Comparative DNA Analysis – Part II
DNA Evidence & Evolution
How do scientists use DNA to figure out what organisms are most
closely related?
1. Go to
http://bioquest.org/bedrock/problem_spaces/whippo/index.php or search for
“Whippo” using Google and find the website this way. WHAT DOES “WHIPPO” REFER TO?
2. Click on “Background” on the left side of the webpage. Read “The big picture of whale
evolution.” WHAT ANIMALS ARE WHALES RELATED TO?
3. An ungulate is a hoofed animal. Although whales no longer have hooves, they are similar to
ungulates in other ways, and scientists think that whales and other ungulates evolved from a
common ancestor. There are different hypotheses about the evolutionary relationships
among the whales and various ungulates. Study the 2 trees. WHICH TREE SEEMS MORE
LIKELY TO YOU AND WHY?
In this “tree”, the whales are not
closely related to any one group
in particular. The scientist is
inferring that the whales had a
common ancestor with hippos,
pigs, ruminants, and camels that
branched off from the odd-toed
ungulates a long time ago.
In this “tree”, the whales are
most closely related to hippos.
The scientist is inferring that the
whales had a common ancestor
with hippos that branched off
from the ruminants in the past,
but not as far back in time as in
Tree A. The scientist is also
inferring that the whales are
more closely related to hippos
than ruminants, to ruminants
than pigs, to pigs than camels,
and to camels than odd-toed
ungulates.
4. Click on “Data” on the left side of the webpage. Scientists have collected data on the DNA
of the following animals.
Bovidae (sheep, cattle, bison, springbok and antelopes)
Cervidae (deer)
Girafidae (giraffes)
Tragulidae (chevrotains)
Hippopotamidae (hippos)
Camelidae (camels and llamas)
Tayassuidae (peccaries)
Suidae (pigs)
Physeteridae (sperm whales)
Delphinoidea (beluga whale, dolphins and porpoises)
Ziphiidae (beaked whales)
Mysticeti (baleen whales)
Outgroup (horses)
5. In order to compare DNA, scientists must first find sections of DNA that code for the same
thing. We will use the data for the DNA section called b -casein exon 7

Click on the “Get the Data” box.

CAREFULLY: Scroll down and find “b -casein exon 7” and click on “raw”.

These are actual DNA sequences from the animals listed! Important: DO NOT
CHANGE ANYTHING ABOUT THIS DATA. IT IS ALREADY WRITTEN IN THE
FORMAT THAT WE WILL NEED LATER.

Save this information on your computer by using “Save as” and saving it to your
desktop. Your file should be named __bcas__. If you do not understand, ask your
teacher for help.
6. Go to Biology Workbench at http://workbench.sdsc.edu
7. Log in by clicking on “Click to Enter the Biology Workbench 3.2”
Username: __computer
Password: keyport
No capitals
Type in the number of the computer that you are using
followed by the word “computer” (no spaces).
8. Scroll down and find the grey “Session Tools” box and click on it.
9. Note: If you do not see the correct screen on this next step, you may have to click once or
twice on “click here to toggle between menus and buttons” in the Biology Workbench box at
the top of the page. (Ask your teacher for help if you cannot figure this out.)
Go to the pull down menu that says “Select Session: Then Choose Tool” and change it to
“Start New Session”
10. Name your session “Hour __ Whippo” under Session Description and press “Start New
Session” again.
Your hour.
11. Now find the grey “Nucleic Tools” box and click on it.
12. Go to the pull down menu that says “Select Sequence(s): Then Choose Tool” and change it to
“Add New Nucleic Sequence”
13. Now upload your DNA sequences by clicking on “Browse”, selecting the file you saved
earlier, and then clicking on “Upload File”
14. Now find the grey “Save” box and click on it.
15. Go to the pull down menu that says “Select Sequence(s): Then Choose Tool” and highlight
“Select All Sequences” instead.
16. Go to the pull down menu that says “Select Sequence(s): Then Choose Tool” and highlight
“CLUSTALW - Multiple Sequence Alignment” instead.
17. On the left side of the screen, go to the pull down menu that says “Unrooted Tree” and
change it to “Rooted and Unrooted Trees”. Then find the grey “Submit” box and click on it.
18. Wait PATIENTLY for results. This can take a minute or more at times.
19. Scroll down to see how the sequences line up and see what the Phylogenetic Trees look like.
Do they look like the Phylogenetic trees below and on the next page? ______
20. WRITE THE COMMON NAMES NEXT TO THE FAMILY NAMES USING THE INFORMATION FROM THE
SECOND PAGE. Do the same on both phylogenetic trees so that they are easier to interpret.
Rooted
Phylogenetic
Tree
Unrooted
Phylogenetic
Tree
Analysis Questions
1. Rooted and Unrooted Phylogenetic Trees are helpful in making some determinations about
how closely related organisms are. Based on your Rooted Phylogenetic Tree, what group are
the whales most closely related to?
2. By looking at the Unrooted Phylogenetic Tree, do you come to the same conclusion?
3. The Unrooted Phylogenetic Tree is actually more accurate to look at. Not only can you see
how the animals are grouped, but the distances of the lines represent the amount of
differences that exist in the DNA sequences. In other words, short lines mean that the DNA
sequences were more similar than long lines. According to the Unrooted Phylogenetic Tree,
what groups are the most closely related?
4. According to the Unrooted Phylogenetic Tree, what group is the least closely related to all of
the other groups?
5. According to the Unrooted Phylogenetic Tree, what group are hippos most closely related to,
whales or to pigs?
6. Think and Discuss: Do you think that the common ancestor of all of these animals lived in
the water or on land? Why? What do scientists currently think about this same question?