TAPHONOMY

Taphonomy
Process and Bias Through Time
second edition
Aims & Scope
Topics in Geobiology Book Series
Topics in Geobiology series treats geobiology - the broad discipline that covers the
history of life on Earth. The series aims for high quality, scholarly volumes of origi-
nal research as well as broad reviews. Recent volumes have showcased a variety of
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these organisms-their ecology, phylogeny, and mode of life and in addition, their
fossil record their distribution in time and space.
Other volumes are more theme based such as predator-prey relationships, skeletal
mineralization, paleobiogeography, and approaches to high resolution stratigraphy,
that cover a broad range of organisms. One theme that is at the heart of the series
is the interplay between the history of life and the changing environment. This is
treated in skeletal mineralization and how such skeletons record environmental
signals and animal-sediment relationships in the marine environment.
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Taphonomy
Process and Bias Through Time
second edition
Peter A. Allison David J. Bottjer

●
Editors
Editors
Peter A. Allison David J. Bottjer
Department of Earth Science & Engineering Department of Earth Sciences
South Kensington Campus University of Southern California
Imperial College London 90089-0740 Los Angeles
SW7 2AZ London California
United Kingdom USA
[email protected] [email protected]
ISBN 978-90-481-8642-6 e-ISBN 978-90-481-8643-3

DOI 10.1007/978-90-481-8643-3
Springer Dordrecht Heidelberg London New York
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Cover illustration: Main Image Caption – Illustration of Lower Devonian Hollardops from Bou Tserfine,
Morocco (see p. 131)
Small figure top left – Eurypterus dekayi from the Late Silurian Williamsville Formation in Ontario,
Canada (see p. 202)
Small figure top middle – Small Nummulites from the late Eocene, Autochthonous Molasse of Upper
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Small figure top right – Modern Limulus (see p. 202)
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Preface
The study of taphonomy has evolved substantially in recent decades. A brief history
of the subject is given in Chapter 1 and will not be repeated here, however it is fair
to say that there is now a first-order understanding of taphonomic processes. It is
particularly noteworthy that taphonomic research breaches the barriers of tradi-
tional research disciplines. The multi-disciplinarity of the subject is evidenced by
the breadth of the publication base that supports the subject; consider for example,
the quantity of vertebrate taphonomy research in the paleontological, archeologi-
cal and forensic domains (e.g. see Chapter 8). The subject is also inter-disciplinary
and this is particularly evidenced by work on inorganic and organic geochemistry
(e.g. see Chapters 5, 6 and 11). It is also true that taphonomic research has always
been quick to incorporate new approaches and techniques. This includes use of the
latest data-bases (Chapters 2 and 16) and analytical methods (Chapters 13 and 14).
Of course paleontological data is ultimately collected by field geologists and
paleontologists and sedimentological and stratigraphic approaches continue to
yield new insights (Chapters 3, 4 and 7).
The great challenges in paleontology are to deepen our understanding of the
origins and evolution of life and elucidate the impact of global change on the bio-
sphere. The first has obvious appeal because it is a basic fundamental question and
the second is relevant to a modern world in the throes of climate change.
Taphonomic research is pertinent to both of these grand challenges, not least
because it is necessary to truly release the data locked in the fossil record. For
example, the controversies surrounding the biogenicity of Archean fossils (see
Chapters 13 and 14) are, in the broadest sense, taphonomic in nature. We also note
that taphonomic research is now being used to evaluate our understanding of large-
scale trends in biodiversity through time (see Chapters 2 and 3). It is also certainly
feasible that global change and mass extinction could impact upon taphonomic
processes. A reduction in the diversity of shell-destroying taxa, a change in the
processing rate of bioturbating organisms, or a change in sedimentary/diagenetic
environment could all influence fossil preservation. This emerging question is
developed in Chapters 9 and 16.
The default assumption for paleontologists is that the fossil record is biased.
The extent of the bias varies between extremes according to depositional circum-
stances (see Chapters 4, 7 and 8) and can be mitigated for by using appropriate
v
vi Preface
research methodologies and statistical approaches, but it is still there. A deeper

understanding of taphonomic process requires an evaluation of how taphonomic
bias has changed over geological time. It is one thing to deal with a biased dataset
and quite another to deal with a bias that has changed with time. This question lies
at the heart of all of the chapters in this book. Chapters 5 and 6 deal with the impact
of biomolecular innovations in the evolution of organic skeletons; Chapters 2, 3, 11
and 12, tackle the issue of secular changes in diagenesis; Chapters 3, 4, 9 and 10
explore the nature of temporal change in taphonomic processes in marine environ-
ments; Chapters 7 and 8 focus on terrestrial environments; and Chapters 14–16
evaluate the extent that taphonomic bias has changed during, or as a result of, major
bio-events. This book as a whole does not define the extent to which taphonomic
bias has changed through time. It does, however, go some way towards properly
defining the questions that need to be asked before that can be done.
It is left to us as editors to thank: the contributors for their patience; the review-
ers of the chapters for their valuable time and insight; our friends, family and col-
leagues who have supported us; and the forbearance and support of the staff at
Springer who have published this work.
Peter A. Allison
David J. Bottjer
Contents
1 Taphonomy: Bias and Process Through Time........................................ 1

Peter A. Allison and David J. Bottjer
2 Taphonomic Overprints on Phanerozoic Trends in Biodiversity:

Lithification and Other Secular Megabiases........................................... 19
Austin J.W. Hendy
3 Taphonomic Bias in Shelly Faunas Through Time: Early Aragonitic

Dissolution and Its Implications for the Fossil Record........................... 79
Lesley Cherns, James R. Wheeley, and V. Paul Wright
4 Comparative Taphonomy and Sedimentology of Small-Scale

Mixed Carbonate/Siliciclastic Cycles: Synopsis
of Phanerozoic Examples.......................................................................... 107
Carlton E. Brett, Peter A. Allison, and Austin J.W. Hendy
5 Taphonomy of Animal Organic Skeletons Through Time..................... 199

Neal S. Gupta and Derek E.G. Briggs
6 Molecular Taphonomy of Plant Organic Skeletons................................ 223

Margaret E. Collinson
7 The Relationship Between Continental Landscape

Evolution and the Plant-Fossil Record: Long Term
Hydrologic Controls on Preservation....................................................... 249
Robert A. Gastaldo and Timothy M. Demko
8 Hierarchical Control of Terrestrial Vertebrate Taphonomy

over Space and Time: Discussion of Mechanisms
and Implications for Vertebrate Paleobiology......................................... 287
Christopher R. Noto
vii
viii Contents
9 Microtaphofacies: Exploring the Potential for Taphonomic

Analysis in Carbonates............................................................................ 337
James H. Nebelsick, Davide Bassi, and Michael W. Rasser
10 Taphonomy of Reefs Through Time....................................................... 375

Rachel Wood
11 Silicification Through Time..................................................................... 411

Susan H. Butts and Derek E.G. Briggs
12 Phosphatization Through the Phanerozoic............................................ 435

Stephen Q. Dornbos
13 Three-Dimensional Morphological (CLSM)

and Chemical (Raman) Imagery of Cellularly
Mineralized Fossils................................................................................... 457
J. William Schopf, Anatoliy B. Kudryavtsev, Abhishek B. Tripathi,
and Andrew D. Czaja
14 Taphonomy in Temporally Unique Settings:

An Environmental Traverse in Search of the Earliest
Life on Earth............................................................................................ 487
Martin D. Brasier, David Wacey, and Nicola McLoughlin
15 Evolutionary Trends in Remarkable Fossil Preservation

Across the Ediacaran–Cambrian Transition
and the Impact of Metazoan Mixing...................................................... 519
Martin D. Brasier, Jonathan B. Antcliffe, and Richard H.T. Callow
16 Mass Extinctions and Changing Taphonomic Processes:

Fidelity of the Guadalupian, Lopingian, and Early Triassic
Fossil Records........................................................................................... 569
Margaret L. Fraiser, Matthew E. Clapham, and David J. Bottjer
Index.................................................................................................................. 591
Contributors
Peter A. Allison
Department of Earth Science and Engineering, South Kensington Campus,
Imperial College London, SW7 2AZ London, UK
[email protected]
Jonathan B. Antcliffe
Department of Earth Sciences, University of Oxford, Parks Road, Oxford
OX1 3PR, UK
[email protected]
Davide Bassi
Dipartimento di Scienze della Terra, Università di Ferrara,
Via Saragat 1, 44122 Ferrara, Italy
[email protected]
David J. Bottjer
Department of Earth Sciences, University of Southern California,
Los Angeles, CA 90089-0740, USA
[email protected]
Martin D. Brasier
Department of Earth Sciences, Oxford University, Parks Road,
Oxford OX1 3PR, UK
[email protected]
Carl E. Brett
Department of Geology, University of Cincinnati, Cincinnati, OH 45221, USA
[email protected]
Derek E.G. Briggs
Department of Geology and Geophysics, Yale University, P. O. Box 208109,
New Haven, CT 06520-8109, USA;
Peabody Museum of Natural History, Yale University, P.O. Box 208118,
New Haven, CT 06520-8118, USA
[email protected]
ix
x Contributors
Susan H. Butts
Division of Invertebrate Paleontology, Peabody Museum of Natural History,
Yale University, P.O. Box 208118, New Haven, CT 06520-8118, USA
[email protected]
Richard H. T. Callow
Department of Earth Sciences, University of Oxford, Parks Road, Oxford,
OX1 3PR, UK
[email protected]
Lesley Cherns
School of Earth and Ocean Sciences, Cardiff University,
Park Place, Cardiff CF10 3YE, UK
[email protected]
Matthew E. Clapham
Department of Earth and Planetary Sciences, University of California Santa Cruz,
1156 High Street, Santa Cruz, CA 95064, USA
[email protected]
Department of Earth Sciences, Royal Holloway University of London,
Egham, Surrey, TW20 0EX, UK
[email protected]
Timothy M. Demko
Department of Geological Sciences, University of Minnesota Duluth,
Duluth, MN 55812, USA;
ExxonMobil Exploration Company, Houston, TX 77210, USA
[email protected]
Steve Q. Dornbos
Department of Geosciences, University of Wisconsin-Milwaukee,
Milwaukee, WI 53201-0413, USA
[email protected]
Margaret L. Fraiser
Milwaukee, WI 53203, USA
[email protected]
Robert A. Gastaldo
Department of Geology, Colby College, Waterville, ME 04901, USA
[email protected]
Neal S. Gupta
Department of Geology and Geophysics, Yale University, P.O. Box 208109,
New Haven, CT 06520–8109 USA;
Contributors xi
Geophysical Laboratory, 5251 Broad Branch Road NW,

Washington, DC, 20015, USA
[email protected]
Austin J.W. Hendy
Center for Tropical Paleoecology and Archaeology Smithsonian Tropical
Research Institute, Panamá, República de Panamá;
Department of Geology and Geophysics, Yale University, New Haven,
CT 06510, USA
[email protected]
Anatoliy B. Kudryavtsev
Institute of Geophysics and Planetary Physics (Center for the Study of Evolution
and the Origin of Life) and NASA Astrobiology Institute, University of California,
Los Angeles, CA 90095, USA
[email protected]
Nicola McLoughlin
Department of Earth Sciences and centre of Excellence in Geobiology,
University of Bergen, 5020 Bergen, Norway
[email protected]
James H. Nebelsick
Institute for Geosciences, University of Tübingen, Sigwartstrasse 10, 72076
Tübingen, Germany
[email protected]
Christopher R. Noto
Department of Biomedical Sciences, Grand Valley State University,
Allendale, MI 49401, USA
[email protected]
Michael W. Rasser
Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
[email protected]
J. William Schopf
Department of Earth and Space Sciences, Institute of Geophysics and Planetary
Physics (Center for the Study of Evolution and the Origin of Life), Molecular
Biology Institute, and NASA Astrobiology Institute, University of California,
Los Angeles, CA 90095, USA
[email protected]
Abhishek B. Tripathi
Advanced Projects Office, Constellation Program, NASA Johnson Spacecraft
Center, 77058, Houston, TX, USA
[email protected]
xii Contributors
David Wacey
Centre for Microscopy, Characterization and Analysis + School
of Earth and Environment, The University of Western Australia,
35 Stirling Highway, Crawley, WA 6009, Australia
[email protected]
Rachel Wood
Grant Institute of Earth Sciences, School of Geosciences, University of Edinburgh,
King’s Buildings, West Mains Road, Edinburgh EH9 3JW, UK
[email protected]
V. Paul Wright
BG-Group, 100 Thames Valley Park, Reading RG6 1PT, UK
[email protected]
J.R. Wheeley
School of Geography, Earth and Environmental Sciences,
University of Birmingham,
Edgbaston, Birmingham B15 2TT, UK
A.D. Czaja
Department of Earth and Space Sciences and Institute of Geophysics
and Planetary Physics (Center for the Study of Evolution and the Origin of Life),
University of California, 90095,
Los Angeles, CA, USA
Chapter 1
Taphonomy: Bias and Process Through Time
Peter A. Allison and David J. Bottjer
Contents
1 Introduction........................................................................................................................... 2
1.1 Taphonomy: A Brief History....................................................................................... 3
2 Is Taphonomic Bias Uniform?.............................................................................................. 4
2.1 Biomolecular Innovation............................................................................................. 5
2.2 Secular Trends in Ocean Chemistry and Skeletal Mineralogy.................................... 6
2.3 Biological Evolution.................................................................................................... 7
2.4 Temporal Trends in Conserving Environments........................................................... 9
3 Taphonomy: A Prospectus?.................................................................................................. 11
References................................................................................................................................... 12
Abstract It is now 18 years since the volume “Taphonomy: Releasing the Data
Locked in the Fossil Record” was published by Plenum Press as part of the successful
“Topics in Geobiology” series. The book was one of several published as the subject
blossomed and diversified. The Plenum book was multi-disciplinary and focused on
processes, including chapters on emerging concepts such as sequence stratigraphy, and
rapidly developing fields such as organic and inorganic geochemistry. In a sense the
book functioned as an entry point for those embarking upon interdisciplinary research
and was quickly out-of-print. Taphonomic bias is now recognized as a pervasive fea-
ture of the fossil record. This is supported by a series of laboratory experiments and
field studies during the last 20 years that have provided a sound first order understand-
ing of the processes at work. A pressing concern, however, is how these processes
have varied through time in different depositional environments. This second-order
understanding is essential if we are to truly fully release the data locked in the fossil
P.A. Allison ()

Department of Earth Science and Engineering, South Kensington Campus, Imperial College
London, SW7 2AZ, UK
e-mail: [email protected]
D.J. Bottjer
Department of Earth Sciences, University of Southern California, Los Angeles,
CA 90089-0740, USA
P.A. Allison and D.J. Bottjer (eds.), Taphonomy: Process and Bias Through Time, 1
Topics in Geobiology 32, DOI 10.1007/978-90-481-8643-3_1,
2 P.A. Allison and D.J. Bottjer
record. It is one thing to work with a biased data set and quite another to work with a
bias that has changed with time. This new book for the “Topics in Geobiology” series
focuses on the extent to which taphonomic bias has changed through time in different
environments. The chapters include work from researchers who are using laboratory,
field and data-base techniques. It does not provide the answers to these questions but
does at least highlight some of the emerging questions.
1 Introduction
Taphonomic processes have exerted a profound and widespread bias to the fossil
record and there are few, if any fossil biotas that are preserved bias-free. The most
striking example of preservational bias is the rarity of fossilized soft parts and
soft-bodied organisms. In “normal” marine near-shore communities such organ-
isms can account for about two thirds of the species and individuals (Allison
1988a) and yet they are rarely preserved. There are of course, examples of biotas
which preserve such tissues and organisms (Bottjer et al. 2002) but it would be
fallacious to assume that the preservation of soft-tissues implied a minimal tapho-
nomic bias. For example, the Iron-Age peat bogs of Europe preserve human car-
casses that include exquisite preservation of soft-tissues (Brothwell 1986; Stead
et al. 1986; Stankiewicz et al. 1997; Glob 2004). Preservation in this instance was
enhanced by the action of organic acids in the peat. However, in some instances
the acids which promoted soft-part decay also promoted mineral dissolution to the
extent that some carcasses are now devoid of bone! The fact that soft-parts are
preserved in preference to skeletal remains underscores the pervasive nature of
taphonomic bias. That is not to say though, that taphonomic processes always
result in signal degradation. Taphonomic bias is influenced by diverse biological,
physical and geochemical processes which are, in turn dependent upon deposi-
tional environment. It is therefore possible to document the nature and extent of
taphonomic bias and invert to infer something of depositional environment; “pale-
ontology’s loss is a sedimentologist’s gain” (Thomas 1986)! Fundamentally, this
aspect of taphonomic bias is incorporated into Walther’s facies concept but was
explicitly developed in the 1980s with the concepts of taphonomic feedback
(Kidwell and Jablonski 1983) and taphofacies (Brett and Baird 1986). Taphonomic
bias in marine environments is most active close to the sediment-water interface:
the Taphonomically Active Zone (Davies et al. 1989), so that sedimentation rate
exerts a strong control on the taphonomy of biogenic remains. Given that the net
rate and episodicity of sedimentation in an aquatic system varies with distance
from land and water depth it is easy to see how relative taphonomic trends can be
used to define sea-level fluctuations (Kidwell 1991; Brett 1995, 1998; Brett and
Baird 1993, 1997) and key trends and surfaces in sequence stratigraphy (e.g.
Courville and Collin 2002; Brett et al. 2009).
1 Taphonomy Through Time 3
Taphonomic research is clearly wide-ranging, and in the Earth sciences impacts

upon all aspects of “soft-rock” research. To put the current work in context it is
necessary to briefly review the history and diversity of research that forms the body
of the subject.
1.1 Taphonomy: A Brief History
Although Efremov (1940) is credited with coining the word, the most obvious and
influential early contributors to the current understanding of taphonomy are the
various German researchers who published in the period between the first and sec-
ond World Wars. That is not to say that these workers were the first to ponder or
make deductions about fossil preservation (see Cadee 1991) but they were the first
to make systematic actualistic observations. In 1927 Weigelt, for example, studied
the fate of diverse modern vertebrate carcasses in and around Lake Smithers in
Texas (Weigelt 1989). He noted the role of insects in carcass degradation and stud-
ied modern mass mortalities and these observations were used in his interpretations
of fossil Lagerstätten. At this point the classic work of Zangerl and Richardson
(1963) should also be highlighted. They conducted a meticulous field study of two
Pennsylvanian Lagerstätten and augmented their interpretations with actualistic
experiments. This was followed by the extensive observations of North Sea tidal
flats made in the influential work of Schäfer (1972 and references therein). These
broad tidal flats provided Schäfer with a low-tech approach for examining marine
taphonomic processes on a daily basis. The abundant and sometimes dramatic
observations that he made on taphonomic systems such as marine animal carcasses
have spurred much additional research. In many ways his observations provided the
modern foundation for actualistic studies of shallow marine systems.
Taphonomic studies assumed ever greater prominence in the 1970s, as demanded
by the rapid growth of the field of paleoecology. Terrestrial studies moved from the
purely observational to those conducted through a time series. One of the pioneers
in this approach has been Behrensmeyer, who focused her earlier studies on the fate
of modern bones in African terrestrial environments and what they can tell us about
the paleoecology of fossil bone assemblages (e.g., Behrensmeyer 1978, 1986;
Behremsmeyer and Hill 1980).
In the 1980s, as taphonomic understanding of different fossil systems matured,
this knowledge was transferred to studies of how taphonomic processes affect
aspects of sedimentary systems and the production of sedimentary deposits. This is
exemplified in the concept of taphofacies coined by Brett and Baird (1986) whereby
different taphonomic processes are considered to characterize particular sedimen-
tary facies. Similarly, taphonomic and depositional processes affecting shell beds,
and the paleoecological and paleobiological meaning of shell beds, have been
extensively investigated through the pioneering work of Kidwell (1985, 1986,
1994, 2002; Kidwell and Jablonski 1983; Kidwell and Flessa 1996; Kidwell and
Brenchley 1996; Kidwell et al. 1986). By the end of the 80s understanding of
taphonomic processes had reached a level requiring broad syntheses of rapidly

accumulating data. This need was met by overview volumes edited by Donovan
(1991), and Allison and Briggs (1991) as well as texts by Lyman (1994) and Martin
(1999), which still provide a useful entry point to the subject.
The concept that some rare fossil deposits have undergone exceptional preserva-
tion, including evidence for soft tissues, was first popularized by Seilacher
(Seilacher et al. 1985). These Fossil Lagerstätten, many of which have exceptional
paleobiological importance, also began to receive important systematic study in the
1980s (Allison 1986, 1988a, b; Allison and Briggs 1993). Such studies fostered
extensive efforts to investigate already-known Lagerstätten and spurred searches
for new Lagerstätten, and the desire to understand the taphonomic processes that
lead to exceptional preservation (e.g., Poinar 1992; Bottjer et al. 2002).
The drive to understand how soft tissues are preserved opened up a new experimental
field of taphonomy. This promoted a stronger focus on understanding process (e.g.,
Martin 1999). Progress developed from the early experiments of Plotnick (1986)
and Allison (1986, 1988a) to more sophisticated levels driven by the work of Briggs
(e.g., Briggs 2003; Briggs and Kear 1993, 1994; Sageman et al. 1999).
Innovative approaches have continually been developed, as taphonomic research
has blossomed into a large discipline within paleontology and sedimentary geology.
Numerous aspects of taphonomy encompassing paleoenvironmental reconstruction
(e.g. Brett and Baird 1997; Martin et al. 1999; Rogers et al. 2007), paleoecology (e.g.
Meldahl et al. 1997; Flessa and Kowalewski 2007), paleobiology (e.g. Kidwell and
Behrensmeyer 1993) and stratigraphy (Kidwell and Holland 2002) are very active
research areas. The latest development is the use of databases to quantify the impact
of taphonomy upon past diversity (e.g., Behrensmeyer et al. 2005). In this context
we embrace the most catholic definition of taphonomy and include the effects of
sedimentation, lithification and rock preservation (e.g. Marshall 1997; Holland
2000; Crampton et al. 2003; Hendy 2009; Sessa et al. 2009; Wall et al. 2009).
2 Is Taphonomic Bias Uniform?
At its heart, paleontology addresses two key concerns that are relevant to mankind:
the origins of life and biodiversity, and the history of past climate change. The first
is relevant because it reveals the evolutionary history of life on the planet (e.g. see
Alroy et al. 2008; Benton 2009; Wagner et al. 2006) and our origins, and the
second is pertinent because the study of past climate change, biodiversity and
extinction (Hallam and Wignall 1997) might warn us of future change. Taphonomy
speaks to both of these endeavours. Given the pervasive nature of preservational
bias, an understanding of that bias is essential to properly decipher the history of
biodiversity (e.g. Powell and Kowalewski 2002) and the impact of climate change
on past biological systems.
Process-based research in the field and in the lab in the last two decades has
gone a long way towards understanding taphonomic bias in modern environments.
A crucial question that remains however, is the extent to which taphonomic bias has
changed through time. It is one thing to work with a data-set where the bias varies
with depositional environment. It is magnitudinally more challenging to work with
data where the bias has also varied with time. There are many reasons to suspect
that this is likely to have been the case, including:
Biomolecular innovation (evolution of the materials from which organisms are
constructed): Some organic molecules and skeletons are more preservable than others
and this has changed with time. The appearance of specific biomolecules such as
lignin and sporopollenin has potentially imparted decay resistance to plants (but see
the chapter by Collinson).
Secular trends in ocean chemistry and skeletal mineralogy: Ocean chemistry has
changed through time and this has influenced the relative preservation of calcite
and aragonite (Sandberg 1975, 1983; Montañez 2002; Cherns and Wright 2000).
Biological evolution: The evolution and diversification of organisms that burrow
into and disturb sediment has clear potential to indirectly promote temporal shifts
in taphonomic bias. Such organisms would disturb and potentially degrade car-
casses that were buried. This bias can be expected to have increased as the depth of
burrowing has increased with time (Thayer 1983; Bottjer and Ausich 1986).
Equally as biodiversity has increased organisms have evolved whose ecology pro-
motes the direct destruction of biogenic remains (e.g. insects, fungi and microbes
that destroy plant material in the terrestrial realm, diverse borers that degrade shelly
remains in aquatic habitats.
Conserving environments through time: Fossil Lagerstätten occur in preserva-
tional windows that are unevenly distributed in time and space (Allison and
Briggs 1991) and clearly reflect temporal trends in fossilization. Similar but more
frequently encountered biases result from variations in lithification! Much of the
sedimentary rock record was deposited in vast shallow epicontinental seas which
lack modern analogues. These seas may have been more prone to stratification and
this could conceivably have enhanced fossil preservation.
Each of these effects can cause changes in taphonomic biases and are discussed
each in turn.
2.1 Biomolecular Innovation
The vast majority of organisms that have lived are not preserved in the rock
record. In a sense, this is fortunate as the complete preservation of biogenic mol-
ecules for a prolonged interval of time would lead to shifts in atmospheric and
Earth surface chemistry. For example, the accumulation of organic carbon subse-
quent to, and during the Devonian-Carboniferous led to marked reductions in
levels of atmospheric carbon dioxide (Berner 1991; Ehleringer et al. 2002). The
evolutionary pressure for space in early terrestrial environments promoted the
development of floral tiering which was facilitated by the complex aromatic
molecule lignin (Kenrick and Edwards 1988). This molecule imparted great
strength to early plants and allowed them to reach substantial heights (Esau
1977). The Carboniferous forests flourished in low-lying areas that were prone
to flooding. Thus, as sea-level waxed and waned to the orbital beat, vast swathes
of forest were periodically waterlogged or drowned. Lignin has traditionally
been considered as particularly decay-resistant in oxygen deficient regimes (but
see Collinson, herein). As well as allowing Carboniferous forests to become tall
it is often considered to have facilitated the accumulation of vast peat deposits,
which subsequently became coal. The carbon cycle was therefore, very different
after the Carboniferous because it included an expanded terrestrial carbon reser-
voir and a new linking process connecting the atmospheric to the lithospheric
reservoirs.
This is a striking example of how taphonomic processes have changed with time
and shows the extent to which those changes can influence the chemical cycles on
the Earth’s surface.
The appearance of molecular novelties that impart some level of decay resis-
tance has of course impacted upon the quality of the fossil record. Chitin is a
polysaccharide that occurs in the exoskeleton of arthropods. The preservation
potential of chitin has long been a source of debate. Prior to the 1950s it was
thought that the biomolecule, chitin was significantly decay resistant (see Richards
1951 for discussion). Taphonomic research in the 1980s (Plotnick 1986; Allison
1988a) showed that arthropod cuticles were degraded over periods of months in
laboratory experiments. In the 1990s however, detailed geochemical investigations
(Baas et al. 1995; Briggs 1999) showed that Richards (1951) was at least partially
correct: there is some evidence that chitin imparts decay resistance immediately
after burial and that chitin derivatives are preserved in geologically ancient depos-
its (Flannery et al. 2001). However, in the majority of cases the chitin has been
diagenetically altered to an aliphatic composition (Briggs 1999). The fossil record
of non-mineralized arthropods may have been significantly enhanced as a result of
this molecule. However, recent work is questioning these paradigms. Chapters by
Gupta and Briggs, and Collinson highlight a growing body of evidence suggesting
that selective preservation is not simply the result of biomolecular composition.
These authors argue that plant and animal biomacromolecules provide a structural
template that is subsequently diagenetically altered to a geomacromolecules in fos-
sils. The authors of these chapters highlight the need for future research and suggest
a tentative agenda of research goals.
2.2 Secular Trends in Ocean Chemistry and Skeletal Mineralogy
The notion that seawater chemistry has changed through time was first mooted by
Sandberg (1975) based upon his work on the mineralogy of Mesozoic ooids. It was
subsequently proposed that the Ca/Mg ratio of seawater influenced the mineralogy
of the dominant abiotic carbonates during the Phanerozoic (Sandberg 1983).
The oscillation between so-called “calcite and aragonite seas” coincides with
Fisher’s (1981) icehouse and greenhouse cycles and this in turn has been linked to
ridge spreading activity and atmospheric PCO2 (Wilkinson and Given 1986;
Wilkinson et al. 1985). Subsequent studies (Dickson 2002, 2004; Harper et al.
1997; Montañez 2002; Stanley and Hardie 1998; Taylor et al. 2009) have shown
that calcareous skeletal mineralogies are also impacted by this secular trend
although the relationship is by no means straightforward. For example clades
whose skeletons evolved in the Ediacaran-Tommotian developed aragonitic skeletons
whilst those that arose between the Tommotian and the Ordovician had a calcitic
skeleton (Porter 2007; Zhuravlev and Wood 2008). Post-Ordovician patterns are
more complex (Taylor 2008; Taylor et al. 2009). This secular variation in seawater
chemistry and skeletal mineralogy clearly has the potential to impart a temporally
variable taphonomic overprint on the fossil record (e.g. see Cherns and Wright
2000; Wright et al. 2003) although the magnitude and pattern of the bias remains
a subject of debate (Bush and Bambach 2004). This theme is touched on in several
of the following chapters but is most pertinent to the chapters by Wood, and
Cherns et al.
Wood highlights the way that taphonomic processes affecting the preservation
of reefs has changed. Many of these taphonomic processes involve biological
destruction, and include an escalation of herbivorous grazers, carnivores, and bio-
erosion that began in the Mesozoic. Changing ocean water chemistry affecting
cementation rates over time also strongly affects the preservation of primary reef
structures. Modern climate change is predicted to strongly affect taphonomic pro-
cesses in reef environments in the future.
The fidelity of the fossil record for paleoecological and paleobiological studies
is affected by the response of skeletons of different original mineralogy to diagen-
esis. The chapter by Cherns et al. explores the well-known problem of differential
preservation of calcitic and aragonitic molluscan fossil faunas. They demonstrate a
number of depositional and diagenetic conditions that are capable of preserving
aragonitic and calcitic shells.
2.3 Biological Evolution
The impact of predator–prey escalation through geological time (Stanley 1974,

1977, 2008; Vermeij 1977, 1987) clearly has the potential to impact upon fossil
preservation. Innovations in predation could potentially lead to a bias against
fossil preservation. Equally, this may have led to the evolution of defence mech-
anisms that included stronger more robust shells that were more likely to be
preserved and more capable of withstanding extended time-averaging (Kidwell
and Brenchley 1994, 1996). The unprecedented diversity of durophagous marine
vertebrates that thrived in the Cretaceous is particularly noteworthy (Walker
and Brett 2002). The crunching jaws of vertebrates are not the only agent of
biological destruction of shells however. Shell borings by diverse inverte-
brates can significantly impact upon shell strength (Kelley 2008) and thereby
reduce preservation potential. The evolutionary diversification of organisms

with this mode of life is therefore likely to have impacted upon hard-part pres-
ervation through time.
Evolution has also impacted upon the depth and nature of burrowing organisms
through time. Modern marine organisms burrow into soft-sediment seafloors to
depths of a meter or more (Bottjer and Ausich 1986). The behavioral activities that
lead to this burrowing range from open burrow systems in which organisms live, to
movement on and through sediment in search of prey, to complex systems in which
microbes are farmed (e.g., Seilacher 2007, 2008). The study of these preserved
burrows, or trace fossils, and the overall fabric it imparts to sediment, or ichnofabric,
has revealed a variety of trends through the Phanerozoic (e.g., Thayer 1983; Droser
and Bottjer 1993). Prior to the Cambrian seafloors were commonly covered with
microbial mats and only in the later part of the Ediacaran did bioturbation first
appear, as trails found at the surface of the seafloor (e.g., Seilacher 1999, 2007).
However, with the Cambrian explosion animals began to evolve the ability to bur-
row into the seafloor for a variety of activities (e.g., Droser et al. 1999; Bottjer et al.
2000). This trend of increasing depth and extent of bioturbation in subtidal environ-
ments continued from low levels in the Cambrian (Droser and Bottjer 1988, 1989)
to where burrows reaching modern depths of one meter or more at the end of the
Paleozoic (Bottjer and Ausich 1986).
The Cambrian is well-known for its exceptional preservation of soft-bodied
faunas in Lagerstätte such as the Burgess Shale. Burgess Shale-type faunas are
found preserved globally, and the Cambrian is a time that has an unusual number
of Lagerstätte with preservation of soft tissues (e.g., Allison and Briggs 1993). The
Cambrian was a time of relatively low depth and extent of bioturbation (Bottjer
and Ausich 1986; Droser and Bottjer 1988, 1989), but with the Cambrian explo-
sion it also saw a proliferation of soft-bodied organisms. Bioturbation can include
scavenging and disruption of carcasses, and it is likely that the low levels of
Cambrian bioturbation led to a greater chance for preservation of soft-bodied
organisms, as compared to the post-Cambrian, when extent of bioturbation
increased significantly (Allison and Briggs 1993; Orr et al. 2003). This intriguing
example of taphonomic bias towards greater preservation under globally-reduced
bioturbation levels is a fascinating example of how the evolution of biological
processes, such as bioturbation, can affect taphonomic processes, and thus intro-
duce bias through time.
The aftermaths of mass extinctions are also times when it might be expected that
bioturbation is reduced, due to extinction of burrowing organisms, with a resultant
effect upon taphonomic processes. This topic is considered as part of the analysis of
the effects of mass extinctions on taphonomic processes in the chapter by Fraiser
et al. Mass extinctions entail a dramatic change in the fossil record through a short
time interval. The question is, how much is this a primary change, and how much
could be due to changes in taphonomic conditions? In this chapter temporal patterns
for Lazarus taxa and distribution of silicified benthic faunas are assessed for the
Permian-Triassic. These analyses show that the fossil record of the end-Permian
mass extinction and the Early Triassic aftermath reflects largely a primary signal, and
is not significantly obscured by a taphonomic megabias due to skeletal mineralogy

or fossil preservation. The impact of mass extinctions on taphonomic processes is
also considered by Nebelsick et al. They document taphonomic attributes of carbon-
ate grains through the Paleogene in a range of facies. They conclude that extinction
events among larger foraminifera that dramatically influence the occurrence and
distribution of facies at this time have little effect on the distribution of taphonomic
features.
2.4 Temporal Trends in Conserving Environments
Fossil lagerstatten are unevenly distributed through time and most abundant in
particular environments (Allison and Briggs 1991, 1993) and it has long been rec-
ognized that this could impact upon estimates of global diversity through time
(Sepkoski 1981). There are for example, times in Earth history when diagenetic
minerals were more likely to preserve fossils. This theme is developed in several
chapters within the book.
Butts and Briggs review the conditions that lead to silicification of marine fos-
sils. The process of silicification is a function of both taxonomic and environmental
factors, which control the rates of carbonate dissolution and silica precipitation.
Silicification is variable through the Phanerozoic, being common in the Paleozoic,
but much less so in the Mesozoic and Cenozoic. This temporal distribution of silici-
fication results in taphonomic biases in the record of biodiversity through time.
Chapters by Brasier et al. and Dornbos detail the nature of phosphatization in the
Precambrian and Phanerozoic respectively. Phosphatization can preserve organisms
ranging from vertebrates to bacteria at the cellular level. The Phanerozoic record of
phosphatization is biased towards taxa with recalcitrant tissues, those with body
parts enriched in phosphate, and those with small body size. Phosphatization is
common in phosphogenic environments, but can also occur in local phosphatizing
microenvironments created by a decaying organism. Phosphatization appears to
have been particularly common from the Cambrian through Early Ordovician and
Cretaceous through Eocene.
The issue of mineralization in the Precambrian is of course fundamental to our
understanding of apostrophe Earth’s earliest fossil biotas where the challenge can some-
times be to determine whether a particular structure is fossil or artifact. This issue is
hotly argued and is addressed in chapters by Schopf et al. and Brasier et al. Preservation
of fine-scale structure at the cellular level has not been adequately documented in the
past because of the lack of appropriate technology to investigate its occurrence. Confocal
laser scanning microscopy (CLSM) and two- and three-dimensional Raman imagery
represent new technological approaches that have successfully been utilized to exam-
ine preservation at the cellular level in animals, plants, fungi, algal protists, and
microbes, preserved variously in phosphorites, cherts, and carbonates. The wide
applicability of this new technology promises to yield an understanding in the future
of how such preservation at the cellular level has varied through time.
Brasier et al highlight a preservational paradox in the early rock record. They
argue that cellular preservation and stromatolite complexity is reduced before the
late Archaean and often considered controversial. They argue that this could be
because scientists have largely been looking in the wrong places: they go on to
identify some exciting and new taphonomic windows, including pillow lavas,
hydrothermal vents and beach sandstones.
The impact of secular changes in bioturbation, geochemistry and climate on fossil
preservation in small scale (10–100 kyr) sedimentary cycles (ubiquitous in offshore
marine successions) is treated in the chapter by Brett et al. In particular, they
characterize the taphonomy of such cycles from Phanerozoioc “greenhouse” times. The
primary taphonomic moderator in these cycles is rate of sedimentation, which varies
exponentially from sediment-starved concentrations to obrutionary deposits. The
occurrence of a persistent motif over this time scale suggests that biological innova-
tions, which might be expected to impact upon fossil preservation, have in fact been
overprinted by the extremes of sedimentation preserved in these small-scale cycles.
For example, having a skeleton, which is more resistant to abrasion, is of little import
when sedimentation is dominated by the extremes: instant obrution or condensation.
Large scale databases, such as the Paleobiology Database (PBDB), can provide
a unique perspective on the effects of taphonomy on the perceived fossil record.
Hendy et al. present an analysis of Phanerozoic data from the PBDB and identify a
variety of taphonomic biases. The availability of fossil assemblages from unlith-
ified sediments, more typical of later Mesozoic and Cenozoic rocks, is likely
related to increases in local as well as global diversity. The occurrence of phosphate
and silica replacement, as well as Konservat-Lagerstätten, is time-restricted.
Similarly, shell beds show increased frequency in middle Paleozoic and Cenozoic
rocks, and fossil molds are most frequent in rocks of early Cambrian and early
Mesozoic age. All of these taphonomic processes are likely to have strong effects
on comparisons of diversity or ecologic complexity through the Phanerozoic.
The nature of terrestrial taphonomic windows is addressed in chapters by
Gastaldo and Demko, and Noto on plants and vertebrates respectively. Gastaldo and
Demko show that in terrestrial settings, plant material is preserved not only in areas
where organic detritus accumulates, but also in burial sites where pore-water geo-
chemistry retards or halts organic degradation. Thus, whereas previously, the lack of
a plant fossil record was interpreted as a function of ecosystem reorganization, extir-
pation, or extinction; it is now apparent that this absence of plant fossils is due to
variations in sediment supply and geochemistry interacting with landscape and cli-
mate. This new understanding of what controls the preservation of plant material
will revolutionize our understanding of the meaning of trends in the plant fossil
record through time.
Noto argues that taphonomic processes are influenced by multiple hierarchical
factors. Every environment contains a specific set of taphonomic conditions and
each biome thus contains a subset of taphonomic conditions termed a taphonomic
regime. As biomes shift through time taphonomic regimes change. Such a perspec-
tive, applied here to the terrestrial vertebrate fossil record, provides a powerful tool
for assessing genuine biotic change through space and time in Earth history.
3 Taphonomy: A Prospectus?
It is clear that our understanding of taphonomy has benefited from diverse approaches
that vary in scale from laboratory and field based studies to the analyses of data-bases.
The latter are growing in number and sophistication and will clearly continue to do
so. That is not to say that there is no place for lab or field based studies. Field-based
studies obviously supply the primary data for subsequent data-base analyses but have
also highlighted potential biases (e.g. Cherns and Wright 2000; Wright et al. 2003;
Bush and Bambach 2004). What though are the ongoing grand challenges for tapho-
nomic research? We argue that they are the same as they are for paleontology in
general and that is to advance our understanding of the diversification of life on Earth
as it evolved and fluctuated in the face of environmental change.
Diversity can be considered to be composed of three components (Whittaker
1972); alpha (within communities), beta (diversity of different communities in a
region), and gamma (diversity of regions). It is clearly important to know how
temporal shifts in taphonomic bias have affected these three components of diver-
sity. The goal is not simply to understand how taphonomic bias has affected the
global headcount of Phanerozoic diversity but also to understand how it has influ-
enced the preserved community structure and ecological evenness. The Paleobiology
Database (PBDB) has of course been a fundamental facilitating endeavour that has
supported the foundation efforts that have already been made in this direction (see
Powell and Kowalewski 2002; Alroy et al. 2008).
An emerging issue relates to the nature of epicontinental seas. Most of the sedi-
mentary rock that is available for paleontological study was deposited in vast shal-
low seas on flooded continents. These seaways lack suitably scaled modern
counterparts and this has long been recognized as a potential problem for uniformi-
tarian analysis (e.g. Hallam 1975; Irwin 1965; Shaw 1964). In essence these sea-
ways were less likely to experience tidal mixing (Wells et al. 2005, 2007) and were
more prone to stratification. This clearly has implications for paleoecology, and
sediment accumulation (Allison and Wright 2005; Allison and Wells 2006) as well
as taphonomic bias (Peters 2007; Smith and McGowan 2008). How this has biased
estimates of diversity is an emerging question.
Predicting the future direction of research is challenging because the very best
research sometimes produces unforeseen results. However, we note the impact of
thorough data-base studies and we can at least predict that this valuable research
tool will be used with greater frequency. We also highlight the need for detailed,
thorough, statistically rigorous fieldwork, because fieldwork always inspires and is
also the raw material for data-base research. But where are the biggest gaps in
taphonomic knowledge? We highlight 3 areas:
1. Precambrian taphonomy: The deepest recesses of Precambrian time included
environments and fossils that lack modern counterparts and are challenging to
identify and interpret. A better understanding of the taphonomy of such systems
will elucidate the early history of Earth and potentially inform the exploration of
other planets.
2. Organic geochemistry: Collinson’s chapter shows that there is still much to learn
about the pathways between organic molecules and preservation of organic carbon.
3. Global biodiversity: The Earth has suffered several mass extinction events.
To what extent do these events impact upon taphonomic processes? Further
development of this work will shed further light on preservational biases and
provide an enhanced understanding of the extinctions themselves.
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Chapter 2
Taphonomic Overprints on Phanerozoic Trends
in Biodiversity: Lithification and Other
Secular Megabiases
Austin J.W. Hendy
Contents
1 Introduction........................................................................................................................... 20
2 Lithification and Diagenesis in the Fossil Record................................................................ 23
2.1 Time-Series Analysis of Lithification and Alpha Diversity: A Global Perspective......... 24
2.2 Time-Series Analysis of Lithification and Alpha Diversity: A Regional Perspective...... 32
2.3 Within-Interval Analysis of Lithification and Alpha Diversity: A Local Perspective...... 37
2.4 Influence of Lithification and Diagenesis on Preservational Quality:
Implications for Taxonomy.......................................................................................... 39
3 Exploring Other Taphonomic Trends in the Quality of the Phanerozoic Fossil Record............ 50
3.1 Preservation as Casts and Molds................................................................................. 50
3.2 Lagerstätten and the Preservation of Soft-Bodied Fossils........................................... 52
3.3 Concentrations of Fossils............................................................................................. 54
3.4 Silicification................................................................................................................. 55
3.5 Phosphatization............................................................................................................ 59
4 Discussion............................................................................................................................. 60
4.1 Evaluation of the Paleobiology Database in Capturing Taphonomic Trends.............. 60
4.2 Research Opportunities and the Mitigation of Taphonomic Biases............................. 64
5 Conclusions........................................................................................................................... 68
6 Appendix............................................................................................................................... 70
References................................................................................................................................... 70
Abstract Taphonomic biases introduce heterogeneity into the quality of the fossil
record and can skew paleontologists’ perception of biodiversity. This paper reviews the
temporal extent and consequences of major taphonomic biases, including lithification
of sediments, skeletal replacement through silicification and phosphatization, concen-
tration of skeletal hard-parts, and the exceptional preservation of soft-bodied faunas.
The frequency of occurrence of particular biases, and their effects of fossil faunas is
identified using occurrence-based datasets, such as the Paleobiology Database.
A.J.W. Hendy (*)
Center for Tropical Paleoecology and Archaeology Smithsonian Tropical Research Institute,
Panamá, República de Panamá
and
Department of Geology and Geophysics, Yale University, New Haven, CT 06510, USA
20 A.J.W. Hendy
Lithification of most Paleozoic and Mesozoic fossiliferous sediments has likely

had a significant influence on perceptions of within-community diversity and
paleoecological composition. The increased availability of unlithified sediments in
rocks of late Mesozoic through Cenozoic age coincides with a two- to threefold
increase in local diversity, a discrepancy that remains even after employing sam-
pling-standardization techniques. Taxa that possess small body size and aragonitic
skeletal mineralogy are preferentially lost or obscured following the cementation of
host sediments. Additionally, morphological details are often obscured or not
preserved in specimens obtained from lithified sediments, suggesting that tapho-
nomic damage could hinder taxonomic practice and estimates of diversity at the
global-scale. Silica replacement, which generally enhances diversity among groups
composed of less stable skeletal composition, appears most frequently among
Permian fossil assemblages. Phosphatic replacement, which plays a key role in the
preservation of soft-bodied and small-shelly faunas, appears commonly in assem-
blages of Cambrian age. Konservat-lagerstätten, while providing a rich source of
information on the rarely preserved soft-bodied biota, are infrequent in the fossil
record, but perhaps are most notable in rocks of Cambrian age. Shell beds are well
known as sources of tremendous diversity and although they are not easily defined
these beds appear to increase in frequency in middle Paleozoic and Cenozoic age
successions. Fossil molds, unlike previously mentioned biases, suggest lost diversity,
and are most frequent in rocks of early Cambrian and early Mesozoic age.
The non-random nature of the above biases raises concerns regarding the com-
parison of diversity or ecological complexity over the course of the Phanerozoic or
between contemporaneous faunal groups. Furthermore, a number of the biases have
tremendous potential to affect community-scale patterns, either degrading (e.g.,
lithification, aragonite dissolution) or enhancing (e.g., silicification, phosphatization)
the relative quality of fossil data. A number of approaches can be undertaken to
minimize these biases, including the selective filtering of datasets to remove tapho-
nomically vulnerable groups or the use of taphonomic control taxa that indicate the
appropriate preservation state of fossil assemblages.
1 Introduction
Documenting trends in biodiversity through geological time is one of the basic goals
of paleontology. Interpretation of these trends has broad implications for understanding
of the evolution of Earth’s environments, the history of life, and the responses of
organisms to environmental change. The observed fossil record of all organisms is,
however, a consequence of taphonomic processes, and diversity data is subject to a
taphonomic overprint. Paleontologists have devoted considerable attention to the
causes, recognition, and mitigation of deficiencies in the record (Donovan and Paul
1998; McKinney 1991; Kidwell and Flessa 1995; Behrensmeyer et al. 2000; Kidwell
and Holland 2002). Attempts to minimize known taphonomic biases are therefore
important to correctly establish underlying evolutionary and environmental signals.
2 Impact of Megabiases on Phanerozoic Biodiversity 21
As a complication, however, the taphonomic biases that affect marine invertebrate

taxa have not only changed over time (Kidwell and Flessa 1995; Kidwell and
Holland 2002), but vary significantly between major groups of taxa (Schopf 1978).
Factors that generate temporal patterns in preservation may include gross changes in
seawater geochemistry (e.g., calcite or aragonite saturation states), the gain or loss
of depositional environments (e.g., microbial mats), changes in the production or
concentration of skeletal sediments, depth and intensity of bioturbation, or the evolution
of durophagous predatory organisms (e.g., piscivorous carnivores) (Thayer 1983;
Wilkinson and Given 1986; Vermeij 1987). Factors that influence variation among
taxonomic groups may include presence, absence, or robustness of skeletons, skeletal
mineralogy (e.g., calcitic, aragonitic) (Fig. 1), and substantive variations in life-habit
(e.g., epifaunal, infaunal modes of life) (Stanley 1968; Behrensmeyer et al. 2005).
Because of their relative ease of preservation, the fossil record is very heavily
biased towards animals with a robust or chemically resistant skeleton (Forey et al.
2004). Nichol (1977) estimated that c. 8% of animal species had a skeleton and
were therefore likely to be preserved. However, having a mineralized skeleton is no
guarantee for preservation and/or fossilization (Smith and Nelson 2003), given the
range of physical, chemical, and biological factors that combine to determine the
ultimate fate of skeletal material. The fossilization potential among skeletonized
organisms is variable but has been estimated to be around 89% of shelled molluscs,
76% of echinoids, and ~50% of crabs (Kidwell and Flessa 1995). While Valentine
(1989) demonstrated that about 80% of shelled mollusc species found living in the
Californian province are preserved in local Pleistocene fossil assemblages, it seems
probable that this figure would be much lower for many non-molluscan groups, like
crabs and echinoids. Alternatively, special deposits are scattered through the geo-
logical record in which soft-bodied and poorly skeletonized organisms are fossil-
ized (Konservat-Lagestätten) (Allison and Briggs 1993). Paul (1998) therefore
considered that it would be reasonable to assume that c. 10% of the biota might
have entered the fossil record, while Forey et al. (2004) went further to conclude
that maybe only 1–5% of species are preserved in the geological record that sur-
vives today. That record, however, is probably most representative for specific
paleoenvironments, geographic regions, or tectonic settings through time.
Our knowledge of past biodiversity represents only a portion of Earth’s former
biota, although it is probably fairly representative for those taxa that possess a mod-
erate to high preservation potential. A recent trend has been towards compiling
comprehensive taxonomic databases for the estimation of diversity (e.g., Sepkoski
2002). The consensus among global analyses such as Sepkoski (1982, 1997) and
Benton (1995) has led to growing confidence that they depict the true history of
biodiversity. However, if there are systematic biases affecting the nature of the fossil
record, then raw systematic counts will give a poor estimation of the underlying
diversity (Alroy et al. 2001, 2008). It is therefore essential that potential biases affecting
the rock record be properly accounted for if paleontologists are to obtain accurate
estimates of past biodiversity. Electronic databases provide the only practical means
for investigating large-scale paleontological patterns and provide direction for inves-
tigation of the processes responsible for such biases (Markwick and Lupia 2002).
22 A.J.W. Hendy
Fig. 1 Variations in the frequency of occurrences for major taxonomic groups of macrofauna
(a) and their skeletal mineralogy (b) through the Phanerozoic. Data from the Paleobiology
Database (downloaded 9/4/2007). Li, Lingulida; Gr, Graptolithina; Cr, Crinoidea; An, Anthozoa;
Ec, Echinoidea; Mg, magnesium; sp, sclero-protein; ph, phosphatic
The development of sophisticated databases, such as the Paleobiology Database

(www.paleodb.org) has not only encouraged the dissection of the fossil record
among geographic regions and paleoenvironments (e.g., Miller 1997; Kiessling and
Aberhan 2007; Bottjer et al. 2008; Wall et al. 2009), but also by the lithologic and
taphonomic context of fossil occurrences (e.g., Foote 2006; Hendy 2009a).
This chapter outlines the nature of past and present assessments of biodiversity
in the light of potential taphonomic biases and in particular the lithification of most
pre-Cenozoic fossiliferous sediments. I not only use data from the Paleobiology
Database (global-scale) and New Zealand Fossil Record Electronic Database
(regional-scale), but also highlight a number of independent basin-scale case stud-
ies (Koch and Sohl 1983; Hendy 2009a; Sessa et al. 2009). These carefully designed
field sampling and specimen-based studies accurately test how taphonomic and
lithologic characteristics of the fossil record influence paleobiological patterns in
the absence of potentially overprinting factors (i.e. paleoenvironmental or biogeo-
graphic heterogeneity of data). Other potentially secular variations in preservational
biases are illustrated using data reposited in the Paleobiology Database. This
exercise serves as both an initial quantitative assessment of these potential biases
and provides an opportunity to critically assess the design and value of
occurrence-based datasets for examining taphonomic trends. The final section of
the chapter summarizes these results, critiques the fidelity of existing data and
design of databases, and suggests future avenues of research.
2 Lithification and Diagenesis in the Fossil Record
A number of authors have noted the potential for secular changes in the nature of the
fossil record associated with lithification and carbonate diagenesis (Raup 1976; Miller
2000; Bush and Bambach 2004; Cherns and Wright 2009). Broadly speaking, altera-
tion of sedimentary rocks and fossils (i.e. dissolution and recrystallization of skeletal
components) is least in younger assemblages. Raup (1976) commented that this may
have the consequence of enhancing apparent species diversity in the younger rocks,
but lamented that quantitative estimates of the effect are not available.
Recently, there has been considerable interest in investigations of the various
spatial components of biodiversity, particularly alpha diversity, or the richness of
individual benthic marine communities. Bambach’s (1977) seminal work revealed
a two- to threefold increase in median community richness from the Paleozoic to
the Cenozoic, an increase also found in subsequent studies (e.g., Sepkoski 1997).
A reinvestigation by Bush and Bambach (2004) not only confirmed this view, but
also suggested that the increase could be even higher after mitigating for such bias-
ing influences as secular variation in aragonite dissolution, environmental cover-
age, and latitudinal variation through the Phanerozoic. Nevertheless, previous
assessments of alpha diversity, while noting the potential bias of secular tapho-
nomic trends, did not attempt to mitigate for the considerable increase of unlithified
fossiliferous sediments in strata of late Mesozoic and Cenozoic age. The following
24 A.J.W. Hendy
section uses several distinct data sources to evaluate the impact of lithification on
biodiversity estimates. Specific focus is applied to three case studies at markedly
different scales to identify lithification bias on (a) a global scale through the
Mesozoic and Cenozoic, (b) regionally through the late Cenozoic, and (c) at basin
scale with carefully collected data that limits the affect of confounding taphonomic,
environmental, and geographic variables. The final section of this chapter focuses
on the biases of lithification and carbonate diagenesis on taxonomic and morpho-
logic data using a specimen-based dataset.
2.1 Time-Series Analysis of Lithification and Alpha Diversity:

A Global Perspective
Using occurrence data from the Paleobiology Database the relationship between
lithification and temporal trends in alpha diversity can be explored. The database
has global, high density coverage of the Phanerozoic fossil record and provides
an excellent resource for evaluating first-order patterns in paleontological data.
Data were downloaded (9/4/2007) only for molluscan and brachiopod compo-
nents of marine invertebrate collections for the Phanerozoic. Collections repos-
ited in the database are typically assigned to one of four lithification categories
(metamorphosed, lithified, poorly lithified, unlithified) during the entry of infor-
mation on the geographic and stratigraphic provenance of faunal lists. The most
appropriate characterization is selected if this information is stated or illustrated
in the bibliographic source of the faunal list. Additional assignments were made
for collections that lack this data, but possessed other lithological or taphonomic
information that is indicative of one of these lithification states. Changes in rela-
tive availability of fossil assemblages assigned to these various lithification states
are presented in Fig. 2.
For much of the Paleozoic, little or no unlithified or poorly lithified fossil material
is available. Skeletal assemblages from metamorphosed sedimentary rock are also
fairly scarce, for the intuitive reason that metamorphism generally destroys fossil
evidence, though some examples are recorded from a range of facies of Cambrian-
Devonian age. The earliest Phanerozoic poorly lithified assemblages of reasonable
number are available from the Jurassic fossil record. Additionally, a number of unlith-
ified assemblages are noted from the Late Jurassic of Greenland, Europe, and Middle
East. Nevertheless, closer inspection of associated data on preservation quality of
these collections, and isolated Paleozoic examples, reveals that many still show diage-
netic alteration through calcite replacement. This suggests that the unlithified state of
at least some older fossil assemblages may be the result of secondary dissolution of
carbonate cement binding sedimentary rocks, perhaps associated with weathering
processes. Notably (Fig. 2) there is an apparent paucity of Early Cretaceous unlithified
assemblages, and, not many more in Late Cretaceous. The precise reasons for this
decrease are not established at this stage, but perhaps relate to the swamping out of a
global signal by large numbers of apparently lithified latest Cretaceous collections
from the Gulf Coastal Plain (see Sohl 1960, 1964a, b; Sohl and Koch 1983, 1984,
Fig. 2 Variation in proportion of collections derived from unlithified and non-lithified (combined
unlithified and poorly lithified) sediments through the Jurassic-Cenozoic. Inset presents the varia-
tion in proportion of collections derived from non-lithified sediments through the Phanerozoic
1987). Easily observed, however, is the sharp increase in availability of unlithified

and poorly lithified assemblages during Paleocene, and maintained through the
Eocene. There is a drop in non-lithified assemblages during the Oligocene, but steady
rise in availability of unlithified assemblages is observed for the remainder of the
Cenozoic. The Oligocene is noted as an interval of increased carbonate production,
as recorded by widespread limestone facies (typically well cemented or lithified) in
many regions of the world (e.g., King et al. 1999; McGowran et al. 2004).
As much as 95% of Pleistocene assemblages are non-lithified (75% of which are
unlithified). This percentage drops to 65% (25% unlithified) during the Middle
Eocene and ranges between 5% and 15% for Late Cretaceous assemblages (typi-
cally less than 5% unlithified). An obvious question to ask is how this secular varia-
tion might affect perceived properties of these collections, such as sample size
(large samples will on average yield more taxa than small samples), preservation of
fossil material (well preserved samples generally appear richer in taxonomic diver-
sity than poorly preserved samples), and composition of those collections (fragile
skeletal elements or shells with reactive mineralogy are known to be more suscep-
tible to destructive diagenetic processes).
The sample size of each of the collections used for this analysis (Fig. 2) is gener-
ally not known. In fact less than 3% of bibliographic references that contribute to
biodiversity data used in these analyses give details of volume or area, although
16% provide abundance data from which the total number of specimens can be
established. On average, unlithified assemblages within this subset contain more
specimens than lithified assemblages (64% and 40% greater sample size for
Neogene and Paleogene collections, respectively). While lithified sediments do not
26 A.J.W. Hendy
Fig. 3 Variation in mean richness of collections from the Jurassic through Cenozoic
necessarily restrict the assembly of particularly large collections, more often than
not the collectors of fossil material will be limited by the volume of sample that can
be removed from the field, or limited by the surface area of rock from which speci-
mens can be extracted or recorded. Collectors may also deliberately obtain espe-
cially large samples, where faunas are particularly well preserved, rich in apparent
taxonomic richness, or of particular paleontologic importance.
With this in mind, it is intuitive to expect that temporal trends in sample size will
have a similar affect on taxonomic richness. The mean richness of collections through
the Jurassic-Cenozoic (Fig. 3). remains relatively low through Jurassic and Early
Cretaceous, ranging from between 7 and 14 genera per collection. A notable increase
in richness is observed between the early Late Cretaceous stages and the latest
Cretaceous (from 7 to 21 genera), increasing further into the Paleocene. Exceptionally
large Campanian and Maastrichtian age collections from the Gulf Coastal Plain of
North America contribute to this jump in richness; the extensive faunal lists of Sohl
(1960, 1964a, b), and Sohl and Koch (1983, 1984, 1987) contribute disproportionately
to Latest Cretaceous occurrence data for this interval. Richness remains relatively high
from the Paleocene through Late Neogene (averaging around 24 genera). These results
point to an increase in apparent marine benthic community richness of around two- to
threefold between the Jurassic-Early Cretaceous and Cenozoic.
In Fig. 4, however, these data are again divided among the three categories of
lithification state (lithified, poorly lithified, unlithified) to determine if these dif-
ferent states have an affect on values of mean richness. Assemblages from lith-
ified collections have relatively low richness through the Jurassic and Early
Cretaceous, ranging from 7 to 14 genera per list, although there is no significant
Fig. 4 Variation in mean richness of collections derived from unlithified, poorly lithified, and
lithified sediments from the Jurassic through Cenozoic
difference in the richness of assemblages from contemporaneous poorly lithified

sediments (where sampled adequately) though this time interval. The richness of
lithified collections climbs steadily through the Late Cretaceous fossil record
from 9 to 18 genera and remains steady throughout the Paleogene and Neogene,
fluctuating between 13 and 19 genera. Poorly lithified assemblages show dis-
tinctly higher diversity from the latest Cretaceous and throughout the Paleogene
and Neogene where sample sizes are large enough to permit meaningful averages.
Notably, the richness of unlithified assemblages is consistently higher than those
of poorly lithified assemblages, and statistically distinct to those lithified collec-
tions (at 95% confidence interval). There are difficulties in accurately measuring
alpha diversity, however. Most notable is the need for abundance data to standardize
for variable sample size. At a global scale, such comparisons are additionally
hindered by latitudinal and environmental heterogeneity among the assemblages
that the dataset comprises.
Koch and Sohl (1983) had previously noted a dramatic disparity in richness
between well-preserved and poorly preserved Late Cretaceous assemblages. They
categorized their dataset of Maastrichtian Gulf Coastal Plain assemblages into one
of six preservation types, ranging from those in which calcite and aragonite shells
were well preserved to those having only calcite shells preserved. Collections in
which both aragonite and calcite were well preserved consistently had more taxa
than those of poorer preservation quality (Fig. 5) and in addition contain many taxa
not found in other collections (Fig. 6). In one of the earlier efforts to standardize
diversity for variations in the number of available fossils (Fig. 7), Koch and Sohl
28 A.J.W. Hendy
Fig. 5 Chart showing the average number of taxa recovered for the six preservation categories
along with variance about the mean and maximum and minimum values. Also shown is the num-
ber of specimens for each category. Preservational types: I, aragonite and calcite well preserved;
II, calcite well preserved, aragonite poorly preserved; III, aragonite preserved as molds; IV, calcite
fossils and molds; V, only molds; VI, calcite only, no molds (From Koch and Sohl 1983)
Fig. 6 Histograms showing abundance (a) and occurrence frequency (b) of 643 taxa used in Koch
and Sohl (1983). Also shown is the distribution for taxa limited to collections in which aragonite
and calcite are well preserved (Type I; see Fig. 5) (stippled). Curve in a is log-normal fit to histo-
gram; curve in b is log-series fit to histogram (From Koch and Sohl 1983)
Fig. 7 Plot of average collection diversity (number of taxa) vs. collection sample size (number of
specimens) after rarefaction of collections; (a) collections with aragonite and calcite well pre-
served (type 1), (b) collections without aragonite and calcite well preserved but with molds and
calcite preserved (types II, III, and IV) and (c) collections from silty fine sands but without well
preserved aragonite. See Fig. 5 for explanation to assemblage types (From Koch and Sohl 1983)
(1983) rarefied specimens from each of three broader preservation categories fur-
ther demonstrating the influence that preservational quality, diagenetic degradation,
and matrix lithology have on sample-level richness. The analysis indicates, for this
example, a modest 25–30% increase in richness between poorly preserved and well
preserved collections at similar sample size. These results also hint at taphonomic
controls on the evenness of abundance distributions, complicating straightforward
interpretation of Phanerozoic trends in community evenness (e.g., Powell and
Kowalewski 2002; Bush and Bambach 2004).
Because the process of lithification commonly involves the cementation of matrix
by precipitation of dissolved carbonate, a likely cause for the genus richness decline
in lithified sediments is the preferential dissolution of aragonitic skeletal hardparts.
Important factors negatively affecting preservation include small size, fragility and
shell composition (Schopf 1978; Koch and Sohl 1983; Paul 1998; Valentine 1989;
Glover and Kidwell 1993; Kidwell and Flessa 1995; Jablonski and Sepkoski 1996;
Cherns and Wright 2000; Wright et al. 2003; Valentine et al. 2006), although recent
analysis (e.g., Kidwell 2005) has suggested that biases that act against skeletal com-
position have little net impact on diversity patterns. Nevertheless, it is argued here
that size and mineralogy are significant factors in the preservation potential of skeletal
components of marine benthic communities through the Mesozoic and Cenozoic.
Additionally, small fossils might also be more readily overlooked by collectors in
30 A.J.W. Hendy
the field because of difficulty in extracting them from lithified sediments (Cooper
et al. 2006). The process of fossil extraction from lithified fossil assemblages in the
field, or preparation in the lab, inherently involves the splitting of hardened slabs or
the fragmentation of larger blocks, processes during which small and fragile specimens
are more likely to be damaged or destroyed.
Data for the analysis of body size composition of taxa were collected from the
literature on Cenozoic and extant Mollusca. Each genus is assigned to one of four
size categories based on the average maximum linear dimension of specimens
belonging to the species of each genus. These sizes, where possible, are based on
multiple species and on multiple specimens of each species where possible, gener-
ally representing type or figured specimens. Each species in the dataset (including
those not contributing measurements) is allotted a size category (maximum linear
dimension) representing their genus; very small (<5 mm), small (6–15 mm), medium
(16–50 mm), and large (>50 mm). Analysis of mineralogical composition used data
derived from the general literature (primarily Coan et al. 2000; Mikkelson and Bieler
2008). As mineralogy is highly conserved among species and genera, composition
was assumed to be consistent within each family (Taylor et al. 1969; Kidwell 2005).
Taxa are here classified as being of dominantly aragonitic, calcitic, or mixed calcite-
aragonite skeletal mineralogies.
The affects of lithification on retrieval of taxa representing various size classes and
mineralogical composition can be assessed a number of ways (Fig. 8). Differences in
composition of lithified and unlithified collections can be estimated using the mean
percentage of taxa in each collection (Fig. 8a), the mean percent of specimens in each
collection (Fig. 8b) (where abundance data are available), the percent of all occur-
rences from a particular time interval (Fig. 8c), and the percent of all taxa from a
particular time interval (Fig. 8d) (summarized in Table 1). Each of the metrics for
composition based on richness or occurrences (Fig. 8a,c,d) reveal a consistent pattern,
a near lack of very small taxa, and reduced numbers of small taxa, among lithified
collections, relative to their unlithified counterparts. Correspondingly, large and
medium-sized taxa tend to contribute a far greater percentage of occurrences among
lithified collections than unlithified ones. Abundance data (Fig. 8b) yields the more
conservative pattern, and although very small taxa and large taxa differ as anticipated
in proportion between lithified and unlithified collections, the differences are minor.
This may be an artefact of the small number of collections available from this time
interval with information on both abundance and lithification state (Table 2).
Any of the above occurrence or richness metrics (Fig. 8) could be used to moni-
tor the affects of lithification through geological time, although an appropriate
choice of measure is probably determined by the scale and resolution of investiga-
tion. For instance, changes in taxic composition measured using abundance data are
probably best limited to investigations of local scale, in which sufficient census
counts are available, and where environmental and taphonomic heterogeneity is
controlled. At a global scale, changes in taxic composition are probably best-
determined using occurrence or richness data, which are available for a consider-
ably larger number of collections that fairly represent a broad range of geographic,
environmental settings and taphonomic conditions.
Fig. 8 Variation in size distribution among fossil data from lithified and unlithified sediments
from the Late Miocene-Pleistocene. (a) Mean percentage of taxa within individual collections.
(b) Mean percentage of specimens within individual collections. (c) Percentage of all Late Miocene-
Pleistocene occurrences. (d) Percentage of all Late Miocene-Pleistocene taxa
Table 1 Estimates of the effect of lithification on small (<15 mm) molluscs using different
protocols. The magnitude by which unlithified sediments contain more specimens, occurrences,
higher mean richness and total diversity than comparable lithified sediments (herein referred to as
the increase factor) is presented for four different data types
Total Total Collection Collection
occurrences richness richness abundance*
Late Miocene- 2.36 1.91 1.50
Pleistocene
Early-Middle 2.61 1.72 1.47
Miocene
Neogene 1.28
Late Eocene 1.86 1.40 1.41
Paleogene 2.17
* = The increase factor calculated with collection abundance is based on samples pooled from the
Neogene and Paleogene to increase sample size
32 A.J.W. Hendy
Table 2 Availability of occurrence and abundance data for which

ithification state is known for three time intervals investigated
Total collections With abundance
Late Miocene-Pleistocene 757 22
Early-Middle Miocene 562 37
Late Eocene 226 23
Figure 9 presents an analysis of differences in composition of lithified and

unlithified collections using the percentage of all occurrences that belong to various
size or mineralogical categories for three time-intervals, the Late Miocene-
Pleistocene (Fig. 9a,b), the Early-Middle Miocene (Fig. 9c,d), and the Late Eocene
(Fig. 9e,f). There is a clear difference between the representation of very small and
small size classes in lithified and unlithified collections. Additionally, there is a
considerable increase (10–20%) in the retrieval of aragonitic molluscs in unlithified
sediments, relative to their lithified counterparts for all time intervals. This further
strengthens the claim that lithification has a considerable impact on the quality of
paleontological data beyond simply influencing the availability of fossil material.
Additionally, this analysis indicates that the pattern is not merely a function of
processes influencing the Late Neogene, but one that is prevalent throughout the
interval for which a non-lithified fossil record in preserved.
2.2 Time-Series Analysis of Lithification and Alpha Diversity:

A Regional Perspective
2.2.1 Cenozoic of New Zealand
A dataset using Eocene-Pleistocene occurrence data from New Zealand’s Fossil Record
Electronic Database (FRED; www.fred.org.nz), is used herein to evaluate the extent that
lithification through time, within a single region, impacts the relationship between regional
and alpha diversity (Fig. 10). In the absence of abundance data spanning the entire time
interval of interest, mean collection richness is used as a proxy for alpha diversity. The
revealed pattern is remarkably similar to that of sampling-standardized total diversity,
except in the latest Pliocene and Pleistocene (Crampton et al. 2006; Hendy 2007). Mean
collection richness declines slightly from the Late Eocene to the Early Oligocene before
increasing to an early peak in earliest Miocene age assemblages. Following the Early
Miocene there is a steady decline in mean richness until the latest Miocene, which appar-
ently represents the most depauperate stage of the Neogene. Collection richness then
increases first to a middle Pliocene peak, declining in the Late Pliocene before climbing
further to a Cenozoic high from Pleistocene assemblages. The nearly threefold increase in
mean collection richness between the latest Miocene (~10 genera) and Pleistocene (27
genera) is remarkable given the time span of only 4–5 Ma between the two intervals. Even
in localized studies, however, difficulties in interpretation of collection richness are posed
by variability in the sample size of assemblages, environmental heterogeneity, biostrati-
nomic and diagenetic effects (including lithification), and time averaging.
Fig. 9 Variation in size distribution and mineralogical composition among fossil occurrences
from lithified and unlithified sediments from Late Miocene-Pleistocene (a, b), Early-Middle
Miocene (c, d), and the Late Eocene (e, f). Percentage was calculated on composition of all occur-
rences in each time interval
34 A.J.W. Hendy
Fig. 10 Mean richness of collections of New Zealand Cenozoic Mollusca. Restricted to collec-
tions >2 occurrences and <100 occurrences. Error bars represent 95% confidence intervals
Fig. 11 Proportional distribution of collection data among three categories of lithification
Though degree of lithification is not often quantified in the literature, the semi-
quantitative category used to describe “hardness” of matrix for collections reposited
in FRED, in addition to anecdotal evidence associated with collections, permit
assessment of how lithification influences richness of individual collections. This is
not without some difficulty given that only about a third of collections are assigned
hardness values (Fig. 11). Two broad scale trends are apparent, the significant
increase in unlithified samples representing the final two stages of the Cenozoic, and
the reduction in lithified assemblages following the Opoitian.
Because of sample size limitations no estimates can be made for a number of
stages during the late Eocene, early Oligocene, and middle Miocene. Indeed, there is
Fig. 12 Mean richness of lithified and unlithified collections of New Zealand Cenozoic Mollusca.
Restricted to collections >2 occurrences and <50 occurrences; means calculated for stages with
>10 collections and whose lithification is accurately determined. Error bars represent 95% confi-
dence intervals
only sufficient sample size to analyze unlithified collections from the latest Pliocene-
Pleistocene, and no collections determined to be lithified are available from the
Pleistocene. Nevertheless, the only stage in which both categories can be assessed is
the Nukumaruan (Fig. 12). The difference in mean richness of Eocene-Early Pliocene
and the latest Late Pliocene-Pleistocene is considerable (approximately two- to three-
fold). While error bars (95% confidence intervals) overlap for the Nukumaruan, the
difference in comparison of diversity in all other stages is significant.
Assuming that the largely lithified Eocene-Early Pliocene fossil record is free of
other secular trends in preservation biases, it appears that there is a strong pattern of
community scale change in biological diversity. If this was indeed a biological signal
then it would suggest that, much of the Eocene-Early Pliocene variation in New
Zealand’s regional biodiversity owes its origin to changing within-community rich-
ness, rather than changes in beta or gamma diversity. This is indeed a significant
result and encourages focused investigation on environmental factors that could play
a role in influencing community-scale diversity, for example, sea-surface temperature
and productivity. The apparently rapid increase in community-richness at the conclu-
sion of the Neogene is, however, overprinted by a lithification bias and any biologi-
cal interpretation of this trend should proceed with caution (Hendy 2009a).
2.2.2 Paleogene of the Gulf Coastal Plain
Sessa et al. (2009) studied the impact of lithification on mollusc-dominated assemblages

of Early Paleogene age from the Gulf Coastal Plain (Texas through Alabama). This
36 A.J.W. Hendy
region is renowned for its well-preserved and diverse record of Paleogene marine
invertebrates, and correspondingly has received considerable taxonomic and biostrati-
graphic investigation. They assembled abundance data from field-collected bulk samples,
and a number of previously published datasets (Toulmin 1977; Hansen et al. 1993a, b;
C. Garvie 2008) that spanned the early to late Paleocene. Using sampling standardiza-
tion procedures they showed a dramatic difference in sample size and diversity between
lithified and unlithified fossiliferous deposits; the latter become the increasingly domi-
nant mode of preservation through the Paleocene and Eocene in this region. On average,
unlithified samples have 2.4 times the diversity of lithified samples of comparable sam-
ple size. Significantly these authors demonstrated that one effect of this bias was to
extend the perceived duration of the recovery period following the Cretaceous-Paleogene
mass-extinction by as much as 7 my. (Fig. 13). An important implication is that observa-
tions of the fate of particular taxonomic or ecologic groups and investigations into the
duration and dynamics of recovery faunas need to be evaluated with respect to tapho-
nomic processes, such as the lithification bias.
An additional dataset, derived from measurements of museum-reposited specimens
from a similar lithology and geography was used to contrast the apparent disparity in
size of taxa recovered from lithified and unlithified units (Fig. 14). Sessa et al. (2009)
Fig. 13 Averaged sample-

level species richness of bulk
samples from the Gulf Coastal
Plain, rarefied to 70 individuals
and with standard deviations,
from the latest Cretaceous
through Paleocene. *, lack of
abundance data for lithified
Cretaceous units (From Sessa
et al. 2009)
Fig. 14 Size frequency

d istribution for museum
reposited specimens indicat-
ing lack of small specimens
from lithified sediments
(n = 1,001) relative to those
from unlithified sediments
(n = 729) (From Sessa et al.
2009)
showed that lithified samples contained individuals with a median size of 11.3 mm
(median of 16.1 mm for unique genera), while unlithified samples possessed individu-
als with a median size of 7.1 mm (median of 6.2 mm). They found that lithification
concealed considerable diversity among small taxa, reduced taxonomic resolution, and
caused the undersampling of already rare taxa. Their study suggested that a size thresh-
old of 5 mm exists, below which specimens were more easily dissolved or more dif-
ficult to identify. Sessa et al. (2009) suggest that while the organisms of particular
interest and preparation techniques will contribute to observed size distributions, speci-
mens of smaller size typically dominate assemblages. Therefore overabundance of
larger specimens in paleontological samples should be cause for concern.
2.3 Within-Interval Analysis of Lithification

and Alpha Diversity: A Local Perspective
An ideal approach to rigorously unraveling the potential effects of this important transition
in preservation should include an attempt to constrain variations in the depositional envi-
ronment, latitudinal position, time-averaging, and temporal variations in biodiversity itself
(Kowalewski et al. 2006). A large dataset of bulk-sampled fossil assemblages in the late
Neogene of New Zealand (Hendy 2009a) provides just such an opportunity to estimate
the loss of taxonomic information associated with lithification bias among contemporane-
ous assemblages. The primary data for this investigation were mollusc-dominated assem-
blages, that ranged in age from Late Miocene to Pleistocene, collected from a narrow
range of sedimentary facies in two sedimentary basins (Wanganui and East Coast) of New
Zealand. The extensive and continuous late Neogene succession in these basins exhibits a
strong lithification gradient between its oldest and youngest sedimentary components.
Sampling was restricted to transgressive shell bed facies (Hendy et al. 2006) to control as
much as possible for between-sample variation in time averaging and to allow the com-
parison of relatively consistent environments through the time series. These samples rep-
resented lower shoreface to mid-shelf bathymetric settings, from sandy or mixed sandy
silty substrates, and exhibited characteristics consistent with within-habitat time-averag-
ing. Additionally, Hendy (2009a) applied consistent methods of collection (stratigraphic
and spatial integrity of samples), preparation, counting and identification, although sample
treatment varied from assemblage to assemblage because of the nature of enclosing sedi-
ments (e.g., weathered or fresh outcrops, lithified or unlithified bedding planes).
If earlier examples of the lithification bias were related simply to the size of the
sample collected from individual localities, then techniques that standardize for varia-
tions in sampling intensity, such as rarefaction, should mitigate this bias (e.g., Bush
and Bambach 2004). Figure 15a shows rarefaction curves for 169 field-collected bulk
samples of Late Miocene-Early Pleistocene age, representing 37 unlithified, 66 poorly
lithified, and 66 lithified fossil assemblages. At comparable levels of sampling, most
unlithified samples yield considerably higher richness than those from lithified sedi-
ments, with poorly lithified assemblages showing an intermediate position, a pattern
that is further amplified by the mean curves for each lithification category (Fig. 15b).
38 A.J.W. Hendy
Fig. 15 Rarefaction of census counts from bulk samples of varying lithification from Late
Miocene-Pleistocene sediments of Wanganui Basin, New Zealand. (a) Rarefaction curves for
individual samples coded by lithification category (poorly lithified samples excluded for clarity).
(b) Means of individual curves in (a) within each lithification category with shaded 95% confi-
dence intervals. (c) Rarefaction curves for individual samples dominated by Tawera. (d) Means of
individual curves in c within each lithification categories with shaded 95% confidence intervals
At a quota of 100 specimens, unlithified sediments yield on average close to 20 genera,

whereas lithified sediments produce slightly fewer than 10 genera for the same
sampling intensity. The disparity was even greater at larger quotas (Table 3).
Hendy (2009a) further constrained environmental heterogeneities in this dataset
by restricting the analyses to a subset of these samples that were dominated by a
single ubiquitous infaunal bivalve, Tawera, which is present throughout late Neogene
fossiliferous deposits in New Zealand (Beu and Maxwell 1990). This subset of sam-
ples represents a single paleocommunity from the shelfal transgressive environmental
gradient through the time series (Hendy and Kamp 2004; Hendy et al. 2006; Hendy
and Kamp 2007). Rarefaction (Fig. 15c, d) of samples dominated by Tawera indicate
again that at comparable levels of sampling most unlithified samples show consider-
ably higher richness than those from lithified sediments, with poorly lithified assem-
blages occupying an intermediate position. Mean curves for each lithification category
confirm this pattern. At a quota of 100 specimens mean richness of unlithified
Table 3 Genus richness in lithified, poorly lithified, and unlithified sediments of the late Neogene
New Zealand from the FRED and from field-collected bulk samples
Data set Subset Unlithified Poorly lithified Lithified
FRED Mean 25.1 9.6 6.0
Max 88 54 19
Field samples All 19.7 (25.1) 15.9 (20.5) 9.9 (10.4)
Pleistocene 20.6 19.6 –
Late Pliocene 17.4 14.8 12.6
Early Pliocene 20.9 16.0 8.8
Late Miocene – – 8.6
Tawera 17.5 (22.5) 13.4 (14.0) 7.8 (8.7)
association
Mean genus richness for FRF data is unstandardized; genus richness for field samples and Tawera
samples rarefied to 100 specimens (and to 200 specimens, in parentheses)
assemblages was approximately two and a half times that of lithified sediments
(Table 3). Unlithified sediments yield on average close to 19 genera, whereas lithified
sediments produce slightly more than seven genera for the same sampling intensity.
A further analysis, reported by Hendy (2009a), restricted comparisons to indi-
vidual time intervals in order to minimize the possibility that temporal variation in
composition of faunas affected the patterns illustrated in Fig. 15. Although unlith-
ified and lithified sediments were lacking from Late Miocene and Pleistocene suc-
cessions, respectively, the pattern of increasing diversity with decreasing degree of
lithification is evident for each time interval analyzed independently (Table 3), but
not through time within any single lithification category. These results demonstrate
that sampling standardization techniques alone cannot reconcile the high diversities
yielded from the easier recovery of fossils from unlithified samples with the lower
diversities of lithified samples, indicating a fundamental difference in the recover-
able taxonomic composition of lithified and unlithified samples.
The results presented in Fig. 16 suggest that skeletal size and mineralogy,
indeed, account for at least part of the difference in taxonomic content between
lithified and unlithified sediment. There is an observable, albeit small, decrease in
the proportion of taxa (and occurrences) with predominantly aragonitic skeletons in
lithified sediment (Fig. 15a). Likewise there is an increase in the proportion of
observed diversity contributed by the smallest and medium sized classes of inver-
tebrates in poorly lithified and unlithified sediments (Fig. 15b). The difference,
while slight, corroborates an independent analysis of the removal of small size
classes on sample-level diversity (Kowalewski et al. 2006).
2.4 Influence of Lithification and Diagenesis

on Preservational Quality: Implications for Taxonomy
Biases in preservational quality at the scale of individual specimens and popula-

tions play an important, yet often overlooked, role in perceptions of biodiversity
and paleoecology. After all, fossil specimens are the raw material in which the
40 A.J.W. Hendy
Fig. 16 Influence of lithification

on taphonomic features of skeletal
assemblages. (a) Relative composition
of aragonitic and calcitic skeletal types.
(b) Relative composition of various
size classes. Error bars indicate 95%
confidence intervals
f ossil record is based. The term preservational quality is used broadly to include the
nature of skeletal material, such as preservation in its original form, replacement by
another mineral, complete dissolution (represented by molds), articulation, fragmen-
tation, abrasion, and the affect of encasement in sediment. Influences on the preser-
vation of taxa may take two forms, either by distortion of sampling probability and
patterns or relative abundance within assemblages (fossil material may be reduced
in frequency or absent due to destructive taphonomic processes), or through influ-
encing taxonomic identifiability (fossil material may be preserved, but not iden-
tifiable to a given taxonomic level). Effects on sampling probability and changes to
the abundance structure of former communities are widely acknowledged in the
literature (e.g., Plotnick and Wagner 2006), although investigations commonly
focus on analyses at fairly coarse resolution, for example, phyla and class (e.g., Foote
and Sepkoski 1999), or clades with typically similar mineralogical composition
(e.g., Kidwell 2005; Valentine et al. 2006). Studies of taxonomic identifiability are,
however, greatly lacking from recent taphonomic and biodiversity literature (but
see Rofthus 2002, 2005). Such affects are especially important given that preserva-
tional quality probably varies fairly predictably through geologic time and across
geographic gradients for given taxonomic groups.
Taphonomic processes may profoundly affect the known fossil record of a taxo-
nomic group, resulting in skewed perceptions of diversity trends and evolutionary
relationships. The diversity history of any group as deduced from fossil data has a
distinct taphonomic overprint (Greenstein 1992), although this may vary from
group to group, depending on the morphological complexity of their body plan,
preservation potential, and their geological age. Additionally, fossil assemblages
themselves are often a mixture of well-specimens with varying degrees of tapho-
nomic alteration (fragmentation, bioerosion, surface alteration). The post mortem
alteration of specimens has the potential to introduce bias into paleoecological data
by preventing taxonomic identification of some portion of the assemblage.
2.4.1 Direct Observation of Fossil Specimens
Assessment of the impact that taphonomy has on taxonomic identification and the
alteration of morphological data cannot be derived from traditional or even occurrence-
based fossil databases. Rather, data must be derived from direct observation of fossil
specimens or whole assemblages. Using data derived from observations of speci-
mens reposited in major natural history museums (collected between 2005 and
2007), the relationships between preservation and facies characteristics are explored.
Variations in preservational quality are determined through observations of morpho-
logical detail for eight families (or superfamilies) of Bivalvia. These families were
chosen for data collection because of their long geological record (in some cases,
Ordovician-Recent), and the diversity of mineralogical composition and skeletal
durability that they comprise (Table 4). Figure 17 presents examples of specimens
of each family from lithified, poorly lithified, and unlithified host-sediments.
Figure 18 illustrates the preservational quality of the eight families (or superfami-
lies) of bivalves through the Phanerozoic. Preservational quality is presented as the
mean percentage of the five or six key types of characters chosen for each family,
potentially observable across all specimens in each interval. Plotted additionally are
the mean values for lithification of host sediment per interval for each family. While
a number of taphonomic conditions could be investigated for their relationship to
preservation of observed morphological details, lithification is explored in this case
study. Table 4 summarizes these character groupings, which will vary from family
to family depending on their inherent morphological characteristics. The character
types chosen in each family are considered essential to the diagnosis of genus-level
taxa in those families, and do not need to be present (i.e. not all Nuculidae possess
crenulation of their inner ventral margin), but must be potentially observable (i.e.
inner ventral margin is exposed for inspection) to be scored as preserved.
Two trends are apparent in each of the family plots in Fig. 18. First, there is a gen-
eral increase in observable characters from the Paleozoic to the Cenozoic, culminating
Table 4 Summary of variations in preservational quality relative to lithification state and geologic time for several families of Bivalvia
42
Character groups Preserved characters Observations (N )

observed Skeletal characteristics
Taxonomic group (generalized) L (%) UL (%) L UL and age range
Nuculidae Shape, sculpture, 39 96 121 62 Aragonitic, nacreous,
inner ventral sculpture fine or
margin, hinge absent; Silurian-
plate, resilifer Recent
Nuculanoidea Shape, sculpture, 53 98 78 54 Aragonitic, sculpture
rostrum, escutcheon, fine or absent;
hinge plate Devonian-Recent
Mytiloidea Shape, sculpture, beak, 54 99 181 31 Aragonitic and calcitic,
inner ventral margin, nacreous, sculpture
hinge plate absent-coarse;
Devonian-Recent
Pinnidae Sculpture, 40 81 40 29 Aragonitic and
ornamentation, calcitic, nacreous,
longitudinal sulcus, sculpture coarse;
adductor muscle Carboniferous-
scar, hinge plate Recent
Limidae Shape, sculpture, 47 100 123 41 Aragonitic and
auricle, byssal gape, calcitic, sculpture
hinge plate fine or coarse;
Carboniferous-
Recent
Anomioidea Shape, presence of right 30 72 30 75 Calcite and aragonite,
valve, muscle scars, subnacreous,
foramen, crura sculpture irregular;
Permian?, Jurassic-
Recent
A.J.W. Hendy
Character groups Preserved characters Observations (N )
observed Skeletal characteristics
Taxonomic group (generalized) L (%) UL (%) L UL and age range
Lucinoidea Shape, sculpture, lunule, 43 89 112 3 Aragonite, sculpture
cardinal dentition, fine or absent;
pallial line Ordovician-Recent
Astartidae Shape, sculpture, lunule, 52 98 102 73 Aragonitic, sculpture
inner ventral margin, fine; Devonian-
cardinal dentition, Recent
lateral dentition
Crassatelloidea Shape, sculpture, 36 97 47 41 Aragonitic, sculpture
umbonal ridge, fine or absent;
cardinal dentition, Permian-Recent
lateral dentition,
posterior truncation
L, lithified; UL, unlithified. Skeletal characteristics and choice of character groups based on Cox (1969), Coan et al. (2000), and Mikkelson and Bieler
(2008)
2 Impact of Megabiases on Phanerozoic Biodiversity
43
44 A.J.W. Hendy
Fig. 17 Examples of the preservation of specimens from unlithified, poorly lithified and lithified
lithification states from several groups of Bivalvia: (a) Nuculanoidea, (b) Nuculanoidea,
(c) Anomiidae, (d) Limidae, (e) Mytiloidea, (f) Astartidae, (g) Lucinoidea, (h) Crassatelloidea.
Identifications and specimen numbers listed in Appendix
in the highest values for the Neogene and Recent (in cases where data were collected).
Second, in many families, peaks may be observable in either the Carboniferous or
Permian intervals. For the Carboniferous, this reflects inclusion in the dataset of either
well-preserved calcite-replaced aragonite taxa from the Mississippian of North
America, or silicified specimens from the type Visean of Belgium. For the Permian,
uncommon, but well-preserved silicified aragonite and calcitic taxa from west Texas
Fig. 18 Temporal trends in preservational quality (black line) and host-rock lithification state
(grey line) for several groups of Bivalvia: (a) Nuculidae, (b) Nuculanoidea, (c) Mytiloidea,
(d) Limidae, (e) Anomioidea, (f) Lucinoidea, (g) Astartidae, (h) Crassatelloidea. Error bars
indicate 95% confidence intervals; dashed lines indicate unsampled intervals
provide a source for well-preserved specimens. Generally Devonian specimens, which

are numerous in museum repositories of North America, are judged to be poorly
preserved (commonly as external molds) and therefore lacking internal skeletal
features such as dentition or muscle scars. In most cases, a significant increase in
preservational quality occurs between commonly lithified specimens of Cretaceous
46 A.J.W. Hendy
age, and those from the Paleogene interval. Most Neogene specimens in the dataset are
from non-lithified host sediment and hence permit observation of most of the key
diagnostic characters that are typically available from Recent material.
In Fig. 19, the preservation quality (mean percent of characters observed) of the
eight taxonomic groups is plotted against degree of lithification. It is clear from
each family that a strong negative trend exists between preservational quality and
degree of lithification. Again, families containing genera that are largely defined on
the basis of internal character groups (e.g., nature of dentition, presence of resilifer,
position of muscle scars, sculpture of interior ventral margin) tend to show highest
decrease (steepest curves) in preservational quality between unlithified and poorly
lithified host sediment categories (i.e. Nuculidae, Nuculanoidea). Carboniferous
and Permian specimens that have undergone silica replacement are not typically
derived from originally unlithified sediments. Nevertheless they indicate that the
process of silicification and subsequent sample preparation techniques (which free
skeletonized specimens from their enclosing matrix), have similar implications for
the preservation and observation of morphological features.
Figure 20a provides more detail on how diagenetic alteration of specimens and
their host sediment can affect morphological details. Data are presented on the five
key character groups required for definition of genus and subgenus-level groups in
the family Nuculidae. Internal features such as the nature of the interior ventral
margin, hinge plate and associated dentition, and resilifer are rarely observable in
specimens from lithified host sediment. Evidence of the latter two character groups
are rarely, if ever, observed on internal molds, whereas evidence of the interior
ventral margin, which is often crenulated, is sometimes preserved by molds. The
shell shape is perhaps the easiest feature (and potentially the least diagnostic for
genus or subgenus level taxonomy) to observe, even among specimens that are
preserved as shells embedded in lithified sediment or as internal and external
molds. Shell surficial sculpture occupies an intermediate position. Being an exterior
feature, it is more readily recognized among embedded specimens and external
molds, although processes of delamination, abrasion and bioerosion often degrade
its appearance even when original shell material remains. Each of the five key char-
acter groups for Nuculidae show improvement in observation probability between
lithified, poorly lithified, and unlithified host sediments. Likewise, when the mean
observation probability is plotted by time interval, a similar increase is noted from
the Paleozoic to the Mesozoic, and the Cenozoic, matching increased representation
among the dataset by specimens from unlithified host sediments.
Figure 20b, presents an independent dataset on the taxonomic resolution of
published occurrences of the Nuculidae, from the Paleobiology Database. These
data represent a random and large sampling of recorded occurrences from the available
literature. The taxonomy largely reflects original published nomenclature and
specifically reported occurrences are not subject to more recent revision, although
nomenclature is corrected for changes in taxonomic rank and synonymy (following
Wagner et al. 2007). The percentage of occurrences that are identified to species
level (Fig. 20b) among recognized genera in this family (e.g., Nucula proxima,
Acila divaricata) increases steadily through the Paleozoic to intermediate levels in
Fig. 19 Relationship between preservational quality and host-rock lithification state for several
groups of Bivalvia: (a) Nuculidae, (b) Nuculanoidea, (c) Mytiloidea, (d) Limidae, (e) Anomioidea,
(f) Lucinoidea, (g) Astartidae, (h) Crassatelloidea. Error bars indicate 95% confidence intervals;
dashed lines indicate unsampled intervals
48 A.J.W. Hendy
Fig. 20 Preservational quality (measured as percent of specimens bearing key characters), lithifi-
cation state of sediments from which specimens were derived, and nomenclatural characteristics
for Nuculidae (Bivalvia). (a) Proportion of specimens preserving individual characters and mean
value plotted against lithification state. Inset shows temporal trends in the mean value and relative
lithification state of those specimens; (b) Proportion of occurrences carrying (I) species-level
identifications, (II) subgenus designations, and (III) identified as Nucula sp. (a potential “waste-
basket taxon”)
the Mesozoic, reaching a plateau near 90% in the Cenozoic. The percentage of
occurrences carrying a subgenus-resolution designation (e.g., Acila (Truncacila))
remains low for Paleozoic and early Mesozoic records, only increasing substantially
with Cenozoic occurrences. Unidentified occurrences of the type genus (Fig. 20b)
for Nuculidae (i.e. Nucula sp.), here regarded as potential “wastebasket taxa”, are
remarkably frequent in rocks of early Paleozoic age, but are fairly uncommon
among records of younger age.
These data series are not necessarily controlled by the degree of lithification of the
sediments from which fossil occurrences are derived, but do reflect quality of preser-
vation of those fossils, which co-varies with lithification. A lack of species-level
identifications among greater than 70% of early Paleozoic occurrences suggests that
while authors can recognize (correctly or incorrectly) the fossils as members of the
Nuculidae, sufficient diagnostic characters are lacking to permit species recognition
or encourage the description of new taxa at species-resolution. The increasing use
(largely post-Mesozoic) of the subgenus rank for identification of Nuculidae appears
to reflect a bias imposed by systematists working with living specimens. The defini-
tions of recent subgenera commonly incorporate anatomical features that are only
available from living material. Systematists working with Cenozoic-age taxa attempt
to conform to the taxonomic framework established for the recent fauna, and relate
fossil taxa to their recent counterparts on the basis of similarity in shell form or
assumed ancestor–descendent relationships. The identification of so many early
Paleozoic occurrences as Nucula sp. is quite troubling, given that the type for the
genus is recent Nucula nucleus (Linné 1758), and although Nucula has a very good
Cenozoic fossil record it probably originated no earlier than the Late Mesozoic (Cox
1969; Wingard and Sohl 1990). The assignment of specimens to Nucula sp. probably
reflects a combination of bad taxonomy on the part of authors, and poor preservation
that would limit subsequent reclassification to true Paleozoic members of the
Nuculidae (e.g., Nuculoidea, Nuculopsis, or Palaeonucula).
2.4.2 Other Studies
Greenstein’s (1992) rigorous study, showed that taphonomic bias affected the diver-
sity history of cidaroid echinoderms, in a systematic, non-random fashion through
time. Greenstein hypothesized that the Jurassic diversification of cidaroids was the
result of evolutionary changes that permitted expansion into new ecospace. The
increased diversity of preservation style noted by Greenstein could have resulted
from occupation of a greater range of environments, which offer differing modes of
preservation, and evolutionary changes that permitted development of more robust
skeletons. An additional observation was that the wider range of preservational
styles following the Jurassic provided additional material for the description of new
taxa, based on the larger number of morphological characters that became available
for description (e.g., lantern muscle-attachment structures). Smith (1990) suggested
that these features are a crucial characteristic in defining and recognizing major
taxonomic groups among Echinoidea.
Rofthus (2002, 2005) investigated the relationship between preservation state
and taxonomic identifiability for bivalves and brachiopods from Silurian and
modern environments. Rothfus found that shell modification by fragmentation
(modifying shell shape characteristics) and surface alteration (modifying sculptural
50 A.J.W. Hendy
features) were among the most important taphonomic variables in reducing

taxonomic identifiability. These processes, and their causes are thought to have
either increased (e.g., through durophagous predation or bioerosion) or remained
constant (e.g., wave energy, abrasion) over the course of the Phanerozoic. This is
an interesting counter to other biases, such as increased sampling intensity and
reduced lithification, which favour the preservation of younger fossil material
(Rofthus 2005). Nevertheless, documentation of taphonomic characteristics, such
as fragmentation frequency, in fossil assemblages may yield additional useful
criteria for grading preservational quality and identifying taxonomic bias in paleo-
biological studies.
3 Exploring Other Taphonomic Trends in the Quality

of the Phanerozoic Fossil Record
Lithification is just one of a range of secular taphonomic biases. Other potential biases,
which are discussed to varying degrees elsewhere in this volume (e.g., Butts and
Briggs, Dornbos, Kidwell this issue), include complete aragonite dissolution (as evi-
denced by preservation of molds), silicification, phosphatization, and preservation of
konservat-lagerstätten. The following section summarizes the presence of these pres-
ervation styles in the published fossil record, as recorded by the Paleobiology Database
(data downloaded 9/4/2007). The nature of any observed trends in their occurrence in
the fossil record and the ways in which they may influence measures of diversity are
described, but more thorough discussion of bio- and geo-chemical processes respon-
sible for these taphonomic and sedimentologic conditions is left for other authoritative
contributions. Nevertheless, their description here provides an initial assessment of
whether large-scale occurrence-based datasets, such as the Paleobiology Database,
adequately capture important taphonomic/sedimentologic trends.
3.1 Preservation as Casts and Molds
The dissolution of mineralized skeletons has long been considered to be a significant

bias on the fossilized record of marine invertebrate organisms (Aller 1982; Flessa and
Brown 1983; Davies et al. 1989). The chemical equilibrium of calcium carbonate in
seawater is balanced between dissolution and precipitation. Dissolution converts solid
CaCO3 into component ions, CO32– and Ca2+, thereby removing skeletal material.
Inorganic precipitation then creates new solid CaCO3 from ions in sea or pore water.
This precipitation often forms cement that binds together existing skeletal and non-
skeletal grains (lithification). Early diagenetic dissolution may also completely
remove aragonite material, resulting in a “dissolution fauna” where susceptible
groups are entirely missing (e.g., Beu et al. 1972). More commonly recognized in the
fossil record, however, are cases where aragonitic material survives dissolution at the
sea floor and become enclosed within host-sediments that experience processes of
cementation and lithification. Dissolution of shell material and concurrent cementa-
tion of surrounding sediments by shell-derived cement preserves traces of former
skeletal hardparts as biomolds (Smith and Nelson 2003; Cherns et al. 2008). Surface
marine waters are less saturated with respect to aragonite than calcite, and aragonite
has a lower thermodynamic stability. Thus aragonite is more likely to dissolve than
calcite (Chave et al. 1962). Furthermore, taxa dominated by organic-rich microstruc-
tures (e.g., nacre) are known to be commonly preserved as molds in the Paleozoic
fossil record, even when co-occurring with taxa bearing organic-poor microstruc-
tures, and preserved with original shell material (Taylor et al. 1969, 1973; Glover and
Kidwell 1993). Given that seawater saturation states of calcite and aragonite have
varied throughout the Phanerozoic (Sandberg 1983; Holland 1984; Wilkinson and
Given 1986) it is appropriate to investigate the fossil record for trends of increased
dissolution (preservation as casts and molds) and to determine the consequences of
skeletal dissolution on perceptions of biodiversity and community composition (see
Cherns and Wright in review, for thorough analysis).
Interpreting trends in the presence of fossil biota preserved as molds through the
geological record is rather complicated, given the secular variation in mineralogy of
skeletal hardparts and multitude of geochemical pathways by which the dissolution
of former skeletons can undergo. Nevertheless, Fig. 21a presents a preliminary analy-
sis of biotas reported in the Paleobiology Database as lacking body fossil preserva-
tion. A significant percentage (75%) of Early Cambrian biotas are reported as being
preserved as internal or external molds. This percentage decreases significantly
through the remainder of the Cambrian, reaching a low of less than 5% through the
Ordovician. A steady increase in representation of fossils as molds is observed from
the Ordovician to the end of the Carboniferous, where values reach around 25–30%.
The Permian is characterized by especially low values (<10%), but a significant
increase in records of cast and mold preservation in observed in the Triassic and early
Jurassic, with values ranching between 20% and 60%. For much of the remainder of
the Mesozoic and Cenozoic, casts and molds contributed to less than 20% of reported
occurrences.
Almost certainly, the complete dissolution of skeletal hardparts has conse-
quences on community-level richness, as shown by comparisons with contempora-
neous silicified biota by Cherns and Wright (2000), Wright et al (2003), and Cherns
and Wright (2009). Figure 21b compares the mean sample richness of those moldic
assemblages plotted in Fig. 20a with background (non-moldic assemblages), sug-
gesting that this bias is prevalent throughout the Phanerozoic. Sixteen of 21 intervals
yield lower mean richness from moldic assemblages than their background coun-
terparts, although the measured difference in richness is never greater than 40%. It
should be noted that this analysis takes no account of the sample size, taxonomic
composition, environmental or geographic origin, and any additional taphonomic
overprints affecting either moldic or background assemblages. The comparison
therefore lacks rigorous control, but provides a starting point for further detailed
investigation.
52 A.J.W. Hendy
Fig. 21 Preservation of marine invertebrate fossils as molds through the Phanerozoic based on data
reposited in the Paleobiology Database. (a) Proportion of collections preserved as molds. (b) Alpha
diversity of contemporaneous assemblages preserved as either molds or as body fossils; collections
with fewer than four taxa (potentially incomplete) are excluded from analyses, and only intervals
with >15 collections with moldic preservation are compared to background assemblages
3.2 Lagerstätten and the Preservation of Soft-Bodied Fossils
Preservation of entirely soft-bodied organisms requires unusual environmental con-

ditions that are geologically rare, such as anoxia or catastrophic burial with rapid
mineral replacement by specialist microbial communities (Allison and Briggs 1991,
1993; Briggs and Crowther 2001). When it occurs, such preservation provides valu-
able windows into the anatomy and habitats of these groups and can be important
simply by virtue of being the earliest record of taxa and morphological characters.
However, stratigraphic horizons with comparable preservation are generally so
dispersed through the stratigraphic record that any time series and evolutionary
conclusions for these groups are highly incomplete (Kidwell and Holland 2002).
Examples of soft-bodied biotas are not well reported or appear not to have been
targeted by the Paleobiology Database, but occur uncommonly during the Early
through Late Cambrian, Carboniferous and then during the Late Triassic through
Late Jurassic (Fig. 22). These include some of the classic konservat-lagerstätten,
such as the Chengiang biota, Burgess Shale, and Alum Shale (‘Orsten’ biota), but
others, including the Hunsrück Slate, Holzmaden and Solnhofen Limestone are
insufficiently represented in the database. Additional soft-bodied assemblages of
Cretaceous and Cenozoic age include preserved remains of non-shelled cephalopods.
While low in frequency, collections exhibiting soft-body preservation comprise a
greater range of taxonomic groups (particularly arthropods and annelids) and body
compositions (including soft-bodied, and chitinous or phosphatic skeletons) than
background (contemporaneous collections with normal preservation).
Allison and Briggs (1993) determined that the Cambrian and Jurassic (Fig. 23)
show significantly higher concentrations of exceptional faunas than predicted by
chance. Those of the Cambrian accumulated in both deep marine (e.g., Kinzers Fm,
Burgess Shale, Wheeler Fm) and shallow water (e.g., Chengjiang biota) settings.
Jurassic faunas, however, tend to be limited to marine environments with restricted
circulation and a stratified water column (Seilacher et al. 1985). The Paleobiology
Database appears not to have captured data from a large number of assemblages.
However, the gross number of exceptionally preserved faunas tabulated by Allison
and Briggs (1993) is itself quite low, with a maximum of only nine reported for the
Cambrian (Fig. 23); by their tabulation an “exceptional fauna” denotes a single
“formation”-scale unit from which konservat-lagerstätten are recorded. Although the
database attempts to assemble data on multiple collections from individual
Fig. 22 Preservation of marine invertebrate fossils in konservat-lagerstätten through the

Phanerozoic (proportion of total collections) based on data reposited in the Paleobiology Database.
Arrows indicated particularly important marine invertebrate lagerstätten
54 A.J.W. Hendy
Fig. 23 Distribution of exceptional faunas in relation to sedimentary outcrop and sea level (sea
level after Hallam 1984) (From Allison and Briggs 1993)
lithostratigraphic units and local sections, it appears as though the few collections
derived from konservat-lagerstätten are overwhelmed by the proportion of faunal
data yielded from fossiliferous sediments with normal preservation. Allison and
Briggs (1993) reported that exceptionally preserved faunas are often omitted from
analyses of evolutionary patterns because of their infrequent occurrences (hence
they can distort diversity metrics) and because their environment of accumulation is
often atypical of the bulk of the fossil record (e.g., deep-water, reduced circulation).
Nevertheless, the taxonomic data from such accumulations does contribute to global
biodiversity estimates (e.g., Sepkoski 2002; Alroy et al. 2008) and their propensity
for recording the first appearances for many higher taxonomic groups with low
preservation potential has relevant implications for paleobiological analyses.
3.3 Concentrations of Fossils
Shell beds (densely packed concentrations of skeletal remains) are a conspicuous

feature of the Phanerozoic (Simões et al. 2000). A number of recent papers have
presented quantitative analyses of changes in the taphonomic quality of the shelly
marine record through the Phanerozoic (Kidwell 1990; Kidwell and Brenchley
1994, 1996; Kidwell this issue). In particular, these studies have demonstrated an
increase in internal complexity and thickness of shell beds through this interval.
These patterns have been suggested to result from Phanerozoic-scale increases in
macrofaunal diversity, average body-size of benthic taxa, the depth and intensity of
infaunalization, the durability of biomineralized skeletons, and the occupation of
high-energy habitats. While not the primary focus of their investigations, the authors
also suggested an increase in the overall abundance of shell beds, independent of
thickness-frequency distributions. As shell beds tend to be a focus for paleontologi-
cal collection effort they are potentially a rich source of data on biodiversity.
Fluctuations in their thickness and frequency in the sedimentary record therefore
might have significant implications on perceptions of past biodiversity.
Records of skeletal concentrations (e.g., shell beds, bioclastic limestones) are
not well documented in the Paleobiology Database due to the lack of specific
descriptive lithology fields concerning such deposits. The time-series of Fig. 24a
was derived from both semi-quantitative lithology descriptor fields (shelly/skeletal)
and informal comments in the lithology comments field, including such terms as
shell bed and coquina. It is unfortunate that objective data (e.g.. dimensions,
packing density) are not readily available to confidently classify collections
following the definitions of Kidwell (1990) and others. Nevertheless, “skeletal
assemblages”, as defined above, comprise between 5% and 18% of collections for
most of the Paleozoic, although their abundance is low (<7%) during the Cambrian,
and again in the late Carboniferous through Late Cretaceous. A significant increase
in skeletal assemblages, reported in the Paleobiology Database, takes place following
the Late Cretaceous, with values ranging between 10% and 25% for most of the
Cenozoic. The mean richness of assemblages derived from skeletal concentrations
was not consistently greater than that assumed to be derived from background sedi-
ments (Fig. 24b), although five of six of the Cenozoic data points did yield higher
collection richness. Given lack of certainty regarding the classification of collec-
tions as shell beds, and the limited availability of abundance data to standardize
sample size, it is difficult to place much emphasis on these results.
3.4 Silicification
Silicified fossils are not only an important component of the Paleozoic fossil record
(Schubert et al. 1997), but preserve data of tremendous significance to paleontology
through their retention of exquisite morphologic detail. Silicification can take place
in a variety of paleoenvironments, including hypersaline and evaporitic shallow
marine settings, oxic through anoxic deep-water sediments, and near hydrothermal
vents (Carson 1991). In addition, the factors involved in silicification vary in each
environment or facies through geologic time. Processes such as evaporation, mete-
oric interaction, changes in redox and pH reactions, and depositional saturation
(e.g., influx of volcanic ash, hydrothermal discharge, and dissolution of biogenic
silica) can contribute, sometimes together, towards silica replacement. The nature
of skeletal material (i.e. carbonate mineralogy), the timing relative to burial history
of the material and the presence of other elements in an organism’s hard-parts or
depositional environment can influence the pathway by which silica replacement
56 A.J.W. Hendy
Fig. 24 Preservation of marine invertebrate fossils in shelly/skeletal rich sediments through the
Phanerozoic based on data reposited in the Paleobiology Database. (a) Proportion of collections
derived from shelly/skeletal rich sediments. (b) Alpha diversity of contemporaneous assemblages
preserved in shelly/skeletal rich sediments and the background fossil record; collections with
fewer than four taxa (potentially incomplete) are excluded from analyses, and only intervals with
>15 collections from shelly/skeletal rich sediments are compared to background assemblages
proceeds. Schubert et al. (1997) found that silicified faunas compose about 20% of
the published record during the Paleozoic, with an almost negligible record silici-
fied during the Mesozoic and Cenozoic (Fig. 25). The post-Paleozoic decline in
silicification has been suggested by a number of authors (Finks 1960, 1970;
Schubert et al. 1997) to correspond to changes in siliceous sponge and radiolarian
abundance or diversity. These authors also found that the dominant locus of silica
Fig. 25 Percentage of analyzed paleontological literature describing benthic marine macrofossils

replaced with silica is shown in histogram. Scale is to left. Line marks number of offshore bedded
cherts, based on data from Hein and Parrish (1987); scale is to right. Confidence intervals 95% for
percentage silicification were calculated following Raup (1991) (From Schubert et al. 1997)
deposition moved to deep-marine environments at the end of Paleozoic, concurrent

with this transition. If silicification is enhanced by the presence of organisms pro-
ducing siliceous skeletons, namely sponges, then the non-random distribution of
these organisms through time and across environmental gradients (Finks 1960;
Brunton and Dixon 1994) may produce another temporal mega-bias in the fossil
record (Schubert et al. 1997).
Analysis of data from the Paleobiology Database in Fig. 26a, indicates that silica
replacement of macrofossils occurs with reasonable frequently throughout Paleozoic.
As much as 15% of Cambrian through Carboniferous fossil occurrences are noted as
showing evidence of silica replacement. A major peak, however, is clear during the latest
Carboniferous and Early Permian, for which greater than 30% of fossil occurrences are
silicified. Post-Paleozoic silicified occurrences are considerably less frequent, but a
clear peak is observed during the Late Triassic with as much as 10% of occurrences
noted as silicified. Fewer than 3% of post-Triassic fossil occurrences are silicified.
The frequency distribution of occurrences with silica replacement derived
from data reposited in the Paleobiology Database (Fig. 26a) agrees with previ-
ously published trends by Schubert et al. (1997) (Fig. 25), in exhibiting a sig-
nificant post-Paleozoic decline in silicification. Nevertheless, the relatively
flat-lying trend observed through the Paleozoic by Schubert is not replicated by
the higher-resolution results in Fig. 26a. This distinction might be related to
greater and more representative sampling of the paleontological literature in the
Paleobiology Database. More likely, however, it is the result of the focused
efforts by Schubert et al. to identify evidence of silicification among their own
literary dataset, and the frequent omission of ancillary taphonomic data for
collections when entered in the Paleobiology Database. It stands to be tested
whether the dramatic increase in the Permian is truly above Paleozoic levels as
58 A.J.W. Hendy
Fig. 26 Preservation of marine invertebrate fossils with silica replacement through the Phanerozoic
based on data reposited in the Paleobiology Database. (a) Proportion of collections preserved
with silica replacement of fossils. (b) Alpha diversity of contemporaneous assemblages pre-
served with silica replacement; collections with fewer than four taxa (potentially incomplete) are
excluded from analyses, and only intervals with >15 collections with silica replacement are com-
pared to background assemblages
suggested with these new data, or an artefact of data entry bias towards well
known rich silicified assemblages (e.g., Cooper and Grant 1972). Figure 26b
compares the mean richness for samples from exhibiting silica replacement
with those from contemporaneous background (normal preservation) assem-
blages. In ten of fourteen cases the silicified assemblages yield higher collection
richness. Early Devonian and the Permian background assemblages were
depleted as much as 30–60% in richness relative to contemporaneous silicified
assemblages. This raises the possibility that estimates of diversity, particularly
those of Permian stages where 20–30% of collections are silicified, could be
significantly inflated relative to adjacent intervals where silicification is less

frequent. Again, it is worth noting that this comparison does not rigorously
ensure that collections are derived from similar environmental and geographic
provenance, reflect similar sampling effort, have consistent preservational
modes, or ensure compatibility in taxonomic composition.
3.5 Phosphatization
Phosphate may preserve calcareous and siliceous skeletons either by replacing the
primary shell mineral or by forming internal or external molds. This type of preserva-
tion is usually rare because of low background phosphate concentrations. Occurrences
of secondarily phosphatized skeletons are therefore predominantly associated with
phosphate beds, or hardgrounds where conditions for apatite precipitation are
enhanced (Prévôt and Lucas 1986, 1990; Lucas and Prévôt 1991). Additionally, it is
possible for soft tissues to be preserved by diagenetic apatite in natural phosphorites.
Replication of soft tissues is rare and requires extraordinary conditions (Allison
1988a), typically occurring in argillaceous sediments deposited in oxygen-depleted
environments (Prévôt and Lucas 1990; Lucas and Prévôt 1991). Phosphatized soft
remains exhibit exceptional preservation, including three-dimensional preservation of
soft-parts and the retention of cellular morphology (Wilby et al. 1996; Wilby and
Briggs 1997). While phosphorite deposits serve as a probable source of phosphorous
involved in replacement of skeletal hard parts, Allison and Briggs (1993) showed no
evidence for global controls on the phosphatization of soft tissue.
Figure 27 presents trends captured by the Paleobiology Database in occurrence
of fossils that have undergone phosphatic replacement. This preservational mode is
recorded at its peak in the Cambrians (ranging between 5% and 9% of recorded
occurrences). Reported occurrences of phosphatic replacement are patchy throughout
the remainder of the Phanerozoic, although another small peak in occurrences is
noted during the Early Cretaceous. It should be noted that this analysis does not
make rigorous estimates of the nature of the fossils that are preserved through phos-
phatic replacement (i.e. original mineralogy) or the type of replacement itself (i.e.
replication of soft parts, replacement of skeletal hard parts, or as internal molds),
and therefore should be regarded as a preliminary attempt to characterize temporal
trends in this mode of fossilization.
The observed pattern of Cambrian and Early Cretaceous peaks in phosphatization
are corroborated by other authors. Numerous recent investigations have detailed
secondary phosphatization among konservat-lagerstätten (e.g., Müller 1985;
Butterfield 1990; Zhu et al. 2005), and small shelly faunas (e.g., Bengston et al.
1990; Brasier 1990; Dzik 1994) of the Cambrian. These fossil occurrences almost
certainly skew perceptions of early Paleozoic biodiversity (Brasier 1990). Small
shelly fossils, for example, dominate Early Cambrian diversity, but suffer a decline
by the Middle Cambrian (Porter 2004), primarily owing to a significant reduction
in phosphogenesis (Cook and McElphinny 1979; Cook 1992). Porter (2004)
suggests that the lack of abundant middle and Late Cambrian small shelly faunas is
60 A.J.W. Hendy
Fig. 27 Preservation of marine invertebrate fossils with phosphatic replacement (proportion of

total collections) through the Phanerozoic based on data reposited in the Paleobiology Database
attributable in part to the closure of this phosphatization window. In additionto phos-

phatized Cambrian konservat-lagerstätten, examples of phosphatized marine inver-
tebrate soft parts are known from the Devonian (Briggs and Rolfe 1983), and are
particularly prevalent in Jurassic (Donovan 1983; Pinna 1985; Allison 1988b), and
Cretaceous (as reported by Allison and Briggs 1993).
4 Discussion
4.1 Evaluation of the Paleobiology Database in Capturing

Taphonomic Trends
It is clear from the examples presented here that particular taphonomic biases can
significantly distort biological trends in biodiversity trajectories. While the focus is
on describing the lithification bias (and associated diagenetic effects), it is clear that
a number of other taphonomic and sedimentology characteristics of fossil assem-
blages show secular variation during the course of the Phanerozoic. The
Paleobiology Database provided the data used to support these claims. Given that
the database is presently regarded as the primary source of data on biodiversity, and
geographic, stratigraphic, and environmental distribution of fossil occurrences in
the Phanerozoic, it is appropriate to assess whether the database has adequately
captured notable taphonomic/sedimentologic trends. Furthermore does the variation
observed between previously noted patterns and those observed from the database
truly reflect the fossil record, features inherent in published paleontologic data, or
simply inadequacies in database structure?
Data used in the global Phanerozoic-scale analyses presented here (lithification,
moldic preservation, silicification, phosphatization, preservation as concretions,
and lagerstätten) were downloaded at a stage in the development of the Paleobiology
Database during which temporal coverage of fossil assemblage data was considered
to have become fairly complete and evenly distributed. Subsequent improvements
to the composition of the database have primarily focused on adding to data from
a few poorly sampled Phanerozoic stages and improving geographic coverage and
evenness of geographic data distribution. A concern, however, remains the taxo-
nomic composition of the database, which tends to be dominated by especially
well-documented groups (e.g., brachiopods, trilobites, corals, bivalves and gastro-
pods) during particular intervals of the Phanerozoic (see Fig. 1). This reflects not
only their ecological dominance (e.g., early Paleozoic collections are dominated by
brachiopod and trilobite occurrences; Cenozoic collections are dominated by bivalve
and gastropod occurrences), but also factors such as paleontological interest (i.e.
biostratigraphic utility), and preservation potential (e.g., echinoids are not well
suited to frequent preservation in the fossil record). With these patterns in mind,
any similar use of the database should attempt to mitigate biases caused by secular
taxonomic variations by limiting investigations to particular taxonomic groups, or
combinations of groups with similar sampling and taphonomic characteristics,
particularly for the purposes of temporal comparisons.
The Paleobiology Database was initially designed (see Alroy et al. 2001,
2008) to collect data in support of analyses of biodiversity change over geological
time, and not necessarily to assemble data appropriate for analyses in a tapho-
nomic framework. Nevertheless, the database does attempt to format taxonomic,
geographic, stratigraphic, sedimentologic, environmental, and taphonomic data
in a standardized framework, by using descriptive values from pulldown lists for
respective fields. Hence, considerable taphonomic and sedimentologic data are
associated with each fossil occurrence, when entered. Fields that have particular
potential for future taphonomic analyses are listed in Table 5, and include those
that consider modes of preservation (e.g., as body fossils, casts, molds, as traces,
in concretions), the nature of original or replaced skeletal mineralogy (e.g., as
original aragonite or calcite, or replaced through silicification or phosphatiza-
tion), preservation as konservat-lagerstätten, the degree of concentration, the
spatial orientation of fossils, the preservation of anatomical data, temporal and
spatial resolution, and biostratinomic damage (e.g., articulation, sorting, frag-
mentation, bioerosion and encrustation). Taphonomic data are also contained
within qualitative comments for each collection, or can be gleaned from
sedimentologic fields (see Table 4). Additional taphonomic analyses can be
undertaken using data pertaining to taxonomic units (e.g., species, genera,
orders), such as information on original skeletal composition, body size, relative
thickness, and the presence of skeletal reinforcement and characteristics of skeletal
architecture. This source of data supported recent analyses on the relationship
62 A.J.W. Hendy
Table 5 Data entry fields in the paleobiology database with applications to taphonomic analysis.
Complete table structure and field definitions can be found at http://paleodb.org/public/tips/tips.
html
Field Example Availability (%)
Sedimentology
Lithification Metamorphosed, lithified, poorly 59
lithified, unlithified
Lithology modifier Bioturbated, concretionary, nodular, 42
pyritic, shelly/skeletal, siliceous
Lithology Dolomite, limestone, sandstone, 93
siltstone
Taphonomy
Modes of preservation Body, cast, mold, impression 57
Original biominerals Aragonite, calcite, chitin 9
Replacement minerals Calcite, pyrite, silica 9
Lagerstätten type Conservation, concentration <1
Concentration of fossils Dispersed, concentrated, lag, hiatal <1
Spatial orientation Life position, random, preferred <1
Anatomical detail Excellent, good, medium, poor 10
Degree of articulation Articulated, associated, disassociated <1
Size sorting Poor, medium, good <1
Fragmentation None, occasional, frequent, extreme 2
Bioerosion None, occasional, frequent, extreme <1
Encrustation None, occasional, frequent, extreme <1
Feeding/pred. traces Drill holes, repair scars, fractures <1
Temporal resolution Snapshot, time-averaged, condensed 5
Spatial resolution Autochthonous, parautochthonous, 5
allochthonous
Availability, percent of all collections that contain field entries (based on data downloaded
9/4/2007)
between skeletal durability and frequency of occurrence in the fossil record

(Behrensmeyer et al. 2005).
A prerequisite to the analyses shown here has been the fundamental shift in
the nature of fossil databases away from compendia that depict only the first and
last known global occurrences of taxa, towards more comprehensive compila-
tions that list occurrences of taxa wherever they are found in the world, regardless
of whether they are the first or last occurrences. Each occurrence can be accom-
panied by a range of supplementary data that can be used not only to assess the
overprint of preservational biases on diversity trajectories, but also potentially
significant paleoenvironmental or paleobiogeographic selectivity in diversifica-
tion and extinction. The Paleobiology Database and numerous other databases
now typically include this kind of information, thereby permitting the kind of
comprehensive assessments of diversity and biases outlined in this chapter.
Nevertheless, the database remains poorly populated with many kinds of data
appropriate for the analyses of taphonomic trends (Table 5), although an increasing
proportion of newly entered fossil assemblages include semi-quantitative tapho-

nomic data (Fig. 28a). Some of this shift is the result of data entry (e.g., avail-
ability of fields, interest and skill of the data enterer), but it may also reflect the
quality of the published literature (Fig. 28b). Modern paleontologic literature
increasingly focuses on the paleoecological or paleoenvironmental interpreta-
tion of fossil data, for which taphonomic information plays a critical role. Much
of the assemblage-level data published through the nineteenth and early twentieth
century, however, were the product of taxonomic treatments or biostratigraphic
reports for particular fossil groups, where aspects of preservation were lacking
or not easily converted into the semi-quantitative data fields that the Paleobiology
Database accepts. As the database continues its growth it should be able to sup-
port broad-scale analyses (where appropriate) of many of the variables listed in
Table 5.
Fig. 28 Growth of semi-quantitative (pulldown fields) and qualitative taphonomic data (key-
stroked comments) reposited in the Paleobiology Database. (a) Historical trends in quality of
entered data; (b) trends in quality of published data
64 A.J.W. Hendy
4.2 Research Opportunities and the Mitigation

of Taphonomic Biases
4.2.1 Taphonomic Biases and the Biodiversity Record
It is clear that for temporal analyses of paleontological data we need to understand

and mitigate for potential biases affecting the fossil record. This has required a
fundamental change in the nature of fossil databases used for large-scale and
coarse-resolution analyses. At the broadest-scale, databases of taxonomic data must
provide data on more than their first and last appearances, but also the nature of
their occurrences and abundance with respect to depositional environments and
past paleogeography (Smith 2001, 2003). Electronic databases now allow high
levels of stratigraphic and environmental dissection of paleontological data that was
not possible in the past. Sampling-standardization techniques are critical in removing
many of the effects (some of which are associated with lithification and taphonomic
biases) on variations in sample size, although these may reveal further issues, such
as variation in heterogeneity of geographic and environmental sampling (see Alroy
et al. 2008). Despite major advances in our analytical approach to reading biodiver-
sity and paleoecological data from the fossil record (e.g., Alroy et al. 2001; Bush
et al, 2004), concerns still remain over the biological veracity of observed results.
Databases are only as good as the data they contain (Markwick and Lupia 2002).
Indeed the quantitative assessment presented here demonstrates the potential of
large-scale occurrence-based datasets in taphonomic investigation, but also reveals
a number of shortcomings, such as heterogeneity in data quantity and quality and
difficulty in establishing causation. Furthermore, the kind of information required
for analysis of biodiversity trends, for instance, can only reveal limited clues about
contemporaneous taphonomic patterns and processes. While large-scale assess-
ments can indicate the temporal scope and magnitude of biases, they will struggle
to fully understand their causal mechanisms without corroboration from small-
scale studies or experiments in which the potential overprint of environmental and
geographic variation is controlled.
Focused taphonomic research on the fossil record needs to continue to collect quan-
titative or semi-quantitative (i.e. rank or relative assessment) data on the preservation
potential of taxa. Improvements in our knowledge of these patterns among taxa, envi-
ronments, and through time will lead to better modelling and empirical analytical
approaches. Such research needs to operate at both the global scale to refine the timing
and magnitude of potential biases, but also at the local scale (field-based) to establish
better constrained magnitudes of taphonomic bias and effective methods to avoid them
either during collecting or data analysis. Experimental (e.g., Flessa and Brown 1983;
Hof and Briggs 1997; Martin et al. 2002; Gupta et al. 2006) and actualistic (e.g.,
Davies et al. 1989; Walker et al. 1998; Parsons-Hubbard et al. 1999; Powell et al. 2002)
studies over the past decade have considerably improved our understanding of the
mechanisms involved in some taphonomic processes, and their rates, at least over short
durations (ecological snapshots rather than geologic time) and in present day condi-
tions of sea water geochemistry and biological activity.
In developing research strategies, it is important to realize that no single bias

applies to all scales of evolutionary analyses or to all taxonomic groups and that no
scale or type of evolutionary analysis or taxonomic group is free of taphonomic
bias. Taphonomic biases may not affect paleontological analyses conducted at
coarse spatial scale and temporal resolution, and indeed, this is one recognized
approach for mitigating potential deficiencies in the fossil record. Nevertheless,
recent basin-scale and high-resolution assessments of the lithification (e.g., Hendy
2009a; Sessa et al. 2009) and aragonite-dissolution (e.g., Cherns and Wright 2000,
in review; Cherns et al. 2008; Wright et al. 2003) biases show such significant
change in community composition and richness that it is difficult not to expect their
manifestation among globally aggregated data. Future effort is therefore required to
better quantify not only the temporal, geographic and taxonomic range of particular
taphonomic biases, but also the ways in which they alter diversity at a range of
spatial scales (i.e. local through global) and the paleoecological properties of indi-
vidual assemblages.
The non-random nature of the above biases raises concern regarding the analysis
of diversity or ecological complexity over the course of the Phanerozoic or comparison
among contemporaneous faunal groups. Furthermore, a number of the biases have
tremendous potential to affect community-scale patterns, either degrading (e.g.,
lithification, aragonite dissolution) or enhancing (e.g., silicification, phosphatiza-
tion) the relative quality of fossil data. Several of approaches can be undertaken to
minimize these biases, including the selective filtering of datasets to remove tapho-
nomically vulnerable groups or the use of taphonomic control taxa that indicate the
consistent preservation state of fossil assemblages (e.g., Jablonski et al. 1997). In
light of recent results indicating that lithification has the potential to alter our percep-
tion of faunal recovery to a mass-extinction event, other recognized extinction and
faunal turnover events should also be revisited to establish their veracity. Sessa et al.
(2009) demonstrated that lithification had a marked effect on perceptions of recovery
dynamics following the Cretaceous-Paleogene mass extinction in one of the most
well known and statigraphically complete regional sections (Gulf Coastal Plain).
With this in mind it is possible that a similar bias influences global compilations of
diversity during this interval. Other intervals of extinction, in which both lithified
and non-lithified fossiliferous facies are represented, should also be treated with
some caution. If other, taphonomic biases (e.g., phosphatization, silicification) are
shown to have similar consequences on community level richness and evenness, and
selective destruction of particular size cohorts or mineralogical components, then
such effects could be widespread throughout the Phanerozoic, and influence many
globally and regionally significant extinction and turnover events.
4.2.2 Implications for Taxonomic and Morphologic Analyses
A number of taphonomic processes have the ability to degrade as well as enhance

the relative quality of fossil material, and in doing so can introduce error into taxo-
nomic practice, skew morphological patterns, and influence evolutionary inference.
Phosphatization and silicification of carbonate skeletons, for instance, plays an
66 A.J.W. Hendy
important role in enhancing the fossil record of the Early Cambrian, preserving
skeletons of thin and small (<40 mm) early metazoans, which were vulnerable to
diagenetic loss (Brasier 1990). These secondarily mineralized specimens are rou-
tinely obtained by acid digestion of limestones, rendering exquisitely preserved
specimens, free of matrix. There is a growing suspicion that this methodology
could be introducing a preservational bias towards small fossils (Runnegar and
Pojeta 1985; Dzik 1991; Mus et al. 2008). Mus et al. (2008) suggested that this has
resulted in the evolutionary model that the earliest molluscs (e.g., helcionellids)
were millimetre-scale animals, despite occasionally reported occurrences of much
larger molluscs in non-carbonate lithologies (e.g., Sundukov and Fedorov 1986).
Most reports of large Cambrian molluscs predate the development of acid-based
extraction techniques and scanning electron microscopy. It appears therefore, at
least in the Early Cambrian, that the excellent preservation of smaller, more easily
phosphatized fossils (phosphatization preferentially occurs in small cavities) has
driven taxonomic effort away from larger poorly preserved material (usually
preserved as molds or through recrystallization), and shifted ideas on the evolution
of body-size among early Paleozoic marine invertebrates. A systematic investiga-
tion of body-size trends in relation to taphonomic properties and preparation tech-
niques for Neoproterozoic and early Paleozoic organisms would be a valuable
prerequisite to further interpretation of early evolutionary trends in diversity or
morphology.
Elsewhere in the Phanerozoic fossil record, changes in quality and preservation
tend to bias against the preservation of small specimens. Indeed few taphonomic
factors act to distort the preservation of larger specimens without also influencing
the smaller cohort. Certainly, the analyses of size composition presented in this
study would suggest that in lithified rocks (Figs. 8, 9, 18) and in cases of complete
aragonite dissolution, small taxa are less likely to be preserved in fossil assem-
blages. Cooper et al. (2006) showed convincingly that the size bias is responsible
for removing as much as 36% of a well-studied, and apparently well-preserved
regional fauna of Cenozoic age. In an independent study, Sessa et al. (2009) also
indicated the selective loss of small specimens, demonstrating that the median size
of specimens from lithified assemblages was nearly 1.5 times as large as those from
unlithified sediments; the median size of unique, lithified genera was over twice
that of unique, unlithified genera. Analyses of Phanerozoic trends in body-size
(Hendy 2009b) reveal a similar pattern for gastropods, with lithified sediments
yielding consistently larger specimens than unlithified sediments or assemblages
having undergone silica replacement. Payne (2005) acknowledged that the size
distribution of silicified species contrasts strongly with other contemporaneous
material, clearly indicating the importance of preservation and preparation for sam-
pling the small end of the size spectrum. It is likely that smaller taxa, particularly
those with less stable carbonate mineralogy (i.e. organic-rich aragonite), are missing
from other time intervals because they are less well preserved. This presents a
particularly problematic bias on estimates of body size or biomass through the
Phanerozoic (e.g., Payne 2005; Payne and Finnegan 2006; Payne et al. 2009).
Useful approaches for mitigating the bias on body-size include choice of proxies
that are independent of the smaller end of the size spectrum (i.e. size maxima; see
Payne et al. 2009), although this greatly restricts the degree to which observed pat-
terns can be generalized to whole faunas, and indeed the interpretation of their
causes. Future studies should dissect trends in body-size among their taxonomic,
geographic, environmental and taphonomic components to ensure correct interpre-
tation of evolutionary and/or paleoenvironmental controls.
Nevertheless, this bias also serves as a reminder that much is lost with respect
to taxonomic composition, thereby influencing assessments of ecological struc-
ture and biodiversity (Hendy 2009a; Sessa et al. 2009). A commonly adopted
strategy to filter the size-frequency distribution of paleontological samples is
through the physical sieving of fossil material, although this is only feasible with
unconsolidated sediments. While this preparation method is often viewed as
degrading neontological as well as paleontological data (Bush et al. 2007), and
hence is termed the size-filtering bias, it offers a useful approach to even the
playing field between unlithified Mesozoic and Cenozoic strata (where small
taxa are easy to collect and identify) and lithified rocks of the Paleozoic (in
which small taxa are difficult to extract, poorly preserved, or missing). In other
words, it is possible to exclude a size-range that has a geologic history of vari-
able preservation. This approach to standardizing paleontological data need not
be restricted to the physical preparation of material; rather it can also be achieved
through analytical sieving (see Kowalewski and Hoffmeister 2003; Bush et al.
2007), whereby measurements of sampled specimens are used to filter the data-
set to appropriate size-ranges. Proxy data (e.g., type specimen or mean dimen-
sions) can be used to provide the information necessary to include or exclude
particular size ranges from paleobiological analyses (e.g., Allmon et al. 1993).
With the growth of taxonomic (e.g., Rosenberg 2005) and occurrence-based
datasets it is becoming easier to filter body size as a routine step during paleo-
biological analyses. The Paleobiological Database now has the ability to collect
not only semi-quantitative data (i.e. the dominant size category for each taxon)
but also the dimensions of individual specimens (i.e. type specimens or popula-
tion-scale datasets).
Heterogeneity in preservation can also place constraints on the amount of mor-
phological complexity that is available to taxonomists, although the taphonomic
nature of studied specimens is seldom reported. Lack of diagnostic characters not
only increases the likelihood of misidentification or error in the classification of
new taxa, but they can provide misleading information on phylogenetic relation-
ships (Grantham 2004). Gastropods, for example, have an extensive fossil record
that stretches back to the Cambrian. However, determining the relationship of
early taxa to one another, and especially to extant forms present major challenges
owing to the limited number of characters preserved and architectural restrictions
apparent among large clades (Frÿda et al. 2008). Features that might be of addi-
tional use in diagnosing these clades, such as shell mineralogy and protoconch
morphology are preserved only infrequently in early fossils. Additionally, the poor
68 A.J.W. Hendy
preservation of type material can present a barrier to establishing relationships

between species and genera within contemporaneous assemblages. Malinky
(1990) in a review of Early and Middle Cambrian hyolithids described how the
poor preservation of many type specimens rendered their generic identification
uncertain and in some cases suggested that their classification to Hyolitha was
quite unlikely. In his systematic treatment of the group Malinky (1990), therefore,
makes a great effort to describe the preservational state of type and other available
specimens. Taphonomic characterization of type material has a role in the future
assessments of taxon validity and such data should be routinely included in systematic
descriptions using standard terminology. The Paleobiology Database recently
added fields to collect similar data where available for type specimens.
5 Conclusions
The quality of the fossil record as an archive of evolutionary and ecological development
has almost certainly changed over the Phanerozoic. Much of the variation in the fossil
record is due to secular taphonomic biases, including those involving diagenetic
alteration of fossils or their host sediments, concentration of skeletal hard-parts, and
the exceptional preservation of soft-bodied organisms. These mega-biases not only
introduce heterogeneity into the quality of the fossil record, but skew paleontolo-
gists’ perception of trends in biodiversity and paleoecology.
The lithification of most Paleozoic and Mesozoic fossiliferous sediments,
typically by carbonate cements, has had a significant influence on perceptions of
within-community diversity and paleoecological composition. Independent investi-
gations of global and regional fossil occurrence datasets reveals that the increasing
availability of unlithified sediments in rocks of late Mesozoic through Cenozoic age
coincides with a two- to threefold increase in local-scale diversity. Previously such
a relationship has been related to the ease of sampling in unlithified sediments; in
other words, a sample-size bias. However, this discrepancy remains even after using
sampling-standardization on a high-quality set of abundance data in which other
taphonomic, environmental, and biogeographic effects have been controlled for.
A significant variation in the body-size and mineralogical characteristics of biota
from lithified and unlithified sediments suggests that assemblages undergo consid-
erable compositional change during the diagenesis associated with lithification.
Compositional differences may also result from preparation difficulties and
decreased taxonomic identification.
A specimen-based analysis indicates that lithified and generally poorly-preserved
specimens, typical of Paleozoic and early Mesozoic sediments, yield fewer diagnostic
characters necessary for precise generic identification than their unlithified and well-
preserved Cenozoic counterparts. Not only are fewer potential characters observable,
but occurrence-based datasets also indicate that late Mesozoic and Cenozoic rocks are
more likely to yield taxa identified to species-resolution, subgenera, and a more even
distribution of species among the constituent genera of families. This analysis indicates
a largely ignored mechanism by which taphonomic damage could hinder taxonomic

practice and estimates of diversity at the global-scale.
Lithification is one of many taphonomic mega-biases that have the potential to
affect biodiversity trends. Occurrence- and specimen-based datasets, in which taxo-
nomic data is tied to information pertaining to the environmental, lithologic, and
taphonomic context of faunal occurrences, are potentially effective tools in highlighting
intervals and particular faunal groups that are susceptible to bias. Silica replacement,
which is thought to enhance diversity among groups composed of less stable skeletal
composition, appears most frequently among Permian fossil assemblages. Phosphatic
replacement, which plays a key role in the preservation of soft-bodied and small-shelly
faunas, appears commonly in assemblages of Cambrian age. Konservat-lagerstätte,
while providing a rich source of information on the rarely preserved soft-bodied
biota, are infrequent in the fossil record, but perhaps are most notable from rocks of
Cambrian age. Shell beds are well known as sources of tremendous diversity in
Neogene sedimentary basins. Although they are not easily defined these beds appear
to show increased frequency in middle Paleozoic and Cenozoic age successions.
Fossil molds, unlike previously mentioned biases, suggest lost diversity, and are most
frequent in rocks of early Cambrian and early Mesozoic age.
The considerable value of paleontological data in evolutionary analyses provides
motivation for thorough understanding of the deficiencies in the fossil record and
developing appropriate protocols to gain the maximum quality and quantity of data
from the fossil record. Taphonomic biases may not affect paleontological analyses
conducted at coarse spatial scale and temporal resolution. However, the non-random
nature of the above biases raises concerns regarding the comparison of diversity or
ecological complexity over the course of the Phanerozoic or between contempora-
neous faunal groups. Furthermore, a number of the biases have tremendous potential
to affect community-scale patterns, either degrading (e.g., lithification, aragonite
dissolution) or enhancing (e.g., silicification, phosphatization) the relative quality
of fossil data. A number of approaches can be undertaken to minimize these biases,
including the selective filtering of datasets to remove taphonomically vulnerable
groups or the use of taphonomic control taxa that indicate the appropriate preserva-
tion state of fossil assemblages.
Future effort is required to better quantify not only the temporal, geographic and
taxonomic range of particular taphonomic biases, but also the ways in which they
alter diversity at a range of spatial scales (i.e. local through global) and the paleoeco-
logical properties of individual assemblages. In the light of recent results indicating
that lithification has the potential to alter our perception of faunal recovery to a mass-
extinction event, other recognized extinction and faunal turnover events should also
be revisited to establish their veracity. The quantitative assessment presented here has
in part relied on large-scale occurrence-based datasets. In doing so, their potential in
taphonomic investigation has been highlighted, but also their shortcomings (e.g., data
quality, objective definitions for taphonomic conditions) are apparent. Additionally, it
is clear that large-scale assessments will struggle to establish the true effect of tapho-
nomic biases and their causal mechanisms without small-scale studies in which the
potential overprint of environmental and geographic variation is controlled.
70 A.J.W. Hendy
Acknowledgments The following institutions and staff are acknowledged for permitting and
facilitating access to museum collections used in this study for analysis of lithification and diagen-
esis on specimens: American Museum of Natural History (Bushra Hussaini), Cincinnati Museum
Center (Brenda Hanke), Paleontological Research Institution (Warren Allmon, Greg Dietel,
Ursula Smith), and the Yale Peabody Museum of Natural History (Susan Butts, Cope MacClintock).
Jessica Bazeley and Penny Benson are thanked for photography and digital archiving of fossil
collections used in this study. Initial research was undertaken while AH was supported by a
University Dean Distinguished Dissertation Award from the University of Cincinnati. A Gaylord
Donnelley Environmental Fellowship from the Yale Institute of Biospheric Studies allowed final
completion of this investigation and funded museum visits. Carlton Brett is thanked for reading
an earlier version of this manuscript, while Arnie Miller, Devin Buick, Katherine Bulinski and
Chad Fergusson, are acknowledged for helpful discussions during its infancy. Lastly, I appreciate
the support of John Alroy in maintaining the Paleobiology Database. This is Paleobiology
Database publication number 99.
6 Appendix
Specimens illustrated in Fig. 19; read from left to right (lithified to unlithified) in

figure (a) Nuculanoidea: Phestia sp. (x0.5), YPM 507054, Mississippian, Indiana;
Phestia bellistriata (x0.5), YPM 507043, Pennsylvanian, Oklahoma; Hilgardia
brogniarti (x.05), YPM 325744A, Eocene, Alabama. (b) Nuculidae: Nuculoidea
corbuliformis (x0.5), YPM 507052–507053, Devonian, New York; Nucula ovata
(x0.5), YPM 383450, Early Cretaceous, England; Nucula percrassa (x0.3), YPM
507066, Late Cretaceous, Tennessee. (c) Anomiidae: “Anomia” sp. (x0.8), YPM
507055, Late Cretaceous, Mississippi; Anomia anomialis (x0.8), YPM 507039,
Eocene, England; Anomia argentaria (x0.8), YPM 507014–507015, Late Cretaceous,
England. (d) Limidae: Lima dichotoma (x0.3), YPM 507051, Late Cretaceous,
Czechoslovakia; Limatula gibbosa (x0.8), YPM 507028, Jurassic, France; Ctenoides
spatula (x0.8), YPM 507012–507013, Eocene, France. (e) Mytiloidea: Phthonia
nodicostata (x0.5), YPM 500843, Devonian, New York; Promytilus swallovi (x0.5),
YPM 507056, Pennsylvanian, Kansas; Modiolus modiolus (x0.3), YPM 309185,
Pleistocene, Scotland. (f) Astartiidae: Neocrassina elegans (x0.3), YPM 507031,
Jurassic, France; Astarte incrassata (x.0.5), YPM 507023, Pliocene, England;
Iocrassina omalii (x0.8), YPM 507065, Pliocene, England. (g) Lucinoidea:
Lucinidae indet. (x0.8), YPM 507048, Late Jurassic, England; Eophysema ozarkana
(x0.5), YPM 6937, Eocene, Alabama; Epilucina concentrica (x0.5), YPM 507036,
Eocene, France. (h) Crassatelloidea: Cypricardella bellastriata (x1.0), YPM 507050,
Devonian, New York; Bathytormus sp. (x1.2), YPM 507034, Oligocene, Mississippi;
Hybolophus speciosa (x0.5), YPM 507030, Pliocene, North Carolina.
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Chapter 3
Taphonomic Bias in Shelly Faunas
Through Time: Early Aragonitic Dissolution
and Its Implications for the Fossil Record
Lesley Cherns, James R. Wheeley, and V. Paul Wright
Contents
1 Introduction........................................................................................................................... 80
2 Environments of Dissolution................................................................................................ 81
2.1 Seafloor Diagenesis..................................................................................................... 81
2.2 Taphonomically Active Zone (TAZ)............................................................................ 82
2.3 Shallow Sub-TAZ Burial Diagenesis........................................................................... 84
3 Taphonomic Windows........................................................................................................... 84
3.1 ‘Skeletal Lagerstätten’................................................................................................. 84
3.2 Other Deposits Capturing Biodiversity........................................................................ 89
4 Discussion............................................................................................................................. 95
4.1 Taphonomic Gradients and Molluscan Preservation: A Model................................... 95
4.2 Molluscan Preservation During ‘Calcite’ and ‘Aragonite Seas’.................................. 97
5 Conclusions........................................................................................................................... 97
References................................................................................................................................... 98
Abstract Early diagenetic dissolution of skeletal carbonate in environments from

seafloor to shallow burial has the potential to skew the marine fossil record of arago-
nitic shells, particularly molluscs. Taphonomic windows leading to the preservation
of labile skeletal components include relatively rare occurrences of early mineral
replacement by silica (skeletal lagerstätten). Another, much more frequent process
is event deposition where dissolution is halted by rapid burial of shells. Shell plas-
ters form in basinal mud or low energy lagoonal environments during temporary
dysoxic episodes, such as are caused by algal blooms. Preservation potential for
L. Cherns (*)
School of Earth and Ocean Sciences, Cardiff University, Park Place,
Cardiff CF10 3YE, UK
J.R. Wheeley
School of Geography, Earth and Environmental Sciences, University of Birmingham,
Edgbaston, Birmingham B15 2TT, UK
V.P. Wright
BG-Group, 100 Thames Valley Park, Reading RG6 1PT, UK
80 L. Cherns et al.
aragonitic fossils may be enhanced by early cementation during shallow burial

