Bio H - Evolution
Determining Evolutionary Relationships:
Now that we know a little about Darwin’s theory and how it works, it’s time to discuss the evidence. Sure it
sounds like a good idea, but what physical evidence do we have that supports the ideas of evolution and
common ancestors.
Part 1: Geologic Evidence
The simplest evidence that organisms have changed over time exists in the organisms themselves, or at
least their remains. Sedimentary rock is a type of rock formed when sand, silt and other particles of eroded rock
are deposited and then exposed to large amounts of pressure. As a result all the particles are compressed into
solid rock. When you look at a cross section of sedimentary rock, you can see distinct layers or strata each of
which formed at a different time. The deeper the layer, the older it is.
Additionally, the remains of organisms that lived during the formation of each layer, get trapped and
fossilize in the rock. We can then dig deep into the strata and uncover the fossils of these organisms. The
further down in the strata a fossil is found, the older it is. Another pattern that we notice is that the further down
a fossil is buried, the simpler it is. It has been a general trend that life began as simple single celled creatures
and has become increasingly more complex as time has passed. Therefore, the older fossils are often the
remains of simpler creatures.
Fossil evidence cannot tell us which organisms are related to one another but it can provide information
about approximately when an organism lived, what environment it lived in and what other organisms it shared
the area with. The latter might provide us with information about possible predators or prey for the fossilized
organism.
In this activity you will propose where fossils from the following organisms might be found in the rock
strata. You have been given a list of organisms and the approximate times during which they lived on earth.
Your job is the following:
a. Assign each organism a symbol to represent its fossil.
b. Position each organism’s fossils in the layers in an appropriate place according to when it lived.
c. Make sure your positions are accurate in terms of when the organism lived as well as who lived during
the same time.
d. For the purpose of this exercise you may assume your rock has many fossils of each organism and
therefore can be shown in multiple layers if appropriate.
You may use the “empty” rock bed below for scratch work, but draw your final product neatly on your answer
sheet.
Organism A lived from 15,000 – 5,000 years ago
Organism B lived from 20,000 – 10,000 years ago
Organism C lived from 100,000 – 3,000 years ago
Organism D lived from 75,000 – 40,000 years ago
Organism E lived from 45,000 – 35,000years ago
Bio H - Evolution
Part 2: Comparative Anatomy
To support the ideas of evolution, we need to do a little more than simple show that organisms change over
time. We also need to prove that some organisms share common ancestors; that they are related. Like members
of the same family, we would expect that related species share some similarities that unrelated organisms don’t.
The simplest comparison we can make is the body parts. Comparative anatomy involves looking at anatomical
structures and determining the following:
Are they built the same way?
Are they used the same way?
The answers to these questions can provide a lot of information.
Homologous structures are body parts that share a common structure but may be used for completely different
things. For example, if you look at the bone structure of a bat wing, a dolphin flipper and a human arm they are
almost identical. (see diagram below) BUT, do you use your arm to fly? Does a bat use its wing to swim? (in
case you’re wondering, the answer is no) So how do we explain the uncanny similarity in bone structure?
The explanation is that once upon a time, Species Q had a body part built much like our arm, a dolphin’s fin
and a bat’s wing. What species Q used this body part for, we don’t know. Somehow a population of species Q
was divided into different groups each of which was subjected to different evolutionary pressures. This is
called divergent evolution. For one group (over a loooooong period of time) it became beneficial to use that
body part for swimming. Mutations that subtly changed the body part into a flipper were favored becoming
more and more common in the population. Eventually that group’s body part had turned into a fin. For another
group, swimming wasn’t necessary, but flying did provide an advantage. So mutations that subtly changed the
body part into a wing were favored until eventually it became a wing.
To make a long story short, the wing, fin and arm all started as the same body part, but each was exposed to
different selective pressures and therefore favored different mutations. They each changed in unique
directions, but maintained their fundamental structure. When two organisms have homologous structures, we
can assume that they share a common ancestor.
Bio H - Evolution
Analogous structures:
Sometimes when we compare organisms we find similarities that are more superficial, in other words they may
have a trait in common, but it is apparent that the two species went about getting that trait very differently.
For example, both bats and insects have wings. BUT are the wings similar on a structural level or just used for
the same thing?
In this case, it seems that the two types of wings have been “built” differently. They share little in terms of structure.
Unlike homologous structures we discussed above, it looks these organisms took completely different approaches to
make their wings.
