Quantifying the risk of hemiplasy in phylogenetic inference

Proceedings of the National Academy of Sciences of the United States of America
Rafael F Guerrero, Matthew W Hahn


Convergent evolution-the appearance of the same character state in apparently unrelated organisms-is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely-or more likely-than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a method to calculate the ratio of these two probabilities (the "hemiplasy risk factor") along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree to identify when and where incongruent traits may be due to hemiplasy.


May 1, 1997·Molecular Biology and Evolution·J Zhang, S Kumar
May 15, 2003·Systematic Biology·John P HuelsenbeckJonathan P Bollback
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Nov 17, 2004·Systematic Biology·Mark PagelDaniel Barker
Aug 4, 2005·Genome Research·Matthew W HahnNello Cristianini
Dec 20, 2005·Genetics·Montgomery Slatkin, Joshua L Pollack
Nov 11, 2006·Molecular Biology and Evolution·Cécile AnéAntonis Rokas
Jul 7, 2007·Current Biology : CB·Pascal-Antoine ChristinGuillaume Besnard
Jun 24, 2008·Systematic Biology·John C Avise, Terence J Robinson
Sep 4, 2008·Evolution; International Journal of Organic Evolution·Emma E Goldberg, Boris Igić
Jul 21, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Marie ManceauHopi E Hoekstra
Oct 13, 2010·BMC Evolutionary Biology·Liang LiuScott V Edwards
Jul 7, 2011·Evolution; International Journal of Organic Evolution·Jonathan B Losos
Mar 9, 2012·Nature·Aylwyn ScallyRichard Durbin
Aug 24, 2012·Nature·Augustine KongKari Stefansson
Sep 29, 2012·Science·Ying ZhenPeter Andolfatto
Jul 5, 2013·Nature·Javier Prado-MartinezTomas Marques-Bonet
Jul 31, 2013·Evolution; International Journal of Organic Evolution·James B Pease, Matthew W Hahn
Dec 4, 2013·Proceedings of the National Academy of Sciences of the United States of America·Joana Projecto-GarciaJay F Storz
Nov 8, 2014·Science·Bernhard MisofXin Zhou
Jul 16, 2015·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Sebastian Duchêne, Robert Lanfear
Dec 8, 2015·Evolution; International Journal of Organic Evolution·Matthew W Hahn, Luay Nakhleh
Dec 29, 2015·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·James MalletMatthew W Hahn
Feb 13, 2016·PLoS Biology·James B PeaseLeonie C Moyle
Mar 2, 2016·Systematic Biology·Fábio K Mendes, Matthew W Hahn
Mar 15, 2016·Nature Reviews. Genetics·Jay F Storz
Sep 17, 2016·Molecular Biology and Evolution·Fábio K MendesMatthew W Hahn
Oct 17, 2016·Molecular Biology and Evolution·Yuan-Yuan LiPeng Shi
Oct 4, 2017·Systematic Biology·Fábio K Mendes, Matthew W Hahn
Oct 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·Dario CopettiMichael J Sanderson


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·Kristin M Lee, Graham Coop
Jun 4, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sangeet LamichhaneyScott V Edwards
May 8, 2020·Scientific Reports·Barbara R HollandGregory J Jordan
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