Chapter 4. Reconstructing evolutionary trees.Chapter 4 and article by Mercer and Roth.

Know the questions related to the squirrel reading. Know the answers to questions in the chapter quiz.

Terms to know:

1. Phylogeny
2. Homoplasy
3. Convergent Evolution
4. Reversal
5. Synapomorphy
6. Parsimony
7. UPGMA method (a type of distance method)
8. Maximum Likelihood method.
9. Outgroup
10. Clade
11. Bootstrapping
12. Molecular Clock
    

1. Questions 1-10, 12-17, 19 at the end of the chapter. Note, answers to these questions are available on the book's web page.
2. How does one use parsimony to identify the best estimate of an evolutionary tree?
3. Why do you have to be careful of homoplastic characters when estimating phylogenies?
4. Be able to interpret various types of trees as we have seen in class, including branching pattern, branch length, and bootstrap support.
5. What is a molecular clock, and how can you use it to find the age of a clade?
6. Discuss and interpret the molecular and morphological evidence that the whales are most closely related to hippos.
7. How do you use fossils to calibrate a molecular clock?
8. What do you use an outgroup for? What must you know about it in order for it to be useful?
9. What are the advantages of using molecular characters to estimate phylogenies?
10. How did phylogenetic analysis of the squirrel family provide insights into factors driving diversification in squirrels? What various kinds of data were required to gain these insights?
11. What do phylogenetic analysis suggest about hybridization between Homo sapiens and H. neandertalis?
12. What are 3 major difficulties in sequencing ancient DNA (these will be presented for Neandertals).