Table of Contents
ISRN Evolutionary Biology
Volume 2013, Article ID 391561, 8 pages
http://dx.doi.org/10.5402/2013/391561
Research Article

The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution

Program in Computational Biology and Bioinformatics, Institute for Genome Sciences and Policy, Duke University, 101 Science Drive, Box 3382, Durham, NC 27708, USA

Received 1 November 2012; Accepted 27 November 2012

Academic Editors: J. Fan, G. Glöckner, and J. A. Norman

Copyright © 2013 Nathan C. Sheffield. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Many commonly used models of molecular evolution assume homogeneous nucleotide frequencies. A deviation from this assumption has been shown to cause problems for phylogenetic inference. However, some claim that only extreme heterogeneity affects phylogenetic accuracy and suggest that violations of other model assumptions, such as variable rates among sites, are more problematic. In order to explore the interaction between compositional heterogeneity and variable rates among sites, I reanalyzed 3 real heterogeneous datasets using several models. My Bayesian inference recovers accurate topologies under variable rates-among-sites models, but fails under some models that account for compositional heterogeneity. I also ran simulations and found that accounting for rates among sites improves topology accuracy in compositionally heterogeneous data. This indicates that in some cases, models accounting for among-site rate variation can improve outcomes for data that violates the assumption of compositional homogeneity.