SimBio Virtual Labs®

EvoBeaker®: Evidence
Evolutionary
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VIRTUAL
LABS
This lab is based on work initially supported with funding from the U.S. National Science
Foundation under Grant No.
0717495.
SimBio Virtual Labs®: EvoBeaker®
Evolutionary Evidence

A WARNING FROM SIMBIO ABOUT CHEATING

You should know that, among other things, we periodically tinker with the underlying models in our
simulations so that the results they produce (i.e. the "right answers") change, and we let instructors know
how to recognize cheating. We hope you do not succumb to the temptation
but, instead, go ahead and dive in. We've tried to make it a truly interesting experience and a fun way to
learn.

Prelude

Nobel-prize winning physicist Richard Feynman was known for being plain-spoken. Here is his description of
how science works:

"In general, we look for a new law by the following process. First, we guess...No! Don't laugh-
it's really true. Then we compute the consequences of the guess to see if this law that we
guessed is right-what it would imply. Then we compare those computation results to
nature-or, we say, to experiment, or experience-we compare it directly with observation
to see if it works. If it disagrees with experiment, it's wrong. In that simple statement is the
key to science. It doesn't make any difference how beautiful the guess is, it doesn't make
any difference how smart you are-who made the guess, or what his name is. It disagrees
with experiment, it's wrong. That's all there is to it."

In this lab we will use the scientific method-that is, the guess-and-check method-to investigate where Earth's
organisms came from.

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 SimBio Virtual Labs" I Evolutionary Evidence

Exercise 2: Designing Lizards

Exercise 1: Organizing Organisms

[1J If you haven't already, start SimUText® by double-clicking the program icon on your computer
or by selecting it from the Start menu. When the program opens, enter your Log In information
and select the Evolutionary Evidence lab from your Assignments window.

[ 2) At the top of the Evolutionary Evidence window, there is a pop-up menu for selecting an exercise.
Use this menu to select Organizing Organisms.

You should now see on your screen a Lab Notebook in which you will be able to organize your
thoughts and ideas. On the lower right hand corner, you have clipped a postcard of a tropical
island. The island is where you will soon be traveling to investigate the origin of several species
of lizards. Before starting your lizard research, however, it will be useful to do some big-picture
thinking.

[ 3) Scattered on the page of your Lab Notebook are photographs of seven different organisms.
There is a SELECTION (arrow) tool in the Tools Panel below the Notebook. Click on the
SELECTION tool to make sure it's active.

[ 4) Using the SELECTION tool, double-click one of the photographs. This will open a pop-up
window showing a list of which traits the animal in the photo possesses.

[5) Move the photos of the seven organisms around in your Notebook. Organize them in a way that
shows how you think the seven organisms are related to each other. You will likely need to try a
few different schemes before you find one that works well.

[ 6) Find and select the PENCIL tool. Use the PENCIL tool's pop-up menu to choose a color. Now
clarify your organization of the seven organisms by circling organisms that are closely related
with the pencil, or drawing lines connecting them. If you need to move a line you've drawn, use
the SELECTION tool. If you need to erase a line, use the DELETE (trash can) tool.

[ 7) If you decide you'd like to start all over again, click the START OVER button at the upper left
in your Lab Notebook.

[ 8) Once you've organized the seven photographs in a way that you like, snap a picture of your Lab
Notebook page. In order to copy your Lab Notebook page, mouse over the center of the page
and right-click (Windows) or Control-Click (OSX) and select "Copy View''. Then open a
document in a word processing program and use the paste command to place the screen shot in
the document. Save the document so that you can look back at it later.

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 SimBio Virtual Labs" I Evolutionary
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[ 8.1 ] Describe your organization scheme here. Explain how the organisms in the photos
are related to each other, and how your arrangement shows this.

Upon deliberation, the group members decided to do this type of organization based upon the activity simulations conducted is
because we decided to based it upon the complexity of an organisms they each are. Despite each of them being related to an
amoeba, they all are however, not related to each other. Thus, each of the organisms are just sharing a common ancestor. As to
which, we can see based on how we are able to organized as a group in regards to this stimulation activity. Which is based upon
the complexity of each organisms from one another.

It is time for you to travel to the tropics to begin your lizard research.

[1] Using the CONTENTS button in the upper left-hand corner of the screen, choose Designing
Lizards.

[ 2] Along the bottom of your Lab Notebook, you should see an Island View with five islands.
Each of the five islands is home to a single lizard. To get a closer look at the lizard on Island 1,
use the SELECTION tool and double-click on the lizard. A trait editor window will appear,
showing a more detailed picture of the lizard and a list of eight traits that the lizard could have.

