Genome Evolution Course 2009-2010

www.yanaiweb.com/genome

Itai Yanai, Technion – Israel Institute of Technology

Exercise Presentation as PP or PDF: Problem Set 3

Problem Set #3 assigned November 1^st, 2009

To be submitted as hard-copy in English or Hebrew on November 15^th, 2009 (at the beginning of class, 9:30am).

E-mail submissions will not be accepted.

Note: The November 8^th Class is canceled and will be made up January 24^th

Molecular Clocks

Problem 1: Warm-up. What’s wrong with the following sentence “Proteins A and B are 90% homologous”?

Problem 2: Homologuephobia. Consider the following gene ancestry (Shown in the figure, M-mouse, R-rat, H-human). An ancestral gene is duplicated forming A and B. A speciation event occurs separating the human and muroid lineage. Following speciation, B is duplicated forming B1 and B2. A speciation event subsequently leads to the modern mouse and rat organisms.

Fill in the blanks using orthologous, co-orthologous, inparalogs, and out-paralogs:

a. MB1 and MB2 are _______ with respect to human.

b. RB1 and RB2 are ________ to HB.

c. HA and HB are ______ with respect to mouse and rat.

d. MA and HA are _______.

Problem 3: Correcting for multiple hits

For this problem, you will need to download MEGA4: http://www.megasoftware.net/ and open the Drosophila_Adh.meg file (this is the Adh region for 11 flies).

Here is a tree of relationships among the flies (we learn what this means in the 5^th lecture).

Calculate the sequence distance between the D. melanogaster and D. pseudoobscura according to:

1. The fraction of bases different between them

2. The Jukes-Cantor corrected distance

Also, explain why the Jukes-Cantor distance is higher or lower.

Hints:

1. In the Distances tab, Select “choose model”. Then in the “model”->”nucleotide”->select you distance metric, then:

2. In the Distances tab, Select “Compute pairwise” then “Compute”

Problem 4: Relative rate test.

Again, use MEGA4 to answer the following question: Can you rule out the molecular clock in the Adh sequences of D. melanogaster and D. pseudoobscura since their divergence with S. lebanonensis? Hint: After opening the same file as in Problem 3: In the “Phylogeny” tab, Select “Relative rate tests”->”Tajima’s test”

Problem 5: Effects on the molecular clock.

Consider a pair of orthologs in mouse and rat. Explain how each of the following changes will affect the molecular clock as kept by the orthologs:

a) The mouse lineage evolves a significantly shorter generation time.

b) The rat lineage evolves very low mutation rates.

c) Changes in the environment cause the mouse orthologs to be unnecessary.