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MBE Advance Access published online on September 29, 2006
Molecular Biology and Evolution, 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
Accepted September 25, 2006

Research Article

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

Denis Baurain 1, Henner Brinkmann 1, and Hervé Philippe 1 *

1 Université de Montréal, Centre Robert-Cedergren, Université de Montréal (D.B., H.B., H.P.); Université de Liège (D.B.)

* To whom correspondence should be addressed.
Hervé Philippe, E-mail: herve.philippe{at}umontreal.ca


  Abstract

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 non-phylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a dataset of comparable size, we use three different strategies to reduce the non-phylogenetic 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 artefactual.

Keywords: animal evolution; phylogenomics; phylogenetic resolution; systematic error; non-phylogenetic signal.
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