MBT/Genetics 541 Homework Assignment 1

Due Tuesday, Apr. 16

1. Make sure you have read the sections of Ewens and Grant (and if possible Durbin et al.) dealing with parsimony.
2. Go to the site ftp://evolution.genetics.washington.edu/pub/dnatree/dnatree.html There you will find a program (available for Windows, Macs, and Unix) which does the following:
   1. Simulates the random branching of lineages to make an evolutionary tree,
   2. Evolves a stretch of DNA sequence along this tree.
   3. Shows you an arbitrary tree for those species and lets you rearrange it interactively to find the most parsimonious tree you can.
3. Do these for a case with 10 species and 200 sites. You may need to try different settings for menu option 0 to get trees to be properly visibile. Use a rate of evolution of 0.1. Write down the true tree. Then look at the data, and then use the interactive rearrangement to try to find the most parsimonious tree. You will need to explore the options which are explained in the Web page.

4. Send Joe (by e-mail:joe@genetics.washington.edu) a report on how it went and how close the most parsimonious tree was to the true tree. If you feel adventurous, try a higher rate of evolution like 2.0 and see what that does to the accuracy.

   Accuracy of a tree is best assessed by seeing if it contains the same groups as the true tree. The trees that we are inferring are unrooted, so what could be compared are the internal branches of the true tree and of the estimate. Each branch divides the species into two sets -- those connected to one end of the branch and those connected to the other. For a tree of 10 species there are 8 (not 9) internal branches of the unrooted version of the tree. How many of them divide the species into the same sets in the two trees?