(hardgrounds) that protects the delicate dissolution moulds from destruction by
bioturbation, or in high energy shoal environments where the drive for microbial
dissolution is reduced. A data-based environmental model summarizes the main
taphonomic zones, and illustrates significant taphonomic bias against aragonitic
shells in lower energy settings of platform interiors and mid-outer ramps/shelves.
The temporal distribution of various taphonomic windows shows the limited occur-
rence of silicified faunas, while the nature and extent of shell beds also change, but
there is no obvious correlation with periods of ‘calcite’ and ‘aragonite seas’.
1 Introduction
A growing weight of evidence points to dissolution of biogenic carbonate as a significant

process in modern carbonate sea-floors in shallow water settings (Morse et al. 1985;
Rude and Aller 1991; Walter et al. 1993). This process, which preferentially affects the
less stable polymorphs, aragonite and high-Mg calcite, is also significant in ancient
shelf environments (e.g. Hendry et al. 1995, 1996; Munnecke and Samtleben 1996;
Munnecke et al. 1997; Sanders 2003). There is now increasing recognition of its poten-
tial to skew the marine fossil record of aragonite shells, particularly molluscs (Cherns
and Wright 2000; Wright et al. 2003; Bush and Bambach 2004; James et al. 2005;
Knoerich and Mutti 2006). Yet the mollusc fossil record is good (Harper et al. 1997;
Harper 1998), and Kidwell (2005) concluded that taphonomic bias was unimportant in
the macroevolutionary record of bivalves. The skeletal lagerstätten represented by early
silicified faunas that have been used to quantify the loss of molluscs (Cherns and Wright
2000; Wright et al. 2003) remain relatively rare in the fossil record. Hence, it appears
that other processes that increased the preservation potential of aragonitic faunas, such
as storms, temporary sea floor anoxia, and synsedimentary cementation, are also impor-
tant in capturing fossil biodiversity (Cherns et al. 2008).
Molluscs biologically mediate the precipitation of their calcareous shells directly
as aragonite and/or calcite layers composed of a variety of crystalline structures
(Lowenstam and Weiner 1989; Falini et al. 1996). The earliest mollusc shells in the
Cambrian were aragonite (Runnegar and Bentley 1983; Porter 2007). As molluscs
evolved and diversified, calcite was incorporated in some groups as the outer shell
layer (pteriomorphs), or forming all but a thin hypostracum (oysters). The func-
tional significance of the evolution of calcitic layers or shells for epifaunal habits
relates to advantages of lower solubility and density (Carter 1980; Carter et al.
1998). In some bivalves, environmental factors such as seawater temperature affect
the secretion of calcite (Carter et al. 1998). There is some evidence that ambient
seawater may have exerted control in the evolution of calcitic shelled groups during
‘calcite sea’ intervals (Harper et al. 1997). However, the wider pattern of mollusc
shell mineralogy over time does not appear to correlate with alternations of ‘arago-
nite’ and ‘calcite seas’ (Stanley and Hardie 1998; Stanley 2006).
Shell mineralogy and microstructure tend to be conservative among species,
genera and families (Taylor et al. 1969), which makes it possible to extrapolate to
3 Aragonitic Dissolution and the Fossil Record 81
fossil taxa even where the shell is poorly or not preserved. Shell microstructures
include prismatic calcite (simple/fibrillar) or aragonite (simple/complex), foliated
calcite, nacreous aragonite, homogeneous aragonite, crossed-lamellar and complex
crossed lamellar aragonite (Carter 1980, 1990). The surface area to volume ratios
of crystallites (SAV), and the content of organic matrix in the shell are both impor-
tant in determining resistance to dissolution through chemical reactivity (Glover
and Kidwell 1993; Kidwell 2005; Valentine et al. 2006). Shells with high SAV and
high organic content, such as nuculoids, are most vulnerable to early dissolution
(Flessa and Brown 1983). Size, shell thickness and ornament are further measures
of robustness (e.g. Behrensmeyer et al. 2005). Juveniles whose shells are thin and
weakly calcified are especially prone to dissolution (Green et al. 2004).
There is a strong correlation between life mode and shell composition. Infaunal
bivalve groups are aragonitic-shelled, while the major epifaunal group, the pteri-
omorphs, are typically calcitic or bimineralic. Therefore, those compositionally
more labile shells, if remaining buried in the sediment during post mortem decay
of soft parts, are already in the taphonomically active zone (TAZ) where the poten-
tial for dissolution is extensive (see below). This contrasts with a presumption of
better preservation potential for infauna because when they die in the sediment they
are protected from seafloor processes of destruction and diagenesis (e.g. Kier 1977;
Cummins et al. 1986). It is however notable that burrowers typically come up to the
surface when stressed (e.g. Oschmann 1988, 1991); in situ preservation of infaunal
bivalves commonly represents rapid burial.
2 Environments of Dissolution
Immediately post mortem, in marine oxygenated settings molluscan remains are

altered by chemical, physical and biological processes. Scavenging and microbial
decay rapidly remove organic tissue, and intraskeletal organics can produce acids
that are corrosive to mineralized skeletal elements. Three diagenetic environments
are important in dissolving aragonite: the seafloor, the TAZ and shallow sub-TAZ
burial (Fig. 1).
2.1 Seafloor Diagenesis
Shells at the seafloor are subject to transport, abrasion, sorting, bioerosion/encrus-

tation, dissolution and cementation. Physical breakdown into constituent compo-
nents increases susceptibility to attrition, abrasion and dissolution, and increases
surface area for boring micro-organisms. Molluscan and other shells are typically
destroyed before they can be buried; if this were not the case shell beds would form
through general accumulation (Davies et al. 1989). Seafloor dissolution of arago-
nite is particularly well known from Recent carbonate undersaturated cool-water
settings (e.g. Alexandersson 1978, 1979; Freiwald 1995). On the other hand, over
82 L. Cherns et al.
Fig. 1 Environments of dissolution close to a carbonate sea floor. Shells are potentially destroyed
through physical processes, bioerosion and by dissolution already on the seafloor. If entering the
bioturbated sediment of the TAZ, acidity raised through decay of organic matter and re-oxidation,
for example producing H2S, leads to differential dissolution of aragonite and high-Mg calcite
shells, further filtering the shell assemblage. Only minor amounts of aragonitic shell material (e.g.
in situ deep burrowing bivalves) survive into the shallow sub-TAZ burial diagenetic environment.
Carbonate liberated from early dissolution, at least partly contributed by shells in TAZ and shal-
low sub-TAZ environments, provides cement through diffusive transfer for limestone beds in
LMA successions (Munnecke and Samtleben 1996; Wheeley et al. 2008)
a 13-year time span, experimental studies in the warm seas of the Gulf of Mexico
and Bahamas show little corrosion of aragonite shells (Powell et al. 2008).
2.2 Taphonomically Active Zone (TAZ)
The TAZ is defined as the upper, bioturbated, mixed zone extending down from the
sediment–water interface (Davies et al. 1989). This is equivalent to the ‘active layer’ of
Sanders (2004) where dissolution of aragonite occurs due to acidity resulting from the
degradation of organic matter that is exacerbated by burrowing (e.g. Aller 1982; Aller
and Aller 1998; Sanders 2001). Most important are dissolution-precipitation reactions
that result from changes to pore-water saturation through bacterially-mediated oxida-
tion of organic matter and re-oxidation of reaction by-products such as solid phase
sulfides (producing H2S), as well as the build-up of CO2 from aerobic oxidation. The
TAZ, however, refers to more than the extent and depth of bioturbation. Aragonitic
Table 1 Net reactions of organic matter oxidation with regard to calcium carbonate saturation in
pore-waters of pure carbonate sediment. Vertical arrangement of reactions 1–4 reflects prevalent
redox reactions down section, or from a burrow wall into the adjacent sediment. In bioturbated/
bio-irrigated shallow-water sediments, reactions 1–4 may proceed adjacent to each other in a
patchy ‘redox-mosaic’ (After Sanders 2004)
Reactions of organic matter oxidation CaCO3 saturation state
1. Aerobic oxidation Down
CH2O + O2 = H2O + CO2
2. Aerobic oxidation of hydrogen sulfide produced by sulfate Down
reduction
HS– + 2O2 = SO42– +H+; H2S + 2O2 = SO42– + 2H+
3a. Sulfate reduction Down-up
2 CH2O + SO42– = HS– +HCO3– + H2O + CO2
3b. Sulfate reduction by methane oxidation (anaerobic methane Up
oxidation)
CH4 + SO42– = H2S + H2O + CO32–
4. Methanogenesis (two step process) Constant-up
4.1. 2CH2O + 2H2O = 2CO2 + 4H2
4.2. 4H2 + CO2 = CH4 + 2H2O
5. Dissolution of calcium carbonate due to production of carbon The role of carbonic
dioxide (reactions 1–3a) acid
CaCO3 + CO2 + H2O = Ca2+ + 2HCO3–
6. Dissolution of calcium carbonate due to production of H+ Control on pH
(reactions 1–3a)
CaCO3 + H+ = Ca2+ + HCO3–
7. Net equation of stoichiometric coupling of carbonate dissolution n/a
to organic matter oxidation (Ku et al. 1999, their equation 7)
2CaCO3 + 2CH2O + 2O2 = 2Ca2+ + 4HCO3–
molluscan bioclasts that survive the burrowed zone pass into the zone of accumulation,
or ‘non-bioturbate’ (i.e., no longer actively bioturbated) layer of Sanders (2004), where
anoxic redox processes and pore-water chemistry also influence their taphonomy.
Detailed reviews of the geochemical processes relating to syn-depositional to early
post-depositional carbonate dissolution are given by Sanders (2003, 2004; also Morse
and Mackensie 1990; Canfield and Raiswell 1991a; Martin 1999; see Table 1).
Bioturbation forces the movement of both solid and dissolved components
through redox mosaics. In Recent carbonate sediments of the Bahamas and South
Florida, the upper 50–350 cm are completely turned over within 100–600 years
(Tedesco and Aller 1997). Organic matter in the active layer of the TAZ is typically
driven hundreds to thousands of times through a cycle of aerobic oxidation to
methanogenesis (Sanders 2004), fuelling dissolution of vulnerable carbonate
components (i.e., aragonite and high-Mg calcite). Residence times for carbonate
bioclasts can vary greatly depending on the depositional setting. For carbonate settings,
components in cool-water regimes typically reside longer in the TAZ because of
lower accumulation rates than in tropical settings (Nelson et al. 2003). In rapidly
deposited and buried shell beds, vulnerable bioclasts may escape the zone of bio-
turbation and with close-packing there is increased potential for ‘self buffering’
(e.g. Kidwell 1991). Burrowing organisms bio-irrigate sediments by actively
84 L. Cherns et al.
pumping and channelling water through burrows (Martin 1999); this process has
been interpreted for burrow networks as far back as the Ordovician (Cherns et al.
2006). This facilitates oxygenation of sediments leading to aerobic decay of
organic matter, and allows back-flux of dissolved calcium carbonate from pore-
waters into the overlying seawater, also increasing sulfate supply and interstitial
water exchange (Sanders 2004). Both the rate and depth of bioturbation have
increased through the Phanerozoic, which may have enhanced the potential for
syn-depositional aragonite dissolution. Early Paleozoic (Ordovician) burrowing
depths are generally £10 cm (Droser and Bottjer 1989), although Orr (2003)
reported bioturbation depth of 4 m in the Arkansas Blakely Sandstone (Middle
Ordovician). Deep burrowing (£1m) becomes common only from Late Paleozoic
times (e.g. Bottjer and Ausich 1986).
2.3 Shallow Sub-TAZ Burial Diagenesis
This is distinct from both well documented near-surface seafloor diagenesis (e.g.
Smith and Nelson 2003), and deeper burial diagenesis characterized by compaction,
pressure solution and late cements. It starts with undersaturation of seawater-filled
pores with respect to aragonite and high-Mg calcite, and thus overlaps partially with
the TAZ, and continues until the supply of aragonite is consumed. Deeper marine pore
fluids are likely to stabilize any vulnerable bioclasts or partially dissolved bioclasts that
have survived processes nearer to the surface (Melim et al. 2002, 2004).
3 Taphonomic Windows
Processes leading to the preservation of the labile skeletal component of fossil

assemblages include early mineral replacement, as in silicified ‘skeletal lagerstät-
ten’, and event deposition involving rapid burial of shell beds. Other taphonomic
windows are produced by dysoxic episodes leading to shell plasters, and by hard-
grounds (Cherns et al. 2008). Here we review the temporal distribution of such
faunas. Reference is made where appropriate to the taphonomic and preservational
model presented in the following section (Section 4).
3.1 ‘Skeletal Lagerstätten’
‘Skeletal lagerstätten’ refer to rare, unusually aragonite-rich fossil faunas preserved

when early aragonite replacement arrests the dissolutional destruction of these
unstable shells. Silicification is one process that can preserve carbonate shells and
fine skeletal detail, and silicified faunas feature prominently among systematic studies
particularly of Paleozoic fossils (Schulbert et al. 1997). Both the primary skeletal
structure, and the relative rates of silica supply and carbonate dissolution, are important
in determining the replacement fabric (Carson 1991). Very early replacement is criti-
cal to preservation of aragonite shells. Holdaway and Clayton (1982) interpreted
pre-lithification replacement of bioclasts and trace fossils by silica as postdating
aragonite dissolution and occurring within the sulfate reduction zone at shallow
depths of 5–10 m. Aragonitic faunas are preserved (if rarely) in cherts forming in
this diagenetic zone; Upper Cretaceous ammonite moulds in flints associated with
chalk hardgrounds may indicate a raised sulfate reduction zone in response to
reduced bottom-water circulation and oxygenation (Carson 1991). Through the
Phanerozoic the source of silica for marine chert and silica-replaced fossils is
predominantly biogenic, derived from sponges, radiolarians and diatoms, but with
input also from volcanic deposits and terrestrial weathering (Maliva et al. 1989;
Kidder and Erwin 2001; Fig. 4a). A decline in shelf silicified fossil assemblages in
post-Paleozoic times corresponds to an offshore shift in biogenic silica and bedded
chert deposition (Kidder and Erwin 2001; also Schulbert et al. 1997; Fig. 4c).
The case studies referred to below range from Ordovician – Jurassic age, all bar
one representing silicified faunas and all indicative of early lithification (Cherns and
Wright 2009). For the Silurian example from Gotland, Sweden, a volcanic source of
silica is indicated by close association with bentonite horizons (Laufeld and Jeppsson
1976; Cherns and Wright 2000). Upper Ordovician silicified faunas from Kentucky,
USA also come from sequences with frequent bentonite horizons (Hoare and Pojeta
2006). The source of silicification in the two other cases is more equivocal. The
Lower Devonian case study from SE Australia has regional association with volca-
nic rocks (Johnston 1993). In the Jurassic example from South Wales, UK (Wright
et al. 2003), Mississippi Valley-type metallic mineralization (Fletcher 1988; Bevins
and Mason 1997) affecting underlying rocks may indicate hot spring environments,
with evidence for very shallow burial mineral replacement coming from silicified
burrow systems. The remaining case, from the Lower Carboniferous of the Mendips,
UK, is represented by faunas with carbonate preservation (Mitchell 1987), but where
very early lithification is indicated by the fine preservation of abundant small and
thin shells, including colour banding on some (Batten 1966).
The faunas are summarized briefly here to illustrate the potential skewing of fos-
sil biodiversity. All are characterized by aragonitic, mollusc dominated assemblages,
which contrast with those characteristically calcitic, mollusc-poor Paleozoic faunas
and the calcitic/bimineralic Mesozoic bivalve faunas that are typical of associated
shelf successions (Sepkoski, 1984; Paleozoic cf. Modern Evolutionary Faunas).
Extensive Upper Ordovician silicified faunas from limestones in Kentucky, USA
have formed the basis for many systematic studies of fossil groups (>55,000 speci-
mens; Pojeta 1971; review in Hoare and Pojeta 2006; Fig. 4c). From Middle Ordovician
times, brachiopods became prevalent among shelly faunas (e.g. Li and Droser
1999; Droser 2002). For example, in the middle Upper Ordovician of Kentucky,
brachiopods dominate faunas from offshore shelf to inshore sand shoals (Holland
and Patzkowsky 2004). In the Cincinnati Arch region, molluscs mostly comprise
<10% in faunas dominated by brachiopods and bryozoans (Novack-Gottshall and
Miller 2003). However, among the silicified faunas, both molluscs and brachiopods
86 L. Cherns et al.
are very numerous. In three faunas across an offshore-onshore environmental gradient

(Hoare and Pojeta 2006), species diversity is dominated by molluscs (58–84%),
with aragonite shells representing up to 71% (mean 47%). By abundance, arago-
nitic molluscs dominate in all three faunas (Fig. 4b-1, -2). The nearshore epifaunal
community is a very diverse, almost entirely molluscan assemblage dominated by
gastropods and pteriomorph (bimineralic) bivalves. The lagoonal community is
dominated by nuculoid bivalves, and chitons are also common. The open shelf
community is characterized by pteriomorphs, gastropods and brachiopods.
Silurian brachiopod-dominated shelly assemblages of level bottom shelf envi-
ronments have been extensively studied, and applied widely in paleoenvironmental
interpretations (e.g., Johnson 1996; Boucot and Lawson 1999). Faunas from
Gotland analysed in detail through a logged Lower Silurian section in inter-reef
carbonates appear typical (Vattenfallet Project; Jaanusson et al. 1979). Brachiopods
are overwhelmingly prevalent (72%), with corals (11%) and trilobites (12%), and
relatively infrequent molluscs (5%) (Fig. 4b-2). A marked contrast in the quality
of preservation between originally calcitic and aragonitic shells contributes to
taxonomic bias. A very diverse brachiopod fauna preserved as calcite shells
comprises >70 species, but includes limited new taxa (two new species, with
several less well represented left in open nomenclature; Bassett in Jaanusson
et al. 1979). This reflects how well known the calcitic faunas are as a conse-
quence of typically good preservation throughout the Gotland succession.
Mollusc preservation is mouldic and poor, except for bimineralic shells (e.g.
some gastropods) where the thin outer calcitic shell layer is preserved; as a result,
much of the taxonomy was left in open nomenclature (Jaanusson et al. 1979).
Lower Silurian silicified material from Gotland comes from comparable inter-
reef carbonate facies, with a brachiopod assemblage characteristic of the same
subtidal environmental zone, Benthic Assemblage 2 that allows direct compari-
son with part of the Vattenfallet section (Högklint b, c; Boucot 1975; Boucot and
Lawson 1999; Fig. 4c). However, although brachiopods are still common they
form a subsidiary component among a mollusc dominated assemblage. Since
both faunas here have been studied extensively and comprise >5,000 specimens,
far above the rarefaction ‘plateau’ for Silurian (and Gotland) shelly faunas
(Watkins 1996, 2000), they can reasonably be compared based on raw diversity
data. The silicified preservation reveals morphological detail also of aragonite
shells. Among a bivalve assemblage of 11 species, seven species (four genera)
were new (Liljedahl 1985), and shell composition by abundance was 96% arago-
nitic. An equally abundant gastropod assemblage, which is at least predominantly
aragonitic, still awaits systematic description but was reported as including 20
species (Liljedahl 1985). A significant and rare, aragonitic polyplacophoran (chi-
ton) assemblage includes seven new species (six new genera; Cherns 1998a, b).
Although brachiopods (15%) are common and diverse in this fauna, they are
hugely outnumbered by molluscs and include no new taxa (M.G. Bassett, N.M.W.
Cardiff, personal communication, 2007). A ternary diagram of shell mineralogy
by abundance illustrates the contrast between the ‘relict’ yet rich calcitic faunas
represented at Vattenfallet, and the silicified assemblage Fig. 4b-2). The silicified
bivalves (mostly nuculoids) and gastropods represent a deposit feeding assem-

blage (Liljedahl 1984). Many small shells and articulated bivalves (20–30%)
among the fauna indicate that this is an in situ to neighbourhood assemblage
(Liljedahl 1983, 1984, 1985).
In the Lower Devonian of SE Australia, brachiopod faunas are again generally
abundant and dominate most level bottom communities, while molluscs are sparse
(Talent et al. 2000). However, silicified limestones yield rich and diverse faunas
among which molluscs are common and greatly increase the known mollusc biodi-
versity. Johnston (1993) described a silicified bivalve fauna comprising 39 species,
of which 22 species (three genera) were new. Along an environmental gradient from
inshore to deeper shelf (Fig. 4c), aragonitic bivalves (nuculoids and heteroconchs)
dominate the inner ramp and deeper subtidal assemblages, while bimineralic pteri-
omorphs are dominant in an intermediate, shallow subtidal setting. Gastropods are
also common and diverse among the silicified faunas (Tassell 1982). Brachiopods
have similar species diversity to bivalves in the two shallower silicified faunas, but
are more diverse in the deeper shelf setting (Chatterton 1973).
The pattern identified from silicified faunas of under-representation of
molluscs in many shelf faunas continues in the Lower Carboniferous Hotwells
Limestone fauna from the Mendips, SW England (Mitchell 1987; Fig. 4c). In the
Carboniferous Limestone of the South Wales-Mendip shelf, coral-brachiopod
shelly assemblages are characteristic (Cossey et al. 2004). A very diverse, small-
shell fauna was obtained through extensive individual study (by Mr Cliff Salter)
of one thin ‘rubbly-weathering bed…with masses of corals’ (Green and Welch
1965, p. 27) in the massive crinoidal-oolitic limestones in Cliff Quarry, Compton
Martin. As well as the typical coral-brachiopod assemblage, there is an excep-
tionally abundant small-sized molluscan fauna. This is dominated numerically by
gastropods (>3,000), which include 98 species (46 genera), of which 18 are new
(Batten 1966). Although not a silicified fauna, the abundant small shells, with
colour banding preserved on some (Batten 1966), indicate a rapidly stabilized
fauna. The less numerous bivalve assemblage (~730 specimens) includes seven
species, and is dominated by aragonitic shells. The aragonitic shelled rostroconch
Conocardium is also common, and the fauna also includes a small chiton
assemblage.
In the Mesozoic, bivalves are by far the dominant shelly benthos. Wright et al.’s
(2003) silicified fauna came from the typically bivalve-rich Blue Lias facies
(Porthkerry Member) of the Lower Jurassic of South Wales, UK (Fig. 4c). Large,
thick-shelled calcitic and bimineralic pteriomorphs (Gryphaea, Plagiostoma,
Pinna) dominate shelly faunas in the alternating nodular limestone and shale facies
that is developed widely across southern Britain (Cox et al. 1999). In such assem-
blages, only anomalodesmatan bivalves represent originally aragonitic shells. Their
mouldic, commonly in situ preservation contrasts with the bedding assemblages of
pteriomorph shells, and they comprise no more than a minor component by abun-
dance (<2%; Wright et al. 2003; Fig. 4b-3). By contrast, in the silicified assem-
blage, where bivalves are still dominant, the characteristic pteriomorph genera form
only part of a far more diverse and well preserved assemblage (Fig. 2). Gastropods
88 L. Cherns et al.
Fig. 2 Lower Jurassic silicified fauna, Bridgend, South Wales, UK showing good preservation of
aragonitic (a–c, e), bimineralic (f) and calcitic (d) shells. (a) Allocosmia; (b) Cardinia – note
beekite rings; (c) ammonites; (d) Gryphaea cluster including articulated shells, single and imbri-
cated shells – note silicification from outer shell layer into inner void at top of cluster; e,
Pholadomya; f, Chlamys. Scale bars 1 cm (Images a, b, e, f courtesy of P. Hodges)
are also very common, and 77% of the mostly small shelled assemblage is arago-
nitic (Fig. 4b-3). The most abundant bivalve genera are a heteroconch and arcoid,
neither of which is present in the typical carbonate fauna. Lower Jurassic bivalves
are well known and this fauna lacks new species (Hodges 1987); the gastropods
include as yet undescribed taxa.
3.2 Other Deposits Capturing Biodiversity
Skeletal lagerstätten remain rare in the fossil record, but all cases described above
are characterized by higher diversity and/or abundance of molluscs than their
comparator faunas. All show aragonite dominated assemblages, whose depletion
from faunas typical of associated successions is represented by a shift toward
calcitic/bimineralic faunas (Fig. 4b). The role of other, more frequent taphonomic
processes that increase the preservation potential of shells vulnerable to early
dissolution is reviewed below.
3.2.1 Storm and Shell Beds
Storm beds and shell beds can halt dissolution of vulnerable aragonite shells through
rapid burial below the TAZ (or zone of bioturbation; Cherns et al. 2008; Fig. 4a).
Storm events are commonly represented by concentrations of epifaunal shells and
exhumed shallow infauna (e.g. Kidwell and Brenchley 1994, 1996). These have
been considered proxies for the dominant faunal components, and hence as records
of paleocommunities (e.g. Li and Droser 1997, 1999; Boyer et al. 2004). Storm
beds and shell coquinas occur abundantly from the early Paleozoic, increasing in
frequency and thickness in late Cenozoic rocks (Kidwell and Brenchley 1994, 1996;
Fig. 4c). In the Cenozoic, molluscs are abundant in shelf faunas, and storm shell
beds in a variety of environmental settings commonly comprise scoured, transported
aragonitic bivalves (Hendy et al. 2006). Molluscan-rich storm event beds in older
rocks are also commonly dominated by such bivalves even when those are otherwise
uncommon in the fossil record (Fursich and Pandey 2003).
Many processes associated with the high energy of storm events, such as shell
disarticulation, fragmentation and abrasion during transport, are destructive for
fossils (Kidwell and Bosence 1991). Sediment erosion and reworking is likely to
bias the record of aragonitic shells through loss of partly dissolved, pitted shells and
early formed moulds. However, some processes increase the potential to preserve
aragonitic faunas. Removal of fine grained sediment and organic matter by winnow-
ing and transport reduces the drive for microbially mediated dissolution (Wright
et al. 2003). Rapid burial of shells reduces or avoids residence time in the TAZ, and
anaerobic decay of organic material within the sulfate reduction zone is associated
with increased alkalinity, favouring shell preservation (Canfield and Raiswell 1991a;
Table 1 (3a and 3b)). In storm concentrations of close-packed shells, buffering of the pore
water through dissolution of fragmented shells can lead to early firmground matrix
in which moulds of aragonitic shells can be preserved (e.g. Sanders 2003, 2004).
Storm beds and other shell beds are discussed here selectively to illustrate the
record of aragonitic biodiversity and abundance represented by these faunas
through the Phanerozoic by comparison with surrounding sediments (Fig. 4c).
A fuller account is given in Cherns et al. (2008).
Trimerellacean brachiopod faunas in storm beds are reported widely from
brachiopod-coral-stromatoporoid carbonate facies of Ordovician-Silurian age (e.g.
90 L. Cherns et al.
Webby and Percival 1983; Bassett 2005). These large, thick-shelled brachiopods
are interpreted unusually as aragonitic shelled because of their consistently mouldic
preservation (Jaanusson 1966). Thick storm beds of mostly disarticulated valves
form high density monospecific concentrations in shallow intertidal-subtidal
carbonate deposits. In situ shell banks are preserved in the shoal zone (Webby and
Percival 1983), where high wave energy ensures a low drive for dissolution (cf.
Wright et al. 2003) because of the removal of fine particulate organic matter.
Storm-winnowed shell beds in the brachiopod-dominated Khuff Formation
(Permian) of Oman were deposited in outer carbonate ramp environments
(Angiolini et al. 2003; Fig. 4b). These coquinas have notably molluscan-rich faunas
of bivalves (Dickins 1999), gastropods and scaphopods, among successions with
brachiopod dominated faunas. From the slightly younger Al Jil Formation (early
Triassic) of Oman, winnowed storm beds of shallow subtidal environments yield
mollusc-dominated faunas that are partly silicified (Krystyn et al. 2003; Fig. 4c).
Shell beds dominated by aragonitic bivalves (Promyalina) represent more proximal,
very shallow subtidal storm beds, while slightly deeper subtidal storm beds have
more pteriomorph bivalves (aviculopectinids); interbedded sediments are poor in
bivalves (Krystyn et al. 2003).
Triassic silicified faunas from shallow subtidal storm beds include diverse micro-
gastropod assemblages from Oman (Wheeley and Twitchett 2005). Other Triassic
silicified microgastropod faunas are also from storm induced shell beds, e.g. the
Sinbad Limestone (Nammalian) of the western USA, which includes scaphopods and
bivalves (Fraiser and Bottjer 2004) and the Gastropod Oolite of northern Italy (Nützel
and Schulbert 2005). Both these represent inner ramp carbonate deposits (Fig. 4c).
The Saltford Shale of the Lower Jurassic (Hettangian) of Worcestershire, UK
includes outer ramp storm-influenced shell beds that contain a diverse and abun-
dant molluscan assemblage, including >15 bivalve and several gastropod species
(Fig. 4c). Many of the originally aragonitic bivalves (e.g. Cardinia, Grammatodon,
Mactromya, Neocrassina, Pholadomya, Modiolus) are well preserved (Fig. 3).
These shell beds most likely formed on oyster-encrusted, exhumed sandy hard-
grounds; they demonstrate taphonomic feedback/ecological succession with evi-
dence for storm and current winnowing and reworking (e.g. Kidwell 1986; Tsujita
et al. 2006).
From the Upper Jurassic-Lower Cretaceous of Kachchh, western India, bivalve-
rich storm beds occur among otherwise unfossiliferous siliciclastic successions
(Fursich and Pandey 2003; Fig. 4c). The storm beds are dominated by large bivalves,
all of which were originally aragonitic (heteroconchs including trigonioids, and
arcoids; Seebachia, Indotrigonia, Pisotrigonia, Megacucullaea). Thin shell lenses of
abraded, robust shells of calcitic Gryphaea accumulated during periods of sediment
starvation, but a notable lack of small, thin and originally aragonitic shells was
ascribed to diagenetic dissolution by Fursich and Pandey (2003).
In the Cenozoic (Miocene-Pliocene) of New Zealand, bivalve-rich shell beds on
a storm-wave dominated siliciclastic shelf comprise mostly aragonitic bivalves from
innermost to outer shelf (Hendy et al. 2006; Fig. 4c). Storm beds dominated by
aragonitic bivalves interrupt sequences with calcitic barnacle-bivalve-bryozoan
Fig. 3 Lower Jurassic Saltford Shale shell bed, Worcestershire, UK. (a) Section through a
winnowed shell bed with convex-up, thin aragonitic bivalve shells (cf. thick oyster shell bottom
right) and abundant microgastropods. (b–d) Details of exquisitely preserved micro-molluscs in
shell bed (a). (e) Plan view of bivalve dominated shell bed showing convex-up orientation of
several originally aragonitic shelled taxa. Scale bars (a), (e) 1 cm, (b–d) 1 mm
faunas (Nelson et al. 2003). Taphofacies range from amalgamated shell beds of
densely packed, disarticulated and broken shells to rapidly buried deposits with in
situ, articulated shallow burrowers (Hendy et al. 2006). By contrast to the shelf-wide
distribution of aragonitic shells, the robust calcitic shells of oysters dominate only in
inner-mid shelf environments in sediment starved beds and proximal tempestites.
92 L. Cherns et al.
Fig. 4 Model for taphonomic gradients and fossil preservation. (a) Environmental profile from
shelf/ramp to basin for siliciclastic and carbonate settings (terminology for carbonate ramps fol-
lowing Burchette and Wright 1992), showing the major controls of water energy, environments
where temporary dysoxia/anoxia may develop, sedimentary facies distribution (nearshore and
shoal grainstones, mid-outer ramp LMA, outer ramp–basin mudstones/shales), and distribution of
taphonomic windows. The drive for aragonite dissolution is higher in organic-rich muddy sedi-
ments of mid-outer shelf/ramp to basin settings and inner shelf/ramp lagoons. (b) Taphonomic
bias resulting from original shell mineralogy of shelly faunas across shelf/ramp to basin zones,
comparing faunas of taphonomic windows (shaded zones) to typical, or‘relict’, faunas (open zones).
1, Inner ramp shoals and lagoons, e.g. Ordovician; 1–1, Lower Ordovician (Cope 1996); 1–2,
Nearshore and 1–3, Lagoonal silicified Upper Ordovician (Hoare and Pojeta 2006); 1–4, trimerellid
banks (Webby and Percival 1983); cf. typical, brachiopod-rich faunas of inner-mid ramp (Williams
et al. 1981; Holland and Patzkowsky 2004). 2, Mid ramp; 2–5, Upper Ordovician open shelf
silicified (Hoare and Pojeta 2006); 2–6, Silurian silicified (Cherns and Wright 2000); cf. typical
brachiopod-rich faunas of Upper Ordovician (Holland and Patzkowsky 2004) and Silurian
3.2.2 Shell Plasters
Shell plasters refer to thin layers or pavements of aragonitic and bimineralic shells
preserved in dark, organic-rich mudstones representing environments prone to
temporary anoxia/dysoxia, such as lagoons and deep ramp or basin settings (e.g. Noe-
Nygaard et al. 1987; Oschmann 1988, 1991; Martill and Hudson 1991; Martill et al.
1994; Fig. 4a, b-4, c). Temporary anoxic/dysoxic events such as those caused by algal
blooms draw infaunal bivalves up onto the sediment surface where they die (Oschmann
1991). Residence time for aragonitic shells in the acidic TAZ remains critical, but rais-
ing of the redox boundary and the sulfide oxidation zone removes them from this zone
even at shallow depths. Without bioturbation to disturb the sediment, local alkalinity
may build up around the shell layers (e.g. Canfield and Raiswell 1991b; Sanders
2003). Diagenetic factors such as organic matter content, sulfate availability and iron
concentration control the style of shell preservation (Hudson in Canfield and Raiswell
1991b). In the dark, sulfide-rich shales of the Lower Oxford Clay, originally aragonite
fossils are preserved as aragonite or as pyritic moulds (Martill and Hudson 1991).
However, in the anoxic/dysoxic shale environments of the Posidonia Shale, shell dis-
solution at very shallow depths is evident from the reduction of mollusc shells to
periostracal (organic) films (e.g. Allison et al. 1995). Similarly, aragonite dissolution
is indicated by shell plasters in black shales restricted to bimineralic pteriomorphs such
as Bositra and Meleagrinella, where very thin shell preservation indicates loss of the
aragonitic inner shell layer (Oschmann 1993; Wilby et al. 2004).
Taphofacies contrasts between fossil preservation in dark grey and black shales,
comparable to those described above, are evident in the Middle Devonian of New
York, USA (Brett et al. 1991). Mass concentrations of nuculoid bivalves are
preserved as pyritized moulds in dark grey shales, while fossils in black shales are
decalcified, even the calcitic brachiopods (Dick and Brett 1986; Speyer and Brett
1991). The nuculoid beds, with many articulated or splayed individuals, likely
represent death assemblages of burrowers drawn to the sediment surface by stressed
conditions associated with the onset of a severe storm event, and then buried by the
later effects of that same event (Speyer and Brett 1991).
3.2.3 Hardgrounds
James et al. (2005) predicted that aragonitic shells should be preferentially
preserved at submarine limestone hardgrounds through rapid cementation of
Fig. 4 (continued) (Jaanusson et al. 1979). 3, Mid-outer ramp; 3–7, Ordovician storm bed (Wilcox
and Lockley 1981); 3–8 Permian storm bed (Dickins 1999); 3–9, Lower Jurassic silicified (Wright
et al. 2003); cf. background faunas, respectively. 4, Outer ramp–basin; 4–10, Jurassic shell plasters
(Oschmann 1991), cf. restricted pterioid faunas (Duff 1975). (c) Temporal distribution of skeletal
lagerstätten, storm bed and hardground faunas, and shell plasters across the environmental zones
(data from text, and Cherns et al. 2008, Table 1)
94 L. Cherns et al.
the host sediment (also Walker and Diehl 1985). This protects the delicate
solution moulds of molluscs from destruction through bioturbation. For exam-
ple, in hardgrounds of the Ordovician cephalopod limestones of Sweden,
large, originally aragonitic orthocone cephalopods are commonly preserved as
moulds (e.g. King 1990). In Ordovician and Jurassic hardgrounds, encrusting
organisms inside the moulds of molluscs were taken to indicate that shell dis-
solution took place very early in diagenesis (Palmer et al. 1988; Palmer and
Wilson 2004). It is not clear whether those moulds formed in direct contact
with overlying seawater, or if dissolution occurred in contact with modified
pore-waters in the near-surface sediment and the moulds were subsequently
exhumed and encrusted. The differential taphonomic vulnerability of aragonite
is evidenced by loss of the inner aragonitic shell layer of bimineralic bivalves
before encrustation of the calcitic inner shell faces (Palmer and Wilson 2004).
Intraformational conglomerates associated with hardgrounds can also preserve
evidence of aragonitic mollusc faunas, e.g. bivalve, cephalopod and gastropod
bioclasts abundant in the Ordovician Kanosh Formation, Utah USA (Palmer
and Wilson 2004).
3.2.4 Shoal Deposits
In high energy inner ramp, shoreface settings, well oxygenated waters and limited
organic matter reduce the drive for microbial dissolution, and thus the preservation
potential for aragonite shells is increased (Fig. 4a). In the coarse conglomeratic
limestones of the Lower Jurassic Sutton Member of South Wales, UK, formerly
aragonitic shells are preserved as open moulds or recrystallized to calcite, by con-
trast to their dissolutional loss in outer ramp Blue Lias facies (Fig. 4b-3; Wright
et al. 2003). Ordovician trimerellid brachiopods from carbonate shoal environments
are preserved as open moulds in situ forming shell banks (Webby and Percival
1983; see Section 3.2.1; Fig. 4c).
In the siliciclastic settings of the early Paleozoic Welsh Basin, rare inshore
shelf faunas are dominated by diverse assemblages of aragonitic bivalves preserved
as moulds, but molluscs are otherwise sparse among the brachiopod-rich shelf fau-
nas (Cope 1996, 1999; Ratter and Cope 1998). The Middle Devonian Hamilton
Group, and many Upper Devonian deposits, of the Appalachian Basin have both
bivalves and brachiopods very well preserved as external moulds in the coarser
siltstones and sandstones of nearshore to mid-shelf environments (Brett et al. 1991;
Speyer and Brett 1991). Preservation of surface ornament and epibionts on moulds
is consistent with relatively late shell dissolution in environments where bottom
circulation and aeration ensured that acid products of decay were flushed through
sediments. The moulds are less compacted and deformed than fossils in more off-
shore mudstones. It is notable that many of the diverse bivalves illustrated by Hall
and Conrad came from such facies (e.g. Bailey 1983), as well as other molluscs
(e.g. Rollins et al. 1971).
4 Discussion
4.1 Taphonomic Gradients and Molluscan Preservation:

A Model
The taphonomic windows outlined above (Fig. 4) define a bias against aragonitic
skeletons and illustrate the potential for early dissolution to skew the fossil record,
both in terms of mollusc biodiversity and of paleocommunity structure. Even in rela-
tively shallow tropical settings, extensive dissolution of aragonite (and high-Mg cal-
cite) takes place during very early burial (Walter et al. 1993). Some facies differential
is likely through higher rates of shell loss for bivalves in carbonate sediments than in
siliciclastics through bioerosion on the seafloor and TAZ dissolution (Kidwell et al.
2005). In low energy, offshore settings, much of the molluscan fauna is likely to have
been removed by shallow, early, microbially-mediated aragonite dissolution, even in
Mesozoic communities where fossil faunas remain mollusc dominated.
In inner ramp, shoreface settings above fair-weather wave base, where low organic
matter content and lack of shallow anoxia reduce the drive for microbial dissolution
in the TAZ, aragonitic shells can be buried until replaced by calcite or preserved as
open moulds (Section 3.2.4). Early cementation forming hardground layers prior to
dissolution allows ghosts of the labile aragonitic fauna to be captured (Section 3.2.3).
Early silicification in inner ramp environments preserves small shell, gastropod-
rich, diverse molluscan assemblages (Hoare and Pojeta 2006; Fig. 4b-1; Nützel and
Schulbert 2005). In the Cenozoic, storm beds increase in thickness and frequency
across inner-mid shelf/ramp environments, and preserve thick molluscan deposits
(Kidwell and Brenchley 1994, 1996; Fig. 4c). In the inner ramp environmental
zone, the preservation potential of aragonitic faunas is probably enhanced by
reduced drive for dissolution compared with quieter and more offshore settings.
In more protected, lower energy lagoonal areas, such as Florida Bay and the inte-
rior of the Great Bahama Bank (Walter and Burton 1990; Walter et al. 1993; Hendry
1993), organic rich sediment increases the drive for synsedimentary loss of aragonite
through microbially mediated dissolution. A silicified Ordovician fauna of molluscs
and brachiopods (Hoare and Pojeta 2006; Fig. 4b-1) demonstrates the potential skew-
ing of the fossil record. In such protected areas, more complete molluscan faunas can
be preserved by storm events (e.g. Radley and Barker 2000; Fig. 4c). Also, thin shell
plasters that formed as a consequence of dysoxic episodes, such as seasonal algal
blooms, comprise aragonitic faunas (Noe-Nygaard et al. 1987; Section 3.2.2; Fig. 4c).
Across the mid to outer ramp zones, current energy becomes generally lower,
and the frequency of storm reworking decreases (Fig. 4a). In bioturbated sediment
that becomes increasingly muddy towards the outer ramp, silicified lagerstätten
faunas suggest that many level bottom shelly faunas are likely to have been selec-
tively affected by aragonite dissolution (Section 3.1; Fig. 4c; Wright and Cherns
2004). In the shallow subtidal mid-ramp, Silurian and Ordovician silicified faunas
provide evidence for significant loss of aragonitic shells (e.g. Cherns and Wright
2000; Hoare and Pojeta 2006; Fig. 4b-2). In the muddier outer ramp setting, the diverse
96 L. Cherns et al.
Lower Jurassic silicified fauna (Wright et al. 2003) is dominated numerically by
two aragonitic bivalve taxa unrepresented in the typical Blue Lias fauna (Porthkerry
Member; Section 3.1; Fig. 4b-3). The potency of the aragonite dissolution process
is clearly evidenced by the abundance of limestone-marl alternations (LMA) in
mid-outer ramp settings through the Phanerozoic record (Westphal and Munnecke
2003; Fig. 4a). Many LMA, and especially those formed during ‘calcite sea’ inter-
vals and in cool-water carbonate environments, were likely sourced from molluscan
aragonite (Wheeley et al. 2008).
In subtidal settings, storm deposits associated with rapid burial that removed
shells from the TAZ can preserve aragonitic molluscs among a more complete fauna
(Section 3.2.1). Storm bed faunas are illustrated (Fig. 4b-3) from the siliciclastic
Ordovician succession of South Wales, UK (Wilcox and Lockley 1981) and Permian
carbonates of Oman (Khuff Formation; Dickins 1999; Angiolini et al. 2003). The
fidelity of such faunas varies with the magnitude of storm scouring, competency of
the storm current and thickness of the storm bed (e.g. Finnegan and Droser 2008).
Some selectivity may also result from physical destruction during transport. Thus it
is relatively rare that a snapshot of the community is captured. Single storm events
are typically thin (£10 cm) beds, and are most likely to show relative enrichment of
aragonitic shells. Thick (³50 cm) beds are mostly amalgamated, multiple event
concentrations (Kidwell and Brenchley 1994), and those formed during periods of
sediment starvation may be depleted in aragonitic shells (e.g. Jurassic Gryphaea
beds of Fursich and Pandey 2003; Section 3.2.1). In the late Ordovician (Cincinnatian)
of Ohio and Kentucky, USA, only the very thin, commonly lenticular shell beds are
rich in molluscs relative to brachiopods, while the widely traceable, major shell beds
have brachiopod–bryozoan–crinoid, calcitic faunas with few, bimineralic (pterioid)
bivalves (Brett et al. 2008; Dattilo et al. 2008).
Some areas of the sea floor are prone to surface dysoxia or anoxia, such as
lagoons where lack of tidal exchange leads to stratification, and in deeper water,
outer ramp to basin settings. In such muddy environments, a typically molluscan
fauna may become preserved as thin shell plasters (Section 3.2.3; Fig. 4b-4). These
represent a limited benthic fauna of small, thin shelled, aragonitic and bimineralic
bivalves, killed by temporary anoxic episodes and preserved as original, recrystal-
lized or pyritic shells (e.g. Oschmann 1988, 1991). Periodic dysaerobic sea floor
conditions in outer carbonate ramp environments are represented by shell beds in
the widespread ‘cephalopod limestone facies’ of early Paleozoic Gondwana (e.g.
Upper Silurian Kopanina Formation, Czech Republic; Gnoli 2003; Fig. 4c). Shell
pavements of large cephalopod shells were colonized by aragonitic bivalve faunas
(Kříž 1992), with all shells preserved recrystallized to calcite.
Temporal trends are evident from the distribution of several types of taphonomic
windows through the Phanerozoic (Fig. 4c). The rare, early silicified, mollusc-rich
skeletal lagerstätten are recorded from Ordovician through Jurassic (Schulbert et al.
1997; Section 3.1). Shell beds are considerably more frequent, but show changes in
thickness and extent; thin (mostly <20 cm), single event storm beds form the majority
among early Paleozoic shell beds, while by Neogene times thick (³50 cm), multiple
event beds are also very common (Kidwell and Brenchley 1994). In dysaerobic mud
environments, the typically sparse benthic faunas are largely infaunal, aragonitic
molluscs, whose preservation potential may be enhanced by episodic raising of the
redox boundary and sulfate oxidation zone (Section 3.2.2).
4.2 Molluscan Preservation During ‘Calcite’

and ‘Aragonite Seas’
An important consideration with regard to differential taphonomy through time is the

influence of ‘calcite’ and ‘aragonite seas’. The dominant abiogenic carbonate seafloor
precipitates are controlled by atmospheric pCO2 and/or Mg:Ca ratios in seawater
(Hardie 1996). In Recent oceans, aragonite, and to a lesser extent high-Mg calcite, are
the main precipitates at the seafloor at least in the tropical realm. Through the
Phanerozoic, similar periods of ‘aragonite seas’ (Precambrian – end Cambrian; end
mid Carboniferous – end Triassic; end Cretaceous – present day) have oscillated with
‘calcite seas’ (Ordovician – end early Carboniferous; Jurassic – Cretaceous; e.g.
Sandberg 1983). These periodic changes in inorganic carbonate precipitation broadly
correlate with patterns of calcification in some invertebrates and algae (Stanley and
Hardie 1998). It may at first seem that periods with more aragonitic taxa (i.e. ‘arago-
nite seas’) were intervals in geological history when taphonomic loss was potentially
higher. However, in an assessment of syndepositional dissolution through time,
Sanders (2003) found no correlation between ‘calcite’ and ‘aragonite seas’ and extent
of syndepositional dissolution, suggesting that site-specific conditions are more
important. The temporal occurrence of the taphonomic windows discussed above
concentrates on ‘calcite sea’ intervals, which cover the main distribution of silicified
fossil assemblages (Schulbert et al. 1997; Fig. 4). The effects of ‘calcite’ or ‘aragonite
seas’ seem to have been more important in influencing the calcification of some
groups (e.g. Ries 2005) rather than on shallow burial dissolution processes.
For the Ordovician, Palmer et al. (1988) and Palmer and Wilson (2004) proposed
that ambient ‘calcite seas’ dissolved aragonite shells directly at the sediment–water
interface (SWI) to form open moulds that became encrusted by contemporaneous
organisms. With recent modelling that predicts those ‘calcite seas’ were in fact super-
saturated with respect to aragonite (Riding and Liang 2005, cf. Locklair and Lerman
2005), it may be that biomoulds formed through dissolution in the shallow sediment,
either through interaction with modified marine pore-waters or through meteoric
leaching, and were later exhumed and encrusted (e.g. Kenyon-Roberts 1995).
5 Conclusions
The taphonomic effects of differential, early aragonite dissolution on the marine

shelly fossil record and biodiversity from carbonate and siliciclastic settings are
highlighted by relatively infrequent faunas capturing aragonitic shells. As well,
98 L. Cherns et al.
early shell stabilization forming skeletal lagerstätten, the processes leading to storm
and shell beds, shell plasters, hardgrounds and shoal deposits all enhance the pres-
ervation potential of originally aragonitic shells. A data-based model for tapho-
nomic gradients and molluscan preservation through the Phanerozoic indicates that
the early aragonite dissolution in lower energy settings such as platform interiors
(including lagoons), mid and outer ramps/shelves and basins was a major process
skewing the fossil record. Dissolution at relatively shallow depths in the TAZ is due
to undersaturation caused by microbially-mediated decay of organic matter and
related reactions. A substantial mineralogical shift in the shelly faunas, quantified
from examples across a shelf/ramp to basin profile, is away from aragonite-dominated
molluscan assemblages towards calcite or bimineralic-dominated, diagenetically
filtered ‘relicts’. Taphonomic windows record aragonitic, molluscan-rich faunas
from Ordovician times onwards. Although the temporal distribution of the several
types of deposit discussed is variable (e.g. silicified faunas), there is no apparent
correlation with the intervals of ‘calcite’ and ‘aragonite seas’.
Acknowledgments We thank Carl Brett (University of Cincinnati) and Peter Allison (Imperial
College, London) for constructive reviews of the original manuscript. JRW is grateful to Robert
Raine (University of Birmingham) for help in collecting Jurassic Saltford Shale material, and for
discussion on the origins of these shell beds.
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Chapter 4
Comparative Taphonomy and Sedimentology
of Small-Scale Mixed Carbonate/Siliciclastic
Cycles: Synopsis of Phanerozoic Examples
Carlton E. Brett, Peter A. Allison, and Austin J.W. Hendy
Contents
1 Introduction........................................................................................................................... 108
2 Small-Scale Sedimentary Cycles.......................................................................................... 111
2.1 Defining Cycles........................................................................................................... 111
2.2 Identifying Analogous Phases of Cycles..................................................................... 112
3 Examples of Small-Scale Cycles in the Phanerozoic........................................................... 115
3.1 Middle Cambrian: Great Basin USA........................................................................... 115
3.2 Late Ordovician; Eastern North America.................................................................... 121
3.3 Early Devonian; Mdaouer-el-Kbir and Khebchia Formations, SW Morocco............. 129
3.4 Middle Devonian; Hamilton Group of New York....................................................... 134
3.5 Lower Jurassic: Lias UK.............................................................................................. 137
3.6 Upper Jurassic to Lower Cretaceous; India................................................................. 145
3.7 Upper Cretaceous: Greenhorn Formation, Western Interior, USA.............................. 146
3.8 Cenozoic: Ashiya Group, Japan, and Punta Judas Formation, Costa Rica.................. 150
4 Discussion: Synopsis of Examples....................................................................................... 152
4.1 Basal Condensed Shell Bed Taphofacies..................................................................... 153
4.2 Dark Mudrocks............................................................................................................ 160
4.3 Proximal Siltstones and Sandstones............................................................................ 168
4.4 Diagenetic Carbonates................................................................................................. 171
5 Inferred Environmental Changes Through Small-Scale Cycles:
Implications for Cycle Genesis............................................................................................. 174
5.1 Environmental Energy................................................................................................. 174
5.2 Oxygenation and Geochemistry................................................................................... 175
C.E. Brett (*)
Department of Geology, University of Cincinnati, Cincinnati, OH 45221, USA
e-mail: C. [email protected]
P.A. Allison
Department of Earth Science and Engineering, Imperial College, London, UK
A.J.W. Hendy
Center for Tropical Palaeoecology and Archaeology, Smithsonian Tropical Research Institute,
Panamá, República de Panamá, USA
and
Department of Geology and Geophysics, Yale University, New Haven, CT 06510, USA
108 C.E. Brett et al.
5.3 Sedimentation Rates and Time-Averaging.................................................................. 176

5.4 Episodicity and Dynamics of Sedimentation............................................................... 176
5.5 Overview...................................................................................................................... 179
6 Long-Term Trends in Cyclic Taphofacies............................................................................. 180
7 Summary: Toward General Cyclic Taphofacies Models....................................................... 182
References................................................................................................................................... 186
Abstract Small scale cycles deposited over 10–100 kyr are a common component
of Phanerozoic shelfal deposits. A combination of detailed outcrop analysis and data-
mining from published literature of cycles largely deposited in greenhouse regimes
reveals a series of recurring sedimentological, paleoecological, and taphonomic
motifs. In general, each cycle is composed of three to four components: (a) a basal
skeleton-rich bed with evidence of condensation and, in some cases mineralization;
(b) a medium-dark gray siliciclastic mudstone/shale interval; (c) a calcareous and/or
silty mudstone interval with common concretionary, diagenetic overprint. A series of
exemplars are highlighted from proximal and distal shelf settings and described using
a depositional sequence approach. The cycles studied include examples deposited
under greenhouse (Cambrian, Ordovician, Devonian, Jurassic and Cretaceous) and,
for comparison purposes, icehouse (Neogene) conditions. The fact that repetitive pat-
terns can characterize deposits that formed over a 500 million year interval is striking.
The primary taphonomic moderator in these cycles is rate of sedimentation, which
varies exponentially from sediment-starved concentrations to obrutionary deposits.
The occurrence of a persistent motif over this time scale suggests that biological inno-
vations, which might be expected to impact upon fossil preservation, have in fact been
overprinted by the extremes of sedimentation preserved in these small-scale cycles.
Having a skeleton, which is twice as resistant to abrasion, is of little import when
sedimentation is dominated by the extremes: instant obrution or condensation.
1 Introduction
Small-scale cyclicity, typically of meter-scale, is pervasive through geologic time

(Fig. 1). The advent of cyclostratigraphy recognizes this ubiquity of cyclic sedi-
mentation as a critical tool not only in stratigraphic correlation (Vail 1987; Vail
et al. 1991; Coe 2003; Catuneanu 2006), but also for understanding the temporal
context of physical and biotic processes (House 1985, 1995). The inference that
many cycles are periodic and related to Milankovitch orbital variations potentially
enables them to be used as a geologic “metronome” (Gilbert 1895; Berger et al.
1992; deBoer and Smith 1994; House and Gale 1995; Hinnov 2000, 2004). This
regular “pulse” is expressed to greater or lesser extent at different times during the
Phanerozoic as a result of long-term secular variations in climate and environmental
regime (Fig. 1). Cycles may be amplified during global icehouse climatic phases as
the result of large amplitude glacioeustatic fluctuations. Calcite vs. aragonite seas
also may play a role in skeletal carbonate preservation (see Wilson and Palmer
1992; Stanley and Hardie 1998). A general sincrease in deep bioturbation has no
doubt had the effect of homogenizing thin beds and producing distinctive fabrics
4 Comparative Taphonomy and Sedimentology of Small-Scale Mixed 109
SKELETAL HARDPART SHELL BED SMALL-SCALE EXPRESSION

DIVERSITY THICKNESS CYCLE MOTIF OF CYCLICITY
0
Neogene
ice
Increasing
biodiversity
a
Paleogene
100 Cretaceous greenhouse
Jurassic
200
Triassic b
Time (Ma)
icehouse
Permian Increasing shell bed
bur r owing
Increased
300
intendsity
thickness
Carbon-
iferous
Devonian
greenhouse
400
Silurian c
Ordovician
500
Cambrian
ice
warm cold
BIOTURBATION GLOBAL CLIMATE
Fig. 1 Schematic of the Phanerozoic time scale illustrating the interplay between the regular beat of
climatic/sea-level cycles and long term, secular changes in climate, the greenhouse-icehouse super-
cycles, changes in biodiversity of skeletonized marine benthic faunas (note: black, medium gray, and
light gray shaded areas represent the biodiversity of “Cambrian”. “Paleozoic”, and “Modern” faunas,
respectively) and bioturbation. Small-scale cycle motifs include: (a) late Neogene decameter-scale
cycle; (b) Carboniferous coal-centered cyclothem, 3–5 m thick; (c) Cambrian meter-scale cycle.
Note amplification of cycles during icehouse times. Diversity curve modified from Sepkoski (1997),
fossil images from Sepkoski (1984); see text for further discussion of the schematic
(Droser and Bottjer 1988). Moreover, the abundance and type of skeletal material
available for formation of shell beds has varied greatly from Cambrian to Neogene
times (Fig. 1). A secular increase in skeletal production and durability may have led
to a general increase in thickness of skeletal limestones, a key component of cyclic
sedimentation (Kidwell and Brenchley 1994; Kidwell et al. 1996).
Milankovitch band oscillations of climate, sea level and ocean chemistry produce
distinctive lithologic, taphonomic and paleoecological signatures that may be modu-
lated by the prevailing climatic regime of greenhouse vs. icehouse megacycles (Fischer
1980, 1984). A number of parameters may co-vary in cycles, including relative water
depth, sedimentation rate, geochemistry, and benthic oxygenation. Milankovitch-
related climatic variations may produce transgressive-regressive, redox, or dissolution
cycles, cyclic variations in sedimentation, or combinations thereof (see Fischer 1980,
1984; Schwarzacher and Fischer 1982; LaFerriere et al. 1987; Einsele and Ricken
1991; Ricken 1991, 1994). These parameters are among the most important in controlling
marine biofacies and their preservation as fossil assemblages (Bennett 1990; DiMichele
et al. 2004). For example, water depth oscillations may cause lateral tracking of dis-
tinctive benthic communities (Brett et al. 2007b) leading to variation in the type and
abundance of skeletal accumulations or trace fossil assemblages (Savrda and Bottjer
1991, 1994). Predictable variations in sedimentation rate, related to sea level or climate
oscillations, in turn, may have a very significant influence on the concentration or dilu-
tion of skeletal material as predicted by the R-sediment model for shell bed accumula-
tion of Kidwell (1985, 1986, 1989, 1991a). In addition, variation in burial rates will
have an important influence on the taphonomy of skeletal material. Modelling predicts
that the degree of taphonomic degradation should be positively correlated with extent
of skeletal concentration, if rates of burial are indeed responsible for skeletal concen-
tration. Alternatively, skeletal concentration may be related to variations in skeletal
production (Tomasovych et al. 2006). In turn, correlated variations in sediment geo-
chemistry may leave a strong imprint in preservation of fossils. For instance, the
development of a persistent zone of sulfate reduction during times of lowered sedimen-
tation may lead to formation of carbonate concretions that encapsulate fossils.
Herein, examples of small-scale cycles through the Phanerozoic (Figs. 1 and 2)
are reviewed and compared, a generalized model of physical–chemical change
through an idealized cycle is proposed, and a standardized approach to describing
cycles and their litho-, bio- and taphofacies is established. This paper begins with
an overview of well-described late Neogene examples of short-term cycles (Fig. 3).
This facilitates a comparison of cycle architecture in ancient examples to those
b
a
d
b
a
d
1m
Fig. 2 Idealized cycles modeled on the Jurassic Blue Lias, showing possible positions for placing
cycle boundaries. (a) At base of thin shell hash; (b) at base of black shale; (c) at base of concre-
tionary carbonate; (d) at top of concretionary carbonate. Note that the sharp base and top of the
concretionary carbonates (marked by arrows) probably do not represent useful cycle boundaries
because they typically represent diagenetic rather than primary sedimentary contacts
MFS
A1
SB
MFS
A2
A1
SB
1m
Fig. 3 Idealized, 40-thousand year cyclothem from the Pleistocene Matemateaonga Formation in
New Zealand. Sequence interpretation following Hendy et al. (2006). SB, sequence boundary;
MFS, maximum flooding surface. Note the following portions of this cycle. (A-1) Basal transgres-
sive shell bed; (A-2) secondary condensed “backlap” shell bed; (B) thick, fine-grained highstand
portion of cycle; may show concretions; (C) regressive or shallowing-upward portion of cycle
showing increasing abundance of graded storm deposited shell hash and sandstone beds
accumulated in an interval from which changes in global sea level oscillation, basin
subsidence, and sediment flux is well understood. This summary is followed by a
review of examples of taphofacies in small-scale cycles from Cambrian to
Paleogene time in order to determine common or unifying features of cycles.
2 Small-Scale Sedimentary Cycles
2.1 Defining Cycles
Herein, small-scale cycles are defined as those that encompass tens to a few hun-
dreds of thousands of years (kyr). Thickness varies substantially within such
sequences and may vary by an order of magnitude across their outcrop area.
We specifically focus on offshore mixed fine-grained siliciclastic/carbonate cycles,
particularly those that show concentrations of skeletal material in portions of the cycle.
Particular focus is applied to evaluating the impact of climatic and sea-level oscillation
on taphonomy and sedimentation. To provide a degree of control on the motifs of
cycles for comparative purposes we concentrate on cycles formed during greenhouse
phases of the Phanerozoic Eon, i.e. early to middle Paleozoic, the Jurassic-Cretaceous,
and Paleogene (Figs. 1 and 2). Future work will be directed towards elucidation and
comparison of cyclic patterns of a similar scale developed during icehouse phases,
including those from the Carboniferous-Permian and Neogene.
An important question that arises is: how are the cycle boundaries to be defined?
If sedimentation is continuous and the cycle is symmetrical, one could arbitrarily
choose to “begin” a cycle at any particular contact of recurring facies, provided that
this point is picked consistently. In many cases, however, sedimentation is discon-
tinuous, and the pattern is more obvious. A sharp surface separates one microfacies
from another forming a logical place to divide cycles. It is important in comparative
taphonomic studies to recognize analogous portions of cycles and to describe them
consistently and systematically with respect to cycle base and top (Fig. 2).
In certain cases the most obvious lithological contacts may not actually represent the
best boundary for cycles (Fig. 2). An excellent example is the well-known Blue Lias
cycles from the Lower Jurassic of southern England (Hallam 1957, 1960, 1964, 1986;
Elliott 1996; see below). These cycles are comprised of sub-tabular limestone and shale
alternations. At first glance it would seem obvious to place the cycle base either at the
top or base of the limestone beds (Fig. 2). However, these bed surfaces are irregular and
actually may cut across primary sedimentary boundaries. They clearly represent diage-
netic boundaries, the positions of fronts of concretionary cementation within pre-
existing sediments. In actuality, sharp primary sedimentary surfaces occur slightly
above the tops of the limestones at the bases of black or dark gray shales, or at thin
skeletal lags along the boundaries between such dark shales and underlying gray marls.
The latter clearly represent the primary sediment from which the concretionary carbonates
have formed by diagenetic enhancement (Hallam 1964, 1986; Weedon 1985; House
1986). Moreover, not every cycle shows the diagenetic cementation (Fig. 2).
Herein, cycle bases are defined as the bases of skeletal lag deposits that sharply over-
lie gray, frequently diagenetically enhanced carbonates. Thus, the concretionary beds,
while probably connected in terms of diagenetic history with overlying sharp surface
and/or skeletal lag deposits, occur in sediments that are portions of the underlying cycles.
The most obvious prominently weathering diagenetic limestones of the Blue Lias and
Collingwood Formations lie completely within cycles, not at their boundaries.
2.2 Identifying Analogous Phases of Cycles
Another problem encountered in a comparative taphonomic approach is to recognize

analogous phases of cycles in terms of pattern and inferred process. Having defined
an arbitrary, but objective, lower boundary, we can examine attributes of basal,
middle, and upper parts of the cycles. Frequently, in fact, three such divisions can be
recognized and we suggest that they are small-scale analogs of the transgressive,
highstand, and falling stage (regressive) portion of larger scale (smaller order) cycles.
That such sequence-like attributes can occur in cycles of just a few 10 s of kyr dura-
tion is strongly suggested by a series of studies on thick successions of mixed silici-
clastic and shell bed carbonates from the Neogene of New Zealand (Abbott and
Carter 1994; Abbott 1997; Naish and Kamp 1997; McIntyre and Kamp 1998; Hendy
et al. 2006), Japan (Kitamura and Kondo 1990; Ito 1992; Kitamura et al. 1994;
Kamataki and Kondo 1997; Kondo et al. 1998), Italy (Rio et al. 1996; Dominici
2001) California (Carter et al. 2002), and South America (Del Rio et al. 2001;
Di Celma et al. 2002; Cantalamessa et al. 2005). These age-constrained cycles were
influenced by 41,000–100,000 year. Milankovitch oscillation; in some cases they
can be linked with oxygen isotope stages and even reasonable estimates of magni-
tudes of sea level fluctuation. They therefore provide an excellent guide for interpret-
ing more ancient and more distal cycles for which age and depth constraints are
typically poorer. Although the Neogene cycles were developed during an icehouse
phase we argue that they supply a model for the general pattern and frequency,
though not the amplitude of sedimentary cycles seen throughout the Phanerozoic.
Despite differences in details, all of these Neogene studies show a common motif for
the cycles: (a) one to two shell-rich beds overlying sharp, erosive surfaces, the lower bed
typically referred to as an “onlap shell bed” (Naish and Kamp 1997), Type-1 shell bed
(Abbott and Carter 1994) or “base of parasequence shell bed” (Banerjee and Kidwell
1991) with mechanical processing and amalgamation of shells, at least in proximal areas.
The upper bed (“backlap shell bed” of Naish and Kamp 1997; “type-2 shell bed” of
Abbott and Carter 1994; “mid parasequence bed” of Banerjee and Kidwell 1991) repre-
sents gradual accumulation during times of sedimentary condensation; (b) a thick, fine-
grained succession with scattered fossils sometimes concentrated as patchy to lenticular
obrutionary, tempestitic, or lag accumulations; (c) an upper vaguely coarsening-upward
part typified by more sparsely fossiliferous coarser sediments with increased numbers of
siltstone, calcisilitite or sandstone layers; fossils are typically sparse and scattered but
may also be concentrated in lenses or at the bases of graded tempestite beds (Fig. 3). In
distal examples the upper portions of the cycles may occur in thicker and more sparsely
fossiliferous, silty mudstone or siltstone; in rare cases, concretions may occur in this por-
tion of the section and its top may be marked by heavy bioturbation.
Not all sedimentary cycles relate to sea level; other possibilities include climatic
variations and changes in storm frequency and intensity (Fig. 3). Nonetheless,
many cycles preserve features that are at least analogous to those expected from sea
level oscillations. These three portions of the cycle could be interpreted, respec-
tively, as (a) early to late transgressive systems tract TST), (b) highstand (HST) and
(c) regressive (RST; Naish and Kamp 1997) or falling stage systems tracts (FSST;
Plint and Nummedal 2000), in some cases with (d) a modified silty-calcareous and
diagenetically altered uppermost division. These lettered divisions (a–c and d,
when present) for analogous phases of cycles will be used throughout this chapter.
In some cases, particularly with distal representatives of cycles, the lower or a)
portion of the cycle may be nearly or completely missing such that a sharp surface
(flooding surface) separates the coarsest (typically shallowest) facies of the lower
cycle from the finer grained (deeper) portion of the overlying one. In such cases,
the small-scale cycles have what may be termed a “parasequence motif ”.
Nearly all of the Neogene shell bed studies have dealt with proximal shelf facies;
there is not a similarly detailed paradigm for distal mixed siliciclastic-carbonate
cycles. There are, however, still many aspects of these cycles that can be interpreted
within the framework of the small-scale sequence paradigm. Complicating factors
arise from the typically much thinner representation or absence of the TST portion,
the addition of dark, organic-rich shale facies, and various early diagenetic phe-
nomena, especially concretionary cementation of the upper HST or FFST sediments
that is typically lacking or subdued in more proximal cycles.
Proximal-distal cycle comparison is complicated by the differing thickness pro-

portions of analogous portions of cycles that are recorded in different areas.
The Late Ordovician (Caradocian) cycles of the Kope Formation and Collingwood
Member (Lindsay Formation; Brett et al. 2006; see below) are a good example of
this problem. In the Kope cycles the most prominent portions (in terms of outcrop
weathering) are ledges of skeletal limestone that define cycle bases (see Figs. 7–9).
In the Collingwood the analogous unit (see Figs. 10 and 11), both in terms of tapho-
facies and inferred sedimentational history, are very thin, lenticular shell hashes
that are not obvious on casual inspection. In several cycles these thin lags may be
absent such that the overlying dark shales rest directly and sharply on underlying
gray mudstones. This clear distinction may relate to rates of skeletal production; in
proximal shelf areas the relatively higher production of robust skeletal items may
lead to development of relatively thick skeletal accumulations during a given inter-
lude of reduced sedimentation. The same or perhaps longer interval of sediment
starvation may lead to a thin veneer of material in deepwater or proximal, high
sedimentation areas, where small, often thin-shelled organisms produce very minor
amounts of debris (Fig. 2). In such cases the cycle could be defined as having a
“parasequence motif”, whereas, in cases of high skeletal production, the relatively
thick skeletal limestone forms an important component of the cycle, analogous to
the transgressive systems tract of a larger scale depositional sequence.
The most prominent beds in a cycle may not be these basal shell-rich lags. In the
Collingwood Member, concretionary limestone ledges, analogous to those of the
Blue Lias, are very prominent. These could easily be confused with the ledge-
forming limestones of the coeval Kope but their taphofacies and inferred origin are
completely different. The concretionary limestone ledges are diagenetically
cemented muds that actually show evidence of having been rapidly deposited. They
are analogous to thin concretionary limestones or discrete concretions present
below ledge-forming skeletal limestones in some distal Kope cycles.
We define the bases of small-scale siliciclastic/carbonate cycles as the sharp
bases of skeletal limestones, or of overlying mudrocks where these skeletal concen-
trations are lacking. This is analogous with depositional sequences; in many cases
the sharp bases of condensed skeletal rich deposits appear to represent an aggrading
to retrograding trend toward more distal facies. However, a key question arises as
to whether these surfaces are merely analogous to or “homologous” to sequence
boundaries in the sense of being generated by the same type of process. It is
conceivable, for example, that sharp surfaces of small-scale cycles may be gener-
ated by a combination of sediment starvation and/or intermittent, storm-generated
erosion that requires no actual change of sea level. Nonetheless, many small-scale
cycles do show a condensed basal shelly carbonate lag with taphonomic evidence
for substantial reworking and processing of sediments; it is the analog of a trans-
gressive lag. This compact interval is followed, often sharply, by a mudrock (shale,
mudstone, marl) interval that is typically thicker than the shelly basal lag and
commonly shows evidence of increased frequency, thickness and episodicity of
mud or silt layers upward. Again, this portion of the small-scale cycle is somewhat
analogous to a larger scale highstand to falling stage systems tract. Early diagenetic
features, such as the above-noted tendency for upper portions of the mudstone to
become cemented into concretionary or tabular layers, complicate this portion of
many small-scale cycles. This cementation actually provides a unique taphonomic
window because contained fossils may be buttressed against compaction.
3 Examples of Small-Scale Cycles in the Phanerozoic
Small-scale cyclicity occurs throughout the Phanerozoic sedimentary record. These recurrent
facies are often inferred to relate to periods of climatic and/or sea level oscillation,
although the forcing mechanisms and frequency of such changes are difficult to deter-
mine. Small-scale cycles from distal and proximal shelf settings not only provide favorable
environmental settings for benthic communities, but also their preservation, through the
interplay of cyclic sedimentation rate and episodicity (through storm action).
In the following sections we review examples of small-scale cycles in a consistent
way that begins with the base of the most prominent skeletal concentrations, treated as
the “shell-rich” hemicycle, and progresses upward through the mudstone/siltstone hemi-
cycle. This paper focuses on offshore mid- to deep-ramp/basinal representatives of small-
scale cycles, rather than nearshore end-members of cycles that have been described
extensively in much previous sedimentological literature (Pattison 1995; Van Wagoner
and Bertram 1995; Hampson et al. 1999; Miall and Mohamud 2001). To improve com-
parability of examples, we have confined our study to the relatively thin cycles typical of
gently dipping ramps of epicontinental seas and distal foreland basins. For each exem-
plar, we discuss shallower and deeper examples, where possible these are correlative
units; for simplicity we refer to these as “proximal” and “distal” cycles although it should
be understood that in no case do we consider examples shallower than lower shoreface,
so that “proximal” examples mainly record medial ramp settings.
We discuss proximal and distal examples of cycles in a systematic way that
includes: (a) age and geographic location; (b) the thickness and variation of cycles;
(c) their regional persistence and variation; (d) characteristics of the cycle base and
top, and how they are defined; (e) variation in lithofacies within cycles; (f) the
variation of ichnofacies and the relative abundance of ichnotaxa; (g) paleoecologi-
cal characteristics of assemblages within cycle components; (h) the variation in
taphofacies, for instance the articulation, fragmentation, and diagenetic alteration
of skeletal hardparts; and, finally (i) variation in diagenetic facies, for instance the
occurrence of concretions, pyrite, siderite, and organic matter.
3.1 Middle Cambrian: Great Basin USA
Meter and decameter-scale cycles from the Middle Cambrian of the Great Basin,
USA (Liddell et al. 1997; Elrick and Snider 2002; Gaines and Droser 2005; Gaines
et al. 2005; Brett et al. 2009; Figs. 4 and 5) accumulated on a distally steepened ramp
a b N
15 0 100 km
Great
Salt Lake
Salt Lake City
D
er Juab Co.
R
UM
v
Ri
Millard Co.
M
MTT
en
Study Area 50 3
Gre
SS.
HOU
WA S A TCH
PL A TE A U
S E RANGE
Delta
70
2
N UT
r o
Marjum Pass
ve ra d
i n
lo 1
irg 0 5 km
r
Co Ri
ive
V
R
c ?
EPOCH FORMATION BIOZONE
Weeks Limestone
HOUSE RANGE
N EMBAYMENT
Bolaspidella
Marjum
Drum Formation
Mts.
MIDDLE CAMBRIAN
House
Range Wheeler Shale
Swasey Limestone
h e lf Ehmaniell a
teS UT
Whirlwind Fm.
o na Dome Limestone
Glossopleura
rb
Ca AZ Chisholm Shale
NV
Howell Limestone
CA
d Pioche Formation
Fig. 4 Location map of study area in south-central Utah and generalized stratigraphic column.
(a) Position of state of Utah in North America and of Delta, Utah and study area within Utah.
(b) House Range and Drum Mountains locations, as follows: (1) Marjum Pass; (2) Wheeler
Amphitheater; (3) Drum Mountains. (c) General paleogeography of the study area showing the
position of the House Range Embayment, a fault-bounded intra-shelf basin in which muddy sedi-
ments of the Wheeler and Marjum formations accumulated. (d) Generalized stratigraphic column
showing position of the Wheeler Shale in the Middle Cambrian (Modified from Hintze and
Robison 1975; Hintze and Davis 2003)
into an intrashelf basin, the House Range Embayment (Rees 1986; Elrick and Snider
2002). Recurrent taphofacies, including both concentrations of disarticulated, frag-
mented debris as well as extraordinarily well preserved trilobites and rare soft bod-
ied organisms, occur predictably within a spectrum of facies in sequences in the
Middle Cambrian Wheeler, and Marjum Formations of the Drum Mountains and
House Range in west-central Utah. The durations of the cycles are somewhat
Fig. 5 Aspects of small-scale cycles in the Wheeler Shale, east flank of Sawooth Ridge, Drum
Mountains. (a) T-1 marker bed, compact oolitic-oncolitic, ledge-forming limestone, sharply over-
lying a bundle of calcisiltites and fine calcarenites at top of underlying cycle; scale bar 50 cm.
(b) T-2 limestone ledge sharply overhanging shales and calcisiltites of third upper Wheeler cycle;
scale bar 50 cm. (c) Detail of the base of limestone ledge showing distinctly incised Planolites
trace fossils indicative of firmground condition of the underlying muds; scale bar 15 cm.
(d) Close-up of basal limestone ledge of T-3 showing intraclasts in oolitic packstone; scale bar
10 cm. Typical fossils of Wheeler gray, calcareous shale facies. (e) Articulated molted exoskeleton
of Elrathia kingi; scale-bar is 1 cm; Wheeler Shale, Wheeler Amphitheater, central House Range,
Millard County, Utah (f) carbonized algal disks; Wheeler Shale, Wheeler Amphitheater, central
House Range, Millard County, Utah; scale bar is 5 mm. (g) Pink sponge spicule mudstone from
condensed bed in lower Wheeler Fm., Stratotype Ridge, Drum Mountains. Mllard Co., Utah; bar
scale is 5 mm (From Brett et al. 2009)
uncertain, but Elrick and Snider (2002) relate them to contemporaneous peritidal
cycles that are inferred to represent precessional and short term eccentricity forcing
of minor sea-level oscillation.
3.1.1 Proximal Cycles
Proximal cycles are 3–20 m thick and comprise alternations of thin carbonates and
calcareous shales (Figs. 5 and 6). Small-scale cycles in the Marjum have been cor-
related over about 10 km within the House Range (Elrick and Snider 2002).
Correlation across ranges is difficult because of facies changes and lack of data
from intervening graben basins.
(a) Each cycle commences at the sharp base of a ledge-forming limestone bed
(Fig. 5a–c). These basal beds are compact, typically 5–50 cm thick, oncolitic to
oolitic and skeletal pack- and grainstones that include minor cross stratification.
In contrast to many later examples, skeletal fragments, including echinoderm
grains, trilobite sclerites, and rare articulate brachiopods, are a minor fraction of
these limestones. Lithoclasts eroded from underlying mudstones are common
within the beds. Beds show sharply-defined, corroded and mineralized upper con-
tacts. Thalassinoides-burrowed firmgrounds are typical of upper surfaces of these
beds and in some cases these burrow galleries have been unroofed, leading to
irregular depressions in the bed tops. Thrombolitic to stromatolitic mounds may
occur at the top surfaces of these beds and extend up into overlying shales.
(b) Basal limestones are overlain by calcareous, medium gray shale, and thin-bed-
ded wacke- to packstones with abundant, largely disarticulated polymeroid and
agnostoid trilobites represent late TSTs; cone-in-cone calcite may occur on trilo-
bites and may form small discoid concretions. These beds are commonly fol-
lowed by pale gray to lavender, siliceous mudstones rich in sponge spicules and
comminuted fossil debris that reflect even more condensed intervals (Fig. 5g).
(c) The overlying thin dark gray to black, fissile shales are typically barren, except
for carbonized discs of putative algae (Fig. 5f), and include rare soft-bodied
animal remains. Interbedded dark gray shales include abundant articulated
agnostoid trilobites and diminutive polymeroids.
(d) Overlying platy, calcareous shales that may make up more than half of the cycle
thickness include bedding planes covered with articulated bodies and molt
ensembles (groupings of associated molted exoskeletal elements) of polymeroid
trilobites, especially Elrathia from rapid blanketing of undisturbed seafloors by
calcareous mud layers (Fig. 5e). The presence of abundant molt ensembles
(i.e., associated articulated thoracopygidia and free cheeks discarded in molt-
ing) provides excellent evidence of in situ activity and an absence of transport.
(e) The Elrathia-rich beds pass upward successively into interbedded sparsely fossilifer-
ous platy to flaggy shale and thin, pale gray weathering calcisiltites and burrow-
mottled to nodular limestones. Lower surfaces of siltstone beds display hypichnial
burrows. Most beds are barren except for rare basal lags of calcisiltites including tri-
lobite sclerites. Rarely, articulated polymeroid trilobites, notably Asaphiscus and the
eocrinoid Gogia, are preserved at bed bases; these represent obrutionary deposits.
The compact oolitic to oncolitic pack- and grainstones are considered to be early
transgressive lag deposits. Their sharp basal contacts are small-scale sequence
boundaries, while sharp, mineralized hardground tops record drowning discontinui-
ties and early transgressive systems tracts (TSTs). The overlying early highstand
a
RELATIVE FOSSIL ABUNDANCE
CYCLES LITHOLOGY WATER DEPTH = 10/m2
T R
meter-
3- 5 m
scale
d a d a
TC MSS?
O, e
O, e T-4 SB
FSST
FS
HST
MFS?
o MSS
O
o
TC
r,e,b T-3 SB
FS
o,e,b
o,e,p
e
FSST
p FS
p
FS
scale (m)
HST
0.5
MFS
e, p 0
e
e
o, b
O,o,e
b
TST
o, p
e
o
o
MSS
O,o SP AG POL
TC
T-2 SB
RELATIVE FOSSIL ABUNDANCE

b WATER DEPTH = 10/m2
T R
CYCLES LITHOLOGY
TST
FSST
HST
scale (m) MFS

1
TST
0
MSS
SP AG AL
TC
SSB
Fig. 6 Detailed log of proximal, medial, and distal small-scale (fifth order) cycles in Middle
Cambrian Wheeler Formation with sequence interpretation, inferred relative water depth curve, and
fossil distribution; the schematic focuses on the meter-scale cycles. Minor cycles are submeter-scale
(HST) intervals are recorded in black to dark gray laminated shales. A combination
of lower dysoxic-anoxic conditions with a fluctuating oxycline and relatively rapid
episodic influx of fine-grained detrital sediment favored repeated burial and preser-
vation of abundant organic detritus and rare soft-bodied animals. Laminated cal-
cisiltites record shedding from nearby proximal carbonate banks during late
highstand to falling stage. Regression triggered a down-ramp progradation of the
carbonate bank and concomitant influx of peloidal carbonate silt and mud. These
rapid inputs of calcareous mud occasionally entombed in situ trilobite molts and
carcasses and Gogia, forming obrution deposits.
3.1.2 Distal Cycles
Distal representatives of meter-cycles in the Middle Cambrian occur in the down-

ramp Wheeler Shale section at Marjum Pass in the House Range (Fig. 6b). In this
case the cycles commence with: (a) thin (0.5–20 cm) lag deposits of skeletal debris,
including sponge spicules and disarticulated agnostoid and small polymeroid trilo-
bites, with rare oncolites. These beds are typically dark gray packstones that may
display yellowish-weathering, dolosilt-filled Thalassinoides burrows. Upper sur-
faces may show evidence of corrosion, commonly are ferruginous and may show
thin rinds of pyrite. The basal hash beds may abruptly pass upwards into (b) light,
purplish-gray spicular platy, siliceous mudstones. Agnostoid trilobites, typically as
disarticulated sclerites, occur in minor concentrations. (c) The major lower portion
of each cycle comprises fissile to friable barren, black shales. In some cycles these
shales lack skeletal fossils, but may include bedding planes covered with carbonized
algae. (d) Overlying, medium-dark gray, platy, calcareous shales that comprise the
bulk of the cycle thickness are mainly barren, but individual bedding planes may
include abundant acrotretid brachiopods and/or agnostoids. The majority of the
trilobites are articulated and dorsal side upward (see tables in Brett et al. 2009). In
some cycles, especially in the upper part of the Wheeler Shale, the polymeroid
Elrathia is present as complete, disarticulated sclerites or as articulated specimens,
including molt ensembles. The upper quarter to third of the cycle may feature: (e)
bundles of thin tabular to nodular, bioturbated calcisiltites. A notable addition to the
motif seen in proximal sections is the occasional presence of horizons of concretion-
ary limestone that lie just slightly below the lag deposits of trilobite skeletal debris.
Fig. 6 (continued) variations within fifth order cycles. (a) Two proximal ramp cycles; upper
Wheeler Fm.; east flank of Sawtooth Ridge, Drum Mountains, Millard County, Utah. (b) Distal
cycles; Wheeler Shale; Marjum Pass, Millard County, Utah. Sequence Stratigraphy: FSST, falling
stage systems tract; FS, flooding surface; MSS, maximum starvation surface; SB, sequence bound-
ary; SSB, sub-sequence boundary; TC, transgressive condensed beds; TST, transgressive systems
tract; note TC is the lower portion of the TST. Relative water depth: T, transgression; R, regression.
Fossils: SP, sponge spicules; AG, agnostoid trilobites; POL, polymeroid trilobites; IN, inarticulate
brachiopods, mainly acrotretids; AL, algae. Taphonomy: d, disarticulated, a, articulated; note bar
widths indicate abundance. Lettered symbols include: b, large burrows; e, echinoderm debris; O,
oncolites; o, ooids; p, phosphatic nodules; r, rip-up clasts (Adapted from Brett et al. 2009)
Differences between proximal and distal cycles include the absence of thicker
basal lag beds of oolitic and oncolitic carbonate and their apparent replacement by
thin (mm-scale) beds of trilobite debris. In only one instance were scattered onco-
lites found in this debris. A second key difference lies in the lesser development of
ribbon bedded calcisiltites in upper portions of the cycles. Finally, early diagenetic
features, particularly carbonate concretions, may be developed preferentially in
upper parts of cycles. Indeed, in places where thin skeletal lag beds are absent,
concretions may represent the primary evidence for cycle tops.
The absence of thicker oolitic/oncolitic limestones and a reduction in frequency
and thickness of “ribbon” limestone facies suggests increasing distance from the
shallow carbonate factory. We infer that concretionary carbonate cementation occurred
during intervals of relative sediment starvation associated with overlying skeletal
debris beds. During pauses in sedimentation cements developed within muds below
the sediment–water interface possibly in the zone of sulfate reduction or near the
upper boundary of the methanogenic zone.
Comparable cycles have been described from the somewhat older Middle
Cambrian Spence Formation in the Wellsville Mountains of Utah and at Oneida
Narrows, Idaho (Liddell et al. 1997).
3.2 Late Ordovician; Eastern North America
Alternating mudstone and carbonate-dominated successions are common in

cratonic settings in the Upper Ordovician (Caradocian/Cincinnatian; Edenian
Stage) of eastern Laurentia (Fig. 7). These intervals consist of distinct, correlatable
alternations of thick (meter- to decameter-scale) mudrock-dominated intervals and
thinner (decimeter- to meter-scale) shell bed-dominated units. These cycles have
been studied extensively from the standpoint of sedimentology (Tobin and Pryor 1981;
Jennette and Pryor 1993; Holland et al. 1997; Brett and Algeo 2001a), paleontology/
quantitative paleoecology (Holland et al. 2001b; Miller et al. 2001; Webber 2002)
and regional stratigraphy (Holland et al. 1997, 2001a; Brett and Algeo 2001b; Brett
et al. 2003, 2006, 2008; Kirchner and Brett 2008). The total duration of the Edenian
stage is debated, but is estimated at between 2 and 3 million years (Sadler and
Cooper 2004). Interpolation suggests that the meter-scale cycles may represent
bundles on the order of a few tens of kyr (possibly precessional or obliquity cycles),
while decameter scale cycles represent 100–400 kyr eccentricity cycles (Ellwood
et al. 2007). Thus, they form a model for early Paleozoic cycles.
The Edenian Kope Formation (Fig. 7b) and its lateral correlatives, the Clays Ferry
and Garrard Formations, are subdivisible into about 40 meter-scale cycles which,
in turn, comprise portions of some 10 decameter-scale cycles that show increased
bundling of limestone beds upward from a thick shale.
Fig. 7 Geologic setting of Cincinnati Arch, Ohio, Kentucky, and Indiana. (a) Paleogeography of
the Late Ordovician Edenian Age in eastern Laurentia: Taconic Highlands (From Brett et al. 2003
modified from Mitchell and Bergström 1991). (b) General stratigraphy of the Upper Ordovician
Cincinnatian Series in the Cincinnati, Ohio area. Kope Formation has been subdivided into
submembers on the basis of decameter-scale cycles of thick mudstone to bundled limestones.
(c) Cross section A-A¢ shows transect from shallow Lexington Platform into the Sebree trough
(Modified from Caster et al. 1955)
Paleontological gradient analysis using detrended correspondence analysis (DCA)

of whole faunal relative abundance data shows patterns of deepening and shallowing
within the decameter scale cycles (Holland et al. 2001a) and a crude (“third order”)
overall shallowing pattern within the Kope to Fairview formations (Fig. 7b). However,
detailed faunal studies of meter-scale cycles failed to find consistent patterns of shal-
lowing or deepening on the basis of DCA scores. A general – but not complete –
similarity exists between faunas of mudstone versus skeletal limestone portions of
any given cycle. However, fossils are extremely concentrated in the limestone por-
tions relative to the shales and include subtle differences in composition.
A typical Kope cycle (Fig. 9) is comprised of several components (Brett and
Algeo 2001b). (a) Bases are delimited by a sharp and typically erosionally-based
bundle of skeletal pack- to grainstones, in some cases expressed as a single compact
amalgamated bed with occasional rip-up clasts of mudstone (Fig. 8c). The lime-
stones are composed of variably disarticulated, fragmented, and in some cases,
abraded brachiopod shells, bryozoans and crinoid ossicles. In a basinward direction
these beds thin and become more compact skeletal grainstones just a few centimeters
Fig. 8 Limestone-mudstone cycles in Kope Formation, Fowler Creek, near Independence,

Kentucky. (a) Alexandria Submember, cycle 28, showing mudstone interval with only minor thin
beds bracketed between bundles of limestone beds. (b) Base of shale overlying limestone bundles
25 and 26; note limestones of bed 26 thinning upward into base of 1.5 m thick mudstone interval.
(c) View of bed 6 (Brent Submember), showing sharp, nearly planar base and prominently rippled
top with foreset beds in cross section; also series of small concretions in shale underlying this bed
(below an additional thin siltstone); Industrial Park off Rte. 17, Covington, KY
thick. Skeletal limestones preserve crude grading and rippled tops; firmground bur-
rows, including Thalassinoides are typical of bed tops. Hardgrounds with borings
(Trypanites) and encrusting organisms also occur on tops of a few of the skeletal
limestones and are indicative of sediment starvation. (b) The sharp, frequently
mounded to rippled tops of the major limestones are commonly overlain by sparsely
fossiliferous olive to dark gray mudstone, typically with thin stringers or lenses of
shelly debris, including highly comminuted and in some cases phosphatized or
pyritized fossil steinkerns. In several instances biostromes of whole bryozoan colonies
occur preferentially in the first few centimeters of shale overlying the limestone beds.
This interval is followed by (c) the main shale-dominated component of the cycle,
comprised of alternating packages of medium to dark gray shale and mudstone.
Fresh surfaces have sharp, scoured contacts between shales of subtly different
a-1 l
d s
s
s
c
s
o
b
o
a-2 l
a-1 l
Fig. 9 Representative meter-scale cycle from Upper Ordovician Kope Formation. Lettered divi-
sions include a-1, a-2; stacked skeletal limestones and thin shales; a-1 shows reworked concre-
tions at erosion surface at base of skeletal limestones (l). (a-2) Ripple-topped bed with hardground,
overlain by obrution deposit. (b) bulk of cycle thickness showing a stacking of event mud beds,
many of which show obrution beds (o) of crinoids or trilobites, or sharply based siltstones/calcisil-
tites (s) with burrows, including Diplocraterion. (c) cluster of siltstones (s) near top of cycle, may
show increasing input of silts during minor falling stage; (d) diagenetically altered siltstone with
concretions formed in older sediment during time of sediment starvation associated with overlying
shell bed. Note that the limestones at base and top are condensed relative to the main thickness of
cycle (see Fig. 32 for interpretation)
coloration or silt or fossil content. Bedding planes covered with shelly debris may
separate the shale packages. Thin and/or lenticular muddy packstones within this
interval are primarily confined to up-ramp facies of the cycles. A number of these
bedding planes preserve obrutionary deposits including articulated trilobites and
crinoid columns, the latter as densely packed, current aligned “logjams”. Most
cycles also include thin beds of parallel to small-scale hummocky cross-laminated
siltstone or calcisiltite. These have sharp bases, typically with distinct tool marks
and very minor lags of skeletal debris. Gutter casts occur associated with specific
widespread siltstone beds. The tops of the beds are hummocky to planar and fre-
quently heavily burrowed with Chondrites, Diplocraterion and other traces (Fig. 9).
In most proximal sections of the Garrard Siltstone, the upper parts of the cycles are
comprised of beds of planar to hummocky laminated siltstone and fine-grained
calcareous sandstones that typically show soft sediment deformation interpreted as
seismites (Seilacher 1982a; McLaughlin and Brett 2004). Lags of bivalves and
concavo-convex brachiopods (Rafinesquina, Strophomena) occur at bases of silt-

stone beds, in some cases as edgewise-stacked shell coquinas.
Kope cycles have been correlated in bed-by-bed detail along nearly 100 km of
the outcrop belt near Cincinnati, Ohio and into the subsurface (Fig. 10). These
detailed correlations demonstrate that not only are the condensed shell-rich beds of
allocyclic origin, but also that many of the subtle obrutionary event beds record
mud deposition of a regional scale.
3.2.2 Distal Cycles
The distal Kope Formation is dominantly dark gray shale but subtle cycles are
picked out by thin (0.2–5 cm) beds of skeletal pack- to grainstones composed of
crinoidal and trilobitic debris and small brachiopods (Kirchner and Brett 2008).
These thin limestones are overlain by medium gray to dark brownish gray shale,
which is largely barren except for fine thread-like pyritic burrows. A few bedding
planes are covered with current aligned graptolites; others display an abundance of
small inarticulate brachiopods (Leptobolus) and disarticulated trilobite sclerites,
including small Triarthrus and less commonly Cyptolithus and Isotelus.
An additional component seen in many distal Kope cycles is one or more hori-
zons of ellipsoidal concretions within the upper 5–15 cm of the mudstone under-
lying the sharp base of the directly overlying skeletal limestone bundle (Fig. 8c).
These concretions are typically nucleated on pyritic burrows. In some cases, the
concretions are laterally amalgamated to form a semi-continuous layer. Kope
concretions rarely contain exceptionally preserved, uncompressed fossils. An
excellent example is provided by elongate concretions that underlie bed 23 which
formed around fillings of shallow scours or gutters. Their silty infill contains
uncompressed current aligned complete rhabdosomes of graptolites (Kirchner
and Brett 2008).
Concretions are commonly re-worked, as evidenced encrustation by bryozoans
and crinoid holdfasts, and are occasionally re-worked into the bases of overlying
skeletal limestone beds. Concretion horizons can be traced from outcrops in which
they occur well below skeletal limestones to others in which they become adnate to
the limestones and/or fully incorporated. Such horizons indicate regional erosion,
typically accentuated in down-ramp directions, along which seafloor currents may
have removed several centimeters of mud (see Figs. 9 and 31).
The Upper Ordovician (Edenian to Maysvillian) Collingwood Member of the
Lindsay Formation, southern Ontario, Canada is a strikingly cyclic package of
shales and carbonates (Figs. 11 and 12; Brett et al. 2006). This unit is approximately
coeval with the upper Kope Formation and provides an outcrop illustration of the
down-ramp expression of similar scale cycles. About 10–12 cycles are 50–150 cm
thick and comprise four major components: (a) very thin lag deposits or in some
cases lenses of skeletal debris, including brachiopod shells, crinoid ossicles and
trilobite fragments; this unit is absent in some cycles, (b) dark gray to black, organic-
rich, laminated shales that grade up-section into, (c) medium to light gray, calcareous
Fig. 10 Correlated stratigraphic sections of the Alexandria sub-member (cycles 25–30) of the Kope
Formation from the vicinity of Cincinnati, Ohio/northern Kentucky. Note persistence of proportional
spacing of limestone bundles and a series of distinctive fossil event beds. Fossil occurrences and
abundances are shown to the left of the column. Black bars denote intervals where a particular fossil
was found at six or more of the seven sites. Intervals marked by dark gray or black bars and which
occur in relatively thin beds are considered to be marker beds (From Brett et al. 2008)
Fig. 11 (a) General time relationships and lithostratigraphy of Upper Ordovician strata in southern
Ontario, Canada. Note position of Collingwood Member. (b) Locality map for Collingwood Member
outcrops, inset map shows location of Craigleith Creek and foreshore, located along the southern
coast of the Georgian Bay (Nottawasaga Bay) near Craigleith Provincial Park. (c) Stratigraphic sec-
tion of the lower Collingwood Member at Craigleith, maximum flooding surfaces (MFS) and cycles
are indicated. See Fig. 12 for detailed log of Cycle III (Adapted from Brett et al. 2006)
a
SB
d
a
d
b
MFS
a SB
1m
Fig. 12 Typical cycle of Collingwood Formation based on Cycle III (see Fig. 11) at Craigleith,
Ontario, showing positions of obrutionary beds and shell hash beds. Note occurrence of well-pre-
served, non-compacted fossils in concretionary limestones. Lettered divisions are portions of cycle
analogous to those shown in Fig. 9. (a) Thin skeletal debris layer; (b) dark shales in lower part of
cycle; (c) gray silty mudstone of falling stage of cycle; (d) thick concretionary bed developed by
early diagenetic cementation of upper obrutionary mudstone (Modified from Brett et al. 2006)
shales or mudstones, and (d) lenticular to tabular concretionary argillaceous lime-

stones and light gray calcareous, fossiliferous mudstones or shales and marls.
Black shale units have a characteristically sharp basal contact and may rest on a
condensed shelly pavement. Fossils within shales are preserved as pavements or string-
ers of trilobite, ostracode and brachiopod debris, with strong taphonomic bias as a
result of prolonged exposure at the sediment–water interface. Bioturbated gray mud-
stones and marls include numerous low diversity orthid brachiopod pavements.
Persistent diagenetic tabular limestone bands include shelly beds that alternate with
less fossiliferous, calcareous mudstones containing non-compressed, spar-filled bur-
rows and articulated, sometimes in situ fossils.Collingwood cycles involve up-section
changes including: (1) benthic oxygenation from lower dysoxic to fully oxic biofacies,
(2) increased frequency and episodicity of sedimentation, (3) higher net sedimentation
rate within gray mudstone to carbonate intervals, (4) increased environmental energy
level, and (5) diagenetic cementation of muds a few centimeters below cycle tops.
A key paradox associated with these cycles is that the best-preserved fossils occur
within the sparsely fossiliferous concretionary carbonates near the tops of the cycles
(Fig. 12). These parts of the cycles record long periods of low sedimentation that
enabled diagenetic redistribution of carbonates. Yet the occurrence of extremely well
preserved trilobites and other fossils in the limestones clearly records episodes of rapid
influx of calcareous mudstone and engulfing of organism carcasses. The in situ lingu-
lids and spar-filled burrows within these beds reflect colonization of stabilized, perhaps
incipiently cemented mudstones. The latter mark the initiation of interludes of low
sedimentation following episodic deposition of up to several centimeters of sediment.
During these times, cementation of the muds ensued while thin veneers of marly, dis-
articulated skeletal hash appear to have accumulated a few centimeters higher.
Variation in fossil abundance in these beds is the result of cyclic variation in
sedimentation, ranging from periods of condensation to rapid burial. Consistency
of these variations, suggests an allocyclic mechanism for the Collingwood cycles
related to short-term eustatic sea level or climatic fluctuation.
3.3 Early Devonian; Mdaouer-el-Kbir and Khebchia

Formations, SW Morocco
The middle Emsian Mdaouer-el-Kbir Formation (formerly Rich 3, Hollard 1967)

of the northeastern Draa Valley in the vicinity of Foum Zguid in south central
Morocco (Fig. 13) includes excellent proximal cycles (1.5–10 m thick) of upward
coarsening mudstone, siltstone and fine-grained sandstone. Cycles are clustered
Fig. 13 (a) Map of study area in SW Morocco, note box: WS, Western Sahara; Maur., Mauritania.
(b) Stratigraphic column of the Lower Devonian showing position of the Hollardops beds
(Modified from Becker et al. 2004b)
into groups that are separated by thicker intervals in siltstone and mudstone, analo-
gous to the “big shales” in the Kope cycles described above. These cycles are pres-
ently under study and have not been fully characterized, but a brief description can
be given here (Jansen et al. 2004).
Each cycle commences with a sharp contact with underlying sandstone; hence
these cycles have a parasequence motif. Nonetheless many of the cycles are based at
distinctive shell rich bioturbated calcareous sandstone beds (a) that form the “caps” of
the sandy beds. The shell rich beds are comprised of disarticulated shells of spiriferids
(e.g. Euryspirifer) and strophomenid brachiopods, crinoid debris, bryozoans, and
homalonotid trilobites and include phosphatic nodules. They have sharp to abruptly
gradational contacts with underlying sandstones and overlying beds. The latter beds
are comprised of heavily bioturbated silty, calcareous mudstones, commonly with
Zoophycos and show stringers and pods of shelly debris. Shells are mainly disarticu-
lated and convex upward, but in some instances articulated specimens occur.
The main portion of each cycle comprises mudstones, siltstones, and muddy
sandstones (b). These are typically barren to sparsely fossiliferous, but include thin
accumulations of moldic brachiopod and bivalve shells. Upper portions of the
cycles (c) consist of hummocky cross-bedded siltstone and sandstone. Symmetrical
and interference ripple marks are present on some bedding surfaces. Nodular
cementation (d) occurs in the upper parts of sandstones in at least two of the 15 cycles.
Nests of articulated, in situ terebratulid brachiopods (Meganteris) in the sandstones
immediately below caps in two cycles are obrution beds comparable to the well-
preserved fossil beds noted at the tops of Ordovician cycles.
Overall, each cycle clearly records a period of sediment starvation and winnowing,
associated with development of fossiliferous, and commonly ferruginous or phosphatic
lag beds. Overlying sediments are characterized by an influx of increasingly
coarse-grained sediments with storm current and wave deposition.
3.3.2 Distal Cycles
The mid Emsian Hollardops Member of the Khebchia Formation is a 5–15 m thick
interval of rhythmically bedded limestones and shales that are well exposed in a series
of anticlines and synclines in the Draa Valley of southwestern Morocco, particularly
at Bou Tserfine, near Assa (Figs. 13–15). It is slightly younger than the proximal
facies of Foum Zguid discussed above but grades upslope into comparable facies.
These beds preserve a rich and well preserved trilobite fauna, including the trilo-
bites Hollardops mesocristata, Phacops saberensis, Psychopyge, Leonaspis, and
Scutellum (see Morzadec 1980; Schraut 2000; Chatterton et al. 2006 for description
of similar but slightly younger trilobite faunas from southern Morocco). Other fos-
sils are scattered, but include abundant large orthoconic nautiloids, small athyrid and
ambocoeliid brachiopods, and small solitary rugose corals (Becker et al. 2004a, b).
The Hollardops Member and overlying Brachiopod Marl and Sellanarcestes
Members interval at its type-section at Bou Tserfine, near Assa, Morocco includes about
160 cycles (238 beds) comprised of calcareous, medium to dark gray shales/
mudstones and decimeter scale concretionary limestones (Figs. 14 and 15). Thicker
shale intervals are not homogenous, but are composed of alternating dark gray, lami-
nated calcareous shale and medium gray marly mudstone, minor skeletal hash beds
include disarticulated and fragmented trilobite segments, cephala and pygidia, crinoid
ossicles, small brachiopods, and flattened molluscan shells (bivalves, gastropods and
orthoconic cephalopods). Thus, a general cycle, analogous to those described above
comprises: (a) thin skeletal lag, (b) medium dark gray to black shales, (c) calcareous
Fig. 14 (a) Typical outcrop of Lower Devonian Hollardops Limestone at Bou Tserfine; note
alternating thin-bedded limestones and dark shales. (b) Close-up of trilobite bearing limestones.
(c) Inset shows specimen of Hollardops in near vertical orientation; scale bar 1 cm (c is adapted
from Chatterton et al. 2006)
Fig. 15 Schematic of cycles in the Lower Devonian Hollardops beds at Bou Tserfine near Assa,
SW Morocco. Left column indicates inferred relative time-richness using hypothetical bars of
equal time increments; stratigraphic profile shows a series of cycles, each commences with thin
skeletal debris beds with trilobite fragments, small brachiopods and small solitary rugose corals,
that are sharply overlain by dark, sub-laminated shale recording minor dysoxic episodes (arrows),
and calcareous mudstones with minor shelly debris and articulated trilobites; note 10–15 cm thick
diagenetic limestone beds within gray marls yield well preserved trilobites in unusual orientations
and pyritic tubes that may extend from overlying soft mudstone into the cemented layer. Columns
to the right show relative benthic oxygenation, sedimentation rate (note pulses of sediment marked
“event”); stratigraphic thickness is partially dependent upon degree of diagenetic cementation, as
noted by arrows in far right column, which may prop open sediments to approximate original
thickness
medium gray mudstone, (d) lenticular to tabular concretionary argillaceous lime-

stones and light gray calcareous, fossiliferous mudstones or shales and marls.
Trilobite remains occurred in 128 (54%) of the beds, with articulated remains in 42
(18%). Limestones were more likely to include obrution beds (27.5%), and in the most
trilobite-rich middle portion of the section (50 alternating shales and limestones) about 40%
of beds and nearly 60% of limestones had articulated remains. Their highly weathered
character undoubtedly biases data collection from shales. Nonetheless, articulated phacopid
trilobites occur in several of the shale intervals and thin skeletal debris layers were com-
monly present in shales just above the contacts with underlying limestones (Fig. 15).
Limestone beds include articulated trilobite remains, including both complete
outstretched, gently reflexed, incompletely and completely enrolled specimens as
well as molt ensembles. The abundance of molt ensembles indicates a near absence
of transport and thus supports the in situ nature of the trilobites. In many cases,
articulated trilobites occur in attitudes perpendicular to bedding and single blocks
incorporate variably oriented specimens (bed parallel, inverted, upright, and vertical;
Fig. 14). All of this evidence strongly suggests that the trilobite and other fossil
remains were physically reoriented within viscous uniform muds, perhaps as mud-
flows that moved carcasses and other skeletal parts very slightly from their living
sites in some cases lifting the bodies or skeletal parts upward within the sediments.
Limestones containing well-preserved trilobites are up to 10 cm thick with
articulated remains running through the entire thickness (Fig. 15). These are essentially
structure-less argillaceous, concretionary micrites. There are no signs of lamination
in most although minor hash stringers are present near the bases and/or tops of some
beds. Cementation of these beds obviously occurred prior to compaction as the delicate
fossils are preserved without distortion. Trilobite bearing limestones commonly
show vertical pyritic burrows that may penetrate the entire thickness of the bed.
The limestone beds are bioturbated and, in a few instances, burrows that partially
disrupted the skeletons have intercepted the buried trilobite carcasses.
Intervening shales do not preserve fossils to the same spectactular extent
although some individuals, including articulated trilobites, were buried in varied
attitudes. The strong compaction of the muds, however, has greatly distorted these
fossils. Very thin skeletal debris layers appear near the bases of many shale intervals,
immediately above the concretionary limestone.
Very similar findings are reported from slightly younger beds at Foum Zguid
(Chatterton et al. 2006). Similar calcareous rhythmite beds occur in the Lower
Devonian Haragan Formation of Oklahoma (Campbell 1977; Ramsköld and
Werdelin 1991) as well as the Schoharie or Needmore Formation in Pennsylvania-
western Maryland (C. E. Brett, unpublished data).
Trilobite bed cycles involve up-section changes comparable in many ways to those of
the Ordovician cycles described above, including: (1) benthic oxygenation from lower
dysoxic to fully oxic biofacies, (2) increased frequency and episodicity of sedimentation,
(3) higher net sedimentation rate within gray mudstone to carbonate intervals, and (4)
diagenetic cementation of muds a few centimeters below cycle tops (Fig. 15).
It is particularly striking that the rhythmic, concretionary limestones appear to
transcend facies, occurring in both dysoxic facies with very low diversity assemblages
near the base of the Hollardops member to more abundantly fossiliferous sections near
the top. Hence, these beds record a regular, recurring cycle superimposed upon an
overall shallowing trend. Time series analysis of magnetic susceptibility data from
Bou Tserfine shows that these smallest cycles are superimposed upon larger trends
that may encompass 100–400 kyr (B. Ellwood, unpublished data). The number and
scale of cycles in relation to dating of the early Late Emsian suggests that these cycles
record overall durations of 10 s of kyr durations, possibly precessional cycles. The
concretionary limestone bands probably formed by carbonate redistribution over
several millennia. Nonetheless, more than a third of the concretionary limestones (in
some intervals nearly 60% of 50 beds) contain well-preserved, articulated trilobites.
Thus, in another sense, they reflect single event deposits of up to several centimeters
of mud within no more than days. The paradox is the same as that noted in the
Collingwood, and to a lesser extent in concretions of the Kope Formation. The non-
random representation of obrutionary muds in the cemented beds appears to reflect
the input of thick, perhaps carbonate rich mudflows in the later portions of short term
cycles, followed by periods of sediment starvation.
3.4 Middle Devonian; Hamilton Group of New York
Typical cycles are well documented from the Middle Devonian (Givetian) Hamilton
Group of the Appalachian basin in eastern North America (Brett and Baird 1985,
1986a, 1996). Proximal cycles are well developed in the upper Hamilton group of
central New York State and Pennsylvania, whereas more distal examples occur in
western New York (Figs. 16 and 17).
Fig. 16 Map of Middle Devonian Hamilton Group outcrop belt in New York State with superim-
posed inferred paleogeography. Numbers: (1) western New York shelf; (2) Finger Lakes trough;
(3) central New York sandy shelf (Modified from Brett and Baird 1986a)
Fig. 17 Decameter-scale cycles in the Middle Devonian upper Hamilton Group in western to
central New York State. Genesee Valley shows distal cycles in thin calcareous successions.
Cayuga Valley basinal cycles, central Finger Lakes. Tully proximal, coarsening-upward cycles of
central New York State. Note relative water depth curves showing the more symmetrical succes-
sions of the western sections as opposed to distinctly asymmetrical, shallowing upward, parase-
quence-type cycles in central sections more proximal to the source area (Modified from Brett and
Baird 1986a; see that paper for details and names of marker horizons shown at letters)
Mudstone-siltstone cycles are well represented in central New York where more
than 30 such cycles have been examined in detail. These are 1- to 5-m thick pack-
ages that commence with relatively thin (up to 0.5 m) shell hash beds and pass
upward into mudstones and or siltstones (Figs. 17 and 18). The typical cycle begins
with (a) a sharply based skeletal debris bed ranging from decimeters upward to
about a meter in thickness. These beds range from silty and muddy packstones to
grainstones, with abundant full valves to highly fragmented brachiopods, crinoidal
debris, bryozoans, and corals. Internal fabric ranges from moderately to densely
packed. Normal grading of shell material is observed in some locations. Admixed
with skeletal material near the tops of beds are lithoclasts and diaclasts in the form
of reworked concretions and bored phosphatic nodules.
a a
b c a
a
a
e
c 2 meters 2 meters d
1 meter
g
d
f
1 1
d
a
e
0 0
0
3
b
c
g d
d d
f
a
1 2 1 2 1 2 e
Fig. 18 Schematic of Hamilton Group distal and proximal meter-scale cycles; based on Wanakah
Shale, “trilobite beds. (a) Distal, calcareous cycles at Lake Erie shore near Eighteenmile Creek.
(b) Basinal cycles, central Finger Lakes. (c) Proximal cycles central New York State. Bars to the
right of each column show spacing of hypothetical time increments; close spacing indicates rela-
tive condensation of that portion of the section owing to winnowing and bypass or sediment
starvation. Large arrows indicate relative vectors of sedimentation (arrow 1) and subsidence
(arrow 2). Note that in the central New York shelf sediment supply may exceed subsidence result-
ing in winnowing and bypass near cycle tops. Concretions and shell beds of western sections (a)
and minor coral bearing layers in the central basin (b), and thin shell hash beds in the central New
York shelf (c) reflect intervals of sediment starvation associated with base-level rise. Facies shown
by letters include: (a) calcareous to concretionary shell-rich beds; (b) shelly limestone beds; (c)
coral-rich beds; (d) gray mudstone; (e) silty, bioturbated mudstone; (f) shell-bearing silt- and
sandstone; (g) reworked phosphatic shell hash associated with sediment starvation (Modified from
Brett and Baird 1986a)
Upper contacts of the beds are planar to rippled. In some cases they are mantled
with a layer of graded silt or calcisiltite. Other examples preserve corrosional dis-
continuities or hardgrounds. Biostromes of rugose and small aulaporid tabulate
corals may occur in these positions (Brett and Baird 1996; Brett et al. 2007a).
Basal shell rich facies pass abruptly into (b) dark gray shales with dysoxic fau-
nas and skeletal beds are sharply overlain by dark gray to black shales with scat-
tered small and brachiopods, especially thin shelled rhynchonellids (“Leiorhynchus”,
Eumetabolotoechia), ambocoeliids, and chonetids, as well as small mollusks. Most
fossils are disarticulated and may be fragmentary and partially decalcified. Medium
gray mudstones that follow typically show sparse, but slightly more diverse assem-
blages of small ambocoeliid and chonetid brachiopods and infaunal deposit-feeding
bivalves (e.g., nuculids, Palaeoneilo) and gastropods. Fossils and burrow tubes may
show pyritic internal molds.
These facies shallow upward into increasingly silty to sandy mudstones (c), which
are typically sparsely fossiliferous, but include lenses of skeletal debris, primarily of
brachiopods and disarticulated bivalves plus crinoid ossicles. Intercalated silty beds
exhibit hummocky cross-stratification and may be locally amalgamated.
Upper portions of cycles (d) are heavily bioturbated, especially by Zoophycos,
and pass gradationally into amalgamated silty to sandy mudstones. The upper 0.5–1 m
of the cycles may exhibit horizons of rusty weathering ellipsoidal to pipe-like con-
cretions, typically nucleated around pyritized vertical shafts of Zoophycos burrows.
These intervals are abruptly overlain by shell, coral biostromes and other skeletal
rich beds associated with the base of the next cycle.
3.4.2 Distal Cycles
More distal cycles from the Middle Devonian are represented by the “Grabau trilobite
beds” of the Wanakah Shale Member and the Smoke Creek bed of the Windom Shale
(Speyer and Brett 1986, 1988; Brett and Baird 1986a, 1996; Batt 1996; Fig. 18). These
cycles are comparable in many ways to the Hollardops beds of the Lower Devonian in
Morocco (discussed above). However, the number of successive rhythms is restricted
to three to ten successive beds, as opposed to the 140+ cycles seen in the Moroccan
section. Evidently, conditions conducive for diagenetically enhancing the environmen-
tal oscillation did not persist nearly as long as in the Moroccan section, although Batt
(1996) recognized the trilobite beds in the Wanakah Shale Member as being a special
case of minor shell beds that he traced throughout the member. These thin shell hash
beds probably record the same scale of cyclicity as the Moroccan rhythms.
Cycles range from about 0.3–0.5 m thick and alternate with medium grey fos-
siliferous shales. The concretionary beds with distinctively preserved trilobites have
each been traced for 80–120 km in outcrops (Speyer and Brett 1985, 1986). The thin
debris layers of brachiopods, small rugose and/or auloporid corals that overlie these
beds appear to grade laterally eastward into proximal shell and coral-rich beds that
occur above minor coarsening upward shale, siltstone cycles in central New York
State. Hence, these beds are associated with persistent discontinuities in sedimenta-
tion. The concretionary diagenetic beds evidently lie beneath these caps and pass
eastward into the upper parts of the mudstone-siltstone cycles discussed above. The
shell-rich beds are more persistent and correlate laterally, eastward with complex
shell beds in thicker and more clastic-dominated successions discussed above. For
example, the “Trilobite beds” pass eastward into complex brachiopod-shell and
bivalve-rich shell beds with bioturbated calcareous silty mudstone matrix.
3.5 Lower Jurassic: Lias UK
Proximal examples of meter-scale cycles are recorded by the 5–10 m thick, coars-
ening-upward successions in the Lower Jurassic (Pleinsbachian) Cleveland
Ironstone Formation of Staithes on the Yorkshire Coast of England (Figs. 19–21;
Yorkshire
South Wales
Dorset
Fig. 19 Outcrop and subcrop map for the Lias Group in England and Wales showing the location
of the main sedimentary basins. Outcrops in Dorset, South Wales and Yorkshire (discussed in text)
are indicated (Modified slightly after Cox et al. 1999; Simms et al. 2004)
Hemingway 1934; Whitehead et al. 1952; Sellwood and Jenkyns 1975; Smith 1989;
Rawson and Wright 1995; Simms et al. 2004; West 2007a, b). The cycles begin
with: (a) thin (mm to cm) bioturbated to cross-bedded, shell rich lags, some of
which are ferruginous, with siderite and oolitic berthierine (e.g., Anderton et al.
1979, p. 206). These beds contain abundant fragmented and sorted shell debris as
well as whole shells including rhynchonellid brachiopods, pectinid bivalves,
59
57 Sulfur Band
Hawskerense 56
Subzone/Zonule
Kettleness Member
55
Elaboratum 54 top
Zonule block
53 Main Seam
52 bottom
Apyrenum block
Subzone ? Solare
Zonule 51
45 Pecten Seam
41 unconformity
40
39 Cycle 5 Two Foot Seam
38
Cycle 4
Cleveland Ironstone Formation
36
Gibbosus 35 Raisdale Seam

Subzone
34
Cycle 3
Penny Nab Member
32
5
31
Avicula Seam
28
metres
Subnodosus
Subzone 27 Cycle 2
0
26 Osmotherley Seam
Nitescens to
Celebratum 25
zonules Cycle 1
Stokesi
Subzone
24
siltstone calcareous and

siderite nodules
silty shale/clay ironstone
shale/clay shell bed
Fig. 20 Section through the Cleveland Ironstone formation between Cowbar Nab, Staithes, and
Rosedale Wyke, Port Mulgrave. After Rawson and Wright (1995) and Simms et al. (2004). Bed
numbers and cycles are from Howarth (1955) and Howard (1985) respectively
Fig. 21 Cleveland Ironstone Formation at Penny Nab, south of Staithes. The Two Foot Seam (a),
the five thin ironstones of the Pecten Seam (b), and components of the Main Seam (c) are indi-
cated (Photo: M.J. Simms, after Simms et al. 2004)
belemnites, and ammonites (Hemingway 1951). (b) The majority of the cycle is
represented by 1–7 m of dark gray shale, mudstone with thin siltstone. (c) Higher
portions of the cycles, characterized as “striped” facies, comprise interbedded dark
gray silty shale and thin siltstone and sandstone beds showing sharp bases and
small-scale hummocky cross-stratification, gutter casts (Greensmith et al. 1980),
and occasional scattered shells. Prominent, condensed sideritic beds mark the
“caps” of several small-scale cycles in the Cleveland Ironstone (Figs. 20 and 21;
Hemingway 1951, 1974).
Upper portions of cycles, (d), are amalgamated siltstone beds up to 0.5 m thick
with abundant burrows, especially Rhizocorallium, suggesting firm sand condi-
tions. In some instances calcitic or sideritic concretions occur in the upper portions
of the cycles below the sharp top (Hallam 1967). The latter nucleated on pipe-like
mineralized burrows. These minor concretions are inferred to be the sedimentologic
analog of the concretionary and tabular cemented limestone beds of more distal
cycles; conversely the main body of the cycle comprising upward coarsening sili-
ciclastic is correlative with thin dark shale and gray marl of the distal carbonate-
shale rhythmic successions.
The Lower Jurassic (Hettangian to lower Sinemurian) Blue Lias, exposed on the
Welsh Coast of the Severn Estuary near Nash Point (Fig. 19), provides a slightly
older and somewhat more distal example (Hallam 1960; Shepard et al. 2006). Here
the cycles range from 0.5 to 2 m in thickness with sharp bases at the bottoms of
shell-rich beds. The latter contain abundant fragmentary bivalve shells, including
gryphaeids, pinnids, and pectinids, crinoid debris and rare, small, solitary sclerac-
tinian corals. These beds are up to 20 cm thick.
Shell beds are overlain by medium to dark gray shale and mudstone. Upper surfaces
of these shell rich beds have gradational to abrupt contacts with dark gray to black
shales. Concretionary limestone beds may occur in the upper portions of the shell beds
but tend to be more lenticular in form compared with the thick tabular beds of the distal
Blue Lias. A high proportion of these concretionary beds contain articulated and
closed Pleuromya, as well as pinnid bivalve shells, vertically to obliquely positioned
in the otherwise sparsely fossiliferous mudstone in apparent life positions.
3.5.2 Distal Cycles
The condensed Jurassic Blue Lias Formation of Dorset, UK (House 1993) contains
numerous fossil-rich shale and concretionary limestone cycles (Figs. 19, 22–25;
Hesselbo and Jenkyns 1996; Moghadam and Paul 2000; West 2007a, b; Paul et al.
2008; Allison et al. in press). About 45 major concretionary limestone beds have
been identified and traced over 10 s km (Lang 1924). Not all cycles show concre-
tionary limestone components. The cyclic pattern is striking because of the alterna-
tion of ledge-forming pale gray weathering concretionary limestones and dark gray
to black shales and marls (Fig. 22). The beds have been a classic source of fossil
Lagerstätten, including ammonites and marine reptiles and fish (Fig. 23).
A typical Blue Lias cycle is 50–150 cm thick and comprises up to five compo-
nent divisions (Fig. 24: Moghadam and Paul 2000). (a) A thin lag (centimeters) of
shelly debris occurs at the tops of the gray marls immediately underlying many
dark shales and seems to be the only representation of the transgressive lag.
(b) Black and dark gray laminated, organic rich shale, typically with Chondrites
burrows pass upward into pale-medium gray mudstone. (c) Medium gray calcareous
Fig. 22 Lower Jurassic Blue Lias Formation, Church Bay, east of Lyme Regis. Cycles composed
of light gray limestone beds and darker shale and marl beds
Fig. 23 Ammonites of bed 29 (Top Tape Bed of quarrymen) of the Blue Lias at Monmouth
Beach, Lyme. (a) Bedding plane from above showing multiple large specimens of the ammonite
Coroniceras; scale 1.5 m. (b) Close-up of ammonites; scale 60 cm (c) chamber fillings showing
different generations of sediment infill; scale: 8 cm (From Allison et al. in press)
shales (marls) may be extensively bioturbated and include scattered fossils. (d) The
prominent 10–25 cm thick ledged-forming, concretionary micritic limestones,
when present, occur within the gray mudstone and are typically overlain by
(e) a few centimeters of shell-rich marl. As such, the Blue Lias shows a distinctive
meter-scale cyclic motif comparable to cycles discussed above for the Upper
Ordovician Collingwood Formation and the Devonian Hollardops member, as well
as classic Cretaceous cycles discussed below (Fig. 25).
These beds have a long history of study from the standpoint of cycle stratigraphy
(Hallam 1960, 1964, 1986; House 1985, 1986, 1993; Weedon 1985, 1986; Weedon
et al. 1999; Moghadam and Paul 2000; Paul et al. 2008; Allison et al. in press).
Interpretations have ranged from a purely primary alternation of calcareous and clay
rich sediment to a diagenetically-induced, rhythmic un-mixing (compare Hallam 1964
with Hallam 1986; Bottrell and Raiswell 1990; Moghadam and Paul 2000; Shepard
marl - mostly blocky or conchoidal fracture (some lamination) Marl
Base of cycle
Top of cycle Burrowed
burrows in section burrow
Thalassinoides, Diplocraterion bivalve Limestone (calcilutite)
Chondrites Many fossils - bivalves, gastropods
Regression? brachiopods, echinoderms; uncrushed
because of early cementation.
c. 80-% calcite, 20% clay.
paired bivalve Burrowed
Marl - c. 65% clay, 35% calcite

log with oysters
Burrowed top
Bituminous Shale
Deeper water? Poor in fossil content
ammonite often c. 85% clay, 10% kerogen etc, 5% calcite
uncrushed
Transgression? bivalve
Marl
Base of cycle Burrowed
Top of cycle
oyster on ammonite
Limestone
4 Comparative Taphonomy and Sedimentology of Small-Scale Mixed
Burrowed
Marl
Fig. 24 Idealized Blue Lias rhythms showing principal lithofacies. In rhythms a and b the pale marl horizon has been diagenetically
cemented into a limestone bed and is overlain by a dark marl bed. Adapted from figure in website Lym Regis-West, Blue Lias, Lower
Jurassic; http://www.soton.ac.uk/~imw/lyme.htm;by Ian West
143
Fig. 25 Stratigraphic section of lower Blue Lias beds at Chippel Bay, Lyme Regis, Dorset,
England, showing recurrent pattern of cycles (From Paul et al. 2008)
et al. 2006). A reasonable alternative is Weedon’s (1985) proposal that the Blue Lias
limestones are actually diagenetically altered marls, i.e. a diagenetic enhancement of
a primary difference in sediment composition. Intervals with an originally higher
content of fossil material and/or carbonate mud were preferentially cemented, prob-
ably in the zone of sulfate reduction (Moghadam and Paul 2000). The overlying
fossil-rich horizons may mark the upper portion of a zone of diagenesis within the
light marls. Both sets of limestone components show signs of early diagenetic altera-
tion. Fossils within the carbonate units are more widely spaced although articulated
specimens, including in situ fauna, are preserved in their original three-dimensional
form.
Large ammonites (up to 80 cm) are abundant in some beds covering up to 40%
of bedding-surface area (Fig. 23). Ammonites are preserved in 3D in nodular lime-
stones and at variable orientation to bedding. Ichnological, sedimentological, and
taphonomic evidence indicates condensation as the primary agent of accumulation
(Allison et al. in press; Paul et al. 2008). However, the occurrence of equally con-
densed Blue Lias limestones lacking ammonite concentrations indicates that this
alone is insufficient to account for concentration. Accumulation likely resulted
from a combination of condensation and environmental conditions favoring the
establishment of ammonites.
Stable isotope values suggest that cements were derived from pore-waters of a
similar composition to contemporary seawater (Moghadam and Paul 2000). A clear
diagenetic trend exists, with limestones having least, and laminated black shales
most, modified stable isotope values. Contrast between trace fossil fills and host
sediment demonstrates that Blue Lias rhythms are primary, but limestone beds are
diagenetically enhanced. Condensation resulted from the interaction of climatic and
sea level fluctuations. Marly skeletal rich sediments formed during minor transgres-
sions. The sharp contacts of the overlying black shales denote maximum flooding
surfaces. These times of prolonged sediment starvation favored concretionary
cementation of underlying marly sediments and the formation of diagenetic lime-
stones. Black shales record stratification under a stable halocline during maximum
high-stands and humid climates. The thicker lower dark to medium gray mudstones
evidence increased flux of mud associated with stable to slightly falling base level,
and/or increased weathering and run-off.
Similar cycles occur in the Upper Jurassic Kimmeridge Formation of east Dorset
Coast (Oschmann 1988; Gallois 2000) and the Lower to Middle Jurassic (Pleinsbachian)
of Spain (Fernandez-López 2007; Fernandez-López et al. 2000, 2002).
3.6 Upper Jurassic to Lower Cretaceous; India
The Upper Jurassic to Lower Cretaceous sedimentary cycles of the Kachchh Basin,
western India (Fürsich and Oschmann 1993; Fürsich and Pandey 2003) are strongly
asymmetric, coarsening upward, and bounded by transgressive surfaces and overlying
skeletal lag deposits (Fürsich and Pandey 2003; see Fig. 29). In proximal settings,
the skeletons of basal shell beds (a) appear to have been reworked and locally trans-
ported, and are moderately time-averaged, with nearly total disarticulation of shells
and preferred convex-up orientation. The fauna generally comprises low-diversity
benthic communities, dominated by bivalves and corals. Fürsich and Pandey (2003)
in contrast to other examples, however, interpret these deposits as the reworked
residues of regressive (RST) sediments. The upper surface of these basal skeletal
deposits, Maximum Flooding Zone (MFZ) shell concentrations of Fürsich and
Pandey (2003) are higher in diversity, poorly-sorted, highly bioturbated, and domi-
nated by mollusks, brachiopods, and randomly oriented, biogenically altered nektonic
cephalopods. Taphonomic feedback (Kidwell and Jablonski 1983) favored coloni-
zation of the seafloor by epifaunal bivalves and brachiopods. Evidence for low rates
of sedimentation include a concentration of iron minerals, with ferruginous ooids
and glauconitic grains.
The overlying early highstand sediments (b) of cycles in the Kachchh Basin are
typically bioturbated (sometimes planar laminated) claystones and siltstones
largely devoid of skeletal accumulations. Fürsich and Pandey (2003) describe well-
sorted shell pavements and lenses from late highstand parts of cycles (c), indicating
paleoenvironments above fair-weather wave base. These skeletal accumulations are
of low diversity, and represent parautochthonous to allochthonous reworked and
transported relicts of benthic communities. Unlike skeletal accumulations of the
TST, those of the RST in the Kachchh Basin (d) are laterally discontinuous and
commonly form lenses, and pods, or form pavements on foresets of large cross-
beds.
The most distal cycles of the Kachchh Basin, for instance the lower portion of
the Bharodia section, are thinner and are dominated by fine-grained siliciclastic
sediments. A well-developed concentration of ammonites, belemnites and bivalves
forms the base of the sequence, which is high ferruginous and bioturbated (a).
Fürsich and Oschmann (1993) report reworked bored concretions from many shell-
rich beds, interpreted as minor transgressive lags, in the Callovian to Oxfordian
Chari Formation. Ferruginous siltstone to silty fine-sandstone (b) overlies the ~1 m
thick MFZ, and is devoid of skeletal accumulations. The overlying sequence (c),
which is more proximal, in contrast to the distal example, is thicker, has a transgres-
sive erosive surface, thicker (~1 m) transgressive lag and thinner MFZ, and is
overlain by a thin package of bioturbated fine sandstone, and thick succession of
trough cross-bedded sandstone.
3.7 Upper Cretaceous: Greenhorn Formation, Western

Interior, USA
Small cycles of the Upper Cretaceous of the Western Interior are similar in scale
and motif to limestone-shale cycles of the Lower Jurassic (Lias) of England (see
above). Using spectral analysis of carbonate content, gray-scale variation, bioturba-
tion index, and geochemical proxies, Sageman et al. (1997, 1998) detected bundled
periodic signatures inferred to represent 20–100 kyr Milankovitch oscillations in
climate and/or minor sea level variation (Figs. 26 and 27). The cycles of the
Greenhorn and Niobrara Formations have been correlated in bed-by-bed detail
from platform facies of Kansas to basinal sections near Pueblo, Colorado (Hattin
Fig. 26 View of Cretaceous Bridge Creek Limestone Member of Greenhorn Formation along
railway cut at Rock Springs anticline, Pueblo, Colorado, showing rhythmic alternation of 10–20 cm
thick, white-weathering, concretionary limestones and dark shales
1971, 1977a, 1982a, b; Kauffman 1982), to proximal and shoreface settings in

central Utah and northern Arizona (Elder et al. 1994).
In the Albian to Cenomanian Greenhorn Formation of southwestern Utah and

