Efficient biased estimation of evolutionary distances when substitution rates vary across sites

Molecular Biology and Evolution
Stéphane Guindon, O Gascuel

Abstract

This paper deals with phylogenetic inference when the variability of substitution rates across sites (VRAS) is modeled by a gamma distribution. We show that underestimating VRAS, which results in underestimates for the evolutionary distances between sequences, usually improves the topological accuracy of phylogenetic tree inference by distance-based methods, especially when the molecular clock holds. We propose a method to estimate the gamma shape parameter value which is most suited for tree topology inference, given the sequences at hand. This method is based on the pairwise evolutionary distances between sequences and allows one to reconstruct the phylogeny of a high number of taxa (>1,000). Simulation results show that the topological accuracy is highly improved when using the gamma shape parameter value given by our method, compared with the true (unknown) value which was used to generate the data. Furthermore, when VRAS is high, the topological accuracy of our distance-based method is better than that of a maximum likelihood approach. Finally, a data set of Maoricicada species sequences is analyzed, which confirms the advantage of our method.

References

Sep 1, 1992·Molecular Phylogenetics and Evolution·H J Bandelt, A W Dress
Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jan 1, 1983·Journal of Molecular Evolution·M NeiY Tateno
May 1, 1981·Die Naturwissenschaften·M Eigen, R Winkler-Oswatitsch
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Jan 1, 1995·Molecular Biology and Evolution·A RzhetskyM Nei
Jul 1, 1994·Journal of Molecular Evolution·Z Yang
Feb 1, 1994·Computer Applications in the Biosciences : CABIOS·G J OlsenR Overbeek
Nov 1, 1996·Molecular Biology and Evolution·A Rzhetsky, T Sitnikova
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·A Rambaut, N C Grassly
Jun 1, 2000·Molecular Biology and Evolution·M Steel, D Penny
Sep 1, 1996·Trends in Ecology & Evolution·Z Yang
Oct 1, 1996·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·K Z LanoueE E Hood

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Citations

Mar 25, 2009·Journal of Molecular Evolution·Alexis Criscuolo, Christian J Michel
Sep 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jimin PeiNick V Grishin
Dec 19, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Richard Desper, Olivier Gascuel
Apr 10, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Vladimir Makarenkov, Pierre Legendre
Sep 16, 2011·Nucleic Acids Research·Alix Boc, Vladimir Makarenkov
Jun 8, 2012·Nucleic Acids Research·Alix BocVladimir Makarenkov
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mark T HolderChristophe Dessimoz
Sep 4, 2012·Algorithms for Molecular Biology : AMB·Daniel DoerrIrad Yavneh
Dec 24, 2013·BMC Evolutionary Biology·Mehdi LayeghifardVladimir Makarenkov
Jul 28, 2005·Gene·Uri GophnaEliora Z Ron
Jun 9, 2010·Systematic Biology·Alix BocVladimir Makarenkov
Nov 2, 2002·Molecular Biology and Evolution·Vincent Ranwez, Olivier Gascuel
Jun 4, 2004·Molecular Biology and Evolution·Hervé PhilippeDidier Casane
Apr 10, 2008·Systematic Biology·Howard A RossWai Lok Sibon Li
Sep 16, 2005·Molecular Biology and Evolution·Uri GophnaW Ford Doolittle
Sep 29, 2017·Molecular Biology and Evolution·Maxime DéraspeJacques Corbeil

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