Homework 2. Tree estimation (search & summary) and Character Evolution
As follow-up to Lab 2, turn in to me by lab next week (or earlier):
1. Your Laboratory 2 handout, with questions on pages 2, 3, and 4 answered. The last question asks you to compare five characters—please choose a few (3-5) characters and compare the parsimony ancestral state estimation with the maximum likelihood ancestral state estimation. What do the differences mean? (1-3 sentences)
2. Which of the Caminalcule character states are synapomorphies?
3. In lab, we ran a parsimony analysis that, in most cases, yielded more than one most-parsimonious tree. We summarized our tree sets using strict consensus and 50% majority rule consensus. Take a look at the pages following this one and tell me, what is the difference between these two techniques? (1-2 sentences)
4. As part of my studies on genus Pyrola, I am proposing that a new species be recognized. As evidence for this new species, I provide you with a 50% majority rule consensus tree showing relationships based on a five-locus dataset. Would a 75% majority rule consensus tree make my argument for recognition of the new species more or less compelling? Why? (1-3 sentences)