[3] For the moment, the Island 1 lizard has none of these traits. But you are the Designer of Lizards, so
you can make the Island 1 lizard look however you like. Pick two or three traits, and use the popup
menus to make them present in the Island 1 lizard. As you do so, the picture of the lizard will
change. If you add a trait you don't like, you can remove it again.
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SimBio Virtual Labs" I Evolutionary Evidence

Exercise 2: Designing Lizards

[ 4] Once you are happy with your Island 1 lizard, close the trait editor window and move on to the
Island 2 lizard. Double-click on it to bring up the trait editor window. Pick another set of two or
three traits to add to the Island 2 lizard. Make at least one of the traits different from the ones you
added to the lizard on Island 1. When you're done, close the trait editor window.

[5] Continue across the chain of islands, designing a lizard species for each one. Give each lizard two
or three traits, but don't make any lizard's set of traits identical to those of another lizard. When
you are finished, close the trait editor window by clicking on its close button.

[6] When you have finished designing a different lizard for each island, click on the GO (single
arrow) button on the left side of the Control Panel. This will allow your lizards to reproduce
and populate the islands. Then click the STOP (square) button.

[7] Now it is time to compare the lizards you have designed and to look for patterns. First, make sure
your mouse is in selection mode by clicking on the SELECTION tool in the Tool Panel. Now
place the tip of the arrow on top of a lizard on Island 1. Click and hold the mouse button while
you drag the lizard onto your Lab Notebook, then release the button. This will save a picture of
the lizard in the Notebook.

[8] Drag a lizard from each of the other islands onto the Notebook as well.

[9] To give yourself more space to work, click on the HIDE triangle in the lower left corner of the
Island View. This will shrink it down to a small square. You can reveal the Island View again
by clicking on the SHOW triangle.

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SimBio Virtual Labs" I Evolutionary
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[ 10] Move the five lizards you have designed around in the window to organize them. Try to arrange
them so that each of the lizards is near other lizards with similar traits. For example, make sure
all of the lizards with frills are relatively near each other, the lizards with back crests are near
each other, and so on. Use the whole Notebook space for your arrangement. It may take some
experimentation to achieve a reasonable arrangement. Do not spend too much time perfecting
your arrangement; this may not be possible.

[ 11 ] Look at the example on the right. Think of

each circle as a group. The solid black
line represents the "Frill" group. The
dotted line represents the "Horns" group.
Using the PENCIL tool, you will make
similar groups for each trait represented
in the lizards you've designed.

[ 12] Start with "Back Crest:' Get the PENCIL

tool, select the color red, and draw a
single red circle surrounding all the
lizards that have back crests.

[ 13] Drag the "Back Crest" label onto the red

circle.

[ 14] Next draw an orange circle

surrounding all the lizards with dewlaps,
and drag the "Dewlaps" label onto it.
Then draw a yellow circle around all the
lizards with head crests, and so on.
Continue circling lizards until all of the
traits are circled.

Remember that if you need to erase a line you've drawn, you can use the DELETE tool. Don't
forget to switch back to the pencil tool before trying to draw a new circle.

[ 15] Once you are finished drawing and labeling circles, save a copy of your Notebook page. Move
your mouse to the center of the Notebook page and right-click (Windows) or Control-click
(OSX). Select "Copy View" and then paste this picture into a word-processor document and save
the document.

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 SimBio Virtual Labs" I Evolutionary Evidence

Exercise 2: Designing Lizards

[ 15.1 ] Consider how your different groups of designed lizards are related to each other. Are
the groups organized in some way? Are the lizards with frills, for example, a subset
of the lizards with side stripes? Or do the groups (circles) intersect in an unsystematic
way? For example, do the lizards with back crests overlap-but only partially-with
the lizards with horns?

The group is organized in such a way which they include lizards with similar traits. However, these traits do not correspond to
each other since the presence of the tail crest of these organisms have nothing to do with how the head crest presence appears
on each of these groups. Where the groups tail crest, head crest, and only the grills in an unsystematic way, partially intersect
with one another.

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SimBio Virtual Labs" I Evolutionary Evidence

Exercise 3: Evolving Lizards

How would the traits of your lizards be organized if, instead of having been independently designed,
the lizards had arisen by descent with modification from a common ancestor?

[1] To find out, go to the CONTENTS button in the upper left-hand corner of the screen and select
Evolving Lizards. Now only one island is inhabited by lizards. Under your direction, the
population on this island will evolve over time, and lizards will occasionally swim from one
island to another to establish new populations.

