Phylogenetics Seminar, Fall 2008, PSPP
500-02 (CRN #26528)
Instructor:
Matt Lavin (email)
Tuesday,
12N-2PM, 339 PBB
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 (Joe Felsenstein -
http://evolution.genetics.washington.edu/phylip.html), ModelTest (David
Posada and Keith Crandall - http://darwin.uvigo.es/software/modeltest.html), MrBayes (Fredrik Ronquist and John P. Huelsenbeck
- http://mrbayes.csit.fsu.edu/), Beast and Tracer (Oxford
Phylogeny Group - http://beast.bio.ed.ac.uk/Main_Page), TreeView (Rod Page -
http://taxonomy.zoology.gla.ac.uk/rod/rod.html), r8s and paloverde (Mike Sanderson -
http://loco.biosci.arizona.edu/r8s/ - this is a Linux-only program), and Phylocom and Phylomatic (Cambell Webb - http://www.phylodiversity.net/phylocom/), as
well as the statistical program R
(http://cran.r-project.org/) 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
(David Swofford - http://paup.csit.fsu.edu/) and have
their own phylogenetic data sets (the PC version of
PAUP is available from Sinauer
for $85 - http://www.sinauer.com/detail.php?id=8060). 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