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MBE Advance Access originally published online on March 2, 2005
Molecular Biology and Evolution 2005 22(5):1161-1164; doi:10.1093/molbev/msi123
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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

Letter

Likelihood, Parsimony, and Heterogeneous Evolution

Matthew Spencer*,{dagger}, Edward Susko* and Andrew J. Roger{dagger}

* Department of Mathematics and Statistics and {dagger} Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

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

Evolutionary rates vary among sites and across the phylogenetic tree (heterotachy). A recent analysis suggested that parsimony can be better than standard likelihood at recovering the true tree given heterotachy. The authors recommended that results from parsimony, which they consider to be nonparametric, be reported alongside likelihood results. They also proposed a mixture model, which was inconsistent but better than either parsimony or standard likelihood under heterotachy. We show that their main conclusion is limited to a special case for the type of model they study. Their mixture model was inconsistent because it was incorrectly implemented. A useful nonparametric model should perform well over a wide range of possible evolutionary models, but parsimony does not have this property. Likelihood-based methods are therefore the best way to deal with heterotachy.

Key Words: Heterotachy • mixture models • likelihood • consistency • simulation


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