[ 2] In Designing Lizards, you played the Designer of Lizards, assigning traits to each of your
lizard populations independently of the others. This time, you are the Introducer of
Evolutionary Innovations. Choose the SELECTION tool in the Control Panel, then double
click on a lizard on the inhabited island. This will open the trait editor window.

[3l Pick one or two traits, and use the lizard's pop-up menu to ORDER TRAIT
make those traits present in the selected lizard. Note the traits
you introduced, in the order in which you introduced them, in
the table at right. Close the trait editor window.

Order Trait
1 Horns
2 Frill
3 Dewlap
4 Backcrest
5 Headcrest
6 Tailcrest
7 Spots
8 Stripes
2
[4]
Click the GO button to start the simulation running. Note how 3
the appearance of a novel trait in your population is indicated
by a change in the color of the lizards. 4

5
[sl Let the simulation run for 20-100 years (generations). If it goes
longer, that is fine! Then click the STOP button. 6

[6 l You are also the Mover of Lizards. Use the SELECTION 7

tool to drag a lizard from the occupied island to one of the
8
unoccupied islands.

[ 7] Introduce one or two new traits into the new population. Note the new traits in the table above.

[ 8] Click the GO button to start the simulation running again. Let the simulation run for 20-
100 generations, then click the STOP button.
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 SimBio Virtual Labs" I Evolutionary
Evidence

[ 9] Repeat steps 6 through 8, taking a lizard from the last island to a new one, until all five islands
are inhabited by lizards, and you have used all of the novel traits. Be sure to run the simulation
for at least 20-100 generations each time you introduce a novel trait, and don't forget to record
the new traits in the table.
* You may have noticed that our model is rigged so that any given trait changed only
once, and a changed trait never reverts to its original state. You also may have noticed
that
every new trait you introduce in to an island population quickly becomes common-and
ultimately universal-among the lizards on the island. These are both simplifications of
real life. In real life, new traits can arise independently in different populations, and
traits can appear and disappear over time. It is also true, of course, that in the real
world, new traits don't always persist in populations. Our simplifications are intended to

help you see the main points of this lab.

[ 10] After you have guided the evolution of five lizard species, drag a lizard from each island onto the
Notebook. Arrange the lizards so those with similar traits are near each other, just as you did in
the last exercise.

[ 11] Use the PENCIL tool to circle groups of lizards sharing traits, and drag labels to the circles, just
as you have done before.

[ 11.1 ] Consider how your different groups of evolved lizards are related to each other. Are
the groups organized in some way? Are the lizards with frills, for example, a subset
of the lizards with stripes? Or do the groups intersect in an unsystematic way?

Based on further deliberation, each of the groups are actually not organized in the same way, since I think they are all
organized in an unsystematic way.

[ 12] Copy your diagram from your Notebook, and paste it into your text document. To do this, move
the mouse to the center of your notebook page and right-click (Windows) or Control-click (Mac
OSX). Select "Copy View" and then paste the picture into your word-processor document.

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 SimBio Virtual Labs" I Evolutionary Evidence

[ 13] Look back at the images you have copied and saved from your Notebook. Compare your
designer lizards to your evolved lizards.

[ 13.1 ] Is there a difference in the way the groups of lizards with different traits are
related to each other when the lizards were independently designed versus when
they evolved by descent with modification from a common ancestor? Try to describe
the nature of this difference in organization in your own words.

Based on the group of lizards, there is a difference in the way each of the different traits are relate to each other. Since, when the
lizards are designed independently, we could trace back some of the certain traits to a common ancestor. Which is why there is a
certain order as to which these traits are passed on to the succeeding generation. A common example of which, is the horn and
frills which appears together always in each of the 5 species.

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 SimBio Virtual Labs" I Evolutionary
Evidence

Understanding the Distribution of Traits

[ 14] You have now seen island chains populated with lizards by two different processes. In the first,
you independently created a lizard species for each island. In the second, your lizard species
descended with modification from a common ancestor. These two processes led to sets of lizards
with different patterns of shared traits.

[ 14.1 ] Can you explain why independent creation is likely to produce organisms
whose traits are organized in just the way you discovered in Designing
Lizards?

The independent generation is most likely to produce organisms whose traits are all organized just the way, we had
discovered in designing lizards particularly because all of the traits have an order by which they are passed on.
Moreover, these traits are also dependent on one another.

[ 14.2] Can you explain why descent with modification from a common ancestor
produces organisms whose evolutionary innovations are organized in just
the way you discovered in Evolving Lizards?

The descent with modification from a common ancestor produces organisms whose evolutionary innovation are
organized in just the way we had discovered in evolving lizards because these evolutionary innovations, particularly each
one of them is optimized to serve a specified function and all of these depends on other mechanisms which that the specie
has.

