Unit 6: Evidence of Evolution

Lesson 6.4
Inferring Evidence of Evolutionary Relationships

Contents
Introduction 1

Learning Objectives 2

Warm Up 2

Learn about It! 3

The Hierarchy of Taxonomic Organization 3
The Hierarchy of Organization 4
Taxonomy 6
Systematics 7
Structural Evidence and the Relatedness of Organisms 9
Molecular Evidence and the Relatedness of Organisms 11
Tools for Studying Evolution 11
Cladograms 11
Phylogenetic Trees 12

Key Points 15

Check Your Understanding 16

Challenge Yourself 18

Bibliography 18
Unit 6: Evidence of Evolution

Lesson 6.4

Inferring Evidence of Evolutionary

Relationships

Introduction
From the previous lessons, you have learned that scientists believe that all living things on
Earth share common ancestors. This means that all life on Earth is related. It is the goal of
scientists to determine how all organisms connect to each other in the evolutionary tree of
life. As such, there are certain ways that they have developed in order to deduce the

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Unit 6: Evidence of Evolution

relatedness between species. Have you ever wondered how humans are related to other
organisms and how scientists know how organisms are related? This will be tackled in this
lesson, along with the molecular, structural, and other pieces of evidence currently known
to science regarding evolutionary relationships.

Learning Objectives DepEd Competency

In this lesson, you should be able to do the

Infer evolutionary relationships
following: among organisms using the
● Describe taxonomy and systematics and evidence of evolution

how scientists use these to study (STEM_BIO11/12-IIIc-g-13)

evolution.
● Explain how organisms are related
through the various pieces of
evolutionary evidence.

Warm Up

Which Animals Are Related? 20 minutes

The students will be asked to choose groups of animals that they will describe. The
characteristics of the animals will be described by the students and they will try to identify
which ones are more closely related based on these characteristics.

Procedure
1. Divide the class into four groups.
2. Together with your group, choose one of the sets of animals below.
a. Set 1: tilapia, shark, whale, goldfish
b. Set 2: tiger, frog, cat, dog
c. Set 3: eagle, sparrow, bat, butterfly
d. Set 4: mosquito, fly, crab, jellyfish
3. For five minutes, discuss among yourselves which of the animals is least likely to be
related to the others.

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Unit 6: Evidence of Evolution

4. Similarly, discuss why you think the remaining animals are likely to be closely related.
5. Make a chart based on how you think the organisms are related. You may do this in
the format of a flowchart or a map.
6. After discussing, divide each group into four. With these new divisions, form four
large groups that contain members from Sets 1 to 4.
7. Share your answers for #3 and #4 with your new group.

Guide Questions
1. What is the basis for determining the relationships in this activity?
2. How do you know if animals are related or not?
3. Which among these animals is the least likely to be closely-related among the
selections?
a. Set 1: tilapia, shark, whale, goldfish
b. Set 2: tiger, frog, cat, dog
c. Set 3: eagle, sparrow, bat, hawk
d. Set 4: dog, frog, hawk, jellyfish
4. What other information can you use for determining the evolutionary relationship
between organisms?

Learn about It!

How do scientists determine evolutionary

relationships between organisms?

The Hierarchy of Taxonomic Organization

Scientists believe, with much evidence, that all life on Earth is related. From the smallest
bacterium to the largest animal, these organisms share a common ancestor somewhere
along with their evolutionary history. In order to properly deduce how all organisms are
related, scientists have devised ways of determining these relationships. Understanding
these relationships and organizing them systematically is crucial to unraveling the mystery
of how all life forms are related to each other.

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Unit 6: Evidence of Evolution

What are some common features among bacteria,

plants, animals, and other organisms that make
scientists think they are truly related?

To organize our understanding of the way organisms are related, scientists have come up
with the hierarchy of organization for all living things.

The Hierarchy of Organization

The process of organizing organisms based on taxonomic hierarchy involves classifying
them into multiple levels of the organization. These levels of organization indicate the
classification of organisms based on general characteristics and how scientists believe they
are related to other similar organisms. Thus, the more similar organisms are based on their
taxonomic hierarchy, the more likely it is for them to be more closely related.

