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Phylogenetic Model Choice: Justifying a Species Tree or Concatenation Analysis | OMICS International | Abstract
ISSN: 2329-9002

Journal of Phylogenetics & Evolutionary Biology
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Research Article

Phylogenetic Model Choice: Justifying a Species Tree or Concatenation Analysis

John David McVay1 and Bryan C. Carstens1,2*
1 Department of Biological Sciences, Louisiana State University, 202 Life Sciences, Baton Rouge, LA 70803, USA
2 Evolution, Ecology and Organismal Biology, The Ohio State Univeristy, 318 W. 12th Ave., Columbus, OH 43210, USA
 
Corresponding Author : Bryan C. Carstens
Evolution, Ecology and Organismal Biology
The Ohio State Univeristy, 318 W. 12th Ave., Columbus, OH 43210, USA
Tel: 614-292-6587
E-mail: [email protected]
Received May 02, 2013; Accepted July 24, 2013; Published July 29, 2013
Citation: McVay JD, Carstens BC (2013) Phylogenetic Model Choice: Justifying a Species Tree or Concatenation Analysis. J Phylogen Evolution Biol 1:114. doi: 10.4172/2329-9002.1000114
Copyright: © 2013 McVay JD, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Abstract

There are two paradigms for the phylogenetic analysis of multi-locus sequence data: one which forces all genes to share the same underlying history, and another that allows genes to follow idiosyncratic patterns of descent from ancestral alleles. The first of these approaches (concatenation) is clearly a simplified model of the actual process of genome evolution while the second (species-tree methods) may be overly complex for histories characterized by long divergence times between cladogenesis. Rather than making an a priori determination concerning which of these phylogenetic models to apply to our data, we seek to provide a framework for choosing between concatenation and species-tree methods that treat genes as independently evolving lineages. We demonstrate that parametric bootstrapping can be used to assess the extent to which genealogical incongruence across loci can be attributed to phylogenetic estimation error, and demonstrate the application of our approach using an empirical dataset from 10 species of the Natricine snake sub-family. Since our data exhibit incongruence across loci that are clearly caused by a mixture of coalescent stochasticity and phyogenetic estimation error, we also develop an approach for choosing among species tree estimation methods that take gene trees as input and those that simultaneously estimate gene trees and species trees.

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