[ 15] Examine the trait groups you circled in the Evolving Lizards exercise. Notice that each nested
set of traits consists of one or more traits that are widespread among lizard populations and other
traits that are restricted to just one or a few populations.

Look back at the table you filled in on page 5. Of the traits exhibited by your lizards:

[ 15.1 ] Which was the first to evolve?

Horns and Frills were the first ones to evolve.

[ 15.2] Which was the last?

Stripes were the last to evolve.

[ 15.3 1 Which are most widespread?

The most widespread are the horns and frill.
[ 15.41 Which are most rare?
The rarest is the stripes.

[ 15.5 1 Within a nested set of traits, what is the relationship between how widespread a
trait is and when the trait evolved?

The relationship between how widespread a trait is and when the trait is evolve happens when within a nested set of traits, if
the trait evolve earlier, then the trait will become more widespread.

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 SimBio Virtual Labs" I Evolutionary Evidence

Exercise 4: Disappearing Traits

[1) In the previous exercises, the original lizard (known as the ancestral lizard) did not have any of the
traits you were examining, and new traits were added as the lizards evolved or were designed.

[ 1.1 ] Make a prediction. What if the original ancestral lizard did have all the various traits
(horns, dewlap, etc.) and these traits were lost through evolution rather than gained.
Would that change how the lizards group together when they change through
evolution?

The group, predicted the yes, it would change how the lizard group together when they change through evolution, since
the reason for this is because the fundamental relationship of certain traits appearing that appear together is more linear
or will be much more as they are opposed to the more random method of gaining traits which is though evolution.

[ 2] To find out, go to the CONTENTS button in the upper left-hand corner of the screen and select
Disappearing Traits. As in Evolving Lizards, lizards inhabit only one island, and you will
direct the evolution of the lizards over time.

[3l Repeat the same steps you followed in Evolving Lizards. In simulation for 20-100
the original population, double click one of the lizards. In your generations each time you
role as Introducer of Evolutionary Innovations, you should remove a trait, and
now remove one or two traits (i.e., make them "absent") from remember to record
this lizard. Note the traits you remove in the table to the right, removed traits in the table.
including the word "no" (e.g., "No Dewlap") to emphasize that
the trait disappeared.

Order Trait
1 No Horns
2 No Dewlaps
3 No Frill
4 No Back crest
5 No Head
Crest
6 No Tail Crest
7 No stripes
8 No spots

[ 4] As before, click the GO button and run the simulation for

20-100 generations. Then move a lizard to another island,
remove one or two traits from the new population, and
continue until lizards inhabit all five islands. Run the
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SimBio Virtual Labs" I Evolutionary
ORDER
Evidence TRAIT

3 7

5 8

[5) After you have guided the evolution of five lizard species, drag a lizard from each island onto the
Notebook. As before, arrange the lizards so those with similar traits are near each other.

* You have been circling lizards that share changes from the original, ancestral lizard. These

changes are known as "derived" traits. In the earlier exercises, the derived traits were

all gains of traits, but in this exercise, the derived traits (changes from the ancestral
lizard) are losses of traits. So now you will circle groups of lizards that are all
missing the same trait.

[ 6) Use the PENCIL tool to circle groups of lizards that are all missing the same traits, and drag
labels to the circles as before. For instance, circle all the lizards that do not have a head crest and
label that group with NO HEAD CREST; circle lizards that do not have stripes and label the
group with NO STRIPES, and so on.

[ 7] Copy your diagram from your Notebook, and paste it into your text document.

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SimBio Virtual Labs" I Evolutionary Evidence

[ 8] Look back at the images you have copied and saved from your Notebook. Compare this set of
lizards that lost traits through evolution to the ones that gained traits through evolution in the
Evolving Lizards exercise.

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 SimBio Virtual Labs" I Evolutionary
Evidence

[ 8.1 ] Does the pattern you see when lizards evolve depend on whether the changes from
the ancestral lizard represent losses of traits or gains of traits?

The primary observation in this exercise is on whether the changes from the ancestral lizard present losses of traits as a
bases of dependency, which is like how the pattern or sequence is observe from the previous exercises which represents a
gain of traits.

[ 9] Now compare this set of lizards that lost traits through evolution to your designer lizards from the
Designing Lizards exercise.

[ 9.1 l When evolution (descent with modification from a common ancestor) produces
organisms whose evolutionary innovations are losses, is the resulting pattern
distinguishable from patterns of traits produced by independent creation? Explain.

