Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy. Classic comparative methods do not account for...

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Auteurs principaux:	Mark S Hibbins, Matthew JS Gibson, Matthew W Hahn
Format:	article
Langue:	EN
Publié:	eLife Sciences Publications Ltd 2020
Sujets:	introgression convergent evolution phylogenetics comparative methods gene tree discordance Medicine R Science Q Biology (General) QH301-705.5
Accès en ligne:	https://doaj.org/article/dbdaeb4e0a8c484a84e432aeba7cca7b
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spelling	oai:doaj.org-article:dbdaeb4e0a8c484a84e432aeba7cca7b2021-11-19T17:51:45ZDetermining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression10.7554/eLife.637532050-084Xe63753https://doaj.org/article/dbdaeb4e0a8c484a84e432aeba7cca7b2020-12-01T00:00:00Zhttps://elifesciences.org/articles/63753https://doaj.org/toc/2050-084XThe incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy. Classic comparative methods do not account for discordance, resulting in incorrect inferences about the number, timing, and direction of trait transitions. Biological sources of discordance include incomplete lineage sorting (ILS) and introgression, but only ILS has received theoretical consideration in the context of hemiplasy. Here, we present a model that shows introgression makes hemiplasy more likely, such that methods that account for ILS alone will be conservative. We also present a method and software (HeIST) for making statistical inferences about the probability of hemiplasy and homoplasy in large datasets that contain both ILS and introgression. We apply our methods to two empirical datasets, finding that hemiplasy is likely to contribute to the observed trait incongruences in both.Mark S HibbinsMatthew JS GibsonMatthew W HahneLife Sciences Publications Ltdarticleintrogressionconvergent evolutionphylogeneticscomparative methodsgene tree discordanceMedicineRScienceQBiology (General)QH301-705.5ENeLife, Vol 9 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	introgression convergent evolution phylogenetics comparative methods gene tree discordance Medicine R Science Q Biology (General) QH301-705.5
spellingShingle	introgression convergent evolution phylogenetics comparative methods gene tree discordance Medicine R Science Q Biology (General) QH301-705.5 Mark S Hibbins Matthew JS Gibson Matthew W Hahn Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
description	The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy. Classic comparative methods do not account for discordance, resulting in incorrect inferences about the number, timing, and direction of trait transitions. Biological sources of discordance include incomplete lineage sorting (ILS) and introgression, but only ILS has received theoretical consideration in the context of hemiplasy. Here, we present a model that shows introgression makes hemiplasy more likely, such that methods that account for ILS alone will be conservative. We also present a method and software (HeIST) for making statistical inferences about the probability of hemiplasy and homoplasy in large datasets that contain both ILS and introgression. We apply our methods to two empirical datasets, finding that hemiplasy is likely to contribute to the observed trait incongruences in both.
format	article
author	Mark S Hibbins Matthew JS Gibson Matthew W Hahn
author_facet	Mark S Hibbins Matthew JS Gibson Matthew W Hahn
author_sort	Mark S Hibbins
title	Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
title_short	Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
title_full	Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
title_fullStr	Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
title_full_unstemmed	Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
title_sort	determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
publisher	eLife Sciences Publications Ltd
publishDate	2020
url	https://doaj.org/article/dbdaeb4e0a8c484a84e432aeba7cca7b
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Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

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