Arizona skeletal beds occur consistently at the bases of shallowing-upwards 10–20 m
thick packages of mudstones, siltstones and sandstones referred to as ‘parase-
quences’ by Elder et al. (1994). The shell-rich deposits (a) comprise disarticulated
gryphaeid shells as well as other bivalves, baculitid ammonoids and gastropods;
they show minor cross stratification and sorting of shells. Concretions are generally
absent. Shell hash beds overlie bioturbated siltstones and sandstones with
Thalassinoides and Planolites burrows (b, c).
Further shoreward, shell hashes were thin to absent but their position was
marked by sharp contacts of bioturbated sandstone and siltstone beds with overlying
shales that were long interpreted as flooding surfaces and were referred to as “low-
stand” shell beds by Sageman (1996) by analogy with widespread thin, shelly
limestone discussed by Brett and Baird (1986a) from the Appalachian basin
Devonian. However, in both cases, these shell beds are better interpreted to repre-
sent lags at the bases of shallowing upward cycles and thus, we interpret them as
Fig. 27 Correlated sections of Cretaceous Greenhorn cycles from Kansas to Colorado, showing
persistence of small-scale cycles (From Hattin 1971)
reworked, time-averaged assemblages that accumulated during intervals of relative

siliciclastic starvation (Brett and Baird 1996).
Such transgressions could be invoked to explain the shell beds as trangressive
lags and would explain the presence of overlying distal dark shale facies.
Progradation of siliciclastics during the alternate highstand/wet interval produced
the coarsening upward motif of the parasequences. Alternatively, the shelley, sediment
starved intervals were associated either with periods of dry climatic conditions during
which offshore transport of terrigenous sediments was greatly reduced during small
base level rises.
The offshore cycles were typically attributed to Milankovitch-band climatic oscilla-
tions, whereas the parasequences were ascribed to local progradation and subsidence of
deltaic lobes, perhaps in response to minor base-level oscillations or to autocyclic
processes (Elder et al. 1994). The careful correlation of the cycles across proximal-
distal profiles provides strong evidence that the typical 10 m-scale cycles of proximal
regions and decimeter scale marl-limestone cycles of distal areas were products of a
common, allocyclic forcing function. These Cretaceous cycles parallel observations on
the Middle Devonian of the Appalachian Basin and in both cases there is now strong
evidence for basin-wide, if not interbasinal oscillations in sea level and/or climate.
Depositional processes responsible for the limestone shale cycles include sediment
bypassing during transgressive erosion and onlap in shoreface to inner shelf depths
and sediment starvation during deepening in inner to mid-shelf depths. Deposition
of entrained relict skeletal material following storm events from shelf depths pro-
duced thin, lenticular shell beds. Rapid sedimentation terminated accumulation of
sediment-starved fauna in mid-outer shelf depths. Storm erosion and re-deposition
of shells occurred above storm wave base in inner shelf and shoreface depths.
Reworking and condensation of shells above fair-weather wave base in inner shelf
to shoreface depths led to deposition of thin time-averaged shell beds comparable
to those of the Jurassic Kachchh basin (Fürsich and Pandey 2003; Fig. 29).
3.7.2 Distal Cycles
The distal facies of the Greenhorn Formation in Kansas and central Colorado are
recorded in chalk facies as very thin shelly lags (a), marly chalk (b) to tabular lime-
stones (c), especially well displayed in the Bridge Creek Formation (Hattin 1971,
1977a, b; Kauffman 1982). The tabular bands are approximately 10–25 cm thick
and alternate with slightly thicker marls. These bands generally display sharp lower
and upper contacts and are overlain by thin lags of inoceramid prisms and other
shell debris. Bed tops are bioturbated by Thalassinoides, Planolites and other large
burrow systems (Hattin 1971). Hattin (1977b) described well-preserved, articulated
barnacles from the tops of some of these beds that indicate pulses of rapid burial;
in situ bivalves may also be present.
Spectral analysis of these rhythmically banded chalky marls and limestones sug-
gest precessional, obliquity, and eccentricity effects (Sageman et al. 1997, 1998).
The latter have been attributed to Milankovitch forced climatic and/or minor sea-
level oscillations.
In basinal sections, cycles comprise thin concretionary shell hash deposits (c)
alternating with calcareous, dark gray shales (b). Shell material is largely disarticu-
lated and fragmented. Rarely, complete, double-valved shells and well-preserved
ammonite shells, primarily Baculites occur within the concretionary limestone
bands. These concretionary intervals thus appear to represent rapidly buried pods
of shells and ammonites accumulated on the seafloor perhaps in low hollows
(cf. Tsujita 1995). These beds are the sedimentological and diagenetic analogs of
concretionary beds with articulated chaotically oriented trilobites in Ordovician
and Devonian samples cited above. As in the latter cases, the overlying hashes of
broken and disarticulated shells (a) are thin, lenticular and subtle. But it is these
surfaces that reflect interludes of sediment starvation during which the concretions
developed in underlying sediment packages, perhaps nucleating around clusters of

rapidly buried shells.
Stratigraphic correlations (Elder et al. 1994) demonstrate that offshore concretionary
beds correlate approximately with the limestone bands of the eastern rhythmically
bedded chalk, and with proximal shell hash beds. However, we infer that the concretions
reflect diagenesis beneath thin shell lags that formed during interludes of low
sedimentation.
Comparative examples include decimeter- and meter-scale Milankovitch cycles of
soft and more indurated beds also have been documented in Cretaceous chalks from
Great Britain and France (Kennedy and Garrison 1975; Hancock 1975). As with the
Greenhorn and Niobrara cycles, and others discussed herein, the compact limestones
show extensive firmground burrows of Thalassinoides, Rhizocorallium, Planolites,
and others; in some cases, Trypanites bored- and oyster-encrusted hardgrounds also
occur at the tops of these cycles (Bromley 1967, 1968; Hancock 1975).
3.8 Cenozoic: Ashiya Group, Japan, and Punta Judas

Formation, Costa Rica
Relative to other intervals little is known of small-scale sedimentary cycles from the
Paleogene. Examples have been noted, however, from the Ashiya Group (Oligocene)
of Japan (Hayasaka 1991; Sakakura 2002), and the San Julián Formation
(Oligocene) of Argentina (Parras and Casadio 2005). Cycles from the Ashiya
Group are reviewed here.
The upper part of the Ashiya Group consists of coarsening-upward sedimentary
cycles of 30–100 m in thickness and comprises a range of sandstone and mudstone
lithologies (Fig. 2 of Hayasaka 1991). Within cycles of the Ashiya Group, a trans-
gressive basal medium sandstone rests on a distinctive erosional surface that trun-
cates the upper part of the underlying cycle, and fines upward to very fine sandstone
(Fig. 28). This basal facies ranges in thickness from 5–20 m in thickness, and is
characterized by coarse lithic granules, smectite, glauconite, and occasional dense
imbricated shelly lenses that overlie minor erosional surfaces. The upper part of the
fining up basal sandstone may contain patches of articulated bivalves. The base of
the cycle (a) is often intensely bioturbated by Thalassinoides and Ophiomorpha.
This upper part of this basal sandstone is rich in glauconite, and is conformably
capped with mudstone that represents the base of a progradational coarsening
upward interval. Most sequences comprise in successive order (b) dark gray lami-
nated or bioturbated mudstone (5–40 m thick), mudstone interbedded with very thin
sandstone beds (3–10 m thick), (c) silty fine sandstone or alternating hummocky
cross-stratified sandstone (HCS) (3–20 m thick), and mudstone and (d) amalgam-
ated HCS (10 m thick). In some cases tabular cross-stratified sandstone may imme-
diately overlie the coarsening upward mudstone, in place of HCS (10–15 m thick).
The shell beds of the basal sandstone facies (a) are densely concentrated as a
parautochthonous accumulation 20–50 cm thick. The erosional surface exhibits
Fig. 28 Typical cycle of the Ashiya Group based on section 7 (Waita Formation), exposed on the
coastline between Sakamizu and Waita, Kitakyushu-Ashiya area, southwest Japan. Lettered divi-
sions are portions of cycle analogous to those shown in Fig. 9. (a) Poorly-sorted pebbly coarse to
fine sand or gravel with an erosional surface and gravel or shell lag at its base; (b) massive, dark
gray siltstone in lower part of cycle; (c) silty very fine sandstone of falling stage of cycle;
(d) well-sorted fine sandstone, amalgamated type HCS, with lags of heavy mineral or shells
(Modified from Hayasaka 1991)
wavy undulation of up to 20 cm in relief. The shell bed comprises typically disar-

ticulated and fragmented bivalve shells, which may be piled up and imbricated
bidirectionally along bedform slopes. The upper part of the transgressive unit in the
Ashiya Group includes both allochthonous shell beds of approximately 20 cm thick,
which rest on wavy erosional surfaces, dispersed assemblages of articulated
bivalves, and shell beds that lack an erosional base. The matrix of these shell beds
consists of shell fragments showing imbrication, articulated shells filled by geopetal,
shells which exhibit high abrasion, and common epifaunal forms (e.g. pectinid and
anomiid bivalves), and widespread encrustation by barnacles.
The mudstone unit that represents highstand conditions in Ashiya Group cycles
(b) yields autochthonous and scattered bivalve shells. Many of these shells are
articulated and in life position. In general the facies lack evidence of bottom ero-
sional or reworking. Occasional shell stringers accumulated along bedding planes
in the mudstone as it coarsens up, and show preferred orientations that result from
unidirectional currents. Primary sedimentary structures in highstand and regressive
parts of Ashiya Group sequences are disturbed by bioturbation. Ichnofossils including

Phycosiphon, Planolites, Palaeophycus, Rosselia and Skolithos are observed in
these facies.
The succession of taphofacies in Ashiya Group cycles suggests an upward
decreasing influence of wave and current energy. The strong wave influence
declines from an erosional and winnowing phase to a quiet muddy phase during
transgressions.
3.8.2 Distal Cycles
Although cycles analogous in scale and pattern to those discussed for the Paleozoic
and Mesozoic are uncommon in the Cenozoic because of changes in depositional
setting (i.e. epicontinental sea vs oceanic shelf), one example described from the
Miocene Punta Judas Formation of Pacific Costa Rica (Krawinkel and Seyfried
1996) provides a number of parallels. A brief synopsis is included for sake of com-
parison. This youngest example comes from a time of transition from greenhouse
to icehouse global climates, but it is derived from a subtropical setting.
Two types of open marine cycles are described by Krawinkel and Seyfried
(1996). Open shelf cycles consist of meter thick cycles that commence with (a)
tempestitic skeletal accumulations and pass upward into mudstones with storm-
reworked parautochthonous to allochthonous shell hashes (b). A few concretionary
beds (d), present within the mudstones host in situ articulated bivalves. Siltstones
and mudstones are heavily bioturbated, with Thalassinoides, Ophiomorpha and
Skolithus burrows in the sands. Upper parts of cycles consist of hummocky cross-
stratified sandstones.
Distal estuarine delta front cycles are also on the order of a meter thick and may
be identified by concretion beds in otherwise monotonous, bioturbated sediments.
Most of these beds show autochthonous bivalves in life position. In most cases the
autochthonous bivalves are associated with concentrations of disarticulated shells of
bivalves, as well as gastropods, echinoids and fish teeth, and in some cases driftwood.
We conclude that these concretionary horizons record episodes of rapid burial during
times of general sediment starvation associated with abrupt sea level rise. Thus, they
are excellent analogs of concretionary shell beds seen throughout the Phanerozoic.
4 Discussion: Synopsis of Examples
Although the age-range of examples considered herein spans nearly 500 million
years, the cycles share striking sedimentologic, paleontologic and taphonomic
characteristics (Tables 1–5; Figs. 29 and 30). Cycles exhibit the same general
sequence of lithofacies. Comparison of the major components of the cycles pro-
vides a basis for understanding meter-scale cycles in general.
In this concluding section we first outline common features displayed by all
cycles in terms of litho-, bio- tapho-, and ichnofacies, and highlight unique features
of small-scale cycles of particular ages. We then consider the underlying causes of

these common features and finally, we briefly outline secular changes and their
influence on cycle appearance.
4.1 Basal Condensed Shell Bed Taphofacies
4.1.1 Base of Cycle Shell Debris Beds
A basal compact bed, yielding evidence of condensation represented by skeletal

and or diagenetic clasts is present in virtually all of the examples of proximal cycles
presented herein (Table 1; Figs. 29 and 30). The prominence of this skeletal bed
varies substantially both from one time to another and with proximality of indi-
vidual cycles, yet this bed is the most persistent feature of the cycles; this bed in
varied guises can be traced from near basinal center to upramp positions, and, in
some cases, to both siliciclastic and carbonate margins of basins.
The extent of development of the condensed shell bed is a complex function of
several factors, including: (a) shell productivity; (b) durability of skeletal remains;
(c) duration of sediment starvation; and/or (d) extent of winnowing and processing
of skeletal material by storm waves and/or bottom currents (see McLaughlin et al.
2008 for review). The basal shell beds of the Ordovician to Cenozoic examples
have all been noted as having sharply erosive bases and abrupt, sometimes rippled
tops with hardgrounds (Fürsich 1978; Fürsich and Pandey 2003). Examples of
phosphatic and hematitic ooids are also present in examples from the Ordovician
(Dabard et al. 2007), Silurian (Van Houten and Bhattacharrya 1982; Cotter and
Link 1993), and Jurassic (Whitehead et al. 1952; Hallam 1966; Hallam and
Bradshaw 1979; Van Houten and Bhattacharrya 1982). Evidence of firmground
and/or hardground features is typical of the upper surfaces of the bed, and in many
instances a coating or impregnation of iron oxide occurs along this sharp contact
(Fig. 29).
In distal facies (Fig. 30) this bed is typically subtle and consists simply of a
single layer or pavements of shelly debris. It may be represented by a thin interval
of shell-rich marls or mudstones and may directly drape concretionary beds at the
top of subjacent cycles.
Despite differences in thickness the basal shell beds of small-scale cycles show
comparable taphonomic patterns. Key features of the proximal shell bed taphofa-
cies include: (a) a high degree of concentration and varied preservation of skeletal
clasts, ranging from intact skeletal elements and rare articulated material to variably
fragmented, abraded and/or corroded and coated grains and prefossilized steinkerns;
(b) presence of reworked material including shale clasts, reworked concretions, pre-
fossilized steinkerns, coated and mineralized grains, phosphatic, hematized and or
pyritic clasts; (c) evidence of reworking and winnowing; typically packstone to
grainstone fabrics; (d) for thicker beds, complex internal amalgamation of varied
lenses and pods of skeletal debris; (e) shell beds are dominated by single valves,
Table 1 Comparative taphonomic and paleoecologic aspects of basal (transgressive) shell-rich beds
154
Age
Formation # Cycles Lithology Common taxa Trace
Location References Duration Bedding Guilds Fossils Taphonomic features
Cretaceous Elder et al. (1994) 10–30 cm Sharply based, Inoceramids, gryphaeids Thalassinoides Moderately to densely
sharp packed
Greenhorn Sageman (1996) 20 Cycles firmground top ammonites, belemnites Rhizocorallium disarticulated,
fragmented shells
Utah/Colorado 20–40 kyr sandy packstone Glossifungites inoceramid prisms;
corrosion
tabular, cross encrusting and boring of
bedding skeletons
Early Jurassic Allison et al. (in 1–20 cm Sharply based, Gryphaeids, belemnites Thalassinoides Moderately to densely
press) sharp packed
Blue Lias Paul et al. (2008) 40 cycles firmground top ammonites, crinoid Rhizocorallium disarticulated,
debris fragmented shells and
Dorset, Gt. Britain 40–100 sandy packstone small corals Diplocraterion crinoid ossicles;
kyr corrosion; encrusting
and
Glossifungites boring of skeletons
Mid-Devonian Brett and Baird 1–20 cm Sharply based, Crinoid, rugose/tabulate “Megaburrowed” Moderately to densely
(1985,1996) sharp packed,
Hamilton Group Landing and Brett 40 cycles firm- and corals, thick shelled firm-/hardgrounds disarticulated,
(1987) hardground top fragmented
New York, Ontario 40–100 packstone- brachiopods; rare Glossifungites abraded and corroded
kyr grainstone shells, crinoids
C.E. Brett et al.
Age
phosphatic nodules mollusks, trilobites Trypanites encrusting and boring of
skeletons
Lower Devonian Botquelen et al. 1–20 cm Sharply based, Crinoid, rugose/tabulate Thalassinoides Moderately to densely
(2006) sharp packed
“Type B” shell beds 30 cycles firmground top corals, thick shelled Glossifungites disarticulated,
fragmented, abraded
Spain 20–100 sandy pack-- brachiopods; rare and corroded shells
kyr grainstone
mollusks, trilobites encrusting and boring of
skeletons
Late Ordovician Brett et al. (2003) 5–60 cm Sharply based, Strophomenid/orthid Planolites Moderately to densely
sharp brach packed
Kope Fm. 40 cycles rippled, firmground ramose bryozoans Cruziana disarticulated,
tops fragmented, abraded
Ohio/KY 20–100 sandy pack-- crinoids, trilobites Trypanites and corroded shells
kyr grainstone
encrusting and boring of
skeletons
Late Ordovician Botquelen et al. 2–20 cm Silty packstone Bryozoans, brachiopods, Sharp Planolites Densely packed
(2006)
“Type B” shell beds ~40 sharp bases; cystoids, crinoids Thalassinoides disarticulated; all
cycles phosphatic fragmented shells
Sardinia 20–100 crusts on tops bioeroded and encrusted
kyr skeletons
Mid-Ordovician Boyer and Droser 5–20 cm Pack- to grainstone Orthid brachiopods Sharp Planolites Loosely-densely packed
(2003)
(continued)
155
156
Table 1 (continued)
Age
Kanosh Fm. ~140 sharp bases; echinoderms, Thalassinoides disarticulated; highly
cycles rippled gastropods fragmented shells
W. Utah firm- and ostracodes Trypanites
hardgrounds
Mid-Cambrian Brett et al. (2009) 10–50 cm Peloidal to oolitic, Orthid brachiopods Planolites Loosely packed
and fragmented
Wheeler Fm. ~25 bioclastic pack- to echinoderms; sponge Thallasinoides skeletal material in
cycles grain oolitic matrix
W. Utah ?20–100 stone; sharp bases spicules; trilobite frags. (hypichniia casts)
kyr
sharp hardground
tops
C.E. Brett et al.
4 omparative Taphonomy and Sedimentology of Small-Scale Mixed 157
A-1 early TST
late HST
C
skeletal elements are rare or absent
A-2 MFZ
A-1 early TST

density
shell
orientation
convex-up
disartic.
degree of
alteration
biogenic
shells
% autocthonous
sorting
hydraulic/chemical
diversity
species
averaging
time-
1m
b
MFS
A-1
A-2
MFS
A-1
1m
oxygenated
dysoxic
shallow
anoxic
high
deep
high
well
low
low
Relative Turbulence Sedimentation Oxygenation

depth rate
Fig. 29 Generalized proximal small-scale cycle. Note basal shell debris beds, upper bed may be
amalgamated to the lower bed followed by shale with thin event beds and capped by cross laminated
silt- and sandstone. Bars show relative frequency. (a) Distribution of taphonomic features within
cycle; note high degree of concentration and orientation in basal bed and very high degree of con-
densation of upper shell bed. (b) Distribution of inferred paleoenvironmental parameters through
the cycle. Note spikes on turbulence and sedimentation curves, reflecting instantaneous event beds.
Symbols: SB, sequence boundary; MFZ, late TST; MFS, maximum flooding surface; HST, high-
stand systems tract; TST, transgressive systems tract (Adapted from Fürsich and Pandey 1999)
a
A MFZ
B early TST
late HST
C
early HST
A MFZ
D early TST
density
shell
orientation
convex-up
disartic.
degree of
alteration
biogenic
sorting
hydraulic/chemical
diversity
species
averaging
time-
1m
b
MFS
SB
MFS
SB
1m
oxygenated
dysoxic
shallow
anoxic
high
well
deep
high
low
low
Relati ve Turbulence Sedimentation Oxygenation

depth rate
Fig. 30 Generalized distal small-scale cycle. Note basal shell debris beds followed by dark,
laminated shale and overlain by gray marly mudstone to siltstone with thin shell hash beds and
laminated storm siltstones; also note sparsely fossiliferous (propped open) concretionary diage-
netic limestone with in situ articulated fossils just below basal shell beds at tops of cycles.
(a) Distribution of taphonomic features within cycle; note high degree of concentration, orientation
in basal bed and very high degree of condensation of upper shell bed. (b) Distribution of inferred
predominantly in convex upward positions (see Kidwell and Bosence 1991; Fürsich
and Pandey 2003; Hendy et al. 2006).
4.1.2 Gray Marl Beds with Thin Condensed Hashes
The main skeletal beds are typically followed by millimeter to decimeter scale gray
calcareous claystone/marl with thin stringers of comminuted shelly debris. In some
instances these gray claystones mantle sharp upper surfaces of the shell hash bed
preserving articulated fossils at the base as obrution beds (Figs. 29 and 30).
As noted above, the trilobite and diminutive phosphatic brachiopod faunas of
deeper water facies did not build thick shell beds. The thin veneers of skeletal hash
that typify the Collingwood Shale, as well as the Lower Devonian Hollardops beds
are believed to occupy a position analogous to the condensed shell beds in upramp
areas. Extreme condensation is recorded by thin veneers of fish bones, conodonts,
and teeth that floor black shales in some Devonian as well as Mesozoic cycles
(Martill 1985; Baird and Brett 1991). Here there is little or no preservation of shell,
if indeed such shells were ever present, and the residue is typically strongly
reworked and comminuted. Thus, these distal dysoxic facies still produced
“Cambrian style” shell beds in middle Paleozoic (McKerrow 1979; Li and Droser
1997). Much the same can be said for thin debris layers that appear at cycle bases
in the distal facies of Jurassic and Cretaceous cycles. The bases of cycles in much
of the Blue Lias are marked by thin veneers of fragmentary ammonoids and
bivalves; in many dysoxic facies the cycles commence abruptly with a sharp based
black shale that may be floored a sprinkling of bones and teeth, or nothing at all.
4.1.3 Biostromes-Bioherms
In some cases the top of the skeletal debris bed is terminated by a more or less
in situ accumulation of skeletal remains and/or microbial carbonates. Such examples
include small thrombolitic mounds, bryozoan-algal mud mounds and biostromes if
intact to fragmental bryozoans and corals. These buildups are present as barren
microbial mounds in the Cambrian (e.g. Elrick and Snider 2002), and as thromb-
olites as well as laterally correlative sponge, tabulate, rugosan coral biostromes and
bioherms in the middle Paleozoic. For example, there are numerous examples of
small patch reefs and bioherms from the Ordovician to Devonian based upon hard-
grounds or stabilized crinoidal shoal deposits recording early TST deposits
(Walker and Alberstadt 1975). Sponge, algal mounds have been reported on flooding
Fig. 30 (continued) paleoenvironmental parameters through the cycle. Note spikes on turbulence
and sedimentation curves, reflecting instantaneous event beds; also, spikes on oxygenation curve
that reflect brief interludes of more oxic conditions that permit temporary seafloor colonization.
Symbols: SB sequence boundary; MFZ, late TST; MFS, maximum flooding surface; HST, high-
stand systems tract; TST, transgressive systems tract
surfaces of small-scale cycles from the Middle Jurassic (Bajocian) of the Atlas
Mountains and Europe (Addi 2006); here too the buildups are related to relative
sea-level rise owing to a combination of tectonics and eustasy. Probably analogous
rudistid bivalve patch reefs occur on flooding surfaces in the Albian of Mexico
(Lehmann et al. 2000).
4.2 Dark Mudrocks
4.2.1 Dark Laminated Shales
Distal facies of many cycles, especially in ramp settings (e.g. Collingwood Shale,
Blue Lias of Dorset and Watchet) include dark gray to black, organic-rich, lami-
nated shales (Table 2; Fig. 30). Such beds are invariably sharp based with a slightly
erosive contact with the underlying gray shale or shelly marl and include a very thin
basal lag deposit of reworked phosphatic, pyritic and resistant skeletal grains (Baird
and Brett 1986, 1991).
Although some shales are barren, many have bedding planes covered with
mono- or paucispecific fossil assemblages. Middle Cambrian cycles show a domi-
nance of a few species of agnostoid trilobites, possibly chemosymbiotic olenid
polymeroids, such as Elrathia (Gaines and Droser 2003), and phosphatic brachio-
pods. The Ordovician dark shale biofacies, exemplified by the Collingwood Shale,
are primarily comprised of inarticulate brachiopods and small orthids, such as dal-
manellids, and a few species of trilobites (e.g., Pseudogygites and Triarthrus).
Lingulids and small nuculid bivalves are also relatively common and represent the
only infaunal organisms within the assemblage. Pelagic forms are well represented
on some bedding planes by graptolites. Devonian dark shales typically include low
diversity or monospecific assemblages of inarticulate brachiopods, as well as leio-
rhynchid and ambocoeliid brachiopods, small nuculid bivalves, and gastropods
(Boyer and Droser 2007). Pelagic forms include thin-shelled tentaculitids (e.g.
styliolinids), nautiloids, and the oldest goniatitic ammonoids. Mesozoic examples
such as the Jurassic Blue Lias shale similarly contain a very low diversity assem-
blage of small nektobenthic and pelagic organisms. The assemblage is dominated
by the small bivalve Bositra, ostracodes, small ammonites, and fish scales. In addi-
tion, carbonized logs and woody plant debris are present in many examples, and the
logs may be encrusted by organisms including bivalves and long stalked crinoids
(Seilacher and Hauff 2004).
Low diversity, high dominance fossil assemblages, are typically preserved as
hash-rich pavements and thin stringers. Fossils are generally disarticulated, commonly
fragmented, and dominated by decalcified, and benthic organisms (e.g. small
bivalves, or brachiopods) and/or carbonized and phosphatic remains (e.g. orbiculoid
brachiopods, graptolites, coalified wood and other plant remains). In a few Mesozoic
examples aragonite is preserved as thin films on highly compressed shells, but in
other cases even calcitic fossils are decalcified.
Table 2 Comparative taphonomic and paleoecologic aspects of highstand dark shales
Age Thickness
Formation Number Lithology Common taxa Trace
Mid-Cretaceous Kauffman (1982) 20–100 cm Dark gray to black Small inoceramid Minor small Barren to densely packed
bedding
Greenhorn Fm. Sageman (1996) 20–40 kyr laminated shale pterioid bivalves Chondrites plane assemblages,
disarticulated
Utah/Colo., USA disseminated pyrite small ammonites fragmented; decalcified,
compressed
minor pyrite patinas
Early Jurassic Kauffman (1978, 50–100 cm Black, laminated Bositra, pectenid Small Chondrites Barren to densely packed
1981) shale bivalves bedding
Posidonienschiefer Seilacher (1982b) ? disseminated pyite ammonites in some bedding planes;
disarticulated;fragmented
S. Germany ? crinoids on logs planes decalcified, compressed;
minor
pyrite patinas; horions of
articulated
vertebratres and crinoids
Early Jurassic Mogadam and Paul 30–120 cm Dark gray to black Small “paper Minor small Barren to densely packed
(Moghadam and pectens” bedding
Paul 2000)
Blue Lias Allison et al. (in 40 cycles laminated pterioid, bivalves Chondrites plane assemblages,
press) bituminous disarticulated
(continued)
161
Table 2 (continued)
162
Age Thickness
Dorset, Great Britain Paul et al. (2008) 38 kyr shale small ammonites fragmented; decalcified,
compressed
fish scales, fish, minor pyrite patinas
marine reptiles horizons of articulated
vertebrates
Mid-Devonian Brett et al. (1991) 20–500 cm Dark gray to black Thin shelled Pyritic thread-like Barren to densely packed
rhynchonellid bedding
Hamilton Group Boyer and Droser ~30 cycles laminated shale orbiculoid burrows plane assemblages,
(2007) brachiopods disarticulated
New York, USA 20–100 kyr disseminated pyrite small pterioid fragmented; decalcified,
bivalves compressed
Lower Devonian Becker et al. 20–80 cm Dark gray to black Small athyrid, Pyritic thread-like Barren to densely packed
(2004a), b) ambocoeliid bedding
Hollardops beds Brett, unpub. data ~30 cycles laminated shale & orbiculoid burrows; small plane assemblages,
brachiopods disarticulated
SW Morocco ? 20–40 kyr disseminated pyrite small pterioid Chondrites fragmented; decalcified,
bivalves compressed
Late Ordovician Brett et al. (2006) 20–100 cm Dark gray to black Orbiculoid, lingulid None Barren to densely packed
and bedding
C.E. Brett et al.
Age Thickness
Collingwood Shale 15 cycles laminated oil shale small orthid plane assemblages,
brachiopods, disarticulated
Ontario, Canada 20–40 kyr disseminated pyrite Triarthrus trilobites fragmented; decalcified,
compressed
beds of articulated trilobites;
molts
Mid-Cambrian Gaines et al. (2005) 20–500 cm Dark gray to black, Acrotretid None Barren to densely packed
brachiopods bedding
Wheeler Formation Gaines and Droser 25 cycles laminated shale agnostoid and polymeroid plane assemblages,
(2005) disarticulated
Utah Brett et al. 2009 20–100 kyr disseminated pyrite trilobites (Elrathia) fragmented; decalcified,
compressed
beds of articulated trilobites;
molts
163
A high degree of skeletal fragmentation is typical of dark shales (Fig. 30).

Although the cause of this breakage in low energy, low oxygen environments is
enigmatic, it points to prolonged exposure and may include episodic disturbance of
diagenetically weakened shells by deep currents.
Although fossil debris appears randomly distributed on some bedding planes,
prominent alignment of elongated fossils is observed in many examples of black
shales, as well exemplified by aligned graptolites in Ordovician-Silurian examples
and aligned tentaculitids and orthocones in the mid Paleozoic, or baculitids in the
Cretaceous. This evidence, together with minor stringers or gutter-like accumulations
of debris points to current activity even in these dysoxic settings.
In contrast to the typical poor preservation, a few bedding planes in many dark
shales yield well articulated fossils and even, especially in the Cambrian examples,
soft or weakly sclerotized organisms. Well preserved trilobite exoskeletons, both as
carcasses and as molt ensembles, are noted on certain bedding planes in Cambrian
to Devonian examples, providing direct evidence for episodic rapid deposition.
The molt ensembles are particularly significant in pointing to in situ life activity on
the seafloor and an absence of lateral transport in obrution deposits. Mesozoic
examples typically lack abundant multi-element skeletons making recognition of
burial horizons more difficult. However, beds of articulated crinoids-frequently
associated with carbonized logs and vertebrates, such as fish and marine reptiles,
provide dramatic evidence, for rapid episodic burial (see Kauffman 1978, 1981;
Seilacher 1982b).
Shells are typically very strongly compacted, decalcified, and lack mineralization
with the rare exception of minor pyritic patinas. Robust pyritized fossils and burrows
are nearly lacking in these facies. However, the poor preservation of fossils within
the shales indicates a relatively low sedimentation rate (long exposure time to
seafloor conditions) and a relatively low pH environment. Some fracturing of shells
results from the early compaction of the units. In both cases, aragonitic fossils are
decalcified and highly compressed but most aragonitic shells are preserved as plastically
deformed molds indicative of early dissolution (see Kauffman 1978, 1981,
Seilacher 1982b).
4.2.2 Gray Mudstones and Siltstones
The remainder of simple shelf cycles may comprise gray shales, mudstones and
siltstones or calcisiltites (Table 3; Figs. 29 and 30). The mudstone components of
the middle Paleozoic and Mesozoic examples both include increased faunal abundance
and diversity over the dark shales. In addition, there is a significant increase in
bioturbation. Nearly all examples contain numerous burrows and the sediment may,
in fact be heavily bioturbated.
Mudstone intervals of distal environmental settings, in fresh samples and cores,
reveal discrete, sharply-based packages of relatively uniform muds, up to several
centimeters thick. Thin siltstones, calcisiltites and silty mudstones, when present, are
sharp based with minor lags of disarticulated skeletal debris on the basal surfaces; these
Table 3 Comparative taphonomic and paleoecologic aspects of highstand mudstones
Age Thickness
Cretaceous Elder et al. (1994) 20–100 cm Medium gray, Gryphaea, inoceramids Planolites Dispersed to patchy;
calcareous disarticulated
Greenhorn ~25 cycles silty mudstone; burrowing bivalves pyritic burrows and articulated
shelly shells; minor
fragments
Utah/Colorado 20–40 kyr stringers; echinoids, ammonites pods and stringers of
concretions shell hash
concretions with
fossils
Early Jurassic Allison et al. (in press) 30–120 cm Medium gray, Gryphaea,burrowing Planolites, Dispersed to patchy;
calcareous disarticulated
Blue Lias Paul et al. (2008) 40 cycles silty mudstone; bivalves; crinoids Chondrites and articulated
fragments
Gt. Britain 38 kyr stringers; echinoids, ammonites pyritic burrws pods and stringers of
concretions, pyritic
burrows/fossils
Mid Devonian Brett and Baird (1986a) 20–500 cm Medium gray, Ambocoeliid and Pyritic burrows Dispersed to patchy;
calcareous chonetid disarticulated
Hamilton Group Speyer and Brett ~30 cycles silty mudstone; brachiopods, nuculid and articulated
(1985) shelly and shells; minor
fragment
New York Brett et al. (1991) 20–100 kyr stringers; modiomorphoid pods and stringers of
concretions bivalves shell hash
165
(continued)
Table 3 (continued)
166
Age Thickness
phacopid trilobites concretions, pyritic
burrows, fossils
Lower Devonian Botquelen et al. (2006) 20–80 cm Gray, marly shale Chonetid brachiopods, Small burrows Dispersed to patchy;
disarticulated
Amoricain Massif, ~30 cycles concretions nuculid and modiomorphid and articulated
shells; minor
fragments
France 20–100 kyr bivalves, phacopid pods and stringers of
shell hash
trilobites
Lower Devonian Becker et al. (2004a, b) 20–100 cm Gray, marly shale Small athyrid and Minor small Dispersed to patchy;
chonetid disarticulated
Hollardops beds Chatterton et al. (2006) 15 cycles concretions brachiopods nuculid and burrows and articulated
shells; minor
fragment
SW Morocco 20–40 kyr modiomorphoid pods and stringers of
bivalves shell hash
phacopid trilobites concretions, pyritic
burrows, fossils
articulated trilobites
Late Ordovician Brett and Algeo 20–500 cm Medium gray, Orthid brachiopods Small Planolites Dispersed to patchy;
(2001b) calcareous disarticulated
Kope Fm. Brett et al. (2003) 25 cycles silty mudstone; bryozoans, small trilobite traces and articulated
C.E. Brett et al.
fragment
Age Thickness
Ohio/KY 20–100 kyr stringers; crinoids, bivalves pods and stringers of
calymenid/asaphid trilos beds with articulated
triloibtes, crinoids
Mid Ordovician Boyer and Droser 20–120 cm Medium-olive gray Small brachiopods Small Planolites Dispersed to patchy;
(2003) disarticulated
Kanosh Fm. ~140 cyc.s calcareous shale ostracods, molluscs and articulated
shells; minor
fragments
20–100 kyr pods and stringers of
shell hash
Mid-Cambrian Gaines et al. (2005) 20–500 cm Medium, dark gray Acrotretid brachiopods; Minor Planolites Dispersed to patchy;
disarticulated
Wheeler Fm. Gaines and Droser 25 cycles calcareous polymerid/agnostoid and articulated
(2005) mudsone shells; minor
fragments
Brett et al. (2009) 20–100 kyr nodular micritic ls. eocrinoids pods and stringers of
shell hash
beds with articulated
trilobites, eocrinoids
167
may feature tool marks, scours, gutter and pot casts etc. They are typically strongly
burrowed from the top downward by Chondrites, Planolites, and Diplocraterion. In
some Devonian and later examples more extensive bioturbation by larger traces, such
as Zoophycos, may homogenize these thin beds with intervening muds. This faunally
and ichnofaunally rich assemblage is suggestive of more oxygenated conditions.
Body fossils may be scattered throughout the mudstone but they are typically
concentrated on certain bedding planes. These include minor lenses and stringers
of skeletal debris, typically including remains of varied soft substrate epifaunal and
infaunal benthic fossils. In Cambrian deposits these are mainly trilobites, calcitic
brachiopods, and eocrinoids (McKerrow 1979; Li and Droser 1997). For the middle
Paleozoic these skeletal layers include abundant strophomenid and spiriferid bra-
chiopods, bryozoans, pelmatozoans, such as crinoids, and trilobites (McKerrow
1979). Jurassic and Cretaceous analogues include gryphaeid bivalves, small
bivalves and certain ammonoids. Cenozoic examples feature primarily bivalves and
gastropods as well as shark teeth and occasional crustaceans.
Taphonomic conditions of fossils within all examples are similar, with more numer-
ous whole valves and, less commonly, articulated specimens. Overall, the taphonomic
grade of these mudstones is better than in the black, laminated shales. The mudstones
clearly represent an increase in sedimentation rate. Shells in a majority of beds are
dominantly disarticulated, but rarely fragmented, representing reworked slightly time-
averaged assemblages. Although this material generally shows little evidence of abra-
sion or bioerosion, the shells may show encrustation by bryozoans and worm tubes.
Obrution beds are characterized by the preservation of articulated bivalved and
multi-element skeletons, such as trilobites, crustaceans, echinoids, crinoids and
small vertebrates. They were commonly buried in varied orientations but may have
subsequently been crushed; see for example the Hollardops beds. Articulated lin-
gulid brachiopods and bivalves may occur in burrow position or in orientations that
suggest escape behavior. Not surprisingly, many obrution beds also contain an
abundance of time-averaged, disarticulated and even fragmented material that
records earlier generations of organisms that underwent normal mortality and
taphonomic degradation prior to the final community (Simoes et al. 1998).
Paleozoic examples include clusters or patches of crinoids, as well as brachio-
pods and trilobites (Brett and Seilacher 1991; Simoes et al. 1998). Mesozoic and
Cenozoic rapid-burial beds include infaunal, shallow-burrowing bivalves typical of
offshore, low-energy conditions and clumps of in situ bivalves (Kondo 1997;
Fürsich and Pandey 2003; Krawinkel and Seyfried 1996; Hendy et al. 2006).
4.3 Proximal Siltstones and Sandstones
Proximal representatives of small-scale cycles, such as those described above typically have
a strongly coarsening-upward parasequence motif (Table 4; Fig. 29). The cycle
bases are silty mudstone and siltstone; in many cases, the mudstone-siltstone portion
of the cycle may be very nearly barren of fossils (e.g., Lower Devonian Rich 3
Table 4 Comparative taphonomic and paleoecologic aspects of falling stage shell beds
Age Thickness
Cretaceous Sageman (1996) 20–100 cm Mudstones and HCS Inoceramids, Zoophycos Complete and some
gryphaeids fragmented
Greenhorn 25 cycles Siltstones, sandstone Burrowing bivalves Thalassinoides valves; rare articulated
fossils; occur
Utah/Colorado 20–100 kyr gutters; shell lenses, belemnites escape traces as graded lenses and pods
stringers
Early Jurassic Allison et al. (in press) 30–120 cm Mudstones and HCS Gryphaeids, Zoophycos Complete and some
belemnites fragmented
Blue Lias Paul et al. (2008) 40 cycles Siltstones, sandstone Burrowing myid Teichichnus valves; rare articulated
bivalves fossils; occur
Gt. Britain 38 kyr gutters; shell lenses crinoids as graded lenses and pods
rare articulated, e.g.,
ophiuroids
Mid-Devonian Brett and Baird (1986) 20–500 cm Silty mudstone to fine Orthid, spiriferid and Zoophycos Complete and some
fragmented
Hamilton Group ~30 cycles grained sandstone; rhynchonellid brach Teichichnus valves; rare articulated
HCS fossils; occur

New York 20–100 kyr shelly lenses Pterioid & escape traces as graded lenses and pods
modiomorphid
bivalves, crinoid rare articulated crinoids
debris
Lower Devonian Botquelen et al. (2006) 20–80 cm Sandy mudstone and Spiriferid brachiopods ? Planolites Loosely packed; lenses
and pavements
(continued)
169
Table 4 (continued)
170
Age Thickness
“Type A” shell ~30 cycles sandstone; HCS, Bivalves, gastropods Thalassinoides Disarticulated; slight to
beds gutters complete
Spain 20–100 kyr packstone lenses fragmentation; not
corroded
no bioerosion or encrsting
Late Ordovician Kreisa and Bambach 20–100 cm Silty mudstone and Orthid and Diplocraterion Loosely packed lenses
(1982) strophomenid and pavement
Martinsburg 15 cycles siltstone with graded Brachiopods; bivalves Thalassinoides Disarticulated; slight to
complete
Virginia 20–40 kyr shell beds, sharp erosi fragmentation; not
corroded
basesl HCS some articulated trilobites,
crinoids
Mid-Cambrian Brett et al. (2009) 20–50 cm Rhythmic calcisiltites Orthid brachiopods Planolites Loosely packed; stringers
pavement
Wheeler Fm. 25 cycles shales; thin skeletal Acrotretids; poymerid Thalassinoides Disarticulated; rare
articulated fragile
~20–100 kyr lag beds trilobites; eocrinoids fossils including trilobites
and
eocrinoids
C.E. Brett et al.
cycles in Morocco; Jurassic cycles in Yorkshire). This may be a function of the

combined stresses of low oxygen and rapid sedimentation (Wignall 1993) or may,
in part reflect dissolution in undersaturated sediments (Aller 1982). In some
instances the siltstone and sandstone portion of the cycle (often 1 to more than 10
m in thickness) may commence abruptly at an erosive surface that may even show
evidence of channeling. The soles of the basal bed and subsequent silt and sand-
stone beds may yield gutter casts and tool marks. Cambrian to Devonian examples
may display excellent trilobite trace fossils (Cruziana and Rusphycus) on lower
surfaces (Table 4; Seilacher 2007). Beds are typically coarse silt and sandstones up
to 10 s of centimeters thick that may show grading, with shell debris lags on basal
surfaces and hummocky lamination, ripple bedding or, rarely, flaser structure.
Younger examples may display intense bioturbation of upper surfaces by Planolites,
Teichichnus (“lam-scram” fabrics; Seilacher 2007). Near cycle tops siltstone or
sandstone may be more heavily bioturbated, especially by Rhizocorallium,
Thalassinoides, or Zoophycos. In some instances pyritic pipe-like burrow replace-
ments, rarely with concretionary overgrowths may be present up to 0.5 m below the
sharp cycle top. Such evidence of more intensive bioturbation and mineralization
indicates alteration of older sediments during periods of relative sediment starva-
tion associated with ensuing transgressions.
Shell beds associated with these regressive deposits tend to be thin and discontinu-
ous or lenticular (Table 4). Fossil material is typically concentrated at the bases of
graded beds and may form discontinuous lags or parautochthonous coquinas up to a
few centimeters thick. Fossils are typically whole un-abraded skeletal elements and, if
fragmented, show sharp, non-rounded breakage. Shells may occur as edgewise, imbri-
cated, or nested accumulations suggesting storm processing (Seilacher and Meischner
1964). Shells generally show only minor encrustation by bryozoans and small corals,
and boring by parasitic forms (e.g. Vermiformichnus), which may have been on shells
of live organisms. In Paleozoic examples the most typical fossils in these coquinites
are disarticulated valves of brachiopods and clams and crinoid ossicles and plurico-
lumnals; articulated shells may also occur. Current aligned Tentaculites tend to be
abundant on some sandstone bedding planes in the Late Ordovician to Middle
Devonian. Woody plant debris is also typical of Devonian and younger examples and
in post-Jurassic examples this wood may contain borings of teredinid bivalves.
Such bedding planes may include well-articulated fragile forms such as complete
crinoids or ophiuroids. Excellent examples are provided by the famed ophiuroid
bed from hummocky cross-bedded sandstones of Lower Jurassic Eype Clay of the
Dorset Coast (House 1989).
4.4 Diagenetic Carbonates
One recurring aspect of many small-scale cycles in distal ramp to basinal settings, is
the occurrence of are carbonate cemented concretionary limestones (Table 5; Fig. 29).
These may incorporate one or more thin shell hash beds, but are usually nearly
Table 5 Comparative taphonomic and paleoecologic aspects of calcareous/concretionary mudstones
172
Age Thickness
Mid-Cretaceous Elder et al. (1994) 10–30 cm Chalky, micritic Ostreids, Thallasinoides Dispersed fossils;
shale inoceramids fragmentary
Greenhorn 30 cycles concretionary infaunal bivalves Zoophycos and complete shells;
limestone in situ
Utah/Colo., USA 20–100 kyr rare ammonites Gryphaea and
inoceramids
Early Jurassic Moghadam and Paul 10–30 cm Medium gray Gryphaeaa, pinnids, Thallasinoides Dispersed, articulated,
(2000) calcareous disart shells
Blue Lias Paul et al. (2008) ~30 cycles mudstone, burrowing bivalves Planolites articulated, closed
concretions bivalves in situ
Dorset, Gt. Britain Allison et al. (in press) 40–100 kyr ammonites, crinoids large Chondrites uncompressed burrows
rhynchonellid brachs
Mid-Devonian Speyer and Brett (1985) 10–30 cm Calcareous, tabular Small rugosans Pyritic burrows Dispersed to loosely
packed
Hamilton Group Brett et al. (1991) ~10 cycles concretionary chonetid and small Zoophycos disarticulated and
ambocoeliid articulated
New York 20–40 kyr argillaceous brachiopods Chondrites clusters of trilobites,
limestone including
phacopid trilobites enrolled and molts
Lower Devonian Chatterton et al. (2006) 5–20 cm Calcareous, tabular Small rugosans, Pyritic burrows Dispersed disarticulated
and
Hollardops beds ~80 cycles concretionary chonetid and rare, small articulated trilobites;
ambocoeliid random
C.E. Brett et al.
SW Morocco 20–40 kyr argillaceous brachiopods Zoophycos orientations
limestone
trilobites
Late Ordovician Brett et al. (2006) 10–20 cm Calcareous, tabular Orthid, Planolites Dispersed disarticulated
strophomenid, and and
Collingwood ~10 cycles concretionary lingulid brachiopods Chondrites articulated trilobites;
random
S. Ontario, Canada 20–40 kyr micritic limestone bryozoans, cheirurid orientations; in situ
and Lingula
calymenid trilobites
173
s tructureless argillaceous fine-grained limestone. These horizons range from diffuse,

isolated concretions, centered at approximately the same level in the sediment, to rami-
fying and interlocking concretions, to concretionary limestone and sub-tabular
“micritic” bands (Kauffman 2003). In some instances, these may be the most promi-
nent beds in outcrops, masking their true significance as diagenetically cemented
layers of background sediment. Many of these beds are nearly barren except for hori-
zontal pyritic (frequently weathered to rusty limonite) thread-like burrows and verti-
cal, pyritic, tubular burrows and highly scattered fossils. In other cases, such as the
Collingwood Formation and the Hollardops beds of Morocco, they contain extraor-
dinarily well preserved fossils preserved in varied orientations. Likewise, proximal
examples of the Blue Lias show abundant burrowing bivalves preserved in life
positions.
In more proximal siliciclastic dominated settings the diagenetic interval is mini-
mal or absent. As noted above, however, the position of the stationary zone of
sulfate reduction may be marked by a horizon of pyrite-replaced burrows and/or
calcitic to sideritic concretions that commonly are nucleated on discrete pyritic
tubes representing mineralized burrow linings. Such rusty concretionary zones are
common beneath the tops of small-scale cycles in the Devonian of the Appalachian
basin (Brett and Baird 1986a, 1996). Similar cycle top concretionary horizons are
known in other settings for example, the Lower Jurassic of Yorkshire (Hallam
1967; Anderton et al. 1979); the Upper Jurassic of Spain (Oloriz et al. 2002); and
the Cretaceous of the Western Interior of North America (Kauffman 2003).
5 Inferred Environmental Changes Through Small-Scale

Cycles: Implications for Cycle Genesis
Cyclic variation results in repetitive patterns of taphonomic and biotic response.

Types of variations include: (a) changes in sedimentation rates; (b) changes in frequency
of episodic sedimentation; (c) changes in energy regime; (d) changes in oxygen-
ation; (e) changes in sediment characteristics, particularly TOC values, and (f)
varying degrees of diagenetic alteration (Figs. 31–33).
5.1 Environmental Energy
A progressive increase in energy level (favoring carbonate-rich units) is evidenced

by the upward increase in current-processed sedimentologic features in many cycles.
Within distal cycles black shale bedding surfaces show only minor orientation of
lightweight shell material but variations in shell convex up-down orientation in
different beds suggest subtle fluctuations in energy level. Narrow gutters and uni-
directional alignment of graptolites demonstrate the existence of minor currents. In
the mudstones, larger gutters (up to 10 cm across) are present and more numerous,
Fig. 31 Relationship of sediment accumulation rates to formation and reworking of concretions.

Bar on right shows position of the MZ (methanogenic zone), SRZ (sulfate reduction zone), RPD
(redox potential discontinuity) and SWI (sediment–water interface) at outset of interval. Note that
these zones remain static during period of sediment starvation but migrate upward as sediments
accrete to differing extents. Carbonate concretions will nucleate and accrete during conditions of
sediment starvation in the stable SRZ; however, under conditions of sediment buildup; these zones
will migrate upward in the sediment and no concretions will form; during sediment starved peri-
ods extreme storm erosion may cut down to the SRZ, exhuming concretions. Bar at the bottom
shows possible relationship to sea level oscillations, with starvation/erosion and concretion forma-
tion during transgression (T) (sediment sequestering in source areas) and increasing rates of
sediment aggradation during regression (R) (Modified from Brett et al. 2008)
as are thin beds of convex-up brachiopods. The shelly coquinas, which cap the
cycles may contain imbricated and/or nested shells, and occur as parts of graded,
hummocky cross-stratified beds indicative of storm wave processing.
5.2 Oxygenation and Geochemistry
Organic content within lithofacies decreases up-section within many cycles (see for
example Moghadam and Paul 2000). Changes in oxygenation are evidenced by pro-
gressive increases in bioturbation and faunal diversity/abundance favoring carbonate-rich
units. The increase in ichnofauna and benthic fauna observed in shales up through
limestones suggests a transition from low dysoxic to well-oxygenated conditions.
The lower shales and mudstones show little to no diagenetic enhancement.
Highly compressed molds of originally aragonitic shells suggests early dissolution
and strong compaction of sediments. Fractured molds indicate that shells remained
intact up to the time of initial compaction.
Conversely, the limestones clearly underwent early diagenetic cementation.

Evidence of synsedimentary cementation includes excellent preservation of fossils
(including three-dimensional preservation of material), lack of distortion of bur-
rows, along with the relatively wide spacing of fossil debris horizons, and the
concretionary nature of some of the units. Concretionary limestones representing
packages of uncompacted carbonate-rich mud are often located below dense hash-
rich pavements, indicative of surfaces of maximum sediment starvation (Fig. 31).
5.3 Sedimentation Rates and Time-Averaging
A strong degree of taphonomic alteration of bioclasts in basal skeletal beds indi-

cates low rates of sedimentation coupled with strong reworking (Figs. 32 and 33).
Such thick shelly pavements, result from condensation associated with minor sea-
level rise and minimal sediment input. Bases of the beds indeed suggest minor to
strong erosion of underlying sediments whereas their tops typically evidence sedi-
ment starvation. Overlying dark shales have sharp basal contacts, suggestive of
strong sediment starvation or minor erosion. Fossil assemblages from dark, organic-
rich shales near the bases of cycles are characterized by poor preservation and
strong taphonomic biases (e.g. strongly biased pygidia: cranidia ratios). Although
very rare articulated remains occur, fossils within the shales are typically fully
disarticulated to fragmentary, indicative of long-term exposure to taphonomic pro-
cesses (Kidwell and Bosence 1991).
The upper mudstone to siltstone portions of cycles contain numerous hash pave-
ments but include greater portions of less fossiliferous matrix in which well-preserved,
spar-filled, articulated, and in situ fossils are present. This indicates increasing rates
of sedimentation. However, concretion beds within the tops of cycles indicate periods
of cementation of older sediment during the time of sediment starvation associated
with overlying shell beds.
5.4 Episodicity and Dynamics of Sedimentation
Episodicity is evident throughout the cycles as relatively barren mud layers over
shelly layers (Fig. 33) and the presence of obrutionary layers within the dark shales.
Obrution beds are more numerous and thicker in the upper mudstone and siltstone
Fig. 32 (continued) mud clasts may be torn up; muds are removed and shell debris is further
stacked and concentrated; a thin silt layer may accumulate on top of shell hash. (f) Recolonization;
in MDP:opportunistic burrowers colonize storm silts producing Diplocraterion, Chondrites, and
other traces; in SDP: recolonization of hard substrate adapted taxa, including bryozoans and cri-
noids; exhumed concretions may be encrusted or bored with Trypanites (Modified from Brett
et al. 2008)
MUD - DOMINANT PHASE SHELL BED - DOMINANT PHASE
Fig. 32 Analogous seafloor processes during mudstone dominant phase (MDP; left column), and
shell-bed dominant phase (SDP; right column). Note that both sediment accumulation and erosion
may occur in either phase, but to different effect. (a) Background conditions at outset of interval;
note general accumulation of skeletal debris during pause in sedimentation. (b) Mud-blanketing;
thick layer in the MDP, note obrution deposit with buried intact crinoid; thin mud layer in SDP.
(c) Seafloor erosion by storm currents; in MDP: scouring is effective in cutting down to firm
muds, but does not erode through relatively thick mud blanket; little or no shell lag formed; in
SDP: winnowing removes thin mud blankets aggregating shelly debris buried by several previous
events. (d) Post-event re-deposition and colonization; in MDP relatively thick silt/mud buries
scoured surface, muds colonized by “snowshoe strategist” brachiopods and vagrant trilobites; in
SDP: minimal mud accumulation; re-colonization involves taphonomic feedback with exposed
shell-ground. (e) Scour and re-sedimentation; in MDP storm erosion produces irregular scoured
surface with gutters buried by silt layer; in SDP scouring creates irregular erosion surface and firm
TIME MAJOR EVENTS STRATIGRAPHIC

COLUMN OF DEPOSITION COLUMN
AND EROSION
KEY
TIME COLUMN
STRATIGRAPHIC COLUMN
(basal scour, reworked concretions)
Fig. 33 Schematic of generalized, small-scale cycle typical of cratonic successions, based on
Upper Ordovician Kope Formation, showing key components recognized in descriptions in this
paper. Individual beds shown in stratigraphic column are coded by letters A–O to levels in the time
column. Time intervals 1 and 2 represent intervals of generally low sediment input; intervals 3 and
4 more extreme sediment starvation; note that these intervals have relatively few mud or silt accu-
mulation events; skeletal debris builds up in “background” times. These intervals, comprising
about a third of the total time, are represented by thin complex of shell beds. Time interval 5
encompasses a time of increasing sediment aggradation; note deposition of a series of mud and
silt layers (including obrution deposits); also note that many upper layers are subsequently
removed in an erosional interval, preceding and contemporaneous with, next shell hash accumula-
tion. Portion of preserved mudstone interval comprising about a third of the time occupies the
majority of thickness of the preserved cycle (From Brett et al. 2008)
components. Mudflow type events are sufficiently common toward the ends of
certain small-scale distal cycles that in some instances a majority of the
mudstones-siltstones preserved at cycle tops show evidence of being obrution
deposits. This is especially obvious where early diagnesis has stabilized the upper
obrutionary layers, such as in the famed Moroccan Devonian trilobite beds where
cycle cap beds preserve articulated trilobites (Chatterton et al. 2006; herein). In situ
preservation and greater spacing of fossils within the upper (regressive) portions of
cycles suggests an increased frequency of burial events, more episodic sedimenta-
tion, and higher net sedimentation rate.
The sedimentologic and taphonomic characteristics of both mudrock- and shell bed-
dominated divisions of small-scale cycles are heavily influenced by the relative amounts
of time represented in mudrock- versus shell bed-dominant phases of the succession

(Fig. 31). Both phases record the episodic interruption of low-energy background sedi-
mentation by high-energy events of storm-related scouring and sediment reworking.
Evidence for event deposition is much easier to recognize in bioclastic strata,
particularly shell beds, which can preserve bedforms and display obvious heteroge-
neities in sedimentary fabric and structure such as cross-bedding, grading, edge-
wise stacking of shells, and rip-up clasts. Evidence for storm activity, although
detectable in mudrocks in some instances, is often subtle and is less likely to be
recognized than in bioclastic units due to their tendency to lack significant varia-
tions in mineralogy, grain size, color and fabric.
Relative to the mudrock-dominated intervals, the thinner bioclastic units are
condensed; taphonomic evidence indicates long-term time averaging of skeletal
remains within the beds (Figs. 32 and 33). The mixture of skeletons derived from
hard and soft substrate adapted organisms suggests a complex succession of minor
mud deposition and removal by winnowing (as in the “Jeram” model of Seilacher
1985). The presence of concretions in muds below skeletal hash layers suggests
intervals of carbonate cementation in the underlying muds as a result of prolonged
stability of the sulfate reduction zone as well as infusion of carbonate saturated
waters resulting from dissolution of aragonitic debris in the accumulating skeletal
hash beds above (Krawinkel and Seyfried 1996; Brett et al. 2003; Fig. 30).
Conversely, the formation of the mudrock dominated hemicycle involved episodic
deposition of mud layers up to several centimeters thick. The latter formed by the
long-term accumulation of thin, mud-starved veneers of winnowed/reworked
parautochthonous skeletal debris.
5.5 Overview
Consistent variations in these parameters suggest similar underlying causes of envi-

ronmental change (Figs. 32 and 33). The oxygen cycle appears coupled with the
sediment cycle. Oxygen levels progressively increase as siliciclastic to carbonate
proportions decrease. Increased sedimentation rate in association with an increase
in episodic formation of CaCO3-rich muds suggest a shallowing-deepening relationship
between cycle components. Evidence of sediment starvation low in the cycle seems
associated with a deepening trend, with sequestration of siliciclastics and cutback
on local carbonate input. Increases in sedimentation rate, episodicity and winnowed
shell layers up-section within the carbonate-rich units supports a shallowing trend,
as more numerous event beds and winnowed units represent an increased proximity
to average storm wave base.
Three models have been proposed to explain the origin of mudrock-shell bed
cycles (see Brett et al. 2008 for review). The first two assume that the mudrock
intervals reflect low energy/deep-water conditions and that shell beds are primarily
the product of increased storm wave energy and winnowing that, in turn, resulted
from either (a) relative sea level fall, during which storm wave-base was lowered
closer to the seafloor, or (b) increased intensity/frequency of storms without

significant change in water depth. A third model proposes that, the shell beds
reflect not only storm winnowing, but also the accumulation of time-averaged skel-
etal debris during prolonged periods of siliciclastic sediment starvation, possibly
associated with minor base-level rise. Decimeter-scale shell beds formed during
millennial-scale periods of siliciclastic sediment starvation combined with episodes
of storm-related reworking and winnowing. This constitutes an alternative interpre-
tation of shell bed genesis that is more in accord with taphonomic, sedimentologic
and paleontologic evidence.
6 Long-Term Trends in Cyclic Taphofacies
Comparison of litho-, tapho- and biofacies of small-scale cycles through time highlights
commonalities resulting from the constancy of physical processes and differences
arising from secular changes in the abundance and diversity of skeleton-producing
organisms (Fig. 34). Some differences are obvious particularly between Cambrian
and later cycle taphofacies.
Early to Middle Cambrian shallow shelf deposits rarely contain thick skeletal
accumulations greater than 1–2 cm thick (Li and Droser 1997). Nonetheless, some
basal skeletal lags, of mixed biotic and abiotic carbonate grainstones, particularly
ooids, are comparable in thickness and complexity to those of later time. Such
mixed oolitic, phosphatic and intraclastic and skeletal beds, ranging up to 50 cm
thick exist in shallower facies for example. Comparable shell beds of mixed lingu-
lid brachiopods and ooidal phosphate and hematite beds are well described from the
Middle Ordovician of the Armorican Massif (Dabard et al. 2007).
By the Middle Ordovician, condensed shell beds attained thicknesses of 10–30
cm as evidenced by the shelly limestones of the Kanosh and Lehman Formation in
the Great Basin (Boyer and Droser 2003). These beds are among the earliest
examples of what may be considered relatively typical Paleozoic style shell beds,
they are composed of monospecific to moderate diversity assemblages, dominated
in offshore facies by orthid brachiopods. Similar shell beds are well documented in
the Silurian and Devonian of many areas. For example, brachiopod shell layers up
to 50 cm thick occur in the Silurian of Arisaig, the Appalachian Basin and the
Welsh Basin (Ziegler et al. 1968). Devonian examples are also widely cited, e.g.,
the Lower Devonian of Iberia (Botquelen et al. 2006) describe shell beds compa-
rable to their A-type beds in the Ordovician up to several centimeters thick.
Jurassic and Cretaceous shell beds are composed mainly of epifaunal bivalves, together
with gastropods and some crinoid material, are typically several centimeters to nearly 2 m
in thickness (e.g. Fürsich and Pandey 1999, 2003; Fürsich and Aberhan 1990).
Increased thickness of transgressive shell beds, in part, reflects increased pro-
duction rates of skeletons relative to the mid Paleozoic, while the absence of inter-
nal discontinuities, in contrast to many obviously stacked, amalgamated beds in
the Paleozoic, reflects bioturbational mixing of shells. Kidwell and Brenchley
a Cambrian b mid-Paleozoic c Late Neogene

(expanded cycle motif) (expanded cycle motif) (typical thickness)
1m scaled to typical thickness scaled to typical thickness
Fig. 34 Small-scale cycles through time. (a) Cambrian cycle with thin skeletal lags at bases
composed of trilobites with limited bioturbation. (b) Middle Paleozoic cycle with better-developed
shell beds and more intense bioturbation. (c) Cenozoic example showing basal shell rich interval
several meters thick, with strongly bioturbated shell debris. Note also the greater thickness of this
cycle; this may be an artifact of the site of deposition: most Paleozoic and Mesozoic cycles accu-
mulated in low subsidence epicontinental sea environments, whereas a majority of Cenozoic
examples occur in actively subsiding outer continental shelf to forearc basins
(1994, 1996) have systematically documented thickness trends in shell beds and
note a substantial change in the mid-Cenozoic that they attribute to the faster pro-
duction and greater robustness of molluscan shells (Fig. 34).
Examples of Middle Cambrian transgressive shell beds include large branching
burrow galleries of “Thalassinoides” type within transgressive shell beds. Not sur-
prisingly, however, the degree of bioturbation with the facies steps up from
Cambrian to Middle Ordovician (Droser and Bottjer 1988; Manguno and Droser
2004). Larson and Rhodes (1983) and Thayer (1985) also reported a substantial
increase in shell bed thickness from Ordovician to Devonian, which they attributed
to increased depth and intensity of burrowing. Burrowed firmgrounds are typical of
the bases of these beds (e.g., Landing and Brett 1987).
A diverse guild association can be observed within the more carbonate-rich
transgressive components of cycles (see discussion in McKerrow 1979; Brett 1995,
1998; and below). Both the calcareous mudstone and limestone intervals contain
diverse and abundant assemblages of benthic organisms, in addition to pelagic
organisms. In the Cambrian cycles skeletal components include debris of pelmato-
zoans (eocrinoids), articulate brachiopods, monoplacophorans, and fragments of
larger trilobites, such as Asaphiscus and Olenoides.
In the Middle to Late Ordovician the condensed transgressive lags are more
skeleton-rich intervals that can be characterized as shell beds. These include abun-
dant valves of brachiopods, especially concavo-convex strophomenids, dalmanellids
and other orthids, trilobites, nuculid bivalves, crinoid ossicles, lingulids, nautiloids,
and graptolites. Mid Paleozoic examples include small brachiopods (strophomenids,
athyrids, atrypids), small solitary rugose corals, small tabulates (auloporids,
Pleurodictyum) and nautiloids. Taphonomic feedback became progressively more
important in enhancing diversity in shell-rich sediments (Kidwell and Jablonski
1983).
Mid Mesozoic transgressive shell beds are similar in thickness to those of the
later Paleozoic and are dominated by the bivalve Gryphaea, small rhynchonellid
brachiopods (e.g., Calcirhynchia), crinoids, small ammonites and rare small, thin
flat bivalves. In both mid Paleozoic and Jurassic cases, guild associations are similar
in the limestones to those of the mudstones, with increased diversity and abundance
of benthic fauna. Noteworthy is the addition of small gastropods and echinoids in
Blue Lias limestone biofacies.
Cambrian dark shales are typically fully laminated and show, at most, discrete
minute burrows (Gaines and Droser 2005; Gaines et al. 2005). Post-Cambrian
examples of dark shales show signs of minor bioturbation at the shale bases.
Ordovician Collingwood shales and Devonian black shales display small Chondrites
(Boyer and Droser 2007). Several of the upper mudstone intervals within the
Devonian cycles in New York, and those of the Jurassic Blue Lias and Cretaceous
Greenhorn cyclothems include dark burrows piping from the overlying shales (this
type of piping is unknown in the Ordovician). This evidence of bioturbation, associ-
ated with the laminated shales, suggests that low oxygen levels, associated with
these facies were sufficient to support the small tracemakers by the mid Paleozoic
and Mesozoic examples, but notably less so in the Cambrian, and perhaps during
much of the Ordovician.
7 Summary: Toward General Cyclic Taphofacies Models
Sea-level, climate, and sediment-supply fluctuation have strong biological

impacts, controlling the environmental and spatial distribution of organisms at a
variety of scales (Bennett 1990; Brett 1998; Brett et al. 2007a, b). Bathymetric and
sedimentologic factors, in particular, exert major controls on the distribution patterns
of shallow marine benthic organism (Ziegler 1965; Ziegler et al. 1968; McKerrow
1979; Boucot 1975, 1982; Brett 1995, 1998; Boucot et al. 1999; Abbott and Carter
1997; Scarponi and Kowalewski 2004; Brett et al. 2007b; Hendy and Kamp 2007).
Water depth/turbulence, sedimentation rate/turbidity, substrate consistency, oxy-
genation, and other parameters force regular and predictable change in small-scale
Milankovitch driven cycles (Bennett 1990; DiMichele et al. 2004; Brett et al.
2007b). In turn these fluctuations result in predictable changes in species composi-
tion and preservation of preserved biotas. For example, cyclic variations in relative
water depth may lead to recurrent biotic replacement series of bathymetrically

zoned organisms (Holland et al. 2001b; Brett et al. 2007b). Redox cycles likewise
will show regular variations from low diversity dysoxic adapted assemblages with
a dominance of small epibenthic forms to more diverse epi- and endobenthic spe-
cies; bioturbation fabrics will also reflect changing benthic oxygen levels.
Moreover, the predicted variation in siliciclastic sediment supply will vary from
relatively low during relative sea-level rise or arid climatic phases to perhaps an
order of magnitude higher during sea-level fall or a shift to humid climates with
active run-off of sediment from source areas. Such changes in sedimentation pat-
terns will strongly affect benthic substrates, rates of sediment accumulation, and
water turbidity (Brett 1998). For instance, high diversity assemblages of steno-
topic epibenthic forms are favored by the development of clean, stabilized sub-
strates and shell accumulations during transgressions, whereas limited endofaunal
generalized assemblages dominate more rapidly accumulated, food rich, soft sub-
strates during falling stages.
Fossils can be regarded as sedimentary particles (sensu Seilacher 1973), and
hence provide sensitive gauges of paleoenvironmental processes, particularly those
that relate to dynamics of sedimentation, and geochemistry. Variations in fossil pres-
ervation (taphofacies) can be related to variations in burial of organisms or buildup
of shell beds, turbulence (degree of disarticulation), redox conditions, pH, and early
diagenetic microenvironments. This regular variation leads to predictable variations
in fossil assemblage preservation or taphofacies (Brett and Baird 1986b; Speyer
and Brett 1986, 1988).
It is striking that similar patterns of fossil preservation should persist in cycles
deposited over half a billion years biological evolution and diversification. The
varied examples of small scales cycles given here contain a similar variety of fossil
accumulations, ranging from thin hash pavements to well preserved in situ assem-
blages. The primary taphonomic moderator in these cycles is rate of sedimentation,
which varies exponentially from sediment-starved concentrations to obrutionary
deposits. The occurrence of a persistent motif over this time scale suggests that
biological innovations, which might be expected to impact upon fossil preservation,
have in fact been overprinted by the extremes of sedimentation preserved in these
small-scale cycles. A skeleton, that is twice as resistant to abrasion, is of little
import when sedimentation is dominated by the extremes: instant obrution or
condensation.
During lowstand or early transgressive phases of sea-level cycles skeletons
accumulate in deposits that represent rather shallow water, and accordingly “high”
energy conditions. Additionally, sedimentation rates in shallow water settings tend
to be low during times of sea level lowstand as a result of winnowing and bypassing
of fine-grained sediment. Transgressive phases of sea level change are character-
ized by low sedimentation across the entire shelf and deeper water settings. Rates
of skeletal destruction tend to be high during these times of reduced burial and
increased energy, and hence, skeletal lag deposits of highly broken and abraded
coquina develop across shelf areas (Kidwell 1991b; Brett 1995; Coe 2003;
Catuneanu 2002, 2006).
At times of maximum rate of sea level rise, sedimentation rates in offshore areas
are at their lowest due to the entrapment of siliciclastic sediments in coastal alluvial
areas and the reduced carbonate production of shelf areas now below the euphotic
zone (Vail et al. 1991). Biogenic skeletons therefore tend to be exposed for long
intervals of time on the sea floor. Not only are skeletal accumulations subject to
reduced wave and current energy, they may also experience intense bio-geochemi-
cal corrosion. Hence, the thin-lag deposits that often accumulate during this interval
of sea level change are characterized by geochemically resistant particles, such as
calcitic (e.g., echinoderm plates) or phosphatic skeletons (e.g., conodont elements,
vertebrate bone). These bioclasts may experience reduced abrasion and physical
breakage relative to early transgressive beds. However, bioerosion (e.g., microbor-
ing), corrosion pitting, and other evidence of biogeochemical dissolution processes
may be more prevalent.
During highstand conditions deeper and frequently more dysoxic water masses are
established over broad areas of the shelf even as fine-grained siliciclastic sediments
begin prograding offshore (Vail et al. 1991; Brett 1995; Van Wagoner and Bertram
1995; Coe 2003). This sets the stage for distinctive types of preservation. Typically,
dark shales with fragmented, corroded and decalcified shell material may occur above
the condensed; biogenic disturbance may be minimal if benthic oxygen levels are low
and variable. This factor favors millimetre scale bedding plane assemblages separated
by laminae of barren shale. In some cases this combination of dysoxic conditions and
rapid sediment aggradation may favor nearly barren gray mudstone facies.
The later highstand deposits may be expected to show evidence of increasing
rates of siliciclastic input, together with improved bottom water oxygen. This may
favor a shift to better-preserved benthic epi- and endofauna. These fossils may be
expected to be more widely dispersed in the sediment and to show preservation of
at least whole valves and some articulated, butterflied, or even closed bivalves.
Pulses of sedimentation may be marked by obrution deposits of well-preserved,
articulated fossils. Because of the peculiar conditions of moderately oxygenated
substrate and bioturbated, organic-poor sediment the episodic burial of organism
bodies these facies may be appropriate for the formation of pyritic molds and coat-
ings (Hudson 1982; Brett and Baird 1986b; Brett et al. 1991).
Falling stage – or regressive – deposits (Naish and Kamp 1997; Plint and
Nummedal 2000) are characterized by increasing input of coarser siliciclastics, as
well as the effects of more numerous turbulence and sedimentation events. Rapid
burial should result in dispersed, well preserved fossils (Brett 1995); however, in
proximal areas, discrete turbulence events associated with storms may be expected
to winnow and concentrate skeletal remains. Fragmentation may be expected, but
fossils should generally lack signs of corrosion, abrasion or bioerosion.
In some cases a particular depositional condition may have an effect on more
than one aspect of taphofacies, For instance, interludes of sediment starvation, com-
monly associated with abrupt transgressions, may promote accumulations of variably
reworked skeletal debris at the seafloor and enhance cementation of subjacent sedi-
ment in the zone of sulfate reduction. This would also enhance preservation of
previously buried organism remains.
Although it is beyond the scope of the present paper, further detailed

c omparative studies may elucidate distinctive time-related features that may
relate to large-scale cyclic changes in earth’s climate and geochemistry, such as
(a) greenhouse-icehouse cycles (Fischer 1980, 1984), (b) calcite vs. aragonite
oceans or (c) other secular trends in paleoecology or water mass properties
(e.g. increased nutrient run-off following land plant evolution (Algeo et al. 1995,
2001). One may anticipate, in particular, that during icehouse phases of Earth’s
climatic history, cycles of similar temporal duration to those noted herein will
have much larger amplitude, leading to stronger gradients of facies within rela-
tively thin successions. For example, cycles may more frequently show changes
from offshore marine facies to marginal marine sediments, coals, and paleosols.
Subaerial exposure in many cycles may impart a higher degree of diagenetic
alteration and vadose solution to offshore marine cycles. Because of the more
rapid shifts in water depth one may anticipate that various portions of the cycles
will be thinner and more closely stacked. Improved oceanic circulation during
icehouse times may have led to a lesser tendency toward stagnation during high-
stands and decreased frequency of dark, organic rich facies in small-scale
cycles.
Differences between calcite and aragonite oceans may track greenhouse- ice-
house conditions because of strong correlations between both climate and oceanic
chemistry and rates of ocean floor spreading (Stanley and Hardie 1998, 1999).
Times of calcite or aragonite oceans, typically correlated with greenhouse or ice-
house megacycle phases, will be characterized by differences in shell bed accumu-
lations. For example, during times of aragonite oceans we anticipate a higher
proportion of aragonitic fossils in shell beds. This may permit preservation of
thicker skeletal accumulations, at least in settings favoring molluscs. Even in dark
shales and mudstones we anticipate that aragonitic (and calcitic) fossils will show
a lesser degree of decalcification and compaction than in comparable facies under
calcitic oceans. In addition, evidence for early cementation may be substantially
less than during greenhouse settings; thus firm- and hardgrounds reported in many
examples herein, may be far less typical of the sediment starved transgressive por-
tions of cycles during intervals characterized by aragonitic oceans (Wilson and
Palmer 1992; Palmer and Wilson 2004). In addition, we predict that concretionary
beds and diagenetic limestone underbeds that have been emphasized in this work
may be far less well developed during aragonitic ocean phases and associated ice-
house conditions. The lesser degree of early diagenetic cementation may negatively
affect the preservation of fossils by inhibiting early cementation of internal shell
fillings (leading to more strongly compressed fossils with lesser amounts of internal
sparry calcites).
The long-term increase in nutrient content of oceans has also had potential cascading
effects on the appearance of cycles. Eutrophication not only promotes increased
production of shelly remains that inevitably led to thicker shell beds (Kidwell and
Brenchley 1994; Bambach 2006; Bush et al. 2007) but may have led to increased
tendency toward production of organic rich laminated facies. This latter trend,
however, has inevitably been countered to a degree by the increase in deep
b ioturbating infauna, especially in low oxygen and sulfide rich environmennts that
may have been largely devoid of infauna during the early Paleozoic.
Finally, a general change in depositional settings of marine sediments from a
preponderance of epicontinental seas and distal foreland basins in the Paleozoic to
continental margins in the later Mesozoic and Cenozoic has inevitably had a strong
influence on many aspects of small-scale cycle paleoecology and taphonomy (e.g.
see Allison and Wells 2006; Wells et al. 2007). Most Cenozoic examples of cycles
are thicker by an order of magnitude than Paleozoic-Mesozoic ones, reflecting the
much higher rates of subsidence and sediment input on many narrow continental
shelves, especially in areas of active tectonism. Inevitably, this greater rate of sedi-
ment accumulation may also have an influence of taphonomy and time averaging,
again countered somewhat by increased burrowing rates.
A future program of comparative taphonomy and paleoecology of small-scale
cycles should investigate and test these hypotheses rigorously by compiling consis-
tently collected data on many aspects of the litho-, tapho-and biofacies of cycles of
comparable time-scale. Icehouse-greenhouse, aragonite-calcite, and other mega-
cycles need to be evaluated by comparing deposits laid down in broadly similar
oceanographic and paleogeographic settings. Only in this way can the hypotheses
listed above be rigorously tested. In turn, variations in taphofacies involving
changes in bioturbation, skeletal production and preservation, lithification and
other aspects of cycles may have critical implications for long-term trends in tapho-
nomic bias and resolution of the stratigraphic record (see Hendy, this volume).
Acknowledgements This project is an outgrowth of cooperative research between PAA and CB,
initially funded by grants from NATO and the Royal Society. CB expresses appreciation to the
Donors to the Petroleum Research Fund, American Chemical Society, NSF Grants EAR 0518511
(to W. Huff and C. Brett); and the National Geographic Society for supporting research on the
Devonian of Morocco. We have benefited from hours of discussion of ideas with many colleagues
and students, but especially Gordon Baird, Alex Bartholomew, Sean Cornell, Patrick McLaughlin,
David Meyer, Arnie Miller, Cam Tsujita. AJWH acknowledges funding from the American
Museum of Natural History Lerner-Gray Fund, Geological Society of America, Palaeontological
Society, the American Association of Petroleum Geologists, and the Department of Geology,
University of Cincinnati.
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Chapter 5
Taphonomy of Animal Organic Skeletons
Through Time
Neal S. Gupta and Derek E.G. Briggs
Contents
1 Introduction........................................................................................................................... 200
2 Organic Skeletons................................................................................................................. 205
3 Chemosystematics................................................................................................................. 207
4 Diagenesis............................................................................................................................. 207
4.1 Molecules Are Not Introduced from Sediment............................................................ 207
4.2 Components Contributing to the Composition of the Fossil....................................... 208
4.3 Implications for Kerogen Formation........................................................................... 210
4.4 The Rate of Diagenetic Change................................................................................... 213
5 Future Directions in Molecular Taphonomy......................................................................... 214
6 Appendix: Main Analytical Methods Applied to Organic Remains..................................... 215
6.1 The Soluble Fraction.................................................................................................... 215
6.2 The Insoluble Fraction................................................................................................. 215
6.3 Thermal Maturation Experiments................................................................................ 217
6.4 Investigating Morphology............................................................................................ 218
References................................................................................................................................... 218
Abstract Investigations of organically preserved invertebrate fossils have focused

on abundant taxa such as graptolites and arthropods. Analyses have shown that their
composition cannot be explained either as a result of decay resistance, or the intro-
duction of macromolecular material from surrounding sediment. The fossilization of
organic materials is a result of the diagenetic transformation of lipids in the organism
itself by a process of in situ polymerization which generates a composition with a
N.S. Gupta (*)
Department of Geology and Geophysics, Yale University, P.O. Box 208109, New Haven,
CT 06520-8109, USA
and
Geophysical Laboratory, 5251 Broad Branch Road NW, Washington, DC 20015, USA
D.E.G. Briggs
Department of Geology and Geophysics, Yale University, P.O. Box 208109, New Haven,
CT 06520-8109, USA
and
Peabody Museum of Natural History, Yale University, P.O. Box 208118, New Haven,
CT 06520-8118, USA
200 N.S. Gupta and D.E.G. Briggs
significant aliphatic component. While this process causes the fossilized remains of
different taxa, even plants and animals, to converge in composition they may still
retain differences following diagenesis. Such chemosystematic signatures have the
potential to be used in the identification of organic materials that lack diagnostic mor-
phology. The diagenetic transformation of organic materials in macrofossils is simi-
lar to the formation of kerogen – the final composition depends on original chemistry,
decay and diagenesis. A better understanding of rates and controls on this process
will require more experimental investigation of decay and maturation, as well as
analyses of fossils of different ages and from different environmental settings.
1 Introduction
The fossil record of animals contrasts with that of plants, in being dominated by
organisms with mineralized skeletons: shells, bones and teeth. Such hard parts
account for the extensive representation of the familiar shelly invertebrates:
sponges, corals, trilobites, ostracodes, brachiopods, molluscs, and echinoderms, as
well as the vertebrates. Although they are normally broken down by decay and
oxidation, soft-bodied fossils also provide critical data on the history of life. The
most decay prone tissues, such as muscle, are preserved by replication in authi-
genic minerals as a result of bacterial activity (Briggs 2003). More resistant tissues,
such as cuticle, however, may survive as organic remains (see Briggs 1999 for a
review). They account for the fossil record of a number of important groups includ-
ing graptolites, chelicerates (eurypterids, horseshoe crabs, scorpions and spiders)
and insects. A number of minor groups (e.g. chitinozoans) also have a non-miner-
alized organic cuticle, and others occasionally preserve organic elements in addi-
tion to the mineralized skeleton (e.g., ammonite beaks and some fish scales).
Attempts to understand the organic preservation of animal fossils have focused
inevitably on the more abundant remains, those of graptolites and arthropods. It was
long assumed that their preservation was a product of a skeleton organically
strengthened for rigidity and protection, and consequently more decay resistant than
the rest of the animal, and burial in environments where bacterial breakdown and
scavenging were inhibited (e.g. low oxygen black shales in the case of graptolites, high
salinity in the case of eurypterids). Research in the 1990s, however, showed that this
model, commonly referred to as ‘selective preservation’, is inadequate. This fol-
lowed the discovery that the composition of the fossilized material (e.g., graptolite
periderm, arthropod cuticle) is very different to that of its living precursor.
Graptolites are, of course, extinct. Investigations of well preserved examples using
electron microscopy showed that the ultrastructure of the periderm (the organic skel-
eton) is characteristic of the protein collagen (Towe and Urbanek 1972; Crowther
1981). Confirmation of this interpretation was provided by comparisons with the liv-
ing pterobranchs, encrusting benthic colonial organisms which are the nearest living
relatives of graptolites. Their structure and mode of growth are essentially identical
to that of graptolites, and the periderm is composed of collagen (Fig. 1a). Surprisingly,
however, analyses of fossil graptolites (Briggs et al. 1995) revealed no evidence of
5 Animal Organic Skeletons Through Time 201
a Rhabdopleura
Pro
1 mm
Pro
Pro
Pro Pro
Pro Pro
Pro
Pro
Pro Pro
*
b Graptolite (Dictyonema) 200 microns

Dictyonema
Relative Intensity
200 microns 1 mm
+
C10
_ P2 + +
+ +
_ _ C15
B3 + C
_20
+ _ _ _
_ + + +
_ Gly _ +
_
N _+ _+
Retention time
Fig. 1 Partial py-GC-MS chromatogram revealing the chemistry of (a) modern pterobranch
Rhabdopleura and (b) graptolite Dictyonema peltatum (YPM 202222), Wisby, Sweden, Silurian. Pro,
protein pyrolysis products; B3, C3 benzene; +, n-alk-1-ane; −, n-alk-e-ene; Cn, where n refers to the
carbon chain length; Gly, Glycerine; N, Napthalene; P3, dimethyl phenol/ethyl phenol; *, contaminant.
Inset (a) branching tubular colony of Rhabdopleura; (b) Dictyonema stipe and close-up of thecae
protein; the composition of the graptolite periderm is aliphatic, composed of long

chain hydrocarbons (Fig. 1b). This anomaly was explained at the time by postulating
that the macromolecular material had been introduced into the organic skeleton of the
graptolite from the surrounding sediment (Briggs et al. 1995).
The history of research on organically preserved arthropod fossils parallels that
of graptolites. Until the mid-1990s fossilized cuticles were assumed to be composed
of a chitin–protein complex like that of their living relatives (Fig. 2a). The exoskel-
eton is more decay resistant than the rest of the animal and it survived to become
a Limulus
Pro
Pro
Ch Ch
Ch
Pro Pro
Ch
Pro Pro Pro Pro
Pro Pro
b Eurypterid
Relative intensity
+ + + * *
+ C10
_ _ _ _+ + C15
_ _ +
_
+ + *
_ + C20
_ _ _+
B3 _+ _+ _+
Retention time
Fig. 2 Partial py-GC-MS chromatogram revealing the chemistry of (a) modern Limulus cuticle
and (b) fossil eurypterid cuticle Eurypterus dekayi (YPM 209619), Ridgemount Quarry, Ontario,
Canada, Williamsville Formation, Pridolian. Note the striking contrast in composition between the
modern and the fossil. Pro, protein pyrolysis products; Ch, Chitin; B3, C3 benzene; +, n-alk-1-ane;
−, n-alk-e-ene; Cn, where n refers to the carbon chain length; *, contaminant. Scale bars: 1 cm
incorporated into sedimentary rock. However, analyses of fossil examples, using a

range of techniques, showed that they consist mainly of an aliphatic hydrocarbon
very different in composition to the cuticle of living arthropods (Figs. 2b and 3).
Indeed, the composition of fossil arthropod cuticle converges on that of graptolite
Fossil beetle
Elytron
Rostrum
Sternites
Relative intensity
Limbs
Ch 1 mm 1 mm
Ch
Ch
P2 Ch
Py
P1
15
P
B3 −+
−+ *
B2 B4 − + 17 19 21 23
I −+ −+
−+ −+ −+
25
27
−+ −+ −+ − −
+ +
−+ + − + 33
+
Retention time
Fig. 3 Partial py-GC-MS chromatogram revealing the chemistry of a fossil curculionid beetle
from Enspel, Germany, Oligocene, with preservation of chitin. I, indole (derived from amino
acid); Ch, Chitin; Bn, benzene derivative were n refers to the carbon number of the alkyl substitu-
tion; +, n-alk-1-ane; −, n-alk-e-ene; Pn, Phenols numbers refer to the carbon chain length; *,
contaminant (This chromatogram focuses on the incorporated aliphatics in contrast to that in
Stankiewicz et al. (1997a), which emphasized the chitin markers.)
periderm. As in the case of graptolites, this anomaly was explained by arguing that
aliphatic components from the surrounding sediment replaced the original chemistry
on a molecular scale (Baas et al. 1995; Briggs et al. 1995).
A new model for the preservation of fossil organic material like that in graptolites
and arthropods has now emerged, which does not involve the incorporation of compo-
nents from the surrounding sediment. It has become clear that diagenetic transforma-
tion of lipids in the cuticle and other tissues of the organism itself, by a process of
in situ polymerization (Briggs 1999; Stankiewicz et al. 2000), is sufficient to account
for the composition of the fossil. Some of the most compelling evidence that fossiliza-
tion does not involve the introduction of components from an external source comes
from situations where such a process is prevented. Insect (and plant) inclusions trapped
in natural resins are sealed within a natural chamber, and analyses of progressively
older amber fossils showed that their original chemistry is gradually transformed to a
more aliphatic composition over time (Stankiewicz et al. 1998b). Artificial maturation
experiments, where arthropods were sealed in gold bombs and subjected to high tem-
peratures in the laboratory (350°C/700 bars/ 24 h), resulted in an aliphatic composition
that could only have been generated from components within the organism itself (see
discussion on experimental maturation: Section 4). Such experiments do not, of
course, replicate the conditions of fossilization, but they allow an exploration of which
starting components are necessary to generate a particular diagenetic product.
Diagenesis in sediments occurs over millions of years (Briggs et al. 2000). Nucleic
acids (DNA and RNA) are very vulnerable to decay and oxidation and do not contrib-
ute significantly to the bulk composition of fossils; nor do they yield extensive
sequences of base pairs in samples more than 100,000 years old. Traces of proteins and
polysaccharides, in contrast, have been detected in much older examples, although
they tend to be altered significantly in pre-Tertiary fossils, if present at all (Table 1).
204
Table 1 Distribution of biomolecules in organically preserved animal and plant fossils through time (Updated from Briggs et al. 2000)
Biomolecule Source organism Archeological record Tertiary record Mesozoic-Paleozoic record
DNA/RNA All organisms Possibly up to 105 year. Physical None confirmed None
protection (such as in bone) may
enhance preservation
Proteins All organisms 103–106 year in shell and bones Present in Oligocene beetles Detected in T. rex bone fossils
(68 ma) and in kerogen (140 ma);
not known in Paleozoic examples
Cellulose Vascular plants and Present Present in Eocene Metasequoia. Not reported so far
some fungi However these could reflect
melanoidins
Chitin Arthropods and fungi In variable amount. Detected in Present in Oligocene beetles Not reported so far
Quaternary beetles
Lipids All organisms Present Present, significant proportion Present, significant proportion bound
bound to macromolecule to macromolecule
Algaenans Algae Present Present, with greater Present, with greater crosslinking
crosslinking
Resins Vascular plants Present Present Diagenetically modified
Lignins Vascular plants Present Present, but may be Diagenetically modified
diagenetically modified
Sporopollenin Vascular plants Present Present in altered state Diagenetically modified
Cutan Vascular plants Occurrence in modern taxa very Not reported Not reported
limited
N.S. Gupta and D.E.G. Briggs
Cellulose and lignins (aromatic alkoxy phenols), the most important macromolecular
constituents of plants, have not been detected in a biopolymeric form in pre-Tertiary
fossils (see Collinson chapter 6, this volume). Lignin, however, may be present in a
defunctionalized state as part of the aromatic fraction in older plant remains. This
diagenetic alteration of organic fossils is a result of polymerization over time, which
ultimately converts all of them, regardless of their original chemistry, to a composition
converging on kerogen (Gupta et al. 2007b).
2 Organic Skeletons
The periderm of graptolites consists of two layers, an inner fusellar layer, secreted
incrementally during growth, and an overlying cortical layer, which is laid down
externally by the zooids and varies in thickness on different parts of the colony
(Crowther 1981). The periderm of pterobranchs (e.g. Rhabdopleura), the closest
living relatives of graptolites, consists primarily of collagen (Fig. 1a). Additional
components include lipids (a series of n-alkanes and n-alkenes soluble in organic
solvents), and fatty acyl moieties. Decay experiments on Rhabdopleura showed
that this periderm, particularly in the older parts of the colony, is much more
decay resistant than the zooids, which become unrecognizable in normal marine
conditions within a week of death (Briggs et al. 1995). The periderm of grapto-
lites (Fig. 1b) has transformed to a resistant aliphatic polymer and benzene, phe-
nol and naphthalene derivatives in the fossil (Gupta et al. 2006c). The collagenous
jaws of polychaetes are similarly transformed in fossil examples, which are
termed scolecodonts (Fig. 4).
P
B1 B2 PA
Relative Intensity
P1
P2
B3
PA PA
B X
X X
X X X X
X X
X
Retention time
Fig. 4 Partial py-GC-MS chromatogram revealing the chemistry of a scolecodont (YPM 1112997),
Cincinnati, Ohio, Upper Ordovician, Cincinnatian, with dominant aromatic composition.
B, Benzene; Bn, Benzene derived product where n refers to the number of Carbon atoms attached
to the benzene ring; P, Phenol; P1, methyl phenol; P2, dimethyl phenol; PA, polyaromatic com-
pounds; X, alkane/alkene pairs
Arthropod cuticle consists of three layers – an outermost epicuticle and a much

thicker exocuticle and endocuticle. The epicuticle of terrestrial arthropods is waxy
in order to prevent desiccation; the waxes are composed mainly of hydrocarbons,
esters, fatty acids and alcohols (Lockey 1988). The remainder of the cuticle consists
of chitin fibers embedded in a protein matrix, cross-linked by catechol, aspartate
and histidyl moieties (Schaefer et al. 1987). The cuticle may be strengthened by
mineralization, usually in the form of calcium carbonate, but this is a feature of
only a small portion of the range of different arthopod taxa: it occurs in trilobites
and a number of crustacean groups.
There is extensive loss of the protein in arthropod cuticle during the early stages
of decay. Laboratory experiments on shrimps have shown a significant reduction
within 2 weeks, whereas the structure of chitin remained largely intact for 8 weeks
(Baas et al. 1995). Proteins are clearly more decay-prone than chitin (Tegelaar
et al. 1989; de Leeuw and Largeau 1993; but see Nguyen and Harvey 1998) but
they are much more resistant where they have undergone cross-linking, as in the
collagen in graptolite periderm (Briggs et al. 1995) and the jaws of polychaetes
(Briggs and Kear 1993). Protein remnants (Table 1) have been detected in insect
remains from archeological sites (McCobb et al. 2004) and in beetles (weevils) in
lacustrine sediments as old as 24.7 my from the Oligocene of Enspel, Germany
(Fig. 3) (Stankiewicz et al. 1997a; Gupta et al. 2007a). Older traces of proteins
have been reported in other taxa: e.g. in the bone of a 68 m.y. old dinosaur
(Schweitzer et al. 2007; Asara et al. 2007), and even in sedimentary organic matter
140 my old (Mongenot et al. 2001). Protein fragments in these older examples
may have been ‘protected’ chemically: more reactive functional groups and the
bonds that link the carbon chain may be shielded and protected by less charged
species such as alkyl chains (Knicker et al. 2001; Mongenot et al. 2001; Riboulleau
et al. 2001).
Chitin is also present in young fossils. Traces occur routinely in Pleistocene
beetles (Stankiewicz et al. 1997c) but the oldest evidence of chitin is only
Oligocene in age (Table 1). This earliest known chitin was found in a weevil
from Enspel (Fig. 3) but only remnants were detected in the fossil. The composi-
tion of the weevil cuticle is dominated by an aliphatic polymer up to C33 in chain
length (indicated by n-alkane/alkene peaks and consisting mainly of C14, C16 and
C18 fatty acids) with additional aromatic compounds (Stankiewicz et al. 1997a;
Gupta et al. 2007a). Neither chitin nor protein are present in other insects analy-
sed from Enspel, or in older arthropod fossils. The fossilized cuticle of Paleozoic
examples, such as scorpions and their extinct relatives the eurypterids (Gupta
et al. 2007c), is largely aliphatic, consisting of alkane/alkene homologues with
chain lengths ranging from C9 to C22 (Fig. 2b). Eurypterids from some sequences
yield a more aromatic signature (i.e. with phenols and polyaromatic compounds),
which may reflect diagenesis at higher temperatures (thermal metamorphism).
Assuming that the original chemistry of the eurypterid cuticle was similar to that
of its living relatives, the chitin–protein complex has undergone transformation,
including incorporation of the lipid fraction, to a composition with a significant
aliphatic component (Gupta et al. 2007c). A similar transformation occurs in
fossil crustaceans (e.g. shrimps, Stankiewicz et al. 1997b; Gupta et al. 2008a).
3 Chemosystematics
Organisms and their component tissues vary in composition. At the simplest level the
cuticle of terrestrial arthropods like insects, with their waxy outer layer, differs chemically
from that of marine taxa like horseshoe crabs. Even though the chemistry is altered dra-
matically during diagenesis, the composition of a fossil may still reflect its original com-
position, and therefore its biological affinities. Such chemical differences (chemosystematic
signatures) include variation in the chain length of the aliphatic components. These signa-
tures have the potential to help in the identification of fossil fragments that lack diagnostic
morphology. They may also illuminate the nature of the diagenetic process by revealing
how different starting compositions result in different fossil chemistry.
Research on the preservation of chemosystematic signatures is at an early stage, par-
ticularly as applied to animal remains. An example is provided by the Cretaceous of Las
Hoyas, Spain, where the composition of fossils differs depending on their identity (Gupta
et al. 2008a). The cuticle of beetles from Las Hoyas is composed of aliphatics with car-
bon chain lengths ranging from C8 up to C31, presumably reflecting the contribution of
long chain waxes (greater than C30) in the epicuticle. Shrimp cuticles from the same
locality, in contrast, are composed of alkyl benzene and phenols (aromatics); aliphatics
with additional sulfur compounds are also present but they do not range beyond C21. The
composition of fish scales is dominated by aliphatics ranging up to C21/22 and the plant
Montsechia is likewise aliphatic, but with chain lengths ranging from C9 to C25 with very
little aromatic content. Thus the composition of the Las Hoyas fossils provides a poten-
tial means of identifying fragmentary fossil material to at least a major taxonomic group.
Compositional differences between different taxa have also been reported from other
localities: the cuticles of arthropods and plants from the Carboniferous of North America
(Stankiewicz et al. 1998a), for example, differ mainly in the distribution of alkenes/
alkanes rather than total chain length or the proportion of aromatics.
The relationship of starting chemistry to final composition in fossils is compli-
cated by factors other than chemistry. Diagenetic history varies with environmental
setting and time (Briggs 1999; Briggs et al. 2000), and thermal metamorphism may
be reflected in the production of aromatic compounds (Gupta et al. 2007c). In order
to investigate fossil chemosystematics further, a comprehensive analysis of modern
taxa and related fossils from different ages and environments is required. The
development of isotope techniques that target the aliphatic component in the mac-
romolecule, and specifically the incorporated lipids, will provide valuable paleoen-
vironmental, paleodietary and potentially chemosystematic information.
4 Diagenesis
4.1 Molecules Are Not Introduced from Sediment
The resistant aliphatic components that dominate the chemistry of fossil arthropods
are not present in the organic skeleton of living examples. Thus their presence in fos-
sils cannot be explained simply by the survival of a decay resistant biopolymer in the
cuticle. A number of lines of evidence indicate that the introduction of aliphatics from
sediment can also be ruled out. Experiments on materials sealed in gold bombs and
analyses of specimens in amber have shown that input from an external source is not
necessary to explain the presence of an aliphatic component in organic fossils (Gupta
et al. 2007a). The lipids that occur in leaves from the Miocene of Clarkia, Idaho, are
confined to the fossils from which they originate, and were not detected ‘leaking’ into
the sediment (Logan et al. 1995). Aliphatic polymers are even less mobile in sediment
due to their insoluble nature (Briggs 1999). Chemosystematic differences between
the aliphatic signatures found in insect and associated plant fossils in lithologies in
the Cretaceous of Las Hoyas, Spain (Gupta et al. 2008b) and in the Upper
Carboniferous of North America (Stankiewicz et al. 1998a) show that diagenesis did
not involve replacement with components from a common source such as the sedi-
ment. The possibility of migration from sediment was also eliminated in an investiga-
tion of samples from the Oligocene of Enspel: the fatty acyl components of insects,
plants and the sedimentary matrix are all different (Gupta et al. 2007a).
4.2 Components Contributing to the Composition of the Fossil
It is clear that the composition of a fossil is derived primarily from the chemistry of
the living organism. Initial analyses and experiments indicated, surprisingly, that it is
not only the decay resistant components that contribute; some much more labile
decay-prone components, such as lipids, are also essential to this diagenetic process.
Lipids include a diversity of molecules united by their solubility in organic solvents.
It is not a straightforward matter to determine which lipids contributed to the compo-
sition of fossil cuticle; the fossil material becomes insoluble during diagenesis, and it
is necessary to break it down chemically to determine its constituents. The major
technique used to analyse inert materials like fossil cuticles is pyrolysis, which vapor-
izes the sample very rapidly at high temperatures before passing it through a mass
spectrometer (i.e. pyrolysis – gas chromatography/mass spectrometry: Py-GC-MS).
However, such routine pyrolysis breaks down the macromolecule in an unconstrained
fashion and the spectra generated provide little detail of the structure of the aliphatic
component or the identity of the molecules that contributed to it.
More detail can be obtained by using techniques that cleave the fossil macromole-
cule into fragments by breaking specific bonds. The cuticle of fossil eurypterids, for
example, consists largely of long-chain (<C9 to C22) aliphatic components. Like other
fossil arthropod cuticles, it is very resistant to degradation. It is not broken down by base
hydrolysis, for example, suggesting that any ester linkages in the macromolecule are
protected by alkyl chains that resist chemical attack on the ester bond. Pyrolysis in the
presence of tetramethylammonium hydroxide (a technique known as thermochemolysis
or structural analysis: de Leeuw and Baas 1993) cleaves ester linkages, thereby provid-
ing evidence of the compounds that were combined during diagenesis. Thermochemolysis
of eurypterid cuticle yielded fatty acyl moieties, which are derived from lipids, of chain
lengths C7 to C18. C16 and C18 are the most abundant (Fig. 5b) indicating that lipids of
a Limulus
C16FA
o
o
Methylated chitin/ protein products and
short chain acids C18FA
o
o
b Eurypterid
Relative intensity
C16FA
_+ C10
X
* o
+
_
_+ _+ C18FA
o _+ C15
_+ _+
o
o o _+o _+o _+o C20

o o o _+ _+o _+
C16FA
o
m/z 74+87+85+83
C7FA C12FA C18FA

C14FA o
C10 o o _+
+ C15 o _+o _ _+
_ _+ _+o _+o _+o _+o _+ _+o _+ + o
Retention time
Fig. 5 Partial TMAH-py-GC-MS (thermochemolysis) chromatogram revealing the distribution

of fatty acyl moieties in (a) modern Limulus and (b) eurypterid Eurypterus lacustris, Ridgemount
Quarry, Ontario, Canada, Williamsville Formation, Pridolian. FA(o), fatty acid where Cn refers to
the carbon chain length; +, n-alk-1-ane; −, n-alk-e-ene; Cn, where n refers to the carbon chain
length. M/z 74+87+85+83 reveals the distribution of fatty acyl moieties relative to alkane/alkene
homologues; *, contaminant
this length were the primary contributors to the fossil cuticle. A similar analysis of
modern scorpion (Gupta et al. 2007c) and horseshoe crab (Fig. 5a) showed that C16 and
C18 fatty acyl moieties are also dominant in the cuticle of the living relatives of euryp-
terids. Fossilization must have involved the incorporation of lipids of these chain lengths
into the aliphatic polymer. Lipids may also become crosslinked by oxidative reticulation
leading to an ether linked macromolecule, e.g. in fossil cephalopod beaks (Gupta et al.
2008b) and fossil algae (Versteegh et al. 2004).
A similar result was obtained from graptolites, even though the starting compo-
sition was predominantly collagen as opposed to chitin–protein. The aliphatic
polymer (C9 to C21) in graptolite periderm, like that in arthropod cuticle, is immune
to base hydrolysis indicating that here too ester linkages are probably sterically
protected. Thermochemolysis released fatty acyl moieties with chain lengths from
C7 to C18 (Fig. 6b), dominated by C16 and C18. A similar distribution of fatty acyl
moieties was detected in the periderm of living Rhabdopleura (Fig. 6a) indicating
that the fossilization of graptolites involved direct incorporation of lipids mainly of
lengths C16 and C18. Such a process of in situ polymerization of lipids appears to
account for the preservation of organic remains in all those fossil groups so far
analysed (Mösle et al. 1998; Briggs 1999; Stankiewicz et al. 2000; Gupta et al.
2006a–c, Gupta et al. 2007a–c, Gupta et al. 2008a, b). Furthermore, electron
microscopy shows that the internal structure of fossil cuticles is normally destroyed
over an extended period, presumably as a result of the polymerization of the chemi-
cal constituents (Stankiewicz et al. 1998a).
The likely effect of original chemistry on the composition of fossil material is
illuminated by laboratory experiments. When lipids are removed (by solvent
extraction and saponification) from arthropod cuticle prior to thermal maturation in
sealed bombs no n-alkyl macromolecular component (aliphatics) are generated
(Fig. 7; Gupta et al. 2006b). Thermal maturation of different plant molecular com-
ponents in gold bombs also results in products that differ, particularly in the length
of the carbon chain in the aliphatic polymer obtained (Gupta et al. 2007d).
4.3 Implications for Kerogen Formation
Most ancient sedimentary organic matter is a product of the diagenetic alteration of

biological material, which typically yields kerogen, a non-hydrolysable macropo-
lymer, insoluble in common organic solvents (Tissot and Welte 1984). The compo-
sition and type of kerogen depends on the nature of the biological input, the
environment of deposition and the diagenetic pathway (de Leeuw and Largeau
1993). Many kerogens are highly aliphatic (especially Type I/II which is similar in
composition to most organic macrofossils) and these are converted to petroleum
products during thermal maturation (catagenesis). The process of kerogen forma-
tion and preservation is critical to the formation of fossil fuel deposits, impacts the
global carbon cycle, and accounts for the preservation of macroscopic and morpho-
logically intact organic remains in the fossil record.
C16FA
a Rhabdopleura o
C18:1FA
o
Methylated short chain acids and
C16:1FA
collagen derived products C18FA
C14FA o
o
o o
b Graptolite
o
Relative Intensity
C16:1FA C18:1FA
C9FA o
o
o o o
o o o o
o o
m/z 74+87+85+83 C15

o C12FA C16FA
o
alk-1-ene
alk-1-ane
C14FA
o
o o C18FA
C7 FA o o
o o
o o o o
Retention time
Fig. 6 Partial TMAH-py-GC-MS (thermochemolysis) chromatogram revealing the distribution

of fatty acyl moieties in (a) modern Rhabdopleura and (b) graptolite Dictyonema peltatum (YPM
202222), Wisby, Sweden, Silurian. FA(o), fatty acid where Cn refers to the carbon chain length;
M/z 74 + 87 + 85 + 83 reveals the distribution of fatty acyl moieties relative to alkane/alkene
homologues
The preservation of organic fossils is a type of kerogen formation. The formation

of kerogen has been attributed to a number of processes. Neogenesis (Tissot and
Welte 1984) involves random intermolecular polymerization and polycondenzation
of sedimentary organic matter. Natural vulcanization involves the reaction between
reduced sulfur and various functional groups in organic compounds; it results in the
formation of a sulfur-rich macromolecule (Kok et al. 2000). Oxidative reticulation
(de Leeuw et al. 2006; Gatellier et al. 1993; Riboulleau et al. 2001; Versteegh et al.
2004; Gupta et al. 2008b) involves crosslinking of lipids with oxygen. Selective
preservation involves the preferential survival of highly aliphatic and decay-resistant
biopolymers such as algaenan and cutan (Tegelaar et al. 1989; de Leeuw and
Largeau 1993).
a
m/z 83+85
C16FA
C15
X
C9 X
X X X
X X X X XX
A
C18FA
C2Py
A
C3Py
C1P
C2P C3P C16FA
C1Py A
Relative intensity
C2Id C3Id C4Id

C2Pyr
C1In
B2
B1
m/z 83+85
C1P C2P
b
C3Py C P
3
C2Py
C1In C2Id C Id
C1Py 3
C2Pyr
B2
B1 P
Retention time
Fig. 7 Partial py-GC-MS chromatogram of cockroach cuticle matured (a) without chemical treat-
ment (b) after removal of extractable and hydrolysable lipids. Bn, benzene derivatives (n refers to
the number of carbon atoms in the alkyl component); C1In, methyl indole; A, amide derivative
(primarily C16 and C18 derivatives); Cn Py, pyridine pyrolysis products, where n is the number of
carbon atoms in the alkyl substituent; P, phenol derivative; Id, alkyl indenes (Inset mass chromato-
grams m/z 83 + 85 reveal the presence of n-alkane/alkenes: X.)
The preservation of the organic remains of animals cannot be explained fully by

any of the above processes. Fossil arthropods from Pleistocene and Tertiary depos-
its may preserve traces of the more resistant elements of the chitin–protein complex
that make up the cuticle, but older fossils are aliphatic in composition as are many
plant fossils. Such a contrast cannot be explained by selective preservation: the
cuticles of modern arthropods do not contain decay-resistant aliphatic components
and they differ in composition from fossil cuticles (Stankiewicz et al. 2000).
Neither does selective preservation explain the composition of most fossil plant
material. Most modern leaves lack a resistant aliphatic component such as cutan
(Gupta et al. 2006a). The aliphatic signature that dominates the composition of fos-
sil leaves is the result of diagenetic changes (Mösle et al. 1997; Mösle et al. 1998;
Gupta et al. 2007a; b). The convergence in the composition of the organic remains
of fossil animals and plants cannot be explained simply by the selective preserva-
tion of certain components of the living organisms.
Neither selective preservation nor simple chemical transfer can explain the ali-
phatic composition of fossil cuticles and it is not the product of random incorpora-
tion of components from the surrounding sediment. As clearly demonstrated by the
chemical transformation of graptolites, arthropods and other organic structures
like cephalopod beaks and fish scales, more labile chemical components, such as
free cuticular lipids or hydrolysable lipids (such as fatty acids), are incorporated
into the aliphatic dominated fossil cuticle. Such lipid incorporation also has been
observed to contribute significantly to the formation of kerogen, where the role of
selective preservation is likewise limited (Riboulleau et al. 2001). The major propor-
tion of the fossil record of organic animal remains is the result of some process of in
situ polymerization, a process which is also important in the formation of TypeI/II
kerogens (Briggs 1999).
The chains of n-alkanes/n-alkenes in the aliphatic component of marine animal
fossils such as cephalopod beaks and eurypterids do not exceed C25; they are not as
long as those in terrestrial fossils such as leaves and beetles (Gupta et al. 2007a–c).
This presumably reflects the presence of longer chain waxes, which control water
loss, in the cuticles of land organisms. Thus the chain lengths in the aliphatic con-
tent of macromolecular material in fossils and in sedimentary organic matter may
allow marine and terrestrial origins to be distinguished. Neoproterozoic kerogens
(e.g. those from the south Oman salt basin), which are exclusively marine in origin,
show aliphatic contents mainly up to C24 (Höld et al. 1999). Where higher molecu-
lar weight aliphatics are present in marine kerogens they may represent the preser-
vation of the biopolymer algaenan which is present in the outer cell walls of some
algae and has an aliphatic component >C30 (Blokker et al. 2000). In deltaic loca-
tions, where marine and terrestrially derived organic matter mix, longer aliphatic
components may be sourced from terrestrial input. Although animal cuticles may
provide important insight into kerogen formation, kerogen is primarily sourced
from plant material, especially algae and terrestrial higher plants, with some bacte-
rial input (Vandenbroucke and Largeau 2007). Only 0.1% to <1% of the organic
components produced by autotrophic organisms is incorporated into sediments.
The final composition of the kerogen depends on decay prior to sedimentation and
diagenesis thereafter. The origin, evolution and structure of kerogen are reviewed
by Vandenbroucke and Largeau (2007).
4.4 The Rate of Diagenetic Change
Genetic material (DNA/RNA) can be extracted from fossils up to 105 years old,
especially where hard parts such as bone provide physical protection from hydro-
lyzing agents, and sequence data are frequently used in archeological investiga-
tions. These nucleic acids are very prone to decay, however, and are unlikely to
make any contribution to kerogen. Proteins and carbohydrates, on the other hand,
react to form compounds called melanoidins (through the Maillard reaction:
Maillard 1912). Melanoidins may cross link with lipids to form protokerogens
(Larter and Douglas 1980). Lipids, which are present in all organisms, may make a
significant contribution to sedimentary organic matter by becoming incorporated
into macromolecules during early diagenesis. Diagenetic changes ensure that ani-
mal cuticles older then Tertiary do not contain recognizable traces of their original
molecular composition (Table 1). Just how quickly this process of in situ polymer-
ization progresses is unknown. Traces of aliphatics are evident, for example, in
Hymenaea leaves in 20 Kya resin from Kenya even though they are not present in
living Hymenaea leaves (Stankiewicz et al. 1998b). Analyses show that resistant
aliphatics have formed in Oligocene insect cuticles (flies from Enspel have been
transformed even though beetles still reveal traces of chitin and protein: Stankiewicz
et al. 1997c). Previous investigations of Tertiary arthropods have focused on the
search for the oldest traces of macromolecular components like chitin and may have
overlooked the formation of aliphatic components in younger fossils.
5 Future Directions in Molecular Taphonomy
The chemistry of the biopolymeric constituents of invertebrates begins to change in

the early stages of decay (Baas et al. 1995). Future experiments are necessary to
explore the impact of microbes on the chemistry of a decaying carcass over
extended periods of time. Determining the changing structure of biopolymers and
associated lipids using high resolution mass spectrometry and 13C NMR spectros-
copy will illuminate the reactions involved in the transformation of the living
organism to a fossil and its eventual contribution to sedimentary organic matter.
Such a coupled analytical approach is important as spectroscopy, which is non-
destructive, provides complementary data on functional groups to that obtained
from spectrometry (e.g. py-GC-MS and chemolysis).
Preliminary thermal maturation experiments using a hydrothermal apparatus
(see Section 6.3) have revealed the importance of lipids in geopolymer formation
(Gupta et al. 2006b) but it is essential to track the fate of both the soluble (i.e. lipid)
and insoluble fractions to understand the evolution of the macromolecular composi-
tion of a fossil. Similar maturation experiments are necessary to evaluate the role
of different conditions of pressure and temperature during diagenesis, catagenesis
and metagenesis (i.e. the transformation of organic matter with increasing tempera-
ture). Such experimentation will help to determine the relative contribution of dif-
ferent organisms and their constituent lipids and biopolymers to sedimentary
organic matter and kerogen.
The influence of environmental factors on the preservation of organic fossils is
poorly understood. This can be explored by comparing the nature of organic pres-
ervation with sedimentological and paleontological evidence for depositional con-
ditions. Lipid biomarkers can also provide data on conditions in the sediment and
water column during deposition. Systematic investigations of preservation in different

settings are necessary to show how physico-chemical processes generate biases in
the record of organically preserved fossils. Investigations of the morphological
preservation and chemical composition of organic fossils through time are neces-
sary to determine how one reflects the other. Preliminary results do not reveal any
direct correlation (Mösle et al. 1998; Gupta et al. 2006c, Gupta et al. 2007a, b)
especially in samples older than Tertiary, which have undergone significant diage-
netic alteration.
Accumulation of data on the composition of different animal and plant taxa of
different ages and from different settings will lead to an improved understanding of
the nature of organic diagenesis. This in turn will lead to an understanding of how
different compositions (e.g. relative distribution and chain length of aliphatic com-
ponents, nature of chemical linkages) are diagnostic of particular taxa or the condi-
tions in which they lived and were diagenetically transformed. The application of
new x-ray methods (Section 6.3) will enable chemical characterization of samples
at much finer resolutions than are routinely available now, an important consider-
ation when sample size is a limiting factor. Such methods will allow the investiga-
tion of the fate of biopolymers and chemical changes during diagenesis, on a
subcellular (sub-micron) level where such remains are still preserved. In the case of
arthropods that preserve the structure of the cuticle, it will be possible to analyse
the composition of the different layers in the fossil (Gupta et al. 2007a) and show
how these morphologically specific regions change over time.
6 Appendix: Main Analytical Methods Applied

to Organic Remains
6.1 The Soluble Fraction
The soluble fraction (lipids) of organic components in modern and fossil samples
can be analysed using gas chromatography-mass spectrometry (GC-MS) after sol-
vent extraction in dichloromethane-methanol. The lipids isolated in this way can
then be fractionated into different compound classes using column chromatogra-
phy. This reveals the distribution of lipid carbon chain lengths and associated func-
tional groups.
6.2 The Insoluble Fraction
The molecular and isotopic composition of the insoluble fraction of organic fossils
in both modern and fossil specimens is evaluated using a range of analytical tech-
niques. These techniques have specific strengths and biases and it is important to use
them together in order to generate complementary data and ensure more robust interpre-
tations. Organic fossil remains generally are not available in abundance and sample
size is often limiting. Samples of cuticles can be obtained from sedimentary rock by
acid digestion, or by mechanical preparation. Pyrolysis-gas chromatography/mass
spectrometry (py-GC-MS), which is destructive, requires a very small sample (200 µg),
often all that is available for fossils. It is a rapid and efficient tool that is used rou-
tinely for determining the molecular constituents of insoluble organic matter (Larter
and Horsfield 1993) in fossils and their modern counterparts. Py-GC-MS involves
heating a macromolecule to break chemical bonds thermally. The molecular species
generated are then separated using a gas chromatograph (GC) and identified using a
mass spectrometer (MS). This technique can be employed to track the changes that
take place in the molecular composition of material from living sample, through
decay experiments, to progressively older fossils.
Organic fossils often reveal a composition with a dominant aliphatic hydrocar-
bon-rich component linked by C–C, ester and ether linkages (Figs. 1–4). These
functional groups can be targeted specifically using stepwise chemical degradation
techniques that cleave molecular linkages in a systematic fashion, thereby yielding
structural information beyond that provided by py-GC-MS without such treat-
ments. Such degradation techniques include RuO4 (ruthenium tetroxide) oxidation
treatment and thermochemolysis. RuO4 oxidation cleaves ether linked carbon com-
ponents (Blokker et al. 2000) and thermochemolysis (pyrolysis in the presence of
tetramethylammonium hydroxide; de Leeuw and Baas 1993) cleaves ester linkages
in macromolecules providing evidence of the distribution of fatty acids in fossils
(Gupta et al. 2007b). These techniques reveal the distribution of chain lengths and
associated functional groups. In marine fossils, such as graptolites and shrimps,
molecular components may also be linked through C–S bonds. These can be
detected by subjecting the fossils to treatment with Li/NH3 (Adam et al. 1993;
Schaeffer et al. 1995). Thus, following an initial analysis using py-GC-MS, chemo-
lytic methods can be used to cleave specific chemical linkages to provide further
structural information.
Spectroscopic tools provide additional structural data on insoluble organic mat-
ter. Methods commonly used include solid state nuclear magnetic resonance spec-
troscopy (NMR), Fourier transform infrared spectroscopy (FTIR), and Raman
spectroscopy, all of which are non-destructive. Solid state 13C and 15N NMR reveals
bulk molecular and structural characteristics that complement the data obtained
from pyrolysis but these methods may require around 0.5 g of sample material.
FTIR has been used widely to determine the constituent oxygen functional groups
(such as carboxyl, carbonyl, ethers) and their relative importance in fossil plant
material, providing insights into oxygen-linked bonds that are important in the
macromolecule. The application of spectroscopic techniques to animal fossils has
been limited so far. Raman spectroscopy allows microscale analysis of carbona-
ceous samples even when available quantities are very limited. It can be used as an
indicator of thermal maturity and has the potential to provide thermal data on
organic carbon at temperatures as low as 100°C (Rahl et al. 2005). Current research
is also making use of X-ray absorption spectroscopy of carbon, sulfur and oxygen
Sample
Extraction
Hydrolysis py-GC/MS
Thermochemolysis
Hydrolysed Extract Extract Residue 113C NMR, FTIR, Raman Spectroscopy
GC-MS Chromatography Hydrolysis
Hydrolysable Hydrolysed
Neutral Lipids Fatty Acids Phospholipids
Lipids Residue
GC-MS Saponification Saponification GC-MS py-GC/MS
-GC MS- -GC MS- Thermochemolysis
13C NMR, FTIR, Raman Spectroscopy
RuO4 oxidation
GC-irMS
Fig. 8 Schematic analytical protocol used for evaluating the chemistry of modern and fossil
samples
(C,S,O-XANES) to provide more information on the valence state and spatial con-
figuration of the molecular species in the fossils. This method allows sub micron
level characterization of macromolecules where other methods of chemolysis and
pyrolysis are difficult to apply. The presence of lignin, for example, can be mapped
at submicron resolution in fossil plant cell walls (Boyce et al. 2002).
Compound specific stable isotope analysis (CSIA), using gas chromatography-
isotope ratio-mass spectrometry (GC-IR-MS), provides isotope data on individual
molecular components. Such data may be used as a geochemical tracer to analyse
the transformation of biomolecules to geomolecules during diagenesis, and to
determine the origin of molecular constituents in sedimentary organic matter. The
application of compound specific techniques to macromolecules has been problem-
atic due to their insoluble and recalcitrant nature. However, we are currently devel-
oping an approach that first employs RuO4 (ruthenium tetroxide) oxidation
treatment (Sharpless et al. 1981) to generate a series of organic acids that provide
information on the constituent chain lengths. Applying compound specific tech-
niques to these acids has the potential to identify which lipids are incorporated
(Fig. 8).
6.3 Thermal Maturation Experiments
Techniques have been developed recently to explore the chemical transformation of

living materials with confined pyrolysis-accelerated maturation techniques using a
hydrothermal apparatus (Fig. 9). This approach involves experimental heating of
model compounds and modern tissues in a sealed gold cell (within an autoclave) at
temperatures from 260°C to 350°C and a confining pressure of 700 atmospheres for
a day (or longer at lower temperatures). The end products reveal compositions simi-
lar to those of fossils and this provides a means to determine the role of biopoly-
mers in forming geopolymers.
Heater
Heater
Temperature
Control
Heater
Internal
thermocouple High pressure
Gold cell Pressurizing
Stainless steel Valve + line
+Sample medium
reactor
Fig. 9 Confined pyrolysis autoclave and gold cell apparatus used for accelerated maturation of
modern tissues and model compounds
6.4 Investigating Morphology
Transmission and scanning electron microscopy allow surface morphology and

ultrastructural preservation within organic materials to be examined. Surface fea-
tures may be pristine even if the internal structure of the cuticle has been destroyed.
Microscopy in conjunction with rigorous chemical analysis provides the most com-
plete data on the changes that occur in organic fossils though time.
Acknowledgments DEGB’s research in this area has been supported by Natural Environment
Research Council (UK) grants and mass spectrometry facilities, and by the American Chemical
Society Petroleum Research Fund. We are grateful for collaboration and discussions with M.E.
Collinson, G. Eglinton, R.P. Evershed, R. Michels, R.D. Pancost, R.J. Parkes, B.A. Stankiewicz
and R.E. Summons.
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Chapter 6
Molecular Taphonomy of Plant Organic
Skeletons
Contents
1 Introduction........................................................................................................................... 224
1.1 Aims of This Chapter................................................................................................... 224
1.2 Caveats and Barriers to Understanding Resistant Bio- and Geomacromolecules....... 225
2 Leaves and Cuticles.............................................................................................................. 226
2.1 Leaf and Cuticle Preservation...................................................................................... 226
2.2 Polymerization and Future Research Directions......................................................... 232
3 Xylem (Including Wood), Fruit Walls and Seed Coats......................................................... 234
4 Flowers.................................................................................................................................. 237
5 Spores and Pollen.................................................................................................................. 237
6 Phytoplankton and Algal Cysts............................................................................................. 238
6.1 Chlorophyta and Prasinophyta..................................................................................... 238
6.2 Dinoflagellates............................................................................................................. 239
6.3 Acritarchs..................................................................................................................... 240
7 Conclusions and Implications............................................................................................... 241
7.1 Plant Evolutionary Constraints and Temporal Bias..................................................... 241
7.2 Implications for Applied Paleobotany......................................................................... 241
References................................................................................................................................... 243
Abstract Selective preservation of resistant biomacromolecules, such as cutan

in leaf cuticles; lignin in woods, fruit walls and seed coats; sporopollenin in
spores and pollen and algaenan in algal cysts, has previously been invoked in
survival of these tissues and organs in the fossil record. A growing body of
evidence is questioning this paradigm, suggesting that biomacromolecules may
provide the structural template for formation of geomacromolecules in fos-
sils which form as the result of (i) polymerization of labile constituents (e.g.
in situ polymerization of cutin, waxes and internal lipids in cuticles; oxidative
polymerization incorporating an aliphatic component into sporopollenin), (ii) loss
(e.g. loss of cellulose from lignin–cellulose complexes), and (iii) transformation
(e.g. lignin methoxyphenols to phenols). Recommended future research directions
M.E. Collinson ()

Department of Earth Sciences, Royal Holloway University of London,
Egham, Surrey TW20 0EX, UK
224 M.E. Collinson
include: (a) taphonomic experiments to simulate the molecular alteration

sequence in diverse environments, (b) analysis of fossils (time series) from a
range of depositional settings, and (c) identifying those modern plant organs that
lack an expected fossil record. This will require a combination of microscopical
and chemical approaches to monitor alteration and understand specific controls
on plant preservation.
1 Introduction
1.1 Aims of This Chapter
Plants are normally represented in the fossil record by a variety of isolated organs
such as leaves, fruits and seeds, wood, flowers and pollen. Each has a distinctive
combination of organic chemical composition and physical structure and both
factors influence their preservation. Other important taphonomic factors include
the depositional context, the nature of enclosing sediment, the time available for
senescence and decomposition prior to burial and the degree of oxidative expo-
sure prior to and after burial. All of these factors may bias the plant fossil record.
This chapter addresses preservation of the plant organic skeleton as a morpho-
logically and structurally recognizable fossil (compression, adpression or mum-
mification) in the absence of entombing or supporting minerals (permineralization).
For a recent study on chemical characterization of permineralized plant kerogen
see Czaja et al. (2009). The incorporation of plant macromolecular components
into sedimentary organic matter (kerogen) is outside the scope of this chapter and
the reader is referred to Vandenbroucke and Largeau (2007) for a review.
However, it should be noted that that paper was accepted for publication prior to
the publication of much of the work cited here, especially on leaf preservation
(Section 2) and therefore lacks a lot of more recent information relevant to the
origin and structure of kerogen.
To an extent all aspects of applied paleobotany make some degree of assump-
tion that the record of plant fossils is either (i) representative of ancient plants and
vegetation or (ii) that the biases in the fossil record are adequately understood.
With regard to chemical composition the conventional paradigm has been that the
fossil record will be biased in favour of those plants whose organs contain resis-
tant biomacromolecules. Recent research has focussed on a combination of
molecular and morphological (including ultrastructural) analyses. These have
been used, firstly, to further understand the distribution and location of resistant
biomacromolecules within plant groups and plant tissues and, secondly, to estab-
lish if plant fossils are indeed composed pre-dominantly of surviving resistant
biomacromolecules. This chapter will review recent discoveries, suggest future
research directions and reassess the role of resistant biomacromolecules in plant
preservation through time.
6 Molecular Taphonomy of Fossil Plants 225
1.2 Caveats and Barriers to Understanding Resistant

Bio- and Geomacromolecules
To establish the presence, physical location and chemical composition of a resis-

tant macromolecule it is necessary to be able to isolate (purify) both the mole-
cule and the structure in which it occurs. Any chemical isolation procedure has
the potential to alter the chemistry of the target molecules as well as removing
other material.
For modern material this is particularly problematic for most cuticles (some can
be physically stripped off the surface but most cannot) and for pollen and spore
walls that are multilayered and intimately associated with underlying living tis-
sues. Algal cell walls and cyst walls present similar problems and for both these
and pollen and spores the small size of the objects makes physical isolation diffi-
cult. The situation is somewhat less problematic for the lignified cell walls of
woods and thickened sclerotic layers of seed coats and fruit walls where the physi-
cal thickness of the tissue enables parts to be removed more easily. These prob-
lems and their consequences are discussed in more detail in van Bergen et al.
(2004) and de Leeuw et al. (2006).
Mechanical stripping of cuticles (Collinson et al. 1998) and ultrasonic potter
homogenization of algal cells to obtain purified wall samples (Blokker et al. 1998;
van Bergen et al. 2004; de Leeuw et al. 2006) are effective physical isolation treat-
ments. However, even physically isolated cuticles do not always consist only of the
cuticular membrane as will be discussed in Section 2, showing that monitoring of
the structure using transmission electron microscopy (TEM) (or other high resolu-
tion methods) is essential.
Fossil material could be regarded as another potential source of purified
sample on the basis that the resistant materials survive burial and diagenesis
whilst other associated more labile molecules do not. The megaspores and
microspore massulae clusters of water ferns have been used as one classic
example (Van Bergen et al. 1993a), TEM monitoring of the structure was used
to demonstrate that no infill of extraneous organic material was present.
However, recent work on sporopollenin suggests that the chemical composi-
tion of the fossil spore walls has been altered (de Leeuw et al. 2006) as will be
discussed in Section 5, showing that fossil material cannot be simply taken to
represent the original composition of a resistant macromolecule. Furthermore,
in older fossils, characteristic molecular components may be lost preventing
the identification of the original (or altered) macromolecule (see, for example,
Section 3).
Recent research, which is reviewed below, focuses on a combination of micros-
copy and chemistry to closely monitor the effects of isolation procedures and
chemical treatments. Where appropriate multiple chemical analytical techniques
are employed to provide a variety of evidence on molecular structure. Nevertheless
much remains poorly understood and some examples of potential future research
directions are indicated in the following sections.
226 M.E. Collinson
2 Leaves and Cuticles
2.1 Leaf and Cuticle Preservation
The external surfaces of leaves (and other aerial plant organs) are covered by a con-
tinuous extracellular membrane named the cuticle. The base material of the cuticle is
a cross-linked insoluble biopolyester named cutin, the biosynthesis of which is poorly
understood (Suh et al. 2005). The cuticle has many functions including as a perme-
ability barrier and a protective layer (Bargel et al. 2004; Riederer and Müller 2006).
Leaves are extremely well-represented as fossils throughout the geological record as
are herbaceous axes prior to the evolution of leaves. Dispersed cuticles are also wide-
spread in the fossil record, and are amongst the earliest records of probable land-
adapted plants in the Ordovician and Silurian (Raven and Edwards 2004).
The protective role of the cuticle in life might be expected to confer an increased
preservation potential, by comparison to other leaf tissues such as mesophyll with
cellulosic cell walls. However, this would be an assumption as relatively little is
known about the anatomical preservation of leaf tissues. Most paleobotanists study
leaf gross morphology (e.g. for paleoclimate analysis) or venation patterns and
cuticle details (e.g. for taxonomic purposes) and few have examined the internal
anatomy or the ultrastructure of fossil leaves. As Fig. 1a–d shows the structural pres-
ervation of leaf compression fossils is extremely variable. A ‘fossil leaf’ may consist
only of a cuticle envelope (Fig. 1c) or it may also exhibit excellent preservation of
internal cellular details (Fig. 1d). Both these are conifer leaves and are of the same
age and from the same site. Apart from these two extremes ‘fossil leaves’ may totally
lack cuticles (Fig. 1a, b). Furthermore, leaves may exhibit varying degrees of internal
morphological preservation ranging from retaining some evidence of their original
cellular structure (Fig. 1a) to having internal material which shows absolutely no
morphological resemblance whatsoever to that of a leaf (Fig. 1b). Figure 1a, b is from
the same horizon at the same site and these flowering plant leaves originally would
have possessed cuticles, epidermis and palisade and spongy mesophyll like their
modern relatives. This ongoing transmission electron microscope work indicates the
potential importance of factors such as degree of senescence, timing of burial, local
depositional conditions and subsequent diagenesis for each individual leaf.
The fact that fossil leaves survive after cuticles have been lost calls into question
the importance of cuticles in controlling leaf preservation. Equally it is known that
cuticles are recalcitrant in microbial decay experiments (e.g. Kelleher et al. 2006)
and it is abundantly clear that cuticles survive as fossils both with and without other
leaf tissues. It has previously been suggested that cuticles survive as a consequence
of the selective preservation of a highly aliphatic resistant biomacromolecule named
cutan (Nip et al. 1986a, b; Tegelaar et al. 1991) contained within the cuticle (review
in Gupta et al. 2006a and refs cited and de Leeuw et al. 2006). If this were correct
the presence/absence of cutan or varying abundances of cutan might control cuticle
preservation and hence, in some situations, also control leaf preservation, thus bias-
ing the fossil record in favour of plants whose leaves contain cutan as suggested by
Tegelaar et al. (1991).
Fig. 1 The range of anatomical preservation in Miocene fossil leaves as shown by vertical sec-
tions with transmission electron microscopy (TEM). (a and b) Ardeche, France a (top left).
Quercus hispanica with some evidence of original cellular structure and b (bottom left) Castanea
vesca with no recognizable leaf anatomy whatsoever. Neither a nor b possess cuticles. For further
details see Gupta et al. (2007a). (c and d) Clarkia, USA C (top right. Amentotaxus, consisting only
of a cuticle envelope and d (bottom right) Metasequoia exhibiting both a cuticle and full ana-
tomical preservation (cell infills probably of diagenetic origin)
It is clear from multiple repeated analyses in different laboratories that the mono-
cotyledon genera Agave (Agavaceae) and Clivia (Lilliaceae) contain cutan (review in
Gupta et al. 2006a and refs there cited). In Agave, cutan occupies a considerable pro-
portion of the cuticle and cuticle survives as a recognizable entity after treatment with
acetylation and saponification which remove cell walls and cutin respectively (Fig. 2).
However, there are no leaves or cuticles of the genera Agave and Clivia in the fossil
record. There are a few other reported occurrences of cutan (summarized in Gupta
et al. 2006a) including in one Podocarpus species, in Clusia and Prunus laurocerasus
(Boom et al. 2005; Gupta et al. 2006a) and a cutan-like fraction is reported in fruit
cuticles of pepper and apple and leaf cuticles of olive on the basis in NMR and FTIR
studies (Johnson et al. 2007). Collinson et al. (1998, 2000) studied modern conifer and
Ginkgo leaves and concluded that they all lacked cutan but this work was criticized by
Boom et al. (2005) because chemical treatments used to prepare cuticles might have
affected the results. Gupta et al. (2006a) analysed leaves of Ginkgo and the conifers
Pinus and Metasequoia without any chemical pretreatments and confirmed the absence
of cutan. Gupta et al. (2006a) also analysed leaves from eight families of flowering
plants all of which were found to lack cutan whilst Agave, as expected, was found to
228
Fig. 2 Chemistry and ultrastructure of Agave cuticles showing the importance of the resistant
biomacromolecule cutan in this genus. The Py-GC-MS traces of both the extracted cuticle and the
extracted, saponified and acetylated cuticle (= cutan only) reveal the characteristic alkene/alkane
doublets which dominate in the latter. The EM images show that (i) some cell wall material (elec-
tron dense black) remains attached to the extracted cuticle (seen in TEM but not appreciated in
SEM) but that this is removed after saponification and acetylation and (ii) that cutan, which
remains after a combination of extraction, acetylation and saponification, plays a major structural
role in the cuticle and survives as a coherent entity but with much reduced thickness and more
open microlamellar organization than the complete cuticle. EM images are from left to right an
SEM of the internal surface of a cuticle showing a stoma; a TEM vertical section through the
cuticle showing the anticlinal (downward projecting) cuticular flanges which penetrate inwards
Fig. 3 Absence of cutan in leaves of the flowering plant Acer indicated by the absence of alkene/
alkane doublets after base hydrolysis (= saponification) which has removed cutin as shown by loss
of C16 and C18 fatty acids (CNFA) (compare to Fig. 4 of Agave prepared under exactly the same
conditions and without chemical pretreatment and also to Fig. 2). Ps = polysaccharide pyrolysis
products, P, S and G indicate presence of lignin derivates as this material has not been subjected
to acid hydrolysis (acetylation). For further details of chemical treatments and explanation of
chemical annotations see Gupta et al. (2006a). Extracted = chemical extraction with dichlo-
romethane and methanol to remove soluble lipids; Saponified (= base hydrolysis) = chemical
extraction with methanolic sodium hydroxide to remove cutin
Fig. 2 (continued) into the leaf and into the wall of the epidermal cells; a TEM detail. For fur-
ther details of the chemistry and treatments of this Agave see Mösle et al. (1997). Extracted
= chemical extraction with dichloromethane and methanol to remove soluble lipids; Acetylated =
chemical extraction with acetyl bromide and acetic acid to remove polysaccharides and lignin;
Saponified (= base hydrolysis) = chemical extraction with methanolic potassium hydroxide to
remove cutin
230 M.E. Collinson
Fig. 4 Presence of cutan in leaves of Agave indicated by the presence of alkene/alkane doublets
(x) surviving after base hydrolysis which removed cutin. Compare to Fig. 3 prepared under exactly
the same conditions and without chemical pre-treatment. Ps = polysaccharide pyrolysis products,
P and S indicate presence of lignin derivatives as this material has not been subjected to acid
hydrolysis (acetylation). Following base hydrolysis these pyrolysis products dominate the signal
but they are removed by acetylation to leave only cutan which yields a chromatogram dominated
by alkene/alkane doublets as shown in Fig. 2. For further details of chemical treatments and expla-
nations of chemical annotations see Gupta (2006a)
contain cutan (Compare chemical compositions in Figs. 3, Acer and 4, Agave). The
chemical treatments of acetylation (chemical extraction with acetyl bromide and
acetic acid) and saponification (= base hydrolysis, chemical extraction with methanolic
potassium or sodium hydroxide) remove cell wall layers and cutin respectively from
cuticles of the conifer Pinus and the flowering plant Quercus (Figs. 5 and 6). If both
treatments are applied there is no recoverable residue, in striking contrast to the Agave
(Fig. 2). Both Pinus and Quercus (in contrast to Agave) have an extensive leaf fossil
record both as compression and impression fossils as do many taxa now shown to lack
cutan (Gupta et al. 2006a). These data lead to the conclusion that (in spite of its struc-
tural role demonstrated in Fig. 2) the presence or absence of cutan does not exert any
obvious bias on the preservation of leaves in the fossil record.
Fig. 5 TEM images of a prepared cuticle of Recent Pinus, for comparison with Agave in Fig. 2,
monitoring the effects of chemical treatments to reveal chemical composition of various layers and
an absence of cutan. The prepared and extracted cuticle infact consists not only of the cuticle
(paler grey more electron lucent outer layer) but also the cell walls of the epidermal cell and two
sub-epidermal cells (black and pale grey). Saponification removes the cuticle leaving just cell
walls, acetylation removes the cell walls leaving just the cuticle (cutin). A combination of acetyla-
tion and saponification yields no recoverable residue, i.e. no cutan, in contrast to Agave (Fig. 2).
Details of cuticle preparation (removal from the leaf) and chemical treatments are given in Mösle
et al. (1997) and Collinson et al. (1998). Extracted = chemical extraction with dichloromethane
and methanol to remove soluble lipids; Acetylated = chemical extraction with acetyl bromide and
acetic acid to remove polysaccharides and lignin; Saponified (= base hydrolysis) = chemical
extraction with methanolic potassium hydroxide to remove cutin
232 M.E. Collinson
Fig. 6 TEM images of leaf fragments of Recent Quercus showing the absence of cuticle (cutin)
from the outer surface (top of image) after saponification (base hydrolysis). Chemical analysis of
this material is essentially identical to that of Acer (Fig. 3), showing an absence of cutan. The
material remaining after saponification is essentially lignin moieties as expected from the reten-
tion of cell walls seen in the TEM image. See Gupta et al. (2006a) for details.Extracted = chemi-
cal extraction with dichloromethane and methanol to remove soluble lipids; Saponified (= base
hydrolysis) = chemical extraction with methanolic sodium hydroxide to remove cutin
Combining their studies of modern and fossil leaves Gupta et al. (2006a, 2007a, b,
2009) concluded that, in the absence of cutan, other constituents, including cutin,
plant waxes and internal plant lipids contributed to the formation of a highly resistant
resistant geomacromolecule in leaf fossils through a process of in situ polymerization.
Further support for this hypothesis was derived from experimental maturation which
demonstrated that a resistant macromolecule could be generated from plant tissues in
the absence of a resistant precursor such as cutan (Gupta et al. 2007c, 2009) and by
heat treatment of Kalanchoe cuticles where waxy cuticles yielded a chemical signa-
ture comparable to that of plant fossils but dewaxed cuticles did not (Finch and
Freeman 2001). Yang et al. (2005) found evidence to support the in situ polymeriza-
tion model in their studies of Metasequoia fossils as did Aucour et al. (2009) in their
studies of Cretaceous leaf fossils. Polymerization (including oxidative polymeriza-
tion) of labile components such as lipids has also been recognized as an appropriate
mechanism to explain preservation and formation of geopolymers of kerogens, dino-
flagellates and animal remains as well as fossil leaves (Kuypers et al. 2002; Versteegh
et al. 2004; de Leeuw et al. 2006; De Leeuw 2007; Gupta et al. 2007d). See
Stankiewicz et al. (1998), Briggs (1999), Briggs et al. (2000), Gupta et al. (2007d)
and Gupta and Briggs (this volume) for further details on animal remains.
2.2 Polymerization and Future Research Directions
In situ polymerization, in particular of labile cell membrane lipids and free fatty
acids, could be an important factor in the preservation of any plant materials that
contained living cells at the time of death. Even largely dead tissue, such as heartwood,
is traversed by rays containing metabolically active parenchyma cells. Therefore,

this preservational mechanism may be involved for all plant fossils. De Leeuw et al.
(2006) concluded that the aliphatic component of fossil sporopollenin was likely
the result of early diagenetic oxidative polymerization of unsaturated lipids whilst
Versteegh et al. (2004) suggested a similar process to account for unusually pre-
served fossil dinoflagellates. Oxidiative exposure is known to increase the aliphatic
character of kerogen (Hoefs et al. 1998). This mechanism could have operated since
the evolution of cell membrane lipids for which biomarker evidence, in the form of
steranes, exists deep in the Proterozoic alongside eukaryotic single cell plant skel-
etons (Javaux and Marshall 2006). Preservation in the fossil record could thus be
strongly influenced by the existence of conditions, including those favouring oxida-
tive cross-linking (as yet not fully understood), that facilitate either in situ polym-
erization (in the case of cuticles) or incorporation and polymerization of externally
sourced labile constituents (or a combination of both). Having recorded the oldest
fossil carbohydrates in structurally intact leaves characterised by pyrolysis analysis
(polysaccharides in Eocene Metasequoia leaves from litter mats) Yang et al. (2005)
suggested that the presence, in the leaf litters, of structural polyphenolic com-
pounds as decay products such as tannins might have provided resistance against
decomposition. Such possibilities further underscore the importance of the burial
context in preservation of the plant organic skeleton.
To further understand controls on preservation one future research direction would
be a comparative survey of depositional settings containing impression versus com-
pression fossil leaves (i.e. with and without organic preservation) and a microscale
comparison within depositional settings where a range of structural and ultrastruc-
tural preservation occurs. One example of the latter is the Miocene of the lacustrine
Clarkia site. Here some fossil leaves occur with preservation of chloroplasts contain-
ing membrane stacks (Schoenhut et al. 2004; Collinson et al. in progress) and well-
preserved cellular anatomy (e.g. Fig. 1d) whilst others consist only of cuticle
envelopes (Fig. 1c). Yang et al. (2005) and Gupta et al. (2009) noted very poor pres-
ervation of polysaccharides in Clarkia Metasequoia compared with Metasequoia
from other sites. This may be related to poor tissue preservation in specific leaves as
the Metasequoia from Clarkia shown in their SEM’s is stated to have very modified
‘amorphous’ or ‘decayed’ internal tissues (in striking contrast to the specimen from
the same site illustrated in Fig. 1d herein). Variations in individual leaves may result
from different degrees of senescence or from different exposure to oxidative condi-
tions prior to, or after, burial. Combined TEM and chemical studies of fossils are
really necessary to fully evaluate molecular preservation.
Carboniferous leaves consisting only of a cuticle envelope (somewhat compa-
rable to the Eocene fossil in Fig. 1c) are well known in concentrated occurrences in
what are sometimes termed cuticle coals or paper coals. Based on a variety of
chemical and geological evidence Zodrow and Mastalerz (2009) proposed that
internal tissues were lost from these fossilized cuticles, probably at a late to post-
diagenetic time. This may be the result of oxygen rich groundwater initiating in situ
pyritic oxidation and producing sulfuric acid which removed vitrinite (altered inter-
nal fossil leaf tissues) resulting in survival of fossil cuticle only.
234 M.E. Collinson
A second future research direction would be to establish the time frame and condi-
tions over which in situ polymerization occurs. In part this could be accomplished by
a series of taphonomic experiments studying chemical and structural alteration of
distinctive plant organs and tissues, both fresh and senescent, under varying environ-
mental and depositional conditions (including exposure to oxygen), both pre and post
burial. Three studies have investigated both macromolecular chemical composition
and morphological changes during decay – Collinson et al. (1998) studied Ginkgo
cuticles following up to 30 weeks decay, Gupta and Pancost (2004) studied Arbutus
leaves over 20 days decay and Gupta et al. (2009) studied Metasequoia leaves through
stages of senescence and from two sedimentary samples inferred to represent 1 year
decay. None of these studies found evidence of the formation of a highly aliphatic
resistant macromolecule, suggesting that in situ polymerization either had not yet
occurred or was insufficient to be recognized by Pyrolysis GC-MS methods.
Therefore it would also be appropriate to study a time-series of samples through the
Recent, archeological and fossil record from a suite of carefully chosen isotapho-
nomic contexts. The difficulty with this approach is that the degree of senescence and
decomposition prior to burial is likely to be unknown and might be crucial.
A third research direction would be to undertake experiments to artificially
simulate chemical alterations. The experimental approach is problematic as it may
be impossible to adequately mimic changes that occur over geological time scales.
Infact, the purpose of such experiments need not be an attempt to mimic diagenesis
but to demonstrate potential sources for highly aliphatic macromolecules from tis-
sues lacking such precursors (Stankiewicz et al. 2000; Finch and Freeman 2001;
Gupta et al. 2006b, 2007c, 2009; Gupta and Briggs this volume) and to establish
links between physical/visual/structural changes and chemical changes (e.g. in
spores – Yule et al. (2000) and cuticles – Stankiewicz et al. (2000)).
Shechter and Chefetz (2008) compared the sorption properties (for hydrophobic
organic compounds) of cutin and cutan isolated from tomato (Lycopersicon) fruits
and Agave leaves respectively. This type of study could be extended to include fos-
sil geopolymers such as those in fossil cuticles to provide insights into their chemi-
cal interactions in sediments.
3 Xylem (Including Wood), Fruit Walls and Seed Coats
Unequivocal molecular evidence for lignin exists in fossil wood samples from the
early Mesozoic onwards (van Bergen et al. 2004). Prior to this time interpretation
of the fossil record is complicated by diagenetic transformations with loss of char-
acteristic side chains preventing identification of the lignin biomacromolecule (van
Bergen et al. 2004). In Devonian early land plants the presence of lignin is not
demonstrable in the earliest vascular thickenings and it is possible that either lignin
or other polyphenolic compounds may then have been components of water con-
ducting tissues (Ewbank et al. 1996; Edwards et al. 1997; Boyce et al. 2003; Raven
and Edwards 2004; van Bergen et al. 2004). Cell wall lignification may have
occurred first in the outer cortex (Boyce et al. 2003) rather than in vascular tissue.
Almendros et al. (2005) compared their chemical results for Lower Cretaceous fern
leaves to those of Edwards et al. (1997) for Devonian Psilophyton and linked the
loss of diagnostic lignin signals to an advanced state of maturation of the fossils.
Lignin chemical composition varies in modern plants (Van Bergen et al. 2000b,
2004) and the syringyl units in angiosperm woods are less stable (Fengel 1991) and
prone to rapid degradation (Van Bergen et al. 2000b) and preferential removal during
decomposition (e.g. Hedges et al. 1985, other references cited in Van Bergen et al.
(2000b, p. 71). Other studies also indicate preferential degradation of certain
lignins which imply that angiosperm lignin may be less well represented in the fos-
sil record in comparison with gymnosperm lignin (Kim and Singh 2000). In
Miocene lignites (brown coals) wood assemblages and collections of large fossil
wood specimens are often dominated by coniferous woods. However, the palyno-
logical assemblages and small wood fragments and charcoalified wood fragments
may indicate a higher proportion of angiosperms in the original plant community
(Mosbrugger et al. 1994; Figuerial et al. 1999) thereby suggesting a possible bias
against angiosperm woods.
Lignin–cellulose–hemicellulose complexes in sclerotic (= thick-walled, not
cuticular) seed coats and fruit walls survive in a modified form in the Cainozoic
record typically with loss of polysaccharides and hemicelluloses but retaining
lignin markers (Collinson and van Bergen 2004 and refs cited; Stankiewicz et al.
1997). The same is true of woods (Kaelin et al. 2006). In several fruit and seed
examples chemosystematically distinctive signatures survive not only in the scle-
rotesta but also in cuticular layers (van Bergen et al. 1995; Van Bergen et al. 2000a;
Collinson and van Bergen 2004; Sawada et al. 2008). In a study of the sclerotesta
of the seed coats of Stratiotes from the mid Paleogene Hooker et al. (1995) showed
that major alteration of the lignin–cellulose–hemicellulose complex can occur (in
this case resulting in a very simple polyphenolic macromolecule). Nevertheless, the
sclerotesta still remains structurally recognizable and the taxonomic affinity is
determinable in the fossil record. This is comparable to the degree of chemical
alterations known in leaves (Section 2) where a morphologically recognizable fossil
leaf in hand specimen is typically drastically altered chemically. These data suggest
little bias to the fossil record of propagules containing lignin–cellulose–hemicellulose
complexes of appropriate chemistry. Depositional settings and enclosing lithologies
exert some control on chemical preservation of lignin in seed coats (van Bergen
et al. 1994; Hooker et al. 1995) and woods (Kaelin et al. 2006). Somewhat counter-
intuitively preservation of lignin chemistry was better in coarser sediments (sands)
than finer sediments such as muds (van Bergen et al. 1993b, 2004) or organic rich
‘coaly’ layers (Kaelin et al. 2006). Kaelin et al. (2006) suggested that the strong
physical compaction in the coaly layers may have been a key driver of geochemical
changes as all samples showed very low maturity. These more altered woods also
lost some of their structural characteristics due to compaction. In the case of extreme
chemical alteration of seed coats some anatomical details maybe lost (Hooker et al.
1995) but nevertheless the taxon remains identifiable and the entity survives as a
fossil even when drastic chemical alteration has occurred.
236 M.E. Collinson
Chemical alterations to woods during fossilizsation have profound implications

for applied paleobotany. Poole and van Bergen (2006) emphasise the need for a
thorough understanding of the alterations to wood chemistry prior to the application
of wood fossils as proxies for paleoclimates. Poole et al. (2006) demonstrated how
carbon isotope signatures of bulk wood are influenced by the chemical preservation
of the wood and concluded that knowledge of both chemical preservation and
taxonomic identity are essential prerequisites for recognition and interpretation of
real isotopic shifts which can then be applied in paleoenvironmental analysis.
These arguments are strongly underscored by evidence that oxidative degradation
alters carbon isotopic composition of kerogens through removal of carbohydrates
(Hoefs et al. 1998) and that recalcitrant carbon resulting from microbial decay
experiments may be similar despite different plant sources (Kelleher et al. 2006).
Richter et al. (2008) drew attention to the risks in assuming that oxygen isotope
composition of fossil wood cellulose had not changed during burial. They used
XRD to control against mineral contamination and to demonstrate that the crystal-
line form of fossil cellulose was the same as modern cellulose in some cases.
Notably they found that samples from the same site were variable in their preserva-
tion and contamination. Lechien et al. (2006) showed that in some morphologically
well-preserved Miocene gymnosperm woods cellulose was structurally preserved
but was not bioavailable (not degradable e.g. by cellulases) and that lignin had
undergone only slight chemical alteration. They suggested that the lignin transfor-
mations could have maintained the structural integrity of the wood and led to cel-
lulose preservation through reduced bioavailability. It is important to emphasize
that quality of structural preservation need not equate to quality of chemical pres-
ervation as was also shown by the absence of assured derivatives of lignin or cel-
lulose in the kerogen of exceptionally structurally preserved permineralized plants
(Czaja et al. 2009).
In marked contrast to lignins there is strong evidence suggesting that thick-
walled tissues lacking the lignin–cellulose–hemicellulose complex may be biased
against in the fossil record. The propagule wall of Nelumbo (lotus) is composed of
a tannin–polysaccharide complex (Van Bergen et al. 1997b). Although Nelumbo-
like leaves have a long fossil record and the propagule is extremely physically
resistant with high longevity (Shen-Miller et al. 1995) there is no pre-Holocene
morphologically recognisable fossil record of the propagules (Van Bergen et al.
1997b). Other propagules are known with distinctive chemistry. Lignin is lacking
in peas and wheat grains (Braadbaart et al. 2007) and a polyphenolic macromole-
cule, along with protein derivatives, was reported in modern and archeological
(c. AD 600) seed coats of Raphanus (raddish) (Van Bergen et al. 1997a).
The above examples demonstrate that biomacromolecules other than lignin play
a role in structural plant tissues. If, as the Nelumbo example suggests, some or all
of these other biomacromolecules are missing from the fossil record of organic
plant skeletons this clearly creates a bias, but the extent of this bias is essentially
unknown. Fruits and seeds that lack a sclerotic layer containing a lignin–cellulose–
hemicellulose complex and also lack a cuticular layer (see Section 2 for preserva-
tion of cuticles), may be strongly biased against in the fossil record (Van Bergen
et al. 2000a; Collinson and van Bergen 2004). Obviously the absence of a fossil
record is hard to recognize. Future research can be directed in two ways. Firstly
further examples like that of Nelumbo can be investigated where fossils exist of one
organ of a taxon but other organs are lacking. An example may be the fossil record
of legumes where the pods and leaves are characteristic widespread fossils
(Herendeen and Dilcher 1992) but there appear to be no examples of organically
preserved morphologically recognisable legume seed coats as pre-archeological
organic fossils inspite of an extensive fossil record of seed assemblages (e.g. Collinson
and van Bergen 2004). Secondly, well-calibrated molecular phylogenies may be
used to target future chemical studies on the structural entities of taxa with a
predicted early origin but no known morphologically recognizable fossil record.
4 Flowers
Flowers consists of a complex mixture of tissues and organs many of which (esp pet-
als and stamens) are typically short-lived and readily shed or detached from the
flower. Preservation of the entire flower as a compression fossil will be strongly
influenced by conditions which would cause physical break up rather than by chemi-
cal composition of the individual organs. Much of the important information on fos-
sils flowers comes from those that have been charcoalified as a result of wildfires
(Friis et al. 2006). Discussion of this distinctive preservational pathway is outside the
scope of this paper. Compressions fossils of flowers or floral organs are relatively rare
and when present are often dominantly impression fossils with little or no organic
skeleton remaining, even in settings of exceptional preservation. An exception is the
large numbers of flower compression fossils present in the exceptionally preserved
biota from the Eocene oil shales of Messel (Schaal and Ziegler 1992; Wilde 2004),
an extremely tranquil depositional setting with a very high organic content. The exter-
nal surfaces of floral organs (e.g. sepals, petals, carpels) are covered by cuticles
(Riederer and Müller 2006) and cuticle preservation is discussed in Section 2. Pollen
preservation is discussed in Section 5 and fruit walls or seed coats, which will begin
to develop in flowers after fertilization, are discussed in Section 3.
5 Spores and Pollen
The outer walls (exines) of pollen and spores of vascular plants contain a highly
resistant macromolecule named sporopollenin. For a review and history of study
see van Bergen et al. (1993a), Van Bergen et al. (2004) and de Leeuw and Largeau
(1993). This is one of the most resistant organic molecules (argueably the most
resistant) and has been considered to be responsible for the extensive record of land
plant pollen and spores in sediments since at least the Ordovician (van Bergen et al.
2004) and which probably extends back into the Cambrian (Raven and Edwards
238 M.E. Collinson
2004). Spores from at least the latest Ordovician onwards retain a characteristic
ultrastructure suggesting comparable development to their modern analogues
(Wellman 2004).
At least two chemically different types of sporopollenin (one with aromatic
building blocks and the other aliphatic) have been thought to exist, possibly in
different plant groups or mixed within the same entity (Reviews in van Bergen
et al. 2004; de Leeuw et al. 2006). Most fossil spore and pollen walls analysed
consist of both aromatic and aliphatic constituents (de Leeuw et al. 2006). Having
taken account of recent analytical results and previous literature de Leeuw et al.
(2006) concluded that the aliphatic component in fossils is not part of the original
sporopollenin structure but is due to early-diagenetic oxidative polymerization of
unsaturated lipids. This hypothesis requires reconsideration of the previous
assumption that the presence of sporopollenin is responsible for the preservation
of pollen and spore exines in the fossil record. In cuticles (Section 2) it can now
be argued that cutan is of little (perhaps no) importance in cuticle preservation
which is instead mainly controlled by the in situ polymerization of cutin, plant
waxes and internal plant lipids contributing to the formation of a resistant geo-
macromolecule. Equally it is at least possible that the biomacromolecule
sporopollenin plays little role in pollen and spore preservation but that polymer-
ization of lipids and their incorporation into a geomacromolecule (which should
be termed fossil sporopollenin, or given a new name) is the controlling factor.
The role of sporopollenin in the pollen and spore wall (as also perhaps the role of
cutin in the cuticular membrane) could be more as a physical entity providing a
structural template for polymerizations.
6 Phytoplankton and Algal Cysts
6.1 Chlorophyta and Prasinophyta
A detailed recent review (de Leeuw et al. 2006) has been published on the resis-
tant macromolecules of algae with an extensive literature survey of their occur-
rence in fossil and modern examples building on that by Versteegh and Blokker
(2004). Relevant references to previous work can be found in de Leeuw et al.
(2006) on which the text to follow is based. Only a few Recent algae biosynthe-
size a resistant cell wall or resting cyst wall containing the highly aliphatic resis-
tant biomacromolecule algaenan – these include Chlorophyta, Eustigmatophyta,
Prasinophyta and one member of the Dinophyta. Detailed studies of algaenans
(Tegelaar et al. 1989) have been undertaken by Blokker et al. (2000) and by
Metzger et al. (2007, 2008), the latter specifically on Botryococcus. Algaenan (or
an algaenan-like molecule) has been identified in a number of fossil algal cell
walls mostly those of the Chlorophyta including Botryococcus (a widespread fos-
sil from Permian onwards, well known for hydrocarbon generation potential,
Batten and Grenfell 1996), Tetraedron (the alga which played a large part in the
exceptional preservation of biota in the Eocene Messel oil shales, Schaal and
Ziegler 1992) and Pediastrum (an important algal indicator taxon for freshwater
conditions from the Cretaceous onwards, Batten 1996). The fossil prasinophyte
Tasmanites also has a similar aliphatic polymer (but with possible additional
components). Algaenan in resting cyst walls occurs in modern Chlorophyta such
as Chlamydomonas, Spirogyra and Dunaniella. Resting cysts of a variety of
Zygnemataceae (Recent analogues Spirogyra, Mougetia, Debarya and Zygnema)
occur in the fossil record from the Carboniferous onwards (van Geel and Grenfell
1996) but I am not aware of any studies of their chemical composition. Not all
algae whose living members produce algaenan have yet been identified in the
fossil record but their absence may be due to inadequate morphological charac-
teristics preventing their recognition. Many Recent algae do not produce
algaenan, but (with the exception of Dinophyta – see below) it is difficult to name
an example where the organic skeleton is strongly diagnostic such that it should
be recognizable in the fossil record and so could be demonstrated to be absent.
Such cases would be a prerequisite to help to justify an hypothesis that the pres-
ence/absence of algaenan exerted a major bias on the algal fossil record. Kodner
et al. (2009) showed that algaenan is not widespread ecologically or phylogeneti-
cally and argued that it was therefore unlikely to be responsible for a sizeable
proportion of refractory organic matter is sediments. As demonstrated for cuticles
(Section 2) and as suggested as a possibility for pollen and spores (Section 3) the
highly resistant macromolecule (in this case algaenan) may be less important in
fossil preservation then previously thought.
6.2 Dinoflagellates
A number of modern Dinophyta have been shown to produce acetolysis resistant

cell walls and resting cysts (de Leeuw et al. 2006 for a review). The resistant
macromolecule in Lingulodinium is predominantly aromatic and is often referred
to as dinosporin which differs from both algaenan and sporopollenin (de Leeuw
et al. 2006). In contrast the cyst walls of Scrippsiella also have a substantial ali-
phatic component (de Leeuw et al. 2006). Most fossil dinoflagellates analysed
have both an aromatic and aliphatic component (de Leeuw et al. 2006). A number
of modern Dinophyta are also known to lack resistant chemistry in their cell walls
(de Leeuw et al. 2006).
It is well known that there are some apparent gaps in the fossil record of dino-
flagellates, both the group as a whole and for individual families and genera show-
ing the lazarus taxon phenomenon. One possible explanation is that these gaps are
due to phases when resistant cysts were not produced (e.g. Fensome et al. 1996).
De Leeuw et al. (2006) suggested, on the basis of chemical analyses of a few mod-
ern and fossil dinoflagellates and the differential survival of fossil cyst walls under
different extraction procedures, that dinosporin may be variable in its chemical
composition. If this hypothesis is supported by further analyses then both the
240 M.E. Collinson
chemical nature and the presence/absence of dinosporin could be exerting a bias on

the dinoflagellate fossil record.
Versteegh et al. (2004) argued that oxidative polymerization of lipids was
responsible for the preservation of one example of fossil dinoflagellates that
lacked a cell wall but were preserved through an infill acting as a ‘cast’ of the
original morphology. This work demonstrates a similar process of polymeriza-
tion to that discussed above for spores and pollen (Section 5) and cuticles
(Section 2) albeit not in situ in the dinoflagellate cell wall or cyst wall. Because
the cyst walls of the modern dinoflagellate Scrippsiella contain both aromatic
and aliphatic components it is possible that the aliphatic/aromatic compositions
of fossils cysts are little altered from their modern counterparts. However, the
equivalent from the modern genus has not been studied for any of the fossil
resting cyst walls listed in the review by de Leeuw et al. (2006). Until this direct
comparison is undertaken the relative role in preservation of fossils for (i) the
aromatic biomacromolecule dinosporin, or (ii) an original aliphatic component
becoming associated with dinosporin through polymerization during diagenesis
or (iii) some form of in situ polymerization (see Sections 2 and 5 above)
remains unknown.
6.3 Acritarchs
Acritarchs are organic-walled microfossils of unknown biological affinities.

