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MBE Advance Access originally published online on August 17, 2009
Molecular Biology and Evolution 2009 26(12):2689-2697; doi:10.1093/molbev/msp184
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© The Author 2009. 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@oxfordjournals.org

Research Articles

General Heterotachy and Distance Method Adjustments

Jihua Wu and Edward Susko

Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada

E-mail: jihuaw{at}mathstat.dal.ca.

Heterotachy is a general term to describe positions in a sequence that evolve at different rates in different lineages. Kolaczkowski and Thornton (2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980–984.) recently described an intriguing heterotachy model that leads to topological bias for likelihood-based methods and parsimony methods. In this article, we show that heterotachy can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each site. Motivated by this idea, we propose a pairwise alpha heterotachy adjustment model, which gives us much improved topological estimation in the settings by Kolaczkowski and Thornton (2004).

Key Words: heterotachy • covarion model • distance method • tree estimation


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