Date |
Topic |
Reading |
| 1/4 | What is a phylogeny? Parsimony - a small example | Chapter 1 |
| 6 | Parsimony algorithms - small parsimony problem | Chapter 2 |
| 8 | Exact enumeration - the number of trees | Chapter 3 |
| 11 | Searching tree space heuristically | Chapter 4 |
| 13 | Branch and bound | Chapter 5 |
| 15 | Reconstruction of ancestral character states. Branch lengths; Variants of parsimony |
Chapters 6, 7 |
| 18 | Holiday: Martin Luther King, Jr. Day | |
| 20 | Variants of parsimony, cont'd; Compatibility | Chapters 7, 8 |
| 22 | Inconsistency and parsimony | Chapter 9 |
| 25 | " " " | " " |
| 27 | A brief discussion of philosophy, parsimony, history etc. | Chapter 10 | 29 | More on history and philosophy; Distance matrix methods | Chapters 10, 11 |
| 2/1 | Distance matrix methods: Least squares | Chapter 11 |
| 3 | UPGMA, Neighbor-Joining; DNA distances | Chapters 11, 13 |
| 5 | DNA distances incl. rate variation among sites | Chapter 14 |
| 8 | Protein models and distances; Likelihood methods | Chapters 14, 16 (through page 259) |
| 10 | Likelihood methods | Chapter 16 (through page 259) |
| 12 | Likelihood methods; Hidden Markov Models of rate variation | Chapter 16 (page 259 on) |
| 15 | Holiday: Presidents' Day | |
| 17 | Bayesian inference | Chapter 18 |
| 19 | " " " | " " |
| 22 | Testing trees, clocks, etc. by likelihood ratio tests | Chapter 19 |
| 24 | The bootstrap, the jackknife, etc. | Chapter 20 |
| 26 | More bootstraps/jackknifes, Brownian motion trees | Chaps. 20, 23 |
| 29 | Continuous characters and covariances | Chapter 24 |
| 3/2 | Covariances; Comparative methods | Chapters 24, 25 |
| 4 | Another kind of tree: Coalescents | Chapter 26 |
| 7 | More on coalescents | Chapters 26, 27 |
| 9 | Likelihoods on coalescents | Chapter 27 |
| 11 | Consensus trees; Tests based on tree shape. | Chapters 30, 33 |
Owing to the press of time, I have not been able to schedule lectures on several major topics: Quartets methods (Chapter 12), Restriction Site and Short Tandem Repeat data (Chapter 15) Hadamard methods (Chapter 17), Paired Sites Tests (Chapter 21), and Invariants (Chapter 22). The (fun) chapter on drawing trees (Chapter 34) is also not being covered for lack to time. These include methods of particularly great interest 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.