Waksman Challenge I

Developed by the Teachers of BRITE 2006

2006/2007

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 determine which techniques seem to work best.

LEVEL 1

1. What is taxonomy? Why is taxonomy important to biologists?

2. What criteria have been used to traditionally classify organisms?

3. What criteria would you use to classify organisms? 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

4. 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 use molecular criteria to classify organisms. To gain a better understanding of what they are using, define the following:

a. Homology

b. Conserved sequence

c. Phylogenic tree

d. 16S rRNA

e. Cytochrome b

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.

CLUSTALW is a general purpose multiple sequence alignment program for DNA or proteins. It aligns the sequences so that identities, similarities and differences can be seen. Phylogenetic trees can be constructed from these data that allow you the opportunity to see evolutionary relationships between the different organisms.

Use the following link http://align.genome.jp/ to perform CLUSTALW analyses. Paste the sequences provided in the attached files into the text box on the CLUSTALW web page. Be sure you indicate if your sequence is DNA or protein using the button above the text box, and then select the ‘Execute Multiple Alignment’ button. At the bottom of the results page you will see a ‘Select Tree’ pulldown menu allowing you to build a phylogenetic tree using the desired technique. For each CLUSTALW analysis, create two different phylogenetic trees (one must be unrooted).

2. Use the sequences in the attached file to classify the organisms based on their cytochrome b amino acid sequences. (doc) (html)

3. Use the following sequences to classify the organisms based on their 16S rRNA.

4. Compare the classification results using the traditional characteristics vs. cytochrome b sequences vs.16S rRNA. (doc) (html)

a. Did you get the same classification (phylogenic trees) using physical characteristics, DNA comparisons, and amino acid sequence comparisons?

b. What are the 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

1. 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 translated amino acid sequence is shown below. Try to classify this organism using these data. Justify your reasoning. (doc) (html)