Some of these may have been produced by Dinoflagellates (or their close rela-
tives) and some by various algal groups or other groups of life. Acritarch fossils
are amongst the oldest organic plant skeletons recovered from the fossil record
extending back into the Mesoproterozoic. Recent research has used a combina-
tion of transmission electron microscopy and multi-method micro-chemical
analysis in an attempt to further elucidate the biological affinities of some very
early acritarchs (Javaux and Marshall 2006 for a review). A highly aliphatic
signal, similar to that of Recent algaenan, was documented in the wall of the
Neoproterozoic Tanarium; a potentially new class of biopolymer, with aliphatic,
branched aliphatic and saturated/olefinic carbon constituents, in the
Neoproterozoic Leiosphaeridia; and an aromatic polymer in a Mesoproterozoic
Shuiyousphaeridium (Marshall et al. 2005; Javaux and Marshall 2006). These
authors also noted the occurrence of various different multilayered wall ultra-
structures in acritarchs with similar chemical composition. Issues such as those
discussed in Sections 2 and 5, in particular the potential for the diagenetic altera-
tion of biopolymers, mean that it cannot be assumed that chemical compositions
of these very ancient organic skeletons reflect those of the original material. In
situ polymerization or incorporation of external material may well have altered
the chemistry of the fossils. As Javaux and Marshall (2006) state a combination
of microscopy and chemistry will be important for further characterization of
these early eukaryotic fossils.
7 Conclusions and Implications
7.1 Plant Evolutionary Constraints and Temporal Bias
The timing of evolution of resistant macromolecules such as lignin and sporopollenin

and of the evolution of certain tissues and organs (such as xylem, cuticle, wood and seed
coats) is important, but once these had evolved there is no obvious time-related bias.
Some obvious bias is taxon-related with the presence/absence of a particular
chemistry in a given organ/tissue of a given taxon being an important control on
representation in the fossil record. It is predicted that depositional and burial condi-
tions will prove to be extremely important (and possibly the key factor controlling
preservation in at least some components of the plant organic skeleton) as these are
expected to exert a strong influence on the process(es) of in situ (within organ/
tissue) polymerization and oxidative polymerization and have already been shown
to influence quality of chemical preservation.
7.2 Implications for Applied Paleobotany
7.2.1 Floras and Vegetation Reconstruction, Dating First Occurrences Etc.
It has been shown that preservational biases linked to chemical composition may
affect the fossil record of certain organs or tissues of a given taxon. This bias can
be overcome by using the fossil record of multiple organs wherever possible. For
example, a combination of evidence from pollen and spores, leaves, fruits and
seeds and woods can be used to produce a vegetational reconstruction as all are
common fossils. There is no evidence that any one organ is less affected by
biases than others, the bias affects particular organs of selected taxa. Thus there
is no evidence to support preferential selection of particular organ types for any
particular application.
7.2.2 Geochemical Applications
Although plant organs/tissues survive as fossils their chemistry may be drastically

altered. These alterations vary according to the macromolecular composition of the
parent material. The three main categories of alteration involve (i) polymerization
(e.g. in situ polymerization of cutin, plant waxes and internal lipids into a geomac-
romolecule in the cuticle), (ii) loss (e.g. loss of cellulose from lignin–cellulose
complexes), and (iii) transformation (e.g. lignin methoxyphenols to phenols). For
cuticles in situ polymerization involves little or no migration of material from exter-
nal sources whilst oxidative polymerization affecting spore and pollen walls may
involve incorporation of an external aliphatic component. When geomacromolecules
242 M.E. Collinson
or altered biomacromolecules are being applied as paleoenvironmental proxies it

would seem prudent to (i) establish the preservational state of relevant molecules,
(ii) use samples of like preservational state for any comparative study, and (iii) moni-
tor the degree of alteration and the contribution of external materials (which may
render the proxy invalid) both by microscopy and by chemical analysis. In fossil
material, and in modern material which has been physically or chemically isolated
for study, it is necessary to establish the presence of wall layers, cells, tissues and organs
by microscopy prior to making inferences about the sources of chemical signals.
Non-destructive approaches such as Raman microspectroscopy and Scanning
Transmission x-ray Microscopy (Bernard et al. 2009; Czaja et al. 2009) have con-
siderable potential to combine microscopical and chemical analyses.
7.2.3 Ultrastructure, Taxonomic Characteristics and Chemotaxonomy
It is to be expected that chemical alteration may result in loss of taxon diagnostic

morphology and ultrastructure following polymerization, loss or transformation
alterations. In contrast, it is known that taxon diagnostic morphology and ultra-
structure may survive even when chemistry is drastically altered. Although chem-
istry is altered chemical signals of chemosystematic value do sometimes survive
and these also provide evidence of the past occurrences of distinctive biosynthetic
pathways. Current evidence reveals no obvious overriding factors controlling the
survival or loss of taxonomically valuable characters and much more work is
needed to establish the circumstances and processes which affects these signals.
Further understanding of these factors would offer potential to target particular fos-
sil assemblages for future systematic and evolutionary study.
Exceptional preservation of organelle ultrastructure is known, for example, in
some leaf fossils (Section 2). This is variable from specimen to specimen and taxon
to taxon within the same sedimentary horizon. In the same horizon some fossil
leaves exhibit detailed cellular anatomy and organelle preservation whilst others are
composed only of cuticle envelopes. In some other deposits leaves are preserved
but without cuticles (Section 2). These facts underscore just how little is understood
about the specific controls on plant preservation, warn against wide inferences
based on small sample numbers and demonstrate the need for combined micro-
scopical and chemical approaches in studies of plant molecular taphonomy.
Acknowledgments Special thanks are due to Jan de Leeuw and Pim van Bergen for their long
term interest, enthusiasm, support, and friendship in our collaborative studies of the organic geo-
chemistry of plant fossils. I would like to thank Ben van Aarsen, Pim van Bergen, Peter Blokker,
Tony Brain, Derek Briggs, Richard Evershed, Paul Finch, Neal Gupta, Jan de Leeuw, Raymond
Michels, Barbara Mösle, Rich Pancost, Andrew Scott and Gerard Versteegh for their previous, and
in many cases ongoing, collaboration; to the chemists amongst them also my thanks for their
patience with my inadequate knowledge of chemistry. Any errors in the present work are entirely
those of the author. Funding from a Royal Society 1983 University Research Fellowship, the
NERC Biomolecular Palaeontology Special Topic, the NERC Ancient Biomolecules Initiative
(grants GST/02/1030 and 1390) and from the Petroleum Research Fund, American Chemical
Society (the latter to collaborators Pancost, Briggs and Michels) is gratefully acknowledged.
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Chapter 7
The Relationship Between Continental
Landscape Evolution and the Plant-Fossil
Record: Long Term Hydrologic Controls
on Preservation
Robert A. Gastaldo and Timothy M. Demko
Contents
1 Introduction........................................................................................................................... 250
2 Factors Influencing Plant-Part Preservation.......................................................................... 252
2.1 Plant-Part Decay Rates................................................................................................ 252
2.2 Relationship Between Rates of Decay and Sedimentation.......................................... 254
3 Models of Stratigraphic Frameworks and Landscape Evolution.......................................... 257
3.1 Continental Sequence Stratigraphy.............................................................................. 258
3.2 Graded Profiles, Paleosols, and Landscape Evolution................................................. 259
4 A Model for Plant-Part Preservation in Continental Landscapes......................................... 261
5 Case Studies.......................................................................................................................... 264
5.1 Plant Assemblages in Aggradational/Degradational Landscapes................................ 265
5.2 Plant Assemblages in Aggradational Landscapes....................................................... 272
6 Conclusions........................................................................................................................... 277
References................................................................................................................................... 279
Abstract Continental depositional environments preserve the majority of the

macrofloral record since the advent of land-plant colonization in the mid-Paleozoic,
and wetland representatives are encountered more commonly than those that grew
under more seasonal conditions. It has been assumed that preservation potential and
future recovery of plant debris are high once detritus is introduced into any appro-
priate environment of deposition (e.g., fluvial-lacustrine or paludal setting), regard-
less of prevailing associated climate, sediment load, or geochemistry at the time
of emplacement or interval thereafter. If a plant fossil is identified in any part of a
stratigraphic interval, even if it occurs solely as an impression, it has been presumed
that favorable conditions persisted over time to facilitate this record. Conversely, the
R.A. Gastaldo (*)

Department of Geology, Colby College, Waterville, ME 04901, USA
T.M. Demko
Department of Geological Sciences, University of Minnesota Duluth, Duluth, MN 55812, USA
and
ExxonMobil Exploration Company, Houston, TX 77210, USA
250 R.A. Gastaldo and T.M. Demko
absence of fossil plants in a stratigraphic sequence commonly has been interpreted

as the result of catastrophic perturbation across the landscape, rather than the
ascribing their absence to taphonomic filters that may have operated millennia
after burial. Terrestrial landscapes are affected by aggradational, equilibrium, and
degradational processes that control not only the local or regional water table, but
also the long-term fossilization potential of organic debris entombed within these
sediments. Fossil plants have the highest preservation potential when high water
tables are maintained long-term within soils (e.g., histosols, entisols, gleyed soils),
or in settings that are maintained below the maximum draw down of the regional
water table (e.g., channel barforms, abandoned channels, lakes) of aggradational
landscapes. When landscapes reach equilibrium, extensive pedogenesis ensues and
the development of deep mature soils (e.g., calcisols) results in the bacterial deg-
radation of any previously buried plant debris due to extreme penetration of atmo-
spheric gases. When sediment is removed during landscape degradation, the local
and/or regional water table is reset lower in the unconsolidated stratigraphy, once
again promoting rapid decay of previously buried detritus at depth. These processes,
operating under time frames of centuries to millennia and longer (lakh), control the
ultimate preservational mode of plants recovered from the fossil record.
This chapter reviews the factors influencing the preservation of terrestrial plants
in both subaqueous and subaerial environments based on actualistic studies, and
develops a conceptual framework for landscape evolution in continental regimes.
A model is presented in which preservational mode is related to the taphonomic and
sedimentary history of the landscape in which plant detritus is buried. Case studies
of the plant-fossil record, ranging from the Triassic to the Eocene, in exclusively
aggradational and in aggradational/degradational landscapes are presented.
1 Introduction
Plant communities form the base of terrestrial ecosystems, serving multiple functions
including, but not limited to: acting as the primary food resource for life; biogeo-
chemical cycling and carbon storage; development and enrichment of soils; mod-
eration of local and regional temperature; and animal habitats and shelters.
Colonization of land may have occurred very early in the Phanerozoic, with evi-
dence of cryptogam and bryophyte-grade plants found within nearshore marine
deposits (Strother 2000; Baldwin et al. 2004) earlier than fragmentary debris of
multicellular plants preserved in fluvial siliciclastic and associated environments
(Pratt et al. 1978; Gensel and Edwards 2001). As plant clades evolved various
architectures imparting more robust growth statures beginning in the Silurian, both
aerial and subterranean plant parts become more prevalent in the stratigraphic
record. Early preservational modes range from adpressions (Shute and Cleal 1987)
to pyritization (Grimes et al. 2001) and charcoalification (Glasspool et al. 2004).
With the advent of higher vascular plants in the Late Silurian (Edwards and Feehan
1980; Rickards 2000) and the appearance of the seed habit in the Late Devonian
7 Continental Landscape Evolution and the Plant-Fossil Record 251
(Fairon-Demaret and Scheckler 1987; Rothwell et al. 1989), plants evolved strategies
for successful colonization under wide climatic regimes within various enriched or
depauperate soil types. Individual clades developed a broad range of adaptions that
allowed taxa to grow under moderate to extreme climates, although fossil assem-
blages rarely are preserved or encountered in these parts of the landscape for a
variety of reasons (DiMichele and Gastaldo 2008). The principal preservational
mode where such assemblages are found usually is permineralization (Demko et al.
1998) or authigenic cementation (Schopf 1975), promoted by physico-chemical
groundwater conditions interacting with entombed vascular tissues during early
diagenesis (e.g., Drum 1968; Allison and Pye 1994).
There is no doubt that the terrestrial plant record consists of an over-representa-
tion of wetland assemblages (Greb et al. 2006; Wing and DiMichele 1995). But, it
is not unreasonable, and more parsimonious, to hold that deep time landscapes
outside of the wetlands also were vegetated to some degree at least as far back as
the latest Devonian, when the evolution of the seed habit allowed for biogeographic
expansion of clades into more inhospitable regions. Of course, there does exist the
possibility that community representatives could be preserved in these extrabasinal
areas (e.g., Beraldi-Campsei et al. 2006), but their general absence in the pre-Ter-
tiary stratigraphic record generally is construed to reflect their true absence in the
landscape at that moment in geologic time. Lazarus taxa are known, although they
are envisioned as having been wetland-centered species (Mamay 1992) and not
representative of the remaining coeval landscape. Hence, the prevalence of wetland
assemblages appears to have resulted in a prevailing paradigm that when plant-part
debris is buried within a suitable depositional regime, early diagenetic processes
generally will promote preservation. Conversely, when there is an absence of plant
fossils in strata, it is assumed that the landscape was hostile to their successful colo-
nization and they were extirpated from the region (often, in spite of paleopedologi-
cal evidence) or that this absence marks a major extinction event. But, it is equally
probable that the processes that promote preservation also will promote degradation
and recycling via fungal and bacterial activity (Gastaldo 1994; Gupta and Pancost
2004). One must remember that the majority of organic matter is recycled for reuse,
with a very small proportion of biomass sequestered in the rock record. Hence,
concepts tying the presence or absence of the plant-fossil record to the evolution of
continental landscapes generally have been overlooked or neglected.
The plant-fossil record plays a major role in understanding and interpreting the
response of ecosystems to changes in climate, evolution, and crises in Earth systems.
The physical presence (e.g., Gastaldo et al. 2009) or absence (Gastaldo et al. 2005)
of terrestrial plants within any particular depositional regime at any specific point in
time is integrally tied with the packaging of continental sedimentary successions.
Recent workers have suggested methods and frameworks to subdivide continental
rocks based upon differences in rates of accommodation and their relationship to
allogenic and autogenic factors in basin fill (e.g., Shanley and McCabe 1994;
McCarthy and Plint 1998; Etheridge et al. 1998). And with these models in
mind, the preservation of terrestrial plant-fossil assemblages may be more a function
of longer term processes operating within the landscape than any other factor.
It is essential to understand the relationships between the short-term (facies) and

long-term (landscape) controls on the taphonomic biases controlling this record
before using these data in paleoecological, paleoclimatic, and macro-evolutionary
studies. This contribution will provide a model for continental sedimentary succes-
sions constraining the physico-chemical conditions within which terrestrial plant-
fossil assemblages, and their preservational mode(s), can be understood and utilized.
2 Factors Influencing Plant-Part Preservation
Vegetated landscapes vary enormously in systematic composition, plant density,

and vegetational architecture on continental spatial scales that are controlled by
climate, topography, and edaphic conditions. Yet, the prerequisites that allow for
preservation of the continental plant-fossil record are met under relatively restricted
sedimentological and geochemical conditions (Krasilov 1975; Spicer 1989;
Gastaldo 1992, 1994). These prevent incorporation of many types of plant assem-
blages in the deep-time record. In addition, there are a limited number of potential
depositional sites where plant parts accumulate under conditions that may promote
their long-term (101 to 104–5) preservation prior to deeper burial within any land-
scape. Aerial debris must accumulate within a depositional regime where (1) dys-
oxia and/or anoxia prevails (i.e., at the sediment–water interface in a lake system),
(2) micro-environmental geochemical gradients are strong (e.g., fluvial channel-bar
troughs; Gastaldo et al. 1995), (3) resistant and diagnostic phytoclasts persist unal-
tered long after decay has removed all volatiles (e.g., phytoliths – Strömberg 2004),
and (4) sedimentary entombment maintains (preventing degradation) or enhances
(through pore-water interactions with organic ligands) the geochemical environ-
ment within the facies. In the majority of instances, biomass is fated to be reused
within various biogeochemical cycles by the living biota, which is the rule rather
than the exception.
2.1 Plant-Part Decay Rates
The loss of vegetative and reproductive structures, either through physiological or

traumatic disarticulation (Gastaldo 1992, 1994), subjects them to decay through a
myriad of potential interactions including those with saprotrophs, fungi and bacte-
ria, as well as autocatalytic cellular and subcellular breakdown. Although microbial
films may promote preservation under specific environmental conditions (Dunn
et al. 1997), phytoclasts have a tendency to degrade instantaneously in a geological
sense. Subterranean rooting structures, already pre-entombed, may remain less
affected for longer intervals of time, particularly when influenced by a change in
pore-water chemistries promoting the precipitation of carbonate of various miner-
alogical compositions (calcite, siderite, pistomesite, etc.; Retallack 2001).
There is an abundance of actualistic data in the ecological and plant taphonomic

literature focused on rates of forest-litter decay across the latitudinal (climate) spec-
trum (e.g., Bray and Gorham 1964; Gastaldo and Staub 1999 and references
therein). In general, the refractory nature of the original biochemical composition
of the plant organ, or part thereof, will influence the rate of decomposition which
is calculated as the decay constant k (Perry 1994; Fig. 1). A leaf with a decay con-
stant of k = 1 will be completely degraded in 1 year’s time. But, complete decay
can proceed within time frames on the order of weeks (e.g., flowers and leaves),
months (leaves), or years to several decades (wood, gymnospermous cones, fruits,
and seeds; Burnham 1993). It is well documented from neoecological and actuo-
paleontological studies that decay rates not only differ within taxa of a single clade
or between various clades, but also under different climatic conditions (Gastaldo
and Staub 1999). Rates even may vary within microhabitats under the same general
climate (Bray and Gorham 1964). Hence, all plant assemblages essentially provide
a geologically instantaneous (T0) snapshot of preservable landscape constituents.
It is true that certain resistant phytoclasts may be reworked, such as woody debris,
heavily lignitized cones, fruits, seeds, charcoal (Scott 2000), and palynomorphs.
Labile plant parts, such as leaves, flowers, and less reinforced reproductive struc-
tures, will sustain physical abrasion when re-entrained into bedload and reduced to
unidentifiable phytoclasts (Gastaldo et al. 1987). But, published criteria allow for
recognition of such recycled parts (e.g., wood-clast rounding – Gastaldo 1994;
change in palynomorph fluorescence – Traverse 1994) within an allochthonous
Fig. 1 The relationship between the yearly production of plant biomass and the total organic
accumulation in various terrestrial biomes is described by the k constant (Perry 1994). A plant part
with a decay constant of k = 1 will be completely degraded in 1 year’s time. Note that decay
constants differ between the most labile (leaves, fruits, flowers, etc.) and refractory (xylem elements,
wood, amber/dammar, etc.) plant parts
assemblage. And, in reality, most phytoclasts do not possess structural attributes

that allow them to be buried, exhumed, and recycled, if at all, more than once or
twice (in the case of lignitized plant parts) before being reduced to palynofacies-
grade debris.
2.2 Relationship Between Rates of Decay and Sedimentation
Inasmuch as decay rates of the most labile plant parts are, at best, on the order of
months to only a few years, this rate exceeds average sedimentation rates in most
instances, precluding potential preservation anywhere in the landscape.
Sedimentation rate usually is expressed in cm/ka, which is an insufficient rate to
promote plant-part preservation. Hence, a convergence must exist in nature where
the sedimentation rate at some point in time exceeds the decay rate of plants for
there to be any potential preservation of terrestrial vegetation in the stratigraphic
record. In addition, the geochemical conditions associated with entombment that
promote preservation must be maintained in both the short and long term for that
organic debris to be identifiable.
2.2.1 Subaqueous Environments
Plant parts accumulate at the sediment–water interface within discharging and stand-
ing water bodies either when their specific gravity exceeds that of water (Gastaldo
1994) or when flow rate is reduced sufficiently to allow for settling from suspension
(Spicer and Greer 1986; Spicer 1990). Assemblages within active channels include lag
deposits of wood and carpological (fruit and seed) remains (Gee et al. 1997; Gee
2005). Dense accumulations occur within both channel bottoms and various barforms,
as well as isolated coarse woody debris (CWD) scattered within the system
(e.g., Fielding et al. 1997; Alexander et al. 1999; Gastaldo 2004). In contrast, coarse
woody assemblages also have been recognized at the top of fluvial channel fills
preserved as log jams (Gastaldo and Degges 2007). Such relationships require an
understanding of the contextual taphonomic framework before interpreting Late
Devonian (Meyer-Berthaud et al. 1999) to Recent dense woody assemblages in the
fluvial stratigraphic record. Troughs within and between fluvial barforms, particularly
point bars and lateral barforms, are sites where an admixture of aerial plant parts tend
to accumulate when conditions allow for suspension-load settling. This may be in
response either to a decrease in discharge velocities following seasonal changes in
water supply, the lowering of river stage following a high discharge event (either
bankfull or flood stage; e.g., Scheihing and Pfefferkorn 1984), or interactions with
meso- to macro-tidal processes transforming a free flowing river to a standing body
of water at tidal-bore turnaround (e.g., Gastaldo et al. 1996a). Similarly, organic drapes
consisting of various phytoclast components often are found at bounding surfaces
separating foreset laminae created by bedform migration. Preservation potential of all
these assemblages increases when they are buried by continued bedform migration and
maintained below the air–water interface. Geochemical properties inherent within the
accumulation, such as the release of organic acids and tannins, may promote long-term
preservation in spite of the fact that pore-waters are in chemical equilibrium with the
water column. But, when water stage falls to a level below that of the buried organic
debris, sediment oxygenation and fluctuating redox conditions promote bacterial and
fungal activity that reduces most identifiable plant parts to palynofacies-grade detritus
(Gastaldo, 1989). This results in an organic residue in which only the most resistant
phytoclasts (e.g., palynomorphs, cuticle, and structured organic matter = mesofossils
fraction) may be recovered.
Standing bodies of water have the highest preservation potential for plant-
assemblage preservation. These include settings that one envisions as stereotypical
lakes and ponds, although the blockade of drainage systems within watersheds
either through mass wasting or effects of volcanogenic activity within active tec-
tonic settings also will result in a standing body of water equivalent in scale to
lakes (Spicer 1989). In addition, plant parts will accumulate within inactive and
abandoned fluvial (oxbow; Gastaldo et al. 1989) and tidal (Gastaldo and Huc
1992) channels. Plant parts transported through feeder channels into lake bodies
often are sequestered in shallow water, Gilbert-type deltaic deposits (Spicer and
Wolfe 1987) where preservation may result if lake levels are maintained. Lake
margins vegetated by aquatic and semi-aquatic plants may act as filters, trapping
organic debris in the shallows (Gastaldo 1994). But, once lake level falls and suba-
erially exposes these areas, buried organic matter shares the same fate as accumu-
lations noted above within barforms. And, if lake levels fall significantly,
pedogenesis will overprint these to some degree (e.g., Wing 1984; Gastaldo et al.
1998). Assemblages that accumulate at marked water depth in more distal parts of
the water body have a higher probability of preservation if several physical (asso-
ciated high sedimentation rate) and chemical (i.e., redox conditions operating at
and below the sediment–water boundary) conditions are met. Otherwise, debris
that settles to the sediment–water interface will be recycled via microbial, inverte-
brate, or vertebrate activity.
Abandoned (or blocked) channels remaining in connection with an active fluvial
(Gastaldo et al. 1996b) or tidal (Gastaldo and Huc 1992) regime provide very local-
ized sites in which primarily parautochthonous assemblages accumulate in associa-
tion with high sedimentation rates resulting in their entombment. The maintenance
of high water levels in a largely confined and restricted setting promotes redox states
wherein reducing conditions are not controlled, necessarily, by acidic waters but,
rather, by the development of strongly negative Eh values in the sediment. The pH in
these water bodies actually may be near neutral (e.g., Gastaldo and Huc 1992), yet
the rate of decay is retarded and even labile tissues are conserved in the subsurface.
In such settings the promotion of bacterial films, as identified by Dunn et al. (1997),
developed at the sediment–water interface in conjunction with sediment influx, may
be controlling the preservation potential in these assemblages. Hence, there is a
localized geochemistry with its own internal equilibrium very different than the
surrounding landscape that controls the taphonomic character of these regimes.
2.2.2 Subaerial Environments
In subaerially exposed floodplain settings, it is generally held that plant-fossil

assemblages have the highest preservation potential when buried by overbank flood
deposits. High discharge, sediment-laden flood events allow for the spread of fine-
grained clastics away from the trunk channel over a short time interval that may last
a few weeks before flood waters recede and suspension load settles to what previ-
ously was the soil–air interface (Fig. 2). During flooding, the regional water table
is elevated to above the soil interface and standing water may promote site-specific
dysoxyia and a change in redox conditions. But, once flood waters recede and the
regional water table is reestablished at its previous level, normal decay processes
proceed within the buried litters as groundwater levels fluctuate in response to
meteoric water supply, evaporation, and plant growth (transpiration). Fluctuations
in the groundwater table introduce oxygenated waters promoting biochemical and
biogeochemical processes, reducing plant parts to meso- and micro-detrital sizes
without physical abrasion. In effect, the return to the local or regional equilibrium
resets the degradational processes, reducing to null the potential for preservation as
Fig. 2 The fate of organic matter at the soil–air interface within interfluves. (a) Groundwater
fluctuations in hydromorphic (wetland) soils are responsible, in part, for decay of organic matter
at and immediately below ground level. (b, c) During overbank flooding, fine-grained sediment is
transported into the interfluves where it is deposited from suspension load as a thin to thick blan-
ket over the former soil. (d) As flood waters subside and return to the original river stage, ground-
water table also returns to its previous placement in the landscape. Pedogenic and biological
activity, along with yearly-centennial fluctuations in groundwater table, promote decay of buried
plant debris. To isolate the buried litter (O–) horizon and increase the probability of preservation,
the surface must be placed beneath the regional watertable. This may be done either in response
to tectonic subsidence (e) or rapid aggradation of the landscape (f)
pedogenesis becomes the primary mechanism operating within the landscape. This
scenario also holds for landscapes influenced by avulsion unless a perched water-
table is established, preventing root penetration, oxygenation, and microbial decay
of buried debris. Hence, it is only possible to preserve subaerial plant assemblages
that accumulate at the soil–air interface by not only (1) entombing the debris within
overbank (and avulsion) deposits that are relatively thick, but also (2) in an area
where the post-depositional groundwater table has been elevated above the former
soil profile to insure that subsequent pedogenesis and associated biological decay
processes are eliminated (Fig. 2e, f).
Plants in volcanogenic regimes (Spicer 1989, 1991) may be encountered in a
variety of settings ranging from autochthonous litters, preserved at the contact
between the soil and ashfall deposits (Burnham and Spicer 1986; Wing et al. 1993;
Opluštil et al. 2007), to allochthonous assemblages encased within lahars and
debris flows (Fritz 1980; Fritz and Harrison 1985) or reworked tuffaceous sedi-
ments (Jacobs et al. 2005). Besides the possibility for the presence of charcoal,
either the result of temperatures experienced during the blast event (Spicer 1989)
or following burial (Scott and Glasspool 2005), very early diagenetic interactions
as a result of reactive pore-water chemistries may promote sulfide precipitation
enhancing preservation potential of more labile parts (Burnham and Spicer 1986).
Such rapid mineralization may allow for identification of those plants in the strati-
graphic record subsequent to the reestablishment of regional groundwater table and
promotion of degradation in the buried assemblages. In other instances where
mineral-charged groundwaters are transported through xylary conducting tissues
(tracheids in plant steles and tracheids and/or vessel elements in wood), reactions
with organic ligands at the boundaries of cell walls may result in silicification
(Sigleo 1978, 1979). Subsequently, abiotically mineralized plant parts will be
retained in the stratigraphic record even when others may be removed by degrada-
tion. Hence, even in explosive volcanogenic regimes where sedimentation rates
exceeds decay rates the control on potential preservation is linked with maintaining
the assemblage within the phreatic zone.
3 Models of Stratigraphic Frameworks

and Landscape Evolution
With the advent of the sequence-stratigraphy paradigm and its primary application
to marine-influenced sedimentary successions, extension of sequence boundaries
onto continental terrains became necessary to understand how these were expressed
in subaerial environments. Initial models for continental regimes relied upon base-
level changes tied to eustacy (e.g., Posamentier and Vail 1988; Miall 1991; Shanley
and McCabe 1991, 1994), although Wright and Marriott (1993) note that models
controlled by simple base-level changes can not be applied to fluvial systems where
complexity is controlled, in part, by climate. They also dispute the concept of avail-
able accommodation in continental settings by noting that floodplain sedimentation
not only is controlled by the elevation of the channel but also by its bankfull depth.
More recently, Muto and Steel (2000) extended the concept of accommodation,
sensu lato, when they argued that the term “potential accommodation” is equivalent
to the maximum possible accommodation that essentially coincides with water-
column height at a specific place in time. Hence, the depth and extent to which
sediment can accumulate within any continental regime will be controlled by both
the water level within fluvial conduits (including avulsion channels) and at over-
bank stage when sediment is distributed between channel systems that, in effect,
increase the height of confining levees.
3.1 Continental Sequence Stratigraphy
As originally conceptualized, the sequence stratigraphy of continental successions

was placed within the context of base-level change within coastal plain and deltaic,
marginal marine settings (Posamentier and Vail 1988). Posamentier and Vail (1988)
differentiated between fluvial deposition in the coastal plain, at or just above sea
level, and in the alluvial plain, above sea level. In the coastal plain, fluvial deposi-
tion was constrained to incised valleys during lowstand, and during the latter stages
of highstand progradation of the shoreline depositional system. Several authors
were critical of this framework because of the fact that fluvial architecture is related
to concepts of equilibrium-profile change over time (Miall 1991; Wright and
Marriott 1993). With this in mind, Wright and Marriott (1993) modified the model
relating base level and accommodation to alluvial architecture and soil develop-
ment. Although still visualized within the context of eustacy (e.g., Blum and Törnquist
2000), fluvial sediment accumulation was constrained to the coastal plain in trans-
gressive and highstand systems tracts when there is sufficient accommodation to
store sediment within the system. But, as Wright and Marriott (1993) note, their
model is only one of many possible scenarios.
The range of possible controls on stratigraphic base level within continental suc-
cessions was discussed by Shanley and McCabe (1994) wherein they noted an
interdependency of climate, tectonism, and eustacy that may determine fluvial
architectural patterns. Their and subsequent concepts of a continental sequence fol-
lowed that of Mitchum et al. (1977) in which genetically related strata are bounded
at the top and base by unconformities or their correlative conformities. Such bound-
aries mark a depositional hiatus, the origin of which may have been controlled more
by climate and/or tectonic processes within continental sequences than in marine
ones, and are reflected in the character of interfluve paleosols developed within
coastal plain settings (e.g., McCarthy and Plint 1998, 2003; Plint et al. 2001).
Debate continues as to how to confidently identify the boundaries of marine sys-
tems tracts within correlative alluvial strata (e.g., Etheridge et al. 1998), as well as
the application of terminology devised for marine sequences used in continental
settings. General models for continental sequences continue to be proposed (e.g.,
Boyd et al. 2000) although all models, to date, tend to focus on eustatically influenced
coastal plain deposits to a significant degree (Atchley et al., 2004). In this paper,
we use the term continental to refer to settings in the alluvial plain, in the sense of
Posamentier and Vail (1988), which are beyond the reach of marine influences.
3.2 Graded Profiles, Paleosols, and Landscape Evolution
As many authors have noted (e.g., Bull 1991; Quirk 1996; Posamentier and Allen
1999; Muto and Steel 2000), fluvial systems are in a state of disequilibrium when
they are doing stratigraphic “work” (depositing or eroding). Fluvial equilibrium can
be defined as a state when there is no significant erosion or deposition occurring
along the course of a river that would permanently changes that system’s overall
profile (Machin 1948; although see arguments about theory and reality discussed
by Muto and Steel (2000)). This hypothetical graded state results in a rate of bed-
load transport equivalent to that of sediment supply; hence, there is a balance
between the energy required to carry the bedload and the amount of bedload trans-
ported (Quirk 1996). Disequilibrium occurs when either there is: (1) insufficient
discharge or a decrease in alluvial gradient that results in a decrease in stream
power to carry bedload through the system, resulting in aggradation of the alluvial
plain (positive fluvial accommodation of Posamentier and Allen 1999), or (2)
higher discharge than that required to move bedload, or an increase in alluvial gra-
dient that results in an increase in stream power causing degradation (downcutting)
of the alluvial plain by incising channels (negative fluvial accommodation of
Posamentier and Allen 1999). Hence, fluvial systems only contribute additional
strata or surfaces of erosion to the stratigraphic record when in disequilibrium,
although, as Schumm (1993) pointed out, reworking of the landscape occurs due to
channel and channel belt migration during times of relative stasis. Disequilibrium
is promoted by changes in allogenic forcing factors such as tectonic subsidence or
uplift in the basin, climate and precipitation regimes (Cecil and Dulong 2003), rela-
tive height of ultimate base level (sea level or, in the case of closed basins, interior
lakes), and processes operating in both the provenance area and coastal zones
(baselevel change; Schumm 1993). Quirk (1996) remarks that when climate or the
position of relative sea-level are influencing factors, large parts of the drainage
basin are likely to be affected. And, as such, intervals of aggradation and degrada-
tion may provide a means of chronostratigraphic correlation in alluvial strata. With
this in mind, Quirk (1996) introduced the concept of base profile, an idealized
graded profile of a drainage basin constrained in time to a potential chronostrati-
graphic datum. Rivers aggrade up to, or degrade down to, this base profile (referred
to as the “base level of erosion” by Bull (1991)).
Substantial attention has been focused on sandstone-prone channel facies in
alluvial plain stratigraphy due to their economic importance in hydrocarbon and
groundwater exploration and exploitation. Yet, interfluve areas (floodplain, overbank,
etc.) make up the majority of any alluvial plain, with the trunk drainage channels of
major rivers covering a relatively small component of the overall landscape. Hence,
the character of paleosols adjacent to, and coeval with, within-channel deposits
provides critical information about the prevailing climate (e.g., Sellwood and Price
1993; Retallack 2001) and the relative timing of their formation. Because paleosols
that form under a distinctive climatic signature represent an amount of time that is
roughly equivalent to, or less than Milanković-scale cycles, they, in effect, allow for
chronostratigraphic control in alluvial strata (McCarthy and Plint 1998, 2003; Plint
et al. 2001).
When fluvial systems are in equilibrium, paleosols in adjacent areas are not
provided with any significant new sediment supply, outside arid and semi-arid areas
where aeolian deposition may dominate. During this time, climate is the predomi-
nate influence across the landscape and the result is the development of a mature,
complexly overprinted, or amalgamated paleosol with features reflecting the
physio-chemical processes of formation (e.g. histosols – high water tables and
organic production, vertisols – seasonal wetting and drying, aridisols – accumula-
tion of salts, etc.). More mature paleosols record longer durations over which the
fluvial regime remained in equilibrium providing for increased depth of pedogenic
alteration. When fluvial systems are in disequilibrium, one of two general scenarios
will ensue. Landscape degradation will result in the loss of alluvial plain stratigra-
phy due to increased downcutting and floodplain scavenging. Potential evidence for
the conditions that prevailed during equilibrium may be restricted to channel lag
deposits (e.g., reworked soil nodules: Pace et al. 2005) or aerially restricted sites
that were unaffected by, or resistant to, erosion (e.g., Gastaldo et al. 1998).
Conversely, landscape aggradation will result in the rapid buildup of interfluves
with a concomitant rise in watertable. These conditions promote the development
of immature and wetland paleosols (Kraus 2002).
In summary, continental landscapes can be envisioned as existing within one of
three different states at any point in time during their histories – degradation, aggra-
dation, and equilibrium (stasis). During degradation, fluvial systems are downcut-
ting, removing previously deposited material or bedrock because of excess stream
power. The regional water table will follow the downcutting, and floodplain sedi-
ments that may have been stored under saturated or submerged conditions will be
subject to deeper drainage, infiltration, and more oxidizing conditions. During
aggradation, fluvial systems deposit material, filling up potential accommodation
in order to increase the gradient to a point that is adequate to carry the bedload that
is available. Once this gradient is reached, the fluvial system is in a state that will
carry the bedload provided. As the system aggrades, the regional watertable will
rise with the increased elevation of the fluvial/overbank system. Previously depos-
ited channel-fill and floodplain sediments will be buried below this rising water
table and will be cut off from further connection to vadose-zone weathering and/or
oxidation. If this aggradation is taking place within a valley cut during a previous
period of degradation, the fluvial/overbank system will have to first fill the confined
space within the valley before being able to aggrade the regional landscape surface.
This initial period of valley filling may produce a landscape that has both well-drained
oxidized soils on interfluve areas and poorly-drained areas with relatively wet
edaphic conditions within the incised valley. Since only the valley floor is available for
aggradation and storage of channel-fill and overbank material, relative sedimentation

rates may be high while the valley topography is annealed. The volume of valley
accommodation also may increase because of lateral retreat of the valley walls due
to cutbank erosion, slope wash, and mass-wasting during aggradation. If the poten-
tial equilibrium profile of the system is at a higher elevation than the interfluve
areas, the fluvial system will overtop the valley walls and will have a greater area
over which to deposit channel and overbank sediments. At this time, relative sedi-
mentation rates will apparently decrease, and there will be evidence of a related
increase in floodplain soil maturity. Systems subject to repeated or cyclic changes
in the forcing factors that control landscape aggradation and degradation (discharge,
bedload sediment supply, tectonically-controlled gradient, etc.) may have successive
valley fill and post valley-fill strata that have been subject to superimposed pedogenic
and paleohydrologic regimes. The preservation of plant-fossil assemblages with
identifiable remains within these successions will be controlled by the magnitude
and timing of these depositional and hydrological processes.
4 A Model for Plant-Part Preservation in Continental

Landscapes
The potential for encountering fossil plants within a continental framework is

related directly not only to whether or not the organic detritus accumulates within
a potential preservational site, but also whether or not it is maintained in a burial
site where pore-water geochemistry retards or halts degradation. The highest prob-
abilities for preservation exist within bodies of water in which fine-clastic sedi-
ments accumulate at rates greater than those for organic-matter decay. Conversely,
the lowest probabilities exist within subaerially exposed sites, including wetlands
(Gastaldo et al. 1989), where groundwater flux and meteoric water input vary over
diverse time scales promoting pedogenesis and carbon recycling. Hence, for plant
parts to become recognizable (identifiable) biological remains in the stratigraphic
record, they first must be confined to stratigraphic intervals where high A/S
(Accommodation/Sediment Supply) ratios prevailed. And, once buried, these
assemblages also have to be maintained at a stratigraphic level beneath the maxi-
mum draw down of the prevailing watertable to prevent subsequent decay, deterio-
ration, and loss from the sedimentary succession. Envisioned within the framework
of continental landscape evolution, there are limited potential instances where these
criteria are met in space and time.
During periods when the landscape is static and fluvial systems are in equilibrium,
plant-part preservation is confined to: (1) within channel, subaqueous deposits (CWD
concentrated in basal lags or barforms, heteromeric [admixture of plant-part types
and sizes; Krasilov 1975] hydrodynamically equivalent assemblages in barform
troughs or abandoned channels), and (2) lakes where the depth-to-bottom exceeds
the chemical and biological depth of reactivity (Fig. 3). Pedogenesis across the
interfluves and along river-and-lake margins (aquatic and semi-aquatic colonization)
Fig. 3 A model for preservation of plant assemblages in continental regimes. See text for details
promotes decay and carbon recycling, preventing preservation of all but the most
resistant aerial plant parts (e.g., palynofacies debris, palynomorphs; Gastaldo et al.
1996a). Evidence for subterranean rooting structures may be preserved depending
upon the type of vegetation or soil, and the reactivity of pore waters with entombed
organic material (e.g., drab halos, rhizoconcretions, etc.; Retallack 2001).
The onset of fluvial disequilibrium and landscape aggradation promotes sedi-
ment accumulation within the interfluves that, in turn, may bury organic litters once
residing at the soil–air interface or shallow subsurface. As incremental bedload
deposits accumulate within channels in response to discharge rates that are lower
than needed to flush the system, CWD lags may occur within various parts of barforms
(Gastaldo 2004). Incremental deposition of siliciclastics also occurs along channel
margins (levees) which respond to overbank sedimentation or avulsion with an
increase in their vertical height and lateral extent. The change in relative position
of the river’s water surface is reflected in the watertable across the interfluve, and
it ascends in the section in response to sediment buildup (Fig. 3b, c). As the
watertable continues to reestablish at a higher stratigraphic level in response to
aggradation, buried plant debris is maintained within anoxic geochemical condi-
tions that prevent decay past the state of the original organic matter when entombed.
Organic matter that accumulates at the soil–air interface within the new (primarily
wetland) landscape still is subjected to pedogenic activity and carbon recycling.
A phase of continuous aggradation without landscape degradation, accompanied
by a stratigraphic rise in interfluve watertable, will result in a sequence of stacked
fine-grained clastic deposits wherein fossil-plant assemblages will be confined to the basal
unit(s) immediately above the disconformity (previous soil horizon) if geochemical
conditions are met for potential preservation. Where semi-continuous aggradation
occurs without landscape degradation, the possibility exists, but rarely is met, for
fossil-plant assemblages to be preserved at the contact between each soil horizon and
the overlying aggradational, fining upwards sequence if subsequent aggradational
intervals accumulate rapidly (Fig. 3). These plant assemblages will be preserved pri-
marily as adpressions (coalified compressions and impressions) with carbon, lipid,
resin (if present systematically), and cuticular residua. Depending upon the timing
between soft-tissue decay and the rate of sediment influx and final entombment, casts
of axes (e.g., pith casts) also may be found (Allen and Gastaldo 2006).
Once equilibrium is reestablished across the landscape, pedogenesis again domi-
nates the interfluves (Fig. 3d). Depending upon the prevailing climate and associ-
ated distribution of rainfall over the year, deep soil alteration can occur, buried
organic matter recycled, and pedogenic concretions may form. Under more arid or
highly seasonal and restricted precipitation regimes, stable-isotope signatures
sequestered in carbonate concretions will reflect atmospheric gas concentrations
because of formation within a geochemically open system (Tabor et al. 2007). But,
carbonate concretions also may form in geochemically closed systems, wherein
stable-isotope signatures reflect bacterially-mediated decay of organic matter
within saturated soils (Tabor et al. 2007). Hence, the presence, alone, of carbonate
concretions at some depth within a paleosol may not be the sole criterion for inter-
preting prevailing climate at the time of landscape equilibrium and, hence, soil
formation (Gastaldo and Rolerson 2008). But, as long as entombed plant-part
assemblages are maintained below the stratigraphic level of deepest watertable
penetration, their preservation potential remains high (Fig. 3).
The onset of fluvial disequilibrium resulting in landscape degradation, either
through tectonic uplift or tilting, increased river discharge and/or decreased sedi-
ment supply associated with a shift in climate, or base level change, leads to valley
cutting and scavenging of the former landscape due to the downward shift in equi-
librium profile. The removal of strata and establishment of a new base profile,
resets the regional watertable (Fig. 3e). The outcome of such a regional watertable
reset exposes any previously buried plant assemblages to renewed decay processes
if they are positioned now (or at any time) in the vadose zone. Depending upon the
original grain-size, mineralogical parameters, and degree of compaction of the
entombing sediment, a number of different plant-part preservational modes may
result. For example, if non-woody plant parts originally were entombed within
fluvial sand, sediment porosity and permeability will promote complete deterioration
of the most labile organic matrix. The only remnants that may be left behind would
be unrecognizable or unidentifiable debris and “poorly” preserved axial remains,
which could be assigned to a major plant group if distinguishing morphological
characters exist (e.g., sphenopsid axes). In contrast, if the confining sediments were
fine-grained in nature, decay will result in loss of the organic matrix while retaining
the overall impression of the features of the buried plant part in the mudrock.
Impressions will be the result of sediment and organic-matter compaction within the
confining pressures of the matrix (Rex and Chaloner 1983). Plant assemblages that
remain at a stratigraphic depth below the new watertable have the potential for
continued retention in the stratigraphic record, unless landscape degradation in the
future again resets the level of regional watertable. Preservation potential for plant
parts again increases once aggradational processes begin to fill these incised
landscapes, usually resulting in wetland assemblages (Demko et al. 1998).
In summary, plant-fossil assemblages in continental regimes have the highest
preservation potential when there is a turnover from landscape degradational to
landscape aggradational processes. In systems where aggradation is continuous,
the highest preservation potential exists at the contact above the disconformity
between the degradational and aggradational landscapes and within standing bod-
ies of water. There are decreasing probabilities for the preservation of plant debris
higher in these sections depending upon the A/S ratio in effect at the time of
plant-part entry into an aquatic (fluvial or limnic) environment. In systems where
aggradation is semi-continuous without landscape degradation, the highest pres-
ervation potential exists at the contact between fining upwards intervals, each of
which can be considered analogous to a parasequence in marginal-marine set-
tings. In this case, instead of the genetically related strata being bounded by
marine flooding surfaces, they are bounded by surfaces that mark an increase in
relative accommodation rate filled nearly instantaneously by fluvial and overbank
aggradation. As a new, long-term watertable is established at the top of the strati-
graphic section in response to the buildup of the landscape, plant assemblages
maintained stratigraphically within saturated sediments are buffered from decay
and loss from the potential fossil record. When fluvial equilibrium and landscape
stasis are attained, thick mature soils form that can be used as chronostratigraphic
marker beds across the region.
5 Case Studies
The following case studies are provided as examples illustrating the basic premises
between plant-part preservational modes within the landscape model context. By no
means do these cover the full spectrum of possible scenarios over space and time.
Rather, each sedimentary basin within the range of various tectonic settings must
be evaluated independently to determine the relationships between presence or
absence of fossiliferous plant beds within stratigraphic and regional context.
5.1 Plant Assemblages in Aggradational/Degradational

Landscapes
5.1.1 Paleogene Weißelster Basin, Central Europe
The Paleogene Weißelster basin, Germany, is comprised of interfingering continental

and marine sequences, and is paleogeographically in close proximity to the paleo-
North Sea (Krutzsch 1992). The Eocene and Oligocene deposits were subdivided
by Eissmann (1970) into three stratigraphic units. The Borna beds are predomi-
nantly terrestrial and of Middle and Late Eocene in age, the Middle Oligocene
Böhlen beds are predominantly brackish-marine, whereas the overlying Middle
Oligocene Bitterfelder beds are indicative of terrestrial to brackish-marine settings.
The fluvial Borna beds (Halfar et al. 1998) consist of coarse sand and gravel, with
intercalated thick clay deposits representing oxbow lakes and wetland paleosols.
Several thick economic coals occur within the Eocene sequence, in addition to
several well preserved fossil-leaf assemblages that have been used for paleoeco-
logic (Gastaldo et al. 1998) and paleoclimatic (e.g., Mosbrugger et al. 2005) resto-
rations of central Europe.
In the Bockwitz mine near Borna, Germany, a Middle Oligocene flora is preserved
in close proximity to a Late Eocene coal – Oberflöz II – and an overlying interfluve
paleosol (Gastaldo et al. 1998; Fig. 4), which stratigraphically correlates with
sediments below the Late Eocene Oberflöz III coal in the Schleenhain mine several
kilometers to the west (Halfar et al. 1998). Taphonomic criteria (Gastaldo et al.
1996b) allow for the recognition of autochthonous floodplain assemblages,
parautochthnous channel-fill sequences, and allochthonous accumulations either of
coarse woody detritus (Gastaldo 2004) or heteromeric assemblages within trough
fills of channel barforms.
Three autochthonous plant assemblages were exposed in the mine highwall in
the early 1990s; more recently, mine reclamation has left little surface exposure of
any plant-bearing intervals. Besides the lignite bed (histosol of Oberflöz II) of
varying regional thickness, two additional paleosols occur in the stratigraphic
sequence. The first is found terminating the overlying fluvial complex, and repre-
sents the culmination of alluvial plain aggradation following peat cessation. This
Late Eocene paleosol is only a remnant of a laterally extensive, well-developed
soil that attained a thickness of at least 1.7 m. A prominent A-horizon is underlain
by a weathered and stained B interval, beneath which was a well-developed C zone
(Gastaldo et al. 1998, Fig. 4). In situ woody tree bases are preserved in the
A-horizon, with extensive and deeply penetrating roots found in the B and C hori-
zons. Clay mineralogy and major element analyses show little variance. The sec-
ond paleosol is a very thick, at least up to 17 m or more (due to missing section at
ground level), kaolinitic massive and homogenized silt of Middle Oligocene age.
Large diameter woody roots penetrate deeply throughout the interval, accompa-
nied by slickensides and other features that were used to interpret pedogenesis of
a vertisol. This soil formed across a middle Oligocene landscape characterized by
Fig. 4 An example of the effects of an aggradational/degradational landscape on plant-fossil

assemblages in Eocene-Oligocene fluvial deposits of the Weißelster Basin, central Europe.
(a) Illustration of the mine highwall based on photomosaic taken in the Bockwitz mine near
Borna, Germany (Gastaldo et al. 1998). The stratigraphic sequence, exposed above a thick Eocene
coal (Oberflöz II), consists of aspects of both aggradational and degradational landscapes that
encompass approximately 10 MY. (b) Aggradational sequences and boundaries marking the base
of degradational phases in chronostratigraphic context are isolated in a Wheeler-type diagram
depicting the relationship between the type of plant-fossil assemblage and these events. Erect, in
situ, woody trees and an organic (O) horizon are preserved at the top of a Middle Eocene land-
scape, with much of this landform removed by subsequent degradation. Exceptionally well pre-
served leaf assemblages occur only in the base of Middle Oligocene oxbow lake deposits, the
lowest meters of which were not subjected to pedogenic overprinting
the aggradation of one or more meandering fluvial regimes, each of which were
abandoned and filled as oxbow lakes. Pedogenic alteration was subsequent to
channel fill.
Identifiable parautochthonous plant assemblages only are restricted to the low-
ermost 1.5 m of Oligocene channel-fill sequences, although these probably were
more extensive (Gastaldo et al. 1996b) prior to pedogenic overprinting (Fig. 4). The
aquatic fern Salvinia is commonly interbedded with aerial leaf, branch, fruit-and-
seed remains, representing autochthonous elements within this parautochthonous
assemblage. Leaf accumulations occur as isolated leaves or clusters of leaves
(mats) on bedding planes without any preferred abiotic orientation, either solely as
impressions or inclusive of cuticular remains.
Allochthonous assemblages are restricted to channel lags as CWD above scour
contacts (Gastaldo et al. 1998; Gastaldo 2004) and within channel barforms as admix-
tures of leaf, fruit, and seed debris. Due to the grain size of these channel deposits,
ranging from medium and coarse sand to pebble conglomerate, non-woody detritus
is restricted to troughs of bedforms where most exhibit a very low quality of
preservation.
The quality, quantity, and stratigraphic position of these assemblages in the
Bockwitz mine are consistent within the context of the proposed preservation
model. Autochthonous assemblages that include erect woody trees, deeply pen-
etrating rooting systems, and differentiated soil horizons, mark intervals of land-
scape stasis and equilibrium of the fluvial regime. Phases of disequilibrium
occurred when river avulsion or fluvial reactivation occurred in response to
Alpine tectonic activity, climate change, or both. This resulted in the burial of
paleosols and overall continental aggradation in the Late Eocene (Halfar et al.
1998). Oxbow lake deposits and the plant-fossil assemblages preserved therein
were coeval with in-channel deposits of meandering fluvial systems elsewhere in
the region.
The stratigraphic hiatus recognized between the Late Eocene and Middle
Oligocene is a function of disequilibrium that resulted in landscape degradation.
The first preserved degradation event (Fig. 4) emplaced fluvially derived fine-
grained sediment above an erosional contact that removed the latest Eocene depos-
its (including Oberflöz III) and much of the Eocene autochthonous woody
assemblage. Although the base of the channel form that marks the erosional contact
occurs at places below that paleosol, the regional watertable was maintained higher
in the landscape profile. A high regional watertable prevented decay and degrada-
tion of these buried trees, forest-floor litter, and subterranean rooting structures. If
regional watertable had dropped at any time below the stratigraphic position of this
paleosol, organic matter decay and pedogenesis would have proceeded in the same
manner as that found in the overlying Middle Oligocene.
The middle Oligocene experienced renewed aggradation in the landscape, with
the emplacement of at least two stratigraphically stacked fluvial systems (Fig. 4).
Plant-fossil assemblages in coarse fluvial bedforms reflect the persistence of refrac-
tory CWD in the absence of other plant detritus, which underwent decay in oxygen-
rich waters and/or exposure of bedforms during intervals of low discharge.
Abandoned trunk channels filled with a mixture of fine-grained clastics and aerial
plant parts derived from channel margin, riparian communities (Gastaldo et al.
1989, 1996b). Stratigraphic sequences in modern oxbow lakes show a pattern of
interbedded intervals of leaf clusters (mats), representing annual leaf fall, and mud,
deposited during overbank flood events from the base of the abandoned channel to
the top of the channel fill. The Bockwitz fossil assemblage, though, is restricted to
the basalmost 1.5 m of section because of channel-fill sequence overprinting by
pedogenetic activity. The depth of pedogenic activity is marked by the contact
between the well preserved plant-fossil assemblages and the homogenized, kaolinite-
rich and root penetrated paleosol. Hence, the regional watertable at the time of
paleosol development dropped to within 1.5 m of the contact between the bottom
of the oxbow-lake channel and the underlying fluvial barforms. If regional watertable
had dropped below that level, there would have been no evidence of megafloral
remains at this stratigraphic horizon.
5.1.2 Upper Triassic Chinle Formation, Southwestern United States
The Chinle Formation in the Colorado Plateau region of the southwestern United
States was deposited in a fully continental basin along the western margin of equa-
torial Pangaea (Dubiel 1994). The bulk of the Chinle Formation consists of a suc-
cession of fluvial, lacustrine, and minor aeolian strata that fill a dynamic basin
subsiding between the old Permo-Carboniferous Ancestral Rockies Uplift to the
east and the Mogollon Highlands continental volcanic arc to the south (Stewart
et al. 1986), and separated from the Luning marine basin to the west by a back-arc
bulge (Lawton 1994). The lower part of the Chinle is dominated by volcanic-
sourced smectitic mudstone and mineralogically immature sandstone and conglom-
erate with gleysol- and aflisol-type paleosols, while the upper part has more detrital
clay, aeolian sandstone with calcisol-, and aridosol-type paleosols (Dubiel et al.
1991, Demko et al. 1998). Paleosol types, paleobiologic and taphonomic data indi-
cate that the paleoclimate during Chinle deposition was highly seasonal with
respect to precipitation, characterized as megamonsoonal by Dubiel et al. (1991).
Plant fossils are locally abundant in the lower part of the formation, including the
bulk of the described assemblages of adpressions and the cuticular remains of
gymnosperms, cycadophytes, ferns, and other plant types (Daugherty 1941; Ash
1970, 1980) and the justly famous permineralized gymnosperm log assemblages
(e.g., Petrified Forest National Park – Ash and Creber 2000; Creber and Ash 2004).
The upper part of the formation is characterized by rare fossil plant occurrences,
mostly all impressions of robust foliar material (Ash 1987).
A locality in Petrified Forest National Park in Arizona illustrates the relationship
between plant preservation, paleosol type, and timing of landscape degradation and
aggradation in the lower part of the Chinle Formation (Fig. 5). This locality, within
the Tepees area of the central portion of the park, has produced a significant number
Fig. 5 Strata of the Chinle Formation at the Tepees locality, Petrified Forest National Park,
Arizona, were deposited during two periods of fluvial aggradation separated by an episode of
landscape degradation, resulting in a 12–13 m deep valley cut into the underlying aggradational
succession. Fossil plants are preserved in the initial phases of landscape aggradation that onlap the
paleovalley walls. Fossil-plant abundance in the lower Chinle, when compared to a sparse record
in the upper part of the formation, is the result of deposition within aggrading fluvial and overbank
systems confined to paleovalleys under a hydrologic setting characterized by perennially high
watertables. SB = sequence boundary
of the fossil plants that have been described from the Chinle (Ash 1972, 1991,
2001). These strata were deposited by two periods of fluvial aggradation separated
by an episode of landscape degradation that cut a valley 12–13 m deep into the first
aggradational succession (Demko 1995a). The entire succession at the locality can
be divided into three units characterized by different depositional facies, paleosol
types, and fossil-plant taphocoenoces: (1) an initial aggadational succession
characterized by drab purplish-gray floodplain mudstones with discontinuous
coarse-grained sandstone channel-fills; (2) an aggradational valley-fill succession
comprised of light greenish-gray mudstone, and light red and brown siltstone with
climbing-ripple cross-laminated very fine-grained sandstone, and lateral-accretion
beds of fine- to medium grained current ripple cross-laminated and trough cross-
bedded sandstone; and (3) a post valley-fill succession of dark reddish brown
floodplain mudstones with moderately- to well-developed calcareous and vertic
paleosols (Demko 1995a). The light greenish-gray mudstone within the aggrada-
tional valley-fill succession preserve abundant parautochthonous and autochtho-
nous cycadophyte, fern, and other leaf material in distinct litter layers at bed
boundaries. Autochthonous coalified gymnosperm logs are preserved in the base
of, and erect, casted in situ Neocalamites trunks and leaf mats are preserved in the
upper parts of time-equivalent lateral-accretion units.
The fossil plants at the Tepees locality were preserved in the initial phases of
landscape aggradation after a period of fluvial incision and degradation. The purplish-
gray floodplain mudstones and coarse-grained sandstones below the surface of
incision, a sequence boundary, were deposited by aggradation of an avulsion-
dominated fluvial system (Demko 1995a). The floodplain mudstones are character-
ized by pedogenic features such as drab root haloes and color mottles that indicate
groundwater gleyization and fluctuating watertables associated with the aggrada-
tional succession. No fossil plants are preserved in either the partially-filled sand-
stone channel deposits or their associated levee and floodplain deposits. The
surface of incision cuts 12–13 m into these deposits. At the base of this valley cut,
this degradation surface is overlain by lateral-accretion beds of the Newspaper
Rock sandstone and associated levee and overbank wetland deposits. These units
onlap the valley walls and preserve the fossil plants noted above. The overbank
wetland deposits are characterized by meter-scale coarsening-upwards units com-
prised of greenish-gray mudstone, siltstone, and climbing-ripple cross-laminated
fine-grained sandstone. In areas near the facies change into levee and lateral-accretion
beds, the tops of the coarsening-upwards units are pedogenically modified and have
a slight reddish-gray coloration. At interfluve areas along the margins of the valley
cut, a well-developed dark reddish brown calcareous paleosol is developed on
the underlying pre-incision units. A dark red calcareous vertic paleosol is devel-
oped over the valley fill and marks the overlap of the incisional topography, a return
to unconfined fluvial and overbank conditions, and an apparent slowing of deposi-
tional rate.
As discussed by Demko et al. (1998), the distribution of coalified compression-
impressions (adpressions) and preserved cuticle of foliar plant material in the lower
part of the Chinle Formation was controlled by sedimentological and near-surface
geochemical conditions inherent to depositional settings within incised valley-fill

successions. The abundance of plant fossils in the lower Chinle, as compared to
their rarity in the upper Chinle, is the result of deposition within aggrading fluvial
and overbank systems confined to paleovalleys. Evidence from lower Chinle paleo-
sols and trace fossils in areas outside the valley-fills indicates a climatic and hydro-
logic setting characterized by seasonal fluctuations in recharge and groundwater
table (e.g., Dubiel et al. 1991; Hasiotis and Mitchell 1993). However, during aggra-
dation of the valley-fill succession, watertables in these deposits were perennially
high, as they are in modern aggrading alluvial valleys (e.g., Gallaher and Price
1966; Runkle 1985). Burial of plant material within depositional environments in
these paleovalleys (fluvial channels, crevasse splays, lakes, wetlands, and lacustrine
deltas; Demko 1995b) increased the preservation potential because reducing condi-
tions and low biological demand in these areas of high watertables (near and at the
surface), and groundwater discharge were conducive to low rates of decay. Confined
fluvial systems also have a relatively small area in which to store and deposit
aggrading material, contributing to comparatively high rates of vertical aggradation
(Posamentier and Allen 1999). Preservation potential for foliar material was dra-
matically lower in areas outside the paleovalleys during deposition of the lower
Chinle, and in upper Chinle strata overall, conditions of fluctuating and low water
tables, associated with both fluvial depositional styles (e.g., avulsion-dominated
and ephemeral streams) and increasing aridification. Only rare robust (coriaceous)
leaves and stems in areas outside channels, and permineralized wood in channels
filled with, or laterally-adjacent to, facies with abundant volcanogenic material, can
be found (Demko et al. 1998).
5.1.3 Lower Triassic Katberg Formation, South Africa
The Katberg Formation in the Karoo Basin represents deposition within Early
Triassic fluvial aggradational and degradational successions (Pace et al. 2009)
within a fully continental basin. These rocks are assigned to the Tarkastad
Subgroup of the Beaufort Group (Johnson et al. 1997), and were sourced by
sediments transported several hundred kilometers from the Cape Fold Belt (Smith
et al. 1993). The distance from the provenance and overall grade resulted in fluvial
regimes dominated by very fine, feldspathic sand to silt, with overbank interfluves
consisting of silt and thin sheet sand bodies. Pedogenic carbonate pisoliths and
intraformational mudclasts (Smith and Ward 2001) may be concentrated as lags at
the base of each erosional contact marking landscape degradation. Hiller and
Stravrakis (1984) interpreted the sandstone bodies as wide, shallow channels of a
shifting braided pattern, while Retallack et al. (2003) ascribe several climate
attributes to a variety of paleosols across the landscape. Recently, Gastaldo and
Rolerson (2008) were unable to apply the criteria proposed by Retallack et al.
(2003) to paleosols exhibiting bioturbation and pedogenic nodules, resulting in
their recognition of more wetland paleosols in this part of the stratigraphy than
previously interpreted.
Plant-fossil assemblages in this part of the sequence are poorly preserved and,
in many instances, represent impressions of the most resistant parts including sphe-
nopsid and unidentifiable axial remains. Gastaldo et al. (2005) report new collec-
tions from bedform drapes, scour-and-fill structures, and troughs within channel
barforms, and from within overbank deposits in aggradational sequences above
paleosols. Collections from Bethulie and Carlton Heights, to date, have been pre-
served in fine- to very fine sandstone matrices.
The Katberg Sandstone exposed along the N9 highway at Carlton Heights
(Fig. 6) will serve to illustrate the relationships between plant-assemblage preserva-
tion and the role of landscape aggradation and degradation. A sequence of stacked
wetland paleosols (Gastaldo and Rolerson 2008) overlie each principal fluvial
sandstone body, where not removed through subsequent erosion. Each paleosol is
comprised of silt-sized clasts. Thin, very fine-grained and rippled sheet sandstone
bodies are interbedded with the siltstone, along with isolated lenses of pedogenic
carbonate nodule lags. It is within one of the sandstone bodies that scattered, poorly
preserved plant remains occur in a megaripple trough fill. There is no apparent
order to the assemblage, with most fragmentary debris on the order of 5 cm in
maximum dimension. Impressions of sphenopsid axes, dispersed fern pinnules
(identified due to the vascular tissue having been accentuated by iron staining), and
reproductive structures are dispersed in the matrix. The poor state of preservation,
with resistant plant parts remaining solely as impressions, indicates that all soft
tissues were degraded.
The timing when these plant parts underwent degradation is important to inter-
pret the preservational attributes of the assemblage. The plant parts are allochtho-
nous, being emplaced within the bedform trough via suspension-load settling.
There is no evidence for physical abrasion of these parts that would be encountered
during bedload transport (Gastaldo 1994). If the regional watertable had dropped
following deposition, the most delicate plants (i.e., fern pinnules) would have
Fig. 6 An Early Triassic example of the effects of aggradational and degradational landscapes on
plant-fossil assemblages in the Karoo Basin, South Africa. Only poorly preserved impressions of
conducting tissues of fern pinnules, sphenopsid axes, and isolated reproductive structures remain
in overbank interfluvial deposits of fine-grained sandstone that were not removed by subsequent
landscape degradation (dashed black line). The plant debris remained beneath the watertable
established following landscape degradation, but was subjected to oxygenated pore waters resulting
in loss of the most labile tissues
decayed and been removed from the record without any evidence of having been
there. The development of impressions of isolated plant parts in the sediment is not
possible immediately following burial, due to the maintenance of pore-water pres-
sures in the matrix. Some degree of compaction and dewatering must occur before
the outlines of plant parts are imparted to the entombing matrix. Hence, plant-tissue
decay occurred subsequent to continued burial and early compaction.
The Lower Triassic Katberg Formation is characterized by marked degradational
events that removed significant portions of the stratigraphic record (Pace et al.
2009). Landscape degradation in the Katberg exposure at Carlton Heights resulted
in the removal of the paleosol and overbank sheet sandstones in the north of the
outcrop (Fig. 6). A multi-storied sand body exhibiting a braided configuration was
emplaced above the erosional contact. Stratigraphically, the preserved plant-fossil
assemblage occurs just above the lateral equivalent of this channel base. Landscape
degradation and the development of a fluctuating watertable in adjacent sediments
promoted decay of any previously buried organic matter (paleosol TOC values are
very low, £0.5%; Gastaldo and Rolerson 2008). But, because of prior early compac-
tion of the floodplain deposits, impressions of the most resilient plant tissues
remained in the fine-grained sand when volatile tissues were lost. It is probable that
subsequently introduced pore-water chemistries promoted diagenetic staining of
the remaining structural tissues, accentuating their morphologies. The near absence
of plant-fossil assemblages in the Early Triassic of South Africa can be explained
as the result of changes in regional watertable in response to landscape-degradation
events in the basin. Hence, the paucity of a plant-fossil record in this case is a
taphonomic artifact of the basin (Gastaldo et al. 2005) rather than the absence of a
terrestrial flora in response to terrestrial extinction (Ward et al. 2000).
5.2 Plant Assemblages in Aggradational Landscapes
5.2.1 Eocene Willwood Formation, Western United States
The Bighorn Basin in Wyoming, USA, is a large intermontane basin encompassing

approximately 10,000 mi2 of dominantly Cretaceous rock exposures in addition to
localized outcrops of Early Mesozoic and Tertiary successions. Part of the Lower
Eocene stratigraphy is assigned to the Willwood Formation, characterized by allu-
vial deposits consisting of vertically stacked floodplain mudrock (moderate to
strongly developed paleosols), thick, multi-storied sheet sandstone bodies (mean-
dering trunk channels), and heterolithic deposits consisting of ribbon sandstone
surrounded by pedogenically altered mudrock (avulsion deposits associated with
weakly developed paleosols; Kraus 1996, 2001; Fig. 7). Poorly developed paleosols
within their heterolithic facies indicate high sedimentation rates controlled by avul-
sion (Kraus and Gwinn 1997). In contrast, better developed and more mature soils
are indicative of low sedimentation rates on floodplains controlled by overbank
deposition (Kraus 2002). A gleyed, drab-colored hydromorphic paleosol underlies
Fig. 7 An Eocene example of aggradational landscapes in the Willwood Formation, Wyoming,

USA. Stacked poorly developed (immature) paleosols occur throughout the sequence, with inter-
spersed better developed (more mature) paleosols. Fossil plant assemblages are most common
within siltstone channels interpreted as abandoned avulsion channels within the floodplain. Kraus
and Davies-Vollum (2004) recognize four different channel-fill types. Channel-fill Types 2 and 4
may contain well-preserved leaf mats and show the least effects of pedogenic activity. Channel
Types 1 (not illustrated) and 3 rarely preserve plant debris due to pedogenic alteration of
sediments
the carbonaceous shale which, in turn, is overlain by the development of a yellow-

brown paleosol in the former sequence (Davies-Vollum and Kraus 2001). The bet-
ter developed soil types range from vertisols to Fersiallitic paleosols (no direct
equivalent in the Soil Survey Staff 2006; Kraus 2002). Spatial variation in the more
developed paleosols are suspected to be indicative of variations in regional drainage
which are linked to grain size and, hence, permeability.
Plant-fossil assemblages are common in the carbonaceous shale facies, and have
been used to reconstruct not only the paleoecological mosaic but also the paleocli-
mate of the Early Eocene (Davies-Vollum and Wing 1998). Carbonaceous shale
bodies exhibit both tabular and lenticular geometries (Wing 1984), and the plant
accumulations within display the entire spectrum from exceptionally well pre-
served (Davies-Vollum and Wing 1998) to very poorly preserved assemblages
(Kraus and Davies-Vollum 2004). The best preserved material occurs in two facies.
These are mudrock that are relatively low in total organic carbon and unaltered by
soil-forming processes, and carbonaceous shales that also are the least pedogeni-
cally altered. Both facies are interpreted as overbank-wetland deposits (Davies-
Vollum and Wing 1998; Davies-Vollum and Kraus 2001) and, more recently,
lenticular bodies have been recognized as channel-fill sequences associated with
avulsion events. Where plant debris is preserved in carbonaceous shale of a tabular
nature, Davies-Vollum and Kraus (2001) interpreted the overlying paleosols as
having formed on the floodplain during avulsions. The underlying carbonaceous

shale, then, represents forest-floor (in situ) accumulations within the distal flood-
plain. They note that conditions promoting organic-matter accumulation in this
setting require a high water table, at or above the soil surface. Such a state results
in waterlogged, anoxic conditions that may prohibit bioturbation and inhibit decay
of organic material. Hence, the maintenance of a high local (or regional) water table
during the initiation of each aggradational phase, associated with its rise in the
section during the emplacement of stacked soil horizons, resulted in preservation of
backswamp (autochthonous) debris.
Parautochthonous assemblages are found within mudrock facies interpreted as
abandoned crevasse-splay feeder channels (Kraus and Davies-Vollum 2004). These
often are overprinted by pedogenic activity in the later stages of, or following,
channel fill, as plant colonization occurs and the most recent deposits were amal-
gamated into the floodplain (Wing 1984). Based on what can be determined from
the literature, there does not seem to be evidence for the preservation of coeval litter
(O) horizons at the soil–air interface equivalent with channel-fills. Four different
categories of channel-fill successions are recognized by Kraus and Davies-Vollum
(2004) in which plant part preservation varies. Poorly preserved plant assemblages
are found in Types 1 and 3 fills (Fig. 7). In the former, decay of organic matter is
attributed to the presence of circulating oxygenated water and low sedimentation
rates, whereas pedogenesis overprints Type 3 fills and eliminates any buried organic
matter. Type 3 fills seemingly are associated more commonly with more mature
paleosol horizons (Kraus and Hasiotis 2006), resulting in the greater depth of pedo-
genic alteration and soil modification. The depth of root penetration and soil modi-
fication ultimately are controlled by variations in local watertable. Type 2 fills
(Fig. 7) contain lenticular carbonaceous shale that preserves leaf mats as well as
dispersed plant debris. The presence of organic-rich mudrock reflects slower sedi-
mentation rates and a change in prevailing Eh/pH conditions promoting preserva-
tion (Gastaldo and Huc 1992). Lastly, Type 4 fills are characterized by conglomerate
or sandstone basal deposits with allochthonous plant debris, and intervals of inter-
bedded mudstone and siltstone in which moderate-to-well preserved parautochtho-
nous fossils occur. Kraus and Davies-Vollum (2004) attribute the variety of fill
characteristics to the differences in local drainage conditions that followed channel
abandonment, as well as how rapidly the channel was filled. Their assemblages
display similar taphonomic attributes to those described by Gastaldo et al. (1998)
in Germany (see above). Hence, within the aggradational landscape of the Eocene
Willwood Formation, fossil-plant assemblages have the highest preservation poten-
tial when they are maintained below the prevailing watertable, either in the short
term (aggradational phase characterized by poorly developed paleosols) or longer
term (the phase during which more mature soils developed). Once the local/regional
watertable fell below the level of buried plant detritus in Types 1 and 3 channel fills,
pedogenic activity removed most, if not all traces of the remains.
The type and nature of rhizoliths preserved within these aggradational paleosols
recently have been used to identify differences in the paleodrainage of the land-
scape. Kraus and Hasiotis (2006) provide criteria to separate those soil (more
mature) types that formed under relatively well-drained from those formed under
poorly drained (immature) conditions. Iron (hematite) and manganese staining
adjacent to rhizoliths, as well as the presence of calcareous rhizoconcretions are
considered to be indicative of better drained soils (albeit without stable isotope
geochemical constraint), whereas rhizoliths in poorly drained paleosols commonly
are surrounded by goethite rims and may be preserved by jarosite (pyrite oxidation
product). Fluxes in the geochemical conditions of the soil, in response to climate,
result in the variety of preservational states of rooting structures as well as previ-
ously buried litters.
5.2.2 Upper Jurassic Morrison Formation, Western United States
The Morrison Formation was deposited in a broad, continental, retroarc basin in

western North America during the initial stages of collision- and subduction-related
tectonic mountain building processes that eventually culminated in the Sevier orog-
eny (DeCelles 2004). Demko et al. (2004) interpret the Morrison to represent two
aggradational sequences with an intervening degradational episode. The upper and
lower boundaries, and the medial bounding surface separating the two aggrada-
tional successions, were interpreted as basinwide sequence-bounding unconformi-
ties. These were generated by changes in dynamic uplift and subsidence patterns
due to hinterland tectonics and deep crust-mantle reorganization. The initial aggra-
dational episode in the Colorado Plateau region is represented by the restricted-
marine to lacustrine facies of the Tidwell Member and the overlying thick package
of low-sinuosity fluvial sandstones and associated floodplain deposits of the Salt
Wash Member. Overlying a surface marked by a widespread paleosol and minor
incision, the second aggradational succession is represented by the mudstone-prone
fluvial and lacustrine facies of the Brushy Basin Member. Paleosols, trace fossils,
and other sedimentary paleoclimatic proxies indicate that the Morrison was depos-
ited under arid to tropical wet-dry conditions (Demko and Parrish 1998; Demko
et al. 2004; Hasiotis 2004; Turner and Peterson 2004).
Even though outcrop of the Morrison Formation covers a very large area of the
Western Interior of the United States and is, in most cases, very well exposed in the
modern semi-arid climate, plant fossils are typically very rare, with the exception
of the very uppermost beds in the northern reaches of the outcrop belt in a coal and
organic-rich mudstone interval (Parrish et al. 2004). However, traces of roots, mod-
erately well-developed paleosols, a diverse and abundant soil ichnofauna associated
with socialized insects, and the abundant and diverse remains of large herbivorous
saurpod dinosaurs for which the formation is famous, indicate that the landscape
supported extensive vegetation (Demko et al. 2004; Hasiotis 2004; Engelmann
et al. 2004). The plant fossils that do occur include coniferophytes, ginkophytes,
cycadophytes, ferns, and other plants (Tidwell 1990; Parrish et al. 2004).
In a taphonomic study of fossil plants in the Morrison, Parrish et al. (2004) con-
cluded that within the bulk of the formation, surface and near-surface conditions
during deposition were such that even small fragments of carbonaceous debris were
not preserved. They attribute this relative paucity of identifiable plant remains to
oxidation in well-drained soil conditions and the relative scarcity of durable woody
vegetation on the landscape in general. The few well-preserved foliar assemblages
described by Parrish et al. (2004) were associated with wetland and marginal-
lacustrine depositional environments where watertable would have remained season-
ally high in an otherwise well-drained landscape. However, both wetland and shallow
or marginal-lacustrine settings that may have existed in overall net-evaporative
climatic settings like the Morrison basin, must have been subject to regular low lake
or watertable conditions within the realm of typical water budget fluctuations over
tens to thousands of years, reducing the preservation potential of large volumes of
organic material. Also, these types of depositional environments can only exist in the
absence of high siliciclastic sedimentation rates, also reducing the potential for quick
burial before decay or detritivory. Parrish et al. (2004) note that evidence suggests that
the uppermost Morrison strata in the northern part of the depositional basin indicate
of a less restrictive water budget, reflected not only in the type and amount of plant
material preserved, but also in the types of paleosols and other paleoclimatic indica-
tors (Fig. 8). They suggest that this may have been due to a lower overall temperature
regime in that area at that time, rather than any relative increase in yearly precipitation
as compared to the seemingly drier areas to the south.
The plant-fossil record of the Morrison Formation illustrates that even in overall
aggradational settings, preservation of identifiable remains is still intimately linked
to a balance between the A/S ratio and the maintenance of a perennially high
watertable in the area where plants either are growing or introduced into the depo-
sitional environment. Paleosol types, ichnofossils, stable-isotope geochemistry of
pedogenic and lacustrine/palustrine carbonates, and other sedimentary paleocli-
matic indicators in the Morrison indicate that even though the landscape was domi-
nantly aggrading though time, watertables were low or fluctuating (Demko et al.
2004; Dunagan and Turner 2004). Significant assemblages of identifiable plant
material are rare and only present in deposits that accumulated in isolated lows on
the landscape, near lake margins and floodplain ponds.
Fig. 8 Schematic north-south cross-section of the Morrison Formation in the western USA show-
ing distribution of sedimentary paleoclimatic indicators and foliar fossil-plant localities (After
Parrish et al. 2004)
6 Conclusions
There is no doubt that the general processes that promote preservation of a mega-
floral fossil record (or any fossil record) are restricted in space and time. Based on
actuopaleontological studies, it continues to be presumed that once plant detritus is
introduced into an appropriate depositional setting, the chances for its preservation
and retention in the stratigraphic record are high (which is not necessarily the case).
This assumption is particularly true if the debris is buried rapidly, entombing it in
a sedimentary package. Hence, when these environments of deposition are encoun-
tered in a basin without evidence for terrestrial plants, catastrophic perturbation
often has been invoked to explain their absence. In other words, the lack of a plant-
fossil record in a particular stratigraphic interval is considered to be more a function
of ecosystem reorganization, extirpation, or extinction than the mere fact that pre-
vailing conditions at the time of sediment accumulation were outside of the preser-
vational window. In reality, without an understanding of the plant taphonomic
attributes within the sedimentological and regional/basinal context, the absence of
a plant-fossil record may be either a function of (1) sediment supply, attendant
geochemistry, and climate preventing preservation at the onset; or (2) the interac-
tion of landscape and climate, over the short (millennial) and long (lakh to millions
of years) term, rather than extirpation or outright extinction.
Sediment deposition within continental landscapes, regardless of their geo-
graphic position, is a function of disequilibirum within the fluvial (graded) profile
across the drainage system(s). Aggradational landscapes that form adjacent to river
systems in disequilibrium are characterized by wetland (histosols, entisols, gleyed
soils) and moderately drained soil types. Plant-fossil assemblages have the highest
preservation potential in settings that are maintained below the maximum draw
down of the regional watertable (e.g., channel barforms, abandoned avulsion chan-
nels, oxbow lakes, other limnic regimes, etc.). Under normal circumstances, plant
debris that accumulates at the air-soil interface is recycled even when buried by
overbank flood deposits due to the re-establishment of the regional watertable and
exposure to oxygenating interstitial conditions. Preservation potential only increases
when this O-horizon is displaced to a stratigraphic position some distance below
the prevailing water table, and is maintained under geochemical conditions that
retard or eliminate autocatalytic, bacterial, or detritivore activity (Fig. 2). Hence,
the highest fidelity plant-fossil assemblages are preserved within aggradational
landscapes above each disconformity (marked by a soil profile).
When fluvial systems are in equilibrium, the landscape is static providing suf-
ficient time over which pedogenic features indicative of mature soil types form
(e.g., thick O-horizons in histosols, well-developed Bk or K horizons in calcisols,
etc.). Similar to aggradational landscapes, the highest preservation potential for
plants exists in subaqueous environments (permanent standing bodies of water)
when climate variables result in evaporation exceeding precipitation, and within
peat mires/bogs when precipitation exceeds evaporation (and a perched watertable
prevents or retards drainages; Gastaldo, 2010). In most instances where the landscape
is controlled by high evaporation rates under a dry or seasonally dry climate, there
is an improbable chance for plant-part preservation anywhere in that landscape
(although vertebrate assemblages often are preserved under these conditions).
Deep penetration of pedogenic processes and drying by atmospheric gases results
in organic matter disintegration. Preservation potential exists only for those
materials existing below the level of deepest pedogenic penetration. Similarly, and
although it may seem counterintuitive, in most instances where the landscape is
controlled by high precipitation rates under a humid or everwet climate, there is a
low chance for plant-part preservation in the landscape. This is because sediment
that would have been available for transport out of the landscape is sequestered in
soils by the rootstocks of dense vegetation. The perception of muddy rivers in
Recent tropical regimes is a function of human agricultural and silvicultural
activities (e.g., Staub et al. 2000).
Sediment removal within continental landscapes, again regardless of their geo-
graphic position, is a function of disequilibrium within the fluvial profile across the
drainage system(s). Degradational landscapes are characterized by fluvial incision,
sediment excision and re-entrainment of interfluvial deposits, and transport of these
materials, along with any previously entombed organics, to a depositional site
below the new base level. Fluvial incision resets the relative position of the water
table in the “new” landscape in a stratigraphic position below its previous height.
As such, watertable fluctuations in response to whatever prevailing climate now
operating in the region will result in the re-exposure of once buried organic matter
to renewed biogeochemical processes which, in effect, will remove all traces of
organic residuum that may have been present originally.
The long-term fate of buried organic matter and the size of the sediment clasts
in which it was entombed controls the ultimate preservational mode (Schopf 1975)
of fossil-plant material collected in the field. Compressions, where a coalified resid-
uum exists on the bedding-plane surface, are the result of plant debris buried within
aggradational landscapes wherein the subfossil assemblage was maintained below
the prevailing and subsequent water table(s). Devolatilization and depolymerization
leave a residuum of the most refractory chemicals surrounded by matrix. The external
impression (mold) of those plant parts is best developed in fine-grained matrices
(clay and silt-sized clasts), whereas the fidelity of the impression decreases with an
increasing clast size. When both the compression and impression of the original
plant remains exist, this preservational mode has been termed an adpression (Shute
and Cleal 1987). Impressions, where there is no evidence of an organic residual on
the bedding plane, are the result of organic decay following early diagenetic com-
paction by burial. There would be no transfer of plant morphology to the sediment
without a decrease in pore space within the entombing matrix. Hence, for such a
transfer of morphology to exist, pore space must have been reduced through burial
at some depth less than that required for lithification. But, the removal of all organic
residuum from the matrix requires that active decay processes (or thermal heating
in response to tectonic activity) were reestablished prior to cementation. Such
processes occur when landscapes are static (equilibrium) or when the landscape has
been degraded. The larger the size of the entombing clasts, the higher the probability
that once buried plant debris, now exposed to oxygenating waters under a reset
watertable, will be removed from the stratigraphic record. Other preservational
states of plant material, including permineralization, pyritization, replacement,
etc. can be explained as a function of changing geochemical groundwater-solute
concentrations and conditions, and have the potential to occur under all landscape
phases.
Acknowledgments Support for RAG includes: a Forschungspreis from the Alexander von
Humboldt Foundation for studies in the Weißelster basin, Germany; NSF EAR 0417317 and a
Mellon Foundation grant to Colby, Bates, and Bowdoin Colleges for research efforts in the Karoo
Basin, South Africa; and NSF EAR, ACS PRF, NATO, and other agencies for plant-taphonomic
investigations in the southeastern U.S., Kalimantan, Indonesia, Sarawak, Malaysia, and central
Europe. Support for TMD includes: NSF EAR 9305087, USGS-NPS Interagency Agreement
1443-IA-1200-94-003, Chevron, Colorado State University, and the University of Minnesota
Duluth.
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Chapter 8
Hierarchical Control of Terrestrial Vertebrate
Taphonomy Over Space and Time: Discussion
of Mechanisms and Implications for Vertebrate
Paleobiology
Christopher R. Noto
Contents
1 Introduction........................................................................................................................... 288
1.1 Top-Down Versus Bottom-Up Controls on Terrestrial Taphonomy............................ 288
1.2 Hierarchical Integration of Terrestrial Vertebrate Taphonomy.................................... 291
2 The Structure of Vertebrate Bone......................................................................................... 292
3 The Terrestrial Taphonomic Hierarchy................................................................................. 293
3.1 Microscale Processes................................................................................................... 295
3.2 Mesoscale Processes.................................................................................................... 301
3.3 Macroscale Processes.................................................................................................. 305
4 Large-Scale Spatio-Temporal Controls Over Taphonomic Processes.................................. 308
4.1 Geophysical Dynamics................................................................................................ 308
4.2 Atmospheric Carbon Dioxide...................................................................................... 310
4.3 Orbital Cycles in Solar Energy.................................................................................... 310
5 Implications for the Terrestrial Vertebrate Fossil Record..................................................... 311
5.1 The Existence of Terrestrial Megabiases..................................................................... 311
5.2 Examples of Changing Taphonomic Regimes Over Time........................................... 314
6 Implications for Vertebrate Paleobiology............................................................................. 319
6.1 Changing Patterns of Species Diversity....................................................................... 319
6.2 Model of Diversity Gradients and Climate Change..................................................... 320
7 Summary and Conclusions................................................................................................... 323
References................................................................................................................................... 324
Abstract There is no doubt among paleontologists that the fossil record of terrestrial
vertebrates is fragmented and unevenly distributed over space and time. The underlying
causes of this patchiness derive from a combination of factors occurring before and
after the deposition of vertebrate remains. Large-scale vertebrate fossil distribution
patterns present challenges in addressing the effects of small-scale taphonomic pro-
cesses on distribution patterns, and what, if any, effect they may have on biodiversity
reconstructions. This chapter presents a hierarchical model connecting small-scale
taphonomic processes and large-scale fossil preservation patterns. Factors acting at
C.R. Noto (*)
Department of Biomedical Sciences, Grand Valley State University, Allendale, MI 49401, USA
288 C.R. Noto
higher levels in the hierarchy constrain the range of taphonomic processes acting at
lower levels, whereas lower level processes are responsible for determining vertebrate
preservation and the resulting fossil record for an area. Secular changes in climate,
tectonics, sea-level, etc. alter the distribution of both environments and biodiversity
over time. These changes in turn may alter the congruence between standing biodiver-
sity and the fraction of that diversity faithfully represented in the fossil record, skewing
our understanding of extinct vertebrate ecosystems and their evolution over time.
1 Introduction
The growth of terrestrial taphonomic science requires not only developing new ana-
lytical tools and techniques, but expanding the scope of research questions into new
theoretical territory. Research conditions are rapidly changing as the development of
large online databases allow for the compilation of data from a variety of sources into
common, searchable formats (Alroy 2003; Barnosky and Carrasco 2000; Rees and
Noto 2005). This development provides an unprecedented resource for studying the
taphonomy and paleobiology of terrestrial vertebrates, particularly the ability to analyze
regional and global patterns of fossil distribution. The potential for discovering and
analyzing large-scale patterns in fossil distribution has been discussed for decades
(Behrensmeyer et al. 2000), yet it remains to be explored how taphonomic factors,
acting over multiple scales, interact to influence spatio-temporal preservational pat-
terns of vertebrates. Martin (1999) proposed that many taphonomic processes follow
a hierarchical organization (Rule 19, p. 391), though uncertainty remains about the
strength of interaction between different levels. This concept has yet to be compre-
hensively explored in terrestrial systems, least of all its effect on vertebrate preserva-
tion and interpretations of large-scale patterns in fossil distribution.
1.1 Top-Down Versus Bottom-Up Controls on Terrestrial

Taphonomy
In ecology, the processes structuring ecosystems or communities can be described

as being exerted from the “bottom-up” or “top-down”. Bottom-up refers to lower-
level inputs (resources) exerting control over higher-level processes (community
dynamics), whereas top-down control is where the structure of lower levels (such
as species diversity) depends on processes acting at higher levels (predation or
environmental disturbance) (Begon et al. 2006). Taphonomic processes and their
effects on the fossil record also can be approached analogously, as suggested by
Martin (1999). In this case, top-down processes restrict the range of taphonomic
conditions that can act on remains prior to and following fossilization. Bottom-up
processes act at the level of an individual carcass or bone in response to higher-
order restrictions, producing the fossil record for an area and influencing our view
of fossil distribution at that time (Fig. 1).
8 Terrestrial Vertebrate Taphonomy Over Space and Time 289
Fig. 1 The role of top-down and bottom-up processes on the terrestrial vertebrate fossil record.
Large-scale conditions (see text) influence the range of taphonomic modes available in a given
local environment. Generally favorable (+) or unfavorable (−) taphonomic modes drive the prob-
ability of preservation at small scales. The combination of preservation patterns at smaller scales
form the taphonomic filters responsible for creating the fossil assemblage for a given time and
place. The various fossil assemblages available for study inform our view of life on Earth during
the time period in question
Climate, tectonic activity, and solar energy input exert top-down control over
taphonomic processes through driving the distribution of different environments
and the conditions that preserve or destroy vertebrate remains. Rogers (1993) sug-
gested that the tectonic regime alone controls vertebrate fossil-accumulation pat-
terns and therefore would affect paleoecological interpretations. This may be true
in certain regions, especially in tectonically-active areas that experience aggrada-
tional–degradational cycles. However, climate appears to be the more important
factor. Fiorillo (1999), in a review of fossil sites from the Late Cretaceous Foreland
Basin of western North America, found that while regional tectonism did play a
role, climatic influence was paramount in the formation of the area’s vertebrate
fossil record. Many studies across terrestrial vertebrate taxa have noted relation-
ships between the distribution of fossils at local scales and regional-to-global cli-
matic and biogeographic patterns (Benton 1985; Fastovsky 1987; Graham et al.
1996; Lehman 1997; Markwick 1998; Barnosky et al. 2003; Engelmann et al. 2004;
Rees et al. 2004). Preservation patterns also vary over time in response to climate
change. Millennial-scale climate changes due to plate tectonic movements and
Milankovitch oscillations shift prevailing global climate patterns, altering not only
environments and the distribution of species, but the distribution of taphonomic
290 C.R. Noto
modes. Loope et al. (1998) and Brain (1995) found that periods of fossil assemblage
formation in very different environments (eolian and cave, respectively) coincided
with distinct climatic shifts towards greater precipitation, which created sedimentation
events favoring vertebrate burial and preservation. Outside of these intervals the
vertebrate fauna went largely unrecorded. Therefore, large-scale processes determine
when and where preservation may occur at smaller scales by constraining local
environmental conditions and taphonomic modes.
Bottom-up control is a product of local environmental conditions and includes
small-scale processes such as necrolysis, biostratinomy, and diagenesis acting on
individual remains within depositional settings, creating the taphonomic modes that
drive preservation (Table 1). The sum of these processes over time contributes to
Table 1 Terrestrial depositional environments that contribute to the vertebrate fossil record and
some of their important taphonomic attributes. Based on information found in Behrensmeyer and
Hook (1992)
Depositional environment Vertebrate occurrence Taphonomic characteristics
Poorly-drained Present Heavily vegetated; high water table;
floodplain reducing soils; sometimes acidic;
fine-grained sediments frequently
deposited
Well-drained floodplain Present Less vegetated; variable water table;
well-developed, oxidizing soils;
sometimes acidic; infrequent
sedimentation; bioturbation
Eolian (dune, interdune, Uncommon Fine-to-coarse grained sediments; dry
loess) conditions; periods of rapid burial
Lacustrine Common Range of productivity, sedimentation,
temperature, chemistry, and oxygen
content
Fluvial (channel lags, Common Low-to-high energy; rapid burial;
bars) hydraulic transport and sorting
Abandoned channel fill Common Fine-grained sediment; abundant clays;
organic-rich
Crevasse splay Variable Coarse-grained sediment; rapid burial;
hydraulic transport and sorting
Levee Uncommon Heavily vegetated; well-drained, fining-
upward sediment; soil development;
bioturbation
Springs Common Fine-grained sediment; vary in
temperature and mineral content;
bioturbation
Tar seeps Very common Excellent preservation; vertical mixing;
geologically unstable
Karst (caves, sinkholes, Very common Natural sediment traps; subject to
fissures) lacustrine and fluvial influence;
geologically unstable
Volcanigenic (mudslides, Uncommon Excellent preservation; mass death;
ashfall) rapid burial; alter chemistry; climate
independent
the formation of fossil assemblages, the composition of which may differ because
each mode has its own associated set of biases (Behrensmeyer and Hook 1992).
Studies of vertebrate decomposition and diagenesis following burial provide evi-
dence that short-term, environment-dependent processes are vital in determining
the long-term preservation potential of vertebrate remains (Andrews 1995; Bell
et al. 1996; Fernández-Jalvo et al. 2002; Berna et al. 2004; Nielsen-Marsh et al.
2007; Noto 2009). The distribution of environment types determines what part of
the original biological signal is preserved, exerting a well-known filter over the
fossil record that may persist at larger scales, contributing to large-scale spatio-
temporal patterns of vertebrate fossil distribution. Behrensmeyer and Hook (1992)
note that the distribution of various taphonomic modes through time likely reflects
the sum of environmental variation at regional-to-global scales; referred to here as
a taphonomic regime. Such variation in taphonomic regimes likely drives tapho-
nomic megabiases, the existence of which is recognized, although they remain
poorly understood (Behrensmeyer and Hook 1992; Behrensmeyer et al. 2000).
1.2 Hierarchical Integration of Terrestrial Vertebrate

Taphonomy
In order to aid the development of new tools and techniques in the study of terres-
trial vertebrate taphonomy, any hierarchical framework should take into account the
complex relationship between Earth system processes (including climatic and tec-
tonic processes), ecological and evolutionary responses of the biosphere, and the
resulting vertebrate fossil record.
The following sections explore some of the prominent processes acting in the
formation of the terrestrial vertebrate fossil record at different spatial scales. Thus
providing a context and timeframe through which these processes may act and the
degree to which they may be influenced by factors at other levels of the hierarchy.
The purpose is not to examine every possible process that may occur, as many
extraordinary examples have been documented that may not represent the typical
pathway of fossil formation (Dal Sasso and Signore 1998; Chin et al. 2003;
Channing et al. 2005; McNamara et al. 2006; Schweitzer et al. 2007). The focus
when discussing taphonomic processes will be on the production of body fossils
through bone preservation. Because widespread soft tissue preservation in terres-
trial settings is relatively rare, it will not be discussed in detail here. For reviews see
Martin (1999) and Schweitzer et al. (2007).
This chapter is organized into five main sections. The first section presents a
brief overview of vertebrate bone and how it is affected by taphonomic processes.
The second section is an overview of a proposed taphonomic control hierarchy for
terrestrial vertebrates. The third section deals with the connections between these
hierarchical levels and the major factors constraining processes at each level.
Possible effects of the taphonomic control hierarchy on the fossil record over time
and paleobiological patterns reconstructed from the fossil record are discussed in
292 C.R. Noto
the final two sections. Finally a conceptual model is proposed for approaching
changes in the fossil record brought about by environmental change.
2 The Structure of Vertebrate Bone
The interplay between osseous tissue properties and taphonomic processes is often
underappreciated, even though such knowledge allows for better prediction of a
bone’s “behavior” following organismal death. Bone is a general term that describes
a group of biologically-derived materials that use the mineralized collagen fibril as
a fundamental element in its construction (Weiner and Wagner 1998). Bone has
three main constituents: a close-packed framework of collagen fibrils, layers of
carbonated apatite crystals packed in the spaces between fibrils, and a “cement”
consisting of mucopolysaccharides, glycoproteins, lipids, carbonate, citrate,
sodium, magnesium, fluoride, and water (Weiner and Wagner 1998).
The carbonated apatite crystals found in bone and teeth (bioapatite) have the
general chemical composition of Ca10(PO4)3(OH)2, with carbonate making up 5–6
wt% (Pasteris et al. 2004). Often F− or Cl− ions substitute for OH− in the crystal
lattice. Various authors refer to bone mineral as hydroxyapatite, hydroxylapatite,
frankolite, or dahllite. However compared to the geologic standard, bioapatite
demonstrates several characteristics setting it apart as a unique mineral phase,
including extremely small crystal size (50 × 25 × 4 nm), poor crystallinity, and low
OH− content in the crystallites (Weiner and Price 1986; Weiner and Wagner 1998;
Pasteris et al. 2004). Bioapatite is most stable under homeostatic conditions in the
body. Once removed from this environment, the non-stoichiometric nature of
bioapatite crystallites makes them highly unstable and prone to alteration.
In mineralogical apatite, OH− is necessary for maintaining charge balance in
channel sites of the crystal lattice; its removal would lead to a local charge imbalance
(Pasteris et al. 2004; Wopenka and Pasteris 2005). In bioapatite local charge balance
in the channel sites is maintained through ionic bonding between collagen, which
contains many OH− groups (mainly from hydroxyproline), and the bioapatite lattice
(Pasteris et al. 2004). Sharing OH− groups leads to a strong bond that enables simple
chemical means for rapid coupling or decoupling of the mineral-collagen bond in
response to physiological needs, most likely accomplished by altering pH (Pasteris
et al. 2004). Low OH− content and poor crystallinity leads to the low buffering
capacity necessary for bone remodeling; higher OH- and higher crystallinity in tooth
enamel leads to better buffering capacity necessary for resisting acids such as those
that regularly attack teeth (Pasteris et al. 2004; Pasteris et al. 2008). This may also
explain why vertebrate teeth are more readily preserved than bone.
The structural and chemical properties of a juvenile skeleton are inherently dif-
ferent from those of adults. During early stages of bone development amorphous or
poorly-crystalline calcium phosphate is laid down and later replaced by crystalline
bioapatite (Menczel et al. 1965; Termine et al. 1967; Glimcher 1984; Grynpas and
Omelon 2007). Continued bone development involves the incorporation of more
carbonate and/or fluorine into the crystal lattice, especially during periods of bone
growth, after which it reaches a relatively constant level (Rey et al. 1991; Freeman
et al. 2001; Magne et al. 2001; Pasteris et al. 2004). During life this would serve to
further stabilize the mineral in much the same way that fluoride added to drinking
water prevents tooth decay. Juvenile skeletons are less mineralized; mineral density
increases over time as the animal matures (Symmons 2005). Through ontogeny,
ultrastructural changes within the bone also occur, representing changing metabolic
strategies and physical requirements (such as rapid increases in body size) (Barreto
et al. 1993; Horner et al. 2000; Montes et al. 2005). Therefore, the probability of
preservation of an individual may change with ontogeny, especially between early
and late life stages (Symmons 2005).
The ossified tissues of vertebrates are composed of multiple, hierarchically
arranged structures, which vary in chemistry, structure, and organization (Enlow
and Brown 1956, 1957, 1958; Weiner and Traub 1992; Aerssens et al. 1998;
Dirrigl and Frank 2001). Differences in size, shape, and internal structure among
elements exist within a skeleton and between taxa due to age, ecology, and evolu-
tionary history. For example, small, but significant chemical and structural differ-
ences exist between cortical and trabecular bone (Bigi et al. 1997; Aerssens et al.
1998). Small changes to the chemical or crystal structure of a mineral can have
large effects on its properties, altering how the mineral reacts to external condi-
tions (Bigi et al. 1997). Structurally different regions of the same bone may follow
different diagenetic trajectories. For example, the fractionation of various common
elements (Mn, Fe, Cu, and Ba) (Carvalho et al. 2004) and rare earth elements
(REEs) (Williams and Potts 1988; Trueman and Tuross 2002) differ between corti-
cal and trabecular bone tissue. A similar situation exists in the fractionation of
oxygen and carbon isotopes incorporated into bone tissue and dental enamel dur-
ing early diagenesis (Zazzo et al. 2004). Analysis of dinosaur (Pawlicki and
Bolechala 1987; Goodwin et al. 2007) and human (Lambert et al. 1983; Schoeninger
et al. 1989) compact bone show that diagenesis, as measured by elemental concen-
trations of Ca, P, Fe, Mn, and others, proceeds differentially through the vascular
canals and compact lamellae of bone due to differences in the porosity and com-
position of these tissues. Therefore, the diagenetic alteration of bone tissue is not
uniform and can vary due to environmental differences and/or the structural and
chemical properties of the tissue.
3 The Terrestrial Taphonomic Hierarchy
The description of any hierarchy requires a delineation of specific, inclusive levels

