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MBE Advance Access published online on February 24, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp034
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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

Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal

Adrian Schneider* and Gina M. Cannarozzi

ETH Zurich, Department of Computer Science and Swiss Institute of Bioinformatics

* Corresponding author address: ETH Zurich, Universitätsstrasse 6, 8092 Zürich, Switzerland. Phone: +41 44 632 7309, email: schneadr{at}inf.ethz.ch

Received for publication November 26, 2008. Revision received February 10, 2009. Accepted for publication February 18, 2009.

It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Since the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterium in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla-Chiroptera clade.

Key Words: outgroups • phylogeny • Mammalia • reconstruction artifacts


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