Genome Evolution Course 2009-2010

www.yanaiweb.com/genome

Itai Yanai, Technion – Israel Institute of Technology

Tutorial Presentation as PDF or PP.

Problem Set #5 assigned November 22^nd, 2009

To be submitted as hard-copy in English or Hebrew on November 29^th, 2009 (at the beginning of class, 9:30am).

Problem 1: Tree of life. Why was a ribosomal rRNA gene used to make the tree of life instead of the hemoglobin gene, for example?

Problem 2: Molecular Clock trees. Draw the UPGMA tree for the following sequences.

A: CTTAGTCCGTTACGTT

B: CTTTGTTCGTTACGTT

C: GCTTGTCTGCAACGTT

D: GCCTGTCTGTTACGTC

E: GCTTCCCCGTTATAAT

Problem 3: Roots. As shown in slide 7, for 4 OUT’s there are 3 unrooted trees and 15 rooted trees. This means that for each of the unrooted trees there are 5 rooted trees. Here is one of the three possible unrooted trees:

Draw the five possible rooted trees of this tree.

Problem 4: Maximum parsimony: For each of the 3 possible unrooted trees that relate A, B, C, and D, show the sites that suggest it. Overall, which tree is favored by the most sites?

A: CTGACGTCACGC

B: CCGGTATCGTAT

C: CTGGCGTGACGT

D: CCGGTAGGGGAC

Problem 5: Bootstrapping. You have built the following tree:

Resampling from the data 100 times you arrive at the 3 different types of trees with the following frequencies. Consolidate this information into one tree with bootstrap values.