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TAXONOMY
Challenge:
An important goal of biology is the classification of organisms; that is, discovering
the evolutionary relationship of one organism to another. There are continuing
controversies in this field. In this challenge, you will look at some different ways to
classify organisms and attempt to evaluate which techniques seem to work best. You
will also use many of the technologies that scientists in the field use and determine
the classification of an unknown organism.
LEVEL 1
1. What is taxonomy? Why is taxonomy important to biologists?
2. What criteria have been used to traditionally (before the use of DNA and Protein
sequences) classify organisms?
3. List the criteria would you use to classify organisms?
4. Use these criteria to classify the following organisms into three groups. Use the
following website as a reference
(http://animaldiversity.ummz.umich.edu/site/index.html).
Justify why you grouped the organisms as you did.
Aardvark Orycteropus afer
Porpoise Phocoena phocoena
Elephant Elephas maximus
Giant Panda Bear Ailuropoda melanoleuco
Raccoon Procyon lotor
Sea Cow – manatee Trichechus manatus
Black Bear Ursus americanus
Human Homo sapiens
5. Scientists have long debated the relationship among bears, raccoons and pandas.
What reasoning do you think played a role in this debate?
LEVEL 2
1. Many scientists now incorporate molecular criteria (DNA and Protein sequences)
to classify organisms. To gain a better understanding of what they are using, define
the following:
a. Homology
b. Conserved sequence
c. Phylogenic tree
When we have DNA or protein sequences from many organisms, we can compare
them to one another in order to determine which organisms are more closely
related. It is inferred that species sharing similar sequences share a common
evolutionary ancestor
Certain genes and protein sequences have been chosen to be used in evolutionary
studies because their function and structures have been conserved through
evolution and are important to all life forms. Two such genes and /or proteins are:
16S rRNA: this is a gene (DNA) that codes for a ribosomal RNA that makes up part
of the ribosome
Cytochrome b: this protein is a very important part of the electron transport chain
in aerobic respiration.
When comparing DNA sequences OR protein sequences scientists will align the
different sequences together to see how similar they are. The idea is that the more
similar they are the closer they are on the evolutionary (phylogenetic) tree.
In order to compare sequences scientists use a program called a clustalW.
Use the following link http://www.genome.jp/tools/clustalw/ to perform
CLUSTALW analyses. Your teacher will demonstrate how to execute the alignment
and obtain your phylogenetic tree. However simple directs are below as a reference.

Paste the sequences provided in the attached files into the text box on the
CLUSTALW web page. Make sure you copy and paste the entire document it
is already properly formatted for you).

Be sure you indicate if your sequence is DNA or protein using the button
above the text box.

At the bottom of the results page you will see a ‘Select Tree’ pulldown menu
allowing you to build a phylogenetic tree.
2. Use the sequences titled Cytochrome b sequence to make a tree with the protein
sequences. SAVE THE TREE ON YOUR COMPUTER!!!
3. Use the sequences 16S rRNA to make a tree for with a DNA sequence. SAVE THE
TREE ON YOUR COMPUTER!!!
4. Compare the classification results using the traditional characteristics (level 1)
vs. cytochrome b sequences vs.16S rRNA (level 2).
a. Did you get the same classification (phylogenic trees) using physical
characteristics, DNA comparisons, and amino acid sequence comparisons?
b. What are the main differences between the ways each tree is organized?
5. What are some advantages and disadvantages of classifying organisms based on:
a. Physical characteristics
b. Cytochrome b sequences
c. 16S rRNA
6. How can classifying organisms based on just one criterion be misleading?
LEVEL 3
A bone fragment was found at the bottom of an ancient lake in upper New York
State. Because the fragment was so small, the organism from which it came could
not be identified. Instead, scientists extracted DNA from the bone and sequenced it.
One clone yielded a DNA sequence that appeared to be from the cytochrome b gene.
The scientists used the DNA sequence to translate the DNA into the protein.
The translated amino acid sequence is in the document title Unknown Cytochrome
b. Try to classify this organism using these data. Look at the matches and use all the
recourses available to you to determine the best identification of your organism.
Justify your reasoning.