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Topological Estimation Biases with Covarion Evolution

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Abstract

Covarion processes allow changes in evolutionary rates at sites along the branches of a phylogenetic tree. Covarion-like evolution is increasingly recognized as an important mode of protein evolution. Several recent reports suggest that maximum likelihood estimation employing covarion models may support different optimal topologies than estimation using standard rates-across-sites (RAS) models. However, it remains to be demonstrated that ignoring covarion evolution will generally result in topological misestimation. In this study we performed analytical and theoretical studies of limiting distances under the covarion model and four-taxon tree simulations to investigate the extent to which the covarion process impacts on phylogenetic estimation. In particular, we assessed the limits of an RAS model-based maximum likelihood method to recover the phylogenies when the sequence data were simulated under the covarion processes. We find that, when ignored, covarion processes can induce systematic errors in phylogeny reconstruction. Surprisingly, when sequences are evolved under a covarion process but an RAS model is used for estimation, we find that a long branch repel bias occurs.

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Acknowledgments

We thank the two reviewers for useful comments. This research was supported by Discovery grants awarded to E.S. and A.J.R. by the Natural Sciences and Engineering Research Council of Canada. A.J.R. and E.S. are fellows of the Canadian Institute for Advanced Research Program in Evolutionary Biology. A.J.R. is supported by a fellowship from the Peter Lougheed New Investigator Award from the Canadian Institutes of Health Research and the E.W.R. Steacie fellowship from NSERC.

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Authors and Affiliations

  1. Department of Mathematics and Statistics, Dalhousie University, B3H 4H7, Halifax, Nova Scotia, Canada

    Huai-Chun Wang & Edward Susko

  2. Department of Biochemistry and Molecular Biology, Dalhousie University, B3H 4H7, Halifax, Nova Scotia, Canada

    Huai-Chun Wang & Andrew J. Roger

  3. School of Biological Sciences, University of Liverpool, Liverpool, UK

    Matthew Spencer

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  1. Huai-Chun Wang
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  2. Edward Susko
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  4. Andrew J. Roger
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Correspondence to Huai-Chun Wang.

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Wang, HC., Susko, E., Spencer, M. et al. Topological Estimation Biases with Covarion Evolution. J Mol Evol 66, 50–60 (2008). https://doi.org/10.1007/s00239-007-9062-4

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  • DOI: https://doi.org/10.1007/s00239-007-9062-4

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