(see Martin 1999, p. 11). This model includes three major spatial levels: micro-,
meso-, and macroscale (Fig. 2). Each level in the hierarchy contains a set of associ-
ated biological, chemical, and/or physical processes that influence the preservation
potential of vertebrate remains. Conditions present at an overlying level restrict the
range of possible taphonomic processes and biogeochemical conditions acting at
294 C.R. Noto
Fig. 2 Hierarchy of terrestrial taphonomic processes and controls. (a) Macroscale: distribution of
continental landmasses, sea-level, ocean circulation, atmospheric composition and circulation,
intensity and distribution of solar radiation on the surface, and biome distribution. (b) Mesoscale:
landscape characteristics, local weather patterns, species population dynamics, biogeochemical
cycles, predation/death, and scavenging of remains. (c) Microscale: soft tissue decay, bone expo-
sure, desiccation and cracking from solar radiation, invertebrate utilization, bioturbation, nutrient
use and organic acid release by plant roots, leaching of bone mineral (B) and collagen (C), incor-
poration of exogenous ions (I) and humics (H) into bone matrix, bacterial and fungal degradation
(inset), diagenesis, and hydraulic flow of groundwater
lower levels. It should be noted that the temporal extent of some taphonomic pro-
cesses may cross more than one level of the hierarchy. This model is intended to
organize and relate the work of many different researchers and highlight important
relationships among taphonomic processes that, when considered collectively and
at higher scales, will lend insight into the importance of these factors in the preser-
vation of vertebrate remains. It is also worth noting that certain processes may
behave similarly regardless of scale (e.g., temperature).
Processes described at each level are split into two categories: those that act at
the surface and those that act in the subsurface, following a similar approach used
in marine paleontology (Kidwell 1986; Plotnick et al. 1988; Walker and Goldstein
1999; Behrensmeyer et al. 2000). Here, surface processes refer to those acting at or
near the sediment surface. Subsurface processes act beneath the sediment–air or
sediment-water interface and may be independent of and/or influenced by condi-
tions at the sediment surface, especially at shallow burial depths. Together these
two sets of processes describe a taphonomically active zone (TAZ) for the terrestrial
realm [after Davies et al. (1989) and Lyman (1994); see also “highly dynamic
mixed zone” of Behrensmeyer et al. (2000)]. Additionally, the spatio-temporal
extent of processes and the elements (e.g., molecules, tissues, carcasses, assem-
blages) interacting at each level are discussed.
3.1 Microscale Processes
Microscale processes cover spatial scales in the micrometer to centimeter range and
a temporal scale anywhere from £1 day to upwards of 100 ky. A major difficulty in
assigning specific time estimates to the duration of microscale processes results
from an inability to directly observe the processes in action. This creates uncer-
tainty about the amount of time necessary for these reactions to go to completion.
Instead, different authors have inferred the amount of time needed, using qualitative
terms such as “early” or “late” diagenesis. Still, an attempt is made to estimate the
time windows for these reactions when their activity is most prominent during
diagenesis based on indications given in the literature. Elements interacting at this
scale are molecules, cells, and tissues on both internal and external bone surfaces.
This includes the components of bone tissue (collagen, bioapatite, cells, etc.), bac-
teria, fungi, exogenous ions, and water.
3.1.1 Surface Processes
Diagenetic alteration of bone can begin almost immediately following death. Within
hours metabolic processes shut down and body cells undergo autolysis as their struc-
tural integrity deteriorates, releasing contents of the cytoplasm (organelles, etc.) into
interstitial fluid, leading shortly to soft tissue hydrolysis (Tappen 1994; Andrews
1995). In bone, autolysis is restricted to cells only; collagen and extracellular matrix
proteins (“cement”) remain unaffected (Child 1995). Within days the collagen-
mineral bond weakens, and the bioapatite begins to recrystallize into a more thermo-
dynamically stable form, beginning the transition to a composition closer to the
geologic standard and increasing overall crystallite size (Nielsen-Marsh and Hedges
1997; Berna et al. 2004; Trueman et al. 2004). These processes will occur regardless
of surface exposure, rapid burial, or submergence under water, although the extent
to which reaction rate depends on these conditions is not well understood.
296 C.R. Noto
Water is a strong limiting factor in determining the rate at which diagenetic

change and microbial degradation occurs. Large-scale and/or rapid diagenesis and
microbial attack of the remains becomes possible only when the remains are satu-
rated with water. In submerged bodies microbial attack and diagenetic alteration
to bone tissue can take place almost immediately, causing substantial damage to
histological structures and altering chemical composition after only a few years
(Yoshino et al. 1991; Bell et al. 1996; Davis 1997; Zazzo et al. 2004). At the
sediment–air interface this does not occur usually until after burial, although
archeological and experimental evidence indicates that loss of both collagen and
carbonate ions (in the form of CO2) can occur in the absence of mineral dissolu-
tion in water (Person et al. 1995, 1996). This difference between subaerial and
buried bones has been well documented in the archeological literature (Yoshino
et al. 1991; Andrews 1995), although the ability to discern between them depends
on the difference between prevailing climate and surface conditions during expo-
sure versus those below ground. When surface and subsurface conditions are
divergent, different taphonomic signatures will result; when a similar set of condi-
tions occur, such as in moist environments, the taphonomic signatures are indis-
tinguishable (Nicholson 1996).
Bacteria responsible for initiating soft-tissue decomposition are likely of
endogenous origin. As tissues hydrolyze and mucous barriers break down, bacte-
ria from the intestinal lumen proliferate and migrate to other parts of the body
through the vasculature, continuing aerobic decomposition of soft tissue; this can
occur within as little as 24 h post mortem (Dolan et al. 1971; Kellerman et al.
1976). These bacteria similarly could invade the skeleton via the vasculature and
spread intracortically through the bone vascular system (Bell et al. 1996).
Predator or scavenger action that removes large amounts of viscera and vascula-
ture may retard this type of bacterial invasion, although the removal of flesh
exposes bone to potentially destructive abiotic conditions. Some researchers have
noted that regions of the skeleton closest to the abdomen, such as the vertebrae
and ribs, can be more degraded than distal elements due to the production of
organic acids by anaerobic bacterial decomposition of soft tissue (Boddington
1987; Child 1995).
The important abiotic controls at this scale differ between aqueous and subaerial
environments. At the sediment–air interface ambient temperature, ultraviolet (UV)
radiation exposure, the amount and frequency of precipitation, and the composition
of the sediment or substrate where the remains lie, each play an important role. The
rate of most chemical reactions depends on temperature, approximately doubling
for every 10°C increase (Henderson 1987). This relationship is especially important
in determining the rate of soft tissue decay (Shean et al. 1993), collagen hydrolysis
and peptide loss in bone (Collins et al. 2002; Hedges 2002). At very high tempera-
tures, small amounts of carbonate are released from the bioapatite crystallites in the
form of CO2 and OH− ions are incorporated into the lattice (Person et al. 1996;
Nielsen-Marsh and Hedges 1997; Pasteris et al. 2004). Temperature and UV levels
are positively correlated due to their relation to sunlight: unshaded, exposed surfaces
experiencing high temperature are exposed to higher levels of UV radiation. UV
radiation is particularly damaging to organic components and is likely a leading

cause of damage to subaerially-exposed bone (Andrews 1995; Fernández-Jalvo
et al. 2002). UV facilitates the break-down of the collagen matrix by cleaving spe-
cific peptide bonds, lowering the denaturation temperature of the collagen molecule
(Sionkowska 2005).
Precipitation provides moisture that can have a variable effect on the remains:
soft-tissue desiccation (a form of natural mummification) can act to preserve
remains, while bone desiccation leads to cracking and loss of structural integrity
(Behrensmeyer 1978; Cutler et al. 1999; Trueman et al. 2004). Large diurnal fluc-
tuations in temperature and precipitation have an especially destructive effect on
exposed bone (Martin 1999). The overall effect of temperature, UV radiation, and
precipitation on exposed remains varies due to differences in latitude and seasonal-
ity; the presence of vegetation can help mitigate some of these destructive effects
(Behrensmeyer 1978; Tappen 1994; Cutler et al. 1999).
The ground surface itself plays a role in mediating the effects of the above-
mentioned factors (Shalaby et al. 2000). It can act as a reflector and/or radiator of
incoming solar radiation, increasing the temperature experienced by remains well
above that in the air a short distance above the remains. It also may extend the oper-
able time of decomposition processes by releasing stored heat after sundown.
Porous sediments with higher hydraulic flow draw moisture downwards, away from
the surface, thereby accelerating desiccation. Sediment with low hydraulic flow
retains moisture near the remains, retarding water loss. Under particular situations
when evaporation at the surface is extreme, ground water may be drawn up through
the sediment, leading to the formation of destructive evaporite minerals (e.g., gyp-
sum) in the remains (Trueman et al. 2004).
Temperature plays the largest role in driving aquatic decomposition patterns.
Under aqueous conditions, the surrounding water dulls the effect of the above factors
on submerged remains by mediating diurnal fluctuations. Higher temperatures are
associated with more rapid tissue decomposition, due mainly to increased bacterial
activity (Elder 1985; Elder and Smith 1988; Minshall et al. 1991). Oxygen concen-
tration also is important, determining the availability of the remains to macrocon-
sumers and the range of biogeochemical reactions that may occur on the remains
(Elder and Smith 1988). The more anoxic an environment, the more closed it
becomes to consumers. Water pH will play a role only in cases of very low pH,
which is unusual in most terrestrial aquatic environments. Low pH (<5) would
create acidic conditions capable of dissolving bioapatite crystallites and eroding
osseous tissues (Hare 1980).
The formation of adipocere (hydrogenated fatty acids; “grave soap”) is another
byproduct of decay commonly found in submerged or saturated environments, but
is largely absent as a decay stage in subaerial environments (Mellen et al. 1993;
Haglund and Sorg 2002; O’Brien and Kuehner 2007). Adipocere may play a role
in fossilization by preserving soft tissues and/or the three-dimensional arrangement
of skeletal elements through encouraging early calcium carbonate mineralization
(Berner 1968; Martill 1988). Little work has been done to understand these mecha-
nisms, making it an area ripe for experimental work.
298 C.R. Noto
3.1.2 Subsurface Processes
The processes that occur after burial have received far less attention, despite the
fact that diagenesis only begins at the surface. At least over the short-term
(months to years), burial can offer protection from some of the destructive surface
processes described above, such as direct UV radiation, significantly hindering
their effect (Behrensmeyer 1978; Andrews 1995; Martin 1999; Trueman et al.
2004). Once buried, many of the same processes described for surface exposure
continues, however the intensity with which they occur and the factors that control
them change.
Living plants affect buried remains through both physical and chemical means.
Roots physically infiltrate bone, sometimes causing large cracks and opening the
interior to destructive agents. Roots are also capable of chemically digesting bone
as the plant seeks out nutrients and minerals, with the type of attack and its extent
varying depending on the species and community composition (Henderson 1987;
Berner et al. 2004).
Given the highly unstable nature of bioapatite crystallites in the absence of physi-
ological maintenance, it is perhaps more relevant to ask why bioapatite crystals do
not spontaneously dissolve upon death (Berna et al. 2004). Loss of the stabilizing
presence of a strong mineral-collagen bond opens the crystallites to undergo further
alteration by reacting with available pore water. This is accomplished through the
processes of dissolution (preferential loss of less thermodynamically stable crystal-
lites) and recrystallization (crystallites defer to a more stable state, usually incorpo-
rating exogenous ions) (Nielsen-Marsh and Hedges 1997). These two processes are
by no means mutually exclusive, and may be described more accurately as end-
members of a continuum in which ions are lost and gained between the crystallites
and surrounding pore water. The relative difference between rates of ionic loss or
gain determines the prevailing alterations to the bone. This leads to the change in
mineral identity from bioapatite to a more stable apatite phase, usually through the
uptake of F and CO3 (Hedges 2002) and Fe and Si (Johnsson 1997). The degree of
alteration to bioapatite crystal structure and chemical composition is considered a
relative measure of diagenesis in the bone. At this stage the stability of the bone
mineral (i.e., its propensity to dissolve and recrystallize) is controlled by the pH, Eh
(redox potential), and ionic concentration of the pore water.
It is unknown to what degree the intimate relationship between collagen and
bioapatite influences decomposition dynamics, including whether collagen or min-
eral loss must occur first for diagenesis to proceed. Some authors propose that col-
lagen protects the mineral component from significant alteration until its removal
(Person et al. 1996). However, the bulk of empirical data supports the opposite sce-
nario, in which bioapatite crystallites and inorganic matrix protect the collagen from
immediate microbial attack (Yoshino et al. 1991; Collins et al. 1995, 2002; Nielsen-
Marsh et al. 2000; Pfretzschner 2004). Collins et al. (1995) proposed that the intra-
crystalline spaces of the mineral fraction are too small for microbial enzymes to
penetrate, effectively forming a barrier to everything but water. Under this model
collagen loss is controlled mainly by hydrolysis and temperature, with microbial
digestion playing a secondary role until significant mineral loss has occurred.
While the presence and activity of microorganisms (bacteria, fungi, and proto-
zoans) is an accepted tenet of organic decay, the role they play (especially bacteria)
in diagenesis is less clear. Several species of collagenase-producing bacteria and
fungi are known from archeological bones (Child 1995). Both archeological and
experimentally manipulated bones from a variety of species and environments,
covering timescales over 1–40,000 years, show clear evidence of bacterial and
fungal attack (Hackett 1981; White and Hannus 1983; Piepenbrink 1986; Yoshino
et al. 1991; Child 1995; Hedges et al. 1995; Bell et al. 1996; Davis 1997; Trueman
and Martill 2002; Jans et al. 2004). Zones of microbial attack, known as micro-
scopic focal destruction (MFD; Hackett 1981), are observed readily within compact
bone, usually within and surrounding osteons, and consist of individual tunnels or
honeycomb-type structures 0.1–10 µm in diameter (Yoshino et al. 1991; Bell et al.
1996; Jans et al. 2004). These structures hasten collagen and mineral loss by exposing
more internal surface area to dissolution and leaching (Jans et al. 2004 and references
therein). Avascular bone will be less susceptible to this kind of attack, due to the
lack of routes permitting access to the bone interior (Nicholson 1996).
The overall proportion of bone microstructure attacked appears relatively small
and the overall number of collagenase-producing microorganisms isolated from
bones and surrounding soil is low (Child 1995). Some authors conclude that bio-
degradation plays only a minor role in collagen loss and bone degradation, the
main control instead being abiotic conditions (Child 1995; Collins et al. 1995;
Pfretzschner 2004). Alternatively, the incidence of MFD in fossil bones is minimal
or nonexistent compared to archeological specimens, where ~50% exhibit exten-
sive bioerosion of histological structures (Hedges et al. 1995; Trueman and Martill
2002; Chinsamy-Turan 2005). This difference between fossil and archeological
bone suggests that bioerosion is an important determinant of bone preservation
and must be prevented altogether, or halted in its earliest stages, by environmental
conditions for the specimen to be fossilized (Trueman and Martill 2002). However,
microbial activity alone cannot account for all collagen loss during diagenesis,
especially when original histology is preserved, indicating collagen loss in bone is
controlled by a separate process (Hedges et al. 1995). Therefore, bioerosion rep-
resents an early stage of diagenesis that will lead to rapid deterioration of internal
structure unless quickly halted. But, over longer timescales collagen loss is con-
trolled by abiotic factors, such as gelatinization rate (Trueman and Martill 2002;
Pfretzschner 2006).
Others workers have suggested that fossilization cannot proceed without bacte-
rial activity. It has been experimentally shown that bacteria are necessary for authi-
genic mineral deposition within bone (Daniel 2003; Carpenter 2005). Soil-derived
bacteria recently have been shown to mediate CaCO3 mineralization as a byproduct
of their metabolism and it is thought this property may be common to many soil
bacteria (Lian et al. 2006; Barabesi et al. 2007). Archeological bone sometimes is
observed to contain additional mineral deposition lining the walls of bone tissue
presumably damaged by bacterial activity (Yoshino et al. 1991). These mineral
deposits are noted for having different properties from surrounding bone tissue but
few have been recognized to have bacterial origins. These most likely represent the
initial stages of mineral precipitation (see Daniel 2003).
300 C.R. Noto
Given the breadth of environments covered in taphonomic studies, it is more

likely that conditions present in the burial environment are regulating which fraction
of the osseous tissue – organic or mineral – is degraded and/or removed first.
Therefore, as a general precondition, degradation in at least one fraction must occur
in order for diagenesis to proceed. As diagenesis proceeds, especially in the early
stages, bone porosity initially increases as collagen is lost, with the intervening
spaces filled by the mineral as it recrystallizes and increases in size (Hedges and
Millard 1995; Hedges 2002). Where pore-size distribution shifts to larger diame-
ters, a greater surface area is opened to reaction, facilitating mineral loss through
diffusion to the pore water. This process appears to take place over a timescale of
hundreds to a few thousand years. Environmental settings that inhibit this initial
precondition will delay the onset of diagenesis and potentially act to stabilize the
remains against future destructive change from geochemical and/or biological
agents. Binding of collagen with humic substances released from decaying plant
matter can stabilize collagen against hydrolytic loss and biodegradation (Collins
et al. 2002). Clay minerals may have anti-enzymatic properties that could prohibit
many types of biodegradation (Butterfield and Nicholas 1996; see Gaines 2008 for
an alternative view of this mechanism).
Sediment hydrology is the single most important factor determining the decay and
diagenesis of buried remains, influencing numerous biogeochemical properties of the
sediment. Two factors determine the moisture regime: (i) how water moves through
a sediment, called the hydraulic conductivity; and (ii) the potential for that water to
migrate within the pores of the sediment via osmosis or capillary action, called the
hydraulic (matric) potential (Brady 1974; Retallack 1990; Hedges and Millard 1995).
Coarse-grained sediments typically have higher conductivity and lower potential,
while the opposite is true of fine-grained sediments. These two factors determine the
overall solute concentration surrounding a bone and the maximum pore size within a
bone that will be occupied by groundwater (Pike et al. 2001). Diagenesis proceeds
only when internal bone pores are in contact with water (Hedges and Millard 1995).
Osseous tissue appears to undergo the greatest degradation in high conductivity envi-
ronments, while diagenesis may be favored with increasing matric potential (Hedges
and Millard 1995; Nicholson 1996; Pike et al. 2001; Noto 2009).
The hydraulic properties of the sediment control oxygen availability, thereby exert-
ing a strong influence on the nature and depth of the terrestrial TAZ. Water movement
influences organismal abundance and activity, as highly conductive sediments pro-
vide oxygen to the large proportion of aerobic organisms residing in the sediment,
while anoxia resulting from low flow depresses biological activity. Oxygen availabil-
ity also determines the redox potential, which will determine the range of possible
chemical reactions affecting the remains and surrounding sediment (Retallack 1990).
Redox conditions, especially in submerged sediments, may be important to the forma-
tion of certain authigenic minerals such as pyrite (FeS), which are often associated
with fossilized bone (Pfretzschner 2000, 2001a, b; Leng and Yang 2003).
The effect of temperature on decay and diagenesis varies because of differences
in latitude, season, and depth of burial. Areas with little seasonal variation in tem-
perature should experience higher rates of degradation, as opposed to those places
where the ground remains frozen for part of the year (Henderson 1987). This variation
affects not only chemical reactions, but the influence of soil biota as well. Freezing
of the ground causes most biotic activity and water movement to cease.
3.2 Mesoscale Processes
While it may be easier to differentiate between micro- and macroscale processes,

the “middle ground” between them, mesoscale processes, are more difficult to
distinguish. Mesoscale processes form the bridge connecting localized biogeo-
chemical conditions with regional-level distribution patterns of preserved bone.
The spatial scale used here encompasses areas on the order of 100–104 m: a scale
that is expected to include areas subject to the same local environmental conditions
and regional climatic regime. Temporally, mesoscale processes may be more con-
strained than at other levels, covering ~1 day up to 102–103 years. Individual bones
up to whole carcasses will be affected at this level, with alterations brought about
through interactions with local biota, geomorphological features of the landscape
(including river and lake beds), and biogeochemical characteristics of the sur-
rounding sediment.
Disarticulation, skeletonization, desiccation, and bone utilization by vertebrate,

invertebrate, and fungal consumers are among the main forces acting on vertebrate
remains at the surface. In aquatic environments, fresh carcasses may go through a
well-known process of bloating, tissue decay, bone exposure, and finally disarticu-
lation (Haglund and Sorg 2002; Anderson and Hobischak 2004). The soft tissues of
a carcass often are consumed by predators and scavengers and is a well known part
of the taphonomic process, with examples reaching back into the fossil record
(Rogers et al. 2003; Spencer et al. 2003). The rate and extent of soft tissue removal
determines when and how much of the skeleton is exposed to the surface environ-
ment, with important implications for bone survival prior to and following burial
(Behrensmeyer 1978; Andrews and Cook 1985; Henderson 1987; Weigelt 1989;
Andrews 1995).
Subsequent movement by fluid transport will physically abrade and damage
exposed bone after deposition. The degree of movement is regulated by flow rate, bed
morphology, and skeletal element size, shape, density, and degree of articulation
(Voorhies 1969; Boaz and Behrensmeyer 1976; Elder and Smith 1988; Coard and
Dennell 1995; Coard 1999). Both physical transport and consumer behavior can then
lead to the selective removal and/or concentration of certain elements (e.g., limbs), age
classes, and/or species (Norman 1987; Wood et al. 1988; Lyman 1994; Martin 1999).
Following skeletonization various organisms may utilize exposed bone. Many
mammals are known to break open bones to consume the energy-rich marrow
302 C.R. Noto
within or gnaw them to obtain essential nutrients, however there is no direct evidence
of this strategy outside of Mammalia (Fiorillo 1991; Van Valkenburgh and Molnar
2002; Reisz and Tsuji 2006). If the environment contains sufficient moisture, fungi
will colonize any exposed bone, using the surface as a growth substrate while
digesting the composite matrix beneath (Piepenbrink 1986; Nicholson 1996).
Various species of insects also utilize bone, either by excavating the surface or bor-
ing into the interior, consuming the bone tissue and weakening the ultrastructure
(Kaiser 2000; Paik 2000; Roberts et al. 2007). This may also occur following
burial. In aquatic environments, bone may be colonized and consumed by verte-
brates, macroinvertebrates, and algae (Davis 1997; Haglund and Sorg 2002;
Hobischak and Anderson 2002; Haefner et al. 2004; Goffredi et al. 2005). Still,
little is known about freshwater decay processes and their consequences for preser-
vation (Hobischak and Anderson 1999).
Species identity, size, age, sex, and health at the time of death affect how the
remains respond to surface processes (Martin 1999; Behrensmeyer et al. 2003).
Species vary in the chemistry, structure, and organization of their ossified tissues,
which affects the size, shape, and density of elements. Body size determines the
surface-area-to-volume ratio of the entire carcass, and individual elements available
to interact with the environment, with smaller taxa and elements more prone to loss
and destruction than larger counterparts (Von Endt and Ortner 1984; Nicholson
1996; Martin 1999; Munoz-Duran and Van Valkenburgh 2006). Under certain con-
ditions large carcasses may decompose faster because they attract more consumers
(Hewadikaram and Goff 1991).
The age (ontogenetic stage), sex, and health of the individual at death may be
more important than size in determining decay susceptibility because of the close
relationship between these factors and bone structure. Juveniles not only tend to be
smaller than adults but their skeletons are less mineralized and differ chemically
(Symmons 2005). Reproductive status may play an important role, as the females
of many vertebrate groups utilize calcium reserves from the skeleton during gesta-
tion (e.g., egg production) and parental care (e.g., lactation, brooding, protection)
(Randall et al. 1997; Arias and Fernandez 2001; Schweitzer et al. 2005). Many of
the factors described above are also affected by individual health, but diseases that
affect the mineral density and structure of bone may contribute to loss of bone
integrity following death and can occur regardless of age (Henderson 1987).
On the ground surface temperature, precipitation, solar energy input, and sedi-
ment/soil type continue to affect vertebrate remains at the mesoscale. In submerged
environments, temperature, pH, light availability, nutrient availability, flow regime,
and sediment/substrate type play a similar role (Barnes and Mann 1991). Their
interactions, together with local geomorphology, determine the suite of flora and
fauna that forms the local community of which the remains are a part. Both the
diversity and numbers of predators, scavengers, and decomposers influence the
extent of soft tissue removal and bone tissue modification. On land surfaces foliage
can modify local conditions and provide a certain degree of protection for exposed
remains by decreasing diurnal fluctuations in temperature and moisture and/or
obscure the remains from detection. This can lead to the long-term survival of
bones on the surface in vegetated areas compared to those exposed only a short
distance away (Behrensmeyer 1978; Kerbis Peterhans et al. 1993; Shean et al.
1993; Sept 1994; Tappen 1994; Cutler et al. 1999).
The greater habitat heterogeneity a local environment supports, the larger the
number of potentially favorable microenvironments that exist to protect the car-
cass from the most destructive conditions (of course, depending on where the
animal comes to rest after death). The frequency and intensity of changes in the
local environment determines how long surface conditions last, including seasonal
changes (Dubiel et al. 1991; de Carvalho and Linhares 2001; Rogers 2005) and
episodic events such as fires, floods, or mudslides, that may occur over cycles
from decades to centuries (Watson and Alvin 1996; Loope et al. 1998; Greenwald
and Brubaker 2001). The distribution of landscape features (rivers, hills, plains,
caves, etc.) interact with local flora to control rates of sediment aggradation and
erosion over sediment surfaces, which in turn help drive burial of exposed remains
(Lyman 1994).
Mesoscale subsurface processes involve mainly diagenetic alteration of the sedimentary

body and the effects this has on the diagenesis and preservation of buried remains
(Tucker 1991; Lyman 1994). Both aquatic and ground surface sediments are altered
though a suite of physical, chemical, and biological processes that are controlled by
land surface morphology (topography), sediment characteristics (composition,
grain size) and moisture availability (precipitation, water table). Subaerially-
exposed sediments may also undergo weathering, considered a set of specific
alterations related to but separate from diagenetic processes, although significant
overlap exists (Middleton 2003). Weathering reactions play a large role in both ero-
sion and soil formation (Retallack 1990).
Physical processes acting on sediment bodies include loosening/cracking caused
by heating-freezing expansion cycles and the movement of water and gasses.
Chemical alterations result from four principal reactions: hydrolysis, oxidation,
hydration, and dissolution (Brady 1974; Retallack 1990). Hydrolysis leads to the
displacement of cations by hydronium ions, creating a new, insoluble mineral prod-
uct. Oxidation involves reactions in which electron loss forms new compounds.
Hydration includes the addition of water into the mineral structure. Dissolution is
the disaggregation of a compound into ions, a classic example being a salt cube
(NaCl) dissolving in water into Na+ and Cl−. Biotic influences on sediment altera-
tion are profound. Living organisms influence the availability of nutrients through
their life processes and alter the physical structure of the sediment profile through
bioturbation and the release of various byproducts (Retallack 1990). Many groups
of bacteria create biofilms that can significantly slow the movement of water
through sediment, altering biogeochemical conditions from those predicted by
sediment characteristics alone (Vandevivere and Baveye 1992; Baveye et al. 1998;
Battin and Sengschmitt 1999).
304 C.R. Noto
Soils and paleosols are common environments of vertebrate preservation and the
degree of soil development plays an important role in vertebrate preservation. Soil
formation is a complex process involving the interaction of climate, living organ-
isms, the nature of the parent materials, topography of the area, and time that parent
materials are subject to alteration (Retallack 1990; Schaetzl and Anderson 2005).
Over time a dynamic balance is reached between sedimentary and organic inputs
with their biogeochemical modification that may last thousands of years. These
prevailing conditions determine bulk soil properties, making them environment-
specific. Therefore, different environments can be characterized by their soils, even
long after the conditions that created them cease to exist (Retallack 1990). Over the
long-term, soil formation is affected by (i) shifts in regional tectonics, which alter
basin drainage and sediment aggradation patterns; (ii) volcanic activity, depositing
ash and altering atmospheric chemistry; (iii) changes in atmospheric or ocean cir-
culation patterns, altering precipitation patterns; and (iv) alterations in the level of
solar radiation reaching the surface (Retallack 1990; Martin et al. 1999). Over time
the evolution of the sediment profile changes preservation conditions through
alteration of the biogeochemical properties of the sediment, for example the pro-
duction of clays or iron oxides (see Retallack 1990 for detailed description of
processes; Martin 1999).
Changing sediment-moisture content causes many clay minerals, such as
montmorillonite, present in the sediment to shrink or swell, which can physically
distort or damage bones lying within clay-rich sediment. The shrink-swell cycles of
clayey sediments may cause more distortion than sediment compaction can over
time because they occur more frequently and result in movement in multiple direc-
tions, while sediment compaction is a long-term and unidirectional event
(Henderson 1987; Retallack 1990).
Sediment properties along with topography influence local hydrological condi-
tions, including the height and relative flow of the water table. Changing hydrologic
conditions over both space and time have been implicated in patterns of bone decay
and diagenesis by determining the amount of hydrologic recharge and solute con-
centration surrounding the remains (Hedges and Millard 1995). Under these conditions,
it may not be possible for bones to undergo preservative diagenesis (that is, stabili-
zation of the organic and/or mineral components) and fossilization until they are
beneath the water table, where they are buffered against rapidly shifting biogeo-
chemical conditions. The faster remains come to lie beneath the water table, the
greater their chances of preservation. A similar taphonomic model is proposed by
for plants, in which regional changes in sediment aggradation and accommodation
that lead to base level change and subsequent rise in water table are best for plant
preservation (see Gastaldo et al. this volume). Even if the biogeochemical require-
ments for vertebrate and plant preservation differ, the lower the residence time in
the terrestrial TAZ above the water table, the more likely the remains will be pre-
served. This may help explain the relative wealth of vertebrate remains from lacustrine,
palustrine, and fluvial environments, and from those settings with relatively high
water tables such as wet floodplains in close proximity to water sources that fre-
quently deposit sediment (Noto unpublished data).
3.3 Macroscale Processes
The macroscale consists of many large-scale phenomena not often considered in

studies of the vertebrate fossil record. These processes occur over spatial scales of
101–104 km and temporal scales ranging from 102–106 years. Note that the spatial
and temporal boundaries for this level fall within the resolution considered typical
for most terrestrial fossil assemblages (Behrensmeyer and Hook 1992). The leading
control at this level is the global climate regime, driven ultimately by the interplay
of plate tectonics and Milankovitch cycles altering the distribution of land area and
arrangement of continents, eustatic sea-level, atmospheric concentrations of carbon
dioxide and oxygen, volcanism, mean global temperature, and global atmosphere
and ocean circulation patterns (Behrensmeyer and Hook 1992; Martin 1999).
This complex interaction determines the distribution of biomes. Biomes represent
large regions united by similar climatic and ecological conditions, which produce
distinct assemblages of organisms (Begon et al. 2006). Because the range of tapho-
nomic processes acting within a particular area is determined by the environment
and local biota, many areas within the biome are united under a similar taphonomic
regime. The distribution of biomes and their constituent environments will influence
community composition and patterns of biodiversity. When coupled with variation
between taphonomic regimes, these will have a direct impact on how different com-
munities and species are preserved in the fossil record. The relative stability of
these factors will determine the type of fossil accumulation formed (if any at all)
and its fidelity to the original biota.
Large-scale factors control several key processes at this level. First, weathering
processes, while highly variable at small spatial scales, are coordinated regionally,
altering the land surface for thousands of square kilometers in a similar way
(Simon-Coinçon et al. 1997). Changes in weathering regime can be traced through
time and correspond to shifts in sea-level, topography, and climate. Similarly, the
distribution and morphology of water bodies and associated features are influenced
by geomorphology, tectonics, sea-level, biota, and climate (Prothero and Schwab
1996; Blum and Tornqvist 2000; Leier et al. 2005). Second, the dynamics of plant
and animal populations vary with changing abiotic conditions, which can alter the
size and location of species’ geographic ranges (Dynesius and Jansson 2000). The
expansion and contraction of species ranges over time affect the distribution of
biodiversity. For example, large-scale climate patterns have been shown to drive
population dynamics in groups of caribou and musk oxen, each separated by
more than 1,000 km of ice on the coasts of Greenland (Post and Forchhammer
2002). Because individual species can respond differently to climate change,
community assemblages change over time as new communities are created
through species reorganization (Stone et al. 1996). Third, and perhaps of greatest
306 C.R. Noto
interest to paleontologists, is the close relationship between development of Earth’s

abiotic systems and the evolution of its biotic inhabitants. The positions of conti-
nents, sea-level, tectonic activity, and climate regime have all played important
roles in the history of life, influencing the evolution and extinction of taxa. Orbitally-
driven oscillations in climate patterns have been implicated with species-range
dynamics at different latitudes, related to the amount of seasonality and environmen-
tal heterogeneity (Dynesius and Jansson 2000). These dynamics vary spatio-tempo-
rally, affecting speciation rates, speciation mechanisms, and degree of adaptive
specialization. This variation leads to differing evolutionary rates over both space, in
the form of latitudinal gradients in species richness (Wright et al. 2006), and time,
in secular patterns of global species diversity (e.g., Sepkoski 1998).
Changing climate and tectonic conditions over time can effectively alter the subsur-
face environment and establish biogeochemical conditions that promote the physi-
cal and/or chemical decomposition of organic remains. Long-term development of
the soil profile in conjunction with a lowering of the regional water table can lead
to expansion of the terrestrial TAZ, spreading oxidative conditions, bioturbation,
and consumer access to buried remains. This is most common in areas that support
high productivity and biodiversity due to relatively stable climatic and tectonic
conditions over 104–105 year timescales. Not all soil development is necessarily
destructive. Certain soil orders, such as the aridisols and mollisols, contain calcium
carbonate-bearing horizons at relatively shallow depths (~30–60 cm) (Brady 1974),
that can provide a ready source for calcite formation within the bone and/or sedi-
ment during diagenesis. Several productive fossil formations, mainly from the
Mesozoic and Cenozoic, consist primarily of paleosols at low to moderate stages of
development that were formed within seasonal or semi-arid environments (Bown
and Kraus 1981; Winkler 1983; Maas 1985; Badgley and Gingerich 1988; Downing
and Park 1998; Paik 2000; Clyde et al. 2005). As a general rule, environments that
support a greater degree of soil development lead to biogeochemical conditions
promoting organic decomposition and, in extreme cases, leaving only the most
recalcitrant remains behind (see Retallack 1990 for more extensive description).
Water and sediment availability, geomorphology, topography, and tectonic stability
influence riverbed geometry and flow dynamics. These factors affect the sinuosity and
lateral migration rate of the riverbed, as well as the size and distribution of overbank
deposits (Prothero and Schwab 1996; Einsele 2000). Highly sinuous and mobile rivers
cut into the surrounding landscape, reworking the sediment and exhuming previously
buried remains. Over time this reworking process creates time-averaged assemblages
of varying duration and composition (Behrensmeyer 1988; Behrensmeyer and Hook
1992). This process favors the preservation of more resistant skeletal elements, includ-
ing teeth and large bones or fragments within the most active of fluvial systems.
As sediment accumulates on the surface, underlying layers experience compaction,
cementation, and authigenesis as lithification proceeds (Prothero and Schwab 1996).
Since most fossil bones demonstrate some amount of structural deformation,

prolonged sediment compaction likely plays a role in this phenomenon. This distor-
tion has the potential to artificially inflate skeletal element variability and confuse
the taxonomic assignment of the remains (Wilborn 2007). Grain size, pore space,
and bone size and shape determine the extent of compaction and its effect on the
interred bone (Prothero and Schwab 1996; Smoke and Stahl 2004). Cementation
depends on the hydrology and chemistry of the ground water, but silica or calcite
typically forms the cement. Early cementation has been suggested as a pathway for
fossil preservation, especially in soft tissues (Briggs and Kear 1993; Sagemann et al.
1999). The presence of calcite within fossil bone has been implicated as a condition
favoring preservation (Holz and Schultz 1998; Fernández-Jalvo et al. 2002; Berna
et al. 2004; Wings 2004). Diagenetic concretions may even form, preserving small-
bodied and delicate taxa that would otherwise be destroyed (Downing and Park
1998). Authigenesis leads to the deposition of new or altered mineral species within
and around remains and, due to the environmental-specificity of mineral formation,
can provide a detailed diagenetic history (Bao et al. 1998; Clarke 2004).
The extent of diagenetic alteration depends on sedimentary composition, depth
of burial, temperature at depth, and the length of time the unit is exposed to these
conditions. Depth of burial is particularly important, because certain diagenetic
changes – including dewatering, cementation, recrystallization, dissolution, and
replacement – can occur at shallow depths of 1–3 km (Prothero and Schwab 1996).
The survival of fossils within the unit is contingent upon the extent of these altera-
tions, potentially destroying or rendering unidentifiable fossils that were stable at
shallower depths. It appears that plant fossils, which are far more delicate than
bone, can withstand moderate to high diagenetic processes at depths of 3.8–5.2 km
and temperatures between 150°C and 170°C (Howe and Francis 2005).
While the stability of bone apatite at different pressures and temperatures has yet
to be comprehensively studied, the diagenetic behavior of another bioapatite – from
conodonts – has been well described and may provide a useful model. Color
changes in conodont elements have been linked with an increase in the temperature
experienced by the enclosing rock, providing a relatively precise scale from low
(pale yellow, <80°C) to high (black, >300°C) temperatures (Epstein et al. 1977;
Prothero and Schwab 1996). Conodont elements contain structures homologous to
vertebrate bone (Sansom et al. 1992) and undergo a similar change in crystallite
size during diagenesis (Noth 1998). The bone of more advanced vertebrates may
react similarly and help to explain the wide diversity of colors observed in bone
from terrestrial fossil assemblages, providing valuable insight into the diagenetic
conditions experienced by the sedimentary unit.
McKean et al. (2007) hypothesized that bone color change results from geother-
mal alteration of the bone’s remaining organic content. They found that bone color
(yellowish-white to black) and organic content correlate with depth of burial if one
assumes a geothermal gradient of 27.5°C/1,000 m. This represents a promising first
step, but more work on this is certainly necessary. This relationship is relevant to
those studying rare earth element (REE) signatures in fossil bone for use in paleoen-
vironmental reconstruction, because the REE signature of conodont elements is
308 C.R. Noto
altered at high temperatures due to recrystallization (Armstrong et al. 2001). These

results could have a significant impact on environmental reconstructions that use
REE signatures of fossil bones and merits further investigation.
4 Large-Scale Spatio-Temporal Controls Over Taphonomic

Processes
Changes in the global climate regime, the ultimate causes of which are still not fully
understood, have a far-reaching impact on not only the history of life by driving
extinction and evolution, but also the fossil record, by controlling the distribution
of environments and taphonomic modes. Hence, not only do the players change, but
the stage changes as well. Within the relatively narrow temporal window provided
by many fossil occurrences, these long-term secular changes in taxa and environ-
ments play a relatively minor role in fossil assemblage formation, occurring near
the minimum resolution recordable by the fossil record (Behrensmeyer et al. 2000).
The effect of secular changes on preservation cannot be fully appreciated by study-
ing individual fossil assemblages.
Large-scale environmental changes due to changing tectonic activity, atmo-
spheric CO2 concentration, and/or insolation patterns may shift the taphonomic
window of preservation, altering the biota we are likely to recover in the fossil
record. This dynamic may explain why the fossil record can dramatically improve
or deteriorate (widen or narrow the taphonomic window) during suspected periods
of major environmental change (also see Frasier et al. this volume). Alteration to
taphonomic modes can be subtle, such as is often found with changing sedimenta-
tion rates brought about by changes in erosion patterns (Behrensmeyer et al. 1997;
Martin 1999). Changing environmental conditions may create or remove critical
depositional environments and taphonomic modes over time (Smith and Swart
2002; Retallack 2005b; Smith and Botha 2005). On the extreme end, environmental
changes behind mass extinction events may severely perturb preservation condi-
tions, leading to unusual, short-term taphonomic modes. For example, during the
biotic crisis surrounding the Permian-Triassic transition elevated volcanic activity
altered atmospheric chemistry, leading to massive plant die-offs and extensive ter-
restrial erosion that was rapid and short-lived (Huey and Ward 2005; Retallack
2005a; Sephton et al. 2005; Arche and Lopez-Gomez 2006). In all of these exam-
ples, higher-level changes were required before large-scale alterations to environ-
mental distribution and taphonomic modes could proceed.
4.1 Geophysical Dynamics
Above all, vertebrate remains must be buried before they can fossilize. Tectonic
activity, primarily uplift and subsidence, is the ultimate control of sediment erosion
and deposition. Subsidence increases basin accommodation and allows for rapid
burial, even in the absence of high sedimentation rates. Continental accretion and
mountain building affects topography and can generate regionally higher rates of
sediment accumulation in fluvial, lacustrine, and deltaic environments distal to the
uplifted area (Behrensmeyer and Hook 1992; Behrensmeyer et al. 2000). Tectonically
active periods also tend to see an increase in volcanism. Volcanoes deposit various
silica-rich particulates which, when weathered, alter sediment chemistry and provide
an important source of diagenetic materials (Behrensmeyer and Hook 1992; Downing
and Park 1998; Martin 1999). Increased volcanism may form rift valleys in zones of
continental extension, providing a basin for sediment deposition and altering the local
water table, which can create river and lake systems in valley interiors, leading to
important fossil accumulation sites (Rogers et al. 2001; Smith and Swart 2002).
Significant alterations of geomorphology that affect burial can occur even in the
absence of tectonic activity. For example, the development of continental glacial
conditions during “icehouse” periods promotes widespread eolian silt (loess) deposition,
alluvial outwash, and lake formation from meltwater over land surfaces in areas
proximal to the glacial front (Behrensmeyer and Hook 1992; Prothero and Schwab
1996). In other, more distant areas the onset of glaciations leads to a marked shift
in temperature and precipitation patterns. These environments promote burial of
remains, especially those influenced by periodic flooding from glacial meltwater.
Glacial retreat exposes new depositional basins and topographic sources for weath-
ering, and enhances erosion by altering base level following isostatic rebound.
These features create new opportunities for both terrestrial and freshwater preserva-
tion following glaciation. Glacial mass compacts any underlying non-consolidated
sediments. Over larger spatial scales, glacial formation reduces sea-level, expanding
continental area. Larger land areas support an overall greater abundance of species,
although the exact mechanisms underlying the pattern are still under scrutiny
(Rohde 1992; Chown and Gaston 2000; Storch et al. 2005). The species-area effect
has been observed to operate in the late Cenozoic for various taxa and at multiple
scales, signifying its importance in understanding paleobiodiversity patterns (Flessa
1975; Marui et al. 2004; Barnosky et al. 2005).
Continental drift transports a land surface, submitting it to changing climatic
conditions even when global climate remains stable. The effect of drift vs. large-
scale climate change can be difficult to discern from the fossil record of a particular
region if widespread fossil localities are unavailable to place the inferred changes into
a larger context. New technology, in the form of GIS software, coupled with geo-
physical models of crustal plate movement,1 allows paleontologists to reconstruct
the probable pathways and extents of regional movement over time, providing an
additional comparison between climate change and drift-induced changes (of
course these need not be mutually exclusive). If continental drift has a similar effect
on environmental distribution as climate change does, then we can expect the pre-
vailing taphonomic regime to change as a result.
1
Paleogeographic Atlas Project at the University of Chicago (pgap.uchicago.edu) and the
Paleomap Project at the University of Texas, Arlington (www.scotese.com).
310 C.R. Noto
4.2 Atmospheric Carbon Dioxide
The concentration of atmospheric CO2 is one of, if not the most, important drivers
of global taphonomic patterns because of its role in determining both global tem-
perature and biogeochemical cycles at multiple spatio-temporal scales. Two sets of
carbon cycles control CO2 concentration: (i) the short-term exchange between the
biosphere, soil, ocean, and atmosphere, operating on a 100–104 year timescale; and
(ii) a long-term exchange between the atmosphere, rocks, and ocean on a 105–109
year timescale (Rothman 2001 and references therein).
Periods of elevated atmospheric CO2 accelerate chemical weathering of silicate
rocks, providing calcium, bicarbonate, and silicon ions for the formation of CaCO3
and SiO2 in marine and terrestrial environments (Martin 1999). Changing atmo-
spheric CO2 concentrations, due to volcanism or climate change, alter the cycling
of critical elements like C, N, Ca, and P. However, the relationship is complex,
involving several coupled feedback mechanisms between terrestrial, marine, and
atmospheric sources (Igamberdiev and Lea 2006).
Carney et al. (2007) found that experimental doubling of CO2 in a forest com-
munity actually enhanced terrestrial carbon cycling instead of leading to greater
plant assimilation by altering the relative abundance and activity of soil microbes.
This discrepancy is due to differences between photosynthesis and respiration, with
photosynthesis being more temperature sensitive, placing a lower maximum
response limit to CO2 enrichment than respiration (Allen et al. 2005; Igamberdiev
and Lea 2006). In other words, an increase in atmospheric CO2 leads to relatively
minor gains in plant productivity (which will scale with size) while supporting a
much greater increase in decomposition, labile C cycling, and microbial biomass
within soils (Allen et al. 2005).
When metabolically or structurally critical elements are abundant in the burial
environment, extraordinary preservation can result, but their absence leads to exten-
sive biogeochemical recycling and subsequent destruction of remains (Behrensmeyer
and Hook 1992). Many of the extraordinary fossil Lagerstätten, such as the Early
Cretaceous Liaoning deposits (Zhou 2006), were formed during periods of high
atmospheric CO2, when perturbations to major biogeochemical cycles led to periods
of exceptional preservation (Retallack 2005b), perhaps driving tissue carbonization
as a major mode of preservation. As paleogeographic and paleoclimate models
improve, it should become possible to explicitly test changes in biogeochemical
cycles due to climate and tectonic change at varying spatio-temporal scales.
4.3 Orbital Cycles in Solar Energy
The geometry of Earth’s orbit varies over time, causing changes in the amount of solar
energy received on the surface. These Milankovitch oscillations are long-term cyclical
changes in eccentricity (100 ky period), obliquity (40 ky period), and precession
(26 ky period) (Prothero and Schwab 1996). Individually, the adjustments in orbital
geometry are small, but the combination of these cycles over millennia affect how and
where solar energy is distributed, and they have been implicated in causing periods of
rapid regional-to-global climate change (Wright and Vanstone 2001; Rial 2004).
Due to the semi-chaotic nature of Earth’s orbital geometry it is nearly impossible
to accurately project these oscillations into the distant past (>40–50 Ma) (Laskar
et al. 2004). However, the large-scale effect of changes in these values on climate
is observable in the fossil record. Some examples reach as far back as the Devonian
(Yang et al. 1996) and cover climatic responses in both the marine (Yang et al.
1996; Balog et al. 1997; Fenner 2001; Wendler et al. 2002; Gibbs et al. 2004) and
terrestrial (Olsen et al. 1991; Miller and Eriksson 1999; Retallack et al. 2004)
records. Such responses induced major changes to atmospheric and ocean circula-
tion patterns, sea-level, seasonality, precipitation, and surface temperature. Changes
in these patterns have widespread effects on continental weathering and sediment
transport (Van der Zwan 2002; and see below), and therefore the number and
distribution of depositional systems and fossil-bearing units.
Cycles in solar activity have been found to drive short-term increases (100 ky
cycles) in global temperature and CO2 release into the atmosphere (Rial 2004),
although the overall effect on global climate dynamics appears small compared to
that of orbital oscillations (Cubasch et al. 2006).
5 Implications for the Terrestrial Vertebrate Fossil Record
5.1 The Existence of Terrestrial Megabiases
Megabiases result from the combined effect of multiple, often secular, changes in
taphonomic processes controlling the destruction of remains (Behrensmeyer et al.
2000). Megabiases were first recognized and studied in the marine invertebrate fos-
sil record, foremost among them cycles of preservation and biomineralization
(Martin 1999). Together changes in these factors over time profoundly affect recon-
structions of biodiversity and macroevolutionary patterns in the marine fossil
record (Smith et al. 2001; Martin 2003; Bush and Bambach 2004). Although
Behrensmeyer and Hook (1992) noted the possibility of a megabias in the terrestrial
fossil record and recommended further research, actual research into the existence
of terrestrial megabiases similar to those found in the marine realm have yet to
infiltrate large-scale studies of the terrestrial fossil record.
When major trends in terrestrial fossil preservation are considered, they are
interpreted in light of marine trends, i.e., sea-level change as a driver of terrestrial
fossil preservation (e.g., Sereno 1997; Wolfe and Kirkland 1998). Fara (2002), in a
study on gaps in the Late Jurassic–Eocene terrestrial fossil record, found no evi-
dence that sea-level change influenced continental fossil preservation. Instead he
suggests that the marine and continental records behave independently of each
other. However, Van der Zwan (2002) found that sea-level effects on continental
312 C.R. Noto
sediment supply depend on global climate. Milankovitch cycles are more important
during “greenhouse” intervals, whereas sea-level change dominates during “ice-
house” intervals. Regardless, examining marine megabiases should lend some
insight into potential parallel patterns in the terrestrial record. The marine record
demonstrates many processes, acting at similar spatio-temporal scales and falling
under the same influences as the continental fossil record.
Long-term changes in sea-level and atmospheric CO2 lead to multiple, cascading
alterations in the habitat and sediment character of marine environments, affecting:
(i) the spatial distribution of environments, (ii) species diversity and abundance
levels, and (iii) preservation of the biotic assemblage; all these factors changing
predictably with depth (Smith et al. 2001; Martin 2003). A similar pattern exists in
terrestrial systems, where changes in the sedimentary record often are observed to
coincide with noticeable changes in vertebrate fossil accumulations (Maas 1985;
Bown and Beard 1990; Martin 1999; Smith and Botha 2005). In terrestrial environ-
ments elevation and atmospheric CO2 (a factor in long-term climate change) control
the same set of habitat and sediment character changes. These factors change predictably
with elevation: both environmental distribution and taxonomic diversity vary with
altitude (Gaston 2000) and the opportunity for burial and fossilization decreases as
one moves from low-lying areas of net deposition to elevated areas of net erosion.
The poor representation of highland environments is a well-known feature of the
terrestrial record. It has yet to be identified as a true megabias, possibly due to the
difficulty in distinguishing the effect of elevational changes from other factors
(although methods are improving). Regions experiencing increased tectonic activity
or isostatic rebound most likely are affected by this megabias.
Marine CaCO3 saturation decreases at higher latitudes as shallow waters become
cooler – the “latitudinal lysocline” – causing dissolution in CaCO3 skeletons at higher
latitudes (Martin 1999). Atmospheric CO2, tectonic, and climate changes mediate the
strength and steepness of the lysocline over time by shifting water depth and conti-
nental shelf area (Martin 1999; Pearson and Palmer 2000). Bone preservation may be
similarly controlled by the position of the Intertropical Convergence Zone (ITCZ), a
wide belt of precipitation following seasonal north-south movement cycles, which
changes in response to continental arrangement and land area (Ziegler et al. 2003).
Together these factors influence the geographic range and position of moist, season-
ally wet/arid, and arid environments in tropical and temperate regions.
The greatest extent of moist conditions in tropical and temperate regions are sup-
ported during times of high sea-level and continental divergence, forming a continu-
ous latitudinal band at the equator and two others at mid to high latitudes (Ziegler
et al. 2003). Low sea-level and continental accretion lead to greater seasonality and
aridity, reducing the size of the equatorial moist tropical zone while leaving the high
latitude moist temperate zone intact, forming a precipitation gradient extending down
to the low latitude arid zones. Predominantly moist or arid zones contain a lower
diversity of depositional environments and taphonomic modes favorable to bone
preservation (sedimentation rates, sediment biogeochemistry, biotic activity, etc.).
Intermediate regions that receive enough seasonal precipitation to support a variety of
favorable environments for preservation are more likely to form a substantial fossil
record because more opportunities for burial exist. Bone preservation in very moist
or arid regions does occur but may be more infrequent and subject to seasonal pat-
terns or other intermittent changes in climate that shift conditions towards favoring
burial and preservation (Fastovsky et al. 1997; Loope et al. 1998; Rogers 2005). It
appears this pattern has remained relatively stable through most of the Phanerozoic
because of Hadley cell circulation (Ziegler et al. 2003), with the steepness of moist-
arid gradients mediated by sea-level and continental configuration. This taphocline
has important consequences for vertebrate paleobiology, because most of what we
know about extinct life in the terrestrial fossil record comes from seasonal intermedi-
ate regions at mid-latitudes. Such a pattern has been observed in Mesozoic terrestrial
ecosystems (Anderson et al. 1998; Rees et al. 2004; Noto, unpublished data) but
remains to be studied in other vertebrate groups and other times.
Another potentially widespread cause of megabias is the evolution of vascular
land plants, whose morphological and metabolic adaptations have altered biogeochemical
cycles over time (Berner et al. 2004). This is especially true in the replacement of gym-
nosperms by angiosperms as the dominant flora is most terrestrial environments,
starting in the Cretaceous. Many studies have found distinct differences between
each group in their effect on sediment biogeochemical processes, which influences
the type of weathering regime found in the host soil (Kelly et al. 1998; Berner
et al. 2004). Significant disagreement exists as to which group promotes greater
weathering. The evidence is slightly in favor of gymnosperms, although a great
deal of variability exists between taxa (average ratio of angiosperm over gymno-
sperm weathering rate is 0.5–1.5) within each group, requiring much more work
(see Berner et al. 2004).
Geologic measures of weathering may not be as important in bone decomposi-
tion as other soil properties under gymnosperm vs. angiosperm cover. Grown in the
same conditions, soil under gymnosperms tends to be more acidic, contains less
exchangeable Ca (due to lower Ca content of leaf litter), and a lower abundance of
heterotrophic consumers (Reich et al. 2005). The low sediment pH will be more
destructive to buried bone over time than microbial or fungal activity. Each group
alters soil texture and composition differently. Gymnosperm-altered soils are more
organic-rich and sandy, while angiosperm-altered soils are more clayey and dense
(Andrews et al. 2006), affecting soil hydrologic properties and chemistry. Higher
sand content permits greater fluid flow through the sediment and creation of bio-
geochemical conditions detrimental to the stability of osseous tissue. High clay
content reduces fluid flow; slowing bioapatite and collagen loss, while encouraging
early diagensis (see Section 3.2.2).
These differences may have lead to greater bone destruction in the gymnosperm-
dominated communities of the Paleozoic and Mesozoic than later angiosperm-dominated
communities of the Cenozoic, though this may have been offset somewhat by the
higher consumer abundance and decomposition supported in angiosperm-derived
soils. Furthermore, differences between the soils in gymnosperm vs. angiosperm com-
munities are dependent on external environmental factors and therefore will not act
uniformly across environments. Particular combinations of parent sediment, plant taxa
(or functional group), and climate are likely more important than plant type alone.
314 C.R. Noto
The dramatic rise in terrestrial vertebrate diversity starting in the Cretaceous

(Benton 1985) may not only be the result of “pull of the recent” effects or rock
volume/exposure area bias, but a long-term change in the biogeochemical condi-
tions of environments where angiosperms proliferated, creating conditions more
favorable for bone preservation. Further work on paleosols from the late Mesozoic
and early Cenozoic are necessary to track the chemical and physical changes to the
soil profiles before, during, and after angiosperms diversified.
5.2 Examples of Changing Taphonomic Regimes Over Time
5.2.1 Paleozoic
The fossil record of terrestrial vertebrates begins in the late Devonian with the
evolution of tetrapods and their first forays onto land. Early tetrapods inhabited
marginal-marine, deltaic, and fluvial environments in seasonally wet, semi-arid
climates during a time of high global mean temperature and elevated CO2 and low
O2 concentrations in the atmosphere (Fig. 3a) (Berner 2006; Cressler 2006; Scotese
2009). Two major gaps exist in this record: one during the Famennian (374–360
mya) and the other between the late Devonian and early Carboniferous, known as
“Romer’s Gap”. Both gaps have been interpreted as a true decrease is tetrapod
diversity resulting from the sharp drop in atmospheric oxygen concentration during
this period (Ward et al. 2006). However, a comprehensive examination of the fossil
record from this time reveals changes in tetrapod morphology, diversity, and fossil
distribution that are more compatible with a taphonomic interpretation (Clack
2007; Coates et al. 2008).
In early tetrapodomorphs (“stem tetrapods”) such as Eusthenopteron, Tiktaalik,
and Panderichthys, large body size, obligatory aquatic lifestyle, presence of scales,
and well-ossified skeletal elements may have aided in their preservation. Decay
dynamics of these taxa may have been more like those of large, bony fish such as
the alligator gar (Atractosteus spatula). Gars may provide a viable model for early
tetrapod taphonomy, not only because of their large size, but their ecology and
habitat preferences closely match those of the earliest tetrapods. Well-preserved
taxa like Tiktaalik (Daeschler et al. 2006) and Eusthenopteron (Schultze and
Cloutier 1996) demonstrate taphonomic features, such as the broad head resting
parallel to the bedding plane and dorsoventral flattening of the axial skeleton, simi-
lar to those described in carcasses of alligator gar deposited following tropical
storms on the gulf coast of Texas (Weigelt 1989).
Later more derived, limbed taxa like Acanthostega and Ichthyostega inhabited
freshwater fluvial and shallow-water environments under semi-arid climate con-
ditions (Long and Gordon 2004). Under these environmental conditions early
tetrapod remains were at risk of prolonged subaerial exposure. These taxa also
show loss or reduction of scales on the body (Coates et al. 2008). Scale loss
may have made the bodies of these animals more prone to disarticulation due to
Fig. 3 Distribution of terrestrial vertebrate fossil localities. The size of the marker is proportional
to the number of taxa known from a locality: larger markers contain greater vertebrate diversity. (a)
Devonian, 380 MY reconstruction. Location of tetrapodomorph taxa marked with letters:
A = Acanthostega, E = Eusthenopteron, I = Ichthyostega, P = Panderichthys, T = Tiktaalik. (b) Permian,
270 MY reconstruction. Data from the Paleobiology Database. Paleogeographic map software cre-
ated by John Alroy and Chris Scotese
gas bloating and/or scavenger consumption. These factors likely affected their
preservation, as seen in the prevalence of isolated postcranial elements and/or
large, robust skulls, contributing to the lack of fossil material during much of the
Fammenian.
Starting in the late Devonian terrestrial plants underwent a rapid evolutionary
radiation, expanding into a variety of new niches and culminating in the first recog-
nizable forests (Bateman et al. 1998). An overall rise in secondary plant productivity,
as evidenced by larger, woody stems with deeper roots, resulted in deeper weather-
ing of the soil profile. This was especially true in warm temperate and tropical
316 C.R. Noto
everwet environments (Retallack 1997; Algeo et al. 1998; Scheckler and Maynard
2001). During the early Carboniferous the onset of Pangean assembly drove the
development of extensive ice sheets in the southern hemisphere (Rygel et al. 2008).
The ice sheets would have prevented the spread of vertebrates to the south, but cre-
ated ecological opportunities in the north. Glaciation altered global climate and
supported a differentiation and expansion of tropical and temperate biomes, with
retraction of arid regions (Scotese 2009). All of this added up to increased ecological
opportunity for tetrapods, who likely began radiating into these new environments.
However, low atmospheric oxygen favored smaller body sizes (Clack 2007). Smaller
average body sizes and increased weathering of temperate and tropical soils was a
likely driver of Romer’s Gap during the early radiation of terrestrial tetrapods.
This trend continued until the late Carboniferous when widespread glaciation
at high latitudes lead to increasing seasonality and contraction of the tropical
biome. Increasing atmospheric oxygen and development of the amniotic egg
allowed tetrapods to increase in size and expand into more seasonal environments
with higher preservation potential (DiMichele and Hook 1992). Cyclical glacioeu-
static sea-level changes occurred frequently from late Carboniferous to early
Permian (Rygel et al. 2008), driven by Milankovitch oscillations (Wright and
Vanstone 2001). Sea-level changes created repeated cycles of continental sediment
erosion and deposition (Van der Zwan 2002) that increased preservation opportu-
nities during specific intervals.
During the Permian, continued assembly of the large Pangean landmass contin-
ued the drying trend begun in the late Carboniferous (Fig. 3b). The southern hemi-
sphere ice sheet disappeared. Atmospheric circulation and precipitation distribution
(i.e., ITCZ position) was highly monsoonal (Ziegler et al. 2003). With the drying
of the continental interior and strongly seasonal precipitation pattern, tropical ever-
wet and warm temperate conditions were rare on the main continental mass. More
environments favorable for bone preservation became available, as evidenced by
the reasonably good vertebrate record (Sander 1987, 1989; DiMichele and Hook
1992; Smith 1993; Sidor et al. 2005). Extreme aridity in some places led to highly
destructive environmental conditions. Evidence for extensive (³200 K km2) red bed
formation in North America during the mid-Permian shows extremely acidic (~pH 1)
groundwater and soils, which would have destroyed any buried bone (Benison et al.
1998). Given these hostile environments, it is likely that vertebrate diversity in
these regions was also low.
5.2.2 Mesozoic
A rapid increase in atmospheric CO2 concentration at the beginning of the Triassic

(Berner 2006) relaxed the latitudinal temperature gradient as mean surface tem-
peratures increased, establishing even more widespread aridity – perhaps one of the
most arid periods in Earth history. The absence of polar ice caps meant warm tem-
perate conditions extended all the way to the poles for most of the Mesozoic. The
symmetrical arrangement of Pangea about the equator created a “megamonsoonal”
precipitation regime, with a wide latitudinal excursion for the ITCZ that made cli-
mate patterns highly seasonal (Ziegler et al. 2003). Vertebrate preservation was best
at low- to mid-latitudes, where the monsoonal precipitation led to seasonal flood-
ing, rapidly burying exposed remains under poorly developed soils with high water
tables that promoted early diagenesis (Dubiel et al. 1991; Smith and Swart 2002).
Like the Permian, the most hostile desert regions (e.g., much of the continental
USA) sport few fossils due to poor preservation and low diversity.
As CO2 levels declined from the mid-Triassic to mid-Jurassic, tropical and warm
temperate biomes once again expanded their ranges and a seasonally wet tropical
biome was reestablished at the equator. There is no good evidence of tropical everwet
(i.e., rainforest) conditions throughout the Jurassic due to a weakened but still
operational monsoonal circulation (Ziegler et al. 2003). As such, biome distribution
remains more or less stable during the Jurassic, with an increase in global tempera-
ture and humidity as Pangea began to rift apart and CO2 levels once again peak in
the Late Jurassic, before beginning a steady decline in the Cretaceous (Price and
Sellwood 1997; Berner 2006; Sellwood and Valdes 2006).
The Late Jurassic contains spectacular assemblages of dinosaurs and other ver-
tebrates, preserved mostly in the seasonally-dry biomes at mid-latitudes (Fig. 4a).
The number of vertebrate fossils drops sharply at higher latitudes, coinciding with
the transition to the warm temperate biome, where the peak in plant fossil diversity
occurs (Rees et al. 2004). This drop in vertebrate preservation is likely due to the
relatively poor preservation conditions that existed in high latitude forests.
The record for Early and Middle Jurassic vertebrates is not as good but demon-
strates the same pattern: the vertebrate fossil peak follows the north-south migration
of the biome (Noto, unpublished data). It is interesting that the Middle Jurassic
vertebrate record is so poor, considering it contains the same basic arrangement of
continental area and biomes. Further work on this time period will be necessary to
tease out the cause of this idiosyncrasy.
The Cretaceous was perhaps one of the most equable times in Earth history.
Global temperature cooled as CO2 levels fell, most likely due to the increased
weathering and runoff from the diverging continents (Donnadieu et al. 2006). As
the continents drifted further apart, the smaller continental interiors became moister
and the large desert biomes characteristic of the Triassic and Jurassic were greatly
reduced. Instead, widespread seasonally wet savannah-like environments persisted
in the tropics at the low to mid latitudes (Upchurch et al. 1999). Small patches of
tropical rainforest were restricted to the equator, while warm- and cool-temperate
forests reached all the way to the poles. Widespread seasonally wet conditions
persisted across much of North America, Europe, and China. Global temperature
and humidity were still higher relative to today (Scotese 2009).
Cretaceous vertebrate fossils are relatively widespread, found at some abun-
dance in most biomes and latitudes (Fig. 4b). This is in stark contrast to previous
patterns, where the greatest number of vertebrate fossils is restricted to a narrow
range of environments. High sea-level, in concert with the seasonal precipitation
pattern, promoted broad plains proximal to sea shores (Horner 1989; Horner et al.
1992), creating ideal environments for bone accumulation and burial. In tropical
318 C.R. Noto
Fig. 4 Distribution of terrestrial vertebrate fossil localities. The size of the marker is proportional
to the number of taxa known from a locality: larger markers contain greater vertebrate diversity.
(a) Late Jurassic, 150 MY reconstruction. (b) Late Cretaceous, 90 MY reconstruction. Data from the
Paleobiology Database. Paleogeographic map software created by John Alroy and Chris Scotese
environments, these conditions contributed to the formation of lagoons and other

brackish water bodies, which provide an outstanding record of soft-tissue preserva-
tion (Dal Sasso and Signore 1998; Zhou et al. 2003).
By the Late Cretaceous, angiosperms are important members of the flora, found
in every major environment. Their modifications to the burial environment poten-
tially contributed to the apparent rise in diversity by promoting conditions more
amenable to bone preservation. Indeed, a survey of vertebrate fossil distribution does
appear to show more fossil localities near shorelines. The lack of a fossil record
across the K/T boundary may as much be a function of loss of these habitats due to
lowering sea-level and increasing aridity, which destroyed the most faithful recorders
of the terrestrial biota, as it was widespread extinction (Fastovsky 1990).
6 Implications for Vertebrate Paleobiology
6.1 Changing Patterns of Species Diversity
Cycles of evolutionary and ecological change observed in the fossil record are not
surprising, considering the control that the global climate and tectonic regimes
exert on both biogeochemical processes and species’ population dynamics. These
cycles are explicitly linked because they are controlled by the same set of factors,
yet the changes they elicit often are treated separately. Given the hierarchical nature
of both biotic and abiotic response to climate and tectonic changes, how each level
of the hierarchy interacts during these transitions to form the fossil record takes on
special importance.
As Behrensmeyer and Hook (1992, p. 88) observe, “[m]any paleoecologic stud-
ies have emphasized the role of global climate as the major factor controlling biotic
change, but climate pattern alone neither explains nor predicts the composition of
subsequent biotas.” Climate and tectonic changes that bring about environmental
change lead to shifts in not only floral and faunal assemblages but in biogeochemi-
cal cycling as well, thus altering the suite of taphonomic processes operating in the
area, in effect creating the very real problem of distinguishing between local shifts
in species distributions and large-scale biotic events. The use of other time-equivalent
deposits for reference is required to understand the scope and nature of the per-
ceived change (Behrensmeyer and Hook 1992). This idea needs further enhance-
ment by extending the phenomenon to a larger scale.
At the global scale, shifting environmental parameters and species ranges are
symptomatic of long-term alterations to the properties and distribution of the major
biomes, themselves dependent on the state of tectonic activity and insolation. As
the biomes change, this will also significantly change the overall nature and distri-
bution of taphonomic regimes, effectively moving the taphonomic window of
preservation and our view of life during the periods of time in question. It is not the
completeness of the terrestrial fossil record per se that is at issue here but how this
sliding taphonomic window affects our ability to reconstruct the ecology and evolu-
tion of extinct species, specifically the distribution of regional biodiversity. Much
of the research concerning biodiversity patterns has focused on quantifying global
patterns, charting the rise and fall of life’s diversity through time, while neglecting
potentially important dynamics occurring at the regional level (Miller 2003). It is
precisely the nature and effect of these dynamics in determining species distribu-
tions that continues to be a major source of study for ecologists, the most important
pattern being latitudinal gradients in species richness.
The current latitudinal gradient consists of highest diversity in the tropics, which
decreases with increasing latitude toward the poles. This pattern has been demonstrated
in plants, mammals, reptiles, amphibians, insects, and fish (Rosenzweig 1995).
Although well documented, the mechanisms driving this pattern of species distribution
still are debated actively, being most strongly related to productivity and/or evolu-
tionary rate (Gaston 2000).
320 C.R. Noto
Several examples of latitudinal diversity gradients are also known from the fossil
record, found in plants (Silvertown 1985; Crane and Lidgard 1989; Haskell 2001),
dinosaurs (Rees et al. 2004), radiolarians (Kiessling 2002), bivalves (Crame 2002),
and brachiopods and foraminifera (Stehli et al. 1969). Given the growing interest in
the effect of ecological interactions on speciation and evolutionary rates among
paleontologists and neontologists alike, the presence of latitudinal gradients in the
fossil record suggests that the mechanisms driving these patterns are an ancient
phenomenon.
Studying regional patterns of alpha, beta, and gamma diversity in the fossil
record enables a better understanding of the effects of environment and ecology on
micro- and macroevolutionary processes in ways that may only be addressed with
the fossil record (Miller 2003; Jackson and Erwin 2006). Allison and Briggs (1993)
found that, since biodiversity varies with latitude, the latitudinal range sampled by
the fossil record at a particular time will influence estimates of extinction and origi-
nation rates, especially when comparing patterns from times that experienced dif-
ferent global climate regimes.
A global point of view is necessary to place local- and regional-scale fossil dis-
tributions within the context of global taxonomic diversity patterns, but few studies
have addressed this directly. Applying these principles to the terrestrial fossil record
will first require a better understanding of how taphonomic bias due to environmen-
tal differences influences large-scale patterns. Once addressed, it will be possible
to implement correction factors to the diversity data. Such an approach was applied
to Middle Paleozoic and Late Cenozoic marine benthic communities (Bush and
Bambach 2004).
6.2 Model of Diversity Gradients and Climate Change
Modern continental surfaces can be grouped into broad regions of common climate
and ecology to form biomes (see Section 3.3). The latitudinal and longitudinal
extent of each biome depends on the distribution of constituent environments and
biota, which is driven largely by precipitation and insolation patterns (Begon et al.
2006). These same factors also lead biomes to support different levels of biodiver-
sity; moist, high-energy areas support more species than dry, low-energy areas
(Hawkins et al. 2003; Evans et al. 2005; Kreft and Jetz 2007). Specific chemical,
physical, and biological processes present within an environment define a tapho-
nomic mode, with particular modes preserving vertebrates more frequently in cer-
tain environments over others (Behrensmeyer and Hook 1992).
In the proposed model, vertebrate taxa differ in the taphonomic modes necessary
for fossil preservation and vary in abundance due to ecological requirements. The
number of different taphonomic modes together describes the taphonomic regime for
a given biome. The greater the heterogeneity of taphonomic modes, in particular the
proportion of these modes with conditions necessary for preservation of Taxon X, the
greater the possibility of it entering the fossil record. Therefore the fossil record of
Taxon X varies between biomes due to both abundance and preservation require-
ments, creating latitudinal and longitudinal gradients between taphonomic regimes.
The collection of all taphonomic regimes, in conjunction with the level of biodiversity
supported in each biome, produces the overall fossil record for a given time period.
This model then allows one to explore changes to the fossil record over time brought
about by changes in climate, biodiversity, and taphonomic processes.
Consider the following scenario shown in Fig. 5. At Time A the prevailing climate
regime supports three major biomes: a moist, high-latitude Biome 1; a seasonally-
wet Biome 2; and a moist, equatorial Biome 3. Biodiversity is highest in Biome 3,
decreasing with increasing latitude towards the poles (3 > 2 > 1). When living
biodiversity is surveyed at Time A, the resulting diversity pattern is a unimodal
curve, similar to that observed today. However, when forming the fossil record
under the conditions during Time A, the probability of vertebrate preservation in
Biome 2 is greater than either Biomes 1 or 3 (2 > 3 > 1) due to supporting a greater
Fig. 5 Conceptual model of diversity patterns and fossil preservation for a hypothetical landmass
at two different times: Time A and Time B. Global climate patterns have changed in the transition
from Time A to Time B, changing the distribution and types of biomes on the continental surface
(see text), which has altered both biodiversity and vertebrate preservation patterns. The preserved
fossil pattern differs significantly from the living biodiversity curve for each time period. Light
shades represent higher and dark shades lower biodiversity levels in each biome
322 C.R. Noto
variety of taphonomic modes. The resulting paleolatitudinal diversity curve repre-

sented by the fossil record of Time A would appear bimodal instead of the actual
unimodal pattern.
When we move forward to Time B, climate patterns have shifted, altering envi-
ronmental and taxonomic distributions. Thus there is a reorganization of diversity
and taphonomic regime within the biomes. The major biomes at Time B include: a
cool, high-latitude Biome 1; a moist, temperate Biome 2; a seasonally-wet, tropical
Biome 3; and a seasonally-arid, equatorial Biome 4. The diversity pattern is now
3 > 2 > 4 > 1, creating a bimodal diversity curve. Although possessing fewer taxa
in this hypothetical world, Biome 4 contains a wide range of taphonomic modes
due to a seasonal climate. Increasing moisture and decreasing diversity as one
moves away from the equator leads to depressed vertebrate preservation at higher
latitudes. The resulting preservation pattern 4 > 3 > 2 > 1 yields a unimodal paleo-
latitudinal diversity curve from the fossil record of Time B.
Comparing diversity curves between Times A and B, from both the original liv-
ing distribution and reconstructed fossil distribution, reveals two very different and
conflicting patterns. Contrasting interpretations can be drawn regarding ecological
properties of the biosphere at each time and evolutionary responses to climate
change during the transition from Time A to B. For example, based on the fossil
record from both times, Biomes 2 and 4 appear to support the greatest biodiversity,
which could lead to erroneous conclusions about productivity patterns and their
effect on the biota. Biased fossil diversity patterns could further lead to an under-
estimate of morphological and/or adaptive space occupied by a taxon or commu-
nity, because areas of high biodiversity usually contain the greatest ecological
diversity due to intense competition for resources (Pfennig et al. 2007 and refer-
ences therein). From an evolutionary perspective, comparing terrestrial diversity
patterns over time, in the manner of Sepkoski and others, may lead to gross over-
and underestimations of diversity depending on how the living diversity patterns
were filtered by prevailing taphonomic conditions at the time in question. Fossil
diversity estimates could, in part, be a function of alignment between living diver-
sity patterns and favorable taphonomic conditions.
While not quantitative, this model offers a predictive framework for hypothesis
testing. The reconstruction of extinct communities usually is accomplished by
examining the fossil assemblage for patterns, then comparing these patterns with
present knowledge derived from community and landscape ecology to create a
meaningful picture of the biota and its environment. Awareness of the many filters
this information passes through is part of the process. Nevertheless, an incomplete
understanding of the factors controlling these filters may be playing a direct role in
how one interprets biologically relevant information from the fossil record and
consequently how the same patterns are viewed today. If we were to create a fossil
record for the present world based on what we know about preservation, what
would it look like? Does the distribution of fossil diversity from different times in
the past match with what we would predict based on environmental and climatic
reconstructions? Such exercises may prove useful when considering the spatio-
temporal patterns of biodiversity for different times in the past.
7 Summary and Conclusions
Beyond simply cataloging new specimens, paleontologists desire to understand

sparse fossil remains, not only as once living individuals, but within their commu-
nity and ecosystem context. Understanding the dynamics of past ecosystems has
important consequences for how we view biogeographic and evolutionary patterns.
To detect ecological and evolutionary patterns from the fossil record, we need a
comprehensive taphonomic framework that acknowledges the multiple, hierarchi-
cal factors controlling the surface and subsurface destruction of remains in different
environments, herein termed the micro-, meso-, and macroscales. Each level repre-
sents the spatio-temporal extent over which a set of taphonomic processes act.
Every environment contains a specific set of taphonomic conditions that act on
remains above and below the sediment–atmosphere or sediment–water interface,
and together represent the combined influence of local conditions (e.g., landscape,
precipitation, temperature). Local conditions are controlled by global patterns of
climate, tectonics, and insolation. Therefore, the taphonomic processes acting on a
set of remains at the microscale reflect the prevailing conditions at the macroscale
during exposure and diagenesis.
While particular taphonomic processes (modes) are associated with certain
environments, environments, in turn, can be grouped together as biomes. Each
biome contains a subset of taphonomic modes and can be referred to collectively
as a taphonomic regime. As biomes shift in response to macroscale change, the
nature and distribution of taphonomic regimes also changes, creating cascading
effects through the lower levels. These lead not only to ecological and evolution-
ary change but also to changes in taphonomic processes, which directly impact the
subsequent fossil record. Distinguishing between fossil patterns formed by these
very different processes may be difficult unless hierarchical taphonomic change
and initial conditions are explicitly considered.
With a hierarchy of taphonomic control, paleontologists must recognize that
preservation bias is passed on to larger spatio-temporal scales, directly impacting
ecologic, evolutionary, and biogeographic reconstructions. This perspective pro-
vides a powerful tool for analyzing fossil datasets by constraining the range of
potential alteration to the original biotic community, allowing for a more compre-
hensive assessment of information loss (and gain) for different regions of the Earth
at different times.
Acknowledgments This chapter is dedicated to Alfred M. Ziegler (University of Chicago,

retired), who inspired me to think about big problems at big scales and helped me develop the
scholarly tools to approach them. This chapter owes its existence to the intellectual heritage he
instilled in me as a lowly undergraduate working in his lab many years ago. Working for Fred
opened the opportunity to work with David Weishampel (Johns Hopkins University), who
deserves credit for letting me get my hands on the Dinosauria distribution data, which helped get
me interested in the factors behind fossil distribution patterns. I would like to thank Bob Gastaldo
(Colby College) for detailed comments and criticisms on an early draft of the manuscript and to
Catherine Forster (The George Washington University), who further helped shape this mass of
ideas into a coherent whole through multiple drafts. Thanks also go to Kay Behrensmeyer
324 C.R. Noto
(Smithsonian), Tony Fiorillo (Dallas Museum of Nature and Science), Louis Jacobs (Southern
Methodist University), and Ray Rogers (Macalester College) for many fruitful discussions and
encouragement. I am grateful to David Bottjer and Peter Allison for the opportunity to contribute
to this book. Special thanks go to my family and Summer Ostrowski for their continued support
in all my endeavors, paleontological and otherwise, throughout the years. Paleogeographic and
paleoclimate maps produced by the Paleogeographic Atlas Project (pgap.uchicago.edu), The
Paleomap Project (www.scotese.com), and Ron Blakey (jan.ucc.nau.edu/~rcb7/RCB.html) proved
invaluable in the preparation of this manuscript. Some of the symbols used in Fig. 2 are courtesy
of the Integration and Application Network (ian.umces.edu/symbols/), University of Maryland
Center for Environmental Science.
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Chapter 9
Microtaphofacies: Exploring the Potential
for Taphonomic Analysis in Carbonates
James H. Nebelsick, Davide Bassi, and Michael W. Rasser
Contents
1 Introduction........................................................................................................................... 338
2 Taphonomy in Carbonate Environments............................................................................... 339
2.1 Taphonomy as an Inherent Part of Microfacies Analysis............................................ 339
2.2 Concepts and Definitions of Taphonomy in Thin Section Analysis............................ 341
3 Taphonomy of Paleogene Components in Thin Section....................................................... 342
4 Taphonomic Attributes of Major Facies Types..................................................................... 350
4.1 Lateral and Temporal Facies Distribution.................................................................... 350
4.2 Facies Description and Distribution............................................................................. 351
4.3 Taphonomic Processes in Paleogene Carbonates of the Study Area........................... 360
5 Discussion of the Distribution of Taphonomic Features
Among and Between Time Units....................................................................................... 362
6 Conclusions........................................................................................................................... 363
References .................................................................................................................................. 364
Abstract The microtaphofacies of Paleogene carbonates from three time units

(Middle Eocene, Late Eocene and Early Oligocene) from the circumalpine area are
described and compared. These carbonates are dominated by various larger foramin-
iferal and coralline red algal facies with subordinate coral and bryozoan facies.
The taphonomy of different components and the taphonomic attributes for each
facies type are detailed using a semi-quantified scheme describing four different
taphonomic features (abrasion, fragmentation, encrustation and bioerosion). This
allows the distribution and magnitude of taphonomic features to be determined
along the shelf gradient and between different time units.
J.H. Nebelsick ()
Institute for Geosciences, University of Tübingen, Sigwartstrasse 10, 72076 Tübingen, Germany
[email protected]
D. Bassi
Dipartimento di Scienze della Terra, Università di Ferrara, Via Saragat 1, 44122 Ferrara, Italy
M.W. Rasser
Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
338 J.H. Nebelsick et al.
Taphonomic features vary between facies types and time units. Fragmentation,
for example, is greatest in shallow water, inner shelf settings and is due to wave
base water agitation. Abrasion and encrustation are variable throughout different
facies whilst bioerosion varies through time. Middle Eocene facies are generally
less taphonomically altered than the Late Eocene and Early Oligocene facies which
seems to reflect the appearance of coralline algal dominated facies. The extinction
events among larger foraminifera that dramatically influence the occurrence and
distribution of facies have little effect on the distribution of taphonomic features.
1 Introduction
Taphonomic studies have mostly concentrated on the investigation and quantification

of isolated macroscopic faunal and floral elements. These have determined how
taphonomic pathways are influenced by: (1) the primary morphology and mineralogy
of the faunal skeleton or floral supporting systems, (2) numerous environmental
factors including water movement, salinity, temperature, oxygen levels etc., and (3)
transport and time averaging which can mix environmental and temporal signals. A
number of taphonomic processes and features including decay, abrasion, disarticu-
lation, fragmentation, bioerosion, encrustation, micritization and corrosion which
affect preservation have been identified and analysed for different organisms and in
different environments. More encompassing studies using these taphonomic
features have led to their inclusion in paleoecologic analysis and the establishment
of taphonomic gradients and taphofacies as an alternative to bio- and sedimentary
facies (e.g. Brett and Baird 1986; Cummins et al. 1986; Norris 1986; Staff et al.
1986; Speyer and Brett 1988; Allison and Briggs 1991; Donovan 1991a; Kidwell
and Bosence 1991; Scoffin 1992; Flessa 1993; Kidwell and Flessa 1996; Wilson
1988; Martin 1999; Behrensmeyer et al. 2000; Yesares-García and Aguirre 2004).
Actualistic studies have played a seminal role in elucidating these taphonomic
processes and features.
Indurated carbonate rocks, in contrast to isolated macroscopic remains, do not
readily offer material for taphonomic studies. There is, however, an enormous
potential for analysing taphonomic features in carbonates by studying thin sections.
The use of thin section analysis for very detailed ecological reconstruction of carbonate
environments has been common since the inception of this technique (see numerous
examples compiled in Flügel 1982, 2004). Microfacies analyses of limestones
allow the identification and analysis of even highly damaged biogenic components at
a wide range of magnifications. Various quantification techniques and subsequent
statistical treatment of component distributions are in regular use. Temporal
changes from initial deposition over early diagenetic effects to late diagenetic over-
printing can also be determined. A further advantage of thin-section analysis of
indurated rocks is that sampling can be spaces at regular intervals over long strati-
graphic sections, a possibility not necessarily present when studying macroscopic
9 Microtaphofacies 339
fossils as a base for taphonomic investigations. These advantages of microfacies

analysis have obvious potential for taphonomy.
2 Taphonomy in Carbonate Environments
2.1 Taphonomy as an Inherent Part of Microfacies Analysis
Microfacies studies and the subsequent interpretation of depositional environments

inherently take taphonomic processes into account. The fact that the biotic compo-
nents seen in thin section do not necessarily represent original skeletal architectures,
mineralogies or distributions is not a fatal flaw. The component grains, their
preservation and ultimately the limestone fabric is generally understood to result
from a whole slew of taphonomic processes including in situ processes on the sea
floor as well as early and late diagenetic effects.
Numerous reviews (e.g. Flügel 1982, 2004; Scoffin 1987, Tucker and Wright
1990) consider the role of mechanical destruction and biological breakdown of indi-
vidual skeletons and bioclasts, the stability of carbonate build-ups, the production of
micritic muds and the determination of calcium carbonate budgets. The destruction
of biogenic hard substrates and skeletons occurs through diverse means:
1. Surface grazing by polyplacophores (Rasmussen and Frankenberg 1990; Barbosa
et al. 2008), regular echinoids (Bak 1990, 1994; Steneck 1983) and parrot fish
(Bellwood and Choat 1991). Surface grazing, although prevalent in Recent envi-
ronments, is difficult if not impossible to recognize in the fossil record. In some
cases rare traces, for example from echinoid teeth, can be identified, but generally
they are not preserved. The differentiation of abrasion caused by grazing activity
and that caused by sediment agitation is of course difficult.
2. Chemical and mechanical erosion results from the action of a variety of macro-
scopic borers (Neumann 1966; Bromley 1978; Perry 1996, 1998a, 2000; Perry and
Bertling 2000; Scoffin and Bradshaw 2000; Wilson 2007) including clionid sponges
(Goreau and Hartman 1963; Futterer 1974; Acker and Risk 1985) sipunculids
(Perry 1998a) and boring bivalves (Kleemann 1994). Bioerosion not only weakens
the skeletons so infested but also produces sediment (Hutchings 1986; Glynn 1997).
Furthermore, since bioeroders are often filter feeding organisms, high infestation
rates of macroborers are used as an indication of nutrient-rich carbonate environments.
Boreholes can be recognized in thin section especially if the shells of the producers
are still in the holes (as is often the case with lithophagid bivalves).
3. Infestation of bioclasts by bacterial and algal microborers (Golubic 1969, 1990;
Golubic et al. 1975; Rooney and Perkins 1972; Budd and Perkins 1980; Tudhope
and Risk 1985; Vogel 1993; Kiene et al 1995; Vogel et al. 1995, 2000; Perry 1998b;
Glaub et al. 2007) is the factor that can be studied best in the rock record. This has
led to exploration of the evolution of microboring taxa and boring strategies
through time and in different reefal settings. Their use as ecological indicators
(such as light dependency related to depth and water clarity) is well known especially
since relatively small samples are needed for analysis. The identification of these
traces is problematic though since the taxonomy of micro-boreholes is based on
three-dimensional reconstructions as recovered by various casting procedures.
4. Crushing of shells by predation and scavenging (e.g. Lipps 1988; Cate and Evans
1994) is commonplace in shallow water marine settings. Recognizing predation
in thin section, as opposed to macroscopic evaluation of three dimensional
wound morphologies and breakage patterns, is limited by the two-dimensionality
of thin sections.
5. Grain destruction after ingestion by deposit feeders is often underestimated and
is poorly studied (see discussion in Scoffin 1987). Numerous deposit feeders
consume bioclastic components either whole or after mastication (depending on
the consumer involved). The affects on the respective shells after passing through
the digestive tracts is difficult to resolve, but must be important considering the
high turnover rates in some carbonate environments by benthic animals (such as
echinoids).
Perhaps the most important aspect of microboring for carbonate environments is
micritization (Bathurst 1966; Alexandersson 1972; Kobluk and Risk 1977;
Neugebauer 1978; Reid and Macintyre 2000) which can be either destructive or
constructive (Flügel 2004). Pervasive micritization can make identification of
carbonate grains impossible. Micritization, however, is of utmost importance for
the recognition and identification of bioclastic grains originally consisting of
aragonite such as dasycladalean algae, scleractinian corals and most gastropods and
infaunal bivalves (see below). Since the outer surface of the grains becomes
infested by miciritization, their morphology is conserved even after the aragonite
has been completely dissolved and replaced by sparitic cements.
The differential response of various biogenic skeletons to transport has been
elucidated from field observations and experiments (Chave 1964). A commonly
quoted example of degradation is that of the aragonitic skeletons of Halimeda and
other green calcareous algae which disaggregate into their constituent parts and the
aragonite laths of which they are composed (Wefer 1980). The mechanical and
biological degradation of green algae has been construed to be a major source of
aragonite muds in tropical environments.
Diagenesis is obviously of prime importance for the transformation of loose
skeletal and non-skeletal carbonate grains into indurated limestones (e.g. Flügel
1982, 2004; Dullo 1983; Schroeder and Purser 1986; Scoffin 1992; Tucker and
Wright 1990). Of special importance from a taphonomic point of view is the pref-
erential destruction of specific shell mineralogies at different stages of diagenesis.
Aragonitic components including dasycladalean algae, scleractinian corals, gastro-
pods and bivalves, can dominate Recent carbonate environments. That the dissolution of
aragonite can lead to the distortion of our perception of the original biofacies and
carbonate budgets at hand has been a long standing issue (e.g. Bathurst 1964; Budd
1988; Palmer et al 1988; Canfield and Raiswell 1991; Budd and Hiatt 1993; Brachert
and Dullo 2000). Aragonitic components can, however, be recognized in thin section
if they are micritized thus preserving a recognizable shell outline or if they are
encased in fine micritic muds before dissolution (see examples below).
Encrustation clearly plays an important role in carbonate environments, not only in
reefal settings (e.g. Martindale 1992; Rasser and Riegl 2002), but also as a taphonomic
agent affecting small substrates (Taylor 1979, 1992; McKinney 1995; Lescinsky et al.
2002; Taylor and Wilson 2003). Encrusting floral and faunal elements can produce
complex multi-taxon overgrowth sequences which can be ideally resolved in thin section
analysis (e.g. Reolid and Gaillard 2007; Reolid et al. 2007).
2.2 Concepts and Definitions of Taphonomy

in Thin Section Analysis
There are few studies which have specifically approached the taphonomy of
indurated carbonates using thin section analysis. The following terms have been
used to describe the study of taphonomy in thin sections, in part derived from the
different emphasis of these studies:
1. Brachert et al. (1998) coined the term “Microtaphofacies” and used taphonomic
features recognized in thin section to augment standard microfacies analysis
techniques in Miocene carbonates. This term will be used in this paper.
2. Reolid and Gaillard (2007) and Reolid et al. (2007) used the term
“Microtaphonomy” in a similar way as Brachert et al. (1998). These authors use
rigorous quantification techniques following various taphonomic indices of
Olóriz et al. (2004) to assess specific taphonomic features in Jurassic carbonate
facies from Spain. They use this term in the same sense as “microtaphofacies”
– using taphonomic traits recognized in thin section to augment environmental
information gained by component distributions.
3. Sanders and Krainer (2005) coined the term “Taphloss” when analysing Early
Permian benthic assemblages from the Carnic Alps. As the term suggests,
emphasis is placed on the loss of floral and faunal diversity and information in
general due to taphonomic processes on the sea floor and later diagenesis
(Sanders 1999). The difficulties induced by taphonomic loss in reconstructing
carbonate budgets is emphasized (Sanders 2003).
4. “Microfacies taphonomy” (Wright and Burgess 2005) is used for information
loss and stresses the problems involved in reconstructing paleoenvironments
given the role and rate of taphonomic destruction.
The dichotomy of taphonomic “gain” and “loss” (Cummins et al. 1986; Thomas
1986; Wilson 1988) has also been carried into microfacies studies of carbonates.
Taphonomic processes can either be seen as a source of information loss (often the
case) or information gain as taphonomic processes can reveal ecologic patterns and
developments not necessarily present in “normal” thin section analysis.
The present study provides an example of how taphonomic processes and features
change across facies boundaries. It is based on the analyses shallow water carbonate
Fig. 1 Location of the study area within the changing Paleogene paleogeography of the
Mediterranean and Paratethyan seaways. Study area denoted by a circle (maps after Rögl 1998)
facies during the Paleogene (specifically from the Middle Eocene to the Early
Oligocene) of the circum alpine region (Fig. 1). This time period and geographic
area are especially interesting due to dramatic developments in global climate, signifi-
cant paleogeographic changes, extinction events and resulting shifts of major carbonate
facies types. The studied carbonates are dominated by coralline algae and larger
foraminifera with subordinate corals and bryozoans. This qualitative comparison will
serve as a base for future, more detailed quantitative assessments of microtaphofacies.
3 Taphonomy of Paleogene Components in Thin Section
The taphonomic processes affecting coralline algae and larger foraminifera (Table 1
and Fig. 2) are diversely expressed (Figs. 3–11) although encrustation is especially
important in the production of rhodoliths (which can reach diameters greater than
10 cm). Transport is particularly important to the accumulation of large foraminifera-
dominated sediments, especially those containing Nummulites (“nummulithoclastic
sediments” following Beavington-Penney 2004).
Corals have received intensive attention especially with respect to comparing faunal
diversities of living corals to sub-fossil and fossil faunas (e.g. Scoffin 1992; Greenstein
and Moffat 1996; Pandolfi and Minchin 1996; Pandolfi and Greenstein 1997; Greenstein
and Pandolfi 2003; Meyer et al. 2003; Aronson 2007; Greenstein 2007; R. Wood, this
Table 1 Previous work on the taphonomy of Recent and fossil coralline red algae and larger
benthic foraminifera
Main componentsTaphonomic feature Citations
Coralline algae Reviews Nebelsick and Bassi (2000)
Disease and mortality Littler and Littler (1995, 1997)
Abrasion Chave (1964); Bosence (1976); Testa (1997);
Checconi et al. (2007)
Fragmentation including Cabioch (1969); Adey and McKibbin (1970);
maerl formation Bosence (1976, 1980, 1983b); Freiwald et al.
(1991); Freiwald (1993, 1995); Bordehore
et al. (2003)
Encrustation including Bosellini and Ginsburg (1971); Adey and
rhodolith formation MacIntyre (1973); Bosence and Pedley
(Recent) (1982); Bosence (1976, 1983a–c, 1984,
1985b); Adey (1978); Scoffin et al. (1985);
Sebens (1986); Reid and Macintyre (2000);
Littler et al. (1991); Martindale (1992);
Keats and Maneveldt (1994); Keats et al.
(1994); Steller and Foster (1995); Piller
and Rasser (1996); Foster et al. (1997);
Rasser and Piller (1997); Basso (1998);
Gherardi and Bosence (1999); Gischler and
Pisera (1999); Marrak (1999); Foster (2001);
Perry (2005); Piller and Rasser (2005);
Hetzinger et al. (2006); Konar et al. (2006);
Di Geronimo et al. (2002); Bassi et al.
(2009)
Encrustation including Bosence and Pedley (1982); Braga and
rhodolith formation Martìn (1988); Iryu (1997); Bassi (1998,
(fossil) 2005); Hillis and Jones (2000); Braga and
Aguirre (2001); Rasser (2000, 2001); Bassi
et al. (2009)
Bioerosion Checconi et al. (2007)
Predation (herbivory) and Adey and MacIntyre (1973); Lawrence (1975);
grazing van den Hoek et al. (1975); Wanders (1977);
Brock (1979); Steneck (1983, 1987, 1997);
Morse and Morse (1984); Figueiredo (1997);
Johnson et al. (1997)
Early diagenesis Alexandersson (1972, 1974, 1977); Bosence
(1985a, 1991); Martindale (1992)
Larger benthic Reviews Beavington-Penney (2004); Beavington-Penney

foraminifera and Racey (2004)
Abrasion Peebles and Lewis (1988, 1991); Cottey and
Hallock (1988); Yordanova and Hohenegger
(2002); Beavington-Penney (2004)
Fragmentation Yordanova and Hohenegger (2002); Beavington-
Penney (2004)
Bioerosion Kloos (1982); Serra-Kiel (1982); Serra-Kiel and
Reguant (1984); Matteucci and Pignatti (1988)
Dissolution Cottey and Hallock (1988); Murray (1989);
Peebles and Lewis (1988, 1991)
(continued)
Table 1 (continued)
Main componentsTaphonomic feature Citations
Transport and sediment Davies (1970); Hohenegger and Yordanovea
accumulation (Recent) (2001); Hohenegger (2004); Severin and Lipps
(1989); Yordanova and Hohenegger (2002)
Transport and sediment Engel (1970); Aigner (1982, 1983, 1985); Serra-
accumulation Kiel (1982); Serra-Kiel and Reguant (1984);
(fossil) Matteucci and Pignatti (1988); Eichenseer
and Luterbacher (1992); Kondo (1995a, b);
Racey (2001); Beavington-Penney (2004);
Beavington-Penney and Racey (2004); Bassi
(2005); Jorry et al. (2006)
Fig. 2 Taphonomic features of coralline algae as seen in thin section. “Disarticulation” depicts a
geniculate coralline alga, the rest depict non-geniculate coralline algae. “Fragmentation” is
destroying a fructicose growth form. “Abrasion” shows the destruction of a conceptacle on the
surface. “Encrustation” shows multi-taxonomic encrusting thalli on a coral. “Bioerosion” shows
both surface removal by grazers as well as internal holes created by boring organisms (modified
after Nebelsick and Bassi 2000)
volume). An increasing number of studies have also dealt with the taphonomy of corals
in turbid, nutrient rich waters (Perry and Smithers 2006) and deep water environments
(Freiwald and Wilson 1998). The role of taphonomy in reefs through time have been
summarized with respect to the changing organisms involved in reef growth on the
one hand, and the evolution of bioerosion and encrustation strategies on the other
(e.g. Fagerstrom 1987, 1991; Vogel 1993; Wood 1998, 1999, this volume).
Fig. 3 Abrasion and Fragmentation; Small Nummulites Facies showing fragmented and abraded
small Nummulites (1) in a terrigenous rich packstone matrix. Most Nummulites show abrasion and
fragmentation to varying degrees (2). Pressure solution is also present (3). Late Eocene,
Autochthonous Molasse, Upper Austria. Scale bar = 1 mm
Fig. 4 Encrustation and Bioerosion: Detail of a coral dominated rudstone with a packstone matrix
dominated by an encrusted coral. The components are very well preserved and show little abrasion
and fragmentation. The coral colony (1) shows a complex multi-taxon encrustation sequence
which includes coralline algae (2), encrusting foraminifera (3) and bryozoans (4). Bioerosion is
present as a large rounded hole (5) probably representing a lithophagid borehole. Well preserved
small benthic foraminifera are present. The aragonitic coral skeleton as well as an isolated gastro-
pod (7) has been completely replaced by calcite. Early Oligocene, Gornji Grad formation,
Slovenia. Scale bar = 2 mm
Fig. 5 Very well preserved components showing little or no post-depositional taphonomic features
(precluding diagenesis). This section contains two thalli of very well preserved Neogoniolithon
(1) and an echinoid from the Crustose Coralline Algal Facies. The coralline algal thallus on the right
is encrusted by an encrusting acervulinid foraminifera (2). The complete regular echinoid test
(3) shows distinct plates, tubercles and pores for the tube feet and has been eroded around the peris-
tome and periproct. The left hand side with ambulacral pores is a section through an ambulacrum, the
right hand side (without pores) is a section through the interambulacra. The high Mg-calcite of the
echinoderm skeleton has been replaced by low Mg-calcite. Unidentified fragmented bioclastic mate-
rial is present in the micritic matrix. Early Oligocene, Monti Berici, Northern Italy. Scale bar = 1 mm
Fig. 6 Maerl Facies with coralline algal thalli (1) which are bioeroded (2). Protuberances are
present with some branching. Some well preserved small benthic foraminifera (3) are also present.
Late Eocene, Autochthonous Molasse, Upper Austria. Scale bar = 2 mm
Fig. 7 Rhodolith Facies with a sub-ellipsoidal rhodolith showing complex multi-taxonomic

coralline algal crusts. The rhodolith shows dense encrusting growth forms as well as protuber-
ances. At least three growth generations are present (1, 2 and 3). Large spaces within the rhodolith
are filled by skeletal matrix consisting of unidentified skeletal fragments. Late Eocene,
The taphonomy of bryozoans has been especially studied in non-tropical environ-

ments (Nelson et al. 1988; Smith and Nelson 1994; Smith et al. 1996; Smith and
Nelson 2003; Smith 1995) allowing specific taphonomic features such as abrasion,
fragmentation and diagenesis to be identified and utilized in paleoenvironmental
analysis. The differential mineralogy of bryozoans and the corresponding effect on
diagenesis and dissolution is important (Smith et al. 1992; Steger and Smith 2005).
Subordinate components in Paleogene carbonates include smaller benthic fora-
minifera, molluscs and echinoderms (especially echinoids). Taphonomic studies on
smaller benthic foraminifera are rare (e.g. Lipps 1988; Martin and Liddel 1991;
Schroba 1993) and are mostly restricted to actualistic examples. The overwhelming
majority of taphonomic studies concern Recent and fossil molluscs (e.g. Callender
et al. 1994; Kowalewski et al. 1994; Best and Kidwell 2000; Zuschin and Stanton
2001, 2002; Lescinsky et al. 2002; Zuschin et al. 2003; Schneider-Storz et al.
2008). Molluscs, however, are relatively rare components in Paleogene carbon-
ates and are either present as calcite shelled pectinid bivalves and oysters or as
(dissolved) aragonite shelled gastropods and infaunal bivalves. Echinoderms are
well studied as macrofossils (see reviews in Donovan 1991b; Brett et al. 1997;
Ausich 2001; Nebelsick 2004), but comparatively little has been done on the
taphonomy of echinoderms in thin sections.
Fig. 8 The Large Nummulites Facies dominated by prominent Nummulites (1) together with subor-
dinate saddle-shaped orthophragminid foraminifera (2). Rare coralline algae (3) highly abraded and
fragmented. Some components, such as a single isolated planktonic globigerinid foraminifer (4), are
very well preserved. The components generally lie parallel to bedding, with, some “jamming” of
components in a more inclined posture. There are no indication of encrustation and bioerosion. The
foraminifera are generally well preserved, but can be slightly abraded (5) with some fragmentation.
Post-depositional taphonomic features include in situ pressure solution (6) on components contacts.
Pore spaces of the components (especially within the larger Nummulites specimens) are either filled
by micritic mud, or by sparite. Middle Eocene, Monti Berici, Northern Italy. Scale bar = 2 mm
Fig. 9 Orthophragminid Facies dominated by saddle-shaped orthophragminid larger foraminifera (1)

in a micritic matrix. The fabric is component-supported in matrix rich sediments. The larger foramin-
ifera are generally well preserved. In situ fragmentation (2) is also present. The components lie more
or less parallel to bedding. Late Eocene, Autochthonous Molasse, Upper Austria. Scale bar = 2 mm
Fig. 10 Coral Facies showing corals (1) partially abraded and encrusted by coralline algae (2) and
foraminfera (3). A broken fragment of a thecedine brachiopod (4) and a gastropod (5) are also
present. Bioerosion (6) can be recognized. Late Eocene, Autochthonous Molasse, Upper Austria.
Scale bar = 2 mm
Fig. 11 Bryozoan Facies showing cyclostome (1) and cheilostome (2) bryozoans lying more or
less parallel to bedding plane. Bilaminar upright growth-forms dominate. Some cylindrical
branching forms are also present. The bryozoans are generally well preserved. Some fragmenta-
tion has occurred. The primary pore spaces are generally filled by calcite. Late Eocene,
4 Taphonomic Attributes of Major Facies Types
4.1 Lateral and Temporal Facies Distribution
The Eocene/Oligocene boundary marks the transition from “greenhouse” to

“icehouse” condition and is manifested by dramatic cooling at least in higher
latitudes (e.g. Ivany et al. 2000; Zachos et al. 2001). It is, however, not clear
how this cooling event affected the tropics (e.g. Pearson et al. 2007). This is
relevant in the present study as the investigated carbonates lie at the northern
edge of the “tropical” Tethys seaway. Relevant paleographic development dur-
ing the studied time-frame include the establishment of Paratethys, a distinct
geographic and paleogeographic unit north of the Alps reaching into central
Asia (Rögl 1998; Harzhauser and Piller 2007). The connection from Tethys to
the Atlantic remained open during the studied time frame (Fig. 1). Extinction
events relevant to the development of carbonate facies include the disappear-
ance of larger Nummulites species at the Middle-Late Eocene transition and the
extinction of orthophragminid larger foraminifera at the Eocene/Oligocene
boundary. It is not clear if and how these extinction events are related to cli-
matic change.
The development of carbonate facies in the circum alpine area have been
studied in detail by Nebelsick et al. (2003, 2005). A number of Major Facies
Types (MFTs) were defined for the given time interval in the studied area. The
definition of these MFTs is based on detailed microfacies analysis (Nebelsick
et al. 2003, 2005) using quantitative techniques and statistical analysis of com-
ponent relationships. The MFTs have been defined following dominating (name-
giving) components, subordinate components and carbonate fabrics. The
distributions of these facies along a shelf gradient were mapped in three time
units (Middle Eocene, Late Eocene and Early Oligocene, see Figs. 11–19).
Changes in the distribution of these facies along the shelf gradient were impacted
by the extinction of major component types (i.e. larger foraminifera) and subse-
quent replacement of habitat space by other dominatingcomponents (and hence
the MFT). Most of the MFTs are dominated by either coralline algae or larger
foraminifera. Other MFTs are characterized by smaller benthic foraminifera,
corals and bryozoans. In some cases, the MFT types are very distinct as far as
composition and distribution are concerned. In other cases, they are less well
defined. Examples for the former are the Peyssonneliacean MFT in the Late
Eocene and the Acervulinid MFT in the Middle Eocene; both involve few taxa,
occur in distinct shelf settings and are restricted to a single time slice. An
example for the latter is the Rhodolith MFT which can involve various coralline
algal taxa and growth-forms and occurs in a large range of depths and settings,
and is present in all three time units. Although molluscs and other components
such as echinoderms can be locally common, they do not constitute major facies
components and are thus not listed as such.
Fig. 12 Compilation of taphonomic processes for 14 Major Facies Types of the Middle Eocene
to Early Oligocene of the circumalpine region
4.2 Facies Description and Distribution
The following descriptions summarize the components of each MFT along with
their texture and taphonomic traits. The stratigraphic distribution as well as the
changes of distribution between the different time units is also noted (see Nebelsick
et al. 2003, 2005 for detailed information).
4.2.1 Maerl Facies
The Maerl Facies is dominated by fragments of coralline algal branches often derived
from rhodoliths. Nummulitid larger foraminifera, smaller miliolids and textulariid
foraminifera are subordinate. It occurs as massively bedded rudstones with grain- and
packstone matrix with little or no orientations or gradations. This facies represents a
higher energy environment with grains being highly fragmented and abraded.
Encrustation along with bioerosion is moderate. The taxonomic identification of
highly fragmented algal remnants is difficult due to the lack of diagnostic characters.
The Maerl Facies first appears in the Late Eocene and continues to the Early
Oligocene. It changes its distribution from the middle to inner outer shelf in the
Middle Eocene to the inner to middle shelf in the Late Eocene and Early Oligocene.
Fig. 13 Distribution of abrasion along a shelf gradient from the Early Eocene to the Early
Oligocene
4.2.2 Rhodolith Facies
This facies is dominated by non-geniculate coralline algae, peyssonneliacean algae

and encrusting acervulinid foraminifera. All three of these components contribute
to rhodolith formation, though coralline algae dominate. Encrusting serpulids,
agglutinated foraminifera (e.g. Haddonia) and unilaminate and multilaminate
bryozoans also contribute to the rhodoliths which can reach sizes up to 10 cm.
The rhodoliths occur as spherical, ellipsoidal, discoidal and boxwork shapes.
The rhodoliths can be constrained to a single coralline algal taxon and growth-form,
but often show complex encrusting sequences. The texture of these limestones is
dominated by rudstones with grain- and packstone matrix. Abrasion rates are high
and fragmentation rates moderate. Encrustation rates are, given the dominance of
encrusting components, very high as is bioerosion which can be pervasive.
The Rhodolith Facies first appears in the Middle Eocene and continues into the
Early Oligocene. It changes its distribution from the middle to inner outer shelf in the
Middle Eocene to the inner to middle shelf in the Late Eocene and Early Oligocene.
Fig. 14 Distribution of fragmentation along a shelf gradient from the Early Eocene to the Early
Oligocene
4.2.3 Crustose Coralline Algal Facies
This facies is dominated by encrusting crustose coralline algae, along with

rhodoliths, encrusting foraminifera and locally abundant nummulitids. Smaller
miliolid and textulariid foraminifera, bryozoans, peyssonneliacean algae, echino-
derms and serpulids are subordinate. Meter-thick bindstones composed of 0.5–1
mm thick algal crusts are characteristic of this facies. Due to their growth-forms,
crustose coralline algae serve as binding agents and include sub-discoidal and
sub-ellipsoidal rhodoliths with a loosely ordered inner arrangement. The algae
themselves can be encrusted by encrusting foraminifera and bryozoans with unilami-
nate and multilaminate encrusting growth-forms. The algal crusts are predominantly
horizontally oriented. Taphonomic features include very high rates of encrustation,
high rates of bioerosion and low rates of abrasion and encrustation.
As in the previously described examples, this facies first appears in the Late Eocene
and continues into the Early Oligocene. It reduces the distribution range from the middle
to inner outer shelf in the Middle Eocene to the middle shelf in the Early Oligocene.
Fig. 15 Distribution of bioerosion a shelf gradient from the Early Eocene to the Early
Oligocene
4.2.4 Coralline Algal Debris Facies
This widely distributed facies incorporates a wide range of sediments dominated by

coralline algal debris, larger foraminifera, bryozoans, corals, peloids, and siliciclastics.
Subordinate components include peyssonneliacean algae, molluscs and smaller
benthic rotalid and textulariid foraminifera. The texture of the limestones of this
facies is a rudstone with grainstone/packstone matrix. Taphonomic rates vary; abra-
sion and fragmentation rates can be very high as opposed to the low presence of
encrustation and bioerosion. Highly fragmented and abraded components are
difficult to identify.
This facies occurs in all three time units from the Middle Eocene to Early
Oligocene. It shows a disjunct distribution in the Middle Eocene, and is found in
the inner to middle shelf in the Middle Eocene to Late Oligocene.
Fig. 16 Distribution of encrustation along a shelf gradient from the Early Eocene to the Early
Oligocene
4.2.5 Peyssonneliacean Facies
In this facies, the peyssonneliacean species Polystrata alba forms sub-spheroidal

rhodoliths with coralline algae as subordinate components. The fabric of these
limestones consists of rudstones with a packstone matrix with no grading, sorting
or preferred orientation. This facies is characteristic of low energy conditions and
fragmentation rates are low and abrasion moderate. Encrustation is high due to the
habitat of the dominating component, bioerosion is moderate. The Peyssonneliacean
Facies is restricted to a few occurrences in the Late Eocene.
4.2.6 Larger Nummulites Facies
Various species of larger Nummulites dominate this facies. Other larger and small
benthic foraminifera, molluscs and echinoderms are subordinate. The components
Fig. 17 Compilation of taphonomic processes for the Middle Eocene
can occur in very high densities and include numerous species of larger Nummulites.
The largest Nummulites microspheric forms of Nummulites gizehensis can reach
diameters of up to 10 cm. The texture is represented by rudstones with packstone
matrix showing both orientated and chaotic fabrics.
Various reconstructions for this facies have been offered in the literature (e.g.
Aigner 1985; Eichenseer and Luterbacher 1992; Racey 2001; Beavington-Penney
and Racey 2004; Bassi 2005) for both autochthonous as well as allochthonous
larger Nummulites dominating sediments. Edge abrasion and fragmentation leads
to the production of abraded Nummulites fragments. Encrustation and bioerosion
levels are low.
Fig. 18 Compilation of taphonomic processes for the Late Eocene
Larger Nummulites are common in the middle shelf of the Early to Middle
Eocene and disappear at the Middle/Upper Eocene boundary.
4.2.7 Small Nummulites Facies
In this association, numerous different species of smaller Nummulites occur with

subordinate coralline algal debris, other larger and smaller benthic foraminifera,
bivalves, echinoids, brachiopods and corals. The texture consists of packstones and
rudstones with packstone/grainstone matrix or siliciclastic matrix. Graded bedding
Fig. 19 Compilation of taphonomic processes for the Early Oligocene
can occur. Small Nummulites include moderate edge abrasion and fragmentation;
encrustation and bioerosion are rare.
The Small Nummulites Facies occurs from the Middle Eocene to the Early Oligocene.
It shows a dramatic shift in its distribution range from the outer middle shelf in the
Middle Eocene to inner to middle shelf in the Late Eocene and Early Oligocene.
4.2.8 Orthophragminid Facies
This facies is dominated by various species of large, thin, disc- and saddle shaped ortho-
phragminids along with coralline algal crusts. Larger and smaller benthic foraminifera
(rotaliids and textulariids), bivalves and planktic foraminifera are subordinate.
These components occur in rudstones with wacke- to packstone matrix. A horizontal
o rientation is usually present. The Orthophragminid Facies shows low values for all
taphonomic features except for encrustation. The orthophragminids are often nested.
Orthophragminid occur from the Middle and Late Eocene after which these
larger foraminifera disappear. This facies shifts its range from the middle and outer
shelf in the Middle Eocene to the outer shelf in the Late Eocene.
4.2.9 Orbitolites Facies
This facies is dominated by the larger foraminifer Orbitolites along with small
miliolid foraminifera. Peneroplid foraminifera, bivalves and gastropods are
subordinated in rudstones with pack- to grainstone matrix. Graded bedding can be
present. The Orbitolites Facies shows low values for all taphonomic features except
for encrustation, despite the fact that they occur in shallow water settings.
Encrustation can occur by coralline algae and bryozoans. This facies is restricted to
the inner shelf of the Middle Eocene.
4.2.10 Smaller Miliolid Facies
Diverse small benthic miliolid foraminifera, peneroplids and alveolinid foraminifera

dominate this facies along with subordinate textulariid foraminifera, Sphaerogypsina,
bivalves, echinoderms, geniculate and non-geniculate coralline algae. The miliolid
small benthic foraminifera are primarily quinqueloculine and triloculine forms. The
fabric is represented by grainstones and packstones with moderately to well preserved
components. No grading, sorting or orientation is present. Abrasion and fragmenta-
tion is moderate, with low values of encrustation and bioerosion. This facies expands
its range from the Middle (inner shelf) to the Late Eocene (middle shelf ).
4.2.11 Alveolinid Facies
This facies is dominated by alveolinids together with small miliolid benthic foramin-
ifera, asterigerinid and nummulitid larger foraminifera. Small benthic rotaliid foramin-
ifera, coralline algae, echinoderms are subordinated in pack- and grainstones. Both
oriented and chaotic fabrics occur. Due to the rigid skeletons and high resistance of
alveolinids, this facies shows low values for all taphonomic features except for abra-
sion. This facies shows a restricted range on the middle shelf of the Middle Eocene.
4.2.12 Acervulinid Facies
Acervulinid macroids formed by Acervulina ogormani and A. linearis and tubular

aggregates of A. multiformis dominate in this association along with subordinate
coralline algae, serpulids, homotrematid foraminifera as well as larger foraminifera
and smaller miliolid benthic foraminifera. The acervulinids construct dense macroids
which can show complex encrusting successions including various coralline algae,
serpulids and other encrusting foraminifera within rudstones. The macroids can be
up to 10 cm in diameter with laminar-encrusting growth-forms, and do not show
grading, sorting or preferred orientations. Encrustation rates are correspondingly
very high with moderate bioerosion. Fragmentation and abrasion is rare. The facies
is restricted to the outer shelf of the Middle and Later Eocene.
4.2.13 Coral Facies
Corals and coralline algal crusts dominate this facies along with subordinate small
Nummulites, bryozoans, thecideidean brachiopods and small benthic foraminifera.
They occur in rudstones with wackestone to grainstone matrix and include both
branching and encrusting corals as isolated colonies or in patches.
The aragonitic shelled corals are usually dissolved and often replaced by calcite.
In many cases, corals are easily recognizable due to dense micritic muds which
encase the specimens and fill in the space between the septa. In some cases dissolu-
tion is such that the corals are only recognizable as “ghost” structures. Corals are
often at the core of complex encrustation successions being encrusted by coralline
algae, foraminifera, unilaminate and multilaminate bryozoans and thecideidean
brachiopods. These composite encrustation sequences are often heavily bioeroded.
This facies is represented by low abrasion rates and moderate rates. It is most common
on the middle shelf of the Late Eocene and Early Oligocene.
4.2.14 Bryozoan Facies
Both cheilostome and cyclostome bryozoans dominate in this facies along with
smaller quantities of larger foraminifera, smaller benthic rotaliid foraminifera and
coralline algae. The bryozoan growth forms are dominated by upright growing
cylindrical and bilaminate forms. Bryozoans can be encrusted by coralline algae.
The bryozoans occur in rudstones with wackestone matrix as well as marly
packstones. The components lie nearly parallel to bedding planes. The Bryozoan
Facies represents a low energy system and includes well preserved components
with moderate encrustation rates and sparse abrasion, fragmentation and bioero-
sion. This facies expands from the outer shelf in the Late Eocene to include the
middle shelf in the Early Oligocene.
4.3 Taphonomic Processes in Paleogene Carbonates

of the Study Area
The degree of abrasion, fragmentation, encrustation and bioerosion within each

facies was qualitatively assessed (designated as low, moderate, high or very high;
Fig. 12) in the study area. These taphonomic features were then mapped with
respect to facies distribution along a shelf gradient (Nebelsick et al. 2003, 2005).
The assessment of taphonomic features necessarily concentrates on the name-
giving components. Taphonomic processes will obviously differentially affect the vari-
ous components within the facies. Taphonomic gradients will also exist along shelf
gradients, especially for those facies which show a wide distribution. The interpreta-
tion of taphonomic features is problematic as different processes can lead to similar
features. Nonetheless, the first order comparison does show some general trends.
Abrasion represents destruction of surface characters and the rounding of parti-
cles. It can be caused by grain agitation during transport processes and/or biological
activity. Abrasion is very high in the Coralline Algal Debris Facies and high in
other coralline algal facies. It is low in the Orthophragminid, Orbitolites,
Acervulinid, Coral and Byrozoan Facies. Both the Larger and Small Nummulites
Facies show moderate values.
Fragmentation leads to diminution of components and is recognized by frag-
mented grains with sharp edges and abrupt termination of skeletal characters. As in
abrasion, fragmentation can be caused by both grain agitation and biological activ-
ity. Fragmentation generally shows similar distributions to abrasion in its distribu-
tion among major facies types with the highest values in the Maerl and Coralline
Algae Debris Facies, moderate values in the Larger and Small Nummulites Facies
as well as the Rhodolith, Smaller Miliolid and Coral Facies. Fragmentation is least
in some larger foraminiferal facies and the Bryozoans and the Crustose Coralline
Algal Facies.
Encrustation is easily recognized in thin section by bio-immuration of compo-
nents by encrusting organisms. Encrustation leads to an increase of (aggregate)
component size and can stabilize components and sediment surfaces. Encrustation
sequences can subsequently be affected by other taphonomic features especially
bioerosion. Encrustation is especially high in the Rhodolith, Crustose Coralline
Algal as well as Acervulinid and Coral Facies. It is rare in the Coralline Algal
Debris, Small Nummulites and Acervulinid Facies.
Bioerosion can also be readily recognized in thin section if it extends into the
biogenic substrates and can be caused by an array of micro- and macroborers.
Bioerosion is very high in the Coral Facies and common in the Rhodolith and
Crustose Coralline Algal Facies. The other facies show low or moderate values.
Other taphonomic processes which occur on or near the sediment–water surface
include disarticulation which can be easily recognized in isolated genicula of genic-
ulate coralline algae, disassociated echinoid spines, isolated elements of cellariform
bryozoans and most obviously disjunct bivalve shells.
Post-depositional taphonomic features include dissolution of aragonitic compo-
nents (see discussion above). In the study area, this affects dasycladalean and hal-
imedacean algae, scleractinian corals, aragonitic shelled bivalves and gastropods.
The presence of these components can often be easily recognized due the fact that
they have been encased by a fine micritic matrix. High Mg-calcite skeletons are
invariable transformed to low Mg-calcite in coralline algae and echinoderms. The
later can be accompanied by syntaxial cements if enough pore space was present
into which the cements could expand. Another post-depositional feature is contact
breakage due to compaction. This is common in those facies in which the

component packing is very dense including the larger Nummulites and the
Orthophragminid Facies. Pressure solution is also a feature seen at contact points
between components in these facies.
5 Discussion of the Distribution of Taphonomic Features

Among and Between Time Units
Abrasion magnitude varies in time and space (Fig. 13). In the Middle Eocene, abrasion
occurs in the middle shelf in the Larger Nummulites Facies where it may represent
shoal settings. It is also very high in the Coralline Algal Debris Facies. In the Late
Eocene and Early Oligocene, abrasion dominates in shallow water facies and is rare
in the outer middle and outer shelf. The fact that abrasion does not follow a general
depth gradient may reflect the fact that this taphonomic features can be caused not
only by water movement and grain agitation, but also by surface grazing in deeper
water.
Fragmentation shows the most clear cut spatial distribution with similar trends
in all three time units (Fig. 14). Highest values are found in shallow water inner
shelf settings. Moderate values are also present in shallow water and extend to
middle shelf environments. Deeper water outer shelf facies show low rates of frag-
mentation. This may, in fact, reflect the simple correlation between water depth,
wave base and water movement. The well preserved Middle Eocene Orbitolites
Facies is the exception as it represents sheltered shallow water environment. The
role of predation and bioturbation in the fragmentation of the constituent biogenic
components is not well enough known in the studied facies to postulate on its
influence.
Encrustation does not show as clear a distribution as the other taphonomic fea-
tures (Fig. 15). Thus middle to outer shelf facies show the highest rates in the
Middle Eocene. In the Late Eocene and Early Oligocene, higher values for encrus-
tation are found in both inner and middle shelf setting. The inner shelf environ-
ments in the two younger time units, in fact, show three different levels of
encrustation values. Encrustation seems to be least affected by different environ-
mental parameters such as water energy levels or depth. The fact that components
become encrusted seems to be more related to the size and encrusting potential of
the specific components at hand. This is especially important for the encrusting
foraminifera (acervulinids in the Acervulinid Facies) and calcareous algae which
can encrust surfaces and construct self-encrusting macroids or rhodoliths (Rhodolith
Facies and Peyssonneliacean Facies). Corals can also be encrusted during life as
well as after death and offer various substrates for a number of different encrusters in
both exposed and cryptic microhabitats. More detailed analysis of growth patterns
and encrustation strategies are needed to interpret different encrustation types.
Bioerosion (Fig. 16) varies between Middle and Late Eocene-Early Oligocene.
In the Middle Eocene bioerosion is highest in middle and outer shelf settings but in
the Late Eocene and Early Oligocene it is high in the inner and middle shelf.
Overall however, the highest values are found in the middle shelf (with the Coral
Facies). This may reflect an ecological related to water depth. Of importance for
the presence and preservation of bioerosion is the initial size and skeletal architec-
ture of the potential biogenic substrates. Relatively large corals and rhodoliths are
thus more conducive to the harbouring and preserving endolithic organisms than,
for example, smaller foraminifers or branching bryozoans.
There is thus a general trend for those taphonomic features which can be related to
physical processes such as transport and grain agitation to occur preferentially in shal-
lower setting than in deeper setting. This is due to wave base and associated water
movement. This is not always the case however as some shallow water facies (for
example the Orbitolites Facies) represent quiet water settings and some abrasion and
fragmentation may be biogenic in origin and may be affected by substate availability.
Of primary interest is the cause for differences in the distribution of taphonomic
features between the time units. The main change in this respect occurs between the
Middle Eocene on the one hand and the Late Eocene and Early Oligocene on the
other. Middle Eocene facies (Fig. 17) generally show lower taphonomic values than
the Late Eocene (Fig. 18) and Early Oligocene (Fig. 19). The extinction events that
dramatically influence the occurrence and distribution of facies (extinction of larger
Nummulites and most of the alveolinids at the Middle Eocene/Upper Eocene
boundary and the extinction of orthophragminids at the Eocene/Oligocene bound-
ary) have little effect on the distribution of taphonomic features. This is due to the
fact that the Larger Nummulites, the Alveolinid and the Orthophragminid Facies
show low to moderate values for all taphonomic features. More dramatic as far as
taphonomy is concerned is the appearance in the study area of the Coral, Rhodolith
and Maerl Facies in the Late Eocene. These facies show very high values of encrus-
tation and bioerosion (Coral Facies) and abrasion and fragmentation (Rhodolith and
Maerl Facies) and thus dominate the distribution of taphonomic features.
6 Conclusions
The long tradition of microfacies studies on carbonate rocks have resulted in vast
collection of thin sections. These collections represent a largely untapped source of
taphonomic data. The thin sections are typically all of the same size (depending on
the specific tradition of the thin section laboratories – typically 5 × 5 cm in Central
Europe for example), of uniform thickness, usually vertically orientated to the bedding
plane, and taken at regular distances within stratigraphic sections. Furthermore, broad
facies assignments are usually already known. Microtaphofacies analysis can poten-
tially add new insight into paleoecological interpretations. More studies are not only
needed on fossil carbonate successions, but also using an actualistic approach on
modern components in different carbonate settings. The direct taphonomic analysis of
particulate grains and the same material embedded in resin and cut into thin sections
will allow two- and three dimensional taphonomic attributes to be compared.
This study represents a rather coarse, semi-quantitative treatment of taphonomic

features at broad time scales (sub-stages) over a wide geographic range. Further
studies could include more precise evaluation of taphonomic attributes and extend
the analyses to further time units and a wider geographic area. Closer analyses can
include detailed bed-by-bed quantification of specific taphonomic features (e.g.
Reolid and Gaillard 2007) or document disparities among successive sequence
stratigraphic units (e.g. Brachert et al. 1998). Inclusion of broader geographic areas
would reveal taphonomic patterns across latitudinal and temperature gradients from
more tropical (in this case further southwest in the tropical Tethys) to more temper-
ate settings as well as longitudinal gradients between the study area and both the
Eastern Tethyan and Caribbean provinces.
The quantification of taphonomic features such as encrustation and bioerosion
can be used to follow not only the variations in the intensities of these features, but
also the evolution of encrusting and bioeroding strategies (e.g. Fagerstrom 1987,
1991; Vogel 1993; Wood 1998, 1999, this volume). This can be extended to evalu-
ate co-evolutionary scenarios between substrates and encrusters and bioeroders
through time (e.g. Steneck 1983, 1986).
The carbonates which form the basis for this paper cross important stratigraphic
boundaries marked by extinction events. Of great potential is the study of how
taphonomic features change across other seminal boundaries including (1) major
(and minor) extinction events, (2) the change in climatic (greenhouse/icehouse)
regimes, and (3) marine geochemical turnovers (calcite/aragonite seas – see Palmer
et al. 1988). As has been often appreciated (among taphonomists at least) taphonomy
is an essential factor in determining the presence (and absence) of key biotic
components on which biotic turnover is essentially measured. More detailed studies
on the taphonomy of sedimentary sequences (including carbonate successions
using the microtaphofacies approach presented here) can thus help to more com-
pletely understand key events in Earth history.
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Chapter 10
Taphonomy of Reefs Through Time
Rachel Wood
Contents
1 Introduction........................................................................................................................... 376
2 Spatial and Temporal Variation in Modern Coral Reef Communities.................................. 377
3 Taphonomy of the Modern Coral Reef Environment........................................................... 380
3.1 Loss due to Non-Preservation...................................................................................... 381
3.2 Mode of Life, Skeletal Robustness and Rates of Skeletal Production......................... 381
3.3 Bioerosion, Abrasion, Transport, and Burial............................................................... 382
3.4 Early Diagenesis: Dissolution and Cementation......................................................... 386
3.5 Changing Rates of Accumulation................................................................................ 387
3.6 Detection of Critical Events......................................................................................... 388
4 Taphonomic Bias in Ancient Reefs: Insight from the Pleistocene Record........................... 389
5 Changes in Reef Taphonomy Through the Phanerozoic....................................................... 390
5.1 Rise of Biological Disturbance.................................................................................... 390
5.2 Response to Increase in Disturbance........................................................................... 391
5.3 Response to Changing Seawater Chemistry: Secular Changes in Mineralogy........... 397
6 Current Global Change and Taphonomy.............................................................................. 399
6.1 Loss of Herbivores and Higher Predators.................................................................... 399
6.2 Changing Storm Patterns............................................................................................. 399
6.3 Rise in Sea Level......................................................................................................... 400
6.4 Rises in CO2 and Global Temperature......................................................................... 400
6.5 Changes in Sea-Water Chemistry................................................................................ 401
7 Summary............................................................................................................................... 402
References................................................................................................................................... 404
Abstract Reefs are susceptible to multiple physical, chemical and biological

taphonomic processes. Bioerosion, in particular has escalated through time and
might be expected to have influenced the taphonomy of reefs. The following biases
can be predicted: (1) In the absence of grain-reducing activities by reef biota (fish,
echinoids, and clionid sponges) abrasion on Paleozoic reefs would have been
dominated by physical processes and sediment grains may have been more coarse.
R. Wood ()
Grant Institute of Earth Sciences, School of Geosciences, University of Edinburgh,
King’s Buildings, West Mains Road, Edinburgh EH9 3JW, UK
376 R. Wood
(2) Increased bioerosion since the Jurassic is such that modern reefs are quickly
reduced to rubble and sand leaving only the resilient branching corals and thick
coralline algae. By contrast, many pre-Jurassic reefs commonly preserve intact,
in situ frameworks that include massive or laminar, often soft-sediment-dwelling,
growth forms. (3) After the appearance of reef fish in the Eocene, sediment production
and distribution within reef complexes is likely to have increased markedly but this
has not yet been fully elucidated. (4) Escalation in rates of bioerosion from the
Miocene onwards are such that it can be expected that substantial aprons of reef-
slope sediment may not have been present on pre-Miocene reefs.
Evidence is persuasive that changing global seawater chemistry has exerted
secular changes in the dominant carbonate mineralogy of reef organisms and early
diagenetic cements but the subsequent effects upon reef taphonomy remain to be
documented.
The current phase of climate change will exert a profound effect upon reef
ecology and taphonomy. Reduction of reef herbivore populations will almost
certainly lead to an increase in soft-bodied algal biomass, and a decrease in coral
cover, particularly in areas of eutrophication or outbreaks of disease. Bleaching as
a result of global warming may lead to significant or widespread coral mortality.
Calcification rates are already between 6% and 20% lower than they were under
pre-industrial conditions due to ocean acidification. These processes will reduce
the structural integrity of reefs. Future death assemblages and the subsequent
fossil record of reefs will be dominated by highly degraded coral fragments and
grains with limited in situ reef frameworks, endolithic algal activity, and intense
bioerosion.
1 Introduction
As records of in situ benthic communities, ancient reefs offer considerable

paleoecological information, but the utility of this record is controlled by the
fidelity of their geological expression. Reefs are complex environments of both
hard (reef framework) and soft-substrate (reef sediment) communities that are
exposed to a range of intense physical and biological exposure, transport, and
burial processes. These processes have changed markedly over geological time
due to extrinsic physicochemical controls and particularly an escalation in
bioerosion.
The formation of a reef framework is dependent upon the maintenance of stability
of an epibenthic marine community. But reef frameworks and their surrounding
areas of soft-sediment support a huge variety of closely-interacting immobile and
mobile organisms of varying skeletal durability and ability to withstand biological
and physical attack. For example, reef sediment itself may be the result largely of
abrasion and transport of skeletal debris derived from the reef framework. The
varying rates of skeletal production, breakdown and subsequent transport, as well
as overall sedimentary accumulation rates, control the concentration or dilution of
10 Taphonomy of Reefs Through Time 377
any given component. Only through quantification of the degree of taphonomic

information loss in reef death assemblages will comparisons between living,
sub-fossil, and fossil assemblages be possible.
This review first summarizes the major controls on the post mortem history of
modern reef communities, with an emphasis on the fate of coral skeletons. These
include modes of life and death, abrasion, transport, burial and diagenetic pro-
cesses. Reefs are defined here as discrete carbonate structures that form by in situ
or bound organic components that develop topographic relief upon the sea floor
(Wood 1999). As such, a reef (be it a deep-water mud mound or a shallow coral
reef) is an elevated sessile benthic community that can resist the ambient hydrody-
namic regime, but as reef formation involves both constructional and destructive
processes these may present as any variant between an intact framework or a pile
of skeletal debris in the geological record.
Physical disturbance, grazing pressure and spatial competition are important
determinants of living coral reef community structure. Biological disturbances,
such as predation, herbivory, and deep bioturbation, have evolved in tempo and
strength over the Phanerozoic (Vermeij 1987). The second part of this review will
explore the effects of this ecological escalation on taphonomic processes in reef
communities.
Reefs worldwide are undergoing dramatic change, and many of these changes
are historically recent (Hughes 1994; Jackson et al. 2001; Pandolfi et al. 2003;
Hughes et al. 2003). Most notable is the decline of acroporoid corals in the
Caribbean, and an increase in soft-bodied algal cover and biomass. The shift from
coral to algal dominance has led to a marked reduction in coral biodiversity over
whole regions and a notable decline in rates of reef calcification (Kleypas et al.
1999; Gardner et al. 2003; Kleypas 2007). In particular, the demise of Acropora
palmata and Acropora cervicornis over the last few decades has removed zonation
patterns now considered to have been characteristic of Caribbean reefs for at least
the last 125 Kyr (Jackson 1991, 1992; Pandolfi and Jackson 2007).
The recent decline in coral reefs means that a geologic context is required to
establish a baseline independent of any anthropogenic influence that also accounts
for natural, often cyclical, factors (Bak and Nieuwland 1995). The final section
reviews how the taphonomy of living coral reefs may change as a result of the cur-
rent regime of marked human impact and climate change.
2 Spatial and Temporal Variation in Modern Coral Reef

Communities
The modern reef primary framework is dominated by photosynthetic coralline

algae or corals, with the more slow-growing suspension-feeding and filtering
benthos being restricted to cryptic niches. Secondary, encrusting framebuilders
flourish upon the primary framework above the level of accumulating sediment.
Early lithification can aid frame integrity, but mechanical destruction and bioerosion
378 R. Wood
reduces reef framework to rubble and sand (Fig. 1). Reefs however, generally have
a high preservation potential, such that detailed ecological inter-relationships are
often preserved in the ancient record (Fig. 2).
Modern coral reefs grow rapidly, with extension rates in branching corals
exceeding 15 mm/year (Kleypas 1997), and so it has been supposed that some
short-term processes may be preserved in the reef record (Jackson 1983). Coral
growth decreases exponentially with depth and light. However, recently com-
piled data from cores show that reef accretion does not change significantly with
either water depth or dominant coral species within the upper 20–30 m of the
water column (Hubbard 2006). Bioerosion can progress at comparable rates to
coral growth: reef accretion is therefore not constrained by rates of coral growth
alone.
Physical disturbance, grazing pressure and spatial competition are all known to
control the modern coral reef community structure (Wood 1999). Disturbance
shows marked differences in distribution and intensity across a reef profile. Physical
disturbance, predation (and herbivory) and bioturbation all decrease with depth,
Fig. 1 Reconstruction of a modern Indo-Pacific coral reef and its sedimentological expression. 1. Brain
coral (Leptoria phrygia); 2. Feather star (Comanthus bennetti); 3. Parrotfish (Scarus sp.); 4. Staghorn
coral (Acropora sp.); 5. Emperor angelfish (Pomacanthus imperator); 6. Gorgonian; 7. Vase sponge
(Callyspongia sp.); 8. Anemone with clown fish; 9. Giant clam (Tridacna gigas); 10. Encrusting
corals (Montipora and Hydnophora); 11. Brittle star (Ophiarachella gorgonia); 12 and 13. Echinoids;
14. Cowrie gastropod; 15. Sea cucumber (Thelenota ananus); 16. Sea star; 17. Boring bivalve
(Lithophaga sp.); 18. Cement botryoids; 19. Internal sediment; 20. Cone gastropod (Conus textile);
21. Wrasse (Coris gaimard ) (From Wood 1999; copyright John Sibbick)
Fig. 2 (a) Lower Cambrian (Botomian) cryptic reef community showing a variety of pendent
archaeocyath sponges and coralomorphs attached to the walls and ceiling of a crypt constructed
by the calcimicrobes Renalcis (upper left) and Ephiphyton (upper right). Pockets of micrite within
the crypt have been extensively microburrowed. Scale bar = 1 mm. (b) Reconstruction of a Lower
Cambrian reef community (Atdabanian). 1. Renalcis (calcified cyanobacterium); 2. Branching
archaeocyath sponges; 3. Solitary cup-shaped archaeocyath sponges; 4. Chancelloriid;
5. Radiocytahs; 6. Small archaeocyath sponges; 7. ‘Coralomorphs’ 8. Okulitchicyathus (archaeo-
cyath sponge); 9. Fibrous cement; 10. Microburrows (traces of a deposit feeder); 11. Cryptic
archaeocyath and coralomorphs. 12. Cribricyaths; 13. Trilobite trackway; 14. Botryoid cement;
15. Sediment with skeletal debris (From Wood 1999; copyright John Sibbick)
being usually greatest from the lower intertidal zone to about 20 m, particularly on
reef slopes with substrates of high topographic complexity (Hay 1984). Herbivory
is low above mean low water, often reaching a peak at 1–5 m depth on the forereef,
and then declining rapidly with depth (Steneck 1988). Regardless of depth however,
the effects of biological disturbance may be highly patchy and vary markedly
according to local environmental differences.
Problems exist in extrapolating ecological processes to their manifestation in the
geological record, in particular the results of experiments that operate over ecologi-
cal timescales to observations in the fossil record. Inference of cause and effect
require correlation between independent measures of environmental conditions and
biological change, but reduced variability becomes apparent over broader temporal
and spatial scales. Such issues impose an apparent uniformity on community struc-
ture that was, in fact, far more dynamic and labile.
Reef communities are often highly patchy by nature, such that differences in
community structure apparent within a living reef, within core samples, or across
restricted outcrop exposures may not reflect any significant changes in the com-
munity structure as a whole. In addition, methodological differences in data collection,
e.g., quadrat vs. line transects vs chain transects, can produce significantly different
results from the same modern reef (Hubbard 2006).
On a small scale, reef communities are clearly dynamic and to a large extent
unpredictable, but on larger scales (over tens of kilometers and centuries to thou-
sands of years) patterns that show considerable consistency become apparent
(e.g. Pandolfi 1996, 2002). Variation at the smallest scales may be higher than
even biogeographic differences. This suggests that ‘order’ in reef coral communities
380 R. Wood
is lowest at smaller scales, highest at intermediate scales, and intermediate at the

broadest spatial scales within the same biogeographic province (see Pandolfi and
Jackson 2007). Similar trends in predictability are apparent over varying tempo-
ral scales (e.g. Tanner et al. 1994; Pandolfi 1996; Aronson and Precht 1997;
Connell 1997).
3 Taphonomy of the Modern Coral Reef Environment
By definition, all reefs are autochthonous and produced by a local biota. Because
they represent a record of a community that reflects ecological relationships modi-
fied by pre or post mortem disturbance and/or time averaging of generations, reef
deposits can be termed an association (sensu Fürsich 1977).
The taphonomy of living reefs is controlled by the complex interaction and
feedback of many factors (Scoffin 1992). These can be resolved simplistically into
(a) the proportion of the community with preservable hard parts, (b) the source and
rate of skeletal supply, (c) the resilience of both individual reef builders and reef
framework to ambient physical and biological erosion, (d) the environment of accu-
mulation, and (e) and time scale of accumulation (Fig. 3). Many feedbacks occur in
this system. For example, the presence of skeletal hard parts provides substrates for
further colonization, and the accumulation of skeletal material can influence pore
water chemistry and hence subsequent diagenesis. Indeed, reef framework growth
itself may be self-regulating as over-supply of framework-derived sediment will
bury the framework, so terminating growth, arrest bioerosion, and reducing sediment
production (Scoffin 1992).
LIVING REEF PHYSICO-CHEMICAL

COMMUNITY ENVIRONMENT
SKELETAL SUPPLY TAPHONOMIC ROBUSTNESS ENVIRONMENTAL SETTING TIME SCALE OF

- Proportion of - Skeletal morphology - Hydrodynamic regime ACCUMULATION
community with and microstructure - Rates of dissolution and - Rate of accommodation
hard parts - Life habit cementation space change
- Life cycle - Cause of death - Rates of sedimentation - Length of exposure
- Rates of production and exhumation
- Sources - Rates of bioerosion
Fig. 3 The major factors affecting the preservation of reef communities (adapted from Kidwell
and Bosence 1991)
3.1 Loss due to Non-Preservation
Many organisms on reefs have no preservable hard parts, and so this biota will only
leave a record if their tissues have become bio-immured (Taylor and Todd 2001).
Biota with skeletons composed of loose spicules (e.g. sponges and ascidians) will
become dispersed upon death unless buried rapidly in fine-grained sediment.
One insurmountable problem is that the fossil record is virtually mute on many
key ecological players and processes: for example, fleshy and filamentous algae
leave at best a very poor fossil record, and the record of herbivorous reef fish and
higher predators is highly incomplete.
Few studies have considered the proportion of skeletal taxa within reef commu-
nities. Open reef surfaces in Jamaica show an average of 70% skeletal taxa in shal-
low water (60 m), with deeper waters yielding progressively lower proportions
decreasing to 1.8% skeletal taxa at 120 m depth (Liddell and Ohlhorst 1988). In a
reef cave habitat, skeletal taxa represented less than 40% of total species richness
and covered only 15% of the total surface area (Brett 1988).
3.2 Mode of Life, Skeletal Robustness and Rates

of Skeletal Production
Reef environments offer substrate habitats ranging from hard substrates (rock;
cemented substrates; other organisms), to rubble, gravel, sand or muddy soft
sediments. The relative stability of these substrate types is broadly coincident with
the energetics of the ambient hydrodynamic regime, with hard substrates dominat-
ing in the highest energy environments (the reef crest), and muddy sediments in the
lowest (the lagoon). Hydrodynamic action can be provided by tidal currents, wave
action, gravity flows, or intermittent storms.
The mode and timing of death relative to the life cycle will, in part, control
abundance, size and state of preservation of reef material (Scoffin 1992). Skeletal
organisms may be variously killed and crushed by predation, fragmented by storms,
but left intact by pathogens, bleaching of photosymbionts, overgrowth by encrusters,
or rapid burial by storm-generated sediment. All skeletal elements will suffer
bioerosion and encrustation unless buried rapidly beyond the reach of bioturbators,
bioeroders or physical reworking.
Many of the specific causes of mortality for either individuals or whole com-
munities are either difficult or impossible to detect in fossil skeletal reef material.
The range of bioerosive trace fossil morphologies is vast due to the diversity of
organisms involved (Bromley 1992). Of these traces, however, very few are suffi-
ciently characteristic to allow an unequivocal pairing of a particular predator with
a given trace. For example, while Steneck (1983) noted considerable evidence of
predatory damage in fossil solenoporacean and corallinacean algal thalli, he was
unable to determine their origin.
382 R. Wood
Parrotfish (scarids) do produce distinctive stellate marks on the upper surfaces

of scleractinian colonies or algal thalli. Likewise, camerodont echinoderms produce
characteristic pentaradiate grazing traces (Gnathichnus and Radulichnus) due to the
action of strengthened teeth in a stirodont lantern (Bromley 1975). Both these
traces occur in living and dead modern coral material.
The rate and site of skeletal production, the organism longevity, as well as the
aerial coverage, all determine the initial potential contribution of any given organism
to the reef sedimentary record. Reef organisms vary greatly in their rates of skeletal
production as well as their durability in the face of a multitude of destructive forces.
While corals may occupy 90% of a reef framework and the green alga Halimeda
only 10% (Scoffin 1992), the high rate of Halimeda growth and the robust nature
of its skeleton results in 25% of all modern reef sediment being composed of
Halimeda material. By contrast, the relatively fragile platy coral, Agaricia, while
representing 54% of the living community on the shelf-edge of St. Croix, US Virgin
Islands, is completely absent from cores taken though the underlying reef sediment
(Hubbard et al. 1986).
Patterns of fidelity and time-averaging, that is the mixing of successive genera-
tions, are highly complex and there may be no general rules that can be applied
consistently to all ancient reefs. Analyses show that the resolution provided by the
fossil record will vary with different environments, habitat, and facies, such that
each must be evaluated individually (Greenstein 2007). Inter-provincial differences
are likely to be related to differences in live coral diversity, especially for branching
species of Acropora which are difficult or impossible to distinguish when repre-
sented only as rubble.
Size-frequency distributions are controlled by recruitment, growth rate, and
survivorship of a particular population or species (Scoffin 1992), but are also biased
towards the larger size classes such that these data have most value in assessing
post mortem transport history (Cummins et al. 1986). Staff et al. (1986) found that
taxonomic composition, particularly of adults, and the biomass of the death assem-
blage most accurately reflect characteristics of the living community.
3.3 Bioerosion, Abrasion, Transport, and Burial
A considerable proportion of modern reefs are preserved in the geological record as

rubble, sand, and voids as a result of physical and biological destruction (Hubbard
et al. 1990). In addition, storms often remove reef sediment from its origin, and redis-
tribute and reincorporate this material within the reef interior (Hubbard 1992).
Modern coral reefs are characterized by diverse active predators and herbivores,
and non-predatory borers, which prey upon or otherwise attack sessile organisms
and are capable of removing and ingesting calcareous skeletal material (Table 1).
Epilithic predators feed directly upon sessile invertebrates or algae by etching, rasp-
ing or biting, so causing incidental skeletal or substrate damage. These include
excavators that exert deep bites that result in the removal of large areas of substrate,
Table 1 Major groups of bioeroders and bioturbators on modern coral reefs and their first appearance
in the fossil record
Group Ecology First appearance
Cyanobacteria* Borers ?Neoproterozoic (Vermeij
1987)
Fungi* Borers ?Cambrian (Vermeij 1987)
Chlorophyta Borers ?Ordovician (Vermeij 1987)
Rhodophyta Borers ?Ordovician (Vermeij 1987)
Porifera
Clionidae* Borers ?Jurassic (Vermeij 1987)
Annelida
Spionidae (Polychaetes) Deep burrowers Triassic (Thayer 1983)
Mollusca
Polyplacophora Herbivores (scraping) Late Cretaceous (van Belle
1977)
Gastropoda
Patellacea* Herbivores (scraping) Late Cretaceous (Lindberg and
Dwyer 1983)
Diverse Deep burrowers Late Triassic (Thayer 1983)
Bivalvia
Lithophagidae* Borers and live-borers Boring: Jurassic (Vermeij
1987)
Live boring: Eocene (Savazzi
1982)
Arthopoda
Acrothoracica (Barnacles) Borers Boring:
Live boring: Eocene (D.S.
Jones, pers. comm.)
Decapoda Deep burrowers Early Jurassic (Thayer 1983)
Echinoderms
Holothuroidea Sediment disturbers Devonian (Thayer 1983)
Echinodea
Diadematoida* Herbivores and Late Triassic (Smith 1984)
corallivores
Arbacioida Herbivores (excavating)
Echinoida Herbivores (excavating)
Spatangoida (Irregular echinoids) Deep burrowers Early Jurassic (Thayer 1983)
Pisces
Chondrichthyes (Rays & Skates) Sediment disturbers Devonian (Vermeij 1987)
Scaridae* Herbivores (excavating) Miocene (Bellwood and
Schulz 1991)
Mamallia
Trichechidae (Manatees) Sediment disturbers Eocene (Thayer 1983)
*Indicates most important groups (After Vermeij 1987; Wood 1999)
and scrapers that have weaker jaw apparatuses that take smaller bite sizes with
resultant limited substrate removal. The most important excavators and scrapers on
modern coral reefs are limpets, chitons, some regular echinoids, and acanthuroids
(surgeonfish) and scarids (parrotfish). Corallivores include crustaceans (hermit
384 R. Wood
crabs), polychaetes (amphinomids), gastropods (prosobranchs and nudibranchs),

echinoids (diadematoids), starfish, and numerous fish, which are arguably the most
diverse of all reef predators.
Living and dead corals can carry massive and multiple simultaneous or successive
infestations of endolithic organisms, particularly algae, fungi, sponges, and bivalves.
Often only the final generation of borings is clearly preserved after fossilization
(Scoffin 1992). The rise of the endolithic habit is thought to be a direct response to
the rise of predation, as it provides protection from predators: many endoliths have
reduced skeletal defences compared to open surface dwellers or their epifaunal
ancestors (Harper and Skelton 1993). Endoliths severely weaken the skeleton, and
may ultimately lead to the death of the coral, as well as the reduction of the skeleton
to rubble or sediment. Some have estimated that the biomass of endoliths alone can
equal, or exceed, that of the surface biota on coral reefs (Grassle 1973).
Sediment production by bioeroders in reef habitats varies from 0.2 to 16 kg/m2/
year (Scoffin 1987); some estimates suggest that up to 60% of all carbonate produced
is reduced to sediment by bioerosion (Hubbard et al. 1990). Bioerosion by microbor-
ing is most prevalent in quieter water settings (see summary in Scoffin 1992), and
rises substantially in areas of higher nutrient input. Highsmith (1980) has shown that
the proportion of massive corals bored by bivalves increases proportionally with
phytoplankton productivity.
Only a limited number of bioeroders produce diagnostic grains, e.g. clionid
sponge chips. Although many grains may be the result of compounded bioerosion
and physical abrasion, Scoffin (1987) found that in situ mechanical breakdown of
skeletons produces a broad range of grain sizes (from 0.01 to 256 mm), whereas
boring alone produces predominantly fine grains (0.016–4 mm).
The most important bioeroders on Indo-Pacific reefs are scarids (parrottfish),
which are characteristic of reef crests and fronts. Scarids feed on living or dead
convex surfaces, and pass substantial amounts of sediment through their guts which
is then redistributed as fine grain sediments (0.063–1 mm; Scoffin 1987) at the base
of the reef to form large sediment aprons. Estimates suggest that up to 5.6 kg m/
year may be removed by excavating scarids at Lizard Island, on the Great Barrier
Reef (Bellwood 1995). Here, a single male bumphead parrotfish can remove a
staggering 5 t of reef per year (Bellwood 1996).
Scarids thus modify reefs by (a) direct erosion; (b) decrease in particle size due
to erosion and sediment reworking, and (c) the net removal and transport of reef
material directly from the area of most carbonate production (the reef crest and
front) to deep reef sites. As such, they may significantly control the rate of reef
progradation and removal of fine material from the reef system (Bellwood 1995).
Greenstein (2007) argues that any analysis of death or fossil reef assemblages
must compensate for the facts that coral growth forms are differentially susceptible
to degradation. In Papua New Guinea, Pandolfi and Minchin (1995) found that high-
energy reef environments showed a greater loss in fidelity of coral composition
between life and death assemblages than low energy reef environments. But while
high energy environments produced the best-preserved corals, they also preserved the
most biased assemblage. This was in contrast to that found in a comparable study of
contemporary molluscan assemblages. In Florida Keys, deep-water death assemblages
are more diverse than their living counterparts (Pandolfi and Greenstein 1997),
perhaps due to either slower rates of coral growth and sedimentation.
The degradation of corals is determined by the residence time of dead coral
material in the taphonomically active zone (TAZ) which extends a several centi-
metres below the sediment–water interface (Fig. 4). The majority of physical and
biological destruction occurs to skeletal material post mortem. Massive, rather
than branching or free-living, corals are both the preferred site for most borers
(particularly worms, bivalves, and sponges) as well as showing higher rates of
dissolution (Pandolfi and Greenstein 1997). In any reef environment, massive
forms will survive longer in the TAZ than other forms, but in high energy settings
they will be destroyed, transported or buried before extensive taphonomic altera-
tion can occur (Greenstein 2007). In low–energy environments (leeward or
deeper water sites), any colony growth form will survive longer in the TAZ than
in higher energy environments. With the exception of encrusting foraminifera,
however, epibiont encrustation was found to be higher in deep-reef (20–30 m)
settings (Greenstein and Pandolfi 2003).
Encruster succession with reef frameworks or storm-generated coral debris can
be very sensitive to decreasing light levels, so aiding interpretation of the history of
reef framework burial (Scoffin and Hendry 1984).
OPEN WATER
SATURATED OR OVERSATURATED
pH>7
Intense bioerosion
Micritization
TAPHONOMICALLY ACTIVE ZONE (0-10 cm)
NO BIOTURBATION BIOTURBATION
Oxidising, supersaturated Undersaturated

Minimal dissolution High pCO2; pH<6
Marked dissolution
If detritalFe present = pyrite
formation by sulphate reduction
NO IRRIGATION (~10 cm +)
Anaerobic decomposition; pH>8
Supersaturated pore waters
Carbonate preservation
Micritization
Mollusc valve Bioerosion
Encrustation
Coral fragments Dissolution
Pyrite formation
Fig. 4 The major taphonomic processes occurring within reef sediment

