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MBE Advance Access originally published online on September 29, 2006
Molecular Biology and Evolution 2007 24(1):6-9; doi:10.1093/molbev/msl137
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© The Author 2006. 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

Letters

Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors?

Denis Baurain*,{dagger}, Henner Brinkmann* and Hervé Philippe*

* Canadian Institute for Advanced Research and Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
{dagger} Département des Sciences de la Vie, Université de Liège, Liège, Belgium

E-mail: herve.philippe{at}umontreal.ca.

Accepted for publication September 25, 2006.

A recent phylogenomic study reported that the animal phylogeny was unresolved despite the use of 50 genes. This lack of resolution was interpreted as "a positive signature of closely spaced cladogenetic events." Here, we propose that this lack of resolution is rather due to the mutual cancellation of the phylogenetic signal (historical) and the nonphylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a data set of comparable size, we use 3 different strategies to reduce the nonphylogenetic signal: 1) increasing the number of species; 2) replacing a fast-evolving species by a slowly evolving one; and 3) using a better model of sequence evolution. In all cases, the phylogenetic resolution is markedly improved, in agreement with our hypothesis that the originally reported lack of resolution was artifactual.

Key Words: animal evolution • phylogenomics • phylogenetic resolution • systematic error • nonphylogenetic signal

Scott Edwards, Associate Editor


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