There are eight levels of organization in today’s taxonomic hierarchy of organisms. The eight
levels, starting from the highest and ending with the lowest level, are found in Table 6.4.1.:

Table 6.4.1. The taxonomic hierarchy of organisms

Description

The highest level of classification which separates eukaryotes and

Domain
prokaryotes (bacteria and archaeans).

The kingdoms were traditionally the highest level before domains

Kingdom
were introduced. Examples of kingdoms are Animalia and Plantae.

This is the uppermost level of organization within kingdoms.

Phylum
Examples are Chordata, Arthropoda, and more.

The class is a rank below phylum and above order. An example

Class
includes the class Mammalia.

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Unit 6: Evidence of Evolution

Orders are classifications under each class and organisms within

Order them show many similar characteristics. An example is Primata,
where humans are classified under.

The family is one of the lowest levels of classification denoting close

Family
relationships between organisms.

Organisms of the same genus are very closely related and usually
Genus
with small differences.

Those that share the species level are known as conspecifics,

Species
which have genetic similarities.

All organisms have a corresponding classification in the taxonomic hierarchy. Take for
example the following animals whose complete hierarchical classification can be seen in
Table 6.4.2.

Table 6.4.2. The taxonomic hierarchy for selected animals

Great White Shark Basking Shark Philippine Eagle

Domain Eukarya Eukarya Eukarya

Kingdom Animalia Animalia Animalia

Phylum Chordata Chordata Chordata

Class Chondrichthyes Chondrichthyes Aves

Order Lamniformes Lamniformes Accipitriformes

Family Lamnidae Cetorhinidae Accipitridae

Genus Carcharodon Cetorhinus Pithecophaga

Cetorhinus
Species Carcharodon carcharias Pithecophaga jefferyi
maximus

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Unit 6: Evidence of Evolution

Organisms that are more closely related, such as the great white shark and basking shark,
share much more in common with their taxonomic hierarchy compared to a more
distantly-related organism like the Philippine eagle. As you can see in the table, the lower
the common classification (order for the two sharks, compared to phylum for the sharks
and Philippine eagle), the more closely related they are to each other. More distant
relations, on the other hand, will have a higher common classification between organisms.

Taxonomy
The field of taxonomy is an important field in biology. This field involves naming and
classifying organisms based on characteristics and relatedness. Giving an organism an
appropriate scientific name, for example, is one of the things that taxonomy is in charge of.
Although it seems like a very simple field, taxonomy is essential to all biological branches
that involve studying organisms.

One significance of giving an organism a scientific name is to prevent confusion. There are
scientists around the world that study organisms and each country have a different
common name for the same organism. Related to this fact is that the common name for an
organism may refer to several organisms that are related to each other. The use of scientific
names as a standard in the scientific community allows easier access for studying the same
organism and prevents confusion between different studies.

All of the birds above can be called “eagles” but they are actually different species. Scientific
names can help in differentiating them from each other.
From left to right: Haliaeetus leucocephalus, Aquila chrysaetos, and Pithecophaga jefferyi

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Unit 6: Evidence of Evolution

A scientific name, in most cases, is composed of two components: the genus name and the
specific epithet. These two must be included in a complete scientific name, with both
names being italicized if in a digital format or separately underlined if handwritten. For
example:

The scientific name of the Philippine eagle: Pithecophaga jefferyi

Genus: Pithecophaga
Specific epithet: jefferyi

It is italicized since it is in a digital format, typed on a computer. However, if it is

handwritten, then it should be underlined as Pithecophaga jefferyi. Take note that space in
between the genus name and the specific epithet is not underlined.

Did You Know?

Scientific names are mostly in Latin.

One of the reasons for this is that Latin is a dead language,

meaning that the definition for Latin words is already static and
unchanging. This is in contrast with languages that are currently still
being used whose definitions can still change over time.

