EXERRCISE - 2 Phylostrat Guideliens PDF
EXERRCISE - 2 Phylostrat Guideliens PDF
EXERRCISE - 2 Phylostrat Guideliens PDF
Do the traits of
organisms provide
evidence for evolution?
Consider two hypotheses about where Earth’s organisms came from.
The first hypothesis is from John Ray, an influential British naturalist
of the 17th century. Ray believed that all species were independently
created:
“A species is never born from the seed of another species.”
The second hypothesis is from Charles Darwin, who published On
The Origin of Species in 1859. Darwin believed that all species were
derived, by descent with modification, from a single common ancestor:
“...all the organic beings which have ever lived on this earth have
descended from some one primordial form...”
Designer lizards
Launch the application PhyloStrat. The first thing you will see is an
advertisement for my book. You can click on it to make it go away, or
you can wait a few seconds for it to go away on its own. After the ad
disappears, you should see a window titled Designer Lizards. Lined up
near the top are seven lizards, each of which looks like the one at left.
Note the small black triangle just below each lizard’s tail. Click on
this triangle. It will change orientation to point downward, and reveal a
menu of traits you can bestow on the lizard.If you click the Back Crest
box, for example, a check mark appears in the box and a crest appears
along the lizard’s back. If you change your mind about giving this lizard
a back crest, you can click on the box again. Both the check mark and
the crest itself will disappear.
Your task now is to design seven lizards, by adding traits to each of
the lizards in the window. You can give any lizard any combination of
traits you like, but do give each lizard at least two or three traits. That
will make your next task more interesting and instructive.
Designer lizards 3
After you have designed your seven lizards, look near the bottom of
the window and notice the array of tools you can use:
Current marker
Tool palette color Marker color palette Marker clear button
Try the hand tool first. When you click on the hand tool, the mouse
cursor becomes a hand. You can use the hand to move your lizards
around in the window. Just place the hand over the lizard you want to
move, hold the mouse button down, and drag the lizard to its new loca-
tion.
Now try the marker tool. When you click on the marker tool, the cur-
sor becomes a marker. Pick a color from the marker color palette (by
clicking on it), then use the marker to draw in the window. Place the
marker anywhere in the window, hold the mouse button town, and drag.
The marker will draw a line (or squiggle) in the color you have chosen.
Play with the marker a bit to get the feel of it, then erase your scribbles
by clicking on the marker clear button.
Now that you know how to use the tools, here is your task. Move the
seven lizards you have designed around in the window to organize
them. Try to arrange them so that the lizards with dewlaps are near each
other. And so that the lizards with head crests are near each other. And
so that the lizards with back crests are near each other, and so on. It
4 Do the traits of organisms provide evidence for evolution?
Evolving lizards
Leave the Designer Lizards window open, so you that later you can go
back and look at your work again. Under the Window menu select
Evolving Lizards. This will open a new window, with just one lizard sit-
ting near the bottom. Click the Run button at the bottom right. When
you do so, the lizard will slowly move up the window, dragging a black
line behind it. Note that you can pause at any time by clicking the same
button, now labelled Pause, again. Click the pause button now.
While the simulation is paused, give the lizard a trait, just like you
did in the Designer Lizards window. Now run the simulation again. Note
that a label has appeared on the line below the lizard, marking the time
at which the first trait, a dewlap perhaps, appeared.
Evolving lizards 5
Now, while the simulation is running, click directly on the lizard itself.
It will become two lizards, each representing a different species. And
the line it was dragging will split as well. Note that both lizard species
have inherited dewlaps (or whatever trait you chose) from their common
ancestor, and that you can trace their evolutionary history by following
the branching lines up from the bottom of the window.
Pause the simulation and give one of the lizard species a new trait.
Note that, as before, the time at which the trait appeared is automati-
cally marked on the evolutionary tree. Now run the simulation, let a bit
of time go by, and click on one of your lizards to cause another specia-
tion event. Let some more time pass, then pause the simulation and
give one of your lizards another new trait. At this point, your evolution-
ary tree might look something like this:
This tree shows that the common ancestor of all three lizard species
had a dewlap. The common ancestor split into two daughter species,
and the daughter on the right evolved a tail crest. The tail crested spe-
cies then split, and one of its daughters evolved a collar.
Continue letting your own lizards evolve, occasionally adding new
traits and occasionally causing species to split, until you have seven
species and have used up all of the traits. (You will notice that this sim-
ulation will let each trait evolve only once, and will not let traits disap-
6 Do the traits of organisms provide evidence for evolution?
If you want to try again with either the designer lizards or the evolv-
ing lizards, you can reset either window by choosing the Reset com-
mand under the File menu.
A challenge
To explore the consequences of Darwin’s hypothesis in more detail, and
to test your own understanding of descent with modification, go to the
Windows menu in PhyloStrat and select Challenge. The Challenge win-
dow presents these seven lizards:
example, predicts that dewlaps should appear in the fossil record first,
then back crests, then head crests, then side blotches (if we can see Higher primates
them in fossils), then tail spots, and finally side stripes. This test, which
involves checking the correspondence between evolutionary trees, or
evolulationary trees
pared scatter plots showing the predicted order of trait appearance
based on reconstructed evolutionary trees versus the actual order of
trait appearance in the fossil record. If the predictions match the fossil
record perfectly, then the points in the scatter plots will fall on a diago-
nal line rising from lower left to upper right. In some cases, such as the
higher primates shown at right, top, the predictions based on recon-
structed trees are not especially good. In most cases, however, like the Horses
dinosaurs and horses shown at center and bottom right, the predictions
match the fossil record well. Norell and Nocacek concluded that predic-
tions based on reconstructed evolutionary trees are generally consis-
tent with the fossil record. This is evidence in favor of Darwin’s theory.
For other examples see Benton and Hitchin (1997) and Benton (1998).
Actual order of
appearance in the
fossil record
10 Do the traits of organisms provide evidence for evolution?
Literature cited
Benton, Michael J. 1998. Molecular and Morphological Phylogenies of
Mammals: Congruence with Stratigraphic Data. Molecular Phyloge-
netics and Evolution 9: 398–407.
Benton, Michael J. and Rebecca Hitchin. 1997. Congruence between
phylogenetic and stratigraphic data on the history of life. Proceed-
ings of the Royal Society of London, B 264: 885-890.
Norell, Mark A., and Michael J. Novacek. 1992. The fossil record and
evolution: Comparing cladistic and paleontologic evidence for ver-
tebrate history. Science 255: 1690-1693.