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“Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error
The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce the di...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10263008/ https://www.ncbi.nlm.nih.gov/pubmed/37243541 http://dx.doi.org/10.1093/gbe/evad094 |
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author | Yan, Zhi Ogilvie, Huw A Nakhleh, Luay |
author_facet | Yan, Zhi Ogilvie, Huw A Nakhleh, Luay