Systematics
The field of taxonomy alone is not enough to organize the classification of organisms based
on common characteristics. This field is commonly closely-partnered to another biological
field, which is systematics. The study of systematics focuses on the diversity of organisms
and how related these organisms are. Simply put, systematics deals with building the tree
of life which shows how organisms have diversified and how their evolutionary histories
have played out over time.

Scientists use multiple methods of inferring whether organisms are closely related to each
other or not. Most of these methods have already been discussed in Lessons 1, 2, and 3 of
this unit. In general, however, structural evidence and molecular evidence are the primary

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Unit 6: Evidence of Evolution

methods by which scientists classify organisms based on relatedness. Molecular data is

usually seen as more accurate, although both molecular and structural evidence is used in
current scientific studies in order to determine evolutionary relationships.

An early rendition of the tree of life by Ernst Haeckel

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Unit 6: Evidence of Evolution

Morphology Morphology + Molecules

A comparison of trees created using morphology and a mix of both. In the molecular and
morphological tree, a more accurate representation of the evolutionary relationship as to
how it happened in the phylogenetic history is reflected.

Structural Evidence and the Relatedness of Organisms

It has been discussed in this unit that closely-related organisms have more common
characteristics compared to organisms that they are more distantly related to. Recall the
concepts of homologous structures and vestigial structures that were discussed earlier
in this unit, which serve as proof of relatedness.

How do homologous structures show evolutionary

relationships?

In studying structural evidence, scientists primarily focus on certain morphological and

anatomical characteristics that may indicate common descent between organisms. Similarly,
the presence of common characteristics in organisms that are not found in others outside
of the classification is an excellent indicator of relatedness.

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Unit 6: Evidence of Evolution

For example, all chordates have five characteristics that appear at some point in their lives.
These characteristics are the following (Fig. 6.4.1):
1. the presence of a notochord, which is a cartilaginous tube in the organism for
structural support;
2. the presence of a dorsal hollow nerve cord, which may eventually develop into the
central nervous system;
3. the presence of a post-anal tail used for movement or balance;
4. the presence of pharyngeal slits which are openings close to the mouth, and
5. the presence of an endostyle, which is an organ used for feeding.

All of these characteristics are present in all chordates, even in humans. In humans,
however, some of these are only found during embryonic development. The appearance of
these five characteristics in an animal’s life history means that it is a chordate. In contrast,
no other organisms apart from chordates have all five characteristics appearing in their life
histories. This implies that these characteristics were present in one of the ancestors of
chordates and that these characteristics were passed on which means that all chordates
share an ancestor based on these characteristics which imply relatedness.

Fig. 6.4.1. The characteristics of chordates as seen in a lancelet,

which is a primitive chordate

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Unit 6: Evidence of Evolution

Molecular Evidence and the Relatedness of Organisms

Molecular evidence for the relatedness of organisms involves studying molecules like DNA,
RNA, and proteins to allow scientists to deduce how species are related to each other. As
you have learned in the previous lessons of this unit, close similarities between the DNA or
protein sequences between species may indicate close evolutionary relationships.

An example of molecular evidence for the relatedness of organisms can be seen in reptiles.
Traditionally, the reptiles that we know are the scaly, four-legged organisms like lizards,
crocodiles, and turtles. However, more recent scientific evidence shows that birds can also
be classified as reptiles. This classification is on the basis of the common ancestry
between reptiles and birds (specifically, crocodiles and birds), structural evidence, and DNA
evidence of their close evolutionary relationships.

Tools for Studying Evolution

Studying the relatedness of organisms is done through molecular and structural means.
Scientists use certain tools in order to properly classify organisms based on evolutionary
history or structural characteristics. In order to do so, the construction of cladograms and
phylogenetic trees is necessary.

Cladograms
A cladogram is a diagram that shows
relationships between organisms
based on characteristics. It does not
necessarily show evolutionary history
but may still give an idea of how
organisms are related based on their
common characteristics. The important
parts of a cladogram are the following:
● The terminal nodes show the
groups or the organisms that
are being compared. Terminal
branches lead to these nodes.

