READINGS
Jan. T 20 1) Reading a phylogenetic tree; 2) Trait evolution on a phylogenetic tree
Lab 1 Data for phylogenetic analysis
R 22 1) Historical inference and the Hennigian method; 2) History (optional)
T 27 Parsimony I
R 29 Parsimony II
Feb. T 03 Clade support
R 05 Comparing data sets
T 10 Rooting
R 12 Gene duplication
Optional: a) Concordance; b) Species as ranked taxa
T 24 Introduction to ML
R 26 ML (Lewis 1998)
Mar. T 03 - R05 ML (Swofford 1996)
R 05 paper : Weins et al 2003
T 10 Molecular Dating, an overview
R 12 Hibbett 2001
Spring Break
T 24 No new reading
R 26 Intro to Bayesian Methods
T 31 Traditional and Bayesian Methods: (Holder and Lewis 2003)
Apr. R 02 More on Bayesian: a) Felsenstein on Bayes; b) Alfaro and Holder 2006
T 07 No new reading
R 09 Ané et al 2007 (Concordance Analysis)
T 14 Optional readings: STEM (Kubatko et al 2009), BEST (Liu 2008),
T 28 Testing correlated evolution in continous traits (Summers & Clough 2001)
R 30 Testing rates of evolution of continous traits (Davis et al 2007; suplemental material
May T 05 Key innovations : Hodges 1997
OPTIONAL: Discrete methods
website: nicacho@wisc.edu