Genome 570

Phylogenetic Inference

Winter, 2010

Joe Felsenstein

Syllabus of lectures

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
     
1/11 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
     
1/18 Holiday: Martin Luther King, Jr. Day  
  20 Variants of parsimony, cont'd; Compatibility Chapters 7, 8
  22 Inconsistency and parsimony Chapter 9
     
1/25    "   "   "   "  "  
  27 A brief discussion of philosophy, parsimony, history etc. Chapter 10
  29 Distance matrix methods: UPGMA, Fitch-Margoliash Chapter 11
     
2/1      "    "      "    : Neighbor-joining, Minimum evolution, etc. Chapter 11
  3 DNA distances incl. rate variation among sites Chapter 13
  5 Protein distances and models Chapter 14
     
2/8 Restriction sites, RAPDs, microsatellites, etc. Chaps. 14, 15
  10 Likelihood methods Chapter 16 (through page 259)
  12 Hidden Markov Models of rate variation Chapter 16 (page 259 on)
     
2/15 Holiday: Presidents Day  
  17 Bayesian inference Chapter 18
  19 Testing trees, clocks, etc. by likelihood ratio tests Chapter 19
     
2/22 The bootstrap, the jackknife, etc. Chapter 20
  24    "   "   "      "   "   
  26 Paired sites tests Chapter 21
     
3/1 Trees from continuous characters and gene frequencies Chaps. 23, 24
  3 Comparative methods Chapter 25
  5 Another kind of tree: Coalescents Chapter 26
     
3/8 Likelihoods on coalescents Chapter 27
  10 Consensus trees. Tree distances. Chapter 30
  12 Tests based on tree shape. Chaps. 33

Final Exam:

2:30-4:30 Wednesday, March 17 in the lecture room.

Textbook:

Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts.

What is being left out

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. The chapter on drawing trees (Chapter 34) is also not being covered for lack to time.