Nonadaptive Amino Acid Convergence Rates Decrease over Time

Molecular Biology and Evolution
Richard A GoldsteinDavid D Pollock

Abstract

Convergence is a central concept in evolutionary studies because it provides strong evidence for adaptation. It also provides information about the nature of the fitness landscape and the repeatability of evolution, and can mislead phylogenetic inference. To understand the role of adaptive convergence, we need to understand the patterns of nonadaptive convergence. Here, we consider the relationship between nonadaptive convergence and divergence in mitochondrial and model proteins. Surprisingly, nonadaptive convergence is much more common than expected in closely related organisms, falling off as organisms diverge. The extent of the convergent drop-off in mitochondrial proteins is well predicted by epistatic or coevolutionary effects in our "evolutionary Stokes shift" models and poorly predicted by conventional evolutionary models. Convergence probabilities decrease dramatically if the ancestral amino acids of branches being compared have diverged, but also drop slowly over evolutionary time even if the ancestral amino acids have not substituted. Convergence probabilities drop-off rapidly for quickly evolving sites, but much more slowly for slowly evolving sites. Furthermore, once sites have diverged their convergence probabilit...Continue Reading

References

Jul 10, 1998·Molecular Biology and Evolution·A L Halpern, W J Bruno
Dec 29, 1998·Molecular Biology and Evolution·Z YangM Hasegawa
Mar 13, 1999·Journal of Molecular Biology·D D PollockN Goldman
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Jul 30, 2003·Molecular Biology and Evolution·Douglas M RobinsonJeffrey L Thorne
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Mar 12, 2004·Molecular Biology and Evolution·Nicolas Lartillot, Hervé Philippe
Sep 14, 2004·Biological Procedures Online·Neeraja M. KrishnanDavid D. Pollock
Dec 9, 2004·DNA and Cell Biology·Neeraja M KrishnanDavid D Pollock
Jul 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ari Löytynoja, Nick Goldman
Jun 23, 2006·PLoS Computational Biology·Paul D WilliamsRichard A Goldstein
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
May 3, 2008·PLoS Pathogens·Benjamin P BlackburneRichard A Goldstein
Jun 28, 2008·Molecular Biology and Evolution·Antonis Rokas, Sean B Carroll
Aug 23, 2008·Bioinformatics·Le Si QuangNicolas Lartillot
May 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Todd A CastoeDavid D Pollock
Nov 17, 2009·PLoS Computational Biology·Asif U TamuriRichard A Goldstein
Feb 5, 2010·Current Biology : CB·Yang LiuShuyi Zhang
Feb 18, 2010·Molecular Biology and Evolution·Claudia L KleinmanHervé Philippe
May 2, 2012·Proceedings of the National Academy of Sciences of the United States of America·David D PollockRichard A Goldstein
Sep 15, 2012·Bioinformatics·A P Jason de KoningDavid D Pollock
Sep 29, 2012·Genome Biology and Evolution·Ken Daigoro Yokoyama, David D Pollock
Sep 6, 2013·Nature·Joe ParkerStephen J Rossiter
Dec 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Orr AshenbergJesse D Bloom
Apr 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·David D Pollock, Richard A Goldstein

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Citations

Jun 10, 2015·Proceedings of the National Academy of Sciences of the United States of America·Premal ShahJoshua B Plotkin
Jun 12, 2016·Current Opinion in Structural Biology·Lucas C WheelerMichael J Harms
Mar 31, 2016·Protein Science : a Publication of the Protein Society·Richard A Goldstein, David D Pollock
Sep 17, 2016·Molecular Biology and Evolution·Fábio K MendesMatthew W Hahn
Jun 9, 2017·Genome Biology and Evolution·Galya V Klink, Georgii A Bazykin
Jan 15, 2017·Molecular Biology and Evolution·Shaohua XuSuhua Shi
Jun 4, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Fábio K MendesMatthew W Hahn
Jun 4, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Carine ReyBastien Boussau
Feb 3, 2016·Protein Science : a Publication of the Protein Society·Tyler N Starr, Joseph W Thornton
Mar 15, 2016·Nature Reviews. Genetics·Jay F Storz
Mar 3, 2017·Proceedings. Biological Sciences·Sarah Z Dungan, Belinda S W Chang
Feb 24, 2017·Journal of the Royal Society, Interface·Ashley I Teufel, Claus O Wilke
Apr 8, 2018·Proceedings of the National Academy of Sciences of the United States of America·Tyler N StarrJoseph W Thornton
Sep 9, 2020·Molecular Biology and Evolution·Noor YoussefJoseph P Bielawski
May 20, 2016·Genetics·David M McCandlishJoshua B Plotkin
Oct 25, 2017·Nature Ecology & Evolution·Richard A Goldstein, David D Pollock
Aug 16, 2017·Nature Ecology & Evolution·Xing-Xing ShenAntonis Rokas
Aug 16, 2017·Nature Ecology & Evolution·Kenji FukushimaMitsuyasu Hasebe
Sep 16, 2020·Nature Communications·A V StolyarovaG A Bazykin
Nov 4, 2017·Current Opinion in Structural Biology·Jay F Storz
Dec 29, 2020·Plant Communications·Shaohua XuSuhua Shi
May 19, 2021·Proceedings of the National Academy of Sciences of the United States of America·Magdalena BohutínskáFilip Kolář
Jul 30, 2021·Protein Science : a Publication of the Protein Society·Noor YoussefJoseph P Bielawski

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Methods Mentioned

BETA
amino acid exchange

Software Mentioned

PRANK
MrBayes
MrModeltest
ClustalX

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