Genome 570

Phylogenetic Inference

Winter, 2016

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
     
  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

Final Exam:

2:30-4:30 Wednesday, March 18 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.