Date |
Topic |
Reading |
| 3/31 | What is a phylogeny? Parsimony - a small example | Chapter 1 |
| 4/2 | Parsimony algorithms - small parsimony problem | Chapter 2 |
| 4 | Exact enumeration - the number of trees | Chapter 3 |
| 4/7 | Searching tree space heuristically | Chapter 4 |
| 9 | Branch and bound | Chapter 5 |
| 11 | Reconstruction of ancestral character states. Branch lengths; Variants of parsimony |
Chapters 6, 7 |
| 4/14 | Variants of parsimony, cont'd; Compatibility | Chapters 7, 8 |
| 16 | Inconsistency and parsimony | Chapter 9 |
| 18 | " " " | " " |
| 4/21 | A brief discussion of philosophy, parsimony, history etc. | Chapter 10 |
| 23 | Distance matrix methods: UPGMA, Fitch-Margoliash | Chapter 11 |
| 25 | " " " : Neighbor-joining, Minimum evolution, etc. | Chapter 11 |
| 4/28 | DNA distances incl. rate variation among sites | Chapter 13 |
| 30 | Protein distances and models | Chapter 14 |
| 5/2 | Restriction sites, RAPDs, microsatellites, etc. | Chaps. 14, 15 |
| 5/5 | Likelihood methods | Chapter 16 (through page 259) |
| 7 | Hidden Markov Models of rate variation | Chapter 16 (page 259 on) |
| 9 | Bayesian inference | Chapter 18 |
| 5/12 | Testing trees, clocks, etc. by likelihood ratio tests | Chapter 19 |
| 14 | The bootstrap, the jackknife, etc. | Chapter 20 |
| 16 | " " " | " " |
| 5/19 | Paired sites tests | Chapter 21 |
| 21 | Trees from continuous characters and gene frequencies | Chaps. 23, 24 |
| 23 | Comparative methods | Chapter 25 |
| 5/26 | HOLIDAY (Memorial Day; last day of NW Folk Life Festival) | |
| 28 | Another kind of tree: Coalescents | Chapter 26 |
| 30 | Likelihoods on coalescents | Chapter 27 |
| 6/2 | Consensus trees. Tree distances. | Chapter 30 |
| 4 | Tests based on tree shape. | Chaps. 33 |
| 6 | Drawing rooted and unrooted trees | Chaps. 34 |
Owing to the press of time, I have not been able to schedule lectures on three major topics: Quartets methods (Chapter 12), Hadamard methods (Chapter 17), and Invariants (Chapter 22). These are all methods of particularly great interests to those concerned with the mathematical structures underlying the inference of phylogenies. Students will not be held for this material but are encouraged to read it anyway.