This sequence of traits that is observe in this exercise is produced by evolution which is actually distinguishable from one
sequence or pattern produced by an independent creation, because of the primary reason that in this exercise and the
one before it----evolving lizards; the lineage for the origin of a specific trait tracing back to a common ancestor between a
specie or even sub-species. Which, in an independent design, the traceable lineage is actually unavailable, but instead
correlative straits will become very random.

* Through the rest of this lab, we will use an ancestral lizard that lacks all adorning
traits, because focusing on trait gains will make the lab less confusing than
mixing trait gains
and losses. However, if you think about looking for changes in traits over time, the
conclusions you draw will be the same regardless of whether changes represent gains
or losses. Indeed, when biologists examine this type of evidence, they consider gains

and losses of traits equivalently.

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SimBio Virtual Labs" I Evolutionary Evidence

Exercise 5: Predicting Patterns

You have discovered that when organisms evolve by descent with modification from a common ancestor, they
form nested sets of trait groups, like boxes inside boxes. The lizards that share trait Z are a subset of the
lizards that share trait Y, which are a subset of the lizards that share trait X. As a result, if we come across a
group of organisms whose traits naturally group into nested sets, we can make an educated guess that the
organisms arose by descent with modification from a common ancestor.

We can check the validity of this guess by the method described by Richard Feynman in the quotation on
page 1. We can compute a consequence of our guess and compare it to observations of the real world. If
our guess is wrong, we'll know it.

The consequence we can compute is the order in which the traits in a series of nested sets must have evolved.
Look at these lizards, and the nesting of their shared evolutionary innovations:

If we assume an ancestral lizard that was undecorated, this pattern of trait nesting predicts that horns
evolved before frills, and that back crests evolved before horns. Note that the pattern does not allow us to
predict when dewlaps evolved relative to frills, horns, and back crests. Nor does it allow us to predict
whether dewlaps evolved before or after spots.

Once we have identified a series of traits whose order of evolution we can predict, we can look at the order
in which the traits appear in the fossil record. In the real world, the fossil record is the collection of all the
fossils that have ever been found. In general, a fossil is any trace of an organism that lived in the past.
Commonly, we think of fossils as the petrified remains, or an impression preserved in rock, of an organism
that lived in the past. Examples include a mineralized tree trunk and a dinosaur's footprint. However, other
examples of fossils include an organic molecule found in a sample of crude oil, a mummy, and a penguin
frozen in an Antarctic glacier. To consult the fossil record is to refer to everything we know about earlier

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 SimBio Virtual Labs" I Evolutionary Evidence
organisms based on the physical clues they have left behind.

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SimBio Virtual Labs" I Evolutionary Evidence

For the computer-generated lizards above, the fossil record consists of snapshots of earlier generations of

lizards that have been preserved in the computer's memory. If our guess that the lizards were
generated by descent with modification is correct, then the actual order in which the traits appear in

the fossil record should match our predicted order.

This exercise will let you practice this method.

[1] Using the CONTENTS button in the upper left-hand corner of the screen, choose
Predicting Patterns.

In this exercise, seven populations of lizards will evolve by descent with modification
from an undecorated common ancestor. The populations are hidden from you as evolution and
migration are taking place. The island that is inhabited at the start, the order of appearance of the
evolutionary innovations, and the order of migration are different each time the simulation is run.
The lizards will automatically appear on the screen once all seven islands are inhabited.

[ 2] Click the GO button, wait until the lizards appear (about 750 generations), then click the STOP
button.

[3] Drag a lizard from each of the seven islands onto your Lab Notebook.

[ 4] Hide the Island View by clicking on the HIDE triangle in the lower left corner. You can reveal the
Island View again by clicking on the SHOW triangle.

[5] Organize the lizards in a row along the top of the page by their shared traits.

[ 6] Select the PENCIL tool. Hold down the SHIFT key and draw a single straight horizontal line
underneath all the lizards that share the rarest trait (there may be only one lizard). Now draw
another single line underneath all the lizards that share the second rarest trait. Continue
underlining all the lizards that share each of the other traits, going from rarest to most common
trait. The illustration on the previous page provides an example.

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 SimBio Virtual Labs" I Evolutionary Evidence

[ 7] Find a series of at least three or four traits whose order of evolution you can predict. In the first
column of the table below, list those traits in the order in which you predict they will appear in
the fossil record (1 for the trait that evolved first, proceeding to 3, 4, or 5 for the last trait to
appear). Note that the traits that evolved first are at the bottom of the table and the traits that
evolved later are listed above them. Don't fill in the middle column now; you'll do that later.