Our explanation suggests that we started with two unrelated organism with different body parts. BUT since both lived in
an environment in which flying was beneficial, any mutations that created “wing-like” structures were favored in both
organism. Overtime, wings independently developed in both organisms. So, even though they started out as different
organism, they converged by developed similar traits after being exposed to similar selective pressures. This would be
convergent evolution.
Another example would be the shape of dolphins and penguins. Hopefully we know that dolphins are mammals and
penguins are birds. So obviously these two are not close relatives. BUT they are both aquatic and therefore need to be
“hydrodynamic” so they swim smoothly through the water.
In this case, their body shape is an analogous structure. Not because it started the same, but because it ended up the
same because of the similarity of environment.
Bio H - Evolution
Part 3: Comparative Embryology
Body parts are pretty visible, but as science has advanced it has allowed us to study less obvious
similarities to determine relationships. Comparing the embryos of different organisms and their patterns of
development also gives insight into which organisms might be more closely related.
In early stages of development many species look similar even if their adult forms are very different. Let’s face
it: a zygote is a zygote. You can’t visibly tell the difference between a single chimp cell and a single human
cell. BUT as the phases continue, the differences become more and more apparent.
Think about it this way. Let’s say you and your friend were each handed a lump of clay. You were told to
sculpt a chimp and your friend told to sculpt a flower. Probably pretty quickly we’d be able to tell that you
were sculpting different things. BUT if we told your friend to sculpt a human instead of a flower, you’d
probably both sculpt a head, a body, two arms and two legs. It wouldn’t be until we got to the details that we
could tell your sculpture from your friend’s. The same thing goes for developing embryos.
Depending on how long into development two embryos look alike, you can tell whether they are closely or
distantly related. Organisms that look different at early stages of development are probably not closely related.
Organisms that still look similar at late stages probably are closely related.
For example: The embryo on the far right is a human. Number the remaining embryos in order of
similarity to the human. (1 being the most similar, 5 being the least).
Bio H - Evolution
Now let us look at a slightly later stage in development. Again, the human is on the right. Number the
remaining 5 in order as you did above. Actually look at the pictures because they aren’t in the same order as
above.
Finally the easy phase. These should be easy to order.
Once you have the three stages above in the proper order, ask to see the key to see if you got all three stages
correct. Then complete the questions for this section.
Part 4: Comparative Biochemistry
The most modern mechanism of comparison relates to the biochemistry of the species. For starters ALL living
things have certain biochemical characteristics in common:
a. They all encode their genetic information in DNA
b. They all rely on ATP as the main energy molecule
c. They all use the same genetic code when translating their RNA messages into amino acid sequences.
It is unlikely that each and every organism alive happened to all evolve these mechanisms on their own. It is
more likely that one organism evolved these mechanisms and, since they worked so well, they were maintained
through years and years of evolution. Evolution follows the “if it ain’t broke, don’t fix it” philosophy of life.
Genetic traits that continue to help an organism survive do not change much at all.
But what else? Well, we know that if we examine your DNA and the DNA of your sibling, that the two
samples are going to be pretty close with a few key differences. Those differences make you unique, but are
usually only superficial. For example, chances are both of your DNA codes for two arms and two legs. You
both have a head. You both breathe oxygen and grow hair. Perhaps, it is just the shade of your hair or the
length of your leg that makes you different. But in the end, all the DNA that makes you living, an animal, a
mammal, a human is all the same.
Bio H - Evolution
The same is true for different species. We can think of the species on the great tree of life as a big family tree.
The more similar species are close relatives, while the very different species are distant relatives. Animals have
a lot in common. They all have to make the same type of animal cells and fit all the requirements of being an
animal. For this reason they share all the DNA that provides them with those traits. Mammals are a subsection
of animals. They share all the animal DNA PLUS any DNA that gives them the traits they need to be a
mammal. Therefore their DNA is more similar to each other than it would be to a fish’s DNA (who shares the
animal DNA, but not the mammal DNA.) At the end we can say that members of the same species are the most
closely related, followed by members of the same genus, followed by families, etc. Remember all the groups of
classification?
To sum up, comparing actual DNA sequences and actual protein sequences can tell us how many changes have
occurred between the two species. The more changes, the further apart the two species have grown. For this
exercise we are going to compare actual DNA sequences for a bunch of species and see if we can determine
who is more closely related. You will need access to the internet and word processing software.
