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Systematics Section / ASPT

Kelchner, Scot A. [1].

Fiddly phylogenetics: A report on model choice in published phylogenetic analyses.

A probability approach to phylogenetic analysis often involves a considerable number of parameters in the applied model of character evolution. Most commonly, these include corrections for transition bias, positional rate heterogeneity and unequal base frequencies. Although adding parameters to the model can potentially improve accuracy of phylogenetic analyses, it may also reduce precision of the estimate and in some cases result in systematic error and an incorrect topology. Do we need all these parameters in a probability-based analysis of molecular data? Can we determine if parameters exist that are generally useful in phylogenetics and others that are not? In this study, we broadly survey recent systematics publications that use the hierarchical likelihood ratio test (LRT) to select a "best fit" model of evolution for phylogenetic analysis of DNA sequences. Data sets include nuclear, chloroplast and mitochondrial regions from fungi, vertebrates, invertebrates, algae and plants. Our meta-analysis demonstrates clear trends in the selection of parameters for all molecular data sets and provides insights about the nature of DNA sequence evolution, phylogenetic analysis, and LRTs.


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1 - Idaho State University, Department of Biological Sciences, Campus Box 8007, Pocatello, Idaho, 83209-8007, USA

Keywords:
phylogenetic methods
model selection
phylogenetic inference
rate heterogeneity
meta-analysis.

Presentation Type: Oral Paper
Session: 38-8
Location: 400/Hilton
Date: Tuesday, August 16th, 2005
Time: 4:00 PM
Abstract ID:76


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