Comparing Genomes to Determine Evolutionary Relationships

Using Bioinformatics (NCBI Database)

In this activity, you will be analyzing the genomes and evolutionary relationships of a variety of species. By utilizing The NCBI (National Center for Biotechnology Information) database, you will have access to thousands of genomes. The amount of information available (as you will soon see) is absolutely astounding!! (TYPE RESPONSES IN RED or BLUE)

Directions

I. Visit the NCBI Homepage https://www.ncbi.nlm.nih.gov/ and click on “Genomes and Maps”. Next click on “Genome” (blue link in the center of the page/also found in right side bar). Next click on “Browse by Organism”.

1. What types of genomes are currently available for making comparisons?

2. How many genomes are currently available to view?

II. Next, click on “Eukaryotes” at the top. Click on a species name that looks interesting. If there is a common name for this species, it will be shown in parenthesis after the species name. Keep searching until you find a species that displays a common name and record both of the following below:

Species Name: _____________ ________________ Common Name: ____________________

III. Next, return to the “Genome” Page and click on “Genome Data Viewer”. Here you will see a phylogenetic tree that encompasses over 660 eukaryotic genomes. If you hover over the names/pictures of the organisms, it will provide the species name for each. If you click on the “+” symbols, you will be shown more detailed phylogeny (common ancestry).

3. Click on the “+” symbol to the left of Humans. Then click the single arrow symbol two more times until you see the phylogeny for all primates. Which primate has a closer common ancestor to humans, a monkey or a chimpanzee?

4. Which species has a closer common ancestor to gorillas, a monkey or a human?

5. Which species shown on the diagram has the closest common ancestor to a chimpanzee?

IV. Click on the “<<” symbol to return to the original phylogenetic tree. Hover over the “Open” circle on the very left side of the tree (common ancestor to the eukaryotes). It will indicate how many eukaryotes are classified in this phylogenetic tree. Record that number below: Number of eukaryotes in the Phylogenetic Tree: __________ If you click and hold on this open circle, you will see that the eukaryotes are further subdivided. Continue to click and hold on the open circles displaying the GREATEST number of species (so the next one you should click & hold on is Opisthonkonta (and so on). Toward the end of the phylogeny you will see that both Whales and Pecora still have several remaining species. Click and hold on “Whales” and continue on. 6. What are the two major groups of whales displayed on the phylogenetic tree? 7. Click on a toothed or baleen whale. What is the species name? What is the common name? (You may need to hover over the blue or green circle to find the common or species name). 8. There are several genera (groups) shown for marine dolphins. Click on the genus Tursiops. What is its species name? What is its common name? 9. On the right side of the screen, click on “Browse Genome” (this page may take a minute or two to load). Here you will see a short chromosome that is ______________ base pairs in length (right corner of chromosome). On the left side of the screen, it is indicated that this is a “non-nuclear” chromosome. This means that the chromosome is outside the nucleus. It is actually found in one of the organelles of this dolphin species. “MT” is the abbreviation for this organelle. Which organelle do you think it is? 10. Hover over some of the colored boxes (these are the genes). Describe three different genes found here. (Hint: find the “Title” in the box that pops up). 11. Now go back to the Genome Data Viewer Page with the Phylogenetic Tree of Eukaryotes (you should be able to just click the back button at the top left side of the page). Click the “<<” button next to the dolphin phylogeny to get back to the original phylogenetic tree. The circles with pictures have complete genomes that can be displayed. Click on the human link. Then click on Browse Genome on the right side of the screen.