ORDER
TRAIT IN
FOSSIL RECORDORDER PREDICTED FROM NESTING
5 = Last trait to evolve; will be found only in the
youngest rock layers
4
3

2
1 = First trait to evolve; will be found in the oldest
rock layers
TRAIT ORDER IN FOSSIL RECORD ORDER PREDICTED FROM
NESTING
Stripes 8th 8th = Will be found in the youngest rock
layers
Spots 7th 7th = will be found in the 7th oldest layer
Back Crest 6th 6th = will be found in the 6th oldest layer
Tail Crest 5 th
5th = will be found in the 4th oldest layer
Horns 4 th
4th = will be found in the 4th oldest layer
Dew Lap 3 rd
3rd= will be found in the 3rd oldest rock
layers
Frill 2nd 2nd= will be found in the 2nd oldest rock
layers
Head Crest 1st 1st = will be found in the oldest rock
layers

[ 8] Is your prediction correct? Notice that there is a Fossil Record panel at the lower right of
the Simbio Virtual Labs window. Click the OPEN triangle.

[ 9] Once the Fossil Record panel is open, you should see layers of rock in which you can dig for
fossils. Get the SHOVEL tool from the Tool Panel and start digging. Just like in the real world,
you'll have to dig from the top down. Unlike the real world, we've arranged columns of rock
layers from all seven islands right next to each other.

[ 10] Dig all the way to the bottom.

[ 11 ] At the bottom of the Fossil Record, in the oldest rocks, you will see the oldest fossil
you've uncovered. Double-click it to get a closer look at the lizard it represents.

[ 11.1 ] Which trait does it have? This is the first trait that evolved among the seven
lizard species. Is it one of the traits in the series you listed in the table above? If so,
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SimBio Virtual Labs" I Evolutionary Evidence
put a "1" next to the trait in the "Order in Fossil Record" column in the table
above.

[ 12] In all later layers of rock, the oldest fossil showing each trait is indicated with a red dot. Work
your way up the fossil record from the bottom, examining all the fossils with red dots.

[ 12.1 ] If the new trait the fossil carries is not part of your series, ignore the fossil. If the
new trait is part of your series, add its order of appearance within the series to
your table above.

You may also want to look at a few of the other fossils to get a more complete sense of the fossil
record for your lizards.
* You may be skeptical that traits such as spots and stripes would ever be preserved in fossil
lizards. We have taken some liberties in our choices, picking traits that are easy to
show in pictures rather than traits that preserve well. Note, however, that
extraordinarily well preserved fossils do sometimes reveal the color patterns of

animals. For an example see Vinther et al. (2008).

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 SimBio Virtual Labs" I Evolutionary Evidence

[ 12.2] For each of the traits listed in

your table, place a dot on the
graph at right. The x-value
for the dot is the trait's order
of appearance in the fossil
record; the y-value is the
trait's predicted order of
appearance based on nesting.

[ 12.3 ] Draw, by eye, a best-fit line

through the points on your
graph.

[ 13] The graph you have drawn represents a method for checking your prediction about the order
traits would appear in the fossil record.

[ 13.1 ] What should your graph look like if your prediction is correct? What would
your graph have looked like if your prediction were wrong?

[ 14] The exercise of preparing this graph to check your predictions may seem unnecessary. After all,
you already knew that the computer had generated your lizards by descent with modification. But
look back at your saved Notebook diagram for your designer lizards.

[ 14.1 ] What would happen if you tried to carry out this same test on lizards that had
been created independently, like in the Designing Lizards section? Would you have
been able to predict the order in which the traits would appear in the fossil
record?

If we carry out the same test, which should have been done independently, like for example the designing lizard section then, we
would not have been able to showcase our prediction of the order of which each of the traits will appear in the fossil record.

© 2022, SimBio. All Rights Reserved. I

15
SimBio Virtual Labs" I Evolutionary Evidence

Exercise 6: Testing Darwin's Theory

You have completed your field work on tropical lizards. It's time to return home to the lab and think again
about the big picture.

[ 1 ] From the CONTENTS button in the upper left-hand corner of the screen, choose Testing
Darwin's Theory. Your Lab Notebook once again shows photographs of the seven real
organisms we started with.

Consider two claims about where Earth's organisms came from. The first is from John Ray, an
influential British naturalist of the 17th century and the first scientist to give a biological
definition of species. Ray believed that all species were created independently:

''...[O]ne species never springs from the seed of another."

The second claim 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..."

You now have a method for determining which claim is correct, and for testing Darwin's theory in
particular.

[ 2] Using the method you have practiced with lizards, assume a common ancestor lacks the seven
traits of interest, and arrange the seven real organisms along the top of your Notebook by the
key traits they share. Remember that double-clicking a picture will reveal a checklist of traits.