386 R. Wood
3.4 Early Diagenesis: Dissolution and Cementation
Aragonite is a metastable mineral that will tend to either neomorphose to calcite

with loss of microstructural detail, or may dissolve completely to form a vug if
exposed to an open system of undersaturated water. The solubility of high-Mg
calcite can exceed that of aragonite; low-Mg calcite is relatively stable.
Rates of change are dependent upon sediment permeability, local water chemistry,
and particularly climate (Fig 5). If reef material remains in contact with trapped
interstitial sea water, mineralogical stabilization can take place over 1–3 million
years, but exposure to freshwater may speed up this process to 100,000–200,000
years in the vadose zone, or 5,000–20,000 years in the phreatic zone (Humphrey
et al. 1986; Matthews and Frohlich 1987).
Micritization occurs in warm, oversaturated waters (Alexandersson 1972), and
chemical leaching or microbial attack can lead to chalky textures of both long-lived
and dead skeletal material. Undersaturation of open or pore waters with respect to
carbonate minerals can lead to etching, leaching, or dissolution of skeletal material.
Cryptic biotas that inhabit caves may suffer preferentially the effects of corroding
solutions which may be flushed through the reef framework (Scoffin 1972).
Smoothing and dissolution of skeletal material has been noted to be greatest in
corals from reef-crest and patch reef environments; encrustation (except by fora-
miniferans) is highest in deep-reef settings (Greenstein 2007).
Upon shallow burial, reef sediment passes into the TAZ. Near-surface pore
waters are generally oxidising and supersaturated due to good exchange with the
overlying saturated water; this generally compensates for the acids produced by
aerobic decomposition of organics (Fig. 4). By contrast, in areas of active bioturba-
tion, undersaturated waters with high pCO2 and low pH may develop which pro-
Proportion of
skeletal biota
Wave energy
In situ preservation
Fragmentation
Bioerosion
Cementation
Dissolution
LAGOON BACK-REEF REEF REEF-SLOPE TOE-OF-SLOPE
CREST
KEY
abundant
present common
Fig. 5 Distribution of the key taphonomic determinants and processes across a generalized reef
transect
motes carbonate dissolution. If reactive detrital Fe is present, diagenetic Fe-sulfides

may form by local sulfate reduction. Below the zone of sediment irrigation (TAZ),
anaerobic decomposition leads to high pH which promotes carbonate preservation,
and early cementation (Fig. 4).
Peterson (1976) studied weight loss in buried shells over 7.5 months. After 50 cm-
deep burial in sand or muddy sand, high-Mg calcite (echinoderm ossicles) lost 10–20%
weight; aragonitic shells lost only 0–4%, and low-Mg calcite (scallop shells) lost
0.14%. In a similar study, Best et al. (2004) studied net weight change in mollusc and
coral material from reef sites in Papua New Guinea. She found that the dominant con-
trol on taphonomic condition was the interaction of environmental energy with skeletal
form and size (affecting exposure), with a secondary control of skeletal microstructure.
Net weight change was positive for exposed bivalves and negative for buried ones,
in both cases within 10% of the initial weight. By contrast, weight loss among corals
was ubiquitous with the exception of a few Acropora, and often ranged between 10%
and 20%. Both bivalves and corals showed lower surface alteration if originally buried;
exposed specimen surfaces showed dull to chalky surface textures.
Cementation is pervasive in reef-fronts and reef-crests where water flux is
high and de-gassing occurs as a result of the pumping action of waves (James
et al. 1976). Walled reef complexes present a prominent steep surface to wave and
current action so that the force of sea water flux is high; low-angle reef profiles
undergo far less cementation (Kendall and Schlager 1981).
Modern reef cements range from aragonitic calcite crusts, fans, and botryoids, and
high-Mg calcitic peloids, equant micrite, and acicular crusts or blades (Macintyre and
Marshall 1988). Cements can grow remarkably rapidly in both shallow and deeper
marginal parts (Grammer et al. 1999), but in high energy areas cementation occurs close
to the framework surface, whereas in sheltered lagoonal patch reefs cementation takes
place several centimeters below the sea floor (Scoffin 1992). Marine lithification pres-
ents further hard substrates for colonisation by reef biota, both encrusters and bioerod-
ers. Pavement-like micrite crusts can form during a hiatus in reef growth, which can
protect underlying reef deposits from diagenetic alteration (Macintyre 1985): rates of
cementation are generally lower during rapid reef growth (Lightly 1985).
3.5 Changing Rates of Accumulation
Rates of terrigenous sediment supply will vary with the proximity of the reef to the
land, with fringing reefs often being most affected. Increased clastic sediment will
introduce nutrients into the system which will stimulate higher rates of bioerosion
(Highsmith 1980).
Rates of reef sediment accumulation also affect the rates of taphonomic pro-
cesses. The longer the period of accumulation, the more likely it is that the taxo-
nomic and size composition of the assemblage will be modified by differential
preservation (Kidwell and Bosence 1991). Geologically very short-term changes in
reef community structure may be preserved only under sedimentation regimes that
favour rapid burial of both living and dead corals, such as during periods of rapid
388 R. Wood
sea-level rise and accommodation space increase that favours the growth of ‘keep-
up’ reefs (Greenstein and Pandolfi 2003). During sea-level fall, reefs may be
exposed to fresh water diagenesis and erosion.
3.6 Detection of Critical Events
In the past few decades, some modern reefs have been subject to ecologically
critical events, such as the Caribbean-wide mass mortality in the early 1980s of
the herbivorous sea urchin, Diadema antillarum, the outbreak of the crown-of-
thorns starfish Acanthaster planci in the Indo-Pacific, and coral bleaching events
and disease. All these highly significant and sometimes catastrophic occurrences
have proven difficult or impossible to detect in the sedimentary record. For
example, even though reef substrates were littered with Diadema spines and tests
several weeks after the mass mortality, less than 1 year later, the impact of rapid
sedimentation and bioturbation was such that evidence of this event was absent
(Greenstein 1989).
Glynn (2000) outlines a variety of potential indicators of past mass bleaching
events that might be applied to fossil material. These include isotopic and trace
metal markers in coral cores indicative of ENSO events, alterations in skeletal
banding, protuberant growths on massive corals, and accelerated bioerosion in reef
sediments. All of these phenomena may, however, be caused by factors other than
bleaching, so greatly limiting their utility. There is also evidence that some bleached
corals may fail to secrete a growth band (see Halley and Hudson 2007). To date, no
historical or fossil record of mass bleaching events at regional scales has been iden-
tified prior to 1982 (Glynn 1993).
Statistical methods, however, such as a probabilistic approach can help to place
bounds on information loss in interpreted event preservation in sets of hierarchi-
cally sampled reef cores (Aronson and Ellner 2007). DeVantier and Done (2007)
also offer a potential methodology to evaluate the frequency of feeding scars of
starfish on living coral heads, so potentially enabling the detection of outbreaks in
the geological record.
A signature for hurricane and storm events has been sought in coral death assem-
blages from San Salvador (Bishop and Greenstein 2001). All metrics of fidelity
increased after Hurricane Floyd, suggesting that each reef setting received a pulse
of storm-derived coral material. Such a signature would only be detectable where
both the life and death assemblages were preserved, and could be distinguished, in
the fossil record. In the Pleistocene of the Bahamas and the Dutch Antillies, reefs
that grew in areas which today receive a lower frequency of hurricanes were found
to have a greater proportion of in situ colonies (Meyer et al. 2003).
Using epibiont colonization sequences, Perry (2001) was able to distinguish
between those Acropora palmata-dominated horizons that were derived from storm
deposition, and those that had accumulated through normal reef accretion. Indeed,
he noted repetition of the same reef succession following each storm horizon, each
culminating in an Acropora palmata community.
The recent (~20 years) shift from coral-dominated (75–5%) to algal-dominated

live (<5 to >65%) cover in Jamaica has also been detected in reef sediment. Prior to
1981, reef sediment was composed of >50% Halimeda and >35% coral, but post-
1981, coral fragments have dominated due to widespread coral mortality and bioero-
sion (Precht and Aronson 1997). This suggests that for corals at least, their presence
in ancient reef sediment may be indicative of widespread coral mortality.
Detection of critical events depends in part on the type of reef facies studied
(Greenstein 2007). Due to the inverse relationship between wave energy and taphonomic
alteration, high-energy reef facies could produce well-preserved fragile corals should
rapid burial occur. However, in reefs with relatively low coral diversity the absence of a
coral species from the death assemblage may be ecologically significant. Geologically
very short-term changes in reef community structure may be preserved only under sedi-
mentation regimes that favour rapid burial of both living and dead corals.
4 Taphonomic Bias in Ancient Reefs: Insight from

the Pleistocene Record
Pleistocene and Holocene coral communities have been widely heralded as offering
a record of pre-anthropogenic reef community ecology (Macintyre 1988; Jackson
1992; Greenstein et al. 1998; Greenstein 2007). While there is considerable
ecological information preserved in Pleistocene reefs, numerous taphonomic pro-
cesses have conspired to change, degrade or remove the evidence of events from
future fossil communities that appear vital to understanding the functioning of
present-day reefs (Greenstein and Moffatt 1996). Knowledge of which processes
can be justifiably explored by analysis of the fossil record – and those that cannot
– is therefore vital before any conclusions can be drawn.
Many authors have concluded that Pleistocene strata preserve a composite of
both the living reef and the associated death assemblages (e.g. Goreau 1959;
Ginsburg 1964; Edinger et al. 2001). Reef-coral death assemblages are therefore
not reasonable proxies for fossil assemblages (Greenstein 2007), and it is possi-
ble that such composite assemblages where reef structure is integrated over
ecological time may be the norm for all ancient reefs (Edinger et al. 2001).
Relative abundance data are available in fossil reefs and can be used to deter-
mine ecological patterns over broad temporal and spatial scales (Pandolfi and
Jackson 2007), but other potential sources of data may be highly biased. For
example, Acropora cervicornis growing in Pleistocene high-energy facies have
been found to be significantly less degraded than these species from modern
death assemblages; indeed branching growth forms are consistently over-represented
in death assemblages due mainly to far higher rates of growth and fragmentation
(Greenstein and Moffatt 1996).
It appears that patterns of fidelity and time-averaging are highly complex, and
there may be no general rules that can be applied to all ancient reefs. What is clear
is that the resolution provided by the fossil record will vary in different environ-
ments and within each habitat, and that facies must be evaluated individually.
390 R. Wood
5 Changes in Reef Taphonomy Through the Phanerozoic
The modern coral reef ecosystem is geologically very young. Scleractinian corals
appeared in the mid-Triassic, and had almost certainly acquired photosymbionts by
the late Triassic at the latest (Stanley and Swart 1995). Most modern coral genera
appeared in the Eocene–Miocene (55–5.3 Ma), and many extant species extend
back no further than the Pliocene (5.3–1.8 Ma) (Rosen 1984). Modern reef fish
appeared in the Eocene (50 Ma), but the oldest record of parrotfish (scarid) remains
are from Miocene sediments dated at 14 Ma.
During the Oligocene, the compression of climatic belts and the rise of the
Isthmus of Panama created two distinct regions of reef growth to the Caribbean and
Indo-Pacific. As a probable result of climatic cooling or habitat loss, a major episode
of coral faunal turnover ensued between 4 and 1 Ma in the Caribbean (Budd et al.
1994). Extinction of genera in the Pocilloporidae and Agaricidae was most marked,
but many of these genera continued to persist in the Indo-Pacific. A similar differen-
tial extinction coincident with corals removed all large excavating scarids, herbivo-
rous siganids, and plantivorous caesionid fish from Atlantic reefs (Bellwood 1997).
Although acroporid corals appeared in the Eocene, pocilloporids appear to have
dominated Caribbean reefs from 5 to 6 Ma, but following a 1 Myr transition period
of mixed acroporid-pocilloporid asemblages, acroporids became dominant in reef
communities in the early Pleistocene (approx. 1.6 Ma). Acroporids may not, how-
ever, have achieved levels of extreme abundance until the late Pleistocene (approx.
0.5 Ma) (Budd and Kievman 1994). With this as yet unexplained rise to dominance
of branching Acropora, and a corresponding decline in massive, domal corals, coral
reef communities with a completely modern aspect appeared about 0.5 Ma. Except
for the extinction of Pocillopora in the Caribbean at about 60 ka, the patterns of
community membership and dominance of coral species appears to have been
highly predictable for at least the past 125 Kyr (Pandolfi and Jackson 2001).
The Phanerozoic witnessed major turnovers of reef biotas, mass and minor
extinction events, and profound changes in the chemistry of sea water. This section
explores the effects of biological innovations and extrinsic controls upon reef ecology
and taphonony.
5.1 Rise of Biological Disturbance
Many researchers have emphasized the importance of herbivores and large marine
vertebrates to the healthy functioning of coral reefs (see Wood 1999), and this is
corroborated by analysis of the fossil record. A dramatic escalation of new organ-
isms with innovative and destructive feeding methods occurred from the mid-
Jurassic to Miocene (Table 1); indeed a taxon-independent morphological signal of
herbivory is not recorded until the Eocene (Bellwood 2003). In particular, the
arrival of piscine herbivores had the potential to fundamentally alter the dynamics
of reef and other benthic marine communities.
In general, herbivorous grazers and carnivores throughout the Paleozoic and

early Mesozoic were relatively small individuals with limited foraging ranges inca-
pable of excavating calcareous substrates. A radiation during the Devonian of
durophagous, mobile predators has been proposed by Signor and Brett (1984), but
these forms probably relied upon manipulation only to crush or ingest (Harper and
Skelton 1993). By the early Mesozoic, sessile organisms had to contend with an
increasing battery of novel and more advanced feeding methods, as well as sediment
disruption due to deep bioturbating activity (see summary in Vermeij 1987). Most
notable was the rise of efficient excavation behaviours.
Bioerosion notably increased in intensity from the mid- to Late Jurassic. A
radiation of endoliths occurred from the Triassic onwards, with deep borers (capa-
ble of penetration greater than 50 mm) appearing from the Jurassic. Clionid
sponges – one of the major bioeroders on modern coral reefs – had become abun-
dant by the latest Jurassic. The first live-borers are known from the Eocene (Krumm
and Jones 1993), as are fishes similar to modern reef faunas (50 Ma) (Bellwood
1996). The ability for substantial excavation of hard substrata over large areas
increased considerably from the latest Cretaceous-Early Tertiary when deep-grazing
limpets, camerodont sea urchins, and especially the reef fishes appeared. The com-
plex pharyngeal apparatus of labrids was present at this time, and major labrid
clades were already differentiated (Bellwood 1997). Balistids first appeared in the
Oligocene, and the oldest scarid fossil capable of deep excavation currently known
is from the Miocene (14 Ma) (Bellwood and Schulz 1991). It seems likely that
sometime during the Oligocene – Miocene, reef bioerosion gained a modern caste
(Pleydell and Jones 1988).
The abundance of reef fishes is assumed to be of great importance on coral reefs,
as evidenced by the dramatic increase of algal growth as a result of their decline on
Jamaican reefs (Hughes 1994). Tropical marine hard substrata are usually sparsely
vegetated, but a rich algal flora develops when herbivorous fish are excluded and/
or nutrient input increases. Grazers not only promote the dominance of corals and
coralline algae on coral reefs, they also contribute notably to carbonate sediment
production and redistribution, algal ridge formation, and the maintenance of overall
diversity. Like other predators, they can also ameliorate the effects of competition
and may combine with physical controls to produce the characteristic zonation of
modern coral reefs.
The major causes and indirect effects of predation, particularly herbivory, on
coral reef communities (Table 2) are such that a series of effects on reef ecology
and taphonomy can be predicted. In the sections following, these predictions
are tested.
5.2 Response to Increase in Disturbance
Only skeletal anatomy and morphology, spatial distribution, and skeletal attack or
breakage, and regeneration might be detected – or inferred – in the fossil record of
reef organisms.
392 R. Wood
Table 2 Predicted changes in reef community ecology and taphonomy based on the rise to abun-
dance of new predatory methods and endoliths as evidenced in the fossil record (After Wood 1999)
Event Prediction Timing
The rise of macroherbivores A shift to more conspicuous, Late Mesozoic-Eocene
well-defended macroalgae
(coralline algae) on reefs
The rise of specialized Increase in diversity and
predators retardation of dominance;
reducing or preventing
competition
Limiting of foraging ranges Late Mesozoic-Eocene
Zonation: Interaction of physical Eocene
controls with differential effects
of damselfish in the survival
of different coral species
The rise of excavatory A shift to organisms with deterrent Late Mesozoic to
grazers and predators traits and those which tolerate Miocene
partial mortality
Increase in multiserial, branching Cretaceous onwards
corals
Increase in the diversity of Jurassic onwards
the cryptos and other
spatial refugia
Algal ridge formation by coralline Eocene
algae
Rise of intense bioerosion Reduced reef framework Late Mesozoic to
and endoliths preservation Miocene
Sediment grain size Late Mesozoic to
reduction Miocene
An increase in skeletal Late Jurassic
sediment production
Increase in multiserial Throughout history of
scleractinian corals the group
The rise of parrotfish Formation of sediment aprons Miocene
Thick coralline algal crusts Miocene
Reduction in rate of reef Miocene
progradation
Herein, the origin and diversification of such fossilizable traits are considered
for Paleozoic reef-building cnidarians and skeletal sponges, coralline algae and
scleractinian corals. The appearance of excavatory herbivores paralleled pro-
found changes in reef ecology, including the rise of well-defended, highly tolerant
coralline algae (Steneck 1985), a notable increase in branching corals since the Late
Cretaceous (Jackson and McKinney 1991), and the loss of many functional organisms
that prove to be intolerant to excavatory attack (Table 2). This suggests a cause-
effect system where adaptation to predatory attack has been intimately bound to the
origin and assembly of modern reefs.
5.2.1 Secure Attachment to a Hard Substrate
Organisms without secure attachment to a stable substrate are susceptible to the

effects of disturbances. In modern shallow shelf seas, immobile epifauna are typically
excluded from most soft-substrates, which are dominated by mobile deposit feeders.
While immobile, but unattached corals are common today, they are restricted mainly
to areas protected from high biological and physical disturbance. Most modern sus-
pension-feeders require a hard-substrate, even if these are only isolated patches
within areas of unstable, soft-substrate (‘benthic islands’, or in dense aggregations).
Possession of an edge zone in all but the most primitive scleractinian corals
allows them to gain permanent attachment to a stable substrate. As a result, scler-
actinian corals dominate modern reef framework environments, especially those in
high-energy settings where there is also an abundance of wave-swept, extensive
hard substrata for colonization. Permanent attachment also allows the development
of very large branching morphologies.
Cambrian archaeocyath sponges usually bore small holdfasts that enabled lim-
ited attachment to hard substrates (Fig. 2). But many mid- to late Paleozoic reefs
were dominated by large, sheet-like invertebrates (stromatoporoid sponges, tabulate
and rugose corals, and trepostome and cystoporate bryozoans) that were initially
attached to small, ephemeral skeletal debris and then grew over the surrounding
sediment (Fig. 6). Small, branching forms (some stromatoporoids and bryozoans)
lacking extensive attachment sites were also common, and they were presumably
partially rooted in soft-sediment. For most Paleozoic metazoan reef builders there
is little evidence for any active recruitment onto extensive hard substrates; these
forms were unspecialized and immobile.
The late Paleozoic decline of immobile epifauna coincides with the rise of major
bulldozing taxa, which passed through the end-Permian extinction unscathed. This
coincidence must remain conjectural until tested experimentally.
Since their inception 3.5 billion years ago reefs have developed zonation in
response to environmental gradients (see summary in Wood 1999). Detecting the
exact nature of the added affect of damselfish herbivory, known to be an important
determinant of modern coral reef zonation, will therefore be highly problematic to
assess. Likewise, metazoan reefs have been differentiated into open surface and
cryptic reef communities from their inception (Wood et al. 2002), and this together
with the taphonomic loss of soft-bodied and preferential dissolution of skeletal
organisms from cryptic habitats makes any meaningful quantification of changing
diversity of these two settings through geological time virtually impossible.
5.2.2 Resistance to Partial Mortality
Predation that actively excavates underlying skeleton often results in sub-lethal

damage. In such cases, the capacity of the prey to heal or replace damaged areas of
soft tissue becomes critical to survival. Strategies that rely upon herbivores/preda-
tors to remove competing algae therefore often entail the loss of the prey’s own
394 R. Wood
Fig. 6 (a) Permian Capitan reef (Middle Capitan) community of bryozoans (arrowed ) with pen-
dent sphinctozoan sponges. Remaining cavity space is filled with early botryoid cements, origi-
nally aragonitic now pseudomorphed to calcite; Upper Permian, Mckittrick Reef Trail, Texas,
USA. Scale bar = 20 mm. (b) Reconstruction of Permian Capitan reef community 1. Frondose
bryozoan (Polypora sp. and Goniopora sp.); 2. Solitary sphinctozoan sponges; 3. Archaeolithoporella
(encrusting ?algae); 4. Microbialite; 5. Botryoidal cement; 6. Sediment (grainstone-packstone)
(from Wood 1999; copyright John Sibbick), (c) Platy stromatoporoid sponge community, with
cryptic Shuguria. Remaining cavity space is infilled with radiaxial calcite cement and sediment;
Upper Devonian (Frasnian), Geikie Gorge, Western Australia. (d) Reconstruction of platy stro-
matoporoid sponge reef community 1. Domal stromatoporoid (Actinostroma sp.); 2. Laminar
stromatoporoid (Stachyodes australe); 3. Tabular stromatoporoid; 4. Shuguria (calcified cyanobac-
terium); 3. Stalked lithistid sponge; 6. Spiny atrypid brachiopod; 7. Radiaxial fibrous calcite
cement; 8. Sediment (From Wood 1999; copyright John Sibbick)
tissues. Algal turfs grow very rapidly and so can regenerate from basal portions that
have escaped herbivory.
In coralline algae, a protective outer epithallus overlies the more delicate mer-
istem, fusion cells allow the rapid translocation of photosynthates, and conceptacles
that contain reproductive structures are enclosed within the perithallus. These struc-
tures have been demonstrated to protect the delicate reproductive anatomy from
intensive grazing (Steneck 1982, 1983). Conceptacles are, however, no match for
the deep excavation of parrotfishes, perhaps explaining why such structures are
found only on non-tropical, thickened, crusts. Many coralline algae can also toler-
ate intense herbivory due to their ability to rapidly regenerate removed material
(Steneck 1985, 1988). Thickened crusts are more tolerant to attack than thin
encrusting or branching forms (Steneck 1985), but in modern reefs, the dominance
of a particular growth form appears to be a trade-off between the cost of investment
in increased defence, and the reduction in growth rate or competitive ability. As a
result, thickened crusts dominate only in areas of high wave energy and biological
disturbance. After the Eocene, herbivore-susceptible, delicately branched coralline
algae reduced in abundance in the tropics, the proportion of thickened encrusting
forms increased, and the first algal ridges appeared – all coincident with the rise of
excavatory herbivorous fish (Steneck 1985, 1988).
Many sessile reef organisms possess a modular or colonial habit where partial
predation and boring may remove either individual or a few modules, or large areas
may be cleared of living tissue, sometimes together with the excavation of underly-
ing skeleton. But the modular organization also reduces soft-tissue to a relatively
thin veneer over a larger basal skeleton. This not only decreases accessibility and
the ease of prey manipulation by predators, but also minimizes the tissue biomass
while maximizing the cost of collection. For example, in a typical domal colony of
Porites, only about 0.5% of the colony’s radius is occupied by soft tissue (Rosen
1986). In branching and platy colony forms, the relative proportion of skeleton is
even higher.
Cambrian archaeocyath sponges show a steady and marked increase in the pro-
portion of complex modular forms during their history (Wood et al. 1992), as do
scleractinian corals since the mid-Triassic, which appears to be uninterrupted by the
end-Cretaceous extinction event (Coates and Jackson 1985).
5.2.3 Regeneration After Breakage
Some morphologies are more resistant to breakage than others. For example, colo-
nies with closely spaced branches can make predator access difficult by forming
hidden, protected areas. The flattening of branch terminations can also offer greater
resistance to all forms of breakage and shearing, and this character is found in erect
species of bryozoans, gorgonian corals and stylasterine corals.
A multi-serial modular organization, however, in addition to promoting architec-
tural diversity and flexibility (Fig. 7), also allows compartmentalization of damage and
enables some colonies to regenerate from fragments (Jackson and Hughes 1985).
Most significantly, branching corals also show tremendous powers of regeneration:
Acropora palmata has one of the highest rates recorded (Bak 1983). Indeed, unlike
massive, platy or encrusting forms, damage to branching corals often leads to an
immediate increase in growth rate so causing an increase in size rather than simply
repairing damaged tissue.
Populations of the staghorn coral (Acropora cervicornis) frequently form dense,
monospecific stands on shallow Caribbean reefs, but there is little evidence of
396 R. Wood
Fig. 7 The variety of corals found on modern coral reefs showing flexibility of the modular habit,
and the diversity of branching morphologies. 1. Cup-shaped soft-coral; 2. Columnar; 3. Free-
living (solitary); 4. Digitate; 5. Encrusting; 6. Corymbose; 7. Caespitose; 8. Bottlebrush;
9. Massive; 10. Foliaceous (cup-shaped); 11. Foliaceous (whorl-forming); 12. Tables and plates;
13. Massive; 14. Arborescent (staghorn); 15. Arborescent (elkhorn) (From Wood 1999; copyright
John Sibbick)
frequent sexual recruitment (Tunnicliffe 1981). The fragile organization of this spe-
cies results in easy breakage due to high wave activity and bioerosion, especially
by boring sponges that infest the colony bases. However, such corals are able to
re-anchor fragments and rapidly regenerate and grow, often fusing with other colonies,
at rates up to 150 mm/year (Tunnicliffe 1981). Such branching corals have turned
adversity into considerable advantage, and appear to flourish because, and not in
spite, of breakage.
The percentage of scleractinian erect species (mainly low integration phaceloid-
dendroid growth forms) decreased until the Turonian, but increased markedly –
particularly in multi-serial forms with inferred rates of rapid regeneration – after
that time (Coates and Jackson 1985). This spectacular rise of various morphologies
of branching forms (Fig. 7) was coincident with the appearance of new groups of
predatory excavators.
All families of modern scleractinian corals that dominate reefs today spread
throughout Tethys during the Eocene. The poritids, their relatives the actinids, and
the favids (which had survived the Cretaceous extinction) dominate most coral reef
communities throughout much of the Cenozoic (McCall et al. 1994). Although
branching acroporoids appeared in the Eocene, they did not dominate reefs until
early Pleistocene. The rise of this group – with its particularly remarkable powers
of regeneration from fragmentation and rapid growth – would then seem to be
independent of any known changes in predation style.
5.2.4 Patterns of Sediment Removal and Storage
Anecdotal evidence suggests that the proportion of reef framework preserved in situ
before the Jurassic (Wood 1999) is greater than that occurring today. Many
Paleozoic reefs commonly preserve intact reef frameworks, even of fragile biota
such as frondose bryozoans (Fig. 6a, b) or platy stromatoporoid sponges (Fig. 6c,
d). Such preservation was aided, in part, by abundant and probably rapid syn-
sedimentary lithification, particularly cementation.
Almost nothing is known as to possible changes in the style of skeletal sediment
production and distribution within reefs after the appearance of abundant bioero-
sion from the Late Jurassic, especially after the appearance of reef fish in the
Eocene, and the rise of the scarids in the Miocene. We might predict that substantial
aprons of sediment may not have been present on pre-Eocene reefs. Likewise in the
absence of the grain size reduction activities of clionid sponges, echinoids and fish,
mean sediment grain size may have been more coarse prior to the late Jurassic,
perhaps resulting in a reduced net loss of carbonate to the system through the
removal of fines. It is possible also that the modern style of coral reef lagoon may
also not have appeared until the late Jurassic or later.
Also, barely explored are sedimentological consequences of differences in the
geographical distribution of bioeroders – which is especially marked in fish popula-
tions due to differential extinction in the Atlantic during the mid–late Cenozoic
(Bellwood 1997). This extinction resulted in the conspicuous loss of large excavat-
ing scarids from Caribbean reefs. Compared to the Atlantic, it may be predicted that
modern Indo-Pacific reefs show the formation of larger slope sediment aprons,
reduced rates of progradation of the reef crest, and a greater loss of carbonate in the
form of fine grains in suspension from the system. These differences in sediment
dynamics, however, require further quantification.
5.3 Response to Changing Seawater Chemistry:

Secular Changes in Mineralogy
The dominant form of precipitated crystalline CaCO3 has oscillated during the
geological past, with both inorganic and organic production of aragonite and
high-Mg calcite dominating carbonate formation during cool (icehouse) periods,
and low-Mg calcite predominating during warm (greenhouse) periods (Sandberg
1983; Stanley and Hardie 1998). Such mineralogical shifts are interpreted as
markers for major changes in seawater chemistry. Stanley and Hardie (1998)
proposed that it was shifts in Mg:Ca that has controlled the predominance of
calcite versus aragonite secretors, particularly reef builders, due to the inhibiting
effect of high Mg2+ concentration on calcite secretion. Experimental work has
subsequently confirmed the profound influence of Mg:Ca sea water ratios on
398 R. Wood
modern reef builders, including scleractinian corals (Ries et al. 2004) and
Halimeda algae (Ries 2006).
Scleractinian corals were dominant reef-builders in the Jurassic, but they did not
build extensive reefs during the greenhouse period (calcite seas) of the Cretaceous.
During this period, their species diversity remained high but with lower abundance
on carbonate platforms compared to the Jurassic, and with a distribution shifted to
outer platform settings and higher latitudes (~35–45°N; Rosen and Turnsek 1989).
There are many hypotheses offered to explain these observations, including the
high temperatures, restricted circulation, unstable sediment conditions of Cretaceous
platforms, and the favouring of the calcite-producing rudist bivalves over aragonite
corals (Wood 1999; Steuber 2002).
The role of changing seawater chemistry on the selective loss of aragonitic and
high-Mg skeletal faunal is explored further in Cherns et al. (this volume). They
argue that the fossil and skeletal grain record, particularly in siliciclastic and low-
energy carbonate settings are markedly under-represented in these metastable car-
bonate minerals due to selective dissolution of during calcite seas. This is likely to
hold true also to some extent in the reef record, but the loss would be predicted
to be far less in in situ frameworks which became syn-sedimentarily encased by
secondary framework and early marine cements.
5.3.1 Changing Styles of Early Diagenesis
Evidence is persuasive that changing global seawater chemistry has exerted secular
changes in the dominant carbonate mineralogy of reef organisms (Stanley and
Hardie 1998). It is likely, also, that seawater chemistry has also influenced the style
of early diagenesis in carbonate regimes.
Hardgrounds, synsedimentary lithified seafloors, are found almost exclusively
during periods of calcite seas (Wilson and Palmer 1992) due to the elevated abun-
dance of calcium ions. Enhanced rates of calcite cementation during these times
may have aided preservation of otherwise vulnerable biota to disturbance, particu-
larly in crypts, and promoted rapid lithification of the reef framework, but this has
yet to be documented.
The mineralogy of early marine reef cements also seems to follow the same
secular changes (Wood 1999). For example, aragonitc botryoids are known exclu-
sively from phases of aragonite seas (Early Cambrian, mid-Carboniferous to
Early Jurassic, and mid-late Cenozoic), and while radiaxial calcite is unknown
from the Quaternary, it is common in reefs that grew in calcite seas (particularly
the Ordovician to Devonian).
There is also some limited evidence for enhanced sea-floor dissolution of arago-
nite during calcite seas (Palmer et al. 1988), but this requires further documenta-
tion. If present, such dissolution may have direct taphonomic consequences
(explored further in Cherns et al. this volume). The exact nature of the control of
sea water chemistry on all these diagenetic phenomena and the subsequent effects
upon reef taphonomy remain to be quantified and tested experimentally.
6 Current Global Change and Taphonomy
How does the deep past, facilitate prediction of the taphonomic response of reefs to
current global, anthropogenically-mediated, change, and to what extent might the
processes that operated in the absence of anthropogenic change be at work today?
This section concentrates on processes known to be important agents of current
change and destruction in modern reefs.
6.1 Loss of Herbivores and Higher Predators
Many researchers have summarized the case for the importance of herbivores and
large marine vertebrates to the healthy functioning of coral reefs. Jackson et al.
(2001) present multiple historical data over a range of scales and biogeographic
realms to show how overfishing of key marine vertebrates has been the major cause
of the profound ecological changes seen on corals reefs (and other coastal ecosys-
tems). These authors argue that overfishing may also be a necessary precondition
for additional sources of degradation – such as eutrophication, and outbreaks of
disease or gregarious species – to occur. The superimposition of multiple factors
leads to feedbacks that cause increased vulnerability due to complex synergies, and
these are far from understood.
Reduction of reef herbivore populations will almost certainly lead to an increase
in soft-bodied algal biomass, and a decrease in coral cover. In turn, this may lead
to enhanced rates of bioerosion, particularly in areas of eutrophication or outbreaks
of disease. It is likely that such widespread predicted coral mortality will cause
highly degraded coral fragments to dominate death assemblages and the subsequent
fossil record due to widespread coral mortality, endolithic algal activity, and bioerosion
(Precht and Aronson 1997).
6.2 Changing Storm Patterns
The behaviour of hurricanes and storms has been reviewed by Reigl (2007). The
frequency of Atlantic hurricanes appears to follow 15–20 year cycles, and since the
mid-1990s a period of more vigorous hurricane activity has begun. He suggests that
the frequency of such storms is not predicted to increase under conditions of global
warming, but peak intensities and their relative moisture content may increase,
which will notably increase their powers of destruction. Tropical cyclone basins
may also shift, so exposing more (or less) reef areas to their effects. This is likely
to increase damage until acclimatization can take place.
Increasingly powerful tropical storms are predicted to reduce the proportion of
in situ reef framework preserved and to increase all the metrics of coral death
400 R. Wood
assemblage fidelity in the sedimentary record, but such a signature would only be
detectable where both the life and death assemblages were preserved and distin-
guished, perhaps via changed in epibiont encrustation successions.
6.3 Rise in Sea Level
Sea level is expected to rise by about 0.5 m during this century (Houghton et al.
2001), two orders of magnitude less than the 120 m rise since the last glacial maximum.
Reefs are not considered to be directly threatened by sea-level rise in terms of
drowning (except where no suitable substrates for colonization are present) as the
geological record of reefs shows extraordinary robustness in response to cata-
strophic sea-level change (Macintyre 2007). There may, however, be many other
indirect effects of sea-level rise that could have an impact on some reefs: decreasing
light-dependent calcification rates will severely restrict rates of reef growth poten-
tially leading to drowning, and nutrients and sediments released from newly
flooded coastlines could lead to degradation of water quality. Many of these
scenarios will enhance bioerosion rates on reefs.
6.4 Rises in CO2 and Global Temperature
According to the IPCC’s Special Report on Emission Scenarios (Nakićenović and

Swart 2000), atmospheric CO2 concentrations within this century are predicted to
reach between about 555 and 825 ppmv. Such a rise represents a doubling of the
pre-industrial concentration by the middle of this century, and other greenhouse
gases (CH4, N2O, H2O) will increase as well (Houghton et al. 2001). The range of
predicted temperature increase among models included in the Third IPCC Report
is large (1.4–5.8°C for the period 1990–2100; Houghton et al. 2001), with most
coupled models indicating greater warming at high latitudes than within the tropics
(Kleypas 2007).
Carbonate-rich sediments at shallow ocean depths (<200 m) represent a major
CaCO3 reservoir that can rapidly react to decreasing saturation state of seawater
with respect to carbonate minerals produced by rising atmospheric pCO2. Kleypas
(2007) suggest that the current rapid rate of increase in atmospheric CO2 concentration
is potentially catastrophic for regulation of Earth’s climate and carbonate system, as
the timescales of natural feedbacks required to return these systems to equilibrium
are far greater than the timescale of fossil fuel burning. There is also the possibility
that emergent diseases (pathogens) that thrive in warmer oceans will increase. This
may lead to a synergistic effect in that such pathogens may preferentially attack an
already vulnerable and weakened reef biota.
While reefs that formed during the Paleocene and Eocene may provide impor-
tant clues in terms of certain physical reef characteristics such as calcification rates
and distribution patterns, they are probably less useful as analogues for current
ecological response as most of the dominant modern coral reef species, notably
acroporids, had not appeared by that time.
The massive coral reef bleachings of the last two decades which have led to
widspread coral mortality are probably unprecedented within this century and for
several preceding centuries (Aronson et al. 2000). They are closely associated with
abnormally warm sea surface temperature, and the clear inference is that global
warming is their cause, exacerbated by other factors such as subaerial exposure,
increased penetration of UV light, and decreased water circulation.
Reef-building corals and other symbiotic organisms can adapt to increasing
temperatures through a range of mechanisms, including short-term acclimation,
medium-term acclimatization, and even natural selection (Coles 2001). While cor-
als will vary in their required acclimation periods, it is likely, however, that many
corals will be unable to acclimatize sufficiently rapidly such that bleaching events
with increased coral mortality will increase in frequency and strength over coming
decades.
6.5 Changes in Sea-Water Chemistry
Although predicting seawater chemistry changes in the surface ocean over the short
term (e.g. 100–200 years) is fairly straightforward, these predictions are compli-
cated by biological response to increased pCO2. Calcification of reef-building
organisms decreases as pCO2 increases, while organic carbon production may
increase (Riebesell et al. 2001). Accurate prediction of surface seawater chemistry
changes over the next one to two centuries will therefore depend on how well we
predict both atmospheric CO2 changes, and the biological responses and feedbacks
(Kleypas 2007). Results from the Hamburg Model of the Ocean Carbon Cycle
(HAMOCC) coupled with a carbonate sediment diagenesis model (Archer et al.
1997), predict that these processes will, however, require thousands of years to
bring the carbonate system back to pre-industrial conditions.
All experimental work on natural reefs and in artificial conditions shows that
calcification rates decrease and dissolution increases as the calcium carbonate satu-
ration state declines (Gattuso et al. 1996; Suzuki and Kawahata 1999; Kayanne
et al. 2003). Experimental evidence indicates that biogenic calcification rates are
already 10–20% lower than they were under pre-industrial conditions. Kleypas
et al. (1999) estimated that the average calcification rate on reefs may have already
declined by 6–14% as atmospheric pCO2 has increased from 280 ppmv to the
present-day value of 370 ppmv. Halley and Yates (2000) estimated that on a reef in
Hawaii, the dissolution rate will equal the calcification rate when atmospheric CO2
concentrations reach double pre-industrial levels.
Atmospheric pCO2 prior to the Miocene probably remained higher than today
but that Mg:Ca ratio was probably lower than that of today (Wilson and Opdyke
1996), so that the ocean chemistry of the near future cannot be adequately compared
402 R. Wood
to any past Tertiary time period (B.N. Opdyke, pers. comm. in Kleypas 2007).
Ocean chemistry of the near future will be unique and extraordinary, mainly
because the rapidity of the increase in atmospheric CO2 will drive the system out of
equilibrium.
Rates of reef cement precipitation are also likely to change in response to
seawater chemistry changes. As outlined in the review of Kleypas et al.
(2001) these factors together with increased rates of dissolution will almost
certainly lower the net carbonate deposition on reefs, and so reduce reef-
building potential globally.
7 Summary
Reefs have been subject to markedly shifting changes in taphonomic processes

through the Phanerozoic (Fig. 8). Biological disturbance has clearly escalated since
the Mesozoic. Reef biotas have responded with the proliferation of traits with
proven anti-predatory benefits, particularly rapid regeneration after partial mortality.
Indeed some modern dominant reef taxa, such as branching corals and coralline
Environmental Change Evolutionary Taphonomic Processes

Climate Seawater Innovation and Response
Chemistry
Cenozoic
Aragonite Escalation of destruction of reef framework to rubble,

Icehouse transport of sediment from reef front, formation
of sediment apron. Sediment grain–size reduction
Appearance of excavatory Dominance of thick coralline algal crusts; reduction of
fish and live-borers branching forms
Dominance of fragmented, branching corals
Calcite Algal ridge formation
Mesozoic
Greenhouse Increase in dominance of branching corals

Rise of endoliths Favouring of calcitic reef benthos?
Rise of bioeroders Increase in diversity of cryptic reef communities
Rise of excavatory grazers Shift to well-defended coralline algae
and predators Bioerosion of intact reef framework; increase in
Aragonite Rise of macroherbivores sediment production
Reduction of soft-sediment sessile benthos; increased
Icehouse Rise of deep bioturbation time-averaging?
Favouring of aragonitic reef benthos?

Paleozoic
Rise of denuding herbivores
Calcite
Greenhouse Favouring of calcitic reef benthos?
Dominance of soft-sediment massive/laminar reef
benthos
Reef frameworks intact
Aragonite
Fig. 8 Summary of major environmental changes and evolutionary innovations through the
Phanerozoic that created taphonomic processes and responses on reefs. Approximate position of
global climate states (Icehouse; Greenhouse) from Fischer (1983), and seawater chemistry states
(aragonite or calcite seas) from Sandberg (1983)
algae, appear not only to thrive, but actually require conditions of considerable
disturbance for their survival in shallow tropical seas.
Many modern reefs are largely reduced to rubble and sand via physical abrasion
and particularly bioerosion. These reefs, their fossil assemblages, and final geologi-
cal expression, are all dominated by branching corals due to their high diversity and
abundance in living communities, propensity to proliferate via fragmentation, and
resilience to taphonomic destruction. By contrast, many pre-Jurassic reefs, prior to
the escalation in bioerosion, show the common preservation of intact, in situ frame-
works, and a dominance of massive or laminar growth forms. In addition, most of
the unattached, soft-sediment dwelling organisms typical of Paleozoic reefs appear
to have become largely absent from shallow marine tropical reef biotas during the
late Paleozoic to early Mesozoic, perhaps due to intolerance of deep burrowing taxa
and excavatory attack.
Scleractinian corals, in particular branching taxa, show a marked increase in the
proportion of forms with complex modularity from the Eocene onwards, even
though corals displayed the full range of morphological forms and corallite size by
the Late Triassic. Highly defended, thick crusts in coralline algae become more
dominant, and branching forms also become noticeably less conspicuous, on reefs
from the Eocene onwards. This major reorganization of the coral reef ecosystem
coincides with the rapid appearance and radiation of herbivorous and corallivorous
reef fish, but this remains to be tested experimentally.
We know little as to possible changes in the style of skeletal sediment production
and distribution within reefs after the appearance of abundant bioerosion in the Late
Jurassic, especially after the appearance of reef fish in the Eocene, and particularly
with the rise of the scarids in the Miocene. In addition to the loss of common intact
reef frameworks, we might predict that substantial aprons of reef-slope sediment
may not have been present on pre-Miocene reefs, and likewise in the absence of the
grain-reduction activities of reef fish, echinoids, and clionid sponges, the size dis-
tribution of sediment grains may have been more coarse due to the dominance of
physical abrasion on Palaeozoic reefs. We also need to quantify the taphonomic and
sedimentological consequences of differences in the geographical distribution of
bioeroders, particularly a comparison between the Cenozoic history of Caribbean
reefs that lack large excavating scarids after the Miocene, and Indo-Pacific reefs
where they remained and flourish to this day (Bellwood 1997). It is also possible
that the modern style of coral reef lagoon may also not have appeared until the late
Mesozoic-Cenozoic, and that the carbonate budget of reef systems has shifted to
greater net loss due to removal of fines since the late Jurassic.
Evidence is persuasive that changing global seawater chemistry has exerted
secular changes in the dominant carbonate mineralogy of reef organisms (Stanley
and Hardie 1998), and it is likely, also, that seawater chemistry has influenced the
style of early diagenesis in carbonate regimes. Enhanced calcite cementation during
phases of elevated Ca2+ availability (calcite seas) may have aided preservation of
otherwise vulnerable reef biota to disturbance, particularly within cavities, and
promoted rapid lithification of the reef framework, but in turn may have promoted
selective dissolution of aragonitic and high-Mg skeletal biota. Aragonitic reef
404 R. Wood
framework biota preserved by secondary encrusters and early (aragonitic) cements

that grew in aragonitic seas may not suffer such loss. The nature of the control of
sea water chemistry on all these diagenetic phenomena and their subsequent effects
upon reef taphonomy remain to be documented.
Climate change and extinction are a persistent motif of the geological record and
mass-extinctions are likely to impact upon taphonomic processes (Fraiser et al. this
volume). The current phase of climate change and extinction will exert a profound
effect upon reef ecology and taphonomy of reefs. Reduction of reef herbivore
populations will almost certainly lead to an increase in soft-bodied algal biomass,
and a decrease in coral cover, particularly in areas of eutrophication or outbreaks of
disease. Bleaching as a result of global warming may lead to significant or
widespread coral mortality. The indirect effects of sea-level rise and increased
storm intensity may severely restrict rates of reef growth potentially leading to
drowning; nutrients and sediments released from newly flooded coastlines could
lead to eutrophication. Evidence indicates that biogenic calcification rates are
already between 6% and 20% lower than they were under pre-industrial conditions
due to sea water chemistry changes. Continuing accelerating rates of dissolution
and a reduction in reef calcification will almost certainly lower the net carbonate
deposition on reefs, and reduce reef-building potential globally. All these processes
will cause loss of the structural integrity of reefs. Future death assemblages and the
subsequent fossil record of reefs will be dominated by highly degraded coral frag-
ments and grains with limited in situ reef frameworks, widespread coral mortality,
endolithic algal activity, and intense bioerosion.
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Chapter 11
Silicification Through Time
Susan H. Butts and Derek E.G. Briggs
Contents
1 Introduction........................................................................................................................... 412
2 Processes and Controls......................................................................................................... 413
2.1 Experiments................................................................................................................. 417
2.2 Skeletal Factors............................................................................................................ 417
2.3 Diagenesis: Coupled Dissolution/Precipitation........................................................... 419
2.4 Influence of Depositional Environment....................................................................... 421
2.5 Models of Silicification............................................................................................... 423
3 Silicified Faunas Through Time............................................................................................ 423
3.1 Temporal Patterns........................................................................................................ 424
3.2 Global Ocean Chemistry.............................................................................................. 425
3.3 Spatial Patterns............................................................................................................ 426
4 Taphonomic Bias of Selective Silicification......................................................................... 426
4.1 Diversity Through Time............................................................................................... 427
4.2 Paleoecology................................................................................................................ 427
5 Conclusion............................................................................................................................ 429
References................................................................................................................................... 430
Abstract Silicification, which requires dissolution of original shell material and

precipitation of silica, is mediated by numerous biological and environmental factors.
The processes and controls on silicification, the environments and conditions under
which it occurs, and the temporal and spatial distribution of silicified deposits through
the Phanerozoic are reviewed. Selective dissolution of original shell material in
certain taxa or lithological settings results in a taphonomic bias which impacts our
understanding of paleoecology and patterns of diversity over time. The temporal
pattern of silicification is mediated mainly by global ocean chemistry and climate,
S.H. Butts (*)
Division of Invertebrate Paleontology, Peabody Museum of Natural History, Yale University,
P.O. Box 208118, New Haven, CT 06520-8118, USA
D.E.G. Briggs
Department of Geology and Geophysics, Yale University, P. O. Box 208109, New Haven,
CT 06520-8109, USA and Peabody Museum of Natural History, Yale University,
P.O. Box 208118, New Haven, CT 06520-8118, USA
412 S.H. Butts and D.E.G. Briggs
particularly changes in carbonate solubility (the contrast in calcite and aragonite

seas). On a finer scale, silicification of shelly fossils is influenced by taxonomic
factors (shell mineralogy, organic material in the soft tissues and within the shell,
shell ultrastructure) and by depositional factors (from porewater geochemistry,
lithology, porosity, permeability, position within a stratigraphic sequence and
basin characteristics, to global ocean chemistry). Silicification is more prevalent
in the Paleozoic than in younger strata. The relationship between the abundance of
silicified faunas, the greenhouse/icehouse signal, and fluctuations in carbonate rock
volume are complex; the observed pattern may reflect sampling of exceptionally
preserved silicified faunas rather than a global signal in silicification. The influence
of shifts in biodiversity, in carbonate skeletons susceptible to silicification, and sili-
ceous skeletons that provide a source of silica, remains to be determined.
1 Introduction
Silicification of shells normally requires the concurrent dissolution of calcium

carbonate and precipitation of silica, and is mediated by numerous taxonomic and
environmental factors in natural systems. Here we review the processes and
controls on silicification, the environments and conditions under which it occurs,
and the temporal and spatial distribution of silicified deposits through the
Phanerozoic. The impact of selective silicification on biotas is evaluated as an
important taphonomic bias.
Major advances have been made in our understanding of the taphonomy of
marine fossils, particularly the preservation of non-biomineralized tissues, scales of
resolution, taphonomic filters and their impact on compositional fidelity, and mega-
biases (large-scale variations through time) (Behrensmeyer and Kidwell 1985;
Schubert et al. 1997; Behrensmeyer et al. 2000). The dissolution and replacement
of shelly invertebrates, however, particularly in silica, is an important filter that
remains poorly understood. It is clear that silicification of skeletal material has a
significant effect on the representation of some groups, particularly bivalved mol-
luscs and brachiopods, and that it occurs far more frequently in Paleozoic than in
post-Paleozoic units, introducing a potential megabias (Schubert et al. 1997).
Some aspects of silica replacement, such as the chemical constraints on
dissolution of carbonate mineral phases and the transformation of opal-A to
quartz, are well understood. Fundamental issues, however, such as the conditions
under which silicification occurs in the natural environment, are poorly con-
strained even though they determine, on a local scale, whether or not dissolution
and silicification occur. Replacement of calcareous skeletal material by silica
results in fossils that can be extracted and investigated in three dimensions, with
consequent advantages for systematic description. When silicification is concurrent
with dissolution of shell material the original community may be preserved with
exceptional fidelity (Wright et al. 2003). On the other hand, when silicification
post-dates the degradation of skeletal material or selects particular shell mineralogies
11 Silicification Through Time 413
or textures, or when silica neomorphism destroys morphological detail, the

resulting fossil record is skewed.
Selective dissolution and silicification may impact seriously the data available
for paleoecological analysis of fossil communities. Brachiopods, for example, are
generally less susceptible to dissolution than molluscs, although there is some vari-
ability within these taxa. A comparison of coeval Lower Jurassic units in South
Wales revealed a 65% loss of bivalve genera as a result of early aragonite dissolution
relative to their diversity in assemblages preserved by early silicification (Wright
et al. 2003). A similar loss of mainly molluscan faunas has been documented in the
Silurian of Gotland, Sweden (Cherns and Wright 2000). Despite the striking loss of
diversity in these two specific cases, tests comparing silicified faunas with nonsilicified
faunas are rare.
Controls on dissolution/silicification may have important consequences for
patterns of diversity as revealed by the fossil record. Analyses of the occurrence of
silicification through time reveal a notable decline in its prevalence following four
out of five of the major extinction events (Kidder and Erwin 2001), but such
patterns are poorly known at present. Bias in silicification may be mediated by
changes in ocean water chemistry, in the skeletal mineralogy of important organ-
isms at any given period, and in the source of silica (including the diversification
and abundance of siliceous organisms over geologic time).
2 Processes and Controls
Silicification of shelly fossils results in the partial or complete replacement of the

original mineralized skeleton (Fig. 1). Examples of high fidelity morphological
replacement show an intimate relationship between the dissolution of calcium car-
bonate and the precipitation of silica (Newell et al. 1953; Cooper and Grant 1972;
Boyd and Newell 1972; Jacka 1974; Laufeld and Jeppsson 1976; Schmitt and Boyd
1981; Holdaway and Clayton 1982; Misík 1995; Daley and Boyd 1996; Erwin and
Kidder 2000; Butts 2007). The fidelity of replacement (e.g., complete or partial,
pervasive or non-pervasive, as a fine-scale fabric or beekite rings) is influenced by
factors such as the degree to which carbonate phases have been transformed to
more stable forms (e.g., aragonite to calcite), the differential solubility of these
phases, the geochemical conditions generated by their alteration, and the conditions
that give rise to the dissolution and precipitation of silica. Silica availability is often
a limiting factor. Beekite rings form by liesegang diffusion (Hodges 1932) in condi-
tions of limited or episodic silica supply (Holdaway and Clayton 1982) or fluctuating
carbonate dissolution. The formation of chert in sediments is probably subject to
environmental controls similar to those affecting silicification of shells, but it is
influenced less by the unique nature of skeletal material and is not treated here.
The timing and rate of silicification also influence the fidelity of replacement.
More than one silicification texture may be evident in a specimen. In thin section,
silicification of bioclasts is best observed under cross nicols with insertion of the
aragonite calcite calcite and aragonite

(bivalve) (bivalve, brachiopod) (bivalve)
aragonite original structure and original structure and

preserved mineralogy preserved mineralogy preserved
ld
mo
ld
mo
a neomorphic calcite; b silica- c dissolution d complete e replacement f calcite

relics of internal cemented of primary replacement of calcite preserved;
structure void; no layer; partial with silica; with silica; aragonite
primary replacement internal dissolution of neomorphosed
structure with silica structures aragonite
preserved preserved
Fig. 1 Diagenetic pathways of bioclastic materials (After Scholle and Ulmer-Scholle 2003)
first order red (gypsum) plate (Scholle and Ulmer-Scholle 2003). As the stage is
rotated, carbonate changes between first order white and purple, while quartz
(generally as cryptocrystalline chalcedony which has replaced the skeletal fabric)
alternates between first order red, yellow, and blue (Daley 1987). Complete silici-
fication (Fig. 2a, m) involves replacement of the entire shell. Fine-scale textural
replacement (fabric replacive) preserves the shell ultrastructure (barring subsequent
silica transformation) including punctae in spiriferinide brachiopods (Fig. 2b).
Fig. 2 Silicification types and textures in specimens from the Permian of west Texas (a, c, d, g, i, j, k),
the Carboniferous of east-central Idaho (b, e), and the Devonian of New York (f, h) and in thin section
the Carboniferous of east-central Idaho (l–n). (a, b) Complete pervasive silicification of brachiopod
shells. (a) Fine scale replacement of the entire shell of an athyridide; a portion of the shell has been
removed to reveal the silicified spiralia (×3.42). (b) Fine scale replacement preserving ultrastructure,
including punctae (×4.7). (c, d) Incomplete silicification of brachiopod shells leaving parts of the shell
in calcite and subject to dissolution (×3.2). (e) Non-pervasive silicification of a brachiopod shell
affects only the external layers and leaves the inner shell as calcite (×1.8). (f) Partial silicification of a
crinoid ossicle, in which the inner organic canal is also preserved in silica (×3.8). In this case silicification
forms a surface-coating “crust” or “rim” on the bioclast, rather than replacing skeletal material. (g)
Granular silicification of a bivalve shell (×3.2). (h) Spongy silicification of a gastropod shell (×6.8).
(i, j) Beekite rings. (i) A lyttoniidine brachiopod (×3.7). (j) A pectinid bivalve in which the ribs and
inter-rib areas are differentially replaced even though the shell thickness was uniform (×2.7). (k)
Spherulitic chalcedony, which commonly occurs as a surface-coating on bioclasts but is not evident at
the scale of the other textures (×15). (l–n) Brachiopod shells in thin section. (l) Composita, an athyridide,
showing the tertiary prismatic shell layer (p) in original calcite and secondary layer replaced with
spherulitic chalcedony (sc) (scale bar = 1 mm). (m) Pervasive fine scale replacement in silica (s) (scale
bar = 0.5 mm). (n) Non-pervasive fine scale replacement showing a calcite interior (c) and silicified
exterior (s) (scale bar = 0.5mm)
Partial silicification is characterized by a surface irregularly replaced with silica.

Typically, variably developed beekite rings fail to replace the entire shell resulting
in distinctly “scalloped” edges surrounding voids (Fig. 2c, d) or “lacy” silicified
areas.
Pervasiveness refers to the degree to which the shell thickness is silicified. The
shell surface, which was in contact with the matrix, may be preserved, while inner
shell material, still preserved in calcite, is etched away during acidification
(Fig. 2e, l, n). Silicification of the outer shell layers enhances taphonomic stability
by creating a relatively non-reactive barrier; however, it may prevent pervasive
silicification. Non-pervasive replacement is evident in thin section where silicified
outer shell margins enclose a calcitic shell interior (Fig. 2n); in etched hand samples
void spaces occur most notably where the shell is thickest, as in the umbonal region
of many brachiopods. Silicification also may be inhibited by the formation of a
siliceous crust on the surface of a bioclast (Fig. 2f).
Where silicification is not fine-scale fabric replacive a granular (Fig. 2g) or
spongy (Fig. 2h) texture, or beekite rings, may result (Fig. 2i, j). Finely crystalline
granular texture may retain surface microornament but ultrastructure is no longer
evident in thin section. Granular texture may reflect the gradual enlargement of
silica crystals during silica diagenesis. Spongy texture often occurs in originally
aragonitic skeletons, but is common in all kinds of shelly fossils in fine-grained
siliciclastic rocks. Spongy silicification varies in completeness and pervasiveness
but in some cases preserves ultrastructural features. Beekite rings are concentric
rings of silica each delineated by more or less well developed grooves (Fig. 2i).
Where replacement as beekite rings is complete and pervasive it may retain fine
details of the morphology, allowing taxonomic determination, but ultrastructure is
destroyed. Where replacement is partial, on the other hand, identification may be
more difficult (Fig. 2j). Beekite rings may be relatively flat to nearly spheroidal and
in some cases have the appearance of “blebs” rather than well-formed concentric
rings. Chalcedony spherules are much smaller than other common silicification
textures (Fig. 2k, l); they typically form a “crust” or rim on the external surface or
skeletal/shell layer. At higher magnification, the botryoidal nature of the silica is
readily apparent (Fig. 2k).
Early silicification, i.e., concurrent with the dissolution of the original
carbonate shell, shows complete or partial ultrastructural replacement (Fig. 2a,b)
(Holdaway and Clayton 1982; Maliva and Siever 1988; Cherns and Wright
2000; Butts 2005, 2007). Beekite textures (Fig. 2i, j) and spherulitic chalcedony
rims (Fig. 2f, l) may form during early or late silicification. Late silicification,
when the mineral precipitates as a cast (Fig. 1b), is characterized by mega-
quartz grains (which grow perpendicular to the shell boundary and may increase
in size inwards), euhedral crystals and concentric quartz laminae (Boyd and
Newell 1972; Bathurst 1975; Schmitt and Boyd 1981). Silica permineralization
is a different process which involves filling voids within organic tissues such as
wood with silica-rich fluids (Briggs 2003). Here our primary concern is with
early silicification as a major control on the completeness of the marine shelly
fossil record.
2.1 Experiments
Attempts to determine the controls on silicification using laboratory experiments

have met with only limited success. Bacteria, algae, fungi (Francis et al. 1978)
and wood (Leo and Barghoorn 1976) have been permineralized successfully with
silica in experiments, using tetraethyl orthosilicate to deliver silicic acid, but this
only involves precipitation in association with organic matter. Klein and Walter
(1995) showed that some amorphous silica will precipitate on calcite surfaces in
a matter of hours at 25–50°C but they could not replicate the replacement of
shells with silica in the laboratory. They suggested that organic material in shells
may have an effect that was not considered in their study. Bivalve shells, however,
had been replaced by silica in the laboratory some 20 years earlier (Paraguasso
1976). In these experiments shells were suspended by threads in a solution of
sodium metasilicate at a pH adjusted to allow the external shell form, shell ultra-
structure, and organic matrix of the shell to remain stable during dissolution of
carbonate (trials showed that a solution of 2 g/l of SiO2 at pH 2 resulted in suc-
cessful replacement of a 0.5 g shell). After 3 months, silica encrusted the shells
and after 8 months shells removed from the tank and dehydrated in ambient air
were composed of 75% silica with some organic matter and minor constituents
(Paraguasso 1976). The original shell was replaced with a silica gel, which shrunk
slightly during dehydration, but it was only ~10% of the mass of the original
calcium carbonate. Replacement in natural systems incorporates much more silica
and presumably involves much slower rates.
2.2 Skeletal Factors
The mineralogy and distribution of organic material within individual shells influ-
ences their susceptibility to silicification. The original mineralogy and abundance
and location of organic material (within the shell or in the associated soft tissues)
vary by taxon, which may result in a taphonomic bias. In some cases dissolution
destroys skeletal material (e.g., readily soluble aragonite) prior to silicification,
resulting in taphonomic loss.
2.2.1 Original Mineralogy
Three biogenic carbonate phases are common in marine organisms: high magne-
sium calcite (HMC), which contains >4 mol% MgCO3 (14 mol% on average:
Bathurst 1975); low magnesium calcite (LMC), which contains <4 mol% MgCO3
(Stanley and Hardie 1998); and aragonite, an orthorhombic calcite polymorph
(Tucker and Wright 1990). Although aragonite is unstable, original aragonite is
known in shells as old as Devonian and aragonite preservation is ubiquitous even
in some Paleozoic units (e.g., the Upper Carboniferous Breathitt Formation of

Kentucky: Brand 1983). Skeletal aragonite neomorphoses to coarsely crystalline
calcite, but traces of the original aragonite may be retained as crystallites within the
neomorphic calcite or as relict textures (Fig. 1a, f). Due to the high solubility of
aragonite, dissolution of shell material frequently occurs even prior to burial.
Skeletons may consist of a single carbonate phase or include different mineral
phases (as in the shell layers of pectinid bivalves). Differences in the stability of
aragonite, HMC and LMC are reflected in differences in solubility and susceptibility
to neomorphosis, all of which affect the replacement of fossils in silica. The con-
centration of magnesium in skeletal material varies with the latitude at which
organisms live (Chave 1954). To complicate matters, laboratory studies have shown
that an organism with a particular (fixed) skeletal mineralogy may secrete a carbonate
skeleton with a different Mg/Ca ratio depending on the ambient water geochemistry
(Ries and Blaustein 2003) (see Section 3.2), so skeletal composition in a single
taxon may vary through geologic time.
2.2.2 Distribution of Organic Material
The decay of organic material creates conditions conducive to both carbonate dis-
solution and silica precipitation. Shell ultrastructure, i.e., the size of carbonate
crystallites or grains that make up the shell, influences the overall dissolution rate
(Henrich and Wefer 1986; Glover and Kidwell 1993; Harper 2000). Shell structure
and the location and content of organic matter vary between different taxa (e.g.,
brachiopods and mollusks) and within taxonomic groups (e.g., between brachiopod
orders). Organic material forms sheaths surrounding the calcium carbonate crystal-
lites, and also occurs within them. Specialized morphological features, such as
mantle outgrowths within caeca and spines, are present in some brachiopod shells
(Williams 1997). Organic material may also cover the shell surface (e.g., the
periostracum of mollusks and brachiopods).
The organic content of a brachiopod (soft-tissue and shell) is 2.5–4.1% of its
total mass compared to 15–30% in bivalve molluscs (Peck 1993). Forty to fifty
percent of the organic material in all brachiopods is normally in the shell (Curry
and Ansell 1986; Curry et al. 1989), largely in the caeca, which are outgrowths of
the mantle that line the punctae (an organic content of up to 75% has been reported
in the shell of one example: Peck et al. 1987). But to what extent do organic materi-
als within shells influence the likelihood of silicification? As organic material
decays, CO2 and acidity increase and promote the dissolution of carbonate shell
material and the precipitation of silica (Froelich et al. 1979; Holdaway and Clayton
1982). Observations of degradation of modern punctate (terebratulid) and impunc-
tate (rhynchonellid) brachiopods in marine settings show a higher rate of shell
degradation in the former due in part to the greater concentration of organic material
in the shell (Tomasovych and Rothfus 2005). Unfortunately, most investigations of
silicification have involved petrographic examination of the shells of extinct organisms,
without direct information on the distribution and composition of organic material,
so the influence of shell degradation on silicificiation of organic matter-rich shells

(for example, punctate brachiopods) compared to shells that are relatively poor in
organic matter (impunctate brachiopods) is unknown.
2.2.3 Shell Ultrastructure
Studies of silicified faunas reveal a correlation between shell microstructure and

degree of silicification, resulting in a taphonomic bias. Silicification is often initi-
ated in the secondary shell layer of brachiopods (Holdaway and Clayton 1982);
the primary layer frequently is lost through abrasion, erosion (Williams 1997) or
dissolution. The secondary shell layer is fibrous in the rhynchonellates and cross-
bladed laminar in the strophomenates, the two most abundant classes of
brachiopods (Buening 2001). A tertiary prismatic shell layer is also present in a
few brachiopods (Williams 1990). Spiriferids and athyridids (rhynchonellates)
show a greater tendency to silicify than strophomenates (Schmitt and Boyd 1981;
Loope and Watkins 1989; Tucker 1991; Daley and Boyd 1996; Butts 2005) and
punctate brachiopods are more prone to silicification than impunctate (Newell
et al. 1953; Dott 1958). Among bivalves, differences in shell structure and mineral-
ogy within shells also may affect silicification. The calcitic outer shell layer of
pectinids, for example, may be silicified while the inner aragonitic material is lost
through dissolution (Fig. 1e; Schmitt and Boyd 1981). Similar patterns occur in
Permian pseudomonotid bivalves from the Glass Mountains (Newell and Boyd
1970). Laufeld and Jeppsson (1976) noted that bryozoans, brachiopods, and corals
in the Silurian of Gotland are generally more susceptible to silicification than other
taxa. This ‘hierarchy of silicification’ is also found in the Ordovician Tanner Creek
Formation of Indiana (Fox 1962) and in the Permian Glass Mountains of West
Texas (Newell et al. 1953).
2.3 Diagenesis: Coupled Dissolution/Precipitation
Dissolution of calcium carbonate and precipitation of silica occur in conditions

where pH declines from an initial state of pH > 9 (Correns 1969) in environments
supersaturated in silica and undersaturated in calcite (Knauth 1979). The chemical
conditions required for the dissolution and precipitation of calcium carbonate are
well documented (Canfield and Raiswell 1991). Dissolution is affected by the ther-
modynamic stability of the calcite phase, the saturation state of the pore water
solution, and the reactive surface area of the shell or other bioclastic particle
(Walter 1985). HMC with over 8.5 mol% MgCO3 is slightly more soluble than
aragonite, which is more soluble than LMC (<4 mol% MgCO3) in normal (Mg/Ca
ratio) marine seawater (Berner 1975). In field and experimental studies, however,
HMC has been found to dissolve at the same rate as aragonite (Berner et al. 1976;
Walter and Morse 1985). Due to the relative instability of aragonite, it has the
potential to invert to calcite (Land 1967) under favorable conditions at any point in
its diagenetic history.
The reactive surface area of skeletal material varies with microstructure (Walter
1983; Walter and Morse 1984) which therefore affects its solubility. Laboratory
studies on crushed bioclastic material (results on larger fragments or whole shells
might differ) revealed a rank order of degree of dissolution that could not be
predicted simply on the basis of original mineralogy, and varied with the calcite/
aragonite saturation of the seawater used (Walter 1985; Walter and Morse 1985).
Aragonite in the green alga Halimeda, for example, dissolved more rapidly than less
stable magnesian calcites in red algae and forams. The familiar rank order of suscep-
tibility to dissolution and diagenetic alteration (HMC → aragonite → LMC) applied
only in solutions near or above saturation for aragonite. The influence of micro-
structure on dissolution is greatest where calcite is undersaturated and most aragonite
dissolves. Composition becomes a more important influence than microstructure as
calcite and finally aragonite reach saturation; in the last case only HMC dis-
solves (Walter 1985).
The precipitation of silica involves the polymerization of silicic acid to a silica
gel which dehydrates to form opal (unstable), chalcedony, and quartz (Fairbridge
1983). In carbonate sediments, which are alkaline and typically Mg-enriched, a
compound with a ratio of Mg/Ca ~ 1:2 acts as a nucleation site for opal CT lepi-
spheres by attracting silanol groups (Williams and Crerar 1985). The concentra-
tion of dissolved magnesium is increased by the conversion of HMC to LMC.
This change may be reflected in the formation of early diagenetic dolomite
rhombs adjacent to mineralogically stabilized clasts as in the Middle Permian
Gateway Limestone Member of the Cherry Canyon Formation of Texas and New
Mexico (Jacka 1974). Ca2+ released during the solubilization of calcite favors
silica precipitation because it decreases silica solubility (Paraguasso 1976).
Nucleation and polymerization of silica is slower at lower pH values (Hinman
1987). Electrical charges distributed through chains of proteins and amino acids
in organic matter aid in complexing silica molecules (Paraguasso 1976; Iler
1979). Organic matter decomposition by sulfate-reducing bacteria creates low pH
conditions (Schieber 1996), favoring carbonate dissolution and silica precipitation
(Loope and Watkins 1989) and pyrite has been observed in association with silici-
fied skeletal material (e.g., framboidal pyrite in the caeca of brachiopods: Gaspard
and Roux 1974).
Following precipitation, silica goes through a well understood series of diage-
netic transformations: opal-A (amorphous) → opal A¢ (secondary) → opal CT
→opal CT (reordered phase) → cryptocrystalline quartz or chalcedony → micro-
crystalline quartz (Williams and Crerar 1985; Hesse 1989, 1990). The presence of
organic matter (Hinman 1990) and certain ions derived from carbonate and clay
minerals (Lancelot 1973; Hinman 1998) may influence the rate of silica phase
changes. Silicification does not always involve such a transformation; some of the
mineral variation may be primary (Holdaway and Clayton 1982). The increase in
crystal size associated with neomorphism may obliterate structures required for
taxonomic determination (Fig. 1a,f).
2.4 Influence of Depositional Environment
Controls on silicification operate hierarchically. The agents of carbonate dissolution

and silicification are a function of the composition of the sediment and pore water
chemistry, and hence the sedimentary environment. The chemical environment
is also affected by the sediment: composition, grain size, porosity and organic
content.
2.4.1 Sequence Stratigraphic Framework
Preliminary observations indicate that the distribution of silicified faunas is

reflected in sequence and parasequence boundaries. In the Ordovician of Tennessee
(Holland and Patzkowsky 1997, 1998), for example, chertification occurs in laminated
mudstones and bioturbated packstones and wackestones below sequence boundaries
that are overlain by transgressive surfaces. Intervals of subaerial exposure are evi-
denced in these same units by zones of aragonite dissolution (Railsback et al.
2003). However, this pattern may be obscured by the nature of the lithologies
within stratigraphic sequences. In the Arco Hills Formation of east-central Idaho
(S.H. Butts, unpublished), for example, silicified units are most common in the
lower part of parasequences, probably as a result of lithology and porewater geo-
chemistry in the depositional environment. The Arco Hills Formation parase-
quences are capped by either calcareous quartz arenite, pelmatazoan grainstone
(encrinite) with syntaxial cements, or fine-grained siliciclastics, all of which are
unfavorable for silicification. The high porosity quartz arenite was presumably
originally undersaturated in calcite and aragonite and later cemented with calcite.
The early syntaxial cements in pelmatazoan grainstone eliminated porosity and
precluded silicification. Low-porosity lithologies may act as aquitards to protect
fossil-bearing units from diagenetic waters (as in the Breathitt Formation:
Brand 1983). Silicification is reduced where low porosity clay-rich lithologies cap
parasequences. In contrast, where carbonate-rich lithologies cap sequences
or parasequences, silicification may be common. Subaerial exposure may also
provide access for silica-rich meteoric waters (Meyers 1977). Thus an understanding
of how sequence boundaries affect the geochemistry of the depositional environ-
ment and the early diagenetic history of sediments may allow them to be used as
predictors of the occurrence of silicified fossils within a succession.
2.4.2 Silica Source
Extensive silicification requires sufficient available silica to replace dissolved car-

bonate shell material. In marine environments, dissolved silica is mainly from three
sources: detrital, volcanic/hydrothermal, and biogenic (Tréguer et al. 1995). Input
of dissolved silica (generally as monomeric silicic acid, Si(OH)4) to the world
ocean is primarily riverine, comprising 80% of the total input (Tréguer et al. 1995).
To a lesser extent silica is derived from eolian, submarine weathering, and hydro-
thermal sources, and from the dissolution of skeletons (Tréguer et al. 1995). These
inputs are balanced to some extent by coastal and abyssal deposition, but mainly by
the generation of siliceous skeletons by organisms using dissolved silica (Tréguer
et al. 1995). The concentration of dissolved silica in marine waters is approximately
3 ppm, but it reaches 10–50 ppm in pore waters, depending on the local availability
of siliceous shells in the sediment (Lancelot 1973).
The skeletons of modern siliceous organisms – diatoms, radiolarians, and silico-
flagellates – are composed of Opal-A (Tucker 1991). These organisms, as well as
ebridians, sponges (Maliva et al. 2005), alcyonarians and holothurians (Fairbridge
1983), are the common sources of biogenic silica today. During the Paleozoic, the
primary source of biogenic silica was likely sponge spicules and radiolarians (Maliva
et al. 2005). Simultaneous or penecontemporaneous replacement of siliceous
bioclasts with carbonate, and carbonate clasts with silica, may generate an abundant
source of silica, as in the Permian of the Glass Mountains (Newell et al. 1953) and
the Lake Valley Formation (Mississippian) of New Mexico, where siliceous sponge
spicules are replaced with carbonate (Meyers 1977). Devitrified volcanic ash may
also be an important source of silica: silicification is prevalent in association with
bentonite beds (Laufeld and Jeppsson 1976; Cherns and Wright 2000; Butts 2004).
2.4.3 Other Factors
In certain circumstances organisms may be protected from silicification in spite of

favorable conditions for its occurrence. Early isopachous cements, typically calcite
or aragonite, may shield a shell from interaction with pore waters. Such syntaxial
cements commonly occur on crinoid ossicles, for example. The crystals of crinoid
ossicles are large, giving them “high microstructural stability and thus low suscep-
tibility to replacement” (Maliva 1992, p. 169). Crinoid grainstone with pervasive
syntaxial cements has very limited porosity (Butts 2005). Other syngenetic and
early diagenetic coarse cements likewise limit porosity and permeability, and pre-
clude silicification.
Diagenetic “crusts” of low-magnesium calcite or silica, which form on the surfaces
of skeletal material in contact with the matrix, may impede or prevent dissolution
or may prevent pervasive silicification. Specimens from the mid-Carboniferous
Arco Hills Formation of southeast Idaho and the Pennsylvanian/Permian faunas
from the Guadalupe Mountains region of Texas preserve shells that are silicified
only on the external and internal surfaces of the valves. This suggests that silicifica-
tion was initiated by contact with the surrounding matrix/pore water (Newell et al.
1953), but ceased with depletion of silica or buffering of the system beyond condi-
tions allowing silicification.
Ecology and post mortem transport of an organism may influence the chances of
the skeleton becoming silicified. Infaunal invertebrates are favored over epifaunal,
because the chemical environment above the sediment–water interface is more likely
to promote rapid carbonate dissolution (Davies et al. 1989). Bioclasts in storm
deposits are “buried” before organic matter breaks down within the shell; its
subsequent degradation promotes carbonate dissolution and silica precipitation
(Erwin and Kidder 2000). Biological reworking of sediments also influences the
dissolution of carbonate bioclasts. Dissolution of carbonate bioclasts directly below
the sediment–water interface is enhanced when the burrowing activity of organisms
oxygenates the sediment locally, promoting aerobic respiration and degradation of
organic material, thus increasing acidity and skeletal dissolution (Aller 1982).
Burrowing may also rework organic-rich anoxic sediments to the sediment–water
interface where sulfide oxidation occurs and sulfuric acid is produced (Aller 1982).
2.5 Models of Silicification
The silicification of shelly fossils and the formation of chert have been explained in
a number of ways. The mixing zone model of Knauth (1979) was based on the
presumption that diagenetic fluids are undersaturated with calcium carbonate and
supersaturated with silica. Such conditions may prevail at coastal locations due to
the mixing of meteoric and marine waters. In many examples of silicification, how-
ever, there is no link to terrestrial emergence, and the conditions that favor silicification
are generated by the decay of organic matter.
Early silicification commonly takes place in the upper layers of the sedimentary
column where active decay occurs. Organic matter may act as a nucleation site for
silica precipitation (Maliva and Siever 1988) and decay-induced production of
bicarbonate ions (HCO3−) reduces pH and promotes the dissolution of carbonate
(Cherns and Wright 2000). Silicification is associated with decaying organic matter
in a wide range of contexts, as evidenced by examples of silica precipitation
restricted to bioclasts and absent or very limited in non-bioclastic sediments
(Newell et al. 1953; Schmitt and Boyd 1981; Holdaway and Clayton 1982; Misík
1995; Daley and Boyd 1996).
Late stage silicification may occur where shells are in contact with siliciclastic
grains, as reported in the Devonian Oriskany Sandstone of New York (Maliva
1992), perhaps as a result of pressure solution in pore fluids. The force of crystal-
lization during the growth of syntaxial quartz cements may be responsible for the
dissolution of calcite minerals (Maliva 1992). Dissolution/silicification involving
cavity filling does not usually retain shell structure, and is characterized by
megaquartz.
3 Silicified Faunas Through Time
The primary control on the distribution of silicified faunas over time is the pres-
ence and abundance of organisms with siliceous tests, which provide a source of
biogenic silica. Also important is the relative abundance of different carbonate
skeletons at any time and their relative stability within the global ocean. Controls
on dissolution/silicification may operate on a global scale resulting in megabiases
in the fossil record (Kidder and Erwin 2001). Prior to the Paleozoic, early diage-
netic silica was deposited readily as chert in peritidal deposits. During the
Cambrian radiation, silica was incorporated in skeletons, particularly of sponges
(Maliva et al. 1989). During the radiation of radiolarians in the Ordovician, there
was increased incorporation of silica into skeletons (Maliva et al. 1989). Silicified
bioclasts are common throughout the Paleozoic, but far less common in post-
Paleozoic strata. However, patterns in the temporal occurrence of silicified faunas
are not well established, even on the scale of geologic period, and have not been
tied directly to any large-scale geologic events (e.g., widespread volcanism or
ocean anoxia). Only broad associations between the occurrence of silicification
and other geologic processes have been noted, such as the dissolution of aragonite
in calcite saturated seas (Palmer et al. 1988; Cherns and Wright 2000; Brennan and
Lowenstein 2002). Fluctuations in global ocean chemistry and abiogenic sources
of silica, and variation in the relative abundance of organisms with different skel-
etal mineralogies, were important controls on the silicification of shells and
resulted in predictable megabiases in the fossil record. Unfortunately, however, the
complexity of factors that control the silicification of fossils complicates the inter-
pretation of the pattern.
3.1 Temporal Patterns
Silicification is not distributed randomly through the Phanerozoic. Based on data

from 1,863 published papers, Schubert et al. (1997) determined that 21% of
Paleozoic faunas are silicified, compared to 4% of post-Paleozoic faunas. They
attributed this pattern to variation in the abundance of siliceous sponges as a silica
source and the increase in aragonitic faunas in the Mesozoic and Cenozoic. Within
the Paleozoic, the Cambrian, Ordovician, Devonian, and Permian show notably
high levels of silicification whereas silicified faunas are rarer in the Silurian and
Carboniferous (Schubert et al. 1997). The abundance of silicified faunas does not
correlate with marine outcrop area, carbonate rock volume, changes in sea level or
long-term climate, volcanism, or the amount of nearshore chert (Schubert et al.
1997). Analyses of the occurrence of silicification within series revealed a notable
decline following four out of five of the major extinction events, including a pre-
cipitous drop at the end of the Permian (Kidder and Erwin 2001). Peaks in the
Ordovician and Devonian are associated with increases in sponge abundance and
diversity (Schubert et al. 1997).
Throughout the Ordovician cherts occur in increasing water depths, from peritidal
settings to deep marine basins (Maliva et al. 1989), indicating a transition in silica
source and possibly reflecting declining levels of dissolved silica in shallow water
(Kidder and Mumma 2003). At the Permian-Triassic boundary there appears to be
a similar shift in silica sequestration as chert deposits transitioned from shallow
environments toward basinal environments (Schubert et al. 1997). The decline in

silicification in the Mesozoic may correlate with the change in dominant shell
chemistry from calcite to aragonite (Wilkinson 1979; Railsback and Anderson
1987; but see Stanley and Hardie 1998), and a reduction in the diversity and abun-
dance of siliceous sponges (Kidder and Erwin 2001).
3.2 Global Ocean Chemistry
The magnesium/calcium (Mg/Ca) ratio and saturation state of calcium carbonate

are susceptible to the CO2 content of the atmosphere and oceans, which is different
in a greenhouse world (when seas are calcite saturated and undersaturated in
aragonite) to that in an icehouse world (when seas are aragonite saturated) (Fischer
1982). Throughout the Phanerozoic, there is a shift between calcite and aragonite
seas (Fig. 3). Mg/Ca ratios in seawater are known to affect the phase of inorganic
carbonates in cements and ooids (Brennan and Lowenstein 2002). They also may
facilitate the secretion of skeletons of a particular mineralogy (Stanley and Hardie
1998) and thus influence the predominance of particular organisms over time; how-
ever, modern organisms that normally secrete HMC have been shown to secrete
LMC skeletons in low Mg/Ca environments (Ries and Blaustein 2003). No correlation
had been detected between the abundance of biogenic silica (as bedded cherts and
silicified fossils) and the occurrence of greenhouse versus icehouse conditions
(Kidder and Erwin 2001). Higher production of siliceous tests, however, may occur
when calcareous organisms are in crisis, such as during the Frasnian-Famennian
and end-Cretaceous mass extinction events (Racki 1999). Global changes in ocean
chemistry may result in biases in preservation potential, particularly in the case
of aragonitic faunas (Smith 2003). Extensive loss of aragonite bioclasts and
cements occurs in the Upper Ordovician and Jurassic, for example, when calcite
seas (Mg2+/Ca2+ < 2: Brennan and Lowenstein 2002) were undersaturated with
“Aragonite Threshold”
PC CAM. ORD. SIL. DEV. CARB. PER. TR. JUR. CRET. CEN.
ICEHOUSE GREENHOUSE ICEHOUSE GREENHOUSE ICE
HMC and less abundantly, Aragonite

Calcite (Mg content generally lower, increasing toward “Threshold”)
Fig. 3 Secular variation in non-skeletal carbonate mineralogy in seawater and associated climatic
episodes (After Sandberg 1983)
aragonite (Palmer et al. 1988). On a more local scale, a period of major calcite
dissolution occurred in the Norwegian-Greenland Sea during the most recent deglacia-
tion, but the effects were not global (Henrich 1985).
3.3 Spatial Patterns
Tectonic setting and type of sedimentary basin play a role in controlling the preva-
lence of silicification. Basins may be carbonate or siliciclastic dominated, or mixed
carbonate-siliciclastic; they may be active or passive tectonically; they may occur
in greenhouse or icehouse regimes, and through all ranges of latitude. These factors
affect a range of phenomena including rates of weathering, sediment accumulation
and accommodation, facies distribution (vertical and horizontal), faunal composi-
tion, water temperature, and intra-basinal water depths. Weathering rates, the input
of detrital silica, and volcanism also vary depending on the tectonic regime of a
basin (active or passive). Basin characteristics therefore can influence the distribution
of silicified faunas in space and time.
Stratigraphic “traps”, such as reefs (Newell et al. 1953) and Waulsortian mounds
(Meyers 1977), create sedimentological barriers that control local environmental
conditions. Silicification has been reported on the units flanking such traps (e.g.,
Tierra Blanca, Dona Ana, and Alamogordo Members of the Carboniferous Lake
Valley Formation of the Sacramento Mountains of New Mexico: Meyers 1977) but
there is no widely accepted explanation for this localization. Silicified shells of
gastropods, bivalves, chitons and scaphopods are associated with sponge bioherms
in the Permian limestones of the Glass and Guadalupe mountains of West Texas
(Cooper and Grant 1972). The distribution of silicification in association with such
stratigraphic traps may reflect differences in porosity and permeability. Silicification
occurs on the outer margin of reef talus deposits within the Permian of West Texas
(Newell et al. 1953). Pore fluid migration between the reef, with early diagenetic
cements, and the more permeable flanking reef debris (or between the outer flank
deposits and adjacent sediments) was probably inhibited. Within Waulsortian
mounds, a similar barrier may develop between mud-supported and grain-supported
lithologies.
4 Taphonomic Bias of Selective Silicification
Silicification of shelly fossils is influenced by the nature of organisms (shell

mineralogy, organic material in the soft tissues and within the shell, shell ultrastructure)
and by the depositional environment (porewater geochemistry, lithology, porosity
and permeability, position within a stratigraphic sequence, basin characteristics,
and global ocean chemistry). The non-uniform nature of silicification reflects
taphonomic biases that impact interpretations of paleoecology and diversity,
particularly in Paleozoic sequences.
4.1 Diversity Through Time
Selective silicification of taxa may skew the evidence of faunal diversity in a rock
unit and bias the interpretation of diversity through time. Very early silicification
(preceding aragonite dissolution) provides evidence of total diversity, which is lacking
in similar assemblages where silicification occurs after aragonite dissolution. In the
Jurassic of South Wales, for example, there is a 65% decrease in the diversity of
bivalve genera where dissolution of aragonite preceded silicification (Wright et al.
2003). Shallow infaunal bivalves and small epifaunal gastropods were more suscep-
tible to dissolution than large burrowing bivalves and large ammonites.
The transition from predominantly calcite skeletons in the Paleozoic to a greater
proportion of aragonite skeletons thereafter may explain the paucity of post-Paleozoic
silicified faunas. The faunal turnover at the end Permian extinction resulted in the
decline of calcitic stalked echinoderms and trilobites (Schubert et al. 1997) and
the replacement of calcitic brachiopods and rugose and tabulate corals with faunas
dominated by aragonitic bivalves and scleractinian corals (Railsback and Anderson
1987). Changes in conditions during the Triassic favored the precipitation of arago-
nitic skeletons through an increased concentration of seawater sulfate, higher tem-
peratures and possibly high Mg/Ca, all of which affect the rate of dissolution and
precipitation of carbonates (Railsback and Anderson 1987). Aragonitic faunas are
less susceptible to silicification, because dissolution and diagenesis of aragonite
normally outpaces silica precipitation.
4.2 Paleoecology
The potential for silicification varies from taxon to taxon (Section 2.2) and this
clearly has implications for paleoecological inferences based on fossil assemblages.
A good example is provided by a comparison of the Arco Hills Formation (Butts
2007) of east-central Idaho and the Bluestone Formation (particularly the Bramwell
Member) of West Virginia and Virginia (Henry and Gordon 1992), both Mississippian
in age. These formations are similar in lithologies and depositional environments;
they consist of interbedded or heterolithic carbonate-siliciclastic units and yield a
diversity of fossils. The silicified brachiopod-rich assemblages in the Arco Hills
Formation are nearly identical to those in the Bluestone Formation except that they
lack molluscs. The mollusc component of the fauna has presumably been lost as a
result of early dissolution. Preservation in the Bluestone Formation, in contrast, is
primarily calcareous, resulting in a mollusc-dominated assemblage with a signifi-
cant brachiopod component, more closely reflecting the original community struc-
ture, as exemplified by the Bramwell Member. A comparison of silicified and
nonsilicified faunas from the Lower Jurassic of Wales suggests that the shells of
shallow infaunal marine taxa were more impacted by dissolution, due to high rates
of microbial degradation and consequent acidity, than those of deeper burrowers
(Wright et al. 2003).
Silicification is more prevalent in carbonates than in fine grained siliciclastics;

conditions in carbonate and siliciclastic environments differ in terms of the pH of
pore waters, concentration of ions, saturation state of carbonate, rCO2, permeability
and porosity, and there is considerable variation locally. The Devonian Kalkberg
Formation (Helderberg Group) of New York, for example, is a mixed carbonate and
siliciclastic unit which includes the Bald Hills volcanics with K-bentonite ash layers
(Butts 2004). Carbonate bioclasts are preserved in the fine-grained siliciclastic beds
(Fig. 4a, b) but they are normally silicified where they occur in carbonate-rich beds
(Fig. 4c, d). It is clear that dissolution and loss of the carbonate clasts at any stage
in the diagenetic history of the unit would have resulted in a significant loss of
preserved diversity and consequent distortion of paleoecological interpretations of
the fauna.
Lithology may also affect the degree and fidelity of silicification. High fidelity
replacement tends to be more common in open marine, siliciclastic-poor sediments
(Erwin and Kidder 2000; Butts 2007). Spongy silicification is most prevalent in
shallow-water calcareous fine-grained siliciclastic-rich sediments (Butts 2007).
Shells in offshore deeper deposits are more prone to dissolution than those in
Fig. 4 Silicification of brachiopod shells in the Kalkberg Formation, Helderberg Group,

Devonian, New York. (a, b) In fine-grained siliciclastic lithologies shells retain their original
carbonate composition. (c, d) In carbonate lithologies shells are silicified. (c) Fine-scale, non-
pervasive replacement with length-slow chalcedony. (d) Spherulitic length-slow chalcedony on
outer margins of the shell and fine-scale textural replacement in the interior
nearshore shallow settings, because the clean, high energy, oxidized carbonate
sands of the latter lack organic material for microbial degradation and the resulting
increase in acidity (Wright et al. 2003).
5 Conclusion
Fine scale textural silicification of organisms provides high quality data for taxo-
nomic analysis, preserving shell ultrastructure and morphological features in high
resolution. Likewise early silicification can preserve paleocommunities with
extremely high fidelity. However, silicification is influenced by a range of biological
and lithological controls, resulting in taphonomic biases in the record of biodiversity
through time, particularly in the Paleozoic. The nature of such biases is poorly con-
strained with our present knowledge of silicification patterns and processes. Large
scale trends are influenced by global climate and ocean chemistry as well as shifts
in the relative abundance and composition of invertebrate skeletons through time.
Most notable are the transition from dominantly calcite faunas during the Paleozoic
to post-Paleozoic aragonite faunas, and the diversification and extinction of groups
with siliceous skeletons, such as sponges and radiolarians. Silicification is biased
toward preservation of lower solubility LMC organisms; aragonite and, to a lesser
extent, HMC skeletons are susceptible to dissolution prior to silicification.
Silicification is also biased by depositional conditions, including lithology and pore-
water geochemistry. Degradation of organic matter can generate conditions for the
dissolution and silicification of skeletons, a role that has yet to be investigated
experimentally.
The different dissolution rates of carbonate phases in global and local conditions
determine the abundance and selectivity of silicified faunas through time. In global
greenhouse climates deposition is characterized by thick sequences of carbonate
lithologies with little variation laterally and vertically. Silicification is favored in
carbonate lithologies, and therefore may be more prevalent in greenhouse climates.
However, calcite saturated greenhouse seas promote the dissolution of aragonite
thus biasing the composition of silicified faunas (Palmer et al. 1988). In icehouse
climates, in contrast, seas saturated with aragonite favor the dissolution of HMC
and LMC shells while increased deposition of fine grained siliciclastics may reduce
the abundance of silicified faunas. High amplitude, high frequency sea level
changes repeatedly expose sediment to meteoric diagenesis thereby promoting
bioclast dissolution and replacement in silica. Icehouse climates may also create
porosity barriers that likewise favor silicification locally but do not generate a
global signal. In the absence of a correlation between the abundance of silicified
faunas and a greenhouse/icehouse signal (Kidder and Erwin 2001) or fluctuations
in carbonate rock volume (Schubert et al. 1997), the pattern of silicification through
time may reflect sampling of exceptionally preserved, compartmentalized, silicified
faunas rather than a global signal. There remains the task of unravelling the influence
of shifts in biodiversity, specifically the abundance and diversity of carbonate

skeletons that are susceptible to silicification, and of the siliceous skeletons that
provide a source of silica.
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Chapter 12
Phosphatization Through the Phanerozoic
Stephen Q. Dornbos
Contents
1 Introduction........................................................................................................................... 436
2 Phosphatization Processes and Biases.................................................................................. 436
2.1 Phosphatization Processes........................................................................................... 436
2.2 Phosphatization Biases................................................................................................ 438
3 Temporal Distribution with Examples.................................................................................. 439
3.1 Paleozoic Phosphatization........................................................................................... 439
3.2 Mesozoic Phosphatization........................................................................................... 445
3.3 Cenozoic and Recent Phosphatization......................................................................... 448
4 Temporal Distribution Hypotheses....................................................................................... 450
5 Biases Through Time............................................................................................................ 451
6 Summary............................................................................................................................... 452
References................................................................................................................................... 453
Abstract Phosphatization of soft tissues and skeletal remains has varied temporally and
taxonomically through the Phanerozoic. During the Cambrian through early
Ordovician, microscopic arthropods and animal embryos were preferentially
preserved. Phosphatization was uncommon during the rest of the Paleozoic, as
recalcitrant tissues of a few taxa were preserved in hospitable microenvironments.
The Cretaceous through Eocene saw another expansion of phosphatization, with
a strong bias toward fish remains already enriched in apatite. Throughout its
Phanerozoic history, phosphatization exhibited a taphonomic bias toward taxa with
recalcitrant tissues that could resist the early stages of organic decay, taxa with
organic structures already enriched in calcium phosphate, and, in many cases, taxa
with small body sizes. The pulse of phosphatization during the Cambrian through
Early Ordovician may have been facilitated by the generally lower levels of mixed
layer development in the upper few centimeters of seafloor sediments during that
time period, whereas the Cretaceous through Eocene increase in phosphatization
was possibly related to the enlargement of euxinic epicontinental seaways.
S.Q. Dornbos ()
Milwaukee, WI 53201-0413, USA
436 S.Q. Dornbos
1 Introduction
Phosphatization is a rare yet astounding mode of fossil preservation that has the
capability of preserving soft tissues to cellular and even subcellular levels. While it
is high fidelity in nature, phosphatization is also a highly selective and biased
taphonomic pathway. It favors the preservation of recalcitrant tissues that are resis-
tant to decay and those that are already enriched with phosphate. There is also a
size bias in many deposits because phosphatization has either occurred at a limited
depth within seafloor sediments or in a minute microenvironment within/around an
organism.
The goal of this chapter is to examine the Phanerozoic history of phosphatization
in search of large-scale patterns over geologic time. Are there times in Earth history
when phosphatization is more prevalent? What are possible explanations for this
temporal distribution? Are there biases toward the preservation of certain taxa, and
how has that changed over time? These are some of the questions that this chapter
will explore through a review of the available literature.
2 Phosphatization Processes and Biases
2.1 Phosphatization Processes
Dissolved phosphate in the oceans is derived from continental weathering and is a

limiting nutrient for marine phytoplankton. Most phosphate is remobilized or
remineralized in the photic zone, but in upwelling zones a larger amount of organic
material makes it to the seafloor and phosphate-enriched deposits can result. Such
phosphatic deposits account for only a small percentage of phosphate buried in
marine sediments, making phosphatic fossil preservation exceedingly rare.
Phosphatization of soft tissues and replacement of calcareous skeletons by phos-
phate, most commonly in a form of apatite called francolite (carbonate flourapatite),
can take place in either these broad phosphogenic depositional environments or in
a local phosphatizing microenvironment created by the decay of soft tissues in the
organism itself. When phosphatization does take place in a phosphogenic deposi-
tional environment, there are some general paleoenvironmental, biological, and
chemical parameters that play important rolls in the process. Recent phosphorite
deposits are typically forming in environments characterized by low sedimentation
rates, strong seafloor currents, and a large influx of organic material due to high
primary productivity in the water column above (e.g. Föllmi 1996; Baturin 1999).
The low sedimentation rates and large amount of organic input in these environ-
ments combine to create sediment enriched in organic material (e.g. Föllmi 1996;
Baturin 1999). The organic material in the sediment then begins to decay and
releases phosphate into the pore waters. Although many details about the process
are not yet understood, the dissolved phosphate content of the pore waters reaches
12 Phosphatization Through the Phanerozoic 437
supersaturation, allowing phosphogenesis and the phosphatization of organisms to

begin (e.g. Baturin 1999). The concentration of dissolved phosphate within sediment
pore waters is probably strongly assisted by the sealing of microbial mats on the
seafloor (e.g. Briggs and Kear 1993; Wilby et al. 1996; Soudry 2000).
Although sediment pore water is typically saturated with respect to phosphate, under
normal seawater pH conditions (~8) calcium carbonate is more stable than phosphate
and thereby inhibits phosphate precipitation. One way in which phosphate can precipi-
tate is if the pH of the pore waters is reduced to around 7, which destabilizes calcium
carbonate and allows phosphate to begin precipitating (Lucas and Prevot 1991; Briggs
and Wilby 1996; Trappe 1998). It is thought that bacterial metabolic processes serve to
lower the pH of the pore waters during this process, which also results in the release of
phosphate that is bound to iron hydroxides derived from continental weathering
(Froelich et al. 1988; Baturin 1999; Sagemann et al. 1999; Briggs 2003). Once
precipitation of phosphate begins, it is estimated that the process can phosphatize soft
tissues in rapid timescales ranging anywhere from days to weeks (e.g. Föllmi 1996).
Bacteria coating the surfaces of the tissue often appear to serve as the nucleation
points for phosphatization, and are typically phosphatized themselves (Baturin 1999).
After phosphogenesis and phosphatization have taken place currents remobilize
the sediment, transporting and redepositing it elsewhere. A new round of phospho-
genesis then begins in the newly deposited sediment and the cycle continues (Föllmi
1996). This process of remobilization and redeposition of the sediment results in dif-
ferent generations of phosphate being present in the same sediment (Baturin 1999).
Resulting phosphogenic sediments often include a mixture of phosphatic lithologies
including primary phosphatic mud, hardgrounds, pellets, and concretions, all of
which can contain fossils (Glenn et al. 1994). Phosphatic concretions containing
phosphatized fossils can also form in non-phosphogenic settings.
Other models, including strictly geochemical and hydrothermal explanations, have
been proposed to explain phosphogenesis (e.g. Kholodov and Paul 1995), but the bio-
genic model currently has the greatest amount of support because it explains the most
about both ancient and Recent phosphogenic settings (Baturin 1999). In fact, recent work
has indicated that giant sulfur-oxidizing bacteria, such as Thiomargarita, Beggiatoa, and
Thioploca, which are abundant in modern phosphogenic settings may play an important
role in phosphogenesis by releasing large amounts of dissolved phosphate into their sur-
rounding environment in anoxic conditions (Reimers et al. 1990; Krajewski et al. 1994;
Schulz and Schulz 2005). This modern correlation between phosphorites, upwelling
zones, and sulfur-oxidizing bacteria capable of mediating pore water phosphate concen-
trations have led various authors to suggest that certain ancient phosphatized microfossils
represent sulfur-oxidizing bacteria (e.g. Reimers et al. 1990; Bailey et al. 2007).
When phosphatization takes place in non-phosphogenic depositional environments,
it occurs when an organism creates its own phosphatization microenvironment through
organic decay (Briggs and Kear 1993). Such fossils are often preserved in phosphatic
nodules within broader non-phosphatic facies, usually carbonates (e.g. Walossek et al.
1993). Preservational completeness varies tremendously within single organisms, with
more labile soft tissues often absent or heavily decayed and more recalcitrant tissues
such as carapaces or connective tissues extremely well preserved (e.g. Klug et al. 2005).
438 S.Q. Dornbos
The bacterial decay of the labile soft tissues evidently produced enough dissolved
phosphate and lowered the pH sufficiently to phosphatize the remaining undecayed
tissues (Klug et al. 2005). This process would have taken place after the organism had
been buried in the sediment, likely below the oxic–anoxic interface.
2.2 Phosphatization Biases
Phosphatization is a highly biased mode of preservation. These biases primarily

involve the original composition of organic material, the decay resistance of organic
material, and the size of the organism being preserved. There does appear to be a
phosphatization bias toward organic material that is already enriched in phosphate.
This is true of fish coprolites in the Cretaceous through Eocene phosphorites of the
southern Mediterranean, as well as the phosphatized fish and whale bones found in
Pleistocene and Recent phosphorites offshore of Namibia and Peru (Lamboy et al.
1994; Resig and Glenn 1997; Baturin and Dubinchuk 2003). The beginnings of
bacterial decay in these organic remains releases large amounts of dissolved phosphate,
rapidly creating a phosphatizing microenvironment that preserves the undecayed
portions of the remains (e.g. Lamboy et al. 1994). Organic remains that are not
enriched in phosphate are certainly also known to become phosphatized, but this
bias toward previously enriched remains is prevalent in many deposits.
Another persistent bias is that toward the preservation of more recalcitrant
organic tissues. The more labile, decay-prone, portions of organisms are often
decayed to the point of absence, while the resistant organic structures are phos-
phatized (e.g. Klug et al. 2005). This bias is particularly strong in the phosphatized
animal embryos and microarthropods of the Cambrian to Early Ordovician. Both of
these types of fossils are nearly hollow on the inside while the outer surface is
phosphatized (Maas et al. 2003; Dong et al. 2005). The labile inner organic remains
clearly decayed heavily while the outer cuticle remained relatively intact and
became phosphatized as the decay process created the necessary environmental
conditions for phosphatization. Most of the preserved animal embryos were likely
those of ecdysozoans, so initial cuticular development probably contributed greatly
to their preservation (e.g. Donoghue et al. 2006).
Size is also an important bias in phosphatization. In phosphogenic environments,
the thin zone of phosophogenesis in the upper few millimetres of the sediment, as
well as the constant reworking of the sediments, places strong size limitations on
any organic material that is going to become phosphatized or survive the reworking
to end up in the final deposit (e.g. Dornbos et al. 2006). In non-phosphogenic
settings, small body size increases the chances of preservation because the phos-
phatizing microenvironment is often quite small itself. These biases are likewise
evident in the animal embryos and microarthropods found in the Cambrian through
Early Ordovician (e.g. Walossek et al. 1993; Maas et al. 2003; Donoghue et al.
2006). The preserved embryos and microarthropods are both microscopic. Later
developmental stages are not preserved in the same rocks as the embryos and larger
animals are not phosphatized with the meiofaunal arthropods (e.g. Maas et al. 2003;
Donoghue et al. 2006). Phosphatization gives paleontologists an extremely powerful
yet painfully narrow view of ancient life.
3 Temporal Distribution with Examples
The following subsections describe important instances of phosphatized fossils

through the Phanerozoic fossil record. It includes examples of soft tissue replica-
tion as well as replacement of skeletons by apatite. This section is not intended to
be an exhaustive listing of all known occurrences of Phanerozoic phosphatization,
but a description of certain occurrences that are important for understanding long-term
trends. The examples and relevant references are summarized in Table 1.
3.1 Paleozoic Phosphatization
3.1.1 Cambrian Phosphatization
The Cambrian contains a wealth of phosphatized fossils relative to the remainder

of the Phanerozoic. The lowermost Cambrian rocks of the Dengying Formation,
Shaanxi area, China, for example, contain an ontogenetic series of putative cnidarian
embryos, known as Olivooides (Yue and Bengtson 1999). These embryos and early
larval stages exhibit exceptional preservation of their exterior surfaces, which are
both coated and impregnated with apatite. Similarly preserved cnidarian-like
embryos are also described from the Lower Cambrian Manykay Formation of
Siberia (Kouchinsky et al. 1999). In contrast to the putative animal embryos of the
Ediacaran Doushantuo Formation, southwest China, these Cambrian embryos are
not internally impregnated with phosphate (e.g. Xiao and Knoll 1999; Dornbos
et al. 2005). Instead their interiors are mostly hollow with thin strands of phosphate
running between the outer phosphatized walls (Yue and Bengtson 1999). These are
likely the phosphatized remnants of the decayed interior of these embryos.
Similarly preserved animal embryos are also known from the Lower Cambrian
Kuanchuanpu Formation of southern Shaanxi, China (Steiner et al. 2004). The
external features of these embryos are magnificently preserved while the interiors
are mostly hollow. Several possible species of embryo are preserved in these
rocks, but categorizing them taxonomically is difficult. Likely developmental
sequences have been reconstructed for two of these groups of embryos, one of
which includes larval stages with the beginnings of limb development. Affinities
of these embryos with protostomes, specifically ancestral arthropods, are proposed
(Steiner et al. 2004).
Phosphatized microscopic arthropods preserved in three dimensions are also
known from the lower Cambrian. They are found preserved in the Petrolenus
Table 1 Phanerozoic phosphatization examples discussed in the text
440
Age Formation/unit/stage Location Fossil content Representative reference(s)

Early Cambrian Dengying formation China Animal embryos Yue and Bengtson (1999)
Early Cambrian Manykay formation Russia Animal embryos Kouchinsky et al. (1999)
Early Cambrian Kuanchuanpu formation China Animal embryos Steiner et al. (2004)
Early Cambrian Petrolenus limestone UK Microarthropods Siveter et al. (2001)
Middle Cambrian Monastery creek phosphorite fm. Australia Animal embryos, Walossek et al. (1993); Donoghue
microarthropods et al. (2006)
Middle Cambrian Gowers formation Australia Microarthropods Walossek et al. (1993)
Middle Cambrian Inca Shale formation Australia Microarthropods Walossek et al. (1993)
Middle Cambrian Devoncourt limestone fm. Australia Microarthropods Walossek et al. (1993)
Middle Cambrian Kuonamka formation Russia Microarthropods Müller et al. (1995)
Middle Cambrian Wagcun and Wa’ergang China Animal embryos Dong et al. (2004)
sections
Late Cambrian Orsten Sweden Microarthropods Maas et al. (2003)
Late Cambrian Orsten Poland Microarthropods Walossek and Szaniawski (1991)
Late Cambrian Bitiao formation China Animal embryos, Dong et al. (2005)
microarthropods
Late Cambrian Wa’ernang & Paibi sections China Animal embryos Dong et al. (2005)
Early Ordovician Orsten Sweden Microarthropods Andres (1989)
Early Ordovician Middle-arm point formation Canada Microarthropods Roy and Fåhraeus (1989)
Early Ordovician Green point formation Canada Microarthropods Walossek et al. (1994)
Early Ordovician Fairview formation USA Animal embryos Donoghue et al. (2006)
Early Silurian Bardo beds Poland Acritarchs Kremer (2005)
Late Silurian Panuara group Australia Anthozoans, echinoderms Bischoff (1978); Bischoff and Hall
(1980)
Late Devonian Gogo formation Australia Fish Trinajistic et al. (2007)
Late Mississippian Bear Gulch limestone USA Fish, invertebrates Lund et al. (1993); Grogan and Lund
(1997)
Late Pennsylvanian Coffeyville formation USA Cephalopods Tanabe et al. (2001)
S.Q. Dornbos
Permian Arcturus formation USA Cephalopods Mapes et al. (2002, 2003)
Early Triassic Olenekian stage Svalbard Ostracods, ciliates Weitschat (1995)
Middle Triassic Muschelkalk Germany Bivalves Klug et al. (2005)
Middle Triassic Grenzbitumenzone & Meride Italy Reptiles, nothosaurs, fish Etter (2002); Renesto and Avanzini
limestone (2002)
Ealry Jurassic Lombardische Kieselkalk Italy Crustaceans, fish, coleoids, Pinna (1985)
formation polychaetes, nematodes
Middle-Late Jurassic Oxford clay UK Coleoids Allison (1988)
Late Jurassic Portland limestone formation UK Bivalves Wilby and Whyte (1995)
Early Cretaceous Santana formation Brazil Fish Martill (1988)
Middle Cretaceous Marnes Bleues formation France Bacteria, fungi Bréhéret (1991)
Middle Cretaceous DSDP site 369 East Atlantic Bacteria, fungi Bréhéret (1991)
Late Cretaceous Austin group Mexico Fish, crustaceans, Stinnesbeck et al. (2005)
ammonites, pterosuars
12 Phosphatization Through the Phanerozoic
Late Cretaceous Colon formation Venezuela Foraminifera Ghosh (1984)

Late Cretaceous Various formations Tunisia Fish coprolites Lamboy et al. (1994)
Late Cretaceous Various formations Morocco Fish coprolites Lamboy et al. (1994)
Late Cretaceous Various formations Mauritania Fish coprolites Lamboy et al. (1994)
Late Cretaceous Various formations Egypt Fish coprolites Lamboy et al. (1994)
Late Cretaceous Duwi formation Egypt Diatoms Ahmed and Kurzweil (2002)
Paleogene (Paleocene) Various formations Egypt Fish coprolites Lamboy et al. (1994)
Paleogene (Paleocene- Various formations Tunisia Fish coprolites Lamboy et al. (1994)
Eocene)
Paleogene (Paleocene- Various formations Morocco Fish coprolites Lamboy et al. (1994)
Eocene)
(continued)
441
442
Table 1 (continued)
Paleogene (Paleocene- Various formations Mauritania Fish coprolites Lamboy et al. (1994)
Eocene)
Paleogene (Eocene) Various formations Senegal Fish coprolites Lamboy et al. (1994)
Paleogene (Oligocene- Riversleigh limetones Australia Insects, fungi, bacteria Duncan et al. (1998)
Miocene)
Neogene (Miocene) Monterey formation USA Fish, foraminifera, bacteria Garrison et al. (1990)
Neogene (Miocene) Libros basin Spain Amphibians, birds, snakes, McNamara et al. (2004)
leaves
Pleistocene Continental margin India Stromatolites, bacteria Purnachandra Rao et al. (2000),
2002)
Recent Outer shelf Namibia Fish, whales Baturin and Dubinchuk (2003)
Recent Outer shelf/slope Peru Fish, whales Resig and Glenn (1997)
S.Q. Dornbos
Limestone of Great Britain (Siveter et al. 2001). Much like the Olivooides embryos
of China, these microscopic arthropod fossils have largely hollow interiors within a
thin zone of phosphatized soft tissue. These fossils are preserved in phosphatic nod-
ules within a carbonate facies. This is the earliest known example of “Orsten” style
preservation of microscopic arthropods, a preservational mode within nodules that
is particularly common in the upper Cambrian of Sweden (Siveter et al. 2001).
Similarly preserved arthropods are also found in the middle Cambrian of
Australia. Their preservational style is classically Orsten, with phosphatized external
features and nearly hollow interiors (Walossek et al. 1993). These fossils are found
in the Monastery Creek Phosphorite, the Gowers, the Inca Shale, and the Devoncourt
Limestone Formations, all of western Queensland (e.g. Walossek et al. 1993).
Small phosphatized shields of microscopic arthropods, without soft part preservation,
are also preserved in the middle Cambrian of Kuonamka Formation of western
Siberia (Müller et al. 1995).
Phosphatized animal embryos are also known from the middle Cambrian of
Australia and China (Dong et al. 2004; Donoghue et al. 2006). As with those of the
lower Cambrian, their exteriors are phosphatized and their interiors are mainly hollow
with some phosphatized decayed organic remnants. The Australian embryos are pre-
served in the Monastery Creek Phosphorite Formation of western Queensland. These
embryos, named Markuelia, have a distinctive enrolled morphology and have been
interpreted as the late-stage embryos of cycloneuralian nemathelminths (Donoghue
et al. 2006). The Chinese embryos are also Markuelia, and are found in the Wangcun
and Wa’ergang Sections of western Hunan Province (Dong et al. 2004).
Just as in the middle Cambrian, the upper Cambrian is known to contain phos-
phatized micrscopic arthropods as well as the cycloneuralian nemathelminth
embryo Markuelia. Most of these arthropods are found in the classic Orsten locali-
ties in Västergötland, Sweden and have the typical Orsten style preservation (Maas
et al. 2003). These arthropods include larval stages of the trilobite Agnostus, a che-
licerate larvae, crustaceans, and phosphatocopines. Similar fossils are known from
the Isle of Öland in Sweden (Maas et al. 2003). Upper Cambrian rocks of the Hel
Peninsula of Poland also contain Orsten arthropods, including a stem group crusta-
cean and phosphatocopines (Walossek and Szaniawski 1991). One phosphato-
copine arthropod is found in the Bitiao Formation, Wangcun Section, western
Hunan Province (Dong et al. 2005).
Upper Cambrian rocks in China also contain the embryo Markuelia (Dong et al.
2005). These embryos exhibit the same preservational style as those of the middle
Cambrian. They are preserved in the Bitiao Formation, Wangcun Section, western
Hunan Province, and the Wa’ernang and Paibi Sections, also of western Hunan
Province (Dong et al. 2005).
3.1.2 Ordovician Phosphatization
Although phosphatization becomes a scarcer phenomenon after the Cambrian,

there are several known occurrences in the remainder of the Paleozoic. In fact,
444 S.Q. Dornbos
typical Orsten-style preservation and the embryo Markuelia are both known from
the Lower Ordovician. The Lower Ordovician of the Isle of Öland in Sweden
contains abundant microscopic arthropods (Andres 1989). Other microscopic
phosphatized arthropods are known from the Lower Ordovician of Newfoundland,
Canada. These fossils are preserved in the Middle-Arm Point Formation and the
Green Point Formation (Roy and Fåhraeus 1989; Walossek et al. 1994). Lower
Ordovician Markuelia are preserved in the Fairview Formation of Nevada, western
USA (Donoghue et al. 2006).
3.1.3 Silurian Phosphatization
Phosphatized acritarchs, known as Mazuelloids, are known from the Lower Silurian
Bardo Beds of Poland (Kremer 2005). The acritarchs are thought to have sunk to
the seafloor as part of macroaggregates that were later overgrown by cyanobacterial
mats. Phosphatization, which took place on the outer and inner surfaces of the
organic acritarch walls, may have been facilitated by microbial mats – the presence
of which is suggested by the co-occurrence of coccoidal microfossils that resemble
modern cyanobacteria (Kremer 2005). They are preserved in black radiolarian
cherts deposited in a bathyal setting (Kremer 2005).
Silurian phosphatization is also known from Upper Silurian strata in central New
South Wales, Australia (Bischoff 1978; Bischoff and Hall 1980). These fossils
consist of phosphatized anthozoan soft parts and echinoderm skeletal elements
found in the Boree Creek Formation and Borenore Limestone of the Panuara
Group. The echinoderm skeletal elements include crinoid and asteroid fragments
that exhibit exceptional preservation of the original stereom structure, providing
critical insight into the postlarval skeletal growth of echinoderms. All of these
fossils are preserved within carbonates (Bischoff 1978; Bischoff and Hall 1980).
3.1.4 Devonian Phosphatization
The muscle fibers, circulatory tissues, and nerve tissues of placoderm fish are pre-
served in the Late Devonian (Frasnian) Gogo Formation of the Canning Basin,
Western Australia (Trinajistic et al. 2007). These structures are preserved in three
dimensional phosphate likely mineralized under the influence of bacteria in the
small infillings under the headshield of the fish. Currently the oldest soft tissues
described from such fish, the fossilized material supports the hypothesis that the
placoderms are the sister group of the other gnathostomes (Trinajistic et al. 2007).
3.1.5 Carboniferous Phosphatization
Similarly preserved fish soft parts, including phosphatized muscles, are known
from the upper Mississippian Bear Gulch Limestone of the Heath Formation of
central Montana, USA (Lund et al. 1993). Skin coloration, eye pigments, circulatory
system structures, and internal organs are sometimes preserved (Grogan and Lund
1997). One of the most diverse fish fossil deposits in the world, with over 100 fish
species described, the Bear Gulch also contains a diverse array of invertebrates
(Hagadorn 2002). Frequent turbidity currents across the shallow marine basin likely
facilitated such exceptional preservation, as fish and other organisms appear to have
been simultaneously asphyxiated and buried (Grogan and Lund 1997). Phosphatized
cephalopod mouthparts and a radula are preserved in the Upper Pennsylvanian
Coffeyville Formation of Oklahoma, central USA (Tanabe et al. 2001). The fossil
contains an almost complete jaw apparatus and a well-preserved radula, both in life
orientation. They are preserved in a phosphate nodule found within black shales
likely deposited during low-oxygen conditions associated with a marine transgres-
sion. Based on the morphology of the mouthparts, this fossil is likely that of an
ammonoid (Tanabe et al. 2001).
3.1.6 Permian Phosphatization
Partially phosphatized cephalopod fossils are also known from carbonate nodules in
the Permian Arcturus Formation of Nevada, USA (Mapes et al. 2002, 2003). The
specimens have phosphatized intracameral membranes and siphuncular tissues.
These are more labile tissues than the mouthparts and radula preserved in the
Carboniferous example. These fossils, however, are also preserved in nodules within
shales representing deposition in low-oxygen settings (Mapes et al. 2002, 2003).
Although the Permian Phosphoria Formation of the western USA contains phos-
phoritic shales with abundant phosphatic crusts and ooids, no evidence for the
phosphatization of soft tissues or original shell material has been found (Martindale
1986). Considering that apatite in the Phosphoria often encrusts the insides of gas-
tropod and brachiopod shells (Martindale 1986), it would appear that phosphogenesis
took place after the soft tissues of these organisms had already fully decayed.
3.2 Mesozoic Phosphatization
3.2.1 Triassic Phosphatization
Phosphatized ostracods and associated ciliates are preserved in the Lower Triassic
Olenekian Stage of Svalbard (Weitschat 1995). The ostracods are preserved within the
living chamber of the large ammonoid Keyserlingites. Their valves and appendages
are both preserved through phosphatization. The phosphatized ciliates are preserved
within the ostracod valves, usually on the epipodial appendages of the ostracod. It is
thought that the ostracods were scavenging on the decaying ammonoid tissue when
the ammonoids were buried and phosphatizing microenvironments formed within the
living chamber of the ammonoid and within he ostracod valves (Weitschat 1995).
446 S.Q. Dornbos
Middle Triassic bivalves with some soft parts phosphatized are found in the
Muschelkalk carbonates of Germany (Klug et al. 2005). Phosphatized tissues
include the mantle, adductor muscles, inhalant and exhalant siphons, gills and gill
supports, and the labial palps (Klug et al. 2005). These preserved features were
found within internal molds (steinkerns) of articulated trigoniid bivalves. The
infaunal life mode of these bivalves likely contributed to the phosphatization of
their tissues because they were already buried upon death. The gill supports show
the finest level of preservation, with microscopic ultrastructures visible in SEM,
whereas the other structures are preserved by more massive, undifferentiated phosphate
mineralization (Klug et al. 2005). This is likely because the gill supports were
chitinous, while other more labile tissues had begun decaying by the time of
phosphatization.
The Middle Triassic Monte San Giorgio Lagerstätte of southern Switzerland and
northern Italy contains rare phosphatized soft tissues. These include the skin of the
reptile Macrocnemus bassanii (Renesto and Avanzini 2002; Etter 2002), skin of
nothosaurs, and the digestive tracts of fish. These fossils are preserved within the
bituminous dolomites and bituminous black shales of the Grenzbitumenzone and
the Meride Limestone, interpreted as being deposited in a stagnant basin sur-
rounded by carbonate reefs. The anoxic-dysoxic boundary is thought to have been
at the seafloor and prokaryotic microbial mats covered the seafloor. These environ-
mental conditions created the right conditions for exceptional preservation, including
some phosphatization (Etter 2002).
3.2.2 Jurassic Phosphatization
Phosphatized soft tissues are preserved in the Lower Jurassic Lombardische

Kieselkalk Formation of northern Italy, known as the Osteno Lagerstätte (Pinna
1985). Soft part preservation through phosphatization in this deposit includes the
muscles and branchia of crustaceans, fish tissues, and the digestive tracts of
coleoids, polychaetes, and nematodes. These fossils are interpreted as having been
preserved in a stagnant, restricted basing with anoxic conditions likely within the
sediment pore waters (Pinna 1985).
The Middle to Upper Jurassic Oxford Clay of England contains phosphatized
soft-bodied squids (Allison 1988). They are preserved as films of calcium phos-
phate in the Peterborough Member, interpreted as deposited in a low-oxygen set-
ting. The bodies of these squids are almost completely phosphatized, with some
decay evident on their tentacles (Allison 1988).
Bivalves exhibiting a similar style of preservation as those preserved in the
Triassic Muschelkalk of Germany are found in the Upper Jurassic Portland
Limestone Formation of Great Britain (Wilby and Whyte 1995). As in the
Triassic example, these are articulated trigoniid bivalves preserved as internal
molds, in which the phosphatized soft parts are visible (Wilby and Whyte
1995). The preserved features include muscle fibers from the mantle and
the gill axis. Preservation took place through phosphatization of microbes on

the surface of the soft tissues, resulting in external molds with no preservation
of internal features (Wilby and Whyte 1995). The source of the phosphate for
the preservation of these structures was likely the decay of the more labile
tissues of the bivalve itself. This decay elevated the dissolved phosphate levels
within the articulated valves, facilitating the phosphatization of more refractory
soft tissues (Wilby and Whyte 1995).
3.2.3 Cretaceous Phosphatization
Phosphatization becomes more common again during the Cretaceous and early
Cenozoic. One example is the Lower Cretaceous Santana Formation of Brazil, well
known for its fossil fish. These fish are preserved in three dimensions within cal-
careous concretions in bituminous shale and limestone facies (Martill 1988).
Phosphate replaces muscle fibers in the myomeres and encrusts the bones of many
of these fish. This phosphatization happened extremely early, perhaps even pre-
burial. It seems likely that the earliest phases of decay within the fish bodies cre-
ated the microenvironment necessary for rapid phosphatization of these tissues
(Martill 1988).
The Mid-Cretaceous (Aptian-Albian) Marnes Bleues Formation in the Vocontian
Basin of southeast France and the black shales (Albian) of site DSDP 369 on the
African continental slope in the eastern central Atlantic both contain abundant evi-
dence for phosphatized bacteria and possibly fungi (Bréhéret 1991). These fossils
are preserved in phosphatic nodules within black shales that were deposited in
bathyal, low-oxygen settings. Occasional phosphatized fish bones are found in the
nodules as well. The original source of the phosphate in these nodules is unclear,
but it may be that the bacterial or fungal mats themselves created phosphogenic
microenvironments in sporadic localities (Bréhéret 1991). The phosphatized bacteria
include bacilli and cocci, sometimes arranged in rosettes. The possible fungi are
preserved as monolayered mat fragments (Bréhéret 1991).
The Upper Cretaceous Austin Group at El Rosario, northeastern Mexico also
contains phosphatized fish soft parts and intestinal contents. Such preserved struc-
tures include myotomes, gill filaments, scales, and fins (Stinnesbeck et al. 2005).
Other phosphatized soft tissues found include decapod crustacean carapaces,
ammonite siphos, and parts of pterosaurs. These fossils are preserved in laminated,
platy limestones and marls, interpreted as representing deposition in a basin with
dysoxic to anoxic bottom water conditions near the southernmost portion of the
Western Interior Seaway (Stinnesbeck et al. 2005).
Another example of Upper Cretaceous phosphatization is found in the Tres
Esquinas Member of the Colon Formation, Venezuela (Ghosh 1984). Only a few
meters thick, this phosphorite unit was deposited as a condensed sequence during
a trangression and the beginning of a sea level highstand (Ghosh 1984). Although
no soft tissues are preserved, most calcareous shell material has been replaced by
apatite. Such fossils are mostly foraminiferal.
448 S.Q. Dornbos
Upper Cretaceous phosphatization is also known from a series of phosphorites

in Tunisia, Morocco, Mauritania, and Egypt (Lamboy et al. 1994). These phospho-
rites span well into the Cenozoic, reaching as young as Eocene in age. A few of
them will be discussed in the following section. The phosphatized fossils in these
deposits are elongate coprolites, which make up a large percentage of the grains in
these lithologies. Bacteria likely controlled their preservation by causing the initial
decay necessary for the rest of the coprolites to be phosphatized (Lamboy et al.
1994). This scenario is supported by the microstructure of the coprolites which,
when examined with an SEM, are morphologically consistent with abundant phos-
phatized bacteria (Lamboy et al. 1994). Some of these coprolites contain evidence
of fish remains, so it is thought that predatory fish produced them. Excrement con-
taining fish remains would be highly concentrated with phosphate, making only a
small amount of bacterial decay necessary before the proper microenvironment is
produced for phosphatization (Lamboy et al. 1994). This may explain why no other
phosphatized fossils are known from these deposits despite them representing a
broadly phosphogenic environment.
The Upper Cretaceous phosphorites of Egypt, particularly the Campanian-
Maastrichtian Duwi Formation, also contain phosphatized diatoms (Ahmed and
Kurzweil 2002). The Duwi Formation was deposited during the second of four
phosphatization events preserved in the Upper Cretaceous of Egypt, each of which
is linked to a trangression (Ahmed and Kurzweil 2002). These phosphatized dia-
toms include both concentric and pinnate forms. Their frustules are either replaced
or molded on a fine scale by phosphatic minerals. It is likely that the diatoms them-
selves were an important source of the phosphate necessary for the deposition of
these phosphoritic deposits, as in seen in other phosphorites around the world
(Ahmed and Kurzweil 2002).
3.3 Cenozoic and Recent Phosphatization
3.3.1 Paleogene Phosphatization
Eocene phosphorites in Senegal contain abundant phosphatized fish coprolites

(Lamboy et al. 1994). These are found in strata equivalent to part of the previously
discussed Cretaceous to Eocene Mediterranean phosphorite sequence. As such,
these Senegalese phosphorites contain elongate fish coprolites that were likely
formed through initial bacterial decay of the phosphate-rich fecal pellets them-
selves. Eocene fossils of this type are also found in Tunisia, Morocco, and
Mauritania (Lamboy et al. 1994).
A fauna of phosphatized insects is found in latest Oligocene/earliest Miocene
limestones of the Riversleigh area of Australia (Duncan et al. 1998). These fossils
are preserved in three dimensions and include coleopterans, trichopterans, myri-
apodans, and isopods. The internal soft tissues of these arthropods are not pre-
served, only portions of the cuticle and eyes are phosphatized (Duncan et al. 1998).
The eyes are extremely well preserved, allowing for detailed examination of their
morphologies. Fungi and bacteria are also phosphatized within the specimens,
indicating that substantial decay had begun when the cuticle and eyes were phos-
phatized (Duncan et al. 1998). The environment of deposition is interpreted as a
shallow lime-rich pool in a rain forest (Duncan et al. 1998).
3.3.2 Neogene Phosphatization
Evidence for Miocene phosphogenesis is quite abundant and a common example is

the Monterey Formation of California, USA (Garrison et al. 1990). While predomi-
nantly a siliceous diatomite, the Monterey Formation contains richly phosphatic
units in which carbonate skeletal material has been replaced by phosphate, most
commonly with foraminiferal tests (Garrison et al. 1990). Phosphatic fish bones are
also typically preserved. Evidence for soft tissue phosphatization exists in the form
of abundant phosphatized bacterial material. These rocks were deposited in a bio-
logically productive upwelling zone where bacterial mats likely played a crucial
role in creating phosphogenic settings in the midst of a normally siliceous deposit
(Reimers et al. 1990).
The Libros Basin of northeast Spain contains a Late Miocene assemblage of
amphibians, birds, snakes, and leaves, with phosphatization as a common mode of
preservation (McNamara et al. 2004). The fossils are found in laminated mudstones
within lacustrine deposits. Frog fossils are particularly abundant in these deposits.
They exhibit a high degree of articulation and their outer skin is often phosphatized.
Carbonaceous bacteria are preserved within the skin, evidence that decay of the
inner layers of the skin had begun when the outer portion of the skin was phos-
phatized (McNamara et al. 2004).
3.3.3 Pleistocene and Recent Phosphatization
Pleistocene phosphatization of bacteria within phosphatic stromatolites is known

from phosphorites on the continental margin of southeast India (Purnachandra Rao
et al. 2000, 2002). Found at depths between 186 and 293 m, these stromatolites
contain phosphatized microfilaments and coccoid objects consistent with the cells
of cyanobacteria. These stromatolites formed when sea level was lower during the
Pleistocene and are analogous with Cambrian phosphatic stromatolites (Purnachandra
Rao et al. 2000, 2002). The mats sealed off the pore waters from the ocean waters
above, creating conditions favourable to phosphatization when buried microbial
mats decayed, producing dissolved phosphate from the organic material as well as
buried continental detritus (Purnachandra Rao et al. 2000, 2002). Although the
fossils are not phosphatized, the phosphorites in these deposits frequently encrust
and encapsulate calcareous fossils of bivalves, gastropods, foraminifera, scleractinians,
barnacles, serpulids, and algal rhodoliths.
450 S.Q. Dornbos
Recent phosphogenic environments exist in multiple localities around the world

including the continental margins of southeast Africa, Peru, Chile, and Mexico
(Burnett 1977; Jahnke et al. 1983; Baturin et al. 1998). This process is particularly
active on the outer shelf off the coast of Namibia, where phosphates are forming in
a high-productivity shelf zone created by upwelling (Baturin and Dubinchuk 2003).
Periodic blooms of poisonous zooplankton species in this area causes episodic mass
mortality events. Because of these events, the seafloor in this region is covered with
bones of marine vertebrates (Baturin and Dubinchuk 2003). These bones become
phosphatized, and detailed mineralogical studies of some of these bones recovered
from benthic trawls have been performed. These analyses of fish and whale bones
indicate that the primary fibrous structure of the original bone apatite was altered
to a colloform substance that formed globular clots, which were then crystallized.
So, although these bones are being phosphatized, their microstructures are not
being precisely replicated (Baturin and Dubinchuk 2003).
Similarly phosphatized fish and whale bones are common in the Recent active
phosphogenic zone on the slope and outer shelf off the coast of Peru (Resig and
Glenn 1997). These phosphatized bones, as well as the phosphatic seafloor crusts
common in this region, are inhabited by encrusting foraminifera, serpulid worms,
bryozoans, cnidarians, boring organisms, and grazing chitons. Fossil examples of
such phosphatic hardground communities are known from the Jurassic-Lower
Cretaceous of southern Spain and the Upper Cretaceous of the Czech Republic
(Zítt and Nekvásilova 1993; Martín-Algarra and Sánchez-Navas 1995). The
Upper Cretaceous biota is most analogous to that seen in the modern Peruvian
phosphogenic setting, containing a diverse suite of foraminifera, brachiopods,
sponges, scleractinians, octocorals, bryozoans, bivalves, and worm tubes (Zítt and
Nekvásilova 1993).
4 Temporal Distribution Hypotheses
Although the examples described here do not encompass every known instance of
phosphatization in the Phanerozoic fossil record, they do broadly reflect the tempo-
ral distribution and biases of phosphatization during the past 543 million years.
There do appear to be two important pulses in phosphatization during the
Phanerozoic: the Cambrian through Early Ordovician and the Cretaceous through
Eocene (Table 1). In most other times in Earth history, phosphatization is an
exceedingly rare taphonomic window that usually depends on the formation of
amenable microenvironments.
This temporal pattern of phosphatic fossil preservation is similar, but not identi-
cal, to the Phanerozoic distribution of marine phosphogenic events, which addition-
ally shows increased phosphorite occurrence during the Permian and early
Mesozoic (e.g. Föllmi 1996). This discrepancy further emphasizes the rare nature
of phosphatization because it does not universally become more common during
intervals of increased marine phosphogenesis. The reasons for this remain unclear,
but perhaps, as may have been possible with the Permian Phosphoria Formation,
phosphogenesis was occurring at a diagenetically later time when soft tissues had
already decayed away.
The Cambrian through Early Ordovician record consists of phosphatized animal
embryos and microarthropods (Table 1). These fossils are preserved both within
phosphoritic facies and within nodules in non-phosphoritic facies across a broad
spectrum of marine shelf depositional environments. Similarly preserved animal
embryos and meiofaunal arthropods are not yet known from younger strata.
Perhaps the explanation for the closure of this taphonomic window lies in the
evolution of animal life itself. Animal sediment mixing in marine settings did not
reach typical Paleozoic levels until the Ordovician radiation (e.g. Droser 1987). The
creation of a persistent mixed layer in the upper few centimeters of seafloor sedi-
ments may have permanently narrowed the possible range of phosphatizing
microenvironments in the oceans. This mixed layer would have lowered the oxic–
anoxic interface within sediments, making it more difficult for organic remains to
become buried in low-oxygen settings where mineralization of soft tissues is more
feasible. Similar hypotheses have been proposed for the decline of Burgess Shale-
type soft bodied biotas during the Cambrian (Allison and Briggs 1993), but the
phosphatization window apparently persisted until Ordovician bioturbation levels
made these taphonomic processes exceedingly difficult. Thereafter, phosphatiza-
tion was restricted to low-oxygen and/or phosphogenic environmental settings, as
well as microenvironments.
The pulse of phosphatization during the Cretaceous to Eocene may have to do
with broad paleoceanographic patterns. It corresponds well with a general increase
in phosphogenic environments, which may be related to the development of large
euxinic epicontinental seas during this greenhouse time. Cretaceous to Eocene
phosphorites throughout northern Africa, for example, are strongly related to a
series of transgressions by the Tethys Sea (Ahmed and Kurzweil 2002). These
transgressions would have brought zones of high-productivity and low-oxygen bottom
waters onto the continent, where phosphogenesis could take place and phosphorite
deposits could accumulate.
5 Biases Through Time
Phosphatization during the earliest Phanerozoic is highly biased toward ecdysozo-

ans and their embryos (Table 1). Both the Orsten-style microarthropods and the
animal embryos found in the Cambrian through Early Ordovician have well-
preserved exterior layers with almost no internal preservation (e.g. Maas et al.
2003; Dong et al. 2005). In both cases, their recalcitrant cuticles survived initial
decay to become phosphatized, likely as a direct result of the organic decay of their
interiors. In both cases, there is also a strong size bias. Later developmental stages
of the embryos, including adult forms, were not preserved and the arthropod assem-
blages only contain the meiofauna (e.g. Maas et al. 2003; Dong et al. 2005).
452 S.Q. Dornbos
Phosphatization is much rarer in the remainder of the Paleozoic, and shows a

bias toward taxa with recalcitrant tissues (Table 1). Arcritarch organic walls, echi-
noderm plates, and cephalopod mouthparts all would remain intact for phosphatization
well after the rest of the organism began decaying (Bischoff and Hall 1980; Tanabe
et al. 2001; Mapes et al. 2002, 2003; Kremer 2005). All of these remaining
Paleozoic examples rely on phosphatizing microenvironments. None of them are
found in phosphoritic rocks.
This same bias toward the preservation of recalcitrant tissues continues into the
Mesozoic, but a wider array of organisms are preserved and the strong preservation
bias toward fish remains begins to be seen (Table 1). During the Triassic and
Jurassic, phosphatization takes place in either phosphatizing microenvironments,
such as those within the valves of infaunal bivalves, or within larger low-oxygen
environmental settings that preserve a broad range of taxa (Pinna 1985; Allison
1988; Weitschat 1995; Wilby and Whyte 1995; Etter 2002; Klug et al. 2005). The
Cretaceous does contain phosphoritic facies with phosphatized organic remains,
mostly fish skeletal elements and fish coprolites (e.g. Lamboy et al. 1994). The
enrichment of fish bones in calcium phosphate creates a strong bias toward their
secondary mineralization with apatite that begins in the Mesozoic, particularly the
Cretaceous, and continues into the Recent (Table 1).
Cenozoic and Recent phosphatization exhibits this bias toward fish, with whales
also becoming common in Recent settings (Table 1). Phosphatization does seem to
follow phosphogenesis during the Cenozoic, becoming rare as phosphogenesis
decreases in the Neogene. Fish remains dominate Paleocene through Miocene
examples, with a diverse group of taxa being preserved more infrequently (Garrison
et al. 1990; Lamboy et al. 1994; Duncan et al. 1998; Purnachandra Rao et al. 2000,
2002; McNamara et al. 2004). Recent examples are only known from phosphogenic
settings and contain fish and whale bones (Resig and Glenn 1997; Baturin and
Dubinchuk 2003). This also exemplifies the bias toward recalcitrant remains, since
the only part of the fish and whales that are preserved are typically their secondarily
mineralized bones. Bacteria are the one group of fossils that transcends any broad
Phanerozoic bias patterns. Probably owing to their importance during the phos-
phatization process, putative phosphatized bacteria are common throughout the
Phanerozoic. Putative bacterial fossils have been listed in Table 1 only when they
are one of the primary fossil forms found in the deposit, but they are described
as associated with nearly every one of the fossil occurrences discussed in this
chapter (Table 1).
6 Summary
Phosphatization is a high resolution yet strongly biased taphonomic process.

