MBE Advance Access originally published online on February 24, 2009
Molecular Biology and Evolution 2009 26(6):1259-1272; doi:10.1093/molbev/msp034
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Research Articles |
Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal
* ETH Zurich, Department of Computer Science, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
E-mail: schneadr{at}inf.ethz.ch
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. Because 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 criterion 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
Arndt von Haeseler, Associate Editor