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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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Detalles Bibliográficos
Autores principales: Hibbins, Mark S, Gibson, Matthew JS, Hahn, Matthew W
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800383/
https://www.ncbi.nlm.nih.gov/pubmed/33345772
http://dx.doi.org/10.7554/eLife.63753
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author Hibbins, Mark S
Gibson, Matthew JS
Hahn, Matthew W
author_facet Hibbins, Mark S
Gibson, Matthew JS
Hahn, Matthew W
author_sort Hibbins, Mark S
collection PubMed
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.
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spelling pubmed-78003832021-01-13 Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression Hibbins, Mark S Gibson, Matthew JS Hahn, Matthew W eLife Evolutionary Biology 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. eLife Sciences Publications, Ltd 2020-12-21 /pmc/articles/PMC7800383/ /pubmed/33345772 http://dx.doi.org/10.7554/eLife.63753 Text en © 2020, Hibbins et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Evolutionary Biology
Hibbins, Mark S
Gibson, Matthew JS
Hahn, Matthew W
Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
title 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_short 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
topic Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800383/
https://www.ncbi.nlm.nih.gov/pubmed/33345772
http://dx.doi.org/10.7554/eLife.63753
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