Phylogenetics Seminar, Fall 2009, PSPP 500-02

Instructor: Matt Lavin (email)

Place: 339 PBB

Day and Time: TBA

This seminar will cover the essentials of phylogenetic analysis including both parsimony and likelihood. Parsimony approaches to phylogenetic analysis will include combining different data sets and applying different assumptions to each data partition, using a step matrix, constraints analysis, clade support analysis, and analysis of potential conflict among data partitions. Likelihood approaches to phylogenetic analysis will include selection of DNA substitution models, testing for clock-like rates of evolution, and MC3 Bayesian analysis. Evolutionary rates analysis will include rate smoothing of phylogenetic trees that deviate from rate constancy. Depending on time and interest, the interface of ecology and phylogeny will be presented in the context of community phylogenetic structure and neutral biodiversity theory, and perhaps also correlated character evolution and independent contrasts. For all of these approaches, most of the software is free and is optimized to run on a PC with Windows XP (although the most versatile system is a Mac running Parallels and Windows). These programs include Phylip, ModelTest, MrBayes, Beast, Tracer, FigTree, TreeView, r8s and paloverde (a Linux-only program), and Phylocom and Phylomatic), as well as the statistical program R and associated phylogenetics packages such as Analysis of Phylogeny and Evolution (APE, by Emmanuel Paradis). The requirements for attendance, however, are that participants purchase PAUP and have their own phylogenetic data sets (the PC version of PAUP is available from Sinauer for $85). We will be running most programs in the batch file mode, and in this regard the PC version of PAUP runs as well if not better than the Mac and UNIX versions. The goal is to have participants not familiar with some of these methods take their data sets through all of the necessary steps to fully address their specific questions and hypotheses.

Go to the “downloads” page from the PAUP web site and obtain a PDF of the command reference document (2nd draft). We will be using this to find batch file commands to work through the various analyses that PAUP offers (the nexus format is standard in many phylogenetic analysis programs). The PAUP 3.1 Manual provides excellent introductory material for parsimony analysis.

Seminar Schedule (The following text files [.txt] can be renamed to have the Nexus extension [.nex], if so desired). I will finalized these data sets the night before we discuss them (i.e., by 9 PM Tuesday evening).

Parsimony analysis 1: data set 1 (basic parsimony search strategies). See how to import text files for analysis with PAUP: import.txt.

Parsimony analysis 2: data set 2 (multiple data blocks, partitioning, testing for congruence).

Parsimony analysis 3: data set 3 (constraints analysis: testing for congruence).

Parsimony analysis 4: data set 4 (character assumptions: dollo, stepmatrices, etc.).

Maximum likelihood: data set 5 (heuristic searches under likelihood).

Maximum likelihood: data set 6 (model selection via ModelTest).

Maximum likelihood: data set 7 (LRT) and data set 9 (AIC)

Bayesian analysis: data set 10 (MrBayes blocks for analyzing a single locus, or multiple loci simultaneously).

Bayesian analysis: (continued).

Phylogenetic ecology. data set 11 (exporting a phylogenetic distance matrix for import into a statistical program like R).

Plant Sciences and Plant Pathology