Phylogenetic Analysis of Molecular Data- Syllabus
Botany 563 - Spring 2009
Jan. T 20 Introduction
Lab 1 Data formats and generating a data matrix
R 22 Principle of phylogenetic inference
T 27 Introduction to Parsimony
Lab 2 Parsimony searches
R 29 Parsimony continued (Ivalú Cacho)
Feb. T 03 Weighting and decay
Lab 3 Non-parametric bootstrapping
R 05 Evaluating clade support in a parsimony framework
T 10 Comparing data sets
Lab 4 Statistics in a parsimony framework
R 12 Rooting and gene duplication
Take home midterm I
T 17 Gene trees and species trees
Lab 5 Integrative parsimony analysis
R 19 Long branch attraction
T 24 Introduction to maximum likelihood
Lab 6 Maximum likelihood
R 26 Maximum likelihood continued
Mar T 03 Models of molecular evolution
Lab 7 Maximum likelihood continued
R 05 Hypothesis testing with likelihood
T 10 Distance methods
Lab 8 Molecular dating
R 12 Molecular dating
Spring Break
T 24 Relaxed clock methods
Lab 9 Molecular dating with relaxed clocks
R 26 Introduction to Bayesian phylogenetics
T 31 Markov-chain Monte Carlo
Apr Lab10 Bayesian MCMC
R 02 Phylogeny and taxonomy
Take-home midterm II
T 07 Trees and species delimitation
Lab 11Confidence intervals on divergence times
R 09 Bayesian Concordance Analysis (Cecile Ané)
T 14 Using trees to reconstruct the evolution of discrete traits
Lab12 BUCKy
R 16 Correlated evolution of discrete traits
T 21 Modeling the evolution of continuous traits (assigned reading)
Lab13 Comparative methods I (discrete traits)
R 23 Comparative methods II
T 28 Correlated evolution of continuous traits
Lab14 Comparative methods II (continous traits)
R 30 Rates of evolution and continous traits (assigned reading); Paper draft due
May T 05 Key Innovations
Lab15 Comparative methods III
R 07
Final Exam: 12:25-2:25PM P.M. SUN. May 10, HUMANITIES 1217
Paper due: 12:00 A.M, SUN. May 10
(here :) )
website: nicacho@wisc.edu