[3] Draw and label lines to show the trait groups. Start with the most rare trait at the top and work
your way down to the most widely shared trait at the bottom.

[ 3.1 ] How are the trait groups organized? Are they organized like they were for your
independently designed lizards, or like they were for your evolved lizards?

© 2022, SimBio. All Rights Reserved. I 16

SimBio Virtual Labs" I Evolutionary Evidence

[ 4] If Darwin's theory of descent with modification from a common ancestor is correct, you should
be able to accurately predict the order in which the seven traits will appear in the fossil
record. Use the first column of the table below to make your prediction.

ORDER IN
TRAIT FOSSIL RECORD ORDER PREDICTED FROM NESTING

7 = Last trait to evolve; will be

found only in the youngest rock
layers

4
3
2
1 = First trait to evolve; will be
found in the oldest rock layers

[5] Now open the Fossil Record panel. The fossils and text we've included represent the true fossil
record at the time of this writing.

[ 6] Working your way up from the bottom, double-click the seven key fossils indicated by red
dots, examine the photos, and read the text.

[ 6.1 ] In the second column of the table above, record the order in which the seven traits
actually appear in the fossil record.

[ 6.2 1 As you did previously, place

a dot on the empty graph at
right for each of the traits you
listed on the table.

[ 6.3 1 Draw, by eye, a best-fit line

through the points on
your graph.

[ 6.4] Does your evidence support

or refute Darwin's theory of
descent with modification? In
what way?

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17
SimBio Virtual Labs" I Evolutionary Evidence

As you may suspect, we hand-picked the real organisms, because we knew they
would work well and because we knew about the fossils we wanted to
show. Mark Norell and Michael Novacek (1992) performed a similar test of
Darwin's theory using data from two dozen groups of vertebrates. The
researchers picked the groups not because they knew in advance the
exercise would work but because the groups had fairly extensive fossil
records and were well-studied. For each group, they prepared a scatter plot
showing the predicted order of trait appearance based on nested sets of
shared evolutionary innovations 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 diagonal line rising from lower
left to upper right. In some cases, such as the higher primates shown at
right, top, the predictions based on nested sets are not especially good. In
most cases, however, like the dinosaurs and horses shown at center and
bottom right, the predictions match the fossil record well. Norell and
Novacek concluded that predictions based on nested sets of shared traits-
based, that is, on Darwin's theory-are generally
consistent with the fossil record. For other examples, see Benton and Hitchin (1997) and Benton (1998).

[7J The predictions about the fossil record that Norell and Novacek checked were based on Darwin's theory
that organisms are descended, with modification, from a common ancestor. The researchers found that
the predictions were generally correct.

[ 7.1 ] Based on their work, what conclusions do you think we can draw about the validity
of Darwin's theory of evolution by descent with modification?

The research you have done during this lab is consistent with the claim that amoebas, fish, salamanders,
alligators, and birds are all descended with modification from a common ancestor. In fact, biologists are
agreed that all organisms on Earth are descended from a single common ancestor, or at most a small
number of ancestors. This claim can seem extraordinary to someone new to the idea.

We have mostly considered evidence from nested sets of traits and the order in which traits appear in the
fossil record. There are other lines of evidence in favor of Darwin's theory. For example, there are a great
many similarities between alligators and birds beyond the checklist of traits you've looked at. For
© 2022, SimBio. All Rights Reserved. I 18
SimBio Virtual Labs" I Evolutionary Evidence

instance, the forelimbs of birds and alligators are built from the same set of bones in the same relative positions,
despite the fact that one is used for flying and the other for walking.

The striking similarities among Earth's organisms extend beyond anatomy to genetics. The genetic
machinery inside the cells of all organisms is so similar that it has become routine for genetic engineers to
move genes from organism to organism and find that they still work. For example, Shang-Hsun Yang and
colleagues (2008) recently took from a jellyfish the gene for a protein, called green fluorescent protein, and
inserted it into the egg cells of rhesus monkeys. After fertilizing the eggs in a dish, the researchers
implanted them into surrogate mother monkeys. The result was green fluorescent baby monkeys. That a
gene from a jellyfish works inside the cells of a monkey is evidence that jellyfish and monkeys are
descended from a common ancestor. Furthermore, when we use the degree of genetic similarity among
organisms to reconstruct their relationships, we get the same groupings as we do by looking at nested trait
sets. Alligators and birds, for example, are more genetically similar to each other than either is to
salamanders.