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Unit 6: Evidence of Evolution

● The outgroup is usually an organism with very different characteristics to provide a

point of comparison.
● The ingroups are the organisms that are being compared and are more
closely-related compared to the outgroup.
● The nodes show the divergence between the groups, while the internodes lead to
these nodes.

Take note that the length of the branches in a cladogram does not matter, unlike what you
will learn later on with phylogenetic trees. These branches merely indicate ancestry and
descent. Take, for example, another cladogram shown in Fig. 6.4.2.

Fig. 6.4.2. Sample cladogram with four terminal nodes

In Fig. 6.4.2., the terminal nodes are all animals. Each internode is marked with a
characteristic that all the terminal nodes to the left do not have and all the terminal nodes
to the right possess. This shows how these organisms are related based only on the
characteristics that they do or do not have. Again, take note that these diagrams do not
show evolutionary relationships but instead show relationships based on characteristics.

Phylogenetic Trees
Phylogenetic trees are very similar to cladograms in that they also show relationships
between organisms. These diagrams may also be based on physical characteristics but

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Unit 6: Evidence of Evolution

more commonly use genetic data to show the relationships between organisms.
Scientists often create phylogenetic trees by using DNA sequences. The sequences of the
different organisms are compared based on the degree of similarity using computer
software that can analyze the DNA sequences and measure the differences between each
sequence.

The similarities between the DNA sequences are then used as a basis for creating a
phylogenetic tree. Naturally, the sequences that are more similar will most likely indicate a
close evolutionary relationship. A very simple phylogenetic tree can be seen in Fig. 6.4.3.

Fig. 6.4.3. Parts of a phylogenetic tree

As in cladograms, a phylogenetic tree will also have groups of organisms or individual

species that are being compared. The most important parts are the following:
● The root forms the base of the tree.
● The nodes indicate a divergence and indicate a common ancestor between taxa. In
the example above, species A and species B are related which is indicated by the
divergence in the node.
● The branches that lead from nodes usually end in organisms or groups of organisms
that are being studied.
● To properly analyze the phylogenetic tree, one must trace the divergences of the
nodes starting from the root. Each node indicates a divergence in evolutionary
history and usually terminates in another node (which indicates another divergence)

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Unit 6: Evidence of Evolution

or a taxonomic group (indicating descent). Organisms that are more closely-related

are usually closer in terms of ancestry (indicated by divergences) as opposed to the
more distantly related which have more divergences separating them.
● Lineages can also be traced by checking which organisms or groups form a direct
connection from a node to a terminal node.

Fig. 6.4.4. Mammalian phylogenetic tree

Fig. 6.4.4 shows a mammalian phylogenetic tree. To determine the closeness of

evolutionary relationships, the divergences from the nodes can be compared between
organisms. For example, even though guinea pigs and tree shrews are next to each other in
the tree, the common ancestors they most likely have are farther to the left because of the
number of divergences in the nodes. On the other hand, humans, bonobos, and
chimpanzees are closely related on the basis of the closeness of their ancestral

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Unit 6: Evidence of Evolution

relationships. Thus, it is important to trace these divergences in order to determine direct

evolutionary relationships.

Unlike cladograms, the branch length of some phylogenetic trees may be an indicator of
when the divergence occurred. The length may be used as an indicator of the evolutionary
time between groups or divergences. The nodes to the left of the node in question diverged
earlier, while the nodes to the right diverged later on in evolutionary history.

Another example of a phylogenetic tree, with this indicating the evolutionary history of
some mammals, can be seen in Fig. 6.4.4. Some phylogenetic trees also have numbers that
accompany the nodes and branches, as can be seen in Fig. 6.4.4.. These may indicate the
time of evolution or divergence in specific units. This tree shows the numbers in mya
(million years ago).

Key Points
___________________________________________________________________________________________
● The process of organizing organisms based on taxonomic hierarchy involves
classifying them into multiple levels of organization.
● The field of taxonomy involves naming and classifying organisms based on
characteristics and relatedness.
● The study of systematics focuses on the diversity of organisms and how related
these organisms are.
● In studying structural evidence, scientists primarily focus on certain morphological
and anatomical characteristics that may indicate common descent between
organisms.
● Molecular evidence for the relatedness of organisms involves studying molecules
like DNA, RNA, and proteins to allow scientists to deduce how species are related to
each other.

