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MBE Advance Access published online on July 13, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi212
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted July 4, 2005

Letter

Maximum Likelihood Outperforms Maximum Parsimony even when Evolutionary Rates are Heterotachous

Sudhindra R Gadagkar 1* and Sudhir Kumar 2

1 Department of Biology, University of Dayton, 300 College Park, Dayton, OH 46469-2320, USA
2 Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-5301 USA; The School of Life Sciences, Arizona State University, Tempe AZ, 85287-5301 USA

* To whom correspondence should be addressed.
Sudhindra R Gadagkar, E-mail: gadagkar{at}notes.udayton.edu


  Abstract

Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position are unlikely to be the same in different species. In a recent study the influence of heterotachy on the performance of different phylogenetic methods was examined using computer simulation for a four-species phylogeny. Maximum parsimony (MP) was reported to generally outperform maximum likelihood (ML). However, our comparisons of MP and ML methods using the methods and evaluation criteria employed in that study, but considering the possible range of proportions of sites involved in heterotachy, contradict their findings and indicate that in fact, ML is significantly superior to MP even under heterotachy.

Keywords: Heterotachy; Phylogenetic inference; Maximum Likelihood; Maximum Parsimony.
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