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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2020
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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. |
format | Online Article Text |
id | pubmed-7800383 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
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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