Study Questions - Reconstructing Phylogenies
Readings - Chapter 4, 9
1) How do you move from an unrooted tree, which only maps similarities, to a rooted tree that attempts to show ancestor-descendant relationships?
2) What are some of the shortcomings of sequence data for phylogenetic reconstruction?
3) What are the assumptions in UPGMA and how does likelihood estimation differ?
4) At the level of nucleotide substitutions, describe why some character changes might be more likely than others.
5) Given the follow data, calculate branch lengths.
| A | B | C | |
| A | 6 | 15 | |
| B | 12 | ||
| C |
6) What do the percentages above a branch represent in a bootstrapped tree?
7) What are some shortcomings of nucleotide data for reconstructing phylogenies? What are LINE's and SINE's and how do they address some of these problems?
8) Be able to repeat the examples done in class.