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Online Assignment:  Determining the Molecular Clock Using Mitochondrial DNA Comparison.

In doing this online assignment you will become familiar with using an online tool to compare two sources of DNA (in this case Mitochondrial DNA or MtDNA).  The first thing to do is to go to the Sequence Server at the DNA Learning Center at Cold Spring Harbor Lab. 

When you go there you will see three possible servers to use.  You will click on the Sequence Server.  But before you do that you will have to Register.  Click on Register and type in your first initial followed by your last name.  Then you will be able to login on the Sequence Server.

Next you will need to follow the directions displayed on the small window that pops up. 

Here is a summary:

1. Click on the Manage Groups button. 
2. Select Classes
3. Look for a class on 8/17/00 at Applied Biosystems
4. Click on the check box and then on OK at the bottom.
5. You should see it appear on your space.
6. Once there select student 5913 (me)
7. Then select where it says none and add another student
8. Up at the top of your space you see the word Compare.
9. Just to the right it either says Align ClustalW or Phylogenetic Tree
10. Make sure Align ClustalW is displayed
11. Click on Compare.
12. A window should appear that shows the differences between the DNA segments in yellow.
13. Count the # of differences.  Make sure that you count only until you start to see lots of N's.  That means that one sequence didn't read as far as the other.  Look for comparisons that both read the same distance.

Go to the Server and Begin these Tasks:

Compare Me to a classmate

Compare Me to Neaderthal

Compare Me to the Iceman

Compare as many others as you have time.

Calculation of the Molecular Clock (When "Mitochondrial Eve" was around)

Assume that the oldest humanoid fossil diverged from apes anywhere from 5,000,000 to 4,000,000 years ago according to fossil records.

If there were approximately 50 differences from modern humans in mitochondrial DNA then:

4,000,000 years/50 difference = 80,000 years/difference

If there are 80,000 years per mutation  or 80,000/mutation and you find.... lets say 5 mutations, then you multiply them together and you get to cross cancel the mutations and you are left with 400,000 years.  That would be the estimate for our mitochondrial eve. 

Use the 80,000 years/difference stat and try to calculate mitochondrial eve for the number of mutations you get on average for the members of my class.  Do a random sample and then average to get the average number of differences between modern humans.

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