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MBE Advance Access published online on April 2, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg073
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted December 2, 2002
© 2003 Society for Molecular Biology and Evolution

Original Articles

Testing Substitution Models within a Phylogenetic Tree

Gunter Weiss 1* Arndt von Haeseler 2

1 Max-Planck-Institut für evolutiondäre Anthropologie, Leipzig, Germany; Heinrich-Heine Universität Düsseldorf, Germany
2 Heinrich-Heine Universität Düsseldorf, Germany; Forschungszentrum Jülich, Germany

* To whom correspondence should be addressed. E-mail: weiss{at}cs.uni-duesseldorf.de.


  Abstract

Phylogenctic tree reconstruction assumes frequently the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample covari-ance matrix of the set of substitution rate matrices estimated from pairwise sequence comparison. The sample covariance matrix is condensed into a one-dimensional test statistic {Delta}={Sigma}ln(l+{delta}i), where {delta}i are the eigenvalues of the sample covariance matrix. The test does not assume a specific mutational model. It analyses the variation in the estimated rate matrices.

The distribution of this test statistic is determined by simulations on the phylogeny estimated from the data. We study the power of the test under various scenarios and apply the test to X chromosome and mtDNA primate sequence data. Finally, we demonstrate how to include rate variation into the test.

Key Words: sequence evolution, tree reconstruction, test for homogeneity substitution models


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