Review of the available literature indicates pulses of phosphatization during the
Cambrian through Early Ordovician and the Cretaceous through Eocene. The
Phanerozoic record of phosphatization is biased toward taxa with recalcitrant tissues,
those with body parts enriched in phosphate, and those with small body sizes.
Phosphatization can take place in phosphogenic environmental settings, but does
not always do so. It is also likely to occur in local phosphatizing microenvironments
created by a decaying organism. The soft tissues of a wide range of Phanerozoic
taxa, from vertebrates down to bacteria, are preserved through phosphatization,
making this taphonomic process a powerful tool in understanding the details of the
history of life on Earth.
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Chapter 13
Three-Dimensional Morphological (CLSM)
and Chemical (Raman) Imagery of Cellularly
Mineralized Fossils
J. William Schopf, Anatoliy B. Kudryavtsev, Abhishek B. Tripathi,

and Andrew D. Czaja
Contents
1 Introduction........................................................................................................................... 458
1.1 Cellularly Mineralized Fossils..................................................................................... 460
2 Techniques............................................................................................................................ 461
2.1 Confocal Laser Scanning Microscopy (CLSM).......................................................... 461
2.2 Raman Spectroscopy.................................................................................................... 462
3 Applications.......................................................................................................................... 464
4 Mineralized Soft Tissues of Metazoans................................................................................ 464
4.1 Apatite-Mineralized Ctenophore Embryo................................................................... 464
5 Permineralized Plants............................................................................................................ 466
5.1 Quartz-Permineralized Plant Axes............................................................................... 467
5.2 Calcite-Permineralized Plant Axes.............................................................................. 468
6 Permineralized Organic-Walled Microorganisms................................................................. 469
6.1 Quartz-Permineralized Acritarchs............................................................................... 470
6.2 Quartz-Permineralized Filamentous Microbes............................................................ 472
7 Summary............................................................................................................................... 482
References................................................................................................................................... 483
J.W. Schopf ()
Department of Earth and Space Sciences, Institute of Geophysics and Planetary Physics (Center
for the Study of Evolution and the Origin of Life), Molecular Biology Institute, and NASA
Astrobiology Institute, University of California, Los Angeles, CA 90095, USA
A.B. Kudryavtsev
Institute of Geophysics and Planetary Physics (Center for the Study of Evolution and the Origin
of Life) and NASA Astrobiology Institute, University of California, Los Angeles, CA 90095,
USA
A.B. Tripathi
Advanced Projects Office, Constellation Program, NASA Johnson Spacecraft Center,
77058, Houston, TX, USA
A.D. Czaja
Department of Earth and Space Sciences and Institute of Geophysics and Planetary Physics
(Center for the Study of Evolution and the Origin of Life), University of California, 90095,
Los Angeles, CA, USA
458 J.W. Schopf et al.
Abstract Of all modes of fossilization, cellular mineralization, whether by the

n on-biologic process of permineralization (“petrifaction”) or by microbially mediated
mineral precipitation (“authigenic mineralization”), is the most faithful to the pres-
ervation of life-like cells and tissues that is known, yielding fossils that are among
the biologically and taphonomically most informative available from the geological
record. Such preservation spans all forms of life, ranging from vascular plants, such
as those permineralized in calcitic coal balls; to organic-walled algae, fungi and
bacterial prokaryotes, permineralized most commonly in fine-grained quartz; to meta-
zoans that exhibit preserved soft tissues, such as those mineralized in apatite. Though
such fossils can be preserved in exquisite cellular detail, two deficiencies have long
hampered their study: (1) an inability to document fully their three-dimensional
morphology at micron-scale spatial resolution; and (2) the lack of a means to analyze
in situ and at such resolution the chemistry of the carbonaceous matter (kerogen) that
comprises their structurally preserved anatomy. These needs have now been met by
two techniques newly introduced to paleobiology, three-dimensional confocal laser
scanning microscopy (CLSM) and two- and three-dimensional Raman imagery.
We here document the use of these techniques to elucidate the fine-scale structure
and kerogenous composition of representative fossils of each of the major biologic
groups (animals, plants, fungi, algal protists, and microbes) preserved in phosphorites,
cherts, and carbonates, the three principal rock types in which cellular mineraliza-
tion occurs. The examples presented include an apatite-mineralized ctenophore
embryo preserved in a Cambrian phosphorite; quartz-permineralized Eocene fern
rhizomes and a fungal-infested Devonian plant axis preserved in carbonaceous
cherts; a calcite-permineralized plant stem preserved in a calcareous Carboniferous
coal ball; and quartz-permineralized acritarchs (phytoplanktonic algae), cyanobac-
teria, and especially ancient fossil microbes permineralized in Precambrian cherts.
Use of CLSM and Raman imagery can provide new information about the morphol-
ogy, cellular anatomy, taphonomy, carbonaceous composition and geochemical matu-
rity of organic-walled mineralized fossils, whereas Raman imagery used alone can
document the mineralogy of the enclosing matrix and the spatial relations between such
fossils and their embedding minerals. Not only can the use of these techniques eluci-
date the sequence of events and taphonomic processes involved in the cellular mineral-
ization of organic-walled fossils, but the use of Raman to document the geochemical
maturity of their kerogenous constituents can provide new evidence of the biases of
such preservation over time. Because both techniques are non-intrusive and non-
destructive, both can be applied to specimens archived in museum collections. Taken
together, the two techniques represent a major advance in the study of ancient fossils.
1 Introduction
Taphonomic studies of fossils depend critically on the fidelity of the preservation

of the specimens studied and on an ability to investigate and to document at
appropriate spatial resolution the structure of the biologic remnants preserved.
13 Cellularly Mineralized Fossils 459
Among all fossils, cellularly mineralized organisms, studied typically in petrographic

thin sections or cellulose acetate peels, are among the best preserved and,
thus, the biologically and taphonomically most informative. Nevertheless, until
recently it has not been possible to document accurately the three-dimensional
morphology and cellular anatomy of such fossils at high spatial resolution, a
deficiency particularly troublesome to studies of the fine-structural features of
megascopic fossils and the morphology and cellular make-up of minute fossil
microorganisms. Moreover, there has been no means available by which to ana-
lyze directly the molecular-structural composition and geochemical maturity of
the coal-like carbonaceous organic matter (kerogen) that comprises permineral-
ized fossils, factors crucial to an assessment of the fidelity of their preservation.
This chapter documents the use of two techniques newly introduced to paleobiol-
ogy that meet these needs: three-dimensional confocal laser scanning micros-
copy, “CLSM” (Schopf et al. 2006a) and two- (Schopf et al. 2002, 2005)
and three-dimensional Raman imagery (Schopf and Kudryavtsev 2005; Schopf
et al. 2007).
Shown here to be applicable to cellularly mineralized fossils whether studied
in thin sections or in acetate peels, CLSM and Raman imagery, together, can
demonstrate, in three dimensions and at micron-scale spatial resolution, a one-
to-one match of cellular form and kerogenous composition. Particularly useful
for studies of coccoidal and sinuous filamentous Precambrian microbes and
comparably minute Phanerozoic organic-walled microfossils, both techniques
are applicable also to studies of higher plants – where they can provide evidence
of the fine structure and molecular-structural composition of fossilized cells
unavailable by any other means – and of metazoans, where they can yield insight
into the nature and three-dimensional preservation of mineralized soft tissues.
Used in tandem, the two techniques can provide valuable taphonomic informa-
tion about the biological degradation of diverse organically preserved specimens
(e.g., the fungal infestation of plant axes, the enzymatic breakdown of the mid-
dle lamellae of vascular plant cell walls, and the preferential decay of specific
cell wall components in fossil cyanobacteria). Moreover, their use can also elu-
cidate the sequence of events that led to the not uncommonly exquisite preserva-
tion of such fossils (e.g., apatite-mineralization of the organic matter of the soft
tissues of metazoans followed by calcitic infilling of interstices and fluid-filled
cavities) and their fidelity of preservation (measured by use of the Raman index
of preservation, “RIP,” a metric that documents the geochemical maturity of the
kerogenous components of such fossils; Schopf et al. 2005). Properly executed,
both techniques are non-intrusive and non-destructive – factors that permit their
application to specimens archived in museum collections – and unlike standard
two-dimensional optical photomicrographs, the three-dimensional digitized
images provided by CLSM and Raman imagery can be rotated and examined
from multiple perspectives (e.g., in video presentations), a telling advance
over standard optical microscopy of particular relevance to investigations of
taphonomy.
1.1 Cellularly Mineralized Fossils
Of all modes of fossil preservation, cellular mineralization, whether by the non-

biologic process of permineralization (“petrifaction”) or by microbially mediated
mineral precipitation (“authigenic mineralization”), provides the most faithful life-
like representation of biologic anatomy and cellular morphology known in the
geological record.
Of the two processes, permineralization (known commonly, but incorrectly, as
“petrification”) was the first to be described, more than a century ago (White 1893).
The misnomer “petrifaction” (from petrify, “to convert into stone”) dates from this
early study when the process was misinterpreted as reflecting “molecule-by-
molecule…replacement” of cellular organic matter by minerals (White 1893) – an
error repeated in numerous popular books on ancient life and even in some modern
textbooks. In contrast with this stoichiometrically implausible (if historically interesting)
account of the process, permineralization is now known to result from the pervasion
of mineral-charged solutions into biologic tissues during the early stages of diagenesis,
prior to complete decay and cellular disintegration (Schopf 1975). The organic
structures of such fossils, in many specimens preserved in microscopic detail, are
not mineral-replaced. Rather, the permeating fluids infill micellar, intercellular, and
intracellular spaces – replacing the watery milieu of the biomolecular components,
not the organic structures themselves – to produce a mineral-infused inorganic-
organic mix that serves to preserve such physically robust organic-rich structures as
the cell walls of plants, algae, fungi and microbes, and, much less commonly, the
soft tissues of animals (which lack robust cell walls).
Despite such understanding of the products of permineralization, the chemistry
of the process has yet to be defined. It may well be that permineralization merely
reflects the occurrence of infiltration and fine-scale embedding like that performed
routinely by the use of organic resins and/or waxes in the preparation of living
specimens for sectioning and study by optical or transmission electron microscopy.
However, if chemical bonding plays a role in permineralization, the most likely
such chelation would be that involving hydrogen-bonding between the peripheral
hydrogen atoms of the interlinked polycyclic aromatic hydrocarbons (“PAHs”) that
comprise the kerogen of permineralized fossils and oxygen atoms of their embedding
minerals (Schopf et al. 2005). The sequence of events implied by such a process –
from the mineralic infilling of (and chemical bonding with?) the biomolecules of
decaying tissues to the conversion of such material to a chemically bonded mineral-
PAH mix – has yet to be demonstrated. In short, although it is well established that
permineralization results in the fine-scale preservation of mineral-infused, physically
robust cellular organic structures, the chemistry of such preservation has yet to be
elucidated.
In most cases, the fine-scale structural preservation of the soft tissues of animals,
for example in apatite, occurs by a different process: authigenic mineralization.
As an over-simplification, permineralization is a non-biologic chemical process
whereas authigenic mineralization is microbially mediated (for recent detailed
discussions of this process, see Briggs 2003; Briggs et al. 2005). Although most
soft-tissue preservation in apatite is evidently due to bacterially driven authigenic
mineralization, it is possible that some phosphorites represent settings in which
concentrations of phosphate were so high that mineralization of soft tissues in apatite
was more akin to permineralization than to authigenic mineralization (D.E.G.
Briggs, pers. comm. 2007). Similarly, preservation in pyrite, whether of the cellular
structure of fossil plants (e.g., Scheckler 1986; Grimes et al. 2002) or of the soft
tissues of metazoans (e.g., Briggs et al. 1996), is typically due to authigenic miner-
alization, sulfate reducing bacteria using the hydrogen of decaying organic matter
to produce hydrogen sulfide that unites with ferrous iron to produce mineralizing
fine-grained pyrite.
Cellularly mineralized fossils are known from all of the major groups of life –
plants, animals, protists, fungi, and bacteria. Among these, plant fossils have been
the most intensively studied, with in-depth knowledge of the Carboniferous flora,
for example, having been derived almost entirely from studies of plant parts per-
mineralized in calcitic coal balls (e.g., Taylor and Taylor 1993). Similarly, current
understanding of the Precambrian fossil record is dependent largely on studies of
organic-walled acritarchs (planktonic algal protists) and cellular microbes permin-
eralized in cherts (Schopf 1999). Permineralized fungi (Taylor and Remy 1992),
animals (e.g., Chen et al. 2007) and protozoal protists (Bloeser et al. 1977; Schopf
1992, p. 592; Mus and Moczydlodłowska 2000) have also been reported. Although
relatively rare occurrences of plant axes (e.g., Scheckler and Banks 1971;
Scheckler 1986; Grimes et al. 2002) and metazoan soft tissues (e.g., Stuermer 1970;
Stuermer and Bergström 1973; Cisne 1974; Briggs et al. 1996, 2005; Briggs 2003)
authigenically mineralized in pyrite have been recorded, cellularly mineralized
fossils are typically infused by three principal minerals: apatite (as in Cambrian
metazoans preserved in phosphatic limestones); calcite (as in plants permineral-
ized in Carboniferous coal balls); and quartz (as in Phanerozoic plants and fungi,
and Precambrian microorganisms permineralized in bedded cherts and the cherty
parts of stromatolitic carbonates). The use of CLSM and Raman to analyze fossil
animals, plants, fungi, algae and bacteria from each of these matrices is docu-
mented below.
2 Techniques
2.1 Confocal Laser Scanning Microscopy (CLSM)
The confocal laser scanning microscope was developed in the mid-1980s for use in
biology to image in three dimensions the structural components of cells (Amos and
White 2003). In such microscopes, the aperture-constrained light path serves to
restrict the focus of the system to a discrete focal plane. By thus suppressing the
image-blurring input of out-of-focus planes above and below this focal plane,
CLSM provides a crisp image of a thin in-focus plane that cannot be provided by
standard optical microcopy. The laser beam of such systems excites fluorescence in
the material analyzed, for modern cells derived typically from biomolecules having
conjugated ring systems or from introduced fluorescent dyes, but for kerogenous
fossils, such as those analyzed here, emitted from the interlinked PAHs of which
they are primarily composed (Schopf et al. 2005). Such kerogen-derived fluores-
cence, maximum in the red to near-infrared region of the spectrum (Schopf et al.
2005, 2006a), is then collected by the detector of the system. By rapidly rastering
the laser beam of the system across a kerogenous fossil at precisely defined increasing
depths and then processing the digitized sequential series of images acquired – by
use first of the 3-D rendering software of the CLSM system and, if desired, by use
of the more advanced VolView 3-D rendering computer program (Kitware, Inc.,
Clifton Park, NY) – CLSM can produce a three-dimensional image of a specimen
at sub-micron spatial resolution (Schopf et al. 2006a).
CLSM has only recently been introduced to paleobiology. Most such work has
focused on Phanerozoic organic-walled palynomorphs freed from their encompassing
matrices by acid maceration (Scott and Hemsley 1990; Foster et al. 1990; Talyzina
1997; Feist-Burkhardt and Pröss 1999; Mus and Moczydlodłowska 2000; Feist-
Burkhardt and Monteil 2001; Nix and Feist-Burkhardt 2003; Hochuli and
Feist-Burkhardt 2004). Few studies have applied this technique to fossils in petro-
graphic thin sections (Mus and Moczydlodłowska 2000; Nix and Feist-Burkhardt
2003; Schopf et al. 2006a; Chi et al. 2006) and its use to document the anatomy of
mineralized Phanerozoic metazoans (Chen et al. 2007) and the cellular structure
of Precambrian protozoans (Mus and Moczydlodłowska 2000), acritarchs and
microbes (Schopf et al. 2006a) has been barely tapped. The present work records
the first application of CLSM to Phanerozoic plant fossils and infesting fungi, and
its first use for studies of specimens prepared in cellulose acetate peels.
2.2 Raman Spectroscopy
Raman spectroscopy is an analytical technique used widely in geochemistry for the

identification and molecular-structural characterization of minerals (e.g., McMillan
and Hofmeister 1988; Williams et al. 1997), including graphite and graphite-like
mineraloids, studies that have focused on the use of such carbonaceous materials as
indices of high-grade metamorphic alteration (e.g., Pasteris and Wopenka 1991;
Jehlička and Beny 1992; Wopenka and Pasteris 1993; Yui et al. 1996; Spötl et al.
1998; Kelemen and Fung 2001; Jehlička et al. 2003). In contrast, our use of Raman
has centered on the carbonaceous components of less altered and, thus, potentially
fossiliferous, unmetamorphosed to low-grade (greenschist) metamorphic units,
geochemically relatively immature organic matter that has been little investigated
by Raman. Similarly, unlike previous Raman studies – virtually all of which have
been devoted to analysis of carbonaceous matter preserved by compression (in
shales, slates, coals, gneisses and the like) – our work has centered on organic
materials preserved by cellular mineralization, three-dimensionally embedded in

their enclosing mineral matrices (Kudryavtsev et al. 2001; Schopf et al. 2002, 2005,
2007; Schopf 2004a, b; Schopf and Kudryavtsev 2005; Chen et al. 2007).
In analyses of cellularly mineralized carbonaceous matter, CLSM and Raman
studies are complementary, both being used to measure signals derived from prop-
erties of the kerogenous materials analyzed: for CLSM, laser-induced fluorescence
derived chiefly from the interlinked PAHs that predominate in kerogen (Schopf
et al. 2006a); for Raman, laser-induced vibrational transitions in the bonds of such
PAHs and their associated functional groups (Schopf et al. 2005). Only recently
introduced to paleobiology (Roberts et al. 1995; Arouri et al. 2000; Kudryavtsev
et al. 2001; Schopf et al. 2002), Raman can be used to characterize both the molecular
structure and the geochemical maturity of the kerogenous cell walls of organically
preserved fossils – whether megascopic (e.g., plant axes: Dietrich et al. 2001;
Kudryavtsev et al. 2001; Nestler et al. 2003) or microscopic (e.g., metazoan
embryos: Chen et al. 2007; acritarchs and cyanobacteria: Arouri et al. 2000;
Kudryavtsev et al. 2001; Schopf et al. 2002, 2005, 2007; Kaufman and Xiao 2003;
Schopf 2004a, b; Schopf and Kudryavtsev 2005); and whether such fossils have
been preserved by compression (Roberts et al. 1995; Arouri et al. 2000; Kaufman
and Xiao 2003; Marshall et al. 2005) or by cellular mineralization (Kudryavtsev
et al. 2001; Schopf et al. 2002, 2005, 2006a, 2007; Nestler et al. 2003; Schopf
2004a, b; Schopf and Kudryavtsev 2005; Chen et al. 2007).
Two-dimensional Raman imagery, an advanced application of Raman spectros-
copy recently introduced to paleobiologic studies (Kudryavtsev et al. 2001; Schopf
et al. 2002, 2005, 2007; Schopf 2004a, b; Schopf and Kudryavtsev 2005; Chen
et al. 2007), has proven especially useful for analyses of permineralized kerogenous
fossils and associated carbonaceous matter present in petrographic thin sections. In
this technique, documented by Schopf et al. (2005), a large number of point spectra
of the type measured in standard Raman spectroscopy are acquired over a defined
area of a fossil specimen to provide a molecular-structural map in two dimensions
and at micron-scale resolution. Such maps show the distribution of the carbona-
ceous and mineralic matter comprising such fossils in which varying intensities of
the detected Raman signal correspond to the relative concentrations of the molecular
structures present, maps that permit direct spatial correlation of the carbonaceous
material with optically discernable morphology (Kudryavtsev et al. 2001; Schopf
et al. 2002, 2005, 2007).
Three-dimensional Raman imagery of permineralized fossils (Schopf and
Kudryavtsev 2005; Schopf et al. 2007) and micron-scale mineral assemblages
(McKeegan et al. 2007), even more recent extensions of Raman imagery, can
be achieved by the computerized “stacking” and VolView-processing of two-
dimensional images acquired at sequentially increasing depths throughout a thin
section-embedded specimen. The 3-D image thus obtained maps the chemistry
– the molecular-structural characteristics – of the specimen analyzed. Such
images can be compared readily with CLSM images or with photomicrographs
obtained by standard optical techniques. But unlike optical photomicrographs,
the digitized images produced can be rotated or otherwise manipulated in three
dimensions to reveal detailed features of morphology, including those of the

interiors of such specimens that are not discernable by standard optical micros-
copy. Moreover, because the Raman data used to prepare such images record the
distribution not only of carbonaceous matter but also of associated minerals, this
technique can be used to document the three-dimensional spatial relations
between cellularly mineralized carbonaceous fossils and their encompassing rock
matrices.
3 Applications
Our goal here is to document the paleobiologic application of CSLM and Raman
spectroscopy to diverse cellularly mineralized organisms, with particular emphasis
on deciphering their taphonomy. The relevant limitations of the two techniques are
discussed elsewhere (Schopf and Kudryavtsev 2005; Schopf et al. 2005, 2006a;
Tripathi 2007). Below, we discuss results obtained from studies of a fossil metazoan
and fossil plants, fungi, acritarchs and microbes, including examples of fossils that
are among the oldest known in the geological record.
4 Mineralized Soft Tissues of Metazoans
Because carbonaceous animal fossils are typically preserved by compression

rather than cellular mineralization, intact preservation of the soft tissues of fossil
animals, such as that reported for the musculature of mineralized Devonian sharks
(Dean 1902) and Jurassic horseshoe crabs (Briggs et al. 2005), is notably rare.
Nevertheless, exquisitely well-preserved metazoan embryos have recently been
described from latest Precambrian (Xiao et al. 1998; Xiao and Knoll 2000; Chen
et al. 2000, 2006) and Early Cambrian (Bengtson and Zhao 1997; Chen 2004;
Chen et al. 2004, 2007; Steiner et al. 2004a, b) phosphorites and phosphatic lime-
stones of China, including specimens preserved in such detail that they exhibit
convincing evidence of the early stages of cellular cleavage. Late-stage embryos
from these deposits have been relatively little studied, but the one such example
discussed below provides important insight into the taphonomy of such
preservation.
4.1 Apatite-Mineralized Ctenophore Embryo
Shown in Fig. 1 are optical, CLSM, and Raman images of a thin section-embedded
ctenophore embryo from the Lower Cambrian (~540-Ma-old) Kuanchuanpu
Formation of Ningqiang County, Shaanxi Province, China. Described by Chen
et al. (2007), this is the oldest comb jelly and the only embryonic ctenophore
Fig. 1 Optical image (a), CLSM images (b, c, g), Raman spectra (d), and Raman images (e, f,
h–j) of a thin section-embedded apatite-mineralized ctenophore embryo from the Lower Cambrian
Kuanchuanpu Formation of Shaanxi Province, China (Chen et al. 2007). (a) Optical image of the
complete specimen; ac = aboral canal (denoted also in b, c, e, f). (b) Rotated (VolView-processed)
CLSM image of the embryo showing the comb rows, numbered one through eight. (c) CLSM
image of the aboral region showing the numbered comb rows. (d) Overlapping Raman spectra
showing the major bands of the apatite (~965 cm−1), calcite (~1,087 cm−1), and kerogen (~1,350 cm−1,
~1,600 cm−1, ~2,800 cm−1) that comprise the fossil (baseline subtracted). (e, f) Raman images of
the aboral canal and surroundings showing the distribution of kerogen (e, blue; acquired in a
spectral window centered at ~1,600 cm−1) and calcite (f, green; acquired at ~1,087 cm−1). (g) CLSM
image of the distal portion of the embryo in which the red rectangle denotes the region in h–j.
(h–j) Raman images acquired in spectral windows centered at the major Raman bands of kerogen
(h), apatite (i), and calcite (j)
known from the geological record. The ctenophoran affinities of this egg-enclosed
embryo in late development, prior to hatching, are well established by its superb
anatomical preservation that includes such features as the egg membrane, the apical
(aboral) organ, meridional canals, the aboral canal (Fig. 1a–c, e, f) and, perhaps
most notably, the eight sets of ctene-composed comb rows that are diagnostic of
comb jellies (Fig. 1b, c). Such characteristics are especially evident in the CLSM
images that, as is shown in Fig. 1b,c, can be rotated to reveal the anatomy of the
embryo in three dimensions. Moreover, because such images are derived from the
laser-excited fluorescence emitted by the kerogenous components of the specimen,
they provide a firm indication of its carbonaceous composition.
Figure 1d shows the Raman spectra of the apatite, calcite, and kerogen of which
this embryo is composed. Two-dimensional Raman images (Fig. 1e,f,h–j) show
that the soft tissues of the specimen are composed of carbonaceous kerogen
(Fig. 1e,h) infused by mineralizing apatite (Fig. 1i), and that the interstices
between such structures (Fig. 1f, j), as well as such originally fluid-filled cavities
as meridional canals (Chen et al. 2007), have been secondarily infilled by
calcite.
Backed by optical microscopy (Fig. 1a), studies of this specimen by the
combined use of CLSM and Raman imagery (1) establish its ctenophoran affinities,
(2) demonstrate its anatomy and molecular-structural composition, and (3) elucidate
the sequence of mineral emplacement that resulted in its preservation. Use of these
techniques, together, provides biological and taphonomic data unavailable by any
other means. Such data, combined with knowledge of the biology of modern comb
jellies, of the anatomy of their embryos, and of the morphology and paleoecology
of adult members of the group preserved by compression in other Cambrian units
have provided important new insights into the early evolutionary history of the
Ctenophora (Chen et al. 2007).
5 Permineralized Plants
Unlike the cells of animals, those of plants – and of algae (including phytoplank-
tonic acritarchs), fungi, and microbes – are enclosed by robust organic cell
walls. In living organisms the chemistry of such walls varies substantially, for
plants and algae being composed primarily of cellulose with the tracheary xylem
of many plants having been infused secondarily by lignin; the walls of fungi
being composed largely of nitrogen-containing “fungal chitin”; and those of
bacterial microbes, such as cyanobacteria, being composed chiefly of mucopep-
tides such as peptidoglycans. During the diagenesis and resulting geochemical
maturation of such biomolecules, all are driven toward the same end-product,
kerogen, carbonaceous matter composed mainly of stacked, interlinked,
polycyclic aromatic hydrocarbons (Schopf et al. 2005; Vandenbroucke and
Largeau 2007), a precursor of metamorphically produced graphite. Because of
its composition, such kerogen is amenable to investigation by CLSM and
Raman, in cellularly mineralized fossils providing the basis for three-dimen-
sional micron-scale imaging. To illustrate the paleobiologic usefulness of these
techniques in studies of such fossils, the following section of this chapter deals
with their application to quartz- and calcite-permineralized Phanerozoic plants.
Subsequent sections demonstrate their use in the study of Precambrian fossil
microorganisms.
5.1 Quartz-Permineralized Plant Axes
In Fig. 2 are shown optical (Fig. 2a, b, d, f) and CLSM images (Fig. 2c, e, g) of a

transverse section of a quartz-permineralized rhizome (underground stem) of an
Eocene (~45-Ma-old) fossil fern preserved in chert from the Clarno Formation of
Oregon, USA. The CLSM image of the preserved aerenchyma (Fig. 2c), the oxy-
gen-supplying tissue of such underground stems, provides appreciably more infor-
mation than that of a standard optical image (Fig. 2b). This superiority is exhibited
also by CLSM images of the thick-walled cortical cells of this specimen, whether
imaged in a thin section (compare Fig. 2e, a CLSM image, with Fig. 2d, an optical
photomicrograph) or in a cellulose acetate peel (compare Fig. 2g with Fig. 2f). In
the CLSM image of the cortical cells in thin section (Fig. 2e), intracellular middle
lamellae – initially composed of calcium pectate rather than cellulose, the principal
component of the adjacent cell walls – and the spaces resulting from the preferen-
tial degradation of these lamellae, are well displayed. The CLSM image of the same
cells of this specimen in a cellulose acetate peel provides additional information,
showing imprints of the permineralizing cryptocrystalline grains of quartz (Fig. 2g).
Such information, relevant both to the preferential degradation of intercellular
organic cement and the spatial distribution of permineralizing quartz crystals, are
crucial to an understanding of the taphonomy of such specimens.
Figure 3 shows a chert-permineralized Clarno rhizome imaged in a peel of a longi-
tudinal section that similarly illustrates the three-dimensional detail provided by CLSM
imagery (Fig. 3c) in comparison with that of standard optical microscopy (Fig. 3b).
Fig. 2 Optical (a, b, d, f) and CLSM images (c, e, g) of a transverse section of a quartz-permineral-
ized rhizome of a fossil fern (Dennstaedtiopsis aerenchymata) in carbonaceous chert from the Eocene
Clarno Formation of Oregon, USA (Arnold and Daugherty 1964), shown in a petrographic thin sec-
tion (b–e) and a cellulose acetate peel (a, f, g), the area shown in (g) being denoted by the blue rect-
angles in (d–f). (a) Optical image of the rhizome denoting the areas illustrated in (b–g). (b, c) Optical
(b) and CLSM (c) images of aerenchymatous strands and associated interstrand spaces. (d–g) Optical
(d, f) and CLSM images (e, g) of cortical cells in a thin section (d, e) and a peel (f, g); intercellular
middle lamellae (ml) are evident in the CLSM image of the thin section-embedded cells (e) as are
imprints of permineralizing quartz grains (qz) in the CLSM image of the cells in a peel (g)
Fig. 3 Optical (a, b) and CLSM images (c) of a longitudinal section of a quartz-permineralized
rhizome of Dennstaedtiopsis aerenchymata (cf. Fig. 2) in a cellulose acetate peel. (a) Optical
image of the rhizome in which the red circle denotes the area illustrated in (b, c). (b, c) Optical
(b) and CLSM (c) images of tracheids illustrating their prominent annular thickenings
In Fig. 4 are shown optical and CLSM images of a quartz-permineral-ized axis of

Aglaophyton, a prototypical early-evolved land plant, from the Lower Devonian
Rhynie Chert of Aberdeenshire, Scotland. Unlike the other permineralized plants
illustrated here, this specimen was studied in a rock slice several millimeters thick.
Despite the fact that the specimen could therefore not be studied by transmitted light
optical microscopy, CLSM is shown here to be capable of “seeing into” this optically
opaque specimen, analyzing its uppermost surface and underlying cellular structure,
by detection of backscattered kerogen-emitted fluorescence that provides a high qual-
ity image of the xylem cells that compose its haplostelic core (Fig. 4b). Moreover, as
is shown in Fig. 4c, CLSM studies of cellulose acetate peels lifted from the surface
of this fossil provide excellent images of the sporangia of the chitrid fungi that infest
the cortical tissue of this specimen, evidencing the use of this technique to investigate
the biological degradation of such tissues, even in optically opaque rock slices.
5.2 Calcite-Permineralized Plant Axes
The most anatomically informative diverse assemblage of plant fossils known from
the Paleozoic geological record is that preserved by calcite-permineralization in
Fig. 4 Optical (a) and CLSM images (b, c) of a transverse section of a quartz-permineralized axis
of a rhyniophyte (Aglaophyton) from the Devonian Rhynie Chert (Kidston and Lang 1917),
exposed at the surface of a ~3-mm-thick rock slice (a, b) and shown in a peel (c). (a) Optical
image of the axis denoting the areas shown in (b, c). (b) CLSM image of xylem elements of the
central protostele. (c) CLSM image of fungal (chitrid) sporangia, containing spheroidal spores,
permineralized in the cortical tissue of the specimen
Carboniferous coal balls. Though such fossils are not uncommonly excellently
preserved, the processes involved in their permineralization, events documented to
have occurred prior to lithification of the coalified peat beds in which they occur,
are incompletely defined (Schopf 1975; see also Scott et al. 1996). Shown here in
Fig. 5 are optical and CLSM images of one such fossil, the stem of an herbaceous
sphenophyte related to modern Equisetum (the “horsetail” or “scouring-brush”
plant). Importantly, not only do the CLSM images provide crisp images of the cell
walls of the secondary xylem of this specimen, both in a thin section (Fig. 5b) and
in a peel (Fig. 5c), but they also show the morphology of the sparry calcite crystals
in which the cells of this axis have been permineralized. CLSM studies of coal ball-
preserved plant fossils (cf. Schopf et al. 2006b; Tripathi 2007) provide a promising
new approach to investigations of the taphonomy of calcite-permineralization.
6 Permineralized Organic-Walled Microorganisms
Because of the micron-scale spatial resolution provided both by CLSM and by two-
and three-dimensional Raman imagery, these techniques are especially useful for
investigation of permineralized microscopic organisms such as those that comprise
the bulk of the 3,000 million years of Precambrian biologic history. Indeed, before
the recent introduction of these techniques to the study of such ancient minute
fossils (Schopf and Kudryavtsev 2005; Schopf et al. 2005, 2006a), no methods had
Fig. 5 Optical (a) and CLSM images (b, c) of a transverse section of a calcite-permineralized
sphenophyte (Sphenophyllum) in a calcareous coal ball from the Carboniferous of Illinois, USA
(cf. Schopf 1941), shown in a petrographic thin section (a, b) and a cellulose acetate peel (c). (a)
Optical image of the axis in which the red rectangle denotes the area shown in (b, c). (b, c) CLSM
images of the secondary xylem showing the sparry calcite crystals (ca) that have infilled cell
lumina (enclosed by well defined cell walls, cw), particularly evident in the image of the petrified
cells in thin section (b)
been available by which to objectively depict and firmly establish on the basis of
direct analyses in situ either the three-dimensional cellular morphology or the
molecular-structural composition of such specimens. The following sections of this
chapter illustrate the applicability of these techniques to studies of Precambrian
sphaeromorph acritarchs and coccoidal and filamentous microbes; demonstrate
their use to elucidate the taphonomy of such microfossils, including the indirect
evidence they can provide of original biochemistry; and document the cellular
preservation and molecular-structural composition of certain of the oldest
(~3,465-Ma-old) fossils now known.
6.1 Quartz-Permineralized Acritarchs
In Fig. 6 are shown optical and CLSM images of a sphaeromorph acritarch quartz-
permineralized in a thin section of a Neoproterozoic (~650-Ma-old) cherty stroma-
tolite. The optical photomicrographs in Fig. 6a–c show, respectively, the uppermost
surface (“north pole”), equatorial plane, and lowermost “south pole” surface of the
specimen, three views at sequentially increasing focal depths of the type that might
typically be presented in a scientific publication. For comparison, Fig. 6d shows
a CLSM image of the entire acritarch, demonstrating the fine structural detail
Fig. 6 Optical (a–c) and CLSM images (d) of an ensheathed sphaeromorph acritarch in a
petrographic thin section of a conical cherty stromatolite from the ~650-Ma-old Chichkan
Formation of southern Kazakhstan (Schopf and Sovietov 1976); scale in (c) applies also to (a, b, d).
(a–c) Optical photomicrographs showing the uppermost surface (a), equatorial plane (b), and
lowermost surface (c) of the quartz-permineralized unicell for comparison with (d), a CLSM
image of the specimen
Fig. 7 Optical photomicrographs of quartz-permineralized microfossils in petrographic thin

sections of stromatolitic cherts of the ~650-Ma-old Chichkan Fm. of southern Kazakhstan (a–d;
Schopf and Sovietov 1976) and the ~750-Ma-old Bitter Springs Formation of central Australia
(e–j; Schopf 1968; Schopf and Blacic 1971). (a–d) Transmitted (a, c) and plane-polarized light
(b, d) images of large-celled sphaeromorph acritarchs. (e, f) Transmitted (e) and plane-polarized
light (f) images of a small-celled colonial cyanobacterium (Myxococcoides minor), truncated at
the lower left by a quartz-filled vein. (g, h) Transmitted (g) and plane-polarized light (h) images
of a ~25-mm-diameter unicell (Myxococcoides sp.). (i, j) Transmitted (i) and plane-polarized light
(j) images of a ~4-mm-diameter tubular cyanobacterial sheath (Eomycetopsis sp.)
p rovided by only a single such image, the information-rich content of which is even
better depicted in rotating three-dimensional video views of the specimen.
Although typically encompassed by an interlocking three-dimensional mosaic of
irregularly shaped grains of cryptocrystalline quartz, large-sized quartz-permineralized
acritarchs (>40 mm in diameter), such as the sphaeromorphs shown in Figs. 6 and
7a–d, are virtually always filled by swaths of fibrous quartz, known commonly as
“flame chalcedony” (Fig. 7b,d), the robust cell walls of such specimens defining the
boundary between the two forms of quartz. In such fossils, irregularitieson the inner
surfaces of the cell walls have served as points of nucleation for the formation of cell
lumina-infilling chalcedony. In contrast, quartz-permineralized small-celled

spheroidal fossils, whether colonial (Fig. 7e, f) or unicellular (Fig. 7g, h), as well as
small-diameter tubular microbial filaments (Fig. 7i, j), are almost always embedded
within and thoroughly infilled by cryptocrystalline quartz, the grain boundaries of
which transect but do not disrupt their kerogenous walls. Evidently, the particular
mineral phase involved in such quartz-permineralization is dependent primarily on
the dimensions and cell wall thickness of the fossil preserved, small thin-walled cells
being infused by and embedded within small-sized quartz grains, whereas larger
cells, outlined by their relatively thick cell walls, are preserved by an infilling of their
cell lumina by chalcedonic quartz. As is shown above, such permineralization by
large cell-filling crystals is exhibited also by the sparry calcite that infills the cell
lumina of permineralized higher plants (Fig. 5b, c), a similarity suggesting that
detailed taphonomic analyses by CLSM can be expected to yield useful insight into
the processes and products both of quartz- and calcite-permineralization.
In Fig. 8 is shown an additional quartz-permineralized Precambrian sphaeromorph,
included here to illustrate the method used to obtain three-dimensional chemical
(Raman) images of such acritarchs (Schopf and Kudryavtsev 2005). Figure 8a–e
shows representative optical photomicrographs from a sequential “through-focus”
series that extends from the uppermost to the lowermost surface of the specimen,
whereas Fig. 8f–j shows an equivalent series of two-dimensional Raman images.
Computer-aided stacking and processing of such Raman images yielded a micron-
resolution three-dimensional “chemical map” of the acritarch as viewed from
immediately above its uppermost surface (Fig. 8k) and below its lowermost surface
(Fig. 8l). The digitized data used to create such images – like many of the other
images shown here acquired in situ, measured on a specimen entirely embedded
within a petrographic thin section – can be rotated in three dimensions or otherwise
manipulated to provide additional useful information. Thus, for example, Fig. 8m
shows a view of this specimen from which its bottom hemisphere has been
removed, documenting the texture of the inner surface of the spheroid and the
prominent grooves in its upper surface, diagenetically produced tears in the speci-
men that are all but indiscernible in optical photomicrographs (Fig. 8a, b).
6.2 Quartz-Permineralized Filamentous Microbes
Illustrated here by their use for the study of Precambrian microscopic organisms,
CLSM and two- and three-dimensional Raman imagery are particularly applicable
to investigations of minute, sinuous, filamentous microbes.
6.2.1 Precambrian Cyanobacteria
In Fig. 9 are shown an optical image, an interpretive drawing, CLSM images, and a
three-dimensional Raman image of a quartz-permineralized kerogenous cellular
cyanobacterial filament imaged within a petrographic thin section of the ~750-Ma-old
Fig. 8 Optical (a–e) and Raman images (f–m) of a sphaeromorph acritarch in a petrographic thin
section of a conical cherty stromatolite from the ~650-Ma-old Chichkan Formation of southern
Kazakhstan (Schopf and Sovietov 1976); Raman images were acquired in a spectral window
centered at the ~1,600 cm–1 band of kerogen; scale in (c) applies also to (a, b, d–j); scale in (k)
applies also to (l, m). (a–e) Optical photomicrographs showing representative images from a
sequential “through-focus” series from the uppermost surface (left) to the lowermost surface
(right) of the quartz-permineralized specimen. (f–j) Two-dimensional Raman images acquired at
the same focal planes as the corresponding optical images in (a–e). (k–m) Three-dimensional
Raman images as viewed from (k) above the “north pole” of the specimen, showing the two
grooves in its uppermost surface; (l) beneath its “south pole,” showing the hole in its lowermost
surface; and (m) its interior, looking outward toward its “north pole,” showing the inner surface
of the spheroid and the open grooves in its uppermost surface
Bitter Springs Formation of central Australia. The optical image (Fig. 9a) is a
photomontage composed of ten photomicrographs of the medial plane of the fossil, a
presentation necessitated by the minute size of the specimen (and the resultant need
for its optical documentation by use of a high-magnification, but narrow focal-plane,
microscope objective) and its sinuosity, plunging from the upper surface of the thin
section (at the right end of the filament in Fig. 9a–c, and e) to ~20 mm beneath this
surface (at its left end, Fig. 9a–c). The interpretive drawing (Fig. 9b), a stippled
tracingof this photomontage that presents a somewhat more life-like rendering of the
specimen, shares the same deficiencies as the photomontage: both are based on sub-
jective interpretations of the specimen (resulting from the pasting together of photo-
micrographs acquired at differing focal depths). Neither can be regarded as depicting
accurately and objectively the exact morphology of the fossil. In contrast, the CLSM
images of this filament (Fig. 9c,d) faithfully show the sinuosityand cellularity of the
Fig. 9 Optical image (a), interpretive drawing (b), CLSM images (c, d), and a three-dimensional
Raman image (e) of a quartz-permineralized tapering cyanobacterial trichome (Cephalophytarion
laticellulosum) in a petrographic thin section of a flat-laminated cherty stromatolite from the
~750-Ma-old Bitter Springs Formation of central Australia (Schopf and Blacic 1971; holotype
specimen, Harvard University Paleobotanical Collections No. 58571). (a, b) Traditional render-
ings of a sinuous specimen such as this, in which the area shown at higher magnification in the
CLSM image in (d) is outlined by the red rectangle and the area imaged in three dimensions by
Raman spectroscopy (e) is denoted by the red circle, with (a) showing a photomontage composed
of 10 optical photomicrographs (demarcated by the white lines) and (b) illustrating the specimen
by an interpretive drawing. (c, d) CLSM images of the specimen, the right end of which transects
the thin section surface and the left end being situated at a depth of 20 mm within the section.
(e) Three-dimensional Raman image (acquired in a spectral window centered at the ~1,600 cm−1
band of kerogen) of the terminal several cells of the specimen, VolView-processed and rotated to
show the flat uppermost surface of the cells (where they transect the surface of the thin section),
that demonstrates the kerogenous composition of its lateral and transverse cell walls (grey) and
shows the quartz-filled cell lumina (white) that they enclose
specimen (even better depicted in rotating three-dimensional video views of the

specimen), whereas the three-dimensional Raman image (Fig. 9e) shows not only its
cellularity but provides data that establish that its kerogen-defined cell lumina are
infilled by quartz. Optical and CLSM images of an additional filamentous cyanobac-
terium from the same geologic unit are shown in Fig. 10.
As is evident from a comparison of the optical and CLSM images of both of
these examples (viz., Fig. 9a vs. c, and Fig. 10a vs. b), use of confocal laser
scanning microscopy can provide appreciably more information about the fine
Fig. 10 Optical (a) and CLSM images (b) of a quartz-permineralized helical cyanobacterial
trichome (Heliconema funiculum) in a petrographic thin section of a flat-laminated cherty stroma-
tolite from the ~750-Ma-old Bitter Springs Formation of central Australia (Schopf and Blacic
1971; holotype specimen, Harvard University Paleobotanical Collections No. 58595); scale in (a)
applies also to (b). (a) Photomontage composed of five optical photomicrographs (demarcated by
the white lines). (b) CLSM image, showing the fine structural detail that can be depicted by use
of CLSM
s tructural morphology and, thus, the biological affinities and taphonomy of such
specimens, than can standard optical microscopy alone.
Taphonomic Evidence of Original Biochemistry For fossil microbes, CLSM and
Raman imagery can also provide evidence, albeit indirect, of original biochemistry.
Figure 11 shows a many-celled portion of a broken (and at this break, partially
offset) originally ensheathed cyanobacterial trichome compared by Schopf and
Sovietov (1976) to the living oscillatoriacean Lyngbya majuscula. Shown also are
three-dimensional CLSM (Fig. 11b) and Raman images (Fig. 11c, d) of a seven-
celled segment of the specimen. The image in Fig. 11c shows the contours of the
two-dimensional Raman images (oriented parallel to the thin section surface) that
have been combined to produce the three-dimensional image of the portion of the
specimen shown in Fig. 11d. Each of these three-dimensional images has been
rotated to an orientation that permits examination of the central core of the specimen.
Notably, all show the core of the trichome to be “hollow”, a quartz-filled cavity that
in its central region is devoid of the carbonaceous matter that would evidence the
presence of transverse cell walls. The absence or only partial presence of the central
region of such cross walls – on the basis of optical microscopy, cross walls univer-
sally assumed to be preserved in such specimens – is typical of many such
Precambrian cyanobacterial trichomes (Schopf et al. 2006a). In Fig. 12, this same
specimen is shown in an optical photomicrograph (Fig. 12a) and in CLSM images
(Fig. 12b–d) that by illustrating the differing degrees of image quality obtainable
by use of various excitation laser wavelengths and filter arrays (cf. Tripathi 2007)
further show the fine structural detail that can be acquired by use of CLSM (e.g.,
Fig. 12d), data that for this fossil confirm the near-absence of transverse walls and
the “hollow” (i.e., quartz-filled) nature of its trichomic cavity.
Fig. 11 CLSM images (a, b) and Raman images (c, d) of a quartz-permineralized Lyngbya-like
cyanobacterial trichome composed of disc-shaped cells, in a petrographic thin section of a conical
cherty stromatolite from the ~650-Ma-old Chichkan Formation of southern Kazakhstan (Schopf
and Sovietov 1976); scale in (d) applies also to (c). (a, b) Rotated CLSM images of the specimen
in which the red rectangle in (a) denotes the portion of the trichome shown in the VolView-
processed CLSM image in (b). (c, d) Rotated, VolView-processed, three-dimensional Raman
images (acquired in a window centered at the ~1,600 cm–1 kerogen band) of the same part of the
specimen shown in (b), illustrating in (c) the spatial relations between the preserved cell walls and
the two-dimensional Raman slices used to prepare the three-dimensional image in (d), a more
accurate representation of the distribution of the kerogenous components of the specimen
Fig. 12 Optical photomicrograph (a) and CLSM images (b–d) of the thin section-embedded
quartz-permineralized specimen shown in Fig. 11 (but unlike those in Fig. 11, shown here in non-
rotated images); scale in (a) applies also to (b, c). These images illustrate the increased depth of
focus provided by CLSM in comparison with that of optical microscopy (a) and differences in the
quality of CLSM images acquired by use of excitation wavelengths of 488 nm (b, filtered detection
window = 520–560 nm), 543 nm (c, window = 560–600 nm), and 633 nm (d, window = >660 nm),
the last providing the sharpest image of the specimen
This example of the use of CLSM and Raman imagery provides insight into the
taphonomic history of such filamentous fossil microbes that reflects their original
biochemistry. Cell division in oscillatoriacean cyanobacteria occurs by invagination
of septations that grow centripetally from the periphery of the cells to ultimately
divide them into new daughter cells. At their inception termed partial septations,
these inward-growing transverse cell walls are thinner than and differ in biochemical
composition from the exterior (lateral) walls of such microbes. As discussed by

Drews (1973), the lateral cell walls of oscillatoriaceans are composed of four layers
surrounded on the outside in ensheathed taxa by a sheath or slime layer and enclos-
ing within them, toward the interior of such cells, the cytoplasmic membrane.
About half of the total thickness of such lateral walls is made up of the outermost
two layers, the other half by the inner pair of layers (Drews 1973). Notably, the
transverse walls that define the cellular segmentation of such oscillatoriaceans are
composed only of the two innermost layers (Pankratz and Bowen 1963; Lamont
1969; Halfen and Castenholz 1971; Drews 1973) and, thus, are typically only about
half as thick as the lateral walls that define the organismal form of such microbes.
Moreover, biosynthesis of a principal constituent of one of the two innermost layers,
peptidoglycan (known also as murein or mucopeptide and the rigidifying compo-
nent of oscillatoriacean lateral cell walls) ceases in transverse walls after their
initial stages of growth so that the partial septations from which they are derived
are peptidoglycan-rich only near the periphery of such cells (Frank et al. 1962;
Halfen and Castenholz 1971). Relatively thin and peptidoglycan-deficient, such
transverse walls are less robust and relatively more susceptible to diagenetic degra-
dation than the lateral, organismal-form defining cell walls of such microorganisms
(Van Baalen and Brown 1969). Thus, the absence or only partial preservation of
such transverse cell walls in the fossil oscilliatoriacean illustrated in Figs. 11 and
12 meshes well with expectations based on the biochemical and fine-structural
morphology of comparable microorganisms living today.
6.2.2 Raman Index of Preservation (RIP)
Among the paleobiologically useful attributes of Raman imagery is its ability to

characterize the molecular-structural composition of the materials analyzed,
being applicable, as shown above, both to minerals and to mineralized fossils.
Moreover, Raman spectra resulting from studies of the kerogenous materials that
comprise such fossils can themselves be analyzed to yield their Raman Index of
Preservation (Schopf et al. 2005), RIP values that provide a firm basis for the
assessment of their diagenetic alteration, their geochemical maturity (Schopf
et al. 2005).
In Fig. 13 are shown seven Raman spectra, obtained from organic-walled
Precambrian microfossils preserved at various stages of geochemical maturation
(Schopf et al. 2005). As is there illustrated, the two major Raman bands of kero-
gen change markedly as a function of increasing geochemical alteration: the
left-most “D” band becomes increasingly more peaked (and, correspondingly,
less broad and “bumpy”) as the right-most “G” band becomes increasingly nar-
row and ultimately bifurcated. Such data, obtainable from organic-walled fossils
permineralized in rocks subjected even to greenschist facies metamorphism
(Schopf et al. 2002, 2005), can provide definitive insight into the geochemical
maturity (degree of alteration) of fossilized organic matter that is unavailable by
any other means.
Fig. 13 Raman spectra of kerogenous microfossils permineralized in cherts of the ~750-Ma-old Bitter
Springs Fm., central Australia (cf. Figs. 8 and 9); the ~1,900-Ma-old Gunflint Fm., Ontario, Canada;
the ~1,050-Ma-old Allamoore Fm., Texas, USA; the ~3,465-Ma-old Apex chert, Western Australia (cf.
Fig. 14); and of the ~760-Ma-old Skillogalee Dolomite, ~720-Ma-old Auburn Dolomite, and
~775-Ma-old River Wakefield Fm. of South Australia (Schopf et al. 2005). The spectra are ordered by
their RIP values (Schopf et al. 2005) from less (top) to more (bottom) geochemically mature
6.2.3 Archean Bacteria
In recent years, questions have been raised about the biogenicity of certain of the
oldest putative records of life now known (Brasier et al. 2002, 2005), reported from
especially ancient, Archean (>2,500-Ma-old), geological units. Indeed, it has even
been suggested that “true consensus for life’s existence” dates only from “the
bacterial fossils of 1.9-billion-year-old Gunflint Formation of Ontario” (Moorbath
2005). According to this view, all supposed evidence of earlier life, “the many
claims of life in the first 2.0–2.5 billion years of Earth’s history,” is in doubt
(Moorbath 2005).
Notwithstanding such skepticism, the evidence for Archean life seems compelling
(Schopf 2004a, b, 2006a, b; Altermann 2005; Altermann et al. 2006; Schopf et al.
2007). Though markedly less abundant and almost always less well-preserved than
biologic remnants of the younger, Proterozoic, Precambrian – a result, primarily, of the
paucity of Archean rocks that have survived to the present and their pervasive meta-
morphic alteration (Schopf 2006a; Schopf et al. 2007) – diverse microbially pro-
duced stromatolites are known from 48 Archean deposits; 14 such units contain
some 40 morphotypes of described microfossils; and hundreds of carbon isotopic
measurements consistent with the presence of biologic activity have been reported
from Archean rock units dating to 3,500 Ma ago (Strauss and Moore 1992; Schopf
2006a, b). Even more significantly, units 3,200 to 3,500 Ma in age contain abundant
evidence of life: 10 such units are known to be stromatolitic; 11 contain organic-
walled microfossils; and carbon isotopic data consistent with biologic CO2-fixation
are available for nine such deposits (Schopf 2006a, b). In addition, the oldest
metasediments now known, >3,830-Ma-old units of southwestern Greenland, have
recently been shown by 3-D Raman imagery to contain apatite-enclosed graphitic
carbonaceous matter determined by secondary ion mass spectrometry to have an
isotopic value similarly consistent with biological CO2-fixation – a strong hint of
microbial activity arguably suggesting that “the record of life on Earth is as old as
the oldest sedimentary rocks now known” (McKeegan et al. 2007).
Studies of the taphonomy of ancient fossils by CLSM and Raman imagery have
played a pivotal role in resolving the uncertainty about life’s early existence. Shown
in Fig. 14a–c are specimens from the most contentious of the known Archean
microfossil assemblages (Brasier et al. 2002, 2005), minute filamentous structures
reported from the ~3,465-Ma-old Apex chert of northwestern Australia that have
been interpreted to be composed of carbonaceous, kerogenous, cells (Schopf 1993).
As recently documented (Schopf 2004a, 2006a; Schopf et al. 2007), these fossil-
like filaments meet ten separate tests of biogenicity: all exhibit (1) biological
morphology, including (2) structurally distinct carbonaceous cell walls that define
(3) cell lumina. All occur in (4) a multi-member population that includes (5) numer-
ous taxa, members of which exhibit (6) variable preservation. All are (7) preserved
three-dimensionally by permineralization in fine-grained quartz, shown above
(Figs. 9–12) to be a common mode of preservation of such fossils. And all have
(8) biological size ranges, as measured for several hundred specimens, and exhibit
a (9) Raman signal of biogenic kerogen, carbonaceous matter that has an (10) isoto-
pic composition typical of biologically produced organic matter.
Perhaps primary among these criteria for establishment of the biogenicity of
these fossil-like filaments are their organic (kerogenous) and cellular composition.
That they are composed of carbonaceous organic matter that is indistinguishable
from the kerogen of bona fide fossils, an interpretation supported by numerous lines
of evidence (e.g., De Gregorio and Sharp 2003, 2006; De Gregorio et al. 2005),
Fig. 14 Optical (a–c, j), Raman (d–i), and CLSM images (k–n) of permineralized kerogenous
filaments (Primaevifilum amoenum) in petrographic thin sections of the ~3,465-Ma-old Apex
chert of Western Australia; (a) Natural History Museum, London V.63164[5]; (b) V.63166[1];
(c–n) V.63164[6] (Schopf 1993); Raman images were acquired in a spectral window centered at
the ~1,600 cm−1 band of kerogen; scale in (c) applies also to (j–n); scale in (d) applies also to
(e–i); (a–c) show photomontages. (a–c) Photomicrographs of three specimens of P. amoenum, that
in (c) ranging from 3 mm (left end) to 9 mm (right end) below the section surface with the red
is well shown by the Raman spectra presented in Fig. 13: the Apex filaments, hav-
ing an RIP value of 5.0, exhibit an intermediate grade of organic preservation, being
neither as well preserved as the Bitter Springs (Figs. 7, 9, and 10) and other rela-
tively little-altered Precambrian microbes, but exhibiting an appreciably greater
fidelity of preservation than fossils preserved in more metamorphosed Precambrian
geological units. And the cellularity of the Apex filaments is firmly established by
three-dimensional Raman imagery (cf. Schopf et al. 2007). Shown in Fig. 14d is a
three-dimensional Raman image of a portion of the Apex filament illustrated in
Fig. 14c. As is shown by the two-dimensional Raman images in Fig. 14e–i, this
specimen (like numerous others from the deposit; Schopf et al. 2007) is composed
of box-like cells defined by carbonaceous (kerogenous) walls. Such walls are not a
result of petroleum-like carbonaceous fluids having enveloped quartz grains during
recrystallization (Brasier et al. 2005). As is shown by the CLSM images in
Fig. 14k–n, permeation of organic fluids into the Apex chert results in formation of
a three-dimensional chicken wire-like mosaic, not in the formation of discrete,
cylindrical, microbe-like sinuous filaments composed of regularly aligned uniseri-
ate strands of cell-like segments.
Backed by additional factors and subfactors that seem similarly indicative of
biogenicity – including a firm fit with all other reported evidence of comparably
ancient life (Schopf 2004a, b, 2006a, b; Schopf et al. 2007) – demonstration of
organic-walled cellularity in putative filamentous microfossils such as these is a
strong indicator of their biological origin. Such organic-walled cellular structure is
a defining characteristic of bona fide microbial filaments, both extant and fossil.
Indeed, particulate carbonaceous matter like that comprising the Apex filaments is
not known to be produced by any non-biologic means, and pseudofossils that
exhibit such carbonaceous uniseriate cell-like structure are unknown from the
entire geological record, reported not even from petroleum- or anthraxolite-rich
Fig. 14 (continued) rectangle outlining the part shown in (d–i). (d) Three-dimensional Raman
image showing the cylindrical structure of the kerogenous filament (gray) infilled by permineral-
izing quartz (white). (e–i) Two-dimensional Raman images of the part of the filament shown in
(d) acquired at sequential depths below the filament surface (e, at 0.75 mm; f, 1.5 mm; g, 2.25 mm;
h, 3.0 mm; i, 3.75 mm) demonstrating that it is composed of quartz-filled cell lumina (black
“voids” denoted by the arrows in e, evident also in f–i) defined by kerogenous cell walls (white).
(j) Photomicrograph of the upper surface of the thin section showing that the specimen (black
outline) is embedded in a chert matrix composed of irregularly shaped quartz grains (arrows).
(k–n) CLSM images of the filament at sequential depths below the thin section surface (k, at 4 mm;
l, 5 mm; m, 6 mm; n, 7 mm). Heating of the specimen-containing ~150-mm-thick section during its
remounting at the Natural History Museum, London (P. Hayes, pers. comm. to J.W.S. 2005)
separated quartz grains at its upper surface that permitted microscopy immersion oil to permeate
at grain boundaries to a depth of ~7 mm within the section. This separation enabled imaging of the
outlines of quartz grains at the section surface without the use of polarized optics (j) and the fluo-
rescence emission of the permeating oil permitted CLSM imaging of grain margins within the
upper few microns of the section. Arrows in (k, l) point to oil-filled grain boundaries that transect
the uppermost (4- to 5-mm-deep) part of the filament; ellipses in (l–n) denote deeper parts of the
filament (cf. g–i) to which fluorescent oil permeated only partially
deposits where they might be expected to be abundant. As this example shows,

CLSM and Raman imagery, together, can provide important insight into both the
taphonomy and the biogenicity of ancient microscopic fossils.
7 Summary
Cellularly mineralized fossils are among the biologically and taphonomically most
informative known from the geological record. Spanning all of biology, from metazoans
and vascular plants to algae, fungi and bacteria, such fossils can be preserved in
exquisite detail. Two techniques newly introduced to paleobiology and documented
here, three-dimensional confocal laser scanning microscopy (CLSM) and two-
and three-dimensional Raman imagery, provide a means to establish the three-
dimensional morphology as well as the molecular-structural composition and
geochemical maturity of the carbonaceous kerogen that comprises such fossils.
Illustrated here is the use of these techniques to elucidate the preserved anatomy
and cellular structure of examples of all of the major biologic groups (animals,
plants, fungi, algal protists, and microbes), preserved in the three principal cellu-
larly mineralizing rock types (phosphorite, chert, and carbonate). As is shown,
CLSM and Raman imagery, together, can provide new information about the mor-
phology, cellular anatomy, taphonomy, carbonaceous composition, and geochemi-
cal maturity of organic-walled mineralized fossils, and Raman imagery can be used
as well to document the mineralogy of the fossil-enclosing matrix and the spatial
relations between such fossils and their embedding minerals. Together, the two
techniques can provide definitive evidence of the sequence of taphonomic events
involved in such preservation (exemplified here by the study of a phosphate-miner-
alized ctenophore embryo) and the biological degradation of diverse organically
preserved specimens (shown by the fungal infestation of plant axes, the enzymatic
breakdown of the middle lamellae of vascular plant cell walls, and the preferential
decay of specific cell wall components in fossil cyanobacteria). Similarly, the data
presented that permit comparison of chert-permineralized Phanerozoic plants and
Precambrian microbes, and of large-celled and small-celled organic-walled miner-
alized microfossils – coupled with the in situ measurements of the geochemical
maturity of their kerogenous constituents afforded by Raman spectroscopy – pro-
vide new means for assessment of the biases of such preservation over time. Taken
together, these non-intrusive and non-destructive techniques can provide important
new knowledge of ancient fossils and the history of life.
Acknowledgments We thank D.E.G. Briggs, J. Shen-Miller, and the editors of this volume for
helpful comments on the manuscript. The participation of A.B.K. in this work was supported by
CSEOL, the IGPP Center for Study of the Origin and Evolution of Life at UCLA, and by the
UCLA administration in support of UCLA’s membership in the NASA Astrobiology Institute.
Both A.D.C. (supported in part during these studies by a pre-doctoral NSF Fellowship) and A.B.T.
are recent recipients of Ph.D. degrees from UCLA, supported during their graduate studies by
CSEOL Fellowships and by the principal source of funding for this work, CSEOL and NASA
Exobiology Grant NAG5-12357 (to J.W.S).
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Chapter 14
Taphonomy in Temporally Unique Settings:
An Environmental Traverse in Search
of the Earliest Life on Earth
Martin D. Brasier, David Wacey, and Nicola McLoughlin
Contents
1 Introduction: A Preservational Dark Age?............................................................................ 488
2 Early Eden or Distant Planet?............................................................................................... 489
3 New Taphonomic Windows for Old..................................................................................... 490
4 Cellular Lagerstätten............................................................................................................. 491
5 The Challenge of Pseudofossils............................................................................................ 493
6 An Early Earth Taphonomic Traverse................................................................................... 494
6.1 Pillow Basalts.............................................................................................................. 495
6.2 Black Smokers............................................................................................................. 498
6.3 White Smokers............................................................................................................. 500
6.4 Seafloor Banded Cherts............................................................................................... 500
6.5 Stromatolites................................................................................................................ 505
6.6 Siliclastics.................................................................................................................... 509
7 Summary............................................................................................................................... 511
References................................................................................................................................... 512
Abstract There is an apparent preservational paradox in the early rock record.

Cellularly preserved and ensheathed microfossils which are remarkably preserved
from the late Archaean (c.2700 Ma) onward, have rarely been found in the earlier
rock record and when they are their biogenicity is debated. Likewise, the abundance
and morphological complexity of stromatolites appears much reduced in the early
Archaean and even these lack compelling associations with organic remains of micro-
bial mats. This ‘preservational dark age’ may have arisen because microfossils and
M.D. Brasier (*)
Department of Earth Sciences, Oxford University, Parks Road, Oxford OX1 3PR, UK
D. Wacey
Centre for Microscopy, Characterisation and Analysis + School of Earth and Environment,
The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Perth, Australia
N. McLoughlin
Department of Earth Sciences and centre of Excellence in Geobiology, University of Bergen,
5020 Bergen, Norway
488 M.D. Brasier et al.
microbial mats were absent, because conditions for their preservation were rare or, as
we suggest here, because scientists have largely been looking in the wrong places.
To illustrate the potential of looking far beyond ‘chertified Bahamian lagoons’,
we make a traverse across the key potential habitats for early life on Earth and
identify some exciting and new taphonomic windows, in the search for Earth’s
earliest microfossils, trace fossils and stromatolites. Such habitats include hitherto
little explored pillow lavas, hydrothermal vents and beach sandstones. These new
windows are already starting to provide surprising insights into the nature of the
earliest vital processes.
1 Introduction: A Preservational Dark Age?
The fossil record of the Archaean, the interval of time before 2500 Ma BP, is a
preservational paradox. Promising rocks such as isotopically light carbonaceous
cherts are widespread but signals of life are enigmatic and hard to decipher, creating
a so-called ‘preservational dark age’ within the fossil record. This is surprising
given the high fidelity of the younger, Proterozoic (c. 2500–542 Ma) microfossil
record in cherts and carbonates (e.g., Knoll 2003; Brasier and Armstrong 2005) and
the ostensible ease with which microbes can be silicified in modern settings (e.g.,
Konhauser et al. 2003). A conventional explanation for this paradox has been the
relatively low abundance of ancient rocks, most of which have been consumed or
greatly modified by erosion, subduction or metamorphism over the last 3 billion
years (e.g., Schopf 1999). But against this, one may argue that remarkable cellular
preservation is not an unreasonable expectation of the early Archaean rock record.
This is because many of the conditions necessary for preservation would seem to
have been prevalent at this time. For example, low levels of atmospheric oxygen,
abundant carbonaceous matter and high levels of silica supersaturation all seem to
have been the norm in the early Archaean. Together, these should have helped to
deliver a plethora of respectable morphological remains and chemical signatures
for life in rocks of this age. So what, exactly, has been the problem?
It has been argued (Brasier et al. 2005, 2006) that most reports of early
microfossils (e.g., Schopf 1999) and stromatolites (e.g., Hoffman et al. 1999;
Allwood et al. 2006) are not readily distinguishable from self-organizing struc-
tures (SOS) and have yet to pass the null hypothesis of Brasier et al. (2002,
2004). This hypothesis states that microfossils and stromatolite-like structures
of early Archaean age should not be accepted as being of biological origin until
appropriate hypotheses for their abiogenic origin have been tested and falsified
(see also Grotzinger and Rothman 1996; Brasier et al. 2005 and references therein).
Although there have been many reports (e.g., reviews in Schopf 2006; Brasier
et al. 2006), it emerges that rigorously tested examples of cellular preservation
from the early Archaean Dark Age are scarce and still widely debated. In addition,
abiotic scenarios capable of replicating many of the candidate geochemical
signatures for life in these earliest rocks have not been entirely excluded
(e.g., Van Zuilen et al. 2002). Thus, there is as yet, no consensus as to the oldest
14 Taphonomy of the Earliest Life on Earth 489
verifiable evidence of life on Earth and many of the existing claims need further
analysis and testing.
One explanation for this poverty of the early cellular fossil record is that, until
recently, we may have been applying search images that are too restrictive. Armed
with misleading questions, it has become easy to overlook more favourable habitats
and taphonomic windows. The traditional focus on Archaean cherts and silicified
sediments has, for instance, meant that informative lithological windows such as
volcanic glasses, siliciclastics and pyritic deposits have been relatively neglected.
We argue that these taphonomic windows may yet help us to fill the many gaps in
our knowledge about the origins and history of life on Earth.
2 Early Eden or Distant Planet?
Our understanding of Early Archaean Earth environments greatly shapes the strate-
gies adopted for seeking the earliest evidence of life on Earth. A conventional model
for Archaean surface environments is one that can be termed the Early Eden
Hypothesis (Brasier et al. 2004). This hypothesis, which has dominated thinking for
several decades, takes familiar and habitable environments in which primitive
microbes abound today, such as Bahamian tropical lagoons or Shark Bay in Western
Australia, and then uses these to make predictions about the surface of the Early
Earth. This is, of course, a tried and tested method – the so-called Uniformitarian
Principle – advanced by Sir Charles Lyell (1830). This uniformitarian method can be
argued to work reasonably well when applied to the rock record from the Quaternary
back into the Proterozoic (2500–1600 Ma BP) and even as early as the late Archaean
(3000–2500 Ma BP). However, the Principle of Uniformity can be pushed beyond its
limits when extended back into the earliest Archaean. In its most extreme expression,
the Early Eden Hypothesis predicts the presence, on the early Earth, of continents,
subduction zones, carbonate platforms, an oxygenated atmosphere and oxygenic
photosynthesis. Examination of the earliest sedimentary rocks, however, coupled
with an ever-increasing understanding of the nature of the solar system, suggests that
Lyell’s much vaunted Principle of Uniformity may lead towards mistaken conclu-
sions (see Rose et al. 2006). It is useful to remember the warning of Sir Francis Bacon
here: “The subtlety of nature is greater many times over than the subtlety of the senses
and understanding; so that all those specious meditations, speculations, and glosses
in which men indulge are quite from the purpose, only there is no one by to observe
it” (Bacon 1620). In other words, we need to remain aware of the huge gaps in our
understanding at this time. To encourage this caution we recommend that all scientists
view the young Earth as though it were a distant planet.
Once we take this rather unwelcome monster on board, we can see that the
early Earth may have been stranger than we imagine and, perhaps, stranger than
we can imagine. Consider, for example, the following list of conditions is now
thought by many to pertain at the surface of the Earth in the early Archaean: solar
luminosity some 20% lower than now (e.g., Sagan and Mullen 1972); an atmo-
sphere of reducing gases that largely lacked oxygen (e.g., Kasting and Catling
2003; Lowe and Tice 2004); no ozone layer to protect life from ultraviolet light
(e.g., Konhauser et al. 2001); much higher rates of solar and cosmic rays (e.g.,
Delsemme 1998); high rates of meteoritic bombardment, with many over 10km in
diameter (e.g., Byerly et al. 2002; Moorbath 2005); a lack of large continental
landmasses (e.g., Lindsay and Brasier 2002); a hot young crust, with higher rates
of heat flux and hotter oceans (e.g., Knauth and Lowe 2003; Knoll 2003); the
predominance of oceanic crust over granitic crust (Lowe 1994b) and a lack of
extensive, modern style subduction zones and crustal recycling (McCall 2003; Van
Kranendonk et al. 2004).
Given these radically different boundary conditions acting upon the early Earth,
it appears that the planet’s endogenic energy was potentially a much greater source
for the early biosphere than was the solar energy of our star, the sun. A first conse-
quence is that the highly metaliferous crust of the early Earth, when combined with
enormous outflows of energy emanating from hydrothermal and volcanic systems,
is likely to have played a significant role in both the genesis and sustenance of the
earliest forms of life. This message is also delivered to us by the discovery of thriv-
ing life forms around black smokers and modern deep-sea vents (e.g. Jannasch and
Mottl 1985; Teske et al. 2002). In addition, theoretical and chemical studies have
certainly confirmed that a ‘hydrothermal cradle for life’ is indeed plausible (see
Nisbet and Fowler 1996). A second consequence of this view of the early Earth as
a distant planet is that oxygenic photosynthesis need not have been the foundation
for all other forms of life as it might seem to us today. We will return to many of
these concepts below.
3 New Taphonomic Windows for Old
For a generation, conventional wisdom has encouraged us to search for the earliest
cells within bedded siliceous sediments such as Banded Iron Formations (BIF) and
related lithologies (e.g., Schopf and Klein 1992). Such cherts do, indeed, have an
excellent track record, that ranges from the exquisitely preserved cells of microbes
and early land floras in the Lower Devonian Rhynie Chert of Scotland (Trewin and
Rice 2004) to the microbial assemblages of the 1900 Ma Gunflint Chert of Canada
(Barghoorn and Tyler 1965). In both those settings, silica supersaturation appears
to have been achieved as the consequence of high levels of dissolved silica coupled
to low levels of biological silica extraction (Maliva et al. 2005). Preservation of
cellular fossils has then been achieved by their immuration within glassy silica
derived from the surrounding environment, either during life or soon after death
(cf. Konhauser et al. 2003).
The poor cellular fossil record of the early to middle Archaean (3500–3000
Ma) therefore appears puzzling, given that silica supersaturation was common
within the water column (cf. Maliva et al. 2005). One possible explanation for this
(Brasier et al. 2005, 2006), is that the post-depositional history of these sedimentary
cherts is less simple than was at first believed (cf. Schopf 1992a, b, 1993).
This becomes clear when the lithogenesis of these cherts is mapped out on scales
that range from microns to kilometres (e.g. Brasier et al. 2002, 2005). Most impor-
tantly here, we find that the original sedimentary protolith which might be
expected to contain the indigenous cellular fossils has typically been modified,
rather drastically, in one or more of the following ways after burial: by remobiliza-
tion of the silica (especially of carbonaceous cherts); recrystallization of the cryp-
tocrystalline silica components; replacement of one silica phase by another;
dilation, displacement and intrusion of the protolith by many subsequent siliceous
phases, some of which may be quite young in age; metamorphic modification of
the silica, carbon and other phases; and finally, modification of silica and carbon
phases during the prolonged episodes of weathering and exposure in near surface
environments (see Brasier et al. 2005).
Unfortunately, such a convoluted diagenetic history now appears to have been
typical for nearly all banded sedimentary cherts of Archaean age. A pre-requisite
for finding remains of the earliest life in such rocks is, therefore, to attempt to map
out, date and distinguish each of the silica and other mineral phases within the host
rock. This requires time-consuming macro- and microscale mapping and stratig-
raphy and such a program of work is only just beginning (see for example: Brasier
et al. 2002, 2005; Tice and Lowe 2006). When adopted, this approach has revealed
that some putative microfossil like structures, once widely accepted (e.g. Schopf
1993) are not actually located within the primary protolith at all, but reside in later,
probably much younger, post-depositional phases.
There are therefore, a great many concerns regarding the veracity of the earliest
fossil record. Even so, there is a clear way forward – but only if we are prepared to
search for new taphonomic windows onto the early Earth. In subsequent sections,
we describe several rock types in which the post mortem histories are potentially
much less complicated and much better preserved than more conventional materi-
als, so that there is a reasonable hope of discovering, and of constraining, some of
the earliest signs of life on Earth. Three lithologies or taphonomic windows now
appear especially promising in this respect: the formerly glassy margins of early
Archaean pillow basalts (Furnes et al. 2004; Banerjee et al. 2006); the pyritic layers
within hydrothermal black smoker deposits (Rasmussen 2000); and the clasts and
matrix of the earliest beach sediments, comprising quartzose and pyritic sandstones
(Brasier et al. 2006; Wacey et al. 2006, 2008). It is from within these newly
explored habitats, as we explain below, that the nature of the earliest life now seems
likely to emerge.
4 Cellular Lagerstätten
The cell is the fundamental unit of life. The eminent naturalist Jean Baptiste Lamarck
(1809) discovered this major truth, some 150 years after Robert Hooke (1665) had
first described both living and fossil cells. Arguably, many of the most fundamental
steps in evolution have taken place at the cellular level (e.g. Cavalier-Smith et al. 2006).
We here focus on the most primitive type of cellular organisms known as the
prokaryotes, which predate unequivocal eukaryotic cells in the fossil record by
perhaps 2000 Ma or more. Prokaryotes are distinguished from the more advanced
eukaryotes (e.g. algae) by their lack of cellular organelles, including the nucleus.
There must have been many crucial pre-cellular steps leading towards the
origins of life and the first prokaryotes. These steps are likely to have included the
development of an information transfer mechanism (e.g. Cairns-Smith 1985) and
the appearance of a cell wall to hold and concentrate the prebiotic chemicals
(e.g. Hanczyc et al. 2003). Locating these prebiotic precursors in the rock record
is difficult and has not yet been attempted. This means that we are currently
required to focus entirely upon the emergence of cells themselves. The cell
performs three vital roles that help to sustain life. The cell wall provides a compart-
ment in which chemical reactions can be concentrated and controlled and biological
products can be stored. The intra-cellular chromosomes are made of DNA, which
acts as the information store for living cells and reproduction. As a whole, the cell
participates in metabolic processes – chemical reactions – that sustain the cell.
These three actions – compartmentalization, reproduction and metabolism – may
have evolved separately, but they are together responsible for the enormous success
of the cellular unit.
The preservation potential of each of these three features of the cell is rather
different. The products of metabolic processes arguably have the highest chance of
preservation. Although these processes may have little morphological expression,
they must inevitably modify the chemistry in and around the site of life. It is these
chemical signatures that can be preserved. Typical examples of this include metabolic
fractionation of isotopes such as 13C/12C (Schidlowski 2001) and/or 34S/32S (Shen
et al. 2001). To verify such biosignatures in the rock record, however, it is necessary
to discount the role of fractionations arising from purely abiogenic processes.
Plausible abiogenic processes may involve so-called Fischer-Tropsch type reac-
tions for the fractionation of carbon isotopes (Sherwood Lollar et al. 2002; Horita
and Berndt 1999; McCollum and Seewald 2006), or hydrothermal and photochemi-
cal fractionations of sulfur isotopes (cf. Grassineau et al. 2001). Other key indicators
of cellular metabolic processes may involve, for example, the highly localized storage
of biologically-significant, or even biolimiting elements. Enrichments in nitrogen
and phosphorus, as well as Fe, Co, V, Mo and other trace elements are now
being identified, within cellular bodies using high-resolution techniques such as
nanoSIMS (e.g. Robert et al. 2005; Oehler et al. 2006; Wacey et al. 2008).
The characteristic of prokaryote cells with the lowest chances of preservation is
that of reproduction and its associated reproductive apparatus. This may be because
RNA and DNA molecules are intrinsically unstable and are readily degraded over
geological timescales by heat and pressure. And while there are examples of
nuclear preservation in eukaryotes, the nucleus is absent from the prokaryotes
under discussion here.
The cell membrane in the early fossil record seems to have only a low to inter-
mediate chance of preservation. The cell membrane of bacteria is largely composed
of a mureine which, although tougher than the phospholipids of higher plants, is
weaker than cellulose and can be readily degraded, albeit less rapidly than the cell
contents themselves. A morphological record of cell contents and membranes
therefore appears unlikely, but a chemical expression of these cellular components
may nonetheless survive in the rock record. A promising avenue for research
involves the use of ‘molecular fossils’ – cell membrane lipids which can be pre-
served as soluble hydrocarbons in sediments. Where sediments are sufficiently well
preserved, these hydrocarbons may yet indicate the former presence of specific
groups of organisms, such as cyanobacteria (e.g., Summons et al. 1999).
For bacterial cells to preserve, there is therefore a requirement for rapid immuration
of the cell wall within the preservational medium. This medium can include glassy
silica gel (e.g., the 1900 Ma old Gunflint Chert), iron sulfide (e.g., the 3200 Ma
Sulfur Springs deposit), iron oxide (e.g., Galionella in modern hot-springs) and
calcium phosphate (e.g., Doushantuo Formation; see Brasier et al. this volume).
This immuration may be a consequence of the metabolic processes within the
cell itself. For example, encrustation with a mineral precipitate may act as a
UV shield for the organism (cf. Phoenix et al. 2006); or serve to increase the
proton motive force across the cell membrane, as with some iron oxidising bacteria
(e.g. Chan et al. 2004). Conversely, the precipitate may be deleterious to the
cell, restricting the diffusion of reactants and waste products to and from the cell
(e.g., Fortin 2004).
Aggregates of prokaryotic cells are often surrounded by communal extracellular
polymeric substances (EPS) that can have a relatively high chance of preservation.
A good example is the extracellular cytoplasmic sheaths or envelopes found around
the cells of cyanobacteria. The sheath is often preserved when the cells themselves
have collapsed and decomposed, for example in the Bitter Springs Formation
(Oehler et al. 2006). The glutinous substances which comprise EPS have adhesive
qualities, which trap and bind sediment particles onto biofilms and bioaggregates,
leading to the formation of wrinkle structures and stromatolites (e.g., Noffke et al.
2003). These organo-sedimentary structures have a much higher preservation
potential than the constructing organisms themselves.
5 The Challenge of Pseudofossils
The ‘burden of proof’ needed for the demonstration of the earliest cellular life is
very great indeed. Any proposal of this kind requires the demonstration of multiple,
in situ and mutually supporting lines of evidence, including: a well-constrained age
and geological context, a morphology unique to biology, and more than a single
line of geochemical evidence for metabolic cycling. In addition, there must be
falsification of all plausible abiogenic scenarios (see Brasier et al. 2002, 2004,
2005; Altermann and Kazmierczak 2003; Cady et al. 2003; Westall 2005; Rose et al.
2006). Evidence for age and context comes from geological mapping at scales from
kilometres to metres, supported by mapping of petrographic thin sections in order to
show that candidate structures are truly syngenetic and ancient (e.g., Cady et al. 2003;
Brasier et al. 2005 and references therein). Additional evidence for syngenicity can
come from laser Raman spectra (Pasteris and Wopenka 2002, 2003) or atomic force
microscopy (AFM; Altermann and Kazmierczak 2003), though equivocal results
are commonplace here. Evidence for a uniquely biogenic morphology can be
obtained, by in situ imaging and mapping, to distinguish the fields of biotic and
abiotic morphology and by comparing these with self-organising structures (see
below). Geochemical evidence for life requires high-resolution, sub-micron scale,
in situ three-dimensional mapping and analysis, using more than a single line of
contaminant-free evidence. Examples include the in situ study of C and S
isotopes and oxidation states (e.g., House et al. 2000; Ueno et al. 2001; Wacey et al.
2008), major and trace element mapping (Kamber and Webb 2001) and biomarker
analysis (Summons et al. 1999) from putative microfossils and host rocks.
A significant but widely ignored challenge in early life studies, however, con-
cerns our reliance upon inductive lines of reasoning. More specifically, there has
tended to be too much reliance upon evidence that is ‘consistent with’ microbes,
without falsifying or rejecting (sensu Popper 1959) other possible non-biological
scenarios that may likewise be consistent. In particular, the criterion of ‘morpho-
logical complexity’ is widely used as a keystone characteristic for testing the earliest
fossils (e.g., Buick et al. 1981; Buick 1990; Schopf 1999). However, an apprecia-
tion of both self-organizing structures (SOS) and complexity theory suggests that
complex structures do not require complex causes (d’Arcy Thompson 1917).
Complexity can arise naturally in physico-chemical systems through ‘chaotic’
behaviour and it is possible for a spectrum of ‘life-like’ signals to be generated
completely without biology (Brasier et al. 2006, Fig. 2). In other words, a range of
physio-chemical gradients can alone lead to macroscopic stromatoloids and, of
course, ripples, as well as to macrofossil and microfossil-like structures generated
by the growth of dendrites, ‘coffee-ring’ effects, polygonal crystal rims and
spherulites. In each case, these arise from a ‘symmetry-breaking cascade’, which is
a particularly conspicuous phenomenon during the growth and re-crystallization of
spherulites, leading to a natural assemblages of structures that can range from
spheroidal (broadly rotational symmetry), to dendritic (reflectional to slide
symmetry), to arcuate (no clear symmetry). The resulting SOS include spheroids,
filaments, septate filaments, wisps and fluffs (Brasier et al. 2006).
6 An Early Earth Taphonomic Traverse
Now we shall take a tour, like a time traveller, across a spectrum of those early
Archaean habitats in which life should be sought. We will start in deeper waters
around hydrothermal vents and in associated pillow lavas, then work towards the
earliest known shoreline and beach deposits (Fig. 1). In each section, we will assess
the quality of cellular fossil preservation that may be found in that setting, and show
how true fossils may be usefully distinguished from the bewildering plethora of
pseudofossils.
Volcanic edifices
Shallow-water Stratiform bedded chert

sandstones
& stromatolites
Volcanic fissures,
dykes & black
smokers
Caldera collapse
white smokers
Pillow basalts
Fig. 1 Types of environments in which to search for the earliest signs of life
Two Archaean geological domains provide the basis for this traverse: the rocks
of the Barberton Greenstone Belt, South Africa and those of the Pilbara Craton in
Western Australia (see Wacey et al. 2008 for an overview). Early Archaean
Barberton rocks are placed in the Swaziland Supergroup, which comprises the
Onverwacht, Fig Tree and Moodies Groups (Anhaeusser 1973; Lowe and Byerley
1999). The Onverwacht Group, being the oldest, is of most interest and spans the
time interval ~3500–3200 Ma (Armstrong et al. 1990). It is composed of komatiitic
and tholeiitic basaltic rocks interbedded with thin sedimentary units of silicified ash
and black chert, together with rare felsic volcaniclastic and intrusive rock.
The Pilbara craton of Western Australia comprises the three ancient granite
greenstone terranes of East Pilbara, West Pilbara and Kurrana. The East Pilbara
terrane houses the oldest rocks, as ancient as 3515 Ma. The 3515–3420 Ma
Warrawoona Group consists mostly of mafic volcanic rocks interspersed with thin
chert horizons and felsic volcanics. The Kelly Group lies unconformably above
these and it, in turn, is unconformably overlain by the ~3240 Ma Sulfur Springs
Group (for detailed stratigraphy see Van Kranendonk 2006). Together, these rock
units are home to some of the Earth’s oldest purported microfossils, trace fossils
and stromatolites.
6.1 Pillow Basalts
We begin our search for life within rock substrates themselves, especially from
volcanic pillow lavas on the ancient seafloor. We seek micron-sized cavities created
by the metabolic activities of microorganisms (e.g., Bromley 2004). These trace
fossils can preserve evidence for microbial behaviour, ecology and metabolism
in their selection and modification of rock substrates. Endolithic microborings
have long been known from silicified carbonate sediments younger than c.1600 Ma
(e.g., Zhang and Golubic 1987) but have more recently been reported from the
glassy margins of pillow basalts from modern to ancient volcanic rocks (Thorseth
et al. 1992; Fisk et al. 1998; Furnes et al. 2001; Staudigel et al. 2008).
A rock-dwelling ‘endolithic’ mode of life in the Archaean oceanic crust may
indeed have offered many attractions to early life including: proximity to geothermal
heat; a source of reductants, principally Fe and Mn which are abundant in basalts;
and access to both oxidants and carbon sources carried by circulating fluids. In the
early Archaean, especially, an endolithic mode of life would also have offered pro-
tection from the elevated UV radiation, meteoritic and cometary impacts. The latter
may have severely hampered the emergence of life in surface environments.
In addition, given that volcanic pillow lavas constitute an estimated 99% of green-
stone successions from the Barberton and Pilbara cratons, they represent perhaps the
largest potential habitat for early life. We first review of what is known about these
organisms and their trace fossil record in modern volcanic rocks (see also McLoughlin
et al. 2009). Then we will compare these with mineralized, tubular structures from
the Archaean to assess their biogenicity and possible taphonomic pathways.
Traces of euendolithic microbes have been documented over the last 10 years or
more from both in situ oceanic crust world-wide and from Phanerozoic ophiolites
(for a recent review see Furnes et al. 2007). They are preserved as microtubular and
granular structures at the interface of fresh and altered glass, along fractures in the
rims of pillow basalts and around the margins of volcanic glass fragments in hyalo-
clastites (Fig. 2). Importantly, they are both texturally and chemically distinct from
abiotic, palagonite alteration textures found in basalts (cf. Thorseth et al. 2001) so
that, in many samples, evidence for episodes of both biotic and abiotic alteration
can be found along fracture planes. Studies of recent material have found nucleic-
acids, bacterial and archeal RNA concentrated within these bioalteration textures
Fig. 2 Photomicrograph of endolithic microborings in ~10 Ma volcanic glass from ODP Hole
396B in the Mid-Atlantic. This branched ichnotaxon is termed Tubulohyalichnus stipes
(McLoughlin et al. 2009). Such evidence for modern microborings provides an exciting new
search image for signs of early life in early Archaean basaltic glass. Scale bar is 10 mm
(e.g., Torsvik et al. 1998; Santelli et al. 2008). These alteration zones may later be
mineralized by zeolites and clays that can typically preserve localized enrichments
in C, N, and P along the margins of the bioalteration textures themselves. These
concentrations are therefore interpreted to represent the chemical effects of decayed
cellular remains (e.g., Furnes and Muehlenbachs 2003).
Quantitative studies of the distribution and abundance of alteration textures with
depth in the modern oceanic crust have found that, in the upper ~350 m of the
crust, a ‘granular’ type of alteration is dominant. This component decreases steadily
down through the drill core to become subordinate at temperatures of about 115°C
(e.g., Staudigel et al. 2006). The microtubular alteration textures, meanwhile,
constitute only a small fraction of the total zone of alteration and show a clear
maximum at ~120–130m depth, corresponding to temperatures of about 70°C.
Abiotic alteration is seen to dominate at progressively greater depths. Comparisons
of seafloor and drill core samples of different age now suggest that bioalteration
commences early and may take place largely during the first ~6 Ma years after
crystallization of the basalt flows (Furnes et al. 2001).
In the Archaean, pillow basalts may well have been more widespread than
today and microtubular bioalteration textures were first reported from the formerly
glassy rims of pillow basalts and inter-pillow hyaloclastites from the Barberton
Greenstone Belt of South Africa (Furnes et al. 2004). These titanite (CaTiO3)
mineralized microtubes are now preserved in greenschist facies meta-volcanic
glasses that have been described from various units but some of the best preserved
examples have come from the upper Hooggenoeg Formation, dated to about
~3472–3456 Ma (Banerjee et al. 2006). These structures are typically 1–10 mm in
width and up to 200 mm in length (Fig. 3a). They extend away from “root zones”
of fine grained titanite associated with fractures within the basaltic glass that were
later annealed. These Archaean microtubes can have a segmented appearance
brought about by overgrowths of metamorphic chlorite. Morphologically compa-
rable microtubular structures have also been reported from inter-pillow hyaloclastite
layers within the 3350 Ma Eurobasalt Formation of Western Australia (Fig. 3b;
Furnes et al. 2006). The latter are also infilled with titanite that has now been dated
directly using U-Pb systematics. Such dates confirm that the microtubes formed
prior to a late Archaean (c. 2700 Ma) phase of metamorphism (Banerjee et al.
2007). In other words, these microtubes are likely to have formed during, or
shortly after, seafloor colonization of the basaltic lava flows and are therefore
unlikely to be younger contaminants.
Studies thus far have found that microtubular bioalteration textures tend to
predominate in the Archaean Era, and that granular textures are much less
common at this early date. This may, in part, be due to the enhancement and
masking of titanite grains. The early precipitation of titanite within the larger
microtubular textures is suggested to enhance microtube preservation by means
of limiting those morphological changes that would otherwise be caused by
re-crystallization of the host rock (see Fig 7 in McLoughlin et al. (2010a)). It is also
possible, of course, that the smaller granular textures have been obscured by
recrystallization of the glass.
Fig. 3 Photomicrographs of microtubular structures in the glassy margins and inter pillow breccias
of early Archaean basalts. These microtubes are infilled with titanite and emanate from early
fractures in a way that closely resembles modern microborings of biological origin. (a) From the
~3472–3456 Ma Hooggenoeg Formation, South Africa (Furnes et al. (2004)); (b) from the ~3350
Ma Eurobasalt Formation, Western Australia (Banerjee et al. (2007)). Scale bar is 50 mm for a,
and 250 mm for b
6.2 Black Smokers
As we continue along our Archaean environmental traverse, we come across hydro-

thermal vents with chimney shaped deposits of iron sulfide, much like those from
modern mid-oeanic ridges (cf. Corliss et al. 1979; Rona et al. 1986; Von Damm
et al. 1995) and back arc settings (Fouquet et al. 1991). While sulfide-rich black
cherts are well known from hydrothermal rocks some 3500–3400 Ma old in
Australia (e.g., Brasier et al. 2002, 2005; Orberger et al. 2006), it is not until much
later, in the c. 3240 Ma Sulfur Springs Group on the Pilbara craton of Western
Australia, that we can see such hydrothermal black smoker deposits convincingly
preserved in the rock record (Vearncombe et al. 1995). This Sulfur Springs deposit
is associated with a sequence of komatiites, basalts, dacites and rhyolites that
erupted on the seafloor (Van Kranendonk 2006). Thin sections through the well-
preserved drill core materials from the Sulfur Springs region show a wide range of
volcanigenic and hydrothermal fabrics, including laminated pyrite nodules, chalce-
donic silica, vein quartz and hydrocarbon globules (Vearncombe et al. 1995;
Rasmussen and Buick 2000).
Pyritic filaments from within this massive sulfide deposit were first reported by
Rasmussen (2000) and interpreted by him as the fossilized remains of thread like
thermophilic, chemotrophic prokaryotes. These filaments are 0.5–2.0 mm in width
and up to 300 mm long, can be straight, curved or sinuous and exhibit putative bio-
logical behaviour including preferred orientations, clustering and intertwining (Fig. 4).
They only occur in phases of paragenetically early chert plus (interestingly) coarse-
grained quartz that are clearly cross cut by later fractures. The null hypothesis that
needs to be rejected here is that the Sulfur Springs filaments are abiogenic mineral
growths that grew within the hydrothermal setting, and that were later replaced by
pyrite. Abiogenic fibrous mineral growths are a well known feature of hydrothermal
ore deposits, and many of these have been questionably interpreted as of microbial
origin (e.g., Little et al. 2004). We have since recollected and re-examined this
material. Preliminary analyses indicate that these filaments differ from abiogenic
ones in being unbranched, of constant diameter, and distinctively entangled. There
is as yet, however, no evidence for cellular organization nor for metabolic process-
ing. Even so, this is an intriguing discovery that is at least consistent with the
hypothesis of a thermophilic habitat for primitive life forms, in the vicinity of
sub-marine hydrothermal vents (cf. Nisbet 2000; Shock 1990; Stetter 1996).
Fig. 4 Photomicrograph of pyrite filaments from the ~3200 Ma Sulfur Springs Group, Western
Australia. The dark areas are stromatoloidal pyrite laminae. The pale areas are of macrocrystalline
quartz containing pyrite filaments. These filaments have a morphology and context consistent with
their formation by hyperthermophile archaea living in a black smoker setting in the Archaean.
Scale bar is 100 mm
6.3 White Smokers
Continuing our traverse along hydrothermal vent systems, we encounter chimneys

of barium sulfate (barite), silica and subordinate sulfide minerals known today as
white smoker deposits (Mills and Elderfield 1995). Comparable, barite-rich chert
veins and sediments are widely preserved in ~3500–3400 Ma old rocks from the
Pilbara Craton of West Australia. For example, the Dresser Formation (c.3490 Ma,
Nijman et al. 1998; Van Kranendonk 2006) and the Apex Basalt (c. 3465 Ma,
Brasier et al. 2002, 2005), chert-barite veins are both associated with sequences of
tholeiitic basalts and felsic tuffs that erupted on the seafloor, seemingly at times of
granitic intrusion and caldera collapse (Nijman et al. 1998; Van Kranendonk et al.
2001). These veins extend to a depth of up to a kilometre or more down growth faults
and elemental analyses provide evidence for the upward advection of Ba, Pb, Ni and
As along with silica through these structures (Brasier et al. 2002; Orberger et al.
2006). Taking these observations together, several authors have advanced a hydro-
thermal, white smoker type model for these units (e.g. Nijman et al. 1998; Brasier
et al. 2002, 2005; Orberger et al. 2006). Such white smokers with sulfates tend to
form at lower temperatures than sulfide-containing black smokers, and they thereby
increase the spectrum of temperature and venting conditions that were available to
primitive forms of life and proto-life. This conjecture is supported by the close asso-
ciation observed between white smoker deposits and black cherts with 13C depleted
carbonaceous matter (e.g. Ueno et al. 2004). Thin sections through these deposits
show a wide range of volcanigenic and hydrothermal fabrics, including hydro-
breccias, laminated chalcedonic and carbonaceous silica, carbonaceous clots and
clasts, as well as barite domes and veins, and vein quartz (Brasier et al. 2005;
Orberger et al. 2006). In each case, the cherts are found to record a complex history
in which the protolith (typically basalt, felsic tuff and black ‘shale’) has been exten-
sively injected by, and replaced by, fine grained hydrothermal silica. Such displa-
cive-replacive rocks have often been mistaken for the seafloor sediments themselves
(e.g., Schopf 1993; Orberger et al. 2006), making the interpretation of putative bio-
logical signals in ancient white smoker type environments a difficult task.
6.4 Seafloor Banded Cherts
An unusual lithology across large areas of the Archaean seafloor is that of black,
grey and white silica deposits. Such deposits make up less than about 1% of the
thickness of greenstone belts in the Barberton and Pilbara cratons. It seems that
these cherts were deposited as seafloor or stratiform deposits during the final parts
of volcanic cycles through intrusion induced doming and fracturing of seafloor
crust (Van Kranendonk et al. 2001).
Such banded cherts have, until recently, provided the primary search image for
the earliest cellular preservation in the Archaean. That is, perhaps, because the
silicification of microfloras is familiar to us from within much younger banded
cherts, such as the 1900 Ma Gunflint Chert (e.g., Barghoorn and Tyler 1965). In the
Precambrian world, without silica-secreting organisms such as sponges and radio-
larians, much of the ocean was supersaturated with respect to silica (Maliva et al.
2005). Hence, it may have been relatively easy to precipitate silica in a wide range
of settings in which precipitation could not happen today. Banded cherts of
Archaean to Proterozoic age have indeed been found to range from shallow water
and lagoonal environments, through photic zone depths with current rippled sands
(e.g., the Buck Reef chert of South Africa, Tice and Lowe 2004), down to deeper
water, more-distal environments in the vicinity of hydrothermal vents, such as the
Apex chert (Brasier et al. 2005), and ferruginous laminites like the Banded Iron
Formations (BIFs, e.g., Klein 2005).
A wide range of potentially biological signals has been reported from carbona-
ceous material in such banded cherts, the morphologies of which include ‘wisps’,
‘fluffs’, ‘filaments’, ‘spheroids’ and ‘spindles’. Each of these morphologies has
been described in detail by Brasier et al. (2006), accompanied by an explanation of
the plausible abiotic scenarios that need to be excluded in each case. Here, we will
briefly review these signals, with the exception of septate filaments from the 3465
Ma Apex chert, which we will discuss in more detail later in the chapter.
‘Wisps’ are microscopic carbonaceous wrinkled laminae (Fig. 5a). When found
in laminated modern to late Archaean deposits, they are widely interpreted as bio-
logical features derived from microbial biofilms (e.g. Noffke 2000; Noffke et al.
2001, 2003). Wisp-like structures are found in bedded cherts both from the Pilbara
(e.g., Brasier et al. 2005) and the Barberton (e.g., Westall et al. 2001). Using mor-
phological comparisons with modern day examples, as well as their depth-restricted
distribution, and the presence of roll up structures (Fig. 5b), they have often been
interpreted as the remains of anaerobic, photosynthetic mats (Walsh and Lowe 1999;
Tice and Lowe 2004). In these earliest rocks however, an origin for wispy and finely
laminated textures from colloidal sediments, volcaniclastic sediments and prebiotic,
abiogenic films will always need to be falsified. This problem has been highlighted
by recent experimental studies that show how laminated micro-stromatolites and
wrinkle structures can be generated by the diffusion-limited aggregation of synthetic
colloids (McLoughlin et al. 2008).
The role that biology has to play in the generation of ‘fluff’ textures is even more
equivocal. Modern carbonaceous ‘fluff’, sometimes termed marine snow, forms as
a result of decaying planktonic matter settling through the water column, forming
discrete layers within deep-sea sediments. In the Archaean, ‘fluffy’ carbonaceous
grains are common in bedded cherts (Fig. 5b; Walsh and Lowe 1999), but they are
also common in subsurface dyke cherts (Lindsay et al. 2005) where they can form
layers of bush-like shrubs within hydrothermal cavern systems. These bushes arise
from the growth of self-organising dendrites, meaning that similar abiogenic sce-
narios cannot yet be excluded for comparable carbonaceous ‘fluff’ textures found
in seafloor cherts.
Carbonaceous filaments (Fig. 6a) have been at the centre of much controversy
in the search for earliest life. The problem here is that while filaments can be easily
compared with younger examples of prokaryotic microfossils (e.g., Schopf 2006),
Fig. 5 Carbonaceous structures from banded cherts of early Archaean age. Such structures have
been used to argue for the presence of cohesive microbial ‘mats’ on the seafloor at this time.
(a) Carbonaceous wisps (arrowed) from the 3465 Ma Apex chert, Western Australia; (b) fluffy
composite carbonaceous grains (arrowed) and a ‘roll up structure’ from the 3416 Ma Buck Reef
Chert, South Africa. Scale bar is 50 mm for both a and b
they are also one of the most easily formed self organising structures (Brasier et al.
2005, 2006). Filaments can result from the breaking of polygonal, spheroidal or
circular symmetry during crystal growth (see also Buick 1984, 1988; Deegan 2000).
In addition, complex filaments that resemble the earliest Archaean microfossils can
be generated in simple experiments by the precipitation of metallic salts in silica
gels (Fig. 6b) and by subsequent nucleation of carbonaceous material (Garcia-Ruiz
et al. 2003). Furthermore, hollow bacteria-like filaments can be generated by
spark-discharge or FTT-like synthesis of organic polymers in prebiotic experiments
(Folsome 1977; Baker and Harris 1978). This matters because Fischer-Tropsch-
like processes may well have operated in Archaean hydrothermal systems, while
spark discharges are likely to have accompanied all major volcanic eruptions
(Lindsay et al. 2005).
503
Fig. 6 Carbonaceous filaments, spheres and spindles from banded cherts of claimed but question-
able biological origin (a, c–f) and of certain abiological origin (b) The biogenicity of such structures
is proving difficult to demonstrate because they can also arise from complex abiological self orga-
nising structures (see Fig. 7). (a) carbonaceous filament from the 3465 Ma Apex chert, Western
Australia; (b) twisted filamentous pseudofossil made experimentally by precipitating barium-car-
bonate crystals in sodium silicate gel (image courtesy of A Cannerup); (c) septate filament from the
Apex chert interpreted as putative cyanobacterium Archaeoscillatoriopsis disconformis (Schopf 1993)
now explained as d, an abiogenic self-organising structure (boxed area equates to structure shown in
c) formed around a rhombic crystal (arrowed); (e) solitary sphere from the Apex chert formerly inter-
preted as a coccoid cell; (f) spindle structure from the 3400 Ma lower Kromberg Formation, South
Africa (Walsh 1992). Scale bar is 100mm for a; 15 mm for b and e; 25 mm for c; 30 mm for d and f
Carbonaceous septate filaments have been seen as a ‘Holy Grail’ in searches for
the earliest life because they can most closely approach the appearance of younger
authentic prokaryotic microfossils, owing to the presence of cell-like subdivisions
(Fig. 6c). Such filaments have understandably been interpreted as the remains of
bacteria, and at times compared with photosynthetic cyanobacteria because of their
size range (Awramik et al. 1983; Schopf and Packer 1987; Awramik 1992; Schopf
1992a, 1993, 1999; Ueno et al. 2001). On cross-examination, however, many of
these claims falter. For example, it has been shown that the early Archaean, Apex
chert ‘microfossils’ (Schopf 1992a, 1993, 1999) are in truth a population of arte-
facts (e.g., Fig. 6d) that occur within the complex boundary zones of re-crystallized
silica spherulites and crystal rhombs, as well as within jaspilitic and carbonaceous
cherts, volcanic glass and rhyolites. The most parsimonious explanation for these
structures involves their formation during the recrystallization of amorphous glassy
silica to spherulitic chalcedony and other hydrothermal fabrics, as part of a symme-
try-breaking cascade from spheroidal – to dendritic – to arcuate artefacts (see
Brasier et al. 2002, 2004, 2005 for details). A spectrum of artefacts is thereby pro-
duced which depends upon the size of the spherulites, and the purity (carbonaceous
content) of the chert, as illustrated by Fig. 7. Further inaccuracies in the original
reports of the Apex microfossils, in particular the nature of the depositional setting,
their occurrence in late stage fabrics, and the nature of branching, have also been
found by our detailed mapping at a range of scales (e.g. Brasier et al. 2005). The
combined evidence must therefore lead to the rejection of the biological nature of
these putative Apex chert fossils. It also casts doubt on the veracity of other
reported occurrences of early Archaean septate ‘microfossils’.
Carbonaceous spheroids (e.g., Fig. 6e) are also commonplace within Archaean
cherts and some have been regarded as microfossils based upon comparisons with
modern coccoid and baccilate bacteria. The problem with spheroids, however, is
their relatively simple morphology which can be generated by purely physico-
chemical mechanisms in the form of fluid inclusions, vesicles (bubbles), globules,
rings, and spheroidal crystallites (see Folsome 1977; Deegan 2000; Brasier et al.
2006). This makes it difficult to demonstrate the biogenicity of either solitary (e.g.,
Knoll and Barghoorn 1977; Walsh 1992) or clustered spheroids (e.g., Schopf and
Packer 1987; Sugitani et al. 1998, 2006; Westall et al. 2001). The same can be said
for structures which have been regarded as ‘cells in the process of division’ (e.g.,
Schopf 1993, 2006); these likewise can form naturally within complex self-orga-
nizing systems, such as mineral growths (Brasier et al. 2005, 2006).
A further structure of note within banded cherts of the Barberton are ~40 mm
diameter ‘spindles’ (Fig. 6f; Walsh 1992; Westall et al. 2001). These intriguing
morphologies have been interpreted as being either the outer sheaths of colonies of
bacterial cells or as the abiogenic, carbonaceous coatings of ghosted gypsum crys-
tals (Walsh 1992). A further explanation, advanced by Westall et al. (2001) is that
they are similar to the fenestrae of stromatolites and are thus created by bacterially-
produced gas. These scenarios certainly merit further investigation, especially in
light of the recent discovery of similar structures in Western Australia (Sugitani
et al. 2006).
Fig. 7 This three dimensional morphospace model (centre block) of the famous Apex Chert
‘microfossils’(outer images) shows how this spectrum of microfossil-like structures was most
likely created entirely by physicochemical controls during recrystallization of the chert and the
redistribution of carbonaceous material around spherulite and crystal margins. The key controls
here were the relative purity of the chert (vertical axis), the degree of recrystallization of the
fibrous chalcedony to equigranular microcrystalline chert (left horizontal axis), and the diameter
of the spherulites (right horizontal axis). Arrows link theoretical with observed and reported
microfossil-like artefacts sharing similar morphologies
6.5 Stromatolites
Moving into Archaean shallow water environments, our classic expectation is to

find stromatolites. Stromatolites have provided a key search image for the emer-
gence of life on Earth because they are assumed by many workers to be
organosedimentary structures that require a microbial component in order to
grow (e.g., Walter 1976). This view is largely based upon analogous reasoning
from studies of modern examples in Shark Bay, Western Australia and from the
Bahamas, both of which accrete largely as a result of microbial processes of trap-
ping, binding and cementation. In many ancient examples, however, and most
especially in the early Archaean (where the diagenetic destruction of microbial
microfabrics and chemical biomarkers is pervasive), demonstration of such a

biological component to growth is notoriously difficult to demonstrate (e.g.,
Buick et al. 1981; Lowe 1994a).
It is now becoming increasingly apparent that abiotic, chemical precipitation
is an important component of stromatolite accretion and such processes may well
have been prevalent during the earliest periods of Earth history (Grotzinger and
Knoll 1999). These so called “chemical stromatolites” (sensu Pope et al. 2000)
appear to have been common during periods of high levels of seawater carbonate
saturation. Such forms can display a wide-range of morphologies and are charac-
terized by isopachous laminae (i.e. of uniform thickness) with extreme lateral
continuity and a high degree of vertical inheritance of topography from one layer
to the next. In many instances, therefore, demonstrating an active role for
microbes in the growth of such stromatolites has proved extremely difficult (e.g.,
Pope and Grotzinger 2000). For that reason, a non-genetic definition of a stroma-
tolite is adopted here: i.e., an attached, laminated, lithified sedimentary growth
structure that accretes away from a point or limited surface of initiation (Semikhatov
et al. 1979).
Interestingly, both the abundance and diversity of Archaean stromatolites is
much lower than seen in the succeeding Proterozoic interval (e.g., Hofmann 2000)
and their morphologies tend to be less complex over a range of scales. It is also
notable that microfossils of the kind usually inferred to have built these and related
structures have never been found in association with Archaean stromatolites. This
absence of evidence may, of course, be attributed to the low preservation potential
of microfossils in stromatolites generally.
Some of the oldest putative stromatolites have been reported from the ~3490 Ma
Ga Dresser Formation of the Warrawoona Group (Fig. 8a). These occur at several
localities in the North Pole Dome, both in syn-depositional barite mounds and
dykes from a hydrothermal complex (Van Kranendonk et al. 2001; Nijman et al.
1998) as well as within intercalated and silicified, ferruginous carbonates (Walter
et al. 1980). The stromatolites originally described by Walter et al. (1980) were
reviewed by Buick et al. (1981) who concluded that they were only “probable or
possible” biogenic stromatolites. More recent studies have also described domal
and stratiform stromatolites from around the ‘vents’ of barite dykes at the North
Pole and some authors have argued that these mounds were constructed by hyper-
thermophilic microbes (Van Kranendonk 2006). The macro-morphology of these
stromatolites is largely controlled by the thickness of the precipitated barite crusts
and draping chert layers, however, and their distribution more likely reflects the
supply of supersaturated solutions from which they were precipitated. Robust
micro-textural and isotopic evidence for the involvement of microbial mats in the
growth of these baritic stromatolites has not yet been reported, casting some doubt
upon their biogenicity.
Fuel for this debate about Archaean stromatolite biogenicity has been pro-
vided by the discovery of a second Pilbara stromatolite locality, in the ~3430 Ma
Ga Strelley Pool Formation, a marker horizon between the Warrawoona and Kelly
Groups (Hoffman et al. 1999). Conical stromatolites (Fig. 8b) are a characteristic
Fig. 8 Stromatolites of uncertain origin from the Pilbara of Western Australia. (a) Small domal
stromatolite from the ~3490 Ma Dresser Formation interpreted as abiogenic by many authors;
b–d are from the ~3430 Strelley Pool Chert and are of the kind that have been recently claimed
to have a biological origin, but here we show abiological features that include isopachous
laminae and reversible symmetry (b), accretion above crystal fans (c), and intergradation with
asymmetrical linguoid ripples (d). Scale bar is 2 cm for a; 5 cm for b; pen is 15 cm long in
c and d (see also Wacey et al. 2010)
feature of this unit and these were originally considered to be of biogenic origin
(Lowe 1980), a claim that was then rescinded in favour of an abiogenic origin
by means of evaporitic sedimentation (Lowe 1994a). The ‘Trendall locality’
(Hoffman et al. 1999) is notable for possessing an unusually diverse range of
‘conical’ and ‘columnar’ morphologies, plus one example of so-called ‘branching’.
Morphological arguments together with rare Earth element studies have then
been used to argue for their shallow marine setting and their biological origin
(Hoffman et al. 1999; Van Kranendonk et al. 2003; Allwood et al. 2006; Allwood
et al. 2009).
Tellingly, the model put forward by Allwood et al. (2006) for stromatolites in
the Strelley Pool Formation at the ‘Trendall locality’ fails to apply to the same
unit in other areas. In the East Strelley greenstone belt, studied in detail by us
(McLoughlin 2006; Wacey (2010a)), small unbranched ‘coniform’ stromatolites
are typical and these do not show any changes in morphology or distribution with
varying depth across the region. Like the Dresser Formation examples discussed
above, they show a close interrelationship with crystal fan arrays (Fig. 8c). Sadly,
this points clearly towards a strong chemical component for their growth. We also
find that the ‘cones’ intergrade with linguoid and linear current ripples, highlight-
ing a major role for physical processes during their accretion (Fig. 8d). In the
absence of supporting microtextural and geochemical evidence, the biogenicity
of the early Archaean stromatolites from much of the Strelley Pool Formation
remains to be demonstrated (but see especially Wacey 2010).
The case for an entirely abiotic origin for at least some Precambrian stromato-
lites was advanced by Grotzinger and Rothman (1996), who used the Kadar Paris
Zhang (KPZ) equation of interface growth (Kadar et al. 1986), to argue that the
morphologies of some stromatolites can be modelled by abiotic processes alone.
Although some authors dispute their interpretation of the KPZ equation (see Jogi
and Runnegar 2003), this study has reinvigorated the debate surrounding biogenic-
ity of the earliest stromatolites. More recently, McLoughlin et al. (2008) have
shown that synthetic stromatolites, ‘grown’ abiogenically in colloidal media by
diffusion-limited aggregation, can display features at one time believed to reflect
some level of biological participation (Buick et al. 1981), i.e., convex upwards
laminae; laminae that vary in thickness across stromatolite columns (non-isopac-
hous); and laminae with several orders of curvature. We have found that columnar,
branched and digitate stromatolites can all be generated abiologically in our labora-
tory experiments (Fig. 9).
It is curious that the capability of gelatinous or colloidal sediments to produce
stromatolites and wrinkle mat-like fabrics has been largely overlooked, given their
role in laminar to dendritic agate synthesis (e.g., Hopkinson et al. 1998). In the
Precambrian oceans, with a benthic boundary layer that was supersaturated with
silica, diffusion-limited deposition of colloidal sediments such as silica gel must
Fig. 9 Inclined digitate stromatolite structures generated abiologically in the laboratory by means
of diffusion-limited aggregation of three alternating coloured colloids (paints). Here we show that
features such as anisopachous laminae, wrinkled laminae and inclined columns, which have hitherto
been regarded as biological features, can be generated abiologically. (a) Cross section of columnar
digitate paint stromatolite inclined towards the sediment source on the left hand side with bridging
laminae between the columns; (b) cross section of the bulbous head of a paint stromatolite with
multiple branches. Scale bar is 1 mm for both a and b from McLoughlin et al. (2008)
have been capable of generating both laminar wrinkle mat and stromatolite textures
in the absence of microbes (cf. McLoughlin et al. 2008). Given the lack of compel-
ling microbial mat or microfossil remains in many early Archaean stromatolites,
and their close association with non-equilibrium hydrothermal systems supersatu-
rated with silica, questions must therefore remain as to whether, alone, stromato-
lites have anything useful to tell us about microbes or early biology. We would tend
to agree, rather pessimistically with the statement that “it is perhaps impossible, ‘to
prove beyond question’ that the vast majority of reported stromatolites…are assur-
edly biogenic” (Schopf 2006).
6.6 Siliclastics
Moving further towards the Archaean shoreline we encounter quartz arenites.

These have proved to be rather rare because the area of exposed land that could
provide the source material for these sediments was still very small at this early
stage in Earth history (Buick et al. 1995). Nonetheless, quartz arenites are turning
out to provide promising windows into the earliest biosphere, not least because of
the relative ease with which the complex depositional and diagenetic history of
sandstones can be untangled compared with rock types such as cherts and basalts.
A silicified sandstone unit at the base of the ~3430 Ma Strelley Pool
Formation in Western Australia (Brasier et al. 2006; Wacey et al. 2006, 2008,
2010b) is currently revealing multiple, supporting lines of evidence consistent
with a variety of biological activities at this time. The presence of low angle
cross bedding and channels (e.g., Lowe 1983) shows, together with evidence for
relatively high textural and compositional maturity, that deposition took place
during the course of a shallow marine transgression, arguably the oldest such
deposit in the rock record. The sandstones contain well rounded detrital grains
of pyrite that, together with associated rounded grains of chromite, rutile, and
zircon, indicate the formation of heavy mineral placer deposits within the beach
setting (Wacey et al. 2010b). The pyrite grains are associated with carbonaceous
biofilms and pits and channels that are interpreted as microbial trace fossils
(Wacey et al. 2010b). A number of mineral precipitates, including iron oxides
and sulfates, formed in close proximity to the pyrite surfaces and biofilms. These
have been interpreted by Wacey et al. (2010b) as biomineral products of micro-
bial pyrite oxidation.
A second kind of micro-structure present in this sandstone horizon (and
others in the Pilbara) is that of ‘ambient inclusion trails’ (AIT) (Fig. 10). These
are enigmatic structures have, in the past, been confused with both microfossils
and endolithic microborings. However, they can be distinguished by the
following features: (1) presence of a mineral crystal (e.g., a metal sulfide or
oxide) at one end of an AIT, of equivalent diameter to the tube, which may be
pseudomorphed by later minerals (e.g. silica, metallic oxide or phosphate); (2)
longitudinal striations on the AIT created by facets of the propelled mineral
Fig. 10 Photomicrograph of silica-filled ambient inclusion trail (AIT) in a cryptocrystalline silica

matrix from the ~3200 Ma Kangaroo Caves Formation, Western Australia. Such AIT are
microtubes which typically have striated margins and a pyrite crystal at one end. They have often
been mistakenly interpreted for microbial borings, though they may originate through biological
decomposition processes. Scale bar is 15mm
crystal (which may, however, be obscured by later mineral infill); (3) curved or
twisted paths, particularly towards their ends as impedance of the host lithology
affects movement; (4) tendency of AITs to crosscut or form branches of a different
diameter (i.e., where the propelled mineral becomes fragmented or a second crystal
is intercepted), and to make sharp turns; (5) the AIT will likely have a polygonal
cross sectional profile that matches the geometry of the propelled crystal.
Initially, AIT were thought to be a completely inorganic phenomenon (Tyler and
Barghoorn 1963) but a conjecture was later advanced for their formation from the
degassing of decomposing biological material during burial and/or metamorphism
(Knoll and Barghoorn 1974). This hypothesis has now been confirmed by us using
high-resolution mass spectrometry (NanoSIMS) coupled to detailed field and petro-
graphic mapping (Wacey et al. 2008). Further discussion of these AIT formation
mechanisms and a summary of criteria to distinguish them from microtunnels in a
range of rock substrates including sediments and volcanic glass can be found in
McLoughlin et al. (2010b).
Siliclastic deposits of the ~3.2 Ga Moodies Group of S Africa contain hollow
spheroidal organic-walled structures comparable with many younger ‘acritarchs’
(Javaux et al. 2010). These structures pass syngenicity and endogenicity tests and
appear to be the oldest acritarch-like microfossils yet reported. The null hypothesis
here is for an origin from benthic prokaryotic cysts, contemporaneous with benthic
microbial ‘wrinkle structures’ reported from the same rocks (e.g. Noffke et al.
2006). More speculative is their interpretation as bacterial plankton, or even
eukaryotic cells (e.g. Buick 2010). These discoveries will help to define the search
images needed for life in very ancient siliciclastic sediments (see Fig. 11).
Fig. 11 Examples of features sought from early life within siliciclastic sediments, as here found
within some of the earliest known terrestrial ecosystems. (a) petrographic evidence in transverse
section for trapping and binding of sediment grains within organic polymers (arrow); (b) bedding
plane evidence for microbially-induced sedimentary structures in the form of wrinkles or domes;
(c) evidence in horizontal section for organization of cell-like bodies into sheets or mats; (d) detail
of (c) showing evidence for cell walls, cell contents, and growth strategies including binary
fission. All images are from ~1000 Ma siliciclastic lake beds, Torridonian of Scotland. Scale bar
(a) and (c) = 100 micromillimetres; (d) = 10 micromillimetres
7 Summary
In this chapter we have advocated the view that the early Archaean Earth should be
considered as a distant planet. We have reviewed the traditional taphonomic win-
dows, especially carbonaceous cherts, through which the Archaean biosphere has
long been studied. The importance of understanding self-organising structures has
been stressed, along with ways scientists can refute such scenarios when working
to establish the veracity of candidate Archaean fossils. A traverse across early
Archaean environments has highlighted the importance of promising new tapho-
nomic windows into earliest life. These include pillow lavas, pyritic deposits and
siliciclastic sediments, suggesting that life may have been widely distributed at this
time. Further research involving detailed mapping, petrography and geochemistry
is now needed to pin down the specific life processes operating on the early Earth.
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Chapter 15
Evolutionary Trends in Remarkable Fossil
Preservation Across the Ediacaran–Cambrian
Transition and the Impact of Metazoan Mixing
Martin D. Brasier, Jonathan B. Antcliffe, and Richard H.T. Callow
Contents
1 Introduction........................................................................................................................... 520
2 Siliceous (Gunflint-type) Preservation.................................................................................. 523
3 Phosphatic (Doushantuo-type) Preservation......................................................................... 531
4 Siliciclastic (Ediacara-type) Preservation............................................................................. 540
5 Carbonaceous Film (Miaohe-type) Preservation.................................................................. 547
6 Carbonate (Tufa-like) Preservation....................................................................................... 550
7 Conclusion............................................................................................................................ 554
References................................................................................................................................... 555
Abstract A unifying model is presented that explains most of the major changes
seen in fossil preservation and redox conditions across the Precambrian–Cambrian
transition. It is proposed that the quality of cellular and tissue preservation in
Proterozoic and Cambrian sediments is much higher than it is in more recent marine
deposits. Remarkable preservation of cells and soft tissues occurs in Neoproterozoic
to Cambrian cherts, phosphates, black shales, siliciclastic sediments and carbonates
across a wide range of environmental conditions. The conditions for remarkable
preservation were progressively restricted to more marginal environments through
time, such as those now found in stagnant lakes or beneath upwelling zones. These
paradoxes can no longer be adequately explained by recourse to a series of ad
hoc explanations, such as those involving unusually tough organic matter in the
Ediacaran, or unusual seawater chemistry, or even the role of microbial biofilms
alone. That is because the exceptions to these are now too many. Instead, we sug-
gest that elevated pore water ion concentrations, coupled with the almost complete
lack of infaunal bioturbation, and hence the lack of a sediment Mixed-layer,
provided an ideal environment for microbially-mediated ionic concentrations at or
near the sediment–water interface. These strong ionic gradients encouraged early
M.D. Brasier (*) J.B. Antcliffe, and R.H.T. Callow

Department of Earth Sciences, University of Oxford, Parks Road, Oxford OX1 3PR, UK
cementation and lithification of sediments, often prior to complete decomposition

of delicate organic structures. Seen in this way, not only did the biosphere evolve
across the Precambrian–Cambrian transition. Fossilization itself has evolved
through time, and never more dramatically so than across this interval.
1 Introduction
“If my theory be true, it is indisputable that before the lowest [Cambrian] stratum
was deposited, long periods elapsed, as long, or possibly far longer than the whole
interval from the [Cambrian] age to the present day: and that during these vast
yet quite unknowable, periods of time the world swarmed with living creatures.”
(Darwin 1859).
It took a hundred years of research for Darwin’s words of 1859 to be seen for
what they were: a remarkable prediction about the nature of the Precambrian fossil
record. For most of the time since Darwin, there was for example, no concept of the
vast expanse of Precambrian time, nor was there any evidence for a distinct biota.
But we now realize that the Precambrian world was indeed ‘teeming with life’.
Furthermore, it can now be argued that the fossil record is qualitatively better than
anyone of Darwin’s time could ever have dared to imagine (e.g. Brasier 2009).
Analysis of taphonomy in the latest Precambrian (the Ediacaran Period) is intri-
cately linked to one of the most exciting questions in paleobiology: just how real
was the Cambrian explosion? Was it an explosion of animals or merely an explo-
sion of fossils? To answer this, we need to understand not only the nature of fossil
preservation in the Cambrian but also in the preceding Ediacaran Period (c. 635–
542 Ma). Herein we review the concept of a bias in the fossil record towards
remarkable preservation in the Ediacaran interval.
Good preservation can, of course, take place in a variety of ways. Understandably,
the various changes in the quality of preservation, particularly of unmineralized
tissues, across the Ediacaran–Cambrian boundary have received a range of dis-
tinct explanations. Most of these have tended to focus upon oceanic phenomena
such as sea water chemistry, or upon superficial features such as surface mats.
Hence, the decline away from high-resolution siliceous, phosphatic and tufa-like
calcareous preservation of cellular materials have been explained by chemical
causes, such as a decline in sea water silica (Maliva et al. 1989, 2005), phosphate
(Brasier 1992a, b), or pCO2 and alkalinity (Arp et al. 2001; Riding 2006a),
whereas the reduction in siliciclastic preservation has been attributed to a physi-
cal cause, namely the loss of benthic microbial mats (Gehling 1999). Each expla-
nation has its merits but each shares a common problem too – a lack of universal
explanatory power. Put another way, why should each of these different factors
have coincided in time? Could there have been a single ultimate cause or trigger?
In the following review, we consider these ideas and place them alongside the
explanatory potential of the hypothesis illustrated in Fig. 1 (see Callow and
Brasier 2009b).
15 Taphonomy Across the Ediacaran–Cambrian 521
Fig. 1 Model showing how the biosphere revolution from Ediacaran (at left) to Cambrian times
and later (at right) shifted the position of the biogeochemical cycles and hence the quality of
seafloor preservation. The evolution of burrowing, grazing and scavenging across the
Ediacaran–Cambrian boundary introduced an actively maintained mixed layer (see Seilacher
and Pflüger 1994; McIlroy and Logan 1999; Seilacher 1999; Bottjer et al. 2000; Droser et al.
2002, 2004; Bailey et al. 2006 and references in text). This not only brought about the disruption
of formerly pervasive microbial mats (Seilacher and Pflüger, 1994), but it also brought about
seminal changes in the position of important redox boundaries. Each of these five taphonomic
windows discussed in the text was extremely sensitive to Eh and pH. In the Ediacaran, the redox
boundary was rather sharp and typically lay high in the sediment profile so that high levels of
mineral saturation could build up near the sediment-water interface. Early lithogenesis could
often entomb fossil remains before their decay. During and after the Cambrian, expansion in
both the extent and depth of bioturbation pushed down the redox boundary and made it more
diffuse. This increased the recycling of organic matter before it could become fossilized, and
lowered the pH. The associated explosion of biomineralized shells helped to buffer the falling
pH sediments. Zones of ionic saturation and early lithogenesis lay further down within the
sediment profile. The numbered metabolic processes are broadly as follows: (1) Oxygenic pho-
tosynthesis, including cyanobacteria: CO2 + H2O → CH2O + O2. (2) Calcium carbonate pre-
cipitation: Ca2+ + 2HCO3− → CaCO3 + CO2 + H2O. This requires raised pH. (3) Aerobic
respiration, including metazoans: CH2O + O2 → CO2 + H2O. This tends to reduce pH and Eh.
(4) Calcium carbonate dissolution: CaCO3 + CO2 + H2O → Ca2+ + 2HCO3− . This tends to raise
pH. (5) Calcium phosphate precipitation. This requires Ca availability and some alkalinity. (6)
Anaerobic respiration by sulfate-reducing bacteria: 2CH2O + SO42+ → 2HCO3− + HS + H−. This
tends to increase pH and reduce Eh. (7) Anaerobic respiration by methanogenic bacteria:
2CH2O + H2O → CH4 + HCO3− + H−. This tends to increase pH and reduce Eh. Adapted from
Callow & Brasier (2009)
The model shown in Fig. 1 is focussed upon the role of the bioturbated surface
layer – the so-called ‘mixed layer’ (sensu Bromley and Ekdale 1984) – and its asso-
ciated subsurface chemistry. In the Cambrian to modern ocean (shown at right), this
top 10 cm or so of sediment was, and still is, typically mixed and processed by aero-
bic activities including metazoan burrowing and grazing (McIlroy and Logan 1999)
plus metazoan to microbial oxidation of organic matter (cf. Martin and Sayles 2003).
Processes including vertical and lateral particle mixing and bioirrigation within this
zone (e.g. Aller 1978, 1982, 1984, 1994; Martin and Sayles 2003; Burdige 2006)
have a considerable effect upon the distribution of reactive solids such as organic
matter, iron and sulfur minerals, as well as solutes such as O2, CO2, CH4, HCO3−, and
PO43− (see Burdige 2006). Exposure to oxidation in this mixed layer can be quite
long, with a typical residence time for Corg of ~104 years (Martin and Sayles 2003).
This gives ample time for aerobic metabolism to decompose much (about 80%) of
the reactive organic materials. Build-up of metabolic CO2 also takes place in this
zone, leading to a downward decrease in pH that is typically buffered by dissolution
of CaCO3 shells (e.g. Morse 2003). Added to this is the significant ‘weathering’
effect of particle digestion within the digestive tracts of metazoans (McIlroy et al.
2003). Anaerobic processes, such as denitrification, sulfate reduction and methano-
genesis together oxidize 30% or less of the remaining organic matter, mainly in
microbial zones beneath the mixed layer. Since mixing encourages upward diffusion
of products, some of these (especially iron and sulfur compounds) are able to partici-
pate repeatedly as electron donors and acceptors (Martin and Sayles 2003; Burdige
2006). In this way, organic materials will typically be consumed before all available
electron acceptors have been used up. This means that relatively little Corg is left (c.
10%; e.g. Martin and Sayles 2003) to enter the rock record.
Conditions on the seafloor in the Ediacaran and earlier periods (Fig. 1, shown at
left) were significantly different from those of today (Fig. 1; Seilacher 1956; Brasier
1979, 1992b; Seilacher and Pflüger 1994; Droser et al. 1999, 2002, 2004; Hagadorn
and Bottjer 1999; McIlroy and Logan 1999; Bottjer et al. 2000; Jensen 2003; Jensen
et al. 2005). Before the evolution of metazoan burrowers and in the presence of
benthic microbial mats (Seilacher and Pflüger 1994), the mixed layer must have been
confined to the effects of solute diffusion, perhaps compressed within the top ~1 cm
below the sediment–water interface. That being so, the redox boundary will have lain
much closer to the surface, with sulfate-reduction and methanogenesis playing much
more significant roles, as can be seen in some modern estuaries and lacustrine sys-
tems (cf. Martin and Sayles 2003). The contribution of alkaline solutes, arising from
both sulfate-reduction and methanogenesis could then have been much more impor-
tant than now. Being released closer to the sediment surface, they will have increased
pore-water alkalinity, encouraging the precipitation of both calcium phosphate and
calcium carbonate (cf. Morse 2003). Microbial mats and biofilms at or near the sur-
face would have further limited diffusion at the sediment – water interface (e.g.
Gehling 1999) and would have provided ideal sites for crystal nucleation.
In brief, this model predicts that conditions in the Ediacaran to earliest Cambrian
were well-suited to both rapid and high quality impregnation and cementation of
organic materials by a variety of taphonomic mechanisms. This was because the
important zones of fossil lithogenesis lay at, or near, the sediment–water interface.
High quality cellular preservation of this kind may also be connected to higher levels
of oceanic stagnation (e.g. Briggs and Crowther 2001), as indicated by studies of
Cryogenian to Cambrian carbon and sulfur isotopes (Brasier 1992a, b; Shields et al.
1997; Kimura and Watanabe 2001; Fike et al. 2006; Schröder and Grotzinger 2007)
and iron contents (Canfield et al. 2007).
The biological revolution at the base of the Cambrian is defined (see Brasier
et al. 1994) by metazoan recycling of carbonaceous matter through the activities of
bioturbation as well, of course, as by grazing (including zooplankton), scavenging
and biomineralization. The appearance of these new Phanerozoic strategies led to

the development of an actively controlled sediment mixed layer for the first time in
Earth history (Seilacher and Pflüger 1994). Metazoan burrowing led to downward
stretching of the aerobic zone from ~1 to 10 cm or more. A significant change in
the pH of sediments followed from metazoan inputs of respiratory CO2 that was
buffered by raised rate of dissolution of carbonate grains, not least by the ‘newly
invented’ CaCO3 shells of metazoans. Together, these new process are predicted to
have led to an increase in the average depth at which lithogenesis was taking place
in the sediment. Furthermore, these changes are likely to have brought about long-
term decreases in the quality of cellular preservation, as discussed below.
The following review examines the evidence for taphonomic changes, especially
of unmineralized tissues, within five different modes of preservation: siliceous;
phosphatic; siliciclastic; carbonaceous; and carbonate. The review then goes on to
consider various competing models and explanations for these phenomena, including
the role played by the evolution of the mixed layer itself.
2 Siliceous (Gunflint-type) Preservation
Precambrian silica deposits are truly non-uniformitarian (Perry and Lefticariu 2003).
From about 2700 to 1900 Ma, occasionally fossiliferous, siliceous banded iron for-
mations (BIFs; Fig. 2a) dominated deep-sea silica sedimentation in a world generally
believed to have significantly lower levels of atmospheric oxygen (Han and Runnegar
1992; Bjerrum and Canfield 2002). Although the genesis of these unusual sediments
is far from understood, their demise and disappearance after 1800 Ma may be related
in some way to evolution of the atmosphere (see Holland 2006) and/or to ocean pH
and temperature (see Perry and Lefticariu 2003). These laterally extensive sediments
are significant in the Precambrian because they preserve organic-walled microfos-
sils, including coccoid cells and filaments, as for example in the Gunflint Chert
(Barghoorn and Tyler 1965). BIF-like sediments reappear during a brief interval in
the Neoproterozoic (c. 720–580 Ma), coincident with the so-called ‘snowball earth’
intervals (Hoffman and Schrag 2002), although younger BIF-like deposits are only
known from settings of intense hydrothermal activity (e.g. the Red Sea in the
Cenozoic; see Butuzova et al. 1990). Both BIFs and other kinds of widespread
seafloor chert precipitation (e.g. seafloor bedded cherts) largely disappeared after c.
1800 Ma, to be replaced by nodular or lenticular chert within carbonate sediments,
often formed within evaporative and peritidal environments, which sometimes bear
exceptionally preserved microfossil assemblages (Maliva et al. 1989, 2005).
Fossiliferous cherts of Mesoproterozoic to Cambrian age are found across a
range of depositional environments from deep marine to peritidal settings (Figs. 2,
3, 5) where the silicification of organic cellular materials and microbial sheaths can
be remarkably common (Fig. 2b; Table 1). The petrifaction of microfloras within
peritidal cherts is common in these Meso- to Neoproterozoic cherts, such as the
Boorthanna Chert of Western Australia (Fig. 2b) or the Bitter Springs Chert of
central Australia (e.g. Barghoorn and Tyler 1965; Schopf 1968; Schopf and
Fig. 2 (a) before the Cambrian, siliceous sediments, like these banded iron formations (BIFs), can
be found across a wide range of settings from the deep aphotic zone to the supratidal zone and may
be occasionally fossiliferous (e.g. Gunflint Chert). The millimetre scale laminations (arrow) are rich
in iron and maybe seasonal in origin. From the Hammersley Iron Formation Dale Gorge, Karijini
National Park, Western Australia (c. 2400 Ma). Lens cover c. 5cm in diameter. (b) the early silicifi-
cation of cells, such as those of Eoentophysalis sp. from the c. 925 Ma Boorthanna chert of Western
Australia, is common in many Proterozoic sediments (see also Table 1). Arrow shows probable
photosynthetic cyanobacterial coccoid cells undergoing binary fission. Scale bar 1mm for (b)
Fairchild 1973; Schopf and Klein 1992). Such cherts seemingly acted as ‘traps’ that
show a taphonomic bias towards small organic structures including cellulose cell
walls, mucilaginous sheaths, and possibly even subcellular structures (Oehler 1977)
or molecular biomarkers (Hod et al. 1999). Nucleation sites for silica formation
near the sediment surface also appear to have been provided by decaying organic
matter (Knoll 1985). It appears that it was relatively easy, therefore, for silica and/
or silicates to precipitate directly or diagenetically within a range of Proterozoic–
Cambrian marine settings.
Table 1 The changing pattern of soft tissue preservation in siliceous deposits through Earth history, and in particular, across the Ediacaran–Cambrian transition.
This shows how the preservation of coccoid cells and microbial filaments by silicification was abundant and common throughout the Meso- to Neoproterozoic.
The silicification of soft tissues, including cells, is known through the Cambrian, but appears to decrease in frequency and in quality throughout the remainder
of the Phanerozoic, where silicified delicate cellular of subcellular materials and less common. Despite occasional reports of exceptional preservation in nor-
mal marine conditions, silicification in the Phanerozoic tends to be confined either to unusual environments (sinters, alkaline lakes) or to unusually recalcitrant
organic materials (e.g. lignin or biominerals). From sources cited in the text and in references
Acritarch
Coccoid benthic cells Filament sheaths In situ mats (phytoplonkton) Eggs (embryos) Micro-arthropods Micro-faecal pellets
Cainozoic
Cretac +
Jurassic
Triassic
Permian
15 Taphonomy Across the Ediacaran–Cambrian
Carbonif
Devonian + +
Silurian + +
Ordovician + +
U. Camb + + + +
M. Camb + + + +
L. Camb + + + +
U. Ediac + +
M. Ediac + + + +
Proteroz + + +
525
Fig. 3 (a) Relatively deep-water siliceous sediments are widely encountered across the
Ediacaran–Cambrian transition, like these finely laminated cherts from the Tal Formation in
the Lesser Himalaya of India (c. 543–530 Ma). The white layers consist of purer chert while the
darker layers are rich in calcium phosphate and organic matter. Note the cross section through
a sphaeroidal, embryo-like structure (arrow). From Brasier & Callow (2007). (b) Close up
image of the alternating dark and white layers shows the presence of abundant small filaments
and sheaths (arrow) of probable benthic microbial origin, from the latest Ediacaran to basal
Cambrian Tal Formation. Scale bar 1 mm for (a) and 10 mm for (b)
Cellular preservation of acritarchs and other organic-walled microfossils in sil-

ica continued through the Ediacaran interval (e.g. Table 1; Tiwari and Knoll 1994;
Xiao 2004). Some of these cherts, such as those of the Doushantuo Formation of
China, were deposited close to storm wave base where they preserve multicellular
algae (Xiao 2004), giant spiny acritarchs (Zhou et al. 2006) and putative sponge
spicules (Li et al. 1998; Yin et al. 2001). But it is across the Precambrian–Cambrian
Fig. 4 Modern geographic map showing localities studied herein for examples of silicification,
phosphatization or black shale (carbonaceous) preservation during the Ediacaran to early Cambrian.
1, Tal Formation chert, phosphorite and black shale, Uttar Pradesh, Lesser Himalaya, India
(c. 545–530 Ma). B, Hazara chert and phosphorite of Pakistan (c. 545–530 Ma). 3, Doushantuo
Formation chert, phosphorite and black shale of South China Platform (c. 630–580 Ma);
Meishucun Formation phosphorite (c. 535 Ma), Badaowan Formation black shale and chert
(c. 530 Ma), and Chengjiang ‘black shale’ biota (c. 525 Ma), all from the South China Platform.
4, Khubsugul chert and phosphorite of NW Mongolia and Tsagaan Oloom phosphate and chert
beds of SW Mongolia (both c. 550–545 Ma). 5, Fara Formation chert and phosphorite of north
Oman, and Ara Group black shale and chert (‘Athel silicilyte’) of south Oman (c. 545–540 Ma).
6, Soltanieh Formation black shale and phosphorite of the Elburz Mountains of NW Iran
(c. 545–530 Ma). For further details and sources, see the text
boundary that widespread silicification of organic materials in subtidal settings

again becomes prominent, often in association with phosphates and black shales
(Fig. 3; see Mazumdar and Banerjee 1998; Shen and Schidlowski 2000; Amthor
et al. 2005). These lithologies can be used as indicators of high productivity and
eutrophic conditions (e.g. Brasier 1995) and this seems to be the first interval of
Earth history in which these distinctive lithologies can be found as a ‘nutrient trin-
ity’. It is also during this interval that the first volumetrically significant silica
skeletons emerge, including those of hexactinellid sponges and radiolarians (e.g.
Brasier et al. 1997, but see also Porter et al. 2003). Siliceous preservation of soft
tissues in the Ediacaran–Cambrian boundary interval (Fig. 3) seems to be limited
to relatively resistant microbial sheaths, and lacks the delicate coccoidal cellular
clusters known from earlier Proterozoic times (Fig. 2b). This is in spite of abundant
Fig. 5 Model contrasting the wide range of Ediacaran to early Cambrian environments where
cellular preservation occurs by silicification (numbers 1 to 4, outlined below) with the very limited
range of Cretaceous to modern settings, including terrestrial hot springs (asterisk at right) and
biogenic diatomites, radiolarites and flint nodules (asterisk at left). This enormous contraction in
the zone of silica deposition and preservation shows the extraordinary effects of the Cambrian
explosion upon the silica cycle. The Ediacaran to Cambrian examples studied are as follows: 1–2,
Doushantuo Formation of China, Tsagaan Oloom Formation of southwest Mongolia, and Tal
Formation of India. 3, Khufai, Buah and Ara Formations of Oman. 4, Athel silicilyte of southern
Oman. From sources in text and references
silica-rich deposits of this age, such as those from Arabia (Gorin et al. 1982;
Amthor et al. 2005; Schröder et al. 2005). The preservation of possible fungal filaments
alongside discoidal microfossils within aluminosilicate minerals (Callow and
Brasier 2009a; Brasier et al. 2009b) may provide further evidence for the preserva-
tion of unmineralized tissues by silica/silicate minerals during this period.
Silicified cells from marine environments after the Precambrian–Cambrian
boundary become increasingly rare (Table 1). Examples include silicified
Michrystridium-like acritarchs from the Lower Cambrian Yurtus Formation of
South China (Yao et al. 2005), silicified embryo-like structures in Middle Cambrian
cherts in China (Lin et al. 2006) and poorly preserved cells of cyanobacteria in the
Upper Cambrian to Lower Ordovician Durness Formation of Scotland (Brasier
1977 and unpublished data).
Chert-rich sediments remain common throughout the Phanerozoic. Common
examples include flint nodules within the Cretaceous chalk of southern England, or
the radiolarites and diatomites often associated with upwelling zones (e.g. Schubert
et al. 1997; Kidder and Erwin 2001). Silica-rich sediments such as diatomites are
Fig. 6 Examples of the remarkably high-quality of phosphatic preservation that can be seen in
Neoproterozoic phosphorites. (a) and (b) Colonies of presumed photosynthetic cells, from the
Torridon Group of northwest Scotland (c. 1000 Ma). Note the presence of dark structures within
the cells, which may represent contracted cell contents. (c) Cross section through one of the clus-
ters of cells for which the Doushantuo phosphorite is rightly renowned (c. 630–580 Ma). Such
forms have been regarded as cnidarian polyps or stalks. Photo courtesy of Zhou Chuanming. Scale
bar Scale bar 5 mm for (a) and (b) and 200 mm for (c) From Brasier & Callow (2007)
often used as indicators of high levels of nutrient supply or upwelling (Brasier 1995).
However, although chert nodules and silica-rich sediments can be common, the
quality of organic and cellular preservation within younger cherts remains poor in
the vast majority of marine examples. Typically, only the most resistant organic
materials (e.g. wood) or relatively resistant cyanobacterial sheaths are preserved
(Table 1). In other cases, chert can be often be seen replacing biomineral skeletons
(e.g. Mu and Riding 1983; Schubert et al. 1997; Kidder and Erwin 2001), although
this is often a late stage diagenetic process and the chert preserves little of the original
biomineral or its ultrastructure. Examples of high-quality soft tissue and cellular
preservation in Phanerozoic cherts (see Tobin 2004) include reports of preserved
coccoid cells or filaments from evaporative peritidal or marginal marine settings
(Wardlaw and Collinson 1978) and the exceptional preservation of arthropods in
the alkaline lakes of the Miocene Barstow Formation (Park 1995; Park and
Downing 2001). Terrestrial sinter deposits around hot springs, such as the Lower
Devonian Rhynie Chert of Scotland (Trewin and Rice 2004) and silicified algae and
bacteria forming in situ around modern hot spring systems, represent further
examples of exceptional preservation of organic materials by silica (Konhauser
et al., 2001; Jones et al. 2007).
Modern laboratory experiments (e.g. Toporski et al. 2002) and geological obser-
vations around modern hot springs (Konhauser et al. 2001; Jones et al. 2007)
demonstrate that petrifaction of cells is aided by raised concentrations and rapid
precipitation of silica. In modern oceans, silica deposition is typically restricted to
areas of high nutrient flux, as seen for example in regions of equatorial upwelling,
where large volumes of biological opaline silica formed by radiolarians, diatoms
and sponges are deposited on the seafloor. Only about 10% of this silica enters the
geological record, owing to the high surface area:volume ratio of opaline silica
skeletons and their ready dissolution within the undersaturated water masses and
pore waters typical of the modern ocean (e.g. Martin and Sayles 2003).
Cementation within Cenozoic diatomites and radiolarites also seems to be rather
slow and late, taking place around subsurface concentrations of organic matter to
form nodules around faecal pellets, sponges and burrow systems. Cellular materi-
als therefore degrade before they can be encased in silica, allowing only the more-
resistant organic materials such as spores, cysts and wood, to enter the fossil
record. All this clearly suggests that biological innovations near the start of the
Cambrian could have directly influenced both the time and place of silica
authigenesis.
Conditions for siliceous preservation on the Ediacaran to early Cambrian
seafloor were markedly different from those found today. Extraction of silica by
diatoms was lacking and that by radiolarians and sponges was limited (Maliva et al.
2005, but see Porter et al. 2003). This is thought to have favoured significantly
higher silica saturation states in the water column, with potential for direct silica
precipitation and chert formation in deeper neritic to peritidal settings. Added to
this is the likelihood of greater alkalinity in waters near the sediment–water
interface, from the greater activities of sulfate-reduction and methanogenesis (see
Fig. 1). This would have raised the dissolved concentrations of silica in both pore
waters and the local water column. There was, it seems, still considerable potential
at this time for the rapid precipitation and preservation of delicate organic materials
during very early diagenetic lithification by silica. It can therefore be argued that
high-quality cellular and sub-cellular silicification appears to have been more common
in many marine settings during the Meso- to Neoproterozoic (Fig. 5) in comparison
with the Phanerozoic. The zone of exceptional silicification appears to have moved
away from the shallow marine environments and into areas where unusual geochemical
conditions are present, such as evaporative basins, lacustrine settings and terrestrial
hot spring environments.
3 Phosphatic (Doushantuo-type) Preservation
The preservation of fossil organisms by means of diagenetic phosphate arguably

provides a litmus test for the quality of fossil preservation during the emergence of
Metazoa (Cook and Shergold 1984; Xiao and Knoll 1999; Hagadorn et al. 2006;
Brasier and Callow 2007; Brasier 2009; Dornbos 2009 this volume). As a key
biolimiting nutrient, phosphate ions (PO42−) are rapidly utilized by photoautotrophs
and are typically undersaturated in the surface layer of the modern oceans. Phosphate
ions increase in concentration beneath the photic zone in the Oxygen Minimum
Zone (OMZ), where microbial processes remineralize organic materials, thereby
releasing phosphate ions (Föllmi 1996; Compton et al. 2000; Martin and Sayles
2003; Ruttenberg 2003; Burdige 2006). Similar processes of microbially mediated
phosphate ion-release also operate within the sediment profile at the redox boundary
(Fig. 1). Phosphate ions are highly sensitive to the redox state. In oxidizing condi-
tions such as those found within the modern sediment mixed layer and the upper
well-mixed layer of the oceans, phosphate ions tend to complex with ferric oxides,
which removes bioavailable phosphate from both pore waters and the water column
(Föllmi 1996; Compton et al. 2000; Ruttenberg 2003; Burdige 2006). This process
can, however, be reversed under anaerobic and acidic conditions, as for example
during burial beneath the sediment mixed layer or within the oxygen minimum zone
(e.g. Van Cappellen and Ingall 1994; Föllmi 1996; Ruttenberg 2003). Precipitation
of phosphate on the modern seafloor therefore occurs in reducing conditions, such
as those beneath upwelling zones, typically at water depths of c. 200–400m on the
continental slope (Piper and Link 2002). In these settings, phosphatization typically
occurs in moderately alkaline environments where abundant phosphate ions are sup-
plied by the remineralization of organic matter. In modern settings such as this, it is
typically materials such as faecal pellets which become phosphatized.
There is good evidence that phosphate concentrations and distributions are
strongly controlled by microbial processes (Krajewski et al. 1994; Wilby et al.
1996), although in most cases there is no evidence that organisms or microbes act
as preferential sites for phosphate nucleation. Preservation of fossils by diage-
netic phosphate minerals can occur in a number of ways. These include the for-
mation of phosphatic internal moulds within shells, the replacement of calcium
carbonate biominerals, or the replacement or encrustation of organic tissues
(Brasier 1990; Xiao and Knoll 1999). Phosphatic internal moulds or casts provide
little or no information about the soft parts of an organism, or about the details of
unstable or ephemeral biomineral phases. The phosphatic replacement of primar-
ily calcareous skeletons (e.g. Lamboy 1993) is common, as for example in early
Cambrian shelly fossils such as Anabarites (see Kouchinsky and Bengtson 2002;
Feng and Sun 2003) and other small shelly fossils (see Porter 2004). This style
of preservation can replicate the original microstructure of primary biomineral
phases (e.g. unstable aragonite) and therefore provides information which is typi-
cally lost during fossil preservation. The encrustation or replacement of unminer-
alized tissues (e.g. Briggs et al. 2005) also provides valuable paleobiological
information about soft tissues and examples from the Ediacaran–Cambrian inter-
val include the mucilaginous sheaths of putative fossil cyanobacterium Spirellus
(Fig. 7a) and the putative fossil eggs, embryos and hatchlings of cnidarians
(Bengtson and Zhao 1997; Koushinsky et al. 1999; Donoghue et al. 2006b;
Hagadorn et al. 2006).
Some of the earliest described examples of phosphatic preservation are dated
to c. 1000 Ma from the Torridonian of Scotland (Peach et al. 1907; Peat and
Diver 1982; Turnbull et al. 1996; Brasier 2009). These reveal a remarkable
quality of preservation in both cells and cell contents (Figs. 6a, b). Phosphate
Fig. 7 A dramatic transformation took place in the phosphatic preservation of organic matter
between the late Ediacaran and the late Cambrian that is interpreted to be related to a downward
shift of the oxygen minimum zone and the associated zone of phosphogenesis. (a) Phosphatized
cells and extracellular sheaths of spirally twisted cyanobacterium Spirellus, from the Tal Formation
phosphorite of India of Ediacaran–Cambrian boundary age (c. 545–530 Ma). This style of preser-
vation, from within the photic zone, is widely known from the phosphorite localities labelled in
Fig. 4. (b) and (c) Similar examples of late Cambrian age typically show compacted filaments,
which are here interpreted as the gut contents of zooplankton and animal grazers living below the
photic zone, from the Orsten Biota, Agnostus pisiformis Zone of Kinnekulle, Sweden (c. 480 Ma).
After the Cambrian, preservation of phytodetritus became increasingly rare because the phospho-
genic zone began to fall even further below the photic zone. For the majority of the Phanerozoic
it is processed materials and faecal matter that constitutes most phosphate deposits. Scale bar
100 mm for (a)–(c). From Brasier & Callow 2007
does not appear interbedded with other members of the ‘nutrient trinity’ (i.e. chert
and black shale) until much later, however, as for example in the Doushantuo
Formation of China (see Fig. 4, >580 Ma, Condon et al. 2005). These Ediacaran
phosphorites preserve what many now regard as the oldest animal embryos
(Fig. 6c; see Xiao et al. 1998; Xiao and Knoll 1999; Hagadorn et al. 2006),
although they have been interpreted as vesicles of giant sulfur oxidizing bacte-
ria (Bailey et al. 2007). It is also at this time that the primary calcium carbonate
tubes of Cloudina can be replaced by diagenetic phosphate, preserving details
of what is thought to be the original biomineral ultrastructure (Feng et al. 2003;
Hua et al. 2005).
The zenith of phosphatic preservation at any time in Earth history was reached
during the earliest stages of the Cambrian, in particular along the fabled ‘Silk
Route’ (Fig. 4; see Shergold and Brasier 1986; Brasier 1989, 1992a, b). This zone
once lay along the northern margins of a vast ocean (McKerrow et al. 1992) whose
anoxic water masses upwelled into shallow water carbonate lagoons. These early
Cambrian phosphorites typically reveal two modes of phosphatic replacement
(Brasier 1990). The first involves replacement of organic tissues (cf. Briggs et al.
2005), such as can be seen in the mucilaginous sheaths of putative fossil cyanobac-
terium Spirellus (Fig. 7a) as well as in putative fossil eggs, embryos and hatch-
lings of cnidarians (Bengtson and Zhao 1997; Koushinsky et al., 1999), some of
which may represent aphotic fungal microbes (Brasier et al., in press). The sec-
ond mode of phosphatization typically involves replacement of primarily calcar-
eous skeletons (cf. Lamboy 1993), as seen in early Cambrian Anabarites (see
Kouchinsky and Bengtson 2002; Feng and Sun 2003) and other small shelly fossils
(Porter 2004).
Patterns of phosphatization through time shows several interesting trends
(Tables 2 and 3; Brasier and Callow 2007; Dornbos 2009 this volume). Examples
from the c. 1000 Ma Torridonian, for example, as well as those from the >580 Ma
Doushantuo Formation, include clear evidence for preservation of cell walls, and
potentially for sub-cellular architecture (see Fig. 6a, b). By the start of the
Cambrian, however, such remarkable preservation becomes much harder to detect.
This is especially curious given the vast abundance of phosphatic deposits at this
time (e.g. Brasier 1992b). Nor is there evidence for high-quality cellular to sub-
cellular preservation in any marine, post-Ordovician phosphates known to us (other
than of resistant acritarch vesicles, see below).
Of relevance here may be a trend that also can be discerned in the kinds of
organisms that are phosphatized (Table 1). Both the Torridonian and Doushantuo
phosphatic assemblages consist largely of algal thalli, acritarch vesicles and
embryo-like cell clusters. The presence of well preserved algal thalli suggests rapid
phosphatization of the shallow seafloor within the photic zone (e.g. Xiao and Knoll
1999). Preservation of large masses of coccoid benthic algae, however, becomes
rare from the base of the Cambrian. Here, the remains of primary producers seem
to be confined to bundles of cyanobacteria-like sheaths and filaments, like those of
Spirellus (Fig. 7a; see also Zhegallo et al. 2000; Brasier and Callow 2007). By
middle and late Cambrian times, phosphatic preservation of photoautotrophs in the
Table 2 Tables 2 and 3 show the changing pattern of soft bodied preservation in phosphatic deposits through Earth history, and in particular, from the
534
Ediacaran Period and through the Phanerozoic. The tables show how well-preserved embryo-like structures, coccoid benthic algae and cyanobacteria and
microbial filaments are typical of Ediacaran to early Cambrian deposits. The shift towards the preservation of recalcitrant materials, faecal pellets and putative
zooplankton later in the Cambrian is suggested to be related to a deepening of the redox boundary within the water column, coeval with a similar lowering in
the sediment profile. This was followed by continued downwards and offshore migration of the phosphogenic zone through the Phanerozoic. From sources
cited in the text and in references
Subcellular structures Cell walls Eggs/Embroyos Microbial sheaths
Recent x x Laboratory simulations Cyanobacteria sheaths
of Artemia egg and from atolls. Trichet
larvae decay Gostling and Fikn 1997
et al. 2009
Neogene x x x Cyanobacterial sheaths
from NW Arabian
Sea. Rao et al. 2008
Paleogene x x x x
Cretaceous x Coccoids cells from x Cyanobacterial sheaths
Voronezh, Maleokina from Voronezh
2003 Maleokina 2003
Jurassic x Coccoid cells from x Filaments from Nusplingen
Nusplingen lagerstatle, lagerstatle. Briggs
Briggs et al. 2005 et al. 2005
Triassic x x x x
Permian x x x x
Carboniferous x x x x
Devonian x Mazuelloids (acritarchs), x x
Kremer 2005
Silurian x Mazuelloids from Holy x x
Cross mils of Poland
Kremer 2005
Ordovician x Mazuelloids (acritarchs), Markuelia from Vinni Fm. x
Kremer 2005 Donoghue et al. 2006a
M.D. Brasier et al.
Upper Cambrian x x Arthropod embryos from x
Duyun s. China Zhang
and Pratt. 1994
Middle Cambrian x x Markuelia from shallow
marine Georgina Basin
of Queensland Donoghue
et al. 2006a
Lower Cambrian Possible subcellular structures x Olivooides and Markuelia Filaments of the sheath
within embroyos from the L from L. Cam shallow Spirellus from L. Cam
Cambrian Kuanchuanpu Fm. water carbonates. Tal Fm, Brasier and
Donoghue et al. 2006a Bengtson and Zhao Callow 2007
1997
Neoproterozoic Possible organelles within embryos Coccoi cyanobacteria Possible animal embryos Cyanobacterial sheaths
from 580 Ma shallow marine and algal thalli from from 580 Ma shallow and filaments from
Doushantuo Fm. Hagadorn 580 Ma shallow marine Doushantuo 580 Ma shallow
et al, 2006 marine Doushantuo Fm. Hagadorn et al. marine Doushantuo
Fm. Hagadorn 2006 Fm Hagadorn

et al. 2006 et al. 2006
Mesoproterozoic Possible algal nuclei or | Coccoid and filamentous x Cyanobacterial sheaths
plasmolysed cyanobacterial cyanobacteria and from lacustrine
cell contents from lacustrine algae from lacustrine Torridon Group of
Torridon Group of Scotland Torridon Group of Scotland. Brasier
Brasier and Callow 2007 Scotland. Brasier and Callow 2007
and Callow 2007
Paleoproterozoic x x x x
Archean x x x x
535
Table 3 See Table 2 caption
536
Faecal pellets Biominerals Unmineralized arthropods Other Metazoan tissues

th
Recent Lab experiments on lobster √ Various arthopods in 16 x
faecal pellets (Mcllroy century cesspits of York.
pers Comm.) UK McCobb et al. 2004
Neogene √ √ Insects from Riversteigh. x
Queenstand, Arena 2008
Paleogene √ √ Insects from Oligocene x
of Ronheim. Germany
Hellmund and Hellmund
1996
Cretaceous √ √ Ostracods and copepods Fish tissues from Sanatana
from Sanatana Fm Fm of Brazil Martill 1988
of Brazil, Wilkinson
et al. 2007
Jurassic √ √ x Squids from Oxford clay.
Allison 1988
Triassic √ √ Ostracods from Spitsbergen Bivalve soft tissues from
Weitschat 1983 Muschelkalk Klug 2005
Permian √ √ x Goniatite cameral membranes.
Polizotto et al. 2007
Carboniferous √ √ x Goniatite cameral membranes.
Polizotto et al. 2007
Devonian √ √ x x
Silurian x x
Ordovician √ √ Zooplankton crustaceans x
from deep water Orsten
biota Maas et al. 2006
Upper Cambrian Bundles of packaged √ Zooplankton crustaceans x
cyanobacteria from from deep water Orsten
deep water Orsten biota biota Maas et al. 2006
of Sweden, Brasier and
M.D. Brasier et al.
Callow 2007
Middle Cambrian Faecal strings from Mt Molluscs. SSFs and problematica Arthropod integument Burgess Shale Gut contents
Cap Fm, Butterfield common Porter 2004 from shallow marine from Burgess Shale
2001 Georgina Basin. Butterfield 2002
Walossek et al 1993
Lower Cambrian x Molluscs. SSFs problematica in Arthropods from shallow x
shallow water limestones from water Comley Limestone
around the world Bengtson of Shropshire. Siveter
et al. 1990 et al. 2001
Neoproterozoic x Cloudina and Sinotubulites x x
from shallow marine latest
Ediacaran Dengying Fm. Feng
et al. 2003
Mesoproterozoic x x x x
Paleoproterozoic x x x x
Archean x x x x
537
so-called ‘Orsten biotas’ is largely restricted to rare clots of putative cyanobacterial

material (Fig. 7b, c). Here the filaments can be compressed and distorted in a way
consistent with metazoan faecal processing (Butterfield 2001). Benthic algal or
microbial remains preserved in phosphate are seldom seen or reported after this
date, with the exception of a few filaments (e.g. Trichet and Fikri 1997; Rao et al.
2000; Maleokina 2003).
Trends in the preservation of giant spiny acritarchs are equally curious.
Acritarchs like those from the Doushantuo Formation appear almost globally in
the mid Ediacaran (Vidal 1990; Tiwari and Knoll 1994) but are barely known
through the Cambrian to Ordovician. They then ‘reappear’ in some Silurian and
Devonian phosphate deposits, where they are known as mazuelloids or muel-
lerisphaerids (Zhou et al. 2001; Kremer 2005). Their morphology compares with
that of resting-cysts like Baltisphaeridium, a Paleozoic acritarch of widely
assumed pyrrhophyte affinity and phytoplanktonic mode of life (Kremer 2005).
The much larger size of these phosphatized acritarchs (c. 300 µm) has accordingly
been attributed to high levels of nutrients in the water column (Zhou et al. 2001;
Kremer 2005), though this planktonic interpretation is open to question (Butterfield
2007).
We also draw attention to the limited time span over which embryo- or egg
capsule-like structures are preserved in phosphate through time (Table 2 and 3).
They appear in the middle Ediacaran of South China (Hagadorn et al. 2006; Yin
et al. 2007) and remain common in the earliest Cambrian phosphatic deposits
(Koushinsky et al. 1999; Donoghue et al. 2006b; Pyle et al. 2006) but then dwindle
to a few records in the middle and late Cambrian and the early Ordovician (Cheng
and Liu 2004; Donoghue et al. 2006a), with later examples largely restricted to
large, priapulid-like Markuelia. This decline is interesting because laboratory
experiments show that real animal embryos can be fairly resistant to decay (e.g.
Martin et al. 2000; Raff et al. 2006).
Phosphatic preservation of small arthropods, including putative zooplankton,
likewise shows distinctive patterns (Tables 2 and 3). They first appear in the lower
Cambrian of England (Siveter et al. 2001) and become widespread within middle
to late Cambrian phosphates from Sweden (Maas et al. 2006), Newfoundland
(Walossek et al. 1994), Siberia (Müller et al. 1995) and China (Dong et al. 2005).
Younger marine deposits typically lack remarkably preserved small arthropods,
however, despite major phosphatic deposits in the Permian (e.g. Piper and Link
2002), the Cretaceous (e.g. Maleokina 2003) and to a lesser extent the Jurassic (e.g.
Allison 1988; Wilby et al. 1996). Phosphatized small arthropods are found, however,
within lacustrine sediments of Cretaceous to Miocene age (e.g. Bate 1972; Müller
1985; Park and Downing 2001). The rather poor quality of preservation in most
Phanerozoic phosphatic sediments (see below) is not inconsistent with phospho-
genesis taking place fairly slowly at the sediment–water interface, or at greater
depth in the sediment, so that organic materials have degraded before being encased
by phosphate.
Prior to widespread disruption by animal activity across the Ediacaran–