There is one last piece of evidence we'd like to present here. Consider your inference that birds and
alligators are descended from a common ancestor. Birds carry within their bodies hints of a reptilian past.
Just look at a chicken's scaly feet. Most biologists think that birds evolved from within the dinosaurs. If birds
evolved from dinosaurs, then we should be able to find transitional fossils that illustrate this transformation.

Note that transitional fossils are not ancestors. Look back at the lizards on page 7 0 in Exercise 5. The
species with a back crest and horns is a transitional form between the species with a back crest and the
species with a back crest, horns, and a frill. But it is not an ancestor of either. Instead, it is their
contemporary. But it illustrates a transition from the form on its left to the form on its right, and shows
that lizards in this group evolved horns before they evolved frills.

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19
SimBio Virtual Labs" I Evolutionary Evidence

[ 7.2] Take a minute to list some traits, or combinations of traits, that you might expect
to see in a dinosaur-to-bird transitional fossil.

Consider your inference that tetrapods (four-legged animals), such as salamanders,

alligators, and birds, evolved from within the fish.

[ 7.3] Take a minute to list some traits, or combinations of traits, that you might expect
to see in a fish-to-tetrapod transitional fossil.

[ 8] Now go back to the fossil record in Testing Darwin's Theory. Look at the two transitional fossils
indicated by green dots. Examine the photos and read the text.

[ 8.1 ] Microraptor gui, the four-winged dinosaur, has claws on its fingers, a long bony
tail, and feathers. Most modern birds lack claws, have short tails, and feathers. What
does the four-winged dinosaur tell us about how birds evolved their birdness?
Which came first, feathers, or the skeletal modifications typical of modern birds?
How
do the traits of the four-winged dinosaur compare to the predictions you made in
question 7.2?

[ 8.2 ] What does Tiktaa/ik rosaea, the "fishapod;' tell us about how tetra pods evolved
from fish?

[ 8.3 ] Are these transitional fossils consistent with Darwin's theory of descent with
modification from common ancestors?

[ 8.4 ] Overall, whose view about the origin of species seems to be correct, John Ray's or
Charles Darwin's? Why?

© 2022, SimBio. All Rights Reserved. I 20

Graded Questions

[1] Use the CONTENT button to launch Graded Questions.

[ 2] Enter your answers for each of the questions and click the SUBMIT button.
SimBio Virtual Labs" I Evolutionary Evidence

References

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Stratigraphic Data. Molecular Phylogenetics and Evolution 9: 398-407.

Benton, Michael J. and Rebecca Hitchin. 1997. Congruence between phylogenetic and stratigraphic data
on the history of life. Proceedings of the Royal Society of London, B 264: 885-890.

Bonaparte, J.F. and Vicente, M. 1979. El hallazgodel primer nidode dinosauriosTriasicos (Saurischia,
Prosauropoda),TriasicoSuperior de Patagonia, Argentina. Ameghiana 16: 173-182.

Botella, H. 2006. The Oldest Fossil Evidence of a Dental Lamina in Sharks. Journal of Vertebrate
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Botella, H., H. Blom et al. 2007. Jaws and Teeth of the Earliest Bony Fishes. Nature 448: 583-586.

Chen, J. Y., D. J. Bottjer et al. 2004. Small Bilaterian Fossils From 40 to 55 Million Years Before the
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Darwin, C. 1859. On the Origin of Species by Means of Natural Selection, First Edition. London: John
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Downs, J.P., E. B. Daeschler et al. 2008. The Cranial Endoskeleton of Tiktaalik roseae. Nature 455:
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Feynman, R. P. and C. Sykes. No Ordinary Genius: The Illustrated Richard Feynman. New York: W.W.
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Hirsch, K. F. 1979. The Oldest Vertebrate Egg? Journal of Paleontology 53: 1068-1084.

Johanson, Z. and M. M. Smith. 2005. Origin and Evolution of Gnathostome Dentitions: A Question of
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Kundrat, M. 2004. When Did Theropods Become Feathered? - Evidence for Pre-Archaepteryx
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Developmental Evolution 3028: 355-364.

Losos, J.B. 2007. Detective Work in the West Indies: Integrating Historical and Experimental

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Approaches to Study Island Lizard Evolution. Bioscience 57: 585-597.

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 SimBio
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Virtual Virtual I Evolutionary
Evolutionary Evidence Evidence

Miller, R. F., R. Cloutier, and S. Turner. 2003. The Oldest Articulated Chondrichthyan From the Early
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Norell, Mark A., and Michael J. Novacek. 1992. The fossil record and evolution: Comparing
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Ray, J. 1686. Historia Plantarum. London. (Quotation from volume 1, page 40; translated by E.T.
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