Genome 570

Phylogenetic Inference

Winter, 2014

Joe Felsenstein

Syllabus of lectures

Date

Topic

Reading

     
1/6 What is a phylogeny? Parsimony - a small example Chapter 1
  8  Parsimony algorithms - small parsimony problem Chapter 2
1/10 Exact enumeration - the number of trees Chapter 3
     
  13 Searching tree space heuristically Chapter 4
  15 Branch and bound Chapter 5
  17 Reconstruction of ancestral character states.
Branch lengths; Variants of parsimony
Chapters 6, 7
     
1/20 Holiday: Martin Luther King, Jr. Day  
  22 Variants of parsimony, cont'd; Compatibility Chapters 7, 8
1/24 Inconsistency and parsimony Chapter 9
     
  27    "   "   "   "  "  
  29 A brief discussion of philosophy, parsimony, history etc. Chapter 10
1/31 Distance matrix methods: UPGMA, Fitch-Margoliash Chapter 11
     
2/3      "    "      "    : Neighbor-joining, Minimum evolution, etc. Chapter 11
  5 DNA distances incl. rate variation among sites Chapter 13
2/7 Protein models and distances Chapter 14
     
  10 Likelihood methods Chapter 16 (through page 259)
  12 Likelihood methods Chapter 16 (through page 259)
  14 Hidden Markov Models of rate variation Chapter 16 (page 259 on)
     
  17 Holiday: Presidents' Day  
  19 Bayesian inference Chapter 18
  21 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
  28 Trees from continuous characters and gene frequencies Chaps. 23, 24
     
3/3 Continuous characters and covariances Chapter 24
  5 Comparative methods Chapter 25
  7 Another kind of tree: Coalescents Chapter 26
     
  10 Likelihoods on coalescents Chapter 27
  12 Consensus trees. Tree distances. Chapter 30
  14 Tests based on tree shape. Chapter 33

Final Exam:

2:30-4:30 Wednesday, March 19 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 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.