Cambrian transition, the locations and mechanisms of phosphatic preservation
appear to have been significantly different from those observed today. Firstly, it
is predicted that the phosphorus-rich redox boundary layer of the early oceans is
likely to have been much shallower and much sharper (Figs. 1 and 8), making very
early phosphatization possible within the shallow photic zone (Fig. 8). This, and
the associated scarcity of benthic grazers and burrowers, can together explain
the preservation of benthic algae and other photic-zone flora and fauna (e.g.
Xiao and Knoll 1999). From near the start of the Cambrian, however, increasing
oxygenation of the upper water column by both nekton and zooplankton (Signor
and Vermeij 1994; Logan et al. 1995; Butterfield 2007) and of the sediment
surface by bioturbation (McIlroy and Logan 1999) is likely to have forced the
phosphogenic zone downward, not only through the water column but also
deeper into the sediment (Fig. 1). Shallow bioturbation will also have lowered
the pH within the upper mixed layer, encouraging CaCO3 dissolution, raising
Ca2+ levels and increasing Ca-phosphate saturation states yet further (Dr. G.
Shields, pers. comm. 2007).
Fig. 8 Model contrasting Ediacaran to early Cambrian settings where cellular preservation occurs
in phosphate (numbers 1 to 8, outlined below) with the limited range of Cretaceous to modern
settings, including deep slope phosphorites (asterisk at left). This demonstrates the effects of the
Cambrian explosion upon the phosphorus cycle. Ediacaran to Cambrian examples studied are as
follows: 1–2, Doushantuo Formation of China, Khybsugul phosphorite of northwest Mongolia,
Tal Formation of India. 3, Soltanieh Formation of Iran, Dengying Formation of China. 4, Fara
Formation of Oman. 5–7, Chapel Island Formation of Newfoundland. 8, Torridon Group of
Scotland, St John’s Group of Newfoundland. From sources in text and references
4 Siliciclastic (Ediacara-type) Preservation
‘Siliciclastic’ preservation is here used to refer to the style of preservation best-

known from the macrofossils that are commonly known as ‘the Ediacara biota’,
including, Dickinsonia (Figs. 9a and 10a; Brasier and Antcliffe 2008), Charnia
(Fig. 9b; Gehling et al. 2005; Antcliffe and Brasier 2007), Rangea (Fig. 11a) and a
diverse array of related forms analysed in detail by Brasier and Antcliffe (2009).
Such fossils are widely reported from around the world and are typically regarded
as impressions made by macroscopic, flexible, soft-bodied organisms that came to
be preserved beneath event beds, such as storm sands and volcanic ashes (Narbonne
2005; Droser et al. 2006; Fedonkin et al. 2007).
The earliest example of this type of three-dimensional preservation of soft-
bodied organisms within siliciclastic sediments include the unusual ‘string of
beads’ markings on bedding-planes, Horodyskia, of possible protistan-grade (Dong
et al. 2008), which are reported from the 1500 Ma Belt Supergroup (Fedonkin and
Yochelson 2002). The Ediacaran Period witnessed the greatest abundance of this
style of preservation (see below), whereas similar environments from later
Phanerozoic successions typically lack comparable soft-bodied impressions.
Whatever the nature of the taphonomic window, it appears to have narrowed during
the Cambrian. Late Ediacaran examples are scarcer but include the discoidal
Nimbia structures of Crimes and McIlroy (1999) from Norway, Beltanelliformis
markings from England (McIlroy et al. 2005), while rare Cambrian examples
include petalonamaean-type fossils described by Hagadorn et al. (2000) from the
Lower Cambrian of Nevada, and medusae impressions from the Upper Cambrian
of Wisconsin (Hagadorn et al. 2002). Post-Cambrian examples are even more rare
and are of highly limited diversity and include the possible cnidarians from the
Ordovician of Morocco (Samuelsson and Butterfield 2001; Alessandrello and
Bracchi 2003), the enigmatic worm-like organisms from the Devonian of New York
(Conway-Morris and Grazhdankin 2005) and possible medusoid cnidarians from
the Cretaceous (Bell et al. 2001).
Ediacaran fossils preserved within siliciclastic sediments are distributed across
a remarkably wide range of facies that, unfortunately, show rather limited temporal
and geographic overlap (see Grazhdankin 2004). Each taphofacies also tends to
preserve its own distinctive assemblage of fossils, further compounding the problem.
Consequently, it can appear difficult to state whether changes in the biota seen from
one region to another are the result of taphonomic and facies difference alone, or
due to the evolution of the creatures themselves.
Three main types of Ediacaran preservation–lower surface, upper surface and
within-bed (Figs. 9, 10a and 11a) can be distinguished. Rapid cohesion or cementa-
tion of the lower bed of sediments is the mode of preservation typically found across
the Avalon terrane (e.g. England and Newfoundland). Most examples of this kind are
dated to between 575 and 555 Ma (e.g. Brasier and Antcliffe 2004; Narbonne 2005).
Such preservation (Fig. 9b) is accompanied in most cases by Pompeii-like smothering
of frondose fossils beneath layers of waterlain volcanic ash. With fossils like
Fig. 9 Laser scanned images of Ediacara biota preservation of soft bodied macrofossils, showing
the difference between lower- and upper surface preservation of wrinkle-marked sediment layers.
(a) Lower-surface type preservation of Dickinsonia costata here preserves the form of its top
surface topography on the lower bedding surface of a slab from the Rawnsley Quartzite (c. 555 Ma),
Ediacara sheep station, Flinders Ranges, South Australia. (b) Upper-surface type preservation of
the holotype of Charnia masoni here preserves the form of its bottom surface topography, on the
upper bedding surface of fine grain volcanic tuffs from the Maplewell Series (c. 560 Ma),
Charnwood Golf Course, Leicestershire, England. Scale bar 1cm for (a) and (b)
Charnia, Charniodiscus and Bradgatia, the bottom surface was, then, mainly pre-
served as negative impressions made by the organism as it lay against the substrate
(see Brasier and Antcliffe 2009). Such fossils often show some degree of transport
by bottom currents. Interestingly, however, these frondose organisms clearly lived
well below the photic zone, as shown by the evidence for deposition on volcanoclastic
talus slopes well below storm wave base. This means that the wrinkle-marked or
‘elephant-skin’ top surfaces with which they are often associated (e.g. Bailey 2002)
are likely to have been made by microbes of a heterotrophic or chemoautotrophic
nature rather than by photoautotrophs like cyanobacteria (Brasier et al., in press).
Fig. 10 Details showing the nature of preservation of the Ediacara biota in association with
ancient microbial mats, here from lower-surface type preservation. (a) Preservation of Dickinsonia
costata on the under surface of a rock slab, here shown as a optically inverted digital image to
indicate how the fossil and the surrounding seafloor may have looked before its burial by sand.
Note the undulose and pustular structures of inferred microbial origin that not only surround but
also underlie the structur, showing that the fossil was extremely thin. From lower bedding surface
of a slab from the Rawnsley Quartzite (c. 555 Ma), Ediacara sheep station, Flinders Ranges, South
Australia. From Callow & Brasier (2009). (b) Close up of such a surface directly adjacent to a
mould of Dickinsonia costata, showing both parallel and entwined microbial filaments replaced
by pyrite (arrow). From lower bedding surface of a slab from the White Sea area of Russia
(c. 555Ma). From Callow & Brasier (2009). Scale bar 1cm for A and 1mm for (b)
Upper surface preservation takes the form of negative moulds on the base of the
overlying bed, and is best known from South Australia (Gehling 1999) and the
White Sea region of Russia (Grazhdankin 2004). Both assemblages are dated to
about 558–550 Ma (Martin et al. 2000). In these rocks, it is usually the top surface
Fig. 11 Standard photographic images of further kinds of preservation of Ediacaran soft tissue.
(a) Within-bed type preservation of Rangea schneidehorni, here preserves its three dimensional
surface topography (arrow) within a slab of the Kuibis Quartzite from Namibia (c. 550 Ma), from
the Hans Pflug Collection, Geological Survey, Windhoek, Namibia. (b) Bottom surface of a slab
of quartz sandstone bearing the intertwined impressions (arrow) of possible filamentous microbial
or algal impressions known as ‘Arumberia’, from the Masirah Bay Formation (c. 600 Ma), Kufai
Dome, Huqf mountains, central Oman. Scale bar 2cm for (a) and (b)
of an organism like Dickinsonia, that is preserved (Fig. 9a and 10a; Gehling et al.
2005; Brasier and Antcliffe 2008), though positive casts of lower surfaces of less
resistant organisms or structures are also known (Narbonne 2005). Such upper
surface preservation has at times been attributed to the presence of tissues of great
durability (Wade 1968; Seilacher 1992) perhaps like that of modern lichens
(Retallack 1994, but see also Waggoner 1995). A more favoured suggestion,
explored below, is that the fossils were preserved by microbial mats that formed a
kind of ‘death mask’, maintaining selective aspects of external shape (Gehling
1999; Gehling et al. 2005; Narbonne 2005; Droser et al. 2006; Mapstone and
McIlroy 2006).
In South Australia, the sedimentary layers beneath these Ediacaran fossils were
at one time interpreted as a muddy seafloor laid down during relatively quiet condi-
tions at mainly subtidal depths (e.g. Goldring and Curnow 1967). Further studies
have shown, however, that surfaces preserving Ediacara biota often lack mud.
Instead, they typically display a wrinkled texture (Fig. 10a; often called ‘elephant
skin texture’) like that seen on modern microbial mats (Gehling 1987, 1991;
Seilacher 1999; Noffke et al. 2001). Associated features typically include pustules,
over-steepened ridges, current-induced folding, contortion and tearing, suspended
quartz grains, and concentrations of authigenic minerals such as mica in the upper
layers and pyrite beneath (see Hagadorn and Bottjer 1997, 1999; Noffke et al. 2001,
2002). These mats may also have aided preservation by trapping and binding of
sediment (Narbonne 1998; Gehling 1991, 1999; Noffke et al. 2001).
Well-preserved material from the White Sea region of Russia includes surfaces
that were once covered, and locally surrounded, by a mat of filamentous, pyrititized
microbes (Fig. 10b; see also Fedonkin and Waggoner 1997; Gehling 1999; Steiner
and Reitner 2001; Dzik 2005; Grazhdankin 2004; Gehling et al. 2005). In South
Australia, Newfoundland and the Ukraine, comparable surfaces are usually iron-
stained, presumably owing to the oxidation of this pyrite to haematite (e.g. Gehling
1999). Rapid preservation of soft-bodied fossils from these regions have therefore
been attributed to early formation of a death mask of pyrite (Fig. 10b; see Dzik
2003; Gehling et al. 2005) and/or to the early growth of authigenic clay minerals
and mica (Hagadorn and Bottjer 1997; Mapstone and McIlroy 2006) soon after
burial. Preservation of Ediacaran fossils within the Khatyspyt Formation of Siberia
shows some parallels (Dzik 2005) but here, preservation is due to early lithification
by calcium carbonate. A popular hypothesis for upper layer preservation, therefore
involves this cohesive mat of filamentous microbes (perhaps sulfur-oxidizing,
beggiatoan bacteria) upon the seafloor, typically with sulfate-reducing bacteria
thriving just beneath the surface. That sulfate-reduction took place on a massive
scale from the Ediacaran to late Cambrian is clearly confirmed by the sulfur isotope
record (e.g. Shields et al. 1997; Hurtgen et al. 2005). Sulfate-reducers were then
able to produce a thin, post mortem layer of pyrite, especially after the organism
was smothered by an influx of sand. Sand from the underlying beds could then be
mobilized upwards to cast the fossil from below (e.g. Dickinsonia in Gehling et al.
2005, fig. 2).
Cohesive microbial mats of this kind survived into the Cambrian in places (e.g.
Bailey et al. 2006). Their progressive disruption by new metazoan activities has
been used to explain the scarcity of similar preservation at later times in the
Phanerozoic (e.g. Allison and Briggs 1991; Bottjer et al. 2000). Microbial mat
preservation cannot, however, explain the increasing number of observations in
which such a death mask was not involved. Examples of such within-bed preservation
of macrofossils are well seen in sandstones from the Nama Group of Namibia
(Fig. 11a), dated to about 549–542 Ma. Here, soft-bodied fossils such as
Pteridinium, Rangea and Ernietta are typically preserved as three-dimensional
moulds and casts within the sandstone layer itself. Within-bed preservation of
soft-bodied organisms is also known from various taxa in Australia (Glaessner and
Wade 1966), the White Sea (Grazhdankin 2004; Dzik 2005), south-western USA
(Hagadorn and Waggoner 2000) and Newfoundland (Narbonne 2004). This has led
to the controversial suggestion that such organisms may have lived infaunally
(Grazhdankin and Seilacher 2002; but see also Narbonne 2005). It is important to
emphasize here that the disappearance of within-bed preservation during the
Cambrian cannot be explained by the effects of Phanerozoic bioturbation alone.
This is because suitable substrates (well sorted and micaceous quartz arenites with-
out bioturbation) remained common from this time onward; examples of this are
legion from lower Cambrian quartzites of Avalonia and Baltica. Excellent within-bed
preservation of soft-bodied organisms within siliciclastic sediment beds is also a
puzzle because such shallow-water sandstones from near-shore, oxidising, silici-
clastic settings are generally found to have very low preservation potential for
organic materials at later times. One possibility worth exploring, therefore, is that
silica levels in the ocean were still high because of the negligible influence sponges
and the absence of radiolarians at this time. Low pH and Eh in surface layers (see
Fig. 1) then allowed early silicate (including phyllosilicate) cementation before the
body walls had any chance to decay.
Recent discoveries of preserved microbes from bedding planes in argillaceous
rocks of Ediacaran age (Callow and Brasier 2009a; Callow and Brasier, 2009b)
have highlighted the potential for the preservation of a variety of microbes in a
style similar to that of macrofossils during the Ediacaran. Detailed impressions
and moulds of filaments and discoids can occur in high densities on siliciclastic
bedding-planes and may constitute an important and hitherto unrecognized style
of microbial preservation in ancient siliciclastic rocks (Callow and Brasier 2009a,
Callow and Brasier 2009b).
Unusual cohesiveness of sediments may also be used to explain enigmatic struc-
tures called Arumberia (Glaessner and Walter 1975) and Aspidella (see Gehling
et al. 2000), both largely confined to the Ediacaran Period. Arumberia has been
reported from numerous sections around the world at this time, including Australia,
France, England and Newfoundland (Bland 1984; McIlroy et al. 2005) and Oman
(herein). This fossil comprises gently curved or linear subparallel markings, typi-
cally preserved as epichnial grooves or hypichnial ridges. Such markings can cover
bedding-planes for hundreds of square kilometres in Oman (Fig. 11b). In Australia,
they were first interpreted as the remains of a bag-shaped organism (Glaessner and
Walter 1975) but later reinterpreted as abiogenic hydraulic structures caused by
turbulent flow (Brasier 1979). Arumberia is most typically seen on the bottom
surfaces of storm event beds (Mapstone and McIlroy 2006) and seems to have been
enhanced by the presence of a cohesive substrate stabilized by microbial mats
(McIlroy and Walter 1997; McIlroy et al. 2005). New material from the Masirah
Bay Formation of Oman shows that, while the markings clearly reflect the flow of
bottom currents, they can overlie each other or be intertwined in different direc-
tions (Fig. 11b). This suggests that some or all of these lines represent the
remains and impressions of long bundles of organic filaments. At one locality in
the Longmyndian of England, interwoven carbonaceous filaments some 50mm
diameter are preserved in mudrocks from about the same stratigraphic level as
Arumberia (Fig. 13b; see also Peat 1984, Callow and Brasier 2009a). This suggests
that Arumberia structures arose from microbially stabilized substrates somewhat
akin to those indicated by pyritized filaments around Dickinsonia from the White
Sea region (Fig. 10b) but without the formation of extensive pyrite.
Arumberia markings can be associated with circular impressions called
Aspidella, both in Australia (Mapstone and McIlroy 2006) and in Avalonia (McIlroy
et al. 2005; Narbonne 2005). Aspidella has recently been upgraded from a fossil of
dubious biogenic origin to an all-encompassing name for discoid impressions
(Gehling et al. 2000). Some Aspidella may indeed represent the attachment sites of
Ediacaran fronds but others seem likely to be microbial (e.g. Grazhdankin and
Gerdes 2007) and algal impressions or even abiogenic sedimentary structures
(Jensen et al. 2002). Whatever the cause of these circular markings, their sharp
three-dimensional preservation on successive stacks of sedimentary laminae seems
to be largely absent from Phanerozoic marine sandstones and mudrocks.
In summary, the Ediacara-type biota is preserved across a remarkably wide
variety of habitats (Fig. 12) in ways that are barely seen since then (Callow &
Brasier 2009b). This pattern of preservation can best be explained by early cohesion
and lithification of sedimentary laminae on or just beneath the seafloor, before com-
paction could erase all topographic expression.
Fig. 12 Model contrasting the wide range of Ediacaran environments where soft-bodied organ-
isms can become preserved in situ within siliciclastic or calcareous sediments (numbers 1 to 7,
outlined below) with the general lack of such preservation throughout the Phanerozoic. The disap-
pearance of this kind of preservation is here attributed to slower sediment lithification and rising
levels of oxygenation on the seafloor after the Cambrian explosion. The examples are as follows:
1, Charnian Supergroup volcanoclastics of England, and similar rocks of the Conception Group in
Newfoundland (c. 580–555 Ma). 2, Longmyndian Supergroup of England and Drook Formation
of Newfoundland showing microbial preservation. 3, Khatyspyt Formation of Siberia, and
Dengying Formation of South China with calcareous preservation (c. 560–545 Ma). 4, Shuram
Formation of Oman. 5, Masirah Bay Formation of Oman. 6, Rawnsley Quartzite of Flinders
Ranges, South Australia, White Sea biota of Russia (c. 560–550 Ma); Nama Group of Namibia
(c. 550–542 Ma). 7, St John’s Group of Newfoundland. From sources in text and references
5 Carbonaceous Film (Miaohe-type) Preservation
Preservation of macrofossils as compressions and carbonaceous films is well known

from Proterozoic mudrocks (see Hofmann 1994; Steiner 1994; Zhu et al. 2000). The
~1.9 Ga, possible alga or bacterium Grypania is perhaps the first known example
(Han and Runnegar 1992), and Proterozoic fossils such as Chuaria circularis and
Tawuia are also typical of this style of preservation (see Hofmann 1994; Steiner
1994; Zhu et al. 2000; Dutta et al. 2006). By Ediacaran times, such assemblages
commonly contain disc-shaped macroscopic fossils such as Beltanelloides (Fig. 13a).
Fig. 13 (a) Black shale bedding-plane showing clusters of macroscopic, carbonaceous discs of
Beltanelloides sorichaevi, which show concentric wrinkles and folds. From the latest Ediacaran
Pusa Shale (c. 545 Ma), Montes de Toledo, central Spain. The field of view is 15cm.
(b) Petrographic thin-section of shales bearing darker layers packed with abundant entwined car-
bonaceous filaments. From the Lightspout Formation, Longmyndian Supergroup (c. 556 Ma),
Shropshire, England (see Callow and Brasier 2009a). Scale bar 400 mm
Once regarded as eukaryote cells or cell colonies, many of these rounded fossils
have been reinterpreted as the compressed envelopes of prokaryote colonies, perhaps
like those of living cyanobacterium Nostoc (Steiner 1994; Steiner and Reitner 2001;
Xiao et al. 2002, but see also Hofmann 1994). Bedding-planes many tens of square
metres across can be packed with such carbonaceous compressions during the
Ediacaran period, as for example from the Miaohe Formation of China (Xiao et al.
2002), the Pusa Shale of Spain (Fig. 13a; Brasier et al. 1979), the Chapoghlu Shale
within the Soltanieh Formation of Iran (Ford and Breed 1973). It is suggested that
in some settings, similar vesicles can be preserved in three dimensions and infilled
with sediment (Nemiana; see Fedonkin 1990; Hofmann 1994). Interestingly, such
giant vesicles tend to disappear from levels above the Precambrian–Cambrian
boundary.
Petalonamaean organisms such as Charnia can also be preserved as carbona-
ceous films, as for example in the carbonate hosted assemblages of arctic Siberia
(Grazhdankin et al. 2008). Elongate carbonaceous ribbons and filaments are also
common in the Ediacaran Period (Fig. 13b; e.g. Hofmann 1994). Best known of
these is the Miaohe assemblage from the Doushantuo Formation of China, with
over twenty taxa of putative algal remains (Xiao et al. 2002). Ribbon-like compres-
sions of Vendotaenia and Tyrasotaenia are found from the Precambrian–Cambrian
boundary interval in both Europe and Newfoundland (Urbanek and Rozanov 1983;
Peat 1984; Landing et al. 1988; Vidal and Moczydlowska 1992; Callow and Brasier
2009a). Indeed, carbonaceous preservation reaches a peak during a global anoxic
event at this time (Brasier 1992a; b; Kimura and Watanabe 2001; Schröder and
Grotzinger 2007). Higher in the Cambrian, simple algal fossils continue to appear
alongside carbonaceous compression fossils of the Chengjiang biota (such as
arthropod cuticles, Gabbott et al. 2004; Hou et al. 2004) and they can range well
into the middle Cambrian (e.g. Briggs et al. 1993; Yang and Zhao 2000).
Carbonaceous ribbons with transverse markings have also been found in several
Ediacaran assemblages (Peat 1984; Hofmann 1994; Sun 1994; Fedonkin 2003).
These have sometimes been interpreted as the remains of invertebrate fossils, perhaps
even of bilaterians (but see Steiner 1994; Xiao et al. 2002). The first carbonaceous
remains of likely animal and possible bilaterian origin are the organic-walled tubes
of Sabellidites from the latest Precambrian and basal Cambrian of Newfoundland
and the east European Platform (Urbanek and Rozanov 1983; Gnilovskaya 1996).
Simple carbonaceous ribbons known as Vendotaenia are known from around the
world during the Ediacaran and have been suggested to be among of the most abun-
dant of organisms from this interval (Cohen et al. 2009).
Several factors appear to have allowed the frequent preservation of carbona-
ceous compression fossils during Ediacaran times. In a world before burrowers and
grazers, microbial mats were able to colonize the shallow seafloor during intervals
of relatively clay-rich input, directly leading to carbonaceous preservation (Schieber
1986). By the Early Cambrian, when bioturbation and scavenging were becoming
more widespread, such preservation begins to disappear. Real carbonaceous mats
are not seen, for example, in either the lower Cambrian Chengjiang biota of south
China (e.g. Babcock et al. 2001; Gabbott et al. 2004; Hou et al. 2004) nor in the
middle Cambrian Burgess Shale-type biotas of North America, though strands of

algal material occur in both. These famous invertebrate lagerstätte were favoured
by rapid accumulation of clays and silts beneath poorly oxygenated water masses,
somewhat below wave base (Fig. 14). Such stagnant conditions were then able to
help retard the rates of microbially-induced decay (see Allison and Brett 1995;
Butterfield and Nicholas 1996; Hagadorn 2002; Butterfield 2003; Gaines et al.
2005). This ‘Burgess Shale type’ of preservation is rarely observed after the
Cambrian and, even then, is typically limited to a few isolated specimens (Hagadorn
2002; Butterfield 2003).
A complicating factor in studies of carbonaceous preservation is that in many
cases, the original organic materials can be transformed by diagenetic reactions into
secondary phases such as clay minerals or pyrite (Fig. 10b; Schieber 2002; Gabbott
et al. 2004; Page et al. 2008). The high fidelity pyritization of carbonaceous films,
via the activities of sulfate-reducing bacteria (Grimes et al. 2001), is known to be
associated with Ediacaran fronds and discs and can be recognized by the presence
of ancient pyritic laminae (e.g. Mapstone and McIlroy 2006) or by the remains of
pyritized filaments themselves (Fig. 10b). Pyritized microbial mats and stromato-
lites are common across the Precambrian–Cambrian boundary level (e.g. the Tal
Formation of India) but thereafter largely disappear from the fossil record. The high-
quality pyritization of carbonaceous materials is known sporadically from the
Fig. 14 Model contrasting the range of Ediacaran to early Cambrian showing carbonaceous pres-
ervation in marine ‘black shales’ (numbers 1 and 2, outlined below) with the near absence of such
preservation in the marine realm from the Cretaceous onwards. The disappearance of this kind of
preservation is here attributed to more efficient recycling and remineralization of organic materials
and rising levels of oxygenation on the seafloor since the Cambrian. The examples studied include
the following: 1, Miaohe biota of South China (c. 550 Ma); Vendotaenia, Tyrasotaenia and
Sabellidites biota of Baltica and Avalonia (c. 550–540 Ma); Beltanelloides biota of the Pusa Shales
in central Spain, and of Chapoghlu Shale, Soltanieh Formation, Iran (c. 545 Ma); Chengjiang biota
of South China (c. 525 Ma); Burgess Shale of British Columbia (c. 500 Ma). 2, Athel silicilyte of
South Oman. From sources in text and references
Phanerozoic, as for example in sulfide-rich, reducing settings of the Maotianshan

Shales at Chengjiang, China (e.g. Gabbott et al. 2004) or Beecher’s trilobite bed in
New York State (Briggs et al. 1991). In the majority of cases however, Phanerozoic
pyritization is largely confined to the steinkern infills within isolated reducing
microenvironments such as shelly fossils or burrows, as seen in the Lower Cambrian
of southeast Newfoundland and the East European Platform (e.g. Urbanek and
Rozanov 1983; Landing et al. 1988, 1989), which preserve no details of primary
soft-tissue morphology or cellular structures. In other Phanerozoic examples,
organic materials can be replaced during volatilization reactions by diagenetic
aluminosilicate phyllosilicates, as for example in the Burgess Shale and Paleozoic
graptolites (Page et al. 2008).
There is a clear contrast between the Proterozoic and Ediacaran intervals, where
the carbonaceous-pyritic preservation of microbial and/or algal materials abounds,
and Cambrian examples such as the Burgess Shale, which teem with animal fossils
but where algal or microbial remains appear to be more rare. A number of factors
can be identified which appear to help explain these observations. It can be argued
that in a world without burrowers and grazers and with a shallow redox boundary,
buried carbonaceous materials were not effectively scavenged by metazoans and
more rapidly reached potential zones of preservation within the sediment. This
resulted in a greater potential for unmineralized and carbonaceous materials to
enter the rock record (Fig. 1). By the early Cambrian, when bioturbation and scav-
enging were becoming more widespread, such preservation begins to disappear,
because all available organic materials are rapidly remineralized by metazoan and
microbial processes. Settings where comparable preservation could occur were
favoured by rapid smothering of sediment and the accumulation of clays and silts
beneath poorly oxygenated water masses below wave base, as for example in the
lower Cambrian Chengjiang biota (e.g. Babcock et al. 2001; Gabbott et al. 2004;
Hou et al. 2004) and the Middle Cambrian Burgess Shale (Fig. 14). Such poorly
mixed and stagnant conditions may have mimicked those of the Ediacaran. In these
cases it is commonly pyritic veneers and aluminosilicate layers that are preserved,
rather than carbonaceous films themselves, which are rarely seen after the Middle
Cambrian (see Hagadorn 2002).
6 Carbonate (Tufa-like) Preservation
Biological activities such as photosynthesis have major influences upon the aqueous
carbonate cycle. For instance, as a consequence of the uptake of CO2 by cyanobacteria
or algae during photosynthesis, the saturation state of carbonate in surrounding
fluids is increased and this can lead to carbonate precipitation on microbes and their
sheaths as well as on and within algal thalli (cf. Lowenstam 1981; Pentecost and
Spiro 1990). While cyanobacterially-induced microbial mats may have been
present from as early as 2.9 Ga (Noffke et al. 2008), the earliest widely accepted
evidence for calcification of microbes is known from the c. 2.5 Ga Campbelrand
Supergroup of South Africa (Kazmierczak and Altermann 2002; Altermann et al.

2006), where putative cyanobacterial filaments can be found within euhedral dolo-
mite crystals, possibly in association with minute aragonite needles. Photosynthetic
microbes might have been involved in the construction of earlier Archean stromato-
lites, although no body fossils are yet known (e.g. Sakurai et al. 2005). Oxygenic
cyanobacteria were arguably among the major players in facilitating the so-called
‘Great Oxidation Event’ (c. 2.5 Ga), which further suggess the existence of
cyanobacteria by this time (see also Konhauser et al. 2009).
A curious feature of the early fossil record is the poverty of evidence for calci-
fied microbes and cyanobacterial sheaths before ~800 Ma (Riding 2006b), in
spite of their abundance in diagenetic silica deposits. By the late Ediacaran to
earliest Cambrian, however, there was a bloom in the abundance of marine micro-
bial and algal carbonate fossils (e.g. Angulocellularia, Renalcis, Epiphyton,
Girvanella; Grant et al. 1991; Wood 1998; Riding 2006a, b), which may relate to
the evolution of carbon dioxide concentrating mechanisms (CCMs) within
cyanobacteria (Riding 2006b). Some of these calcified cyanobacteria are known
to occur alongside the first putative metazoan carbonate skeletons, including
tubular Cloudina (Fig. 15c; Germs 1972), goblet-shaped Namacalathus (Fig. 15b;
Grotzinger et al. 2000), and the large, modular, possibly colonial fossil Namapoikia
(Wood et al. 2002), not long before the Ediacaran-Cambrian boundary (c. 549 Ma,
Grotzinger et al. 1995). Such microbial carbonates reached an acme during the
early to middle Cambrian and declined thereafter (Riding 2006b). The late
Ediacaran-Cambrian also saw rapid seafloor carbonate cementation in the form of
thrombolites and stromatolites with isopachous laminae, giant oolite grains, carbon-
ate flat pebble breccias, edgewise conglomerates, ‘molar tooth’ carbonate, carbonate
crystal fans, tidal flat ‘tufas’, botryoids and fabric-retentive early diagenetic dolo-
stones (e.g. McCarron 1999; Pratt 1998; Grotzinger et al. 2000; Shields 2002;
Sumner and Grotzinger 2004). This range of features can be seen across a wide
region, from Namibia, Oman, Siberia, Mongolia and China to North and South
America (e.g. Mattes and Conway-Morris 1990; Turner et al. 1993). This suite
of features supports high levels of carbonate ion saturation and raises the pos-
sibility that abiogenic carbonate precipitation was also able to take place widely
onto abiogenic, as well as microbial and/or metazoan templates (i.e. ‘tufa-style’
precipitation).
Some of these indicators of supersaturation (e.g. calcified microbes) are still
found today in settings of unusual geochemical conditions (Fig. 15a). Around many
springs for example, carbonate-saturated waters reach the surface and lead to rapid
deposition of calcium carbonate crusts (tufa) around microbial filaments and even
around chitinous larval skeletons (Fig. 15a), bryophytes, tree stumps, or even
around man-made objects (e.g., Brasier et al. 2009). It is generally accepted (e.g.
Arp et al. 2001; but see also Riding 2006a, b) that the role of organisms in this style
of precipitation is limited to the provision of a suitable substrate plus the involun-
tary promotion of crystal nucleation by extracellular polymeric substances (Turner
and Jones 2005). The subsequent oxidation of the carbonaceous substrates leaves
behind only their external moulds in carbonate minerals.
Fig. 15 Examples demonstrating biologically controlled biomineralization, biologically induced

mineralization and secondary tufa-like calcification in the Ediacaran and Quaternary. (a) Petrographic
thin-section through calcified cyanobacterial filaments (cf. Rivularia sp., white arrow) which have
induced the precipitation of calcium carbonate by the photosynthetic absorption of carbon dioxide.
These dark filaments alternating with abiogenically calcified organic cases of chironomid midge
larvae which appear as open vesicles (red arrow). From Quaternary tufa at Zemeno, Greece, image
courtesy of Dr A.T. Brasier. (b) Longitudinal section through the calcified fossil Namacalathus
showing the irregular thickness of the wall (red arrow) and stalk, from the late Ediacaran of Namibia
(c. 549 Ma). This is here interpreted as having formed in a similar way to the external calcification
of the vesicular midge larvae in (a): by ‘tufa-like’, abiogenic calcification. (c) Transverse sections
through thin calcareous shell layers of Cloudina from the latest Ediacaran Ara Group of Oman,
representing real biologically controlled mineralization. Scale bar is 1mm for (a)–(c)
Such ‘accidental’ calcification relies largely upon pH shifts and hence is favoured
by raised alkalinity (due to degassing or removal of CO2), often from the effects of
turbulence rather than photosynthesis (e.g. Pentecost and Spiro 1990). Interestingly,
our studies of calcification from Namibia show features in Namacalathus (Fig. 15b;
but not in Cloudina, Fig. 15c) consistent with the tufa-like encrustation of an otherwise
unmineralized organism. A comparable tufa-like phenomenon may, we suggest, also
explain the curious calcification of tiny canal-like spaces between soft tissues of
Ediacaran fronds in South China (Xiao et al. 2005). These anomalous carbonates
could therefore be the product of a world in which pCO2 was falling from previously
very high levels (Riding 2006a), though other factors may have been involved,
such as high surface temperature, the absence of crystal inhibitors, an abundance of
calciphilic molecules such as aspartic acid on the seafloor (see Morse 2003) and, of
course, widespread sediment stagnation (Fig. 1; Shields et al. 1997).
Biologically controlled (enzymatically mediated) calcium carbonate biomineralization
seemingly began with Cloudina in the latest Ediacaran and expanded dramatically at
the base of the Cambrian, coincident with the appearance of the major modern animal
phyla, changing the nature of the marine carbonate cycle and the fossil record forever
(Fig. 1, 16; Brasier et al. 1996; Bengtson 2004). One of the consequences of this evo-
lutionary event was that these biominerals acted to greatly reduce the overall saturation
state of carbonate in the oceans (Shields 2002). These first biominerals were often
extremely thin and delicate (e.g. Brasier 1990), allowing their ready dissolution and
thereby raising the local pH of pore waters within the mixed layer. Together, these
processes resulted in a new kind of carbonate, that of pink nodular bioclastic ‘griotte’
limestones, which first appear not far above the base of the Cambrian in Avalonia and
Siberia (e.g. Brasier et al. 1992). Interestingly, we have observed that such limestones
became progressively more offshore in their distribution (e.g. Devonian ‘griotte’ and
‘cephalopodenkalk’, Jurassic ‘ammonitico rosso’) and then largely disappeared after
the evolution of coccolithic-foraminiferid carbonate oozes in the Cretaceous.
Fig. 16 Model contrasting the restricted range of Ediacaran environments where carbonate biom-
inerals are preserved in marine settings (number 1) with the almost ubiquitous presence of biom-
ineral preservation in modern times (asterisks). The first appearance of carbonate biominerals on
carbonate platforms is here attributed to the relatively high levels of carbonate saturation states in
such settings in the Ediacaran. Examples of early carbonate biominerals studied by us are as fol-
lows: 1, Nama Group carbonates of Namibia; Ara Group carbonates of Oman; Dengying carbon-
ates of South China; olistostrome carbonates of central Spain; Reed Dolomite of California
(c. 550–540 Ma). From sources in text and references
7 Conclusion
The need for taphonomic studies of the fossil record during the Ediacaran and
Cambrian periods is of fundamental evolutionary importance and can hardly be
overstated. We argue here for an unexpected bias in the fossil record towards
remarkable preservation of organic remains on the Ediacaran and Cambrian
seafloor. Conditions appear to have been especially favourable to the rapid lithogen-
esis of surface sediments at this time. This is especially well seen in the changing
nature, and decreasing quality, of phosphatic preservation of soft tissues through
time. Soft-bodied preservation in sandstones also began to decline after the onset
of the ‘Cambrian explosion’. Comparable trends can be traced, such as the reducing
incidence and quality of silicification, calcification and carbonaceous-pyritic
preservation of organic matter within marine sediments, especially after the
Cambrian. Suitable conditions seem to have become more and more restricted in
the marine world, though they continued to occur in a few non-marine settings.
Many of these taphonomic changes can be accounted for by a progressive
depression in the depth of the redox boundary and changes in alkalinity, both within
the water column and within the sediment, forcing the zones of lithification both
deeper and later, effectively closing up several important taphonomic windows. The
fact that comparable modes of preservation (especially of cellular features) are seldom
seen again within the marine realm is suggestive of a trigger related to the ‘Cambrian
explosion’. In other words, this inferred ‘fall’ in redox, pH and the zone of mineral
lithogenesis was a likely consequence of major evolutionary innovations taking
place, notably in metazoan respiratory recycling of carbonaceous matter through the
activities of bioturbation, grazing and zooplankton. Of prime importance here is the
directly visible and potentially testable impact of increasingly deep and complex
metazoan bioturbation upon both seafloor porosity and biogeochemistry (see
Brasier 1992b; McIlroy and Logan 1999; Jensen et al. 2005). Carbonate, phosphate
and silica were also being removed at an increasing rate from the water column by
new skeleton builders such as molluscs, brachiopods and sponges. Conceivably,
these organisms chose their biominerals in response to their ready availability as
solutes within the still ‘primitive water masses’ across the Precambrian–Cambrian
boundary interval (see Brasier 1986). Such removal also helped to prevent car-
bonate-, phosphate- and silica-saturated fluids from rapidly building up their concen-
trations to levels approaching the saturated conditions found so widely in earlier
surface sediments. Extreme oscillations in carbon isotopic signatures of
Neoproterozoic carbonates and their falling amplitudes during the Cambrian (e.g.
Lindsay et al. 2005) could likewise reflect the growing influence of bioturbation
upon the carbon cycle, reducing the impact of methane and its oxidized products.
We argue, therefore, that the nature of fossil preservation was progressively
transformed by the impact of a biological revolution across the Precambrian–
Cambrian transition. Given the rather remarkable quality of the Ediacaran fossil
record, we conclude that the ‘Cambrian explosion’ is likely to have been a real
biological revolution of very great magnitude.
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Chapter 16
Mass Extinctions and Changing
Taphonomic Processes
Fidelity of the Guadalupian, Lopingian,
and Early Triassic Fossil Records
Margaret L. Fraiser, Matthew E. Clapham, and David J. Bottjer
Contents
1 Introduction........................................................................................................................... 570
2 Previous Understanding of Biases in the Middle Permian to Early
Triassic Fossil Record........................................................................................................... 572
2.1 End-Guadalupian Extinction and Lopingian Aftermath.............................................. 572
2.2 End-Permian Mass Extinction and Early Triassic Aftermath...................................... 573
3 Methods................................................................................................................................. 574
4 Results................................................................................................................................... 575
4.1 Guadalupian–Lopingian Lazarus Effect...................................................................... 575
4.2 Patterns in Permian Silicification................................................................................. 577
4.3 Early Triassic Lazarus Effect....................................................................................... 580
4.4 Patterns in Early Triassic Silicification........................................................................ 583
5 Conclusions........................................................................................................................... 585
References................................................................................................................................... 586
Abstract The biotic crisis of the Middle Permian through Early Triassic is unmatched
in the Phanerozoic in terms of taxonomic diversity losses and paleoecological reor-
ganization. However, the potential taphonomic bias from post mortem diagenesis
for this crucial time has not been evaluated. We assessed the quality of the fossil
record during this interval by quantifying the number of Lazarus taxa using our own
database, data available in the Paleobiology Database and previous compilations.
M.L. Fraiser (*)
Department of Geosciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53203, USA
M.E. Clapham
Department of Earth and Planetary Sciences, University of California Santa Cruz, 1156 High
Street, Santa Cruz, CA 95064, USA
D.J. Bottjer
Department of Earth Sciences, University of Southern California, Los Angeles,
CA 90089-0740, USA
570 M.L. Fraiser et al.
We also quantitatively tested for paleoecological differences between silicified versus

non-silicified faunas. Herein we report that there is no major taphonomic bias due to
skeletal mineralogy or fossil preservation affecting the Middle and Late Permian fos-
sil record, but that aragonite-shelled molluscs may exhibit a significant Lazarus effect
during the Induan. We propose that a variety of mechanisms affected the fossil record
of the Paleozoic/Mesozoic transition, including ocean chemistry, paleobiology of the
examined groups, and human influences on taxonomic and sampling practices.
1 Introduction
Mass extinctions are geologically short intervals of time when biodiversity losses
are significantly elevated above background rates of extinction (e.g. Jablonski
1986a; Sepkoski 1986; Flessa 1990). They are a prominent feature of the fossil
record and, along with the rise and fall of the three great evolutionary faunas,
shaped the Phanerozoic biodiversity curve (Raup and Sepkoski 1982; Sepkoski
1981, 1984; Courtillot and Gaudemer 1996). Mass extinctions are also important
agents of macroevolutionary change because they eliminate successful groups of
organisms and create new evolutionary opportunities for previously minor groups
(Gould and Calloway 1980; Jablonski 1986a, b, 2001, 2005; Raup 1986, 1994;
Erwin 2001; Bambach et al. 2002). A complete understanding of the evolutionary
role of a mass extinction must include more than just an analysis of the taxonomic
crisis because the effects of mass extinctions extend beyond the biodiversity
losses: the aftermaths may be as important as the extinctions themselves because
of the new ecological patterns arising from survivors that interact in new ways in
less crowded ecological niches (Droser et al. 1997, 2000; Erwin 2001; Bambach
et al. 2002; Jablonski 2001, 2002).
Proper interpretation of the duration, magnitude, and causes of mass extinctions
and the nature of the survival and recovery of organisms during their aftermaths is
contingent upon accurate reconstruction of taxonomic and ecological changes.
Artifacts of sampling methods or taxonomic practice can obscure the real trends
(Sepkoski 1986; Flessa 1990), whereas taphonomic biases inherent in the geologic
record, such as mode of organism preservation (Schubert et al. 1997), rock volume
(e.g., Crampton et al. 2003), and preferential loss of organisms with aragonitic shell
mineralogy (e.g. Cherns and Wright 2000) may also influence observed patterns.
Such taphonomic biases may have obscured the true biotic patterns during the
Permian–Triassic extinction and its aftermath. These potentially confounding
effects have been inferred from the abundance of Lazarus taxa – taxa that temporar-
ily disappear from the fossil record but reappear later unchanged (Flessa and
Jablonski 1983) – and from a decrease in preservation by silicification (Erwin and
Pan 1996; Schubert et al. 1997; Twitchett 2001). Lazarus taxa may be an indicator
of the quality of the fossil record if the phenomenon reflects a failure of certain
organisms to be preserved through taphonomic effects such as the Signor–Lipps
effect, outcrop area bias, paleolatitudinal sampling bias, or reduced preservation
16 Mass Extinctions and Changing Taphonomic Processes 571
quality (Signor and Lipps 1982; Allison and Briggs 1993; Erwin and Pan 1996;
Smith and McGowan 2007). Lazarus taxa abundance may also be due to biological
factors such as reduced population size (which may also affect the chance of sam-
pling a taxon) or reduced geographic range and migration to refugia (Jablonski
1986a,b; Kauffman and Harries 1996; Wignall and Benton 1999; Twitchett 2001;
Rickards and Wright 2002). Taxonomic uncertainty can cause an apparent Lazarus
effect (Wheeley and Twitchett 2005).
Herein we test two aspects of the quality of the fossil record during the
Guadalupian, Lopingian, and Early Triassic. The end-Guadalupian and end-Permian
extinctions marked the end of the Paleozoic (Fig. 1) and heralded major changes in
benthic marine ecology (e.g. Fraiser and Bottjer 2007; Clapham and Bottjer 2007a, b),
but several studies have proposed that taphonomic processes make it difficult to
extract real ecological patterns during these key intervals in evolutionary history
(e.g. Erwin and Pan 1996; Twitchett 2001). First, we quantified the number of Lazarus
taxa among several key taxonomic groups, as an increased number of Lazarus taxa
may indicate reduced preservation quality. Second, a potential source of bias in the
fossil record for this interval, changes in preservation via silicification, was tested
by quantifying the proportion of silicified fossil collections, comparing the alpha
diversity of silicified and non-silicified (preserved as molds and casts) collections,
and assessing the number of taxa exclusive to silicified collections. Silicification is
important because it allows fossils to be acid-etched and freed from calcareous
matrix, often preserving very fine morphological details and improving ease of iden-
tification by taxonomists (e.g. Holdaway and Clayton 1982). It can also preserve a
more faithful record of the original diversity and abundance within an assemblage
(Cherns and Wright 2000; Wright et al. 2003, Butts and Briggs, this volume). Results
of this test will reveal any temporal trends in silicification and the extent to which
silicified faunas preserve a higher fidelity record. Together these tests document the
Fig. 1 Geologic timescale of Middle Permian (Guadalupian), Late Permian (Lopingian), and Early
Triassic stages. Ch = Changhsingian, Ind = Induan. The lower panel shows the per-capita extinction
rates (Foote 2000) for rhynchonelliform brachiopods, bivalves, and gastropods in each stage based
on data from Clapham et al. (2009) (Permian invertebrates), Chen et al. (2005) (Early Triassic
brachiopods), Gastrobase (Early Triassic gastropods), and the Paleobiology Database (Early
Triassic bivalves and gastropods). The per-capita extinction for rhynchonelliform brachiopods is
undefined in the Induan because no genera cross both bottom and top boundaries of the stage
taphonomic quality of the Permian–Triassic fossil record in greater detail and elucidate
the impact of temporal trends of taphonomic bias on the records of the end-Guadalupian
extinction, the end-Permian extinction, and their aftermaths.
2 Previous Understanding of Biases in the Middle

Permian to Early Triassic Fossil Record
2.1 End-Guadalupian Extinction and Lopingian Aftermath
The end-Guadalupian extinction, at the end of the Middle Permian (Guadalupian

Series), was the first phase of the two-stage taxonomic crisis during the Permian–
Triassic interval (Jin et al. 1994; Stanley and Yang 1994). Initial estimates suggested
that biodiversity loss during the end-Guadalupian event was severe with as many as
55–60% of all marine invertebrate and fusulinid genera going extinct (Stanley and
Yang 1994). However, more recent studies have shown that extinction rates were
actually not elevated during the end-Guadalupian interval among most marine
invertebrate groups, including brachiopods, bivalves, and gastropods (Shen et al.
2006; Clapham et al. 2009). Nevertheless, the end-Guadalupian extinction remains
an especially severe event for fusulinids (Stanley and Yang 1994; Yang et al. 2004).
The potential causes of the extinction are unclear, and there may not be a need to
invoke serious perturbations given the negligible invertebrate extinctions.
Environmental changes during the Guadalupian–Lopingian interval include the
Emeishan flood basalts (Wignall 2001), possible climate cooling (Isozaki et al.
2007), and the onset of deep-marine anoxia (Isozaki 1997). Despite the minimal
effects on global invertebrate biodiversity, environmental stress during the
Guadalupian–Lopingian interval caused profound changes in the habitat distribu-
tion of bryozoans during the Lopingian (Powers and Bottjer 2007), shifts in the
relative abundance of rhynchonelliform brachiopods and molluscs in offshore habi-
tats (Clapham and Bottjer 2007a, b), and a dramatic reduction in the number and
size of reefs in the Wuchiapingian (Weidlich 2002; Weidlich et al. 2003).
The potential influences of taphonomic bias on the apparent severity of the end-
Guadalupian extinction were first investigated by Stanley and Yang (1994). They
applied three tests and concluded that the end-Guadalupian extinction peak did not
result from a poor Lopingian fossil record. The preferential extinction of large,
complex fusulinid genera, the inconsistency between observed patterns of extinction
and predicted Signor–Lipps effects, and a strong excess of originations relative to
extinctions in the Wuchiapingian and early Changhsingian all suggest that tapho-
nomic biases only had minor effects on the end-Guadalupian extinction (Stanley
and Yang 1994). However, other taphonomic effects, including changes in the abun-
dance of silicified fossil collections or reductions in preserved rock volume, may
have exacerbated the severity of the end-Guadalupian extinction without producing
a spurious Signor–Lipps effect or completely masking the Lopingian radiation.
2.2 End-Permian Mass Extinction and Early

Triassic Aftermath
The end-Permian mass extinction, approximately 252 million years ago, was the
largest biotic crisis of the Phanerozoic (Bambach et al. 2004; Henderson 2005) with
78% of marine genera going extinct (Clapham et al. 2009). For up to 5 million years
during the Early Triassic aftermath of the end-Permian mass extinction, benthic
marine paleocommunities were characterized by low biodiversity and low ecologi-
cal complexity compared to pre-extinction Permian and later Triassic paleocom-
munities (e.g. Fraiser and Bottjer 2005b; Lehrmann et al. 2006). Macroevolutionary
changes in benthic marine ecology, such as a shift from primarily non-motile organ-
isms to self-mobile taxa and a switch from rhynchonelliform brachiopod-dominated
to bivalve-dominated paleocommunities, were triggered by the end-Permian mass
extinction (Bambach et al. 2002; Wagner et al. 2006; Fraiser and Bottjer 2007).
Sedimentological and geochemical evidence indicate that much of the latest
Permian through the Early Triassic had an atmosphere with elevated CO2 and low
O2, and an ocean rich in H2S and depleted in O2; these conditions were ultimately
linked to extensive volcanism and the supercontinent configuration of Pangea (e.g.
Wignall and Twitchett 1996; Wignall 2001; Berner 2004; Grice et al. 2005; Huey
and Ward 2005; Sephton et al. 2005).
It has been reported that a large portion of Early Triassic taxa are Lazarus taxa
(Batten 1973; Erwin and Pan 1996; Twitchett 2001). For example, there are esti-
mates that 69% of gastropod genera are Lazarus genera during the Griesbachian
(Erwin 1996), and that 90% of sponge families are Lazarus taxa during all stages
of the Early Triassic (Twitchett 2001). Though the Early Triassic Lazarus phe-
nomenon heretofore had been examined for gastropods and sponges only (e.g.
Erwin 1996; Erwin and Pan 1996; Twitchett 2001, Wheeley and Twitchett 2005),
it has been implied that the Lazarus effect was very large for all groups of skele-
toned benthic marine invertebrates during the Early Triassic (e.g. Twitchett 2001;
Erwin 2006).
An absence of faunas preserved by silicification has been proposed as a major
cause of the Early Triassic Lazarus phenomenon and for the apparent delayed
biotic recovery following the end-Permian mass extinction (Erwin 1996, 2006;
Erwin and Pan 1996; Kidder and Erwin 2001). This hypothesis is based on studies
indicating that silicified faunas have a higher fidelity of fossil preservation than
non-silicified faunas preserved as casts and molds (Cherns and Wright 2000;
Wright et al. 2003). Furthermore, it has been proposed that the post-Paleozoic
fossil record suffers from a taphonomic “megabias” because of low numbers of
silicified faunas compared to the Paleozoic (Schubert et al. 1997). Previous
studies of the fidelity of the fossil record following the end-Permian mass extinc-
tion have focused on only one group of benthic marine organisms (e.g. gastro-
pods, Erwin and Pan 1996; or echinoids, Smith 2007), or have examined data
from the Triassic period as a whole (Smith 2007), obscuring any processes that
may have been unique to the aftermath of the end-Permian mass extinction.
The extent of silicification during the Early Triassic has not been quantified
previously, and the characteristics of silicified faunas have not been statistically
compared to those of non-silicified ones.
3 Methods
We compiled a database of Roadian (Middle Permian) through Anisian (Middle

Triassic) rhynchonelliform brachiopod, bivalve, gastropod, and demosponge fossil
occurrences. This was used to examine two additional taphonomic metrics that test
the fidelity of the Permian–Triassic fossil record and its potential influence on the
end-Guadalupian and end-Permian extinctions. The dataset includes (1) more than
53,321 Permian marine invertebrate fossil occurrences, including records of all
marine invertebrate groups, from 9863 collections (the database used in Clapham
et al. 2009); (2) Triassic gastropods modified and updated from Gastrobase, a data-
base of published occurrences of gastropod genera at the stage and substage levels
for the Permian and Triassic periods (http://www.earth.cardiff.ac.uk/people/sum-
maries/GASTROBASEdoc.htm); (3) Triassic bivalves and sponges, and Anisian
brachiopods, from the Paleobiology Database (www.paleodb.org); and (4) Early
Triassic rhynchonelliform brachiopods (Chen et al. 2005). Though the PBDB is not
flawless, it is the most complete database available for comparing benthic marine
organisms from the Lopingian, Early Triassic, and Middle Triassic. Taxonomic
assignments were corrected when necessary and possible.
First, the number of rhynchonelliform brachiopod, bivalve, gastropod, and
sponge Lazarus taxa in each stage from the Roadian to Anisian was quantified to
test for poor preservation, especially in the Wuchiapingian stage immediately fol-
lowing the traditional end-Guadalupian extinction interval and the Induan and
Olenekian stages following the end-Permian extinction (Appendix A). The signifi-
cance of differences between the proportions of Lazarus taxa between stages was
determined using a two-tailed t-test.
Second, the number of Permian and Early Triassic silicified collections was
tallied using the Clapham et al. (2009) database, 211 Paleobiology Database
collections, and 358 additional Induan and Olenekian collections culled from the
primary literature to determine whether a reduction in silicification, particularly
due to the loss of the rich record from western North America, affected diversity
and extinction (Appendix B). Included in the analyses were benthic marine inver-
tebrates from level-bottom marine communities; planktonic, nektonic, and reef
collections were excluded in the Triassic but not in the Permian data. Species
richness (alpha diversity) of each silicified collection was determined and com-
pared to the richness of non-silicified collections. The number of brachiopod,
bivalve, and gastropod genera unique to silicified collections was also quantified
to determine the influence of silicification on large-scale compilations of taxo-
nomic diversity.
4 Results
4.1 Guadalupian–Lopingian Lazarus Effect
During the Guadalupian and Lopingian, the prevalence of Lazarus taxa varied
significantly among different taxonomic groups. At the genus level, a substantial
percentage of gastropod taxa in a given stage, up to 38% of the total genus rich-
ness, are actually Lazarus taxa (Fig. 2a). In contrast, only 20–25% of all bivalve
genera (Fig. 2b) and 18–20% of all rhynchonelliform brachiopods (Fig. 2c) are
Lazarus taxa. Lazarus abundance is calculated by dividing the number of Lazarus
taxa by the total diversity (Lazarus taxa plus taxa sampled within the stratigraphic
interval) in each stage. Despite the pronounced difference between clades, the pro-
portion of Lazarus taxa within most clades typically exhibits little variation (Fig. 2).
There was no statistically significant change in the percentage of gastropod Lazarus
taxa from the Roadian through Wuchiapingian stages (varying between 33.3% and
38.6%). Likewise, the number of bivalve Lazarus taxa remained statistically
unchanged at 19.6–25.2% from the Roadian to the Wuchiapingian. Both aragonitic
bivalves and those with a calcite shell layer (pterioids, pectinoids, and mytiloids)
displayed statistically similar patterns and there is no systematic variation in the
number of Lazarus genera between the two mineralogies, suggesting that the num-
ber of Lazarus taxa is most strongly controlled by the abundance of a group rather
than its skeletal mineralogy. Lazarus taxa accounted for 18.4–20.8% of total rhyn-
chonelliform brachiopod diversity in the Roadian–Capitanian interval, with a
significant decrease to 10% in the Wuchiapingian (Z = 3.03, p = 0.002). However,
in notable contrast to the other groups, demosponges exhibit dramatic variation in
the percentage of Lazarus taxa in a given stage (Fig. 2d). Lazarus genera account
for 50.9% of all present or inferred sponges during the Wuchiapingian, but only
10.2% in the Wordian and 17.0% in the Changhsingian.
Although there are few changes in the percentage of Lazarus taxa from the Roadian
to Wuchiapingian, all investigated groups have substantially fewer Lazarus genera
in the Changhsingian stage (Fig. 2). The percentage of gastropod Lazarus taxa
decreased from more than 37% in the Wuchiapingian to only 18.8% in the
Changhsingian (Z = 2.73, p = 0.006), bivalve Lazarus taxa decreased from 19.6%
to only 4.9% (Z = 2.90, p = 0.003), rhynchonelliform brachiopods decreased from
10% to 0% in the Changhsingian (Z = 4.85, p < 0.001), and demosponges from
50.9% to 17.0% (Z = 3.69, p < 0.001). However, this dramatic reduction in the
percentage of Lazarus taxa does not imply a pronounced increase in the quality of
the fossil record or the fidelity of sampling during the Changhsingian. Rather, it
reflects edge effects due to the severe taxonomic impact of the end-Permian extinc-
tion. Because so many Permian genera became extinct (51% of gastropod genera,
65% of bivalves, and 96% of rhynchonelliform brachiopods, with the remaining
brachiopods disappearing in the Griesbachian), the likelihood of Permian taxa
occurring in the Triassic was greatly reduced and the latest Permian Changhsingian
a 90
80
Genera
70
60
50
40
Lazarus Genera (%)
50
40
30
20
10
b 120
100
Genera
80
60
40
Lazarus Genera (%)
Aragonitic
40 Calcitic
30
20
10
400
c
300
Genera
200
100
0
Lazarus Genera (%)
20
10
90
d 80
70
Genera
60
50
40
30
20
Lazarus Genera (%)
100
75
50
25
Roadian Wordian Capitanian Wuchiapingian Changhsingian Induan Olenekian Anisian
Fig. 2 Total (within-bin and Lazarus) diversity and percentage of Lazarus taxa for gastropods
(a), bivalves, with aragonitic and calcitic forms plotted separately (b), rhynchonelliform brachiopods
(c), and sponges (d) in Middle and Late Permian and Early Triassic stages. Error bars indicate
95% confidence interval for Lazarus percentage
Stage has anomalously low numbers of Lazarus taxa compared to more typical
Permian values. For example, there are no rhynchonelliform brachiopod Lazarus
genera in the Changhsingian stage due to the extreme severity of the end-Permian
extinction event.
The striking stability in the percentage of rhynchonelliform brachiopod,
bivalve, and gastropod genera represented by Lazarus taxa during the Roadian–
Wuchiapingian interval, and especially across the end-Guadalupian extinction,
implies that the quality of the benthic invertebrate fossil record remained consis-
tent across the Guadalupian/Lopingian boundary. Demosponges may be an excep-
tion and the significant increase in Lazarus taxa across the end-Guadalupian
extinction, from 22.5% in the Capitanian to 50.9% in the Wuchiapingian (Z =
−3.49, p < 0.001), could either reflect poor preservation of sponges or small
sponge population sizes in the Wuchiapingian. The Wuchiapingian has few demo-
sponge occurrences compared to the well-sampled surrounding intervals; only 103
generic occurrences of sponges compared to 1,513 in the Capitanian and 223 in the
Changhsingian. In addition, the Wuchiapingian is a time of turnover or crisis in the
reef ecosystem, and the number of preserved reefs is low compared to the Wordian,
Capitanian, or Changhsingian (Weidlich 2002). Thus, the high number of sponge
Lazarus taxa is primarily a result of actual decreases in population size rather than
taphonomic biases due to poor preservation. The overall lack of substantial varia-
tion in the abundance of Lazarus taxa across the end-Guadalupian extinction is
consistent with the conclusions of Stanley and Yang (1994) that taphonomic biases
did not substantially influence the observed pattern of extinction during the end-
Guadalupian crisis.
4.2 Patterns in Permian Silicification
Although variations in Lazarus taxa abundance are not consistent with major
taphonomic biases during the Guadalupian–Lopingian interval, shifts in the amount
of silicification may have independently affected diversity patterns. Early diagenetic
silicification can preserve a higher fidelity record of a fossil assemblage because
of enhanced aragonite preservation (Cherns and Wright 2000; Wright et al. 2003,
Butts and Briggs, this volume), and temporal variations in the amount of silica-
replaced fossils have been argued to influence diversity patterns and extinction
estimates (Schubert et al. 1997). To evaluate the potential effects of silicification
on the end-Guadalupian extinction, we calculated the percentage of collections
with silica-replaced fossils in each Permian stage, quantified the difference in
alpha diversity between silicified and non-silicified assemblages, and counted the
number of genera that are uniquely found in silicified collections.
Diagenetic silica replacement is thought to be a common phenomenon during
much of the Permian, as exemplified by famous silicified localities from Thailand,
the Salt Range in Pakistan, and especially from the Glass and Guadalupe Mountains
in the United States, among others (e.g. Cooper and Grant 1972; Grant 1968, 1976).
However, the number of silicified fossil collections in each stage is actually quite
variable (Fig. 3); for example, 7.5% of the 1,280 Wordian collections contain silica-
replaced fossils whereas 18.1% of the 1,444 collections in the Capitanian have been
silicified. In contrast to the Guadalupian, silicification is much less widespread in
the Lopingian. Only 3.3% of the 1,241 Wuchiapingian collections and 1.5% of the
983 Changhsingian collections have been silicified, suggesting that the substantial
decline in the proportion of silicified fossils across the end-Guadalupian boundary
may contribute to apparent elevated extinction rates.
Collections with silica-replaced fossils also have consistently higher sampled
alpha diversity than non-silicified collections (Fig. 4). Note that overall mean alpha
20
Silicified Collections (% of total)
15
N = 1419
N = 1444
N = 455
10
N = 1241
N = 880
N = 1211
N = 1280
N = 983
5
N = 950
N = 354
N = 162
Assel Sak Art Kung Road Word Cap Wuch Chang Induan Olenek
Fig. 3 Percentage of fossil collections containing silicified fossils in each Permian and Early
Triassic stage. Assel: Asselian; Sak: Sakmarian; Art: Artinskian; Kung: Kungurian; Road:
Roadian; Word: Wordian; Cap: Capitanian; Wuch: Wuchiapingian; Chang: Changhsingian; Ind:
Induan; Ole: Olenekian. The n values indicate the total number of collections from each stage
35
Silicified Collections
Non-Silicified Collections
30
Mean Species Richness
25
20
15
10
Roadian Wordian Capitanian Wuchiapingian Changhsingian Induan Olenekian
Fig. 4 Mean species richness for collections containing silicified fossils (solid line and square
symbols) and non-silicified fossils (dashed line and open circle symbols) in Middle Permian, Late
Permian, and Early Triassic stages. Error bars are 95% confidence intervals
diversity values are a function of the nature of reporting in the published literature
and are not representative of actual alpha diversity; many papers are taxonomic
descriptions and only consider a single taxonomic group and record one or a few
new species of interest from a given locality. In particular, the large discrepancy
between silicified and non-silicified alpha diversity in the Middle Permian is pri-
marily a result of the large taxonomic lists reported from the extraordinarily large
silicified collections from west Texas. Nevertheless, apparent changes in sampled
alpha diversity, whether real biological phenomena or due to changes in the number
of taxa actually reported for a collection in published papers, still affect our percep-
tion of diversity and extinction in the fossil record. During the Roadian and
Wordian, mean silicified alpha diversity is 24.4 species and 14.6 species per collec-
tion, compared to only 3.0 and 3.65 species in non-silicified collections from the
same stages. The difference between silicified and non-silicified alpha diversity is
statistically significant during the Guadalupian, but not in the Lopingian stages (4.5
vs 3.95 species in the Wuchiapingian, p = 0.51; 5.95 vs 4.4 species in the
Changhsingian, p = 0.18). Although the difference in alpha diversity is not always
statistically significant, the consistently higher values in silicified collections may
have acted in conjunction with the significant decrease in the amount of silicifica-
tion to exacerbate apparent diversity loss and increase calculated extinction rates.
However, the major decrease in alpha diversity in silicified collections occurs from
the Roadian to Capitanian stages (Fig. 4), earlier than the traditionally recognized
end-Guadalupian extinction. There is a minor but significant decrease in silicified
alpha diversity across the Guadalupian/Lopingian boundary (7.4–4.5 species; p =
0.05) but non-silicified alpha diversity actually increases significantly (3.45–3.95
species, p = 0.02).
Although there were substantial changes in the extent of silicification during
the Permian, and silicification may preserve a better record of alpha diversity and
relative abundance (Cherns and Wright 2000; Wright et al. 2003), it is not clear to
what extent it affects global diversity patterns. If many genera are known exclu-
sively from silicified collections, silica-replacement may exert an important con-
trol on global diversity patterns. In contrast, if most genera from silicified
assemblages are also found in non-silicified assemblages, the implication is that
silicification itself is not important for reconstructing diversity. During the
Permian, the percentage of genera uniquely known from silicified assemblages in
a given stage is influenced by the percentage of collections that are silicified, and
can be as high as 23% of bivalves, 33% of brachiopods, and 60% of gastropods,
all during the Roadian Stage. However, overall only a small number of genera are
known only from silicified specimens, as many found in silicified collections from
one stage are then recorded from non-silicified assemblages at another time. Only
3.2% of Permian bivalves (6 of 190 genera) are exclusive to silicified collections,
while 17.4% of gastropods (31 of 178 genera, although several of those may be
known from non-silicified collections in the Carboniferous) and 12.9% of brachio-
pods (94 of 727 genera) are uniquely found in silicified assemblages. Total genus
richness is only 5–25% higher when silicified collections are included, compared
to the value obtained solely from non-silicified fossils. However, calculated
extinction and origination rates vary by no more than 5% if silicified collections

are excluded. These results indicate that silicification itself is not necessary for
preserving a good record of diversity during the Guadalupian–Lopingian interval
and that the severity of the end-Guadalupian extinction is not biased by changes
in silicification.
4.3 Early Triassic Lazarus Effect
Only 18.8% of gastropod genera during the Changhsingian and 26.9% during the
Anisian stage are Lazarus taxa, while 34.9% of Induan and 37.2% of Olenekian
gastropod diversity are Lazarus taxa (Fig. 2a). The differences between the propor-
tion of Lazarus gastropod genera from the Changhsingian to Induan is statistically
significant (Z = −2.00; p = 0.045) but the other differences are not significant at
p = 0.05. The proportions of gastropod Lazarus taxa are also lower than those previ-
ously published (Erwin and Pan 1996). Though the proportions of gastropod
Lazarus taxa during the Induan and Olenekian are similar to those of the Middle
Permian (Fig. 2), the predicted proportion of Lazarus taxa in the Induan would be
lower because of extinction edge effects, as in the Changhsingian when less than
20% of taxa were Lazarus genera. The proportion of bivalve Lazarus taxa was 22%
in the Induan and 11.3% in the Olenekian. The differences in the proportion of
bivalve taxa are not statistically significant between the Induan and Olenekian or
from the Olenekian to Anisian, but the change from the Changhsingian to Induan,
is (Z = −2.88, p = 0.004: Fig. 2b). Aragonitic bivalves had a higher proportion of
Lazarus taxa compared to calcitic taxa during the Induan (40% versus 13.3%), but
the difference is not significant due to the small sample size, especially of arago-
nitic taxa (Z = 1.82, p = 0.07). There was also little difference between aragonitic
and calcitic mineralogy during the Olenekian. The proportions of Lazarus arago-
nitic genera were significantly different between the Changhsingian and Induan and
the Induan and Olenekian (Z = −3.65, p < 0.001; Z = 2.01, p = 0.04). The proportions
of calcitic Lazarus taxa did not differ significantly between the Changhsingian
through Anisian stages. There are no rhynchonelliform brachiopod Lazarus genera
during the Early Triassic stages. One hundred percent and 95.8% of demosponge
genera were Lazarus genera during the Induan and the Olenekian, respectively,
while many sponges remained known only as Lazarus taxa in the Anisian.
4.3.1 Controls on Early Triassic Lazarus Taxa
Potential controls on the occurrence of Lazarus taxa during the Early Triassic
include taphonomic processes, sampling, environmental conditions, paleobiology
of the organisms, and taxonomic practices, or a combination thereof.
The Early Triassic Lazarus phenomenon among bivalves and gastropods may
have resulted from taphonomic bias related to their aragonitic composition.
Aragonitic shells typically dissolve during meteoric or burial diagenetic processes

during early diagenesis because aragonite is less stable than calcite at surface
temperatures and pressures, even during “aragonite seas” (e.g. Tucker and Wright
1990). These diagenetic processes may have been compounded by increased acid-
ity and CaCO3 undersaturation of seawater caused by elevated atmospheric CO2
levels during the Early Triassic (Berner 2004). Thus, the large proportion of ara-
gonitic Lazarus taxa could reflect post mortem taphonomic processes in a high
CO2 world. Similar processes have been proposed to explain Triassic–Jurassic
boundary patterns (e.g. Hautmann 2004; Hautmann et al. 2008a), and are observed
in the modern ocean and predicted for the future (e.g. Feely et al. 2004).
Alternatively, low levels and depth of bioturbation during the Early Triassic (e.g.
Twitchett 1999; Pruss and Bottjer 2004; Fraiser and Bottjer 2009, 2010) may have
buffered some shell dissolution during the Early Triassic. Shell dissolution is high
in areas with well-developed infaunal benthic communities because biogenic
reworking of sediments increases oxygen levels in the mixed layer and promotes
oxidative decay of organic matter, thereby increasing acidity near the sediment–
water interface and causing pore waters to become undersaturated with respect to
both aragonite and calcite (Aller 1982; Walter and Burton 1990). Sediment
reworking by infaunal organisms also disrupts mold space left after shells dissolve
(Cherns and Wright 2000). Even if after death benthic calcareous shells were dis-
solved on the seafloor in some regions due to a lowered carbonate saturation state
of seawater (Berner 2004; Feely et al. 2004), the reduction in bioturbating activity
that characterized much of the Early Triassic may have prevented molds from
being disturbed.
Sample size, either as a result of actual sampling effort or of true population size,
is another potential contributor to the Early Triassic Lazarus phenomenon. A good
correlation between a group’s abundance, the number of occurrences, and the num-
ber of Lazarus taxa can be observed in Middle Permian rhynchonelliform brachio-
pods, bivalves, and gastropods, confirming the importance of sampling on Lazarus
abundance. Reduced Early Triassic sampling between two well-sampled stages
tends to increase the number of Lazarus taxa. Very low levels of sampling in the
Early Triassic (378 Induan occurrences and 673 Olenekian occurrences of rhyncho-
nelliform brachiopods, gastropods, and bivalves) relative to the Changhsingian
(4,755 occurrences) and Anisian (2,439 occurrences) may be influenced by sam-
pling effort but more likely reflect reduced marine invertebrate abundance due to
environmental stress following the end-Permian mass extinction (e.g. Fraiser and
Bottjer 2007). A specimen of a Griesbachian Lazarus gastropod taxon was found
recently in a newly discovered Tethyan section (Wheeley and Twitchett 2005),
further highlighting that low numbers of some gastropod taxa contributed to the
Lazarus phenomenon (sensu Wignall and Benton 1999) and suggesting that more
sampling of Lower Triassic strata, especially in largely ignored regions, could aid
in finding missing gastropod taxa that migrated to refugia or that were low in abun-
dance. Future work on physiological and ecological characteristics of Lazarus
gastropod genera could determine the extent to which Early Triassic environmental
conditions contributed to the low numbers of certain gastropod taxa. The prevalence
of sponge Lazarus taxa is also likely tied to sampling; namely, the lack of reef sites
during the Early Triassic (a metazoan “reef gap”, Flügel and Stanley 1984).
Permian–Triassic sponge occurrences are strongly covariant with times of wide-
spread reef-building in the Wordian–Capitanian, Changhsingian, and Late Triassic.
Stages with low reef abundance between those reef episodes have many demo-
sponge Lazarus taxa – e.g. the Wuchiapingian (50.9%), Anisian (the beginning of
the Triassic reef recovery, but still with 53.3% Lazarus taxa), and to an extreme
degree the Induan and Olenekian. As the Early Triassic reef gap may have been due
to elevated atmospheric CO2 and ocean acidification that prevented metazoan reef
organisms from forming skeletons (Stanley et al. 2007), extinction-related environ-
mental factors may have contributed to the reduced sampling through reduced
population size.
Biological factors may have facilitated the Lazarus effect among some Early
Triassic taxa. Most of the aragonitic Induan Lazarus genera had infaunal or
semi-faunal lifestyles. During the end-Triassic mass extinction, aragonitic infau-
nal bivalves suffered greater extinctions than epifaunal bivalves (Hautmann
et al. 2008b), and it has been proposed that this pattern indicates a reduction in
primary productivity as epifaunal bivalves have physiological characteristics
that enabled them to fare better during conditions of reduced food availability
(McRoberts and Newton 1995). A decrease in primary productivity has also
been proposed for the Early Triassic (Twitchett 2001). It is unclear whether the
Lazarus pattern among Early Triassic bivalves resulted more from diagenetic
processes or from biological reasons, but both mechanisms were linked to Early
Triassic environmental conditions (elevated CO2). Furthermore, the reason that
the Lazarus effect among aragonitic bivalve taxa is more pronounced in Induan
versus Olenekian age strata is unknown. However, this temporal pattern supports
the argument for environmental conditions contributing to the Lazarus effect
because it could reflect an amelioration of some aspect of the global environ-
ment later in the aftermath.
Poor taxonomic practice is a plausible hypothesis to explain in part the Early
Triassic Lazarus phenomenon among some groups. For example, partial preserva-
tion has made it difficult to definitively identify some Early Triassic gastropod taxa
(Wheeley and Twitchett 2005). The small size of Early Triassic gastropods could
make it difficult to determine gastropod taxonomy; many Early Triassic gastropods
are microgastropods <1cm in height (Fraiser and Bottjer 2004; Fraiser et al. 2005),
and needles have been required to prepare them to expose areas for proper identifi-
cation (Batten and Stokes 1986). Some Middle Triassic gastropods have been incor-
rectly identified as Elvis taxa (Wheeley and Twitchett 2005), taxa that were
misidentified as having re-emerged after their presumed extinction, but are not
actually descendants of the original taxa (Erwin and Droser 1993). More accurate
gastropod taxonomy across the P/T boundary and into the Middle Triassic could
determine the extent to which the Lazarus effect among gastropods is real and
significant.
4.4 Patterns in Early Triassic Silicification
Contrary to previous reports that shell replacement by silica is absent among Lower
Triassic faunas (e.g. Erwin and Pan 1996; Kidder and Erwin 2001; Twitchett 2001),
5% of Early Triassic collections contain fossils preserved via silicification (Fig. 5).
Silicified Early Triassic faunas have been reported from Oman, China, and the
U.S.A. Although this value likely represents a maximum estimate due to the easily-
accessible literature on silicified faunas, the value is broadly similar to the proportion
of silicification in Permian stages, in the Lopingian in particular. Of the Early
Triassic benthic collections with preservation via silica replacement, 30% are from
Induan and 70% are from Olenekian age strata (Fig. 3). Olenekian U.S.A. collections
comprise 70% of the silicified collections.
Fig. 5 Preservation of Early Triassic fossils. (a) Silicified microgastropods, Virgin Limestone
Member, Moenkopi Formation. (b) Internal molds of microgastropods, Campil Member, Werfen
Formation. (c) Silicified Promyalina, upper member, Thaynes Formation. Scale in mm. From
D. Boyd collection. (d) Internal molds of bivalves (Unionites), Siusi Member, Werfen Formation
(Modified from Fraiser and Bottjer (2005a)
The mean alpha diversity of PBDB Early Triassic collections preserved via
silicification is 7.86 for Induan collections, 2.63 for Olenekian collections, and 4.19
for the series. An independent groups t-test of means indicates that the difference
between the mean alpha diversities of silicified Induan and Olenekian collections is
significant (t = 5.20, p < 0.0001). Non-silicified Induan collections have a mean
alpha diversity of 3.18, and Olenekian ones have a mean alpha diversity of 4.14
(Fig. 4). The mean alpha diversity for all Early Triassic collections preserved
as casts and molds is 3.67. The difference between the means for non-silicified
Induan and Olenekian collections is statistically significant (t = 2.50, p = 0.013).
The difference between means of silicified and non-silicified Induan collections is
statistically significant (t = 4.87, p < 0.0001), but there is no significant difference
between the means for silicified and non-silicified Olenekian collections (t = 1.49,
p = 0.14), or between the means for silicified and non-silicified Early Triassic
collections (t = 0.696, p = 0.49).
Fourteen gastropod genera (Ananias, Anomphalus, Bellerophon, Chartronella,
Coelostylina, Donaldina, Jiangxispira, Laxella, Naticopsis, Omphaloptycha,
Platyzona, Streptacis, Strobeus, and Worthenia) are found in Induan silicified col-
lections, but all but two of those (Jiangxispira, Laxella) also occur in non-silicified
collections at another time. No Olenekian gastropods are known exclusively from
silicified faunas. No Induan bivalve genera are known exclusively from silicified
faunas. At least eight bivalve genera (Elegantinia, Entolioides, Eumorphotis,
Leptochondria, Neoschizodus, Pegmavalvula, “Pleuronectites”, Placunopsis) are
known from Olenekian silicified collections, but Pegmavalvula is the only one of
46 Olenekian bivalves exclusively found in silicified localities throughout its entire
range. No rhynchonelliform brachiopods are known only from shells preserved via
silicification. Therefore, most Early Triassic genera are known from fossil casts
and molds.
Documentation of silicified fossil collections from Lower Triassic strata refutes
the hypothesis that there is a “complete absence of silicified faunas” during the
Early Triassic (Twitchett 2001). Silicified Induan and Olenekian collections are
rare in comparison to some Permian stages, but actually occur as frequently as
silicified collections in the Wuchiapingian or Changhsingian stages of the Late
Permian. There is no change in silicification across the Permian–Triassic boundary,
indicating that changes in preservation style are not the primary contributor to the
unusual Early Triassic record.
The statistically significant differences between silicified Induan and Olenekian
collections and between non-silicified Induan and Olenekian collections supports
previous findings that diversity increased through the Early Triassic (e.g. Schubert
and Bottjer 1995) and could be an indication of biotic recovery following the end-
Permian mass extinction. That there is no statistically significant difference
between silicified and non-silicified Olenekian collections does not support the
hypothesis that silicified faunas record more information than non-silicified ones.
Furthermore, Lazarus taxa have been found in non-silicified collections
(Hautmann and Nützel 2004). The statistically significant difference between silici-
fied and non-silicified Induan collections could reflect a real difference in the
amount of data preserved in silicified and non-silicified collections. However, 22%

of silicified faunas are from one recently discovered Griesbachian-age section in
Oman, and these collections have a mean alpha diversity of 8.5 that skews the mean
alpha diversity for Induan silicified faunas. When these collections are removed
from the analysis, there is no statistically significant difference between the mean
alpha diversities of silicified and non-silicified Induan collections. More sampling
of Lower Triassic sections around the world would probably lead to the discovery
of more silicified faunas.
Only a very small percentage of gastropod, bivalve, or brachiopod genera are known
exclusively from silicified collections, whether in the Permian or in the Early Triassic.
The impact of silicification, or the lack thereof, on global diversity compilations is
therefore minimal.
Differences between silicified and non-silicified collections were likely influ-
enced more by worker-introduced bias and not taphonomic processes. One source
of bias could potentially be the focus of many Early Triassic studies. Publications
of taxonomic lists from Lower Triassic strata commonly report only one higher
taxonomic group, e.g., rhynchonelliform brachiopods (Perry and Chatterton 1979),
ostracodes (Crasquin-Soleau and Kershaw 2005), or pectinoid bivalves (e.g. Newell
and Boyd 1995), even when other taxa have been collected in the field (D.W. Boyd,
pers. comm.). Furthermore, authors commonly report only higher taxa rather than
detailed lists of genera or species. Incompletely reported taxonomic lists mean that
the alpha diversities of both silicified and non-silicified Induan and Olenekian col-
lections are likely underestimates. Bias also could be introduced by the methods in
which data are collected (D.W. Boyd pers. comm.). If only silicified faunas are
searched for and collected from the field for analysis, any data from fossils that are
not silicified are omitted. It is important to note that the only known Smithian (early
Olenekian) collections are from non-silicified collections. Though silicified shells
are easily extracted from their encompassing matrix with weak acids (such as
hydrochloric or acetic acid), acids also cause the dissolution of any non-silicified
material in the sample. Incomplete and incorrectly entered data in the PBDB, i.e.,
preservation entered as silicification when fossils were not actually silicified, incorrect
and outdated taxonomy, and omitted publications, prevent many collections
and taxa (e.g., sponges) from being downloaded when certain searches are per-
formed. Outdated taxonomy, incomplete taxonomic lists, and under-sampling
likely exert a stronger influence on understanding of Early Triassic ecology than
taphonomic processes.
5 Conclusions
A full accounting of the effects of taphonomic biases during mass extinction inter-
vals is critical in any attempt to extract meaningful biological signals from the fossil
record during a biotic crisis and its aftermath. Changes in the fidelity or dominant
style of fossil preservation can have a substantial impact on the composition and
diversity of marine fossil assemblages, and it has been proposed, based on an abun-
dance of Lazarus taxa and a reduction in silicification, that such taphonomic
changes irreparably bias the fossil record of the Permian–Triassic mass extinction.
A new tabulation of the proportion of Lazarus genera in the major Permian–Triassic
taxonomic groups suggests that there was no major bias or change in taphonomic
style in the Late Permian but that aragonitic taxa (gastropods and some, primarily
infaunal, bivalves) may have suffered from reduced preservation in the Induan.
Comparisons between silicified and non-silicified faunas indicate there was little
change in the amount of silicification across the Permian–Triassic boundary;
regardless, silicification is unlikely to be a major taphonomic bias in global compi-
lations because few taxa are known exclusively from silicified collections.
Documentation of Lazarus taxa does not necessarily indicate that the fossil record
is biased. Indeed, taxon outages are a common phenomenon in the fossil record and
are caused by a variety of mechanisms. Rickards and Wright (2002) suggest that the
concept of a Lazarus taxon is not useful as a taphonomic indicator because it repre-
sents nothing more than a taxon’s low abundance during a given interval. The
Permian–Triassic pattern of Lazarus taxa documented here is partially consistent
with this concept; the Early Triassic Lazarus effect is a function of sampling effects,
biological and environmental factors, and actual taphonomic degradation.
Though more sampling and refined taxonomy will improve the reconstruction of
the end-Permian extinction and its unusual aftermath, our current understanding of
the Early Triassic fossil record likely reflects a primary ecological signal (to the
extent that any Paleozoic or Mesozoic fossil assemblage reflects a primary biological
signal) (Fig. 5). Taphonomy remains an important factor that must be assessed in
each fossil assemblage, but analysis of the Permian–Triassic record of Lazarus taxa
and silicification demonstrates that the fossil record of the end-Permian extinction
and the Early Triassic aftermath is not completely obscured by a taphonomic
megabias due to skeletal mineralogy or fossil preservation. Instead of being solely
an indication of the poor quality of the fossil record (e.g., Twitchett 2001; Smith
2007), Lazarus taxa could also provide clues about the environmental conditions
during deposition.
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Index
A Apex chert, 478–481, 501–505

Abrasion, 10, 40, 46, 50, 81, 89, 108, 151, Aragonitc botryoids, 398
183, 184, 253, 256, 271, 338, 339, Aragonite, 5, 20, 21, 23, 27–30, 42–44, 50,
343–345, 347, 352, 353, 355, 356, 51, 61, 65, 66, 69, 80–86, 89, 92–98,
358–363, 376, 377, 382–385, 403, 419 160, 185, 186, 340, 347, 386, 397,
Acanthuroids, 383 398, 413, 417–422, 424–427, 429,
Acervulinid facies, 359–362 532, 551, 577, 581
Acila divaricata, 46 Aragonite seas, 6, 97, 98, 108, 364, 398,
Acritarchs, 240, 440, 444, 458, 461–464, 425, 581
466, 470–473, 510, 525, 526, 528, Arbutus, 234
533, 534, 538 Archaeocyath sponges, 379, 393, 395
Acropora cervicornis, 377, 389, 395 Archean, 478–482, 535, 537, 551
Acropora palmata, 377, 388, 395 Arcoids, 88, 90
Adipocere, 297 Arcturus formation, 441, 445
Agaricia, 382 Argentina, 150
Agave, 227–231, 234 Aromatic alkoxy phenols, 205
Agnostoid trilobites, 118, 120, 160 Arthropod epicuticle, 206
Algaenan, 204, 211, 213, 238–240 Arumberia, 543, 545, 546
Algal blooms, 93, 95 Ashiya group, 150–152
Algal cysts, 238–240 Astartidae, 43–45, 47
Algal microborers, 339 Atmospheric pCO2, 7, 97, 400, 401
Aliphatic components, 200, 203, 206–208, Austin group, 441, 447
212–215, 233, 238–241
Aliphatic hydrocarbon, 202, 216
Al Jil formation, 90 B
Alpha diversity, 23–32, 37–39, 52, 56, 58, Bacteria, 9, 296, 299, 303, 417, 420, 437,
571, 574, 577–579, 584, 585 441, 442, 444, 447–449, 452, 453,
Alum shale, 53 461, 478–482, 492, 502, 504, 521,
Alveolinid facies, 359 530, 544, 549
Amber, 203, 208, 253 Bahamas, 82, 83, 388, 505
Ammonites, 88, 140–142, 145, 149, 154, Baltisphaeridium, 538
160–162, 165, 172, 182, 427, 441 Barium sulphate, 500
Ammonitico rosso, 553 Bear Gulch limestone, 440, 444, 445
Anomioidea, 42, 45, 47 Beekite, 88, 413, 414, 416
Anoxia, 52, 80, 92, 93, 95, 96, 252, Belemnites, 140, 146, 154, 169
300, 424, 572 Beltanelloides, 547, 549
Apatite, 59, 292, 298, 307, 436, 439, Bentonite, 85, 422, 428
445, 447, 450, 452, 459–461, Benzene, 201–203, 205, 207, 212
464–466, 479 Bioapatite, 292, 295–298, 307, 313
591
592 Index
Biodiversity, 4, 5, 9, 12, 19–70, 80, 85, 89–95, 424, 438–440, 443, 449–452, 461,
97, 109, 305, 306, 311, 319–322, 429, 464–466, 519–554
430, 570, 572, 573 Campanian, 26, 448
Bioerosion, 41, 46, 50, 61, 62, 81, 82, 95, 168, Carbonate diagenesis, 23, 24
170, 184, 299, 338, 339, 343–345, 348, Carbon dioxide, 5, 83, 305, 310, 551, 552
349, 351–356, 358–364, 376–378, Carboniferous, 5, 6, 42, 44, 46, 51, 53, 55, 57,
380–385, 387, 388, 391, 392, 396, 85, 87, 97, 109, 111, 207, 208, 233,
399, 400, 403, 404 239, 268, 314, 316, 398, 414, 418, 422,
Biomacromolecules, 6, 224, 226, 228, 234, 424, 426, 444–445, 461, 469, 470, 534,
236, 238, 240, 242 536, 579
Biome, 10, 294, 305, 316, 317, 320–323 Cardinia, 88, 90
Bioturbation, 8, 10, 21, 82–84, 89, 93, 94, 108, Carpels, 237
109, 113, 152, 164, 168, 171, 175, Cell membrane, 232, 233, 492, 493
181–183, 186, 270, 274, 290, 294, 303, Cellular lagerstätten, 491–493
306, 362, 377, 378, 388, 451, 521, 522, Cellularly mineralized fossils,
539, 545, 548, 550, 554, 581 457–482
Bitiao formation, 440, 443 Cellulose, 204, 205, 235, 236, 241, 459, 462,
Bitter Springs formation, 471, 473–475, 478, 466–468, 470, 493, 524
481, 493 Cementation, 7, 20, 29, 51, 80, 81, 93, 95,
Bivalvia, 41, 42, 44, 45, 47, 48, 383 112, 113, 115, 121, 128–130, 132, 133,
Black smokers, 490, 491, 498–500 145, 176, 179, 184, 185, 251, 278, 306,
Bleaching, 381, 388, 401, 404 307, 386–387, 397, 398, 403, 505, 520,
Blue Lias, 87, 94, 96, 110, 112, 114, 522, 530, 545, 551
140–145, 154, 159–161, 165, 169, Chalcedony, 414, 416, 420, 428, 471, 472,
172, 174, 182 504, 505
Body-size, 9, 20, 30, 55, 61, 66–68, 293, 302, Channel, 250, 252, 254–256, 258–262,
314, 316, 438, 453 265–267, 269–274, 277, 290,
Bone diagenesis, 296, 306, 307 292, 509
Boree Creek formation, 444 Chapoghlu Shale, 548, 549
Botryococcus, 238 Charcoalification, 250
Brachiopods, 24, 61, 86, 87, 89, 90, 92, 94, 96, Charnia, 540, 541, 546, 548
122, 125, 128, 130, 137, 159, 180, 349, Chemotaxonomy, 242
394, 414, 418, 427, 428, 445, 573–575, Chengiang biota, 53
577, 580, 585 Chert, 9, 57, 85, 413, 423–425, 444, 461,
Brown coals, 235 467–469, 471, 478–482, 488, 490–491,
Bryophyte, 250, 551 493, 495, 498–507, 509, 511, 523, 524,
Bryozoan facies, 349, 360 526–530, 533
Bryozoans, 85, 90, 96, 122, 123, 125, 130, Chinle formation, 268–270
135, 155, 159, 166, 168, 171, 173, Chitin, 6, 62, 201–204, 206, 210, 212,
176, 342, 345, 347, 349, 350, 214, 466
352–354, 359–361, 363, 393–395, Chlorophyta, 238–239, 383
397, 419, 450, 572 Chondrites, 124, 141, 161, 162, 165, 168, 172,
Burgess Shale, 8, 53, 451, 537, 173, 176, 182
549, 550 Cidaroid echinoderms, 49
Cincinnatian, 96, 121, 122, 205
Cincinnati arch, 85, 122
C Clarkia, 208, 227, 233
Calcification of microbes, 550 Clays Ferry, 121
Calcite seas, 80, 96, 97, 398, 402, 403, 425 Clays Ferry formation, 121
Calcium phosphate, 292, 452, 493, 521, 526 Cleveland ironstone, 137, 139, 140
Cambrian, 8–10, 20, 24, 51, 53, 55, 57, 59, 60, Climate change, 4, 7, 267, 289, 305, 309–312,
66–69, 80, 97, 109, 111, 115–121, 156, 320–322, 377, 404
159, 160, 163, 164, 167, 170, 171, Clionid sponges, 339, 384, 391, 397, 403
180–182, 237, 379, 383, 393, 395, 398, Clivia, 227
Index 593
CLSM. See Confocal laser scanning 272, 274, 276, 278, 293, 294, 296–298,
microscopy 300–302, 304, 314, 338, 418, 423,
Clusia, 227 436–438, 446–449, 451, 459, 460, 482,
Coffeyville formation, 440, 445 521, 534, 538, 545, 549, 581
Collagenous, 205 Decay and sedimentation, 254–257
Collingwood formation, 112, 128, 142, 174 Decomposition, 224, 233–235, 253, 291,
Colon formation, 441, 447 296–298, 306, 310, 313, 386,
Community evennes, 29 387, 420, 510
Complex crossed lamellar aragonite, 81 Dengying formation, 439, 440, 537,
Compression, 224, 226, 230, 237, 263, 269, 539, 546
278, 390, 462–464, 466, 547, 548 Denitrification, 522
Concretionary limestone, 114, 128, 131, 133, Desiccation, 206, 294, 297, 301
134, 141, 147, 149, 171, 172, 174 Devoncourt limestone formation, 440, 443
Condensed, 62, 111, 114, 117, 118, 120, 124, Devonian, 5, 24, 42, 43, 45, 58, 60, 70, 85, 87,
125, 128, 140, 141, 153–160, 179, 180, 93, 94, 129–137, 142, 147, 149, 154,
184, 192, 447 155, 159, 160, 162, 164–166, 168, 169,
Confocal laser scanning microscopy (CLSM), 171, 172, 174, 178, 180–182, 234, 235,
9, 457–482 250, 251, 254, 298, 311, 314, 315, 383,
Continental sequence stratigraphy, 258–259 391, 394, 414, 417, 423, 424, 428, 441,
Coral facies, 349, 360–363 444, 464, 468, 469, 490, 525, 530, 534,
Coralline algae, 342–345, 348–350, 352, 536, 538, 540, 553
353, 355, 359–361, 377, 391, 392, Diadematoids, 383, 384
394, 395, 403 Diagenetic limestones, 112, 132, 145, 185
Coralline algal debris facies, 354, 361, 362 Dinoflagellates, 233, 239–240
Corallivores, 363 Dinophyta, 238, 239
Corals, 61, 86, 87, 89, 130, 132, 135–137, Dinosporin, 239, 240
140, 145, 154, 155, 159, 171, 182, 200, Diplocraterion, 124, 154, 168, 170, 176
340, 342, 344, 345, 349, 350, 354, 357, Disarticulation, 89, 145, 183, 252, 301, 314,
360–363, 377–393, 395– 399, 401–404, 344, 361
419, 427 Dissolution, 2, 9, 20, 23, 24, 29, 40, 50, 51,
Crabs, 210 55, 65, 66, 69, 79–98, 109, 164, 171,
Crassatelloidea, 43–45, 47, 70 175, 179, 184, 298, 299, 303, 307,
Cretaceous, 7, 9, 24–27, 36, 45, 53, 55, 59, 60, 312, 340, 341, 343, 347, 361, 385–387,
65, 70, 85, 90, 97, 111, 142, 145–150, 393, 398, 401–404, 412–414, 416–424,
154, 159, 161, 164, 165, 168, 169, 172, 426–429, 521–523, 530, 539, 553,
174, 180, 182, 207, 208, 232, 235, 239, 581, 585
272, 289, 310, 313, 314, 317, 318, 383, DNA, 203, 204, 213, 492
391, 392, 395, 396, 398, 425, 438, 441, Doushantuo formation, 439, 493, 526–528,
447–448, 450–452, 528, 534, 536, 533, 535, 538, 539, 548
538–540, 549, 553 Durability of biomineralized
Crustose coralline algal facies, 346, 353, 361 skeletons, 55
Cruziana, 155, 171 Durophagous predation, 50
Cryptogam, 250 Dysoxia, 92, 93, 96
Cutan, 204, 211, 212, 226–232, 234, 238
Cutin, 226, 227, 229–232, 234, 238, 241
Cyptolithus, 125 E
Echinoids, 21, 61, 152, 165, 168, 182, 339,
340, 346, 347, 357, 361, 378, 383, 384,
D 397, 403, 573
Dahllite, 292 Edenian stage, 121
Debarya, 239 Ediacaran Period, 520, 534, 540, 545, 548
Decay, 2, 5, 6, 81, 82, 84, 89, 94, 98, 200, 201, Ediacaran preservation, 540
203, 205–208, 212–214, 216, 226, 233, Elrathia, 117, 118, 120, 160, 163
234, 236, 252–257, 261–264, 267, 270, Emsian, 129, 130, 134
594 Index
Encrustation, 61, 62, 94, 125, 151, 168, Gastropod, 61, 66, 67, 86–88, 90, 91, 94, 95,
171, 338, 341–345, 348, 351–356, 131, 136, 147, 152, 156, 160, 168, 170,
358–362, 364, 381, 385, 386, 400, 180, 182, 340, 347, 349, 359, 361, 378,
493, 531, 532, 552 383, 384, 414, 426, 427, 449, 571–577,
End-Permian extinction, 8, 393, 571–575, 577, 579–582, 584–586
581, 586 Geomacromolecules, 6, 225, 241
Eocene, 9, 25, 31–36, 70, 204, 233, 237, Ginkgo, 227, 234
239, 265–267, 272–274, 311, 342, Glauconite, 150
345–360, 362, 363, 383, 390–392, Gogo formation, 440, 444
395–397, 400, 403, 438, 441, 442, Gotland, 85, 86, 413, 419
448, 450–452, 467 Grainstones, 92, 118, 122, 125, 135, 153–155,
Epicontinental seas, 5, 11, 115, 152, 181, 180, 354, 357, 359, 360, 394, 421, 422
186, 451 Grammatodon, 90
Epicuticle, 206, 207 Greenhorn formation, 146–150, 154, 161, 165,
Epifaunal, 21, 80, 81, 86, 89, 146, 151, 168, 169, 172, 182
180, 384, 422, 427, 582 Green point formation, 440, 444
Estuarine, 152 Gryphaea, 87, 88, 90, 96, 165, 172, 182
Euendolithic microbes, 496 Gryphaeids, 140, 154, 169
Eutrophication, 185, 399, 404 Guadalupian, 569–586
Exceptional preservation, 4, 8, 59, 68, Gulf Coastal plain, 24, 26, 27, 35–37, 65
237, 239, 242, 310, 439, 444–446, Gunflint formation, 478, 479
525, 530 Gymnospermous cones, 253
Exines, 237, 238
Extinction, 4, 8–10, 12, 36, 62, 65, 69, 251,
272, 277, 306, 308, 318, 320, 342, 350, H
363, 364, 390, 393, 395–397, 404, 413, Halimeda, 340, 382, 389, 398, 420
424, 425, 427, 429, 569–586 Hamilton group, 94, 134–137, 154, 162, 165,
169, 172
Haragan formation, 133
F Hardgrounds, 59, 84, 85, 93–95, 98, 118, 123,
Fairview formation, 122, 440, 444 124, 136, 150, 153, 154, 156, 159, 185,
Fair-weather wave base, 95, 146, 149 398, 437, 450
Fish scales, 160, 162, 200, 207, 213 Heath formation, 444
Floodplain, 256, 257, 259–261, 265, 269, Hettangian, 90, 140
272–276, 290, 304 High-Mg calcite, 80, 82–84, 95, 97, 386, 387,
Floodplain sediments, 260 397, 398, 403
Flowers, 224, 237, 253 Hollardops member, 130, 133, 142
Foliated calcite, 81 Hollardops mesocristata, 130
Fragmentation, 30, 41, 49, 50, 62, 89, 115, Holothurians, 422
164, 170, 184, 338, 343–345, 347, Holzmaden, 53
348, 352–356, 358, 360–363, 389, Homogeneous aragonite, 81
396, 403 Hunsrück slate, 53
Frankolite, 292 Hurricanes, 388, 389
Fruits, 224, 225, 227, 234–237, 241, 253, Hydroxyapatite, 292
254, 266 Hypostracum, 80
Fungi, 5, 9, 204, 252, 295, 299, 302, 383, 384,
417, 441, 442, 447, 449, 460–462, 464,
466, 468, 482 I
Inca shale, 440, 443
Incised valleys, 258, 260, 270
G Indotrigonia, 90
Garrard siltstone, 126 Infaunal bivalves, 38, 81, 93, 172, 340, 347,
Gas chromatography/mass spectrometry: 427, 446, 452, 586
Py-GC-MS, 208 Infaunalization, 55
Index 595
Inner shelf, 92–94, 149, 359, 362, 414, 416 Leptobolus, 125
Iron-age, 2 Liesegang diffusion, 413
Isotelus, 125 Lignins, 5, 6, 204, 205, 217, 226, 230–232,
Isthmus of Panama, 390 234–236, 241, 466, 525
Limidae, 42, 44, 45, 47, 70
Lindsay formation, 114, 125
J Lingulids, 160, 182
Japan, 112, 150–152 Lingulodinium, 239
Jean Baptiste Lamarck, 491 Lipids, 203–205, 207, 208, 210–215,
Jurassic, 24–27, 42, 49, 51, 53, 60, 70, 85, 87, 217, 229, 231–233, 238, 240, 241,
88, 90, 91, 93, 94, 96, 97, 110–112, 292, 493
137–146, 149, 153, 154, 159–161, 165, Lithification, 4, 5, 19–70, 85, 186, 278, 306,
168, 169, 171, 172, 174, 180, 182, 377, 387, 397, 398, 403, 469, 520, 530,
275–276, 311, 317, 318, 341, 383, 544, 546, 554
390–392, 397, 398, 403, 413, 425, 427, Lombardische Kieselkalk formation, 441, 446
441, 446–447, 450, 452, 464, 525, 534, Lopingian, 569–586
536, 538, 553, 581 Low-Mg calcite, 346, 361, 386, 387, 397
Lucinoidea, 43–45, 47, 70
K
Kachchh Basin, 145, 146, 149 M
Katberg formation, 270–272 Maastrichtian, 26, 27, 448
Keep-up reefs, 388 Mactromya, 90
Kerogen, 204, 205, 211–214, 224, 232, Maerl facies, 346, 351, 363
233, 236, 459, 460, 462, 463, 465, Manykay formation, 439, 440
466, 468, 473, 474, 476, 477, 479, Marjum formation, 116
480, 482 Markuelia, 443, 444, 534, 535, 538
Keyserlingites, 445 Marnes Bleues formation, 441, 447
Khebchia formation, 129–134 Mechanical erosion, 339
Khuff formation, 90, 96 Megabias, 19–70, 291, 311–314, 412, 424,
Kimmeridge formation, 145 573, 586
Kinzers formation, 53 Megacucullaea, 90
Kope formation, 114, 121–126, 134, Meganteris, 130
155, 166, 178 Melanoidins, 204, 214
Kuanchuanpu formation, 439, 440, 464, Mesoproterozoic, 240, 523, 535, 537
465, 535 Metasequoia, 204, 227, 232–234
Methanogenesis, 83, 522, 530
Micritization, 338, 340, 386
L Microbial mats, 8, 21, 437, 444, 446, 449,
Lagersttäte, 3–5, 8–10, 20, 50, 52–54, 59–62, 488, 502, 506, 520–522, 542–546,
69, 80, 84–89, 93, 95, 96, 98, 141, 310, 548–550
446, 491–493, 549 Microfacies, 112, 338–341, 350, 363
Landscape evolution, 249–279 Microgastropod, 90, 91, 582, 583
Larger foraminifera, 9, 338, 342, 348, 350, Microscopic focal destruction, 299
351, 354, 359–361 Middle-arm point formation, 440, 444
Larger Nummulites facies, 355–357, Miocene, 31–34, 37–39, 90, 152, 208,
362, 363 227, 233, 235, 236, 341, 376, 383,
Latitudinal, 23, 27, 37, 253, 306, 312, 316, 390–392, 397, 401, 403, 442, 448,
317, 319–322, 364 449, 452, 530, 538
Lazarus taxa, 8, 251, 570, 571, 573–577, Mississippi Valley-type metallic
580–582, 584, 586 mineralisation, 85
Lazarus taxon, 239, 586 Mixed layer model, 451, 521–523, 531, 539,
Leiosphaeridia, 240 553, 581
Leonaspis, 130 Modiolus, 70, 90
596 Index
Molds, 10, 20, 28, 29, 40, 45, 46, 50–52, 59, Ordovician, 7, 9, 41, 43, 51, 84, 85, 89, 92–98,
61, 66, 69, 136, 164, 175, 184, 446, 114, 121–130, 133, 142, 149, 153, 155,
447, 571, 573, 581, 583, 584 159, 160, 162, 164, 166, 167, 170, 171,
Molluscs, 21, 31, 32, 66, 80, 85–87, 89, 173, 178, 180–182, 205, 226, 237, 238,
91, 94–97, 167, 185, 347, 350, 383, 398, 419, 421, 424, 425, 438, 440,
354, 355, 412, 413, 418, 427, 537, 443–444, 450–452, 525, 528, 533, 534,
554, 570, 572 536, 538, 540
Monastery creek phosphorite, 440, 443 Organic acids, 2, 217, 255, 294, 296
Monte San Giorgio lagerstètte, 446 Organic preservation, 200, 233, 481
Morocco, 129–134, 137, 162, 166, 171, 173, Orsten, 53, 440, 443, 451, 532, 536, 538
174, 441, 448, 540 Orthophragminid facies, 348, 358–359,
Morrison formation, 275–276 362, 363
Mougetia, 239 Overbank flood deposits, 256, 277
Mummification, 297 Oxbow, 255, 265–267, 277
Muschelkalk, 441, 446, 536 Oxbow channels, 255, 267, 277
Mytiloidea, 42, 44, 45, 47, 70 Oxford Clay, 93, 441, 446, 536
Oxidative polymerisation, 233, 238, 240, 241
N
Nacre, 51 P
Nacreous aragonite, 42, 81 Packstones, 118, 120, 124, 135, 357,
Naphthalene, 205 359, 360, 421
Neocrassina, 70, 90 Palaeonucula, 49
Neogene, 25–27, 31, 32, 35, 37–39, 44, 46, Palaeophycus, 152
69, 96, 109–113, 181, 442, 449, 452, Paleobiodiversity, 309
534, 536 Paleobiology database, 10, 11, 22–24, 46,
Neoproterozoic, 66, 213, 240, 383, 470, 523, 50–53, 55–63, 68, 315, 318, 571, 574
525, 529, 530, 535, 537, 554 Paleocene, 25, 26, 36, 400, 441, 442, 452
Non-lithified, 25, 32, 46, 65 Paleogene, 25, 27, 31, 35–37, 46, 65, 235,
Nucleic acids, 203, 213, 496 265–267, 342–349, 360–362, 441,
Nuculanoidea, 42, 44–47, 70 442, 448–449
Nucula nucleus, 49 Paleosols, 258–261, 265, 267–276, 304,
Nucula proxima, 46 306, 314
Nuculidae, 41, 42, 45–49, 70 Panuara group, 440, 444
Nuculid bivalves, 160, 182 Parasequence, 113, 114, 130, 148, 168,
Nuculoidea, 49, 70 264, 421
Nuculoids, 81, 87 Parrotfish, 378, 382–384, 390, 392, 395
Nuculopsis, 49 Peat bogs, 2
Nummulitid, 351, 353, 359 Pectinid bivalves, 138, 347, 414, 418
Pectinids, 139, 140, 151, 347, 414, 418, 419
Pediastrum, 239
O Pedogenesis, 250, 255, 257, 261, 263, 265,
Obrution beds, 124, 130, 133, 159, 168, 176 267, 274
Oligocene, 25, 32, 34, 70, 150, 203, 204, 206, Pennsylvanian, 3, 70, 422, 440, 445
208, 214, 265–267, 338, 342, 345, 346, Permian, 8, 20, 42–44, 46, 51, 57, 69, 90, 93,
350–355, 358, 360, 362, 363, 390, 391, 96, 111, 238, 308, 315–317, 341, 393,
442, 448, 536 394, 414, 419, 420, 422, 424, 426, 427,
Olivooides, 439, 443, 535 441, 445, 450, 451, 525, 534, 536, 538,
Ontario, 125, 127, 128, 154, 163, 173, 202, 570–586
209, 478, 479 Permineralisation, 224
Opal, 420 Petals, 237
Opal-A, 412, 420, 422 Petrolenus limestone, 439, 440
Ophiomorpha, 150, 152 Peyssonneliacean facies, 355, 362
Orbitolites facies, 359, 362, 363 Phacops saberensis, 130
Index 597
Phenol, 201, 203, 205–207, 212, 241 Pyritic, 62, 93, 96, 125, 132, 133, 136, 153,
Pholadomya, 88, 90 160, 162, 164–166, 171, 172, 174,
Phosphate, 9, 10, 59, 180, 292, 436–439, 184, 233, 489, 491, 499, 511, 549,
444–450, 452, 453, 461, 482, 493, 550, 554
509, 520, 521, 526, 527, 531–533, Pyritization, 250, 279, 549, 550
538, 539, 554 Pyrolysis–gas chromatography/mass
Phosphatization, 9, 20, 50, 59–61, 65, 66, 69, spectrometry (Py-GC-MS), 201–203,
435–453, 527, 531, 533, 5539 205, 208, 209, 211, 212, 214, 216, 228
Phosphatized soft tissues, 443, 446, 447
Phosphoria formation, 445, 451
Phycosiphon, 152 Q
Phytoclasts, 252–255 Quartz, 412, 414, 416, 420, 421, 423,
Phytoplankton, 238–240, 384, 436, 538 461, 466–482, 491, 499, 500, 509,
Pillow basalts, 491, 495–497 543–545
Pinnidae, 42 Quercus, 230, 232, 2227
Pinnids, 140, 172
Pisotrigonia, 90
Planolites, 117, 147, 149, 150, 152, 155, 156, R
165–173 Radiaxial calcite, 394, 398
Plant-part decay rates, 252–254 Radiolarians, 85, 320, 422, 424, 429,
Pleinsbachian, 137, 145 527, 530, 545
Pleistocene, 21, 25, 31–33, 35, 37–39, 70, 111, Rafinesquina, 125
206, 212, 388–390, 396, 438, 442, Raman imagery, 9, 457–482
449–450 Raman index of preservation (RIP), 459,
Pleuromya, 141 477–478
Pocillopora, 390 Raman spectroscopy, 216, 462–464, 474, 482
Pocilloporids, 390 Rare earth elements, 293, 307, 507
Pollen, 224, 225, 237–241 Rates of decay and sedimentation, 254–257
Polycyclic aromatic hydrocarbons, Reef-crests, 381, 384, 386, 387, 397
460, 466 Reef-fronts, 387
Polymerization, 203, 205, 210, Reefs, 7, 159, 160, 344, 375–404, 426, 446,
213, 420 572, 577
Polyplacophores, 339 Rhabdopleura, 201, 205, 210, 211
Polysaccharides, 6, 203, 229–231, 233, Rhizocorallium, 140, 150, 154, 171
235, 236 Rhodolith facies, 347, 352, 362
Portland limestone, 441, 446 Rhodoliths, 342, 351–353, 355, 362,
Posidonia shale, 93 363, 449
Prasinophyta, 238–239 Rhynchonellid brachiopods, 138, 182, 418
Preservational quality, 29, 39–50 RIP. See Raman index of preservation
Principle of uniformity, 489 RNA, 203, 204, 213, 492, 496
Prismatic calcite, 81 Rosselia, 152
Prokaryote, 492, 499, 548 Rusphycus, 171
Prokaryote cells, 492
Proterozoic, 233, 479, 488, 489, 501, 506,
524, 527, 547, 550 S
Prunus laurocerasus, 227 Saltford Shale, 90, 91
Pseudofossils, 481, 493–494 San Juliçn formation, 150
Pseudogygites, 160 Santana formation, 441, 447
Psychopyge, 130 Scarids, 382–384, 390, 397, 403
Pteriomorphs, 80, 86, 87, 93 Scleractinian corals, 340, 361, 390, 392, 393,
Pterobranchs, 200, 205 395, 396, 398, 403, 427
Punctae, 414, 418 Scolecodonts, 205
Punctate brachiopods, 419 Scrippsiella, 239, 240
Punta Judas formation, 150–152 Scutellum, 130
598 Index
Seafloor banded cherts, 500–505 Soltanieh formation, 527, 539, 548, 549
Sea level, 2, 6, 54, 109–111, 113–115, 117, Spectral analysis, 146, 149
129, 145, 146, 149, 152, 160, 175, 176, Spirogyra, 239
179, 182–184, 258, 259, 288, 305, 306, Sponges, 57, 85, 200, 339, 379, 381, 384,
309, 311–13, 316–318, 388, 400, 404, 385, 391–397, 403, 422, 424, 425, 429,
424, 429, 447, 449, 2974 450, 501, 527, 530, 545, 554, 573–577,
Seebachia, 90 580, 585
Seeds, 224, 236, 241, 253 Sponge spicules, 118, 120, 422, 526
Sepals, 237 Spores, 225, 234, 237–238, 240, 241,
Sequence stratigraphy, 2, 120, 257–259 469, 530
Severn estuary, 140 Sporopollenin, 5, 204, 225, 233, 237–239, 241
Shell beds, 3, 10, 20, 37, 54, 55, 69, 81, 83, Storm beds, 89–92, 95, 96
84, 89–92, 96, 98, 109–113, 121, 124, Storm waves, 90, 149, 153, 175, 179,
136, 137, 139, 141, 145, 147–159, 526, 541
169–171, 176–183, 185 Strelley pool formation, 506–509
Shell microstructure, 81, 419 Stromatolites, 442, 449, 479, 488, 493, 495,
Shell plasters, 84, 93, 95, 96, 98 501, 504–509, 549, 551
Shoal deposits, 94, 98, 159 Strophomena, 125
Shoreface, 37, 94, 95, 115, 147, 149 Sulphate reduction, 83, 85, 89, 387,
Shoreline depositional system, 258 522, 530, 544
Shuiyousphaeridium, 240 Surface grazing, 339, 362
Sideritic beds, 140 Surgeonfish, 383
Silica gel, 417, 420, 493, 502, 508
Silica replacement, 10, 20, 46, 55, 57, 58, 66,
69, 412, 577, 579, 583 T
Siliceous organisms, 413, 422 Tabulate corals, 136, 427
Silicic acid, 417, 420, 421 Tannins, 233, 255
Silicic preservation, 540–546 Taphocline, 313
Silicification, 9, 46, 50, 55–59, 61, 65, 69, 84, Taphofacies, 2, 3, 91, 93, 110, 111,
85, 88, 95, 257, 411–430, 500, 523, 114–116, 152–160, 180, 182–186,
524, 527, 528, 530, 554, 570, 571, 573, 337–364, 540
574, 577–580, 583–586 Taphonomically active zone (TAZ), 81–84, 89,
Silicified, 8, 44, 51, 55–58, 66, 80, 84–88, 90, 93, 95, 96, 98, 295, 300, 304, 306,
92, 93, 95–98, 412–414, 416, 419–429, 385–387
488, 489, 495, 506, 509, 528, 530, Taphonomic control taxa, 65, 69
571–574, 577–580, 583–586 Taphonomic feedback, 2, 90, 177
Silurian, 42, 49, 85, 86, 89, 92, 95, 96, 153, Taphonomic windows, 10, 84, 92, 95–97,
164, 180, 201, 211, 226, 250, 413, 419, 489, 491, 511, 521, 554
424, 440, 444, 525, 534, 536, 538 Taxonomic databases, 21
Skeletal fragmentation, 164 TAZ. See Taphonomically active zone
Skeletal lag deposits, 112, 145, 183 Teeth, 152, 159, 168, 200, 292, 306,
Skeletal lagerstètten, 80, 84–89, 93, 96, 98 339, 382
Skeletonization, 301 Tentaculites, 171
Skolithos, 152 Terebratulid brachiopods, 130
Smaller miliolid facies, 359 Terrestrial weathering, 85
Small Nummulites facies, 345, 357–358, 361 Thalassinoides, 118, 120, 147, 149, 150, 152,
Snowball Earth, 523 154–156, 169–171, 181
Soft-bodied organisms, 2, 8, 52, 68, 116, 540, Tidal, 3, 8, 11, 86, 87, 90, 95, 96, 117, 254,
544–546 255, 379, 381, 424, 523, 524, 527, 530,
Soft tissues, 2, 4, 8, 59, 271, 297, 301, 307, 544, 551
417, 426, 436–438, 444–448, 451, 453, Tidal channels, 255
459–461, 464–466, 525, 527, 532, 536, Time-averaging, 7, 32, 37, 176, 179, 186, 338,
552, 554 380, 382, 389
Solnhofen limestone, 53 Triarthrus, 125, 160, 163
Index 599
Triassic, 8, 51, 53, 57, 90, 97, 268–272, 308, W

316, 317, 383, 390, 391, 395, 403, 424, Walther’s facies concept, 2
427, 441, 445–446, 452, 525, 534, 536, Waulsortian mounds, 426
569–586 Waxes, 206, 207, 213, 232, 238, 241, 460
Trigonioids, 90 Western interior, 146–147, 174, 275, 447
Trilobites, 61, 86, 116, 118, 120, 124, 128, Wheeler formation, 53, 117, 119, 120, 156,
130, 132–134, 137, 149, 155, 160, 163, 163, 167, 170
166–168, 170, 172, 173, 177, 178, 181, Wheeler Shale, 116, 117, 120, 266
182, 200, 206, 427 White smokers, 495, 500
Trimerellacean, 89 Willwood formation, 272–275
Trypanites, 123, 155, 156, 176 Wood, 160, 171, 224, 234–237, 241, 253, 254,
Tufa, 520, 550–553 257, 270, 416, 417, 529, 530
Tyrasotaenia, 548, 549
X
Xylem, 234–237, 241, 253, 466,
U 468–470
UV radiation, 296–298, 496
Z
V Zoophycos, 130, 137, 168, 169, 171–173
Vendotaenia, 548, 549 Zygnema, 239

TAPHONOMY

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Taphonomy

Process and Bias Through Time

For other titles published in this series, go to

Peter A. Allison David J. Bottjer

ISBN 978-90-481-8642-6 e-ISBN 978-90-481-8643-3

© Springer Science+Business Media B.V. 2011

Printed on acid-free paper

Springer is part of Springer Science+Business Media (www.springer.com)

research methodologies and statistical approaches, but it is still there. A deeper

1 Taphonomy: Bias and Process Through Time........................................ 1

2 Taphonomic Overprints on Phanerozoic Trends in Biodiversity:

3 Taphonomic Bias in Shelly Faunas Through Time: Early Aragonitic

4 Comparative Taphonomy and Sedimentology of Small-Scale

5 Taphonomy of Animal Organic Skeletons Through Time..................... 199

6 Molecular Taphonomy of Plant Organic Skeletons................................ 223

7 The Relationship Between Continental Landscape

8 Hierarchical Control of Terrestrial Vertebrate Taphonomy

9 Microtaphofacies: Exploring the Potential for Taphonomic

10 Taphonomy of Reefs Through Time....................................................... 375

11 Silicification Through Time..................................................................... 411

12 Phosphatization Through the Phanerozoic............................................ 435

13 Three-Dimensional Morphological (CLSM)

14 Taphonomy in Temporally Unique Settings:

15 Evolutionary Trends in Remarkable Fossil Preservation

16 Mass Extinctions and Changing Taphonomic Processes:

Geophysical Laboratory, 5251 Broad Branch Road NW,

Peter A. Allison and David J. Bottjer

P.A. Allison ()

Taphonomic research is clearly wide-ranging, and in the Earth sciences impacts

1.1 Taphonomy: A Brief History

taphonomic processes had reached a level requiring broad syntheses of rapidly

2 Is Taphonomic Bias Uniform?

2.2 Secular Trends in Ocean Chemistry and Skeletal Mineralogy

The impact of predator–prey escalation through geological time (Stanley 1974,

reduce preservation potential. The evolutionary diversification of organisms

is not significantly obscured by a taphonomic megabias due to skeletal mineralogy

2.4 Temporal Trends in Conserving Environments

Efremov, E. A. (1940). Taphonomy: A new branch of paleontology. Pan-American Geologist, 74,

Austin J.W. Hendy

Lithification of most Paleozoic and Mesozoic fossiliferous sediments has likely

As a complication, however, the taphonomic biases that affect marine invertebrate

The development of sophisticated databases, such as the Paleobiology Database

2 Lithification and Diagenesis in the Fossil Record

2.1 Time-Series Analysis of Lithification and Alpha Diversity:

1987). Easily observed, however, is the sharp increase in availability of unlithified

difference in the richness of assemblages from contemporaneous poorly lithified

Table 2 Availability of occurrence and abundance data for which

Figure 9 presents an analysis of differences in composition of lithified and

2.2 Time-Series Analysis of Lithification and Alpha Diversity:

2.2.1 Cenozoic of New Zealand

Fig. 11 Proportional distribution of collection data among three categories of lithification

2.2.2 Paleogene of the Gulf Coastal Plain

Sessa et al. (2009) studied the impact of lithification on mollusc-dominated assemblages

Fig. 13 Averaged sample-

Fig. 14 Size frequency

2.3 Within-Interval Analysis of Lithification

At a quota of 100 specimens, unlithified sediments yield on average close to 20 genera,

2.4 Influence of Lithification and Diagenesis

Biases in preservational quality at the scale of individual specimens and popula-

Fig. 16 Influence of lithification

1.1 Taphonomy: A Brief History

2 Is Taphonomic Bias Uniform?

2.2 Secular Trends in Ocean Chemistry and Skeletal Mineralogy

2.4 Temporal Trends in Conserving Environments

2 Lithification and Diagenesis in the Fossil Record

2.1 Time-Series Analysis of Lithification and Alpha Diversity:

2.2 Time-Series Analysis of Lithification and Alpha Diversity:

2.2.1 Cenozoic of New Zealand

2.2.2 Paleogene of the Gulf Coastal Plain

2.3 Within-Interval Analysis of Lithification

2.4 Influence of Lithification and Diagenesis

2.4.1 Direct Observation of Fossil Specimens

3 Exploring Other Taphonomic Trends in the Quality

3.1 Preservation as Casts and Molds

3.2 Lagerstätten and the Preservation of Soft-Bodied Fossils

attributable in part to the closure of this phosphatization window. In additionto phos-

4.1 Evaluation of the Paleobiology Database in Capturing

4.2 Research Opportunities and the Mitigation

4.2.1 Taphonomic Biases and the Biodiversity Record

4.2.2 Implications for Taxonomic and Morphologic Analyses

A growing weight of evidence points to dissolution of biogenic carbonate as a significant

2.2 Taphonomically Active Zone (TAZ)

2.3 Shallow Sub-TAZ Burial Diagenesis

3.2 Other Deposits Capturing Biodiversity

3.2.1 Storm and Shell Beds

4.1 Taphonomic Gradients and Molluscan Preservation:

4.2 Molluscan Preservation During ‘Calcite’

5.3 Sedimentation Rates and Time-Averaging.................................................................. 176

2 Small-Scale Sedimentary Cycles

2.2 Identifying Analogous Phases of Cycles

3 Examples of Small-Scale Cycles in the Phanerozoic

3.1 Middle Cambrian: Great Basin USA

3.2 Late Ordovician; Eastern North America