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MBE Advance Access originally published online on April 2, 2003
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Mol. Biol. Evol. 20(4):572-578. 2003
DOI: 10.1093/molbev/msg073
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Testing Substitution Models Within a Phylogenetic Tree

Gunter Weiss*,{dagger}, and Arndt von Haeseler{dagger},{ddagger}

* Max-Planck-Institut für evolutionäre Anthropologie, Leipzig, Germany
{dagger} Heinrich-Heine Universität Düsseldorf, Germany
{ddagger} Forschungszentrum Jülich, Germany

Phylogenetic tree reconstruction frequently assumes the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample covariance 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} = {sum} ln(1 + {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 based 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 in the test.

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


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