Statistics 992

Statistical Phylogenetics


Spring 2004 Course Schedule

WeekDateTopicsReadingHomework
1Jan 21, 23 Introduction
Phylogenetic Trees
Parsimony
Felsenstein Chapters 1-3, 9
(We may come back to Chapter 4.)

Due by 6:00AM, Sunday, January 25: Email me two questions about the reading.
Due Monday, January 26: Come to class prepared to discuss the reading.

Due Friday, January 30: Homework 1

[Solution]

2Jan 26, 28, 30 Parsimony Felsenstein Chapters 4 and 11

Due by 6:00AM, Sunday, February 1: Email me two questions about the reading.
Due Monday, February 2: Come to class prepared to discuss the reading.

 
3Feb 2, 4, 6 Distance Methods
Continuous-time Markov chains
Felsenstein Chapter 13

Due by 6:00AM, Sunday, February 8: Email me two questions about the reading.
Due Monday, February 9: Come to class prepared to discuss the reading.

Due Friday, February 13: Homework 2

[Solution]

4Feb 9, 11, 13 Continuous-time Markov chains
UPGMA
Neighbor-joining
Maximum Likelihood
Felsenstein Chapter 16

Due by 6:00AM, Sunday, February 15: Email me two questions about the reading.
Due Monday, February 16: Come to class prepared to discuss the reading.


Notes on Markov Chains

 
5Feb 16, 18, 20 Likelihood Methods Holder and Lewis (2003). Nature Review: Genetics

Huelsenbeck et al. (2001). Science


Note: Please read the articles, but you need not send questions for this reading. You may defer questions until the next week.
 
6Feb 23, 25, 27 Bayesian Phylogenetics Felsenstein Chapter 18

Larget and Simon (1999). Molecular Biology and Evolution

Due by 9:00PM, Monday, March 1: Email me two questions about the reading.
Due Wednesday, March 3: Come to class prepared to discuss the reading.

Due Friday, March 5: Homework 3

[Solution]

[R code]

7Mar 1, 3, 5 Computation, Bayesian Phylogenetics, Bootstrap Felsenstein Chapter 20

Felsenstein (1985)

Efron, Halloran, and Holmes (1996)

Due by 6:00AM, Sunday, March 7: Email me two questions about the reading.
Due Monday, March 8: Come to class prepared to discuss the reading.

oneBranch.C

oneBranch.R

8Mar 8, 10, 12 Bootstrapping Phylogenies Susan Holmes (2003) Statistical Science

Newton (1996) Biometrika


Note: Please read Susan Holmes at some point (the early sections are especially clear).

Please give Newton a read by Friday (but do not become stressed about the details).

 
BreakMar 15, 17, 19      
9Mar 22, 24, 26 Bootstrapping, Reversible Jump MCMC, Model Selection Mark Pagel (1999) Systematic Biology

Rasmus Nielsen (2002) Systematic Biology

Huelsenbeck, Nielsen, and Bollback (2003) Systematic Biology

Due by 6:00PM, Thursday, April 1: Email me two questions about the reading.
Due Friday, March 31: Come to class prepared to discuss the reading.

 
10Mar 29, 31, Apr 2 Reversible Jump MCMC    
11Apr 5, 7, 9 Evolution of discrete characters
Mapping mutations on phylogenies
   
12Apr 12, 14, 16 Goodness-of-fit Tests, Tests of Topology Assigned reading for Monday

Felsenstein Chapter 21.

Shimodaira and Hasegawa (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution.

Goldman, Anderson, and Rodrigo (2000). Likelihood-based tests of phylogenies in phylogenetics. Systematic Biology

Due by 6:00AM, Sunday, April 18: Email me two questions about the reading.
Due Monday, April 19: Come to class prepared to discuss the reading.


Other background reading (not assigned) Posada and Crandall (1998)

 
13Apr 19, 21, 23 Tests of Topology, Genome Arrangements    
14Apr 26, 28, 30 Genome Arrangements (parsimony)    
15May 3, 5, 7 Genome Arrangements (Bayesian)   Due Friday, May 7: Homework 4


Last modified: May 3, 2004

Bret Larget, larget@stat.wisc.edu