Journal Article

A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Nicolas Lartillot and Hervé Philippe

in Molecular Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 27, issue 2, pages 371-384
Published in print February 2010 | ISSN: 0737-4038
Published online October 2009 | e-ISSN: 1537-1719 | DOI:
A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

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  • Evolutionary Biology
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Heterotachy, the variation of substitution rate at a site across time, is a prevalent phenomenon in nucleotide and amino acid alignments, which may mislead probabilistic-based phylogenetic inferences. The covarion model is a special case of heterotachy, in which sites change between the “ON” state (allowing substitutions according to any particular model of sequence evolution) and the “OFF” state (prohibiting substitutions). In current implementations, the switch rates between ON and OFF states are homogeneous across sites, a hypothesis that has never been tested. In this study, we developed an infinite mixture model, called the covarion mixture (CM) model, which allows the covarion parameters to vary across sites, controlled by a Dirichlet process prior. Moreover, we combine the CM model with other approaches. We use a second independent Dirichlet process that models the heterogeneities of amino acid equilibrium frequencies across sites, known as the CAT model, and general rate-across-site heterogeneity is modeled by a gamma distribution. The application of the CM model to several large alignments demonstrates that the covarion parameters are significantly heterogeneous across sites. We describe posterior predictive discrepancy tests and use these to demonstrate the importance of these different elements of the models.

Keywords: heterotachy; covarion; phylogenetics; model violations; posterior predictive discrepancy

Journal Article.  8644 words.  Illustrated.

Subjects: Evolutionary Biology ; Molecular and Cell Biology

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