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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.

How many different chromosomes do humans have not counting our mitochondrial DNA? _______

12. Click on a chromosome of your choice. The chromosome will be displayed in a horizontal position at the top of the screen. You can slide a blue “slider bar” back and forth to highlight certain regions of the chromosome. To do this, click and hold the very right side of the chromosome and drag the highlighted region to the left. You can also do this on the left side of the chromosome to make the region you are investigating a little smaller. The colored bars/boxes are the individual genes that are located below the chromosome. Again, just hover over a gene and you will see an information box pop up. In this same box, click on the first link located under “Links & Tools”. The name of the gene should then be displayed. Record the name of the gene below:

Name of Gene: _______________________

13. Next, hover over a gene labeled with the abbreviation “ENSG” with a long number after it. Once the information box pops up, click on the “View ENSEMBL” link located under “Links & Tools”. On the left side bar, click on “Gene expression”. Here you will see a gene expression atlas of the human body. If you hover over various parts of the body, the parts affected by this particular gene (mostly during embryonic development) will be highlighted. The chart to the right will also highlight the corresponding descriptions of the specific areas affected by the gene. In addition, you can switch between male and female gene expression as well as the brain. Record the following for the gene you have selected:

Gene Name: ______________________

Found on Chromosome: __________

Parts of the Body affected by this gene: ___________________________________________________

____________________________________________________________________________________

14. Continue to research three more human genes and fill in the following information below:

Gene Name: ______________________

Found on Chromosome: __________

Parts of the Body affected by this gene: ___________________________________________________
____________________________________________________________________________________

Gene Name: ______________________

Found on Chromosome: __________

Parts of the Body affected by this gene: ___________________________________________________
____________________________________________________________________________________

Gene Name: ______________________

Found on Chromosome: __________

Parts of the Body affected by this gene: ___________________________________________________
____________________________________________________________________________________

V. Now that you can navigate this database, it is time to research a few species you are interested in. Go back to the “Genome Date Viewer Page” and start browsing. Record your findings below for three species of your choice. Don’t be afraid to click on new links to discover new and exciting information & tools. At this point, you have only “brushed the surface” of this incredible resource!

Organism #1

Species Name: _______________ _______________ Common Name: _________________________

Phylogeny: ____________________________________________________________________________

________

_____________________________________________________________________________________

Number of Chromosomes in genome: ____________

Interesting discoveries:__________________________________________________________________

_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________

Organism #2

Species Name: _______________ _______________ Common Name: _________________________
Phylogeny: ____________________________________________________________________________

_____________________________________________________________________________________________

Number of Chromosomes in genome: ____________

Interesting discoveries:__________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________

Organism #3

Species Name: _______________ _______________ Common Name: _________________________
Phylogeny: ____________________________________________________________________________
_____________________________________________________________________________________________
Number of Chromosomes in genome: ____________

Interesting discoveries:__________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________