PhD course “Advanced topics in phylogenetic analysis”, February 2005
Monday 21Introduction: Tasks and ToolsPeter HovenkampHere I want to set out the main task of phylogenetic analysis as the production of robust phylogenies. What are the problems, what is robustness, how can it be measured? Which tools are available to do so? I would like to introduce robustness against taxon sampling as a common element in the practical work for the rest of the course: robustness of phylogeny estimation, robustness of supertree construction, of date assigments, and perhaps also of alignment? Programs: TNT, WinSupport, PaupNT Tuesday 22Combining trees: supertree methodsPeter HovenkampIn recent years, some methods have been proposed in addition to the well-known MRP method. I wil try to have as many formalized methods available as possible, with a short introduction into the methodology of each of them.
Wednesday 23Bayesian analysisPeter Hovenkamp (introduction to Bayesian statistics and MCMC algorithms)I introduce the conceptual issues in Bayesian statistics, and will examine the working of the MCMC sampling method on basis of a simple graphical representation. Freek Bakker (Bayesian analysis)
Thursday 24Parsimony analysis of unaligned sequence data: theory and practiceJan De LaetStarting from a discussion of general cladistic theory, I will argue that sequence data can be analyzed without being aligned in advance of the analysis. The argument derives from a discussion of classical parsimony analysis of morphological data and concepts such as homology and maximization of explanatory power. Next, I will use POY to show how empirical data can be analyzed in accordance with these theoretical concepts. Insopfat as time permits, participants will be able to familiarize themselves with the necessary operations, with an emphasis on learning how POY integrates tree evaluation and tree search heuristics. Comparisons will be drawn with similar concepts as implemented in other programs such as TNT. I will also deal briewfly with some othe rprograms, in particular a POY-shell (provisionally named "oechel") to conduct jackknife analyses of unaligned sequence data within reasonable time.
Friday 25Molecular clocks and dating methodsJames Richardson
DataThere will be opportunities for all participants to use a dataset of their own, but I will also make a number of different datasets available all based on Rydin & Källersjö’s (2002) dataset. I will draw a number of random subsamples from the total dataset that we can use to examine the effects of taxon sampling in various contexts. Rydin,C., & M.Källersjö. 2002. Taxon sampling and seed plant phylogeny. Cladistics 18: 485-513. ManualsManuals and instructions for the programs to be used:
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