Start off by going to our website and click on Bio J - Unit resources – Marking period 3
- Scroll down to the evolution section and you will see two links that you need
o Click on “Nucleotide BLAST(BLASTn) site” and it should open in a new window leave that
site open for right now.
o Back on our site, click on “Pax6 DNA sequences” This will open up a word document
As we have discussed, certain key genes are conserved or maintained throughout evolution if they continue to
provide an advantage to the organism. Interestingly scientist have learned that during development certain
genes act as “master switches” that turn on the formation of certain body parts.
For example, obviously building an eye requires many proteins and therefore many genes. BUT it turns out that
there is one gene that gets the whole process going. This gene is called (in many species) Pax6. Even more
interesting is the fact that many organisms share this same switch EVEN if they have different types of eyes!
So, in other words, the switch gene is the same, but the genes the switch turns on are completely different!
Once you have both the website and the sequence file open you are ready to begin. The idea is to use the
BLASTn website to compare each DNA sequence to the human sequence. The website does most of the work
so you don’t have to compare each and every nucleotide.
Step one: select the entire Human DNA sequence. Copy it and then switch to the BLASTn website. Paste the
Human sequence into the large text box titled “Enter Query Sequence”
Step two: go back to the file with all the sequences and copy the next DNA sequence. Paste this sequence into
the box titled “Enter Subject Sequence”. If you do not see a second box, make sure the “Align two or more
sequences” check box is checked.
Step three: Scroll down and click on the BLAST button. It may take you to a waiting page while it aligns your
two sequences. The results page should load automatically. Be patient. When the results page loads, scroll
down to the “alignments” heading. In the data you will see your two sequences aligned. Above them you’ll see
the word “Identities” followed by a fraction and a percentage. This represents the percentage similarity
between the two sequences. Record this percentage in your data chart.
Step four: repeat this process for the remaining species. Each time make sure you are comparing to the human
sequence.
Bio H - Evolution
Percent identity in Pax 6 Gene
Species 
Homo
sapiens
% Identity
to Human
gene
100%
Gallus
gallus
Bos
Taurus
Mus
musculus
Rattus
norvegicus
Danio rerio
Caenorhabditis
elegans
Analysis Questions:
Part 1:
Geologic Evidence
1. What is sedimentary rock, how is it formed and what can it tell us about how long ago different
organisms lived? How?
2. Suppose you find a fossil four layers down into the ground. You have looked everywhere but you can’t
find any living organisms that look like the fossil. What might this suggest about the fossilized
organism?
3. Using the rock strata below, draw in your fossils. Next to the layers, create a key to indicate which
symbol represents each organism.
Part 2: Comparative anatomy
1.
Describe the relationship between the following pairs of words and explain how they are different.
Examples may be used in addition to explanations:
a. Convergent vs. divergent evolution
Bio H - Evolution
b. Homologous vs. analogous structures
2. Bird and bat wings present an interesting dilemma. If we examine them closely, the structure is quite
similar but at the same time the common ancestor of the two species did not have wings. So while the
body part is the same, it developed into wings independently in each species. Does this make these
wings analogous, homologous or both? Explain.
Part 3: Comparative Embryology
1. How is embryonic development, (the growth of a single cell into a complex adult) much like the
evolution of organisms on earth?
2. Three species are examined at different stages of development. At stage 1, all three embryos look alike
and are indistinguishable. At stage two, embryos A and C still look alike but embryo B looks very
different. At the final stage, none of the three embryos resemble each other. What information can be
gleaned from this data? Explain.
3. Now that you know what the organisms are, does it make sense that the ones that looked most similar
turned out to be the species they did? Explain by referring to the classification of these organisms.
Bio H - Evolution
Part 4: DNA alignment
1. Use the data to rank the species in order from most similar to humans to most different. Then place the
species IN THAT ORDER from left to right as the column headings in the chart below.
2. Now let’s find out what these creatures are. Do some research on the common names and classification
of the following organisms.
Homo
sapiens
(most similar)
(least similar)
Common
name
Kingdom
Phylum
Class
Order
Family
Genus
Species
2. Remember that the taxons (classification groupings) are like a family tree. Kingdoms are very broad
and include lots of organisms, some of which are very different. Phyla are more specific, classes even
more specific. Explain how these classifications are supported by the DNA data.
3.
You can also do a blast sequence to compare amino acid sequences. If you do this it turns out that the
amino acid sequence for Pax6 is MORE similar to humans than the DNA sequence. How is this
possible when it is the DNA that codes for the protein? (Hint: think back to molecular genetics. Can
DNA change without changing the protein?)