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Unit 6: Evidence of Evolution

Methods for analyzing evolutionary relationships

___________________________________________________________________________________________

Check Your Understanding

A. Identify the term being described by the statements below.

1. This is a diagram that shows relationships between organisms based purely

on characteristics.
2. This is the field of biology involved in naming organisms.
3. This refers to the second name in the scientific name.
4. This is the format that scientific names should follow when handwritten.
5. In diagrams that show relationships between organisms, these refer to the
groups or species that are distantly related and are added for comparison.
6. In reference to #5, these are the groups of organisms that are being
compared.
7. This is a cartilaginous rod found only in chordates.
8. This is the highest level in the taxonomic hierarchy of classification.
9. This is the third-lowest level in the taxonomic hierarchy of classification.
10. These types of nodes indicate a taxonomic group or a specific species.

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Unit 6: Evidence of Evolution

B. Fill in the cladogram below by using the organisms and the

characteristics found in the word bank.

Word Bank

Crocodile Made up of cells

Human Bipedal

Tilapia Animals

Coconut Four limbs

Dog Hair

1. ____________________ 6. ____________________
2. ____________________ 7. ____________________
3. ____________________ 8. ____________________
4. ____________________ 9. ____________________
5. ____________________ 10. ____________________

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Unit 6: Evidence of Evolution

Challenge Yourself

Answer the following questions.

1. Why do taxonomy and systematics often go hand-in-hand?

2. How can the hierarchy of taxonomic classification be an indicator of the relatedness
between organisms?
3. How is DNA used as an indicator of evolutionary history?
4. How do cladograms help in identifying the similarities between organisms?
5. Why are phylogenetic trees important in the study of evolution?

Bibliography

Briggs, John C. “Marine Centres of Origin as Evolutionary Engines.” Journal of Biogeography

30, no. 1 (2003): 1–18. https://doi.org/10.1046/j.1365-2699.2003.00810.x.

Boyer, Rodney F. Concepts in Biochemistry. Hoboken, NJ: Wiley, 2006.

Carpenter, Kent E., and Victor G. Springer. “The Center of the Center of Marine Shore Fish
Biodiversity: the Philippine Islands.” Environmental Biology of Fishes 72, no. 4 (2005):
467–80. https://doi.org/10.1007/s10641-004-3154-4.

Hickman, Cleveland Pendleton, Susan L.. Keen, Allan Larson, William C.. Ober, and Claire W..
Garrison. Animal Diversity. New York: McGraw Hill Education., 2018.

Hickman, Cleveland P. Integrated Principles of Zoology. New York, NY: McGraw-Hill, 2011.

Kardong, Kenneth V. Vertebrates Comparative Anatomy, Function, Evolution. New York, NY:
McGraw-Hill Education, 2019.

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Koonin, Eugene V., and Michael Y. Galperin. Sequence - Evolution - Function: Computational
Approaches in Comparative Genomics. New York: Springer, 2011.

Miller, Stephen A., and John P. Harley. Zoology. New York, NY: McGraw-Hill, 2010.

Russell, Peter J. Biology: The Dynamic Science. Student Ed. Belmont, CA:
Thomson/Brooks/Cole, 2008.

Starr, Cecie, Ralph Taggart, Christine A. Evers, and Lisa Starr. Biology: the Unity and Diversity
of Life. Boston, MA: Cengage, 2019.

“‘Tree’ Facts: Terminology.” National Center for Biotechnology Information. U.S. National
Library of Medicine. Accessed February 12, 2020.
https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo7.html

Voronov, A. S., D. V. Shibalev, and N. S. Kupriyanova. “Evolutionary Relationships between

Reptiles Inferred from the Comparison of Their ITS2 Sequences.” Russian Journal of
Genetics 47, no. 7 (2011): 864–73. https://doi.org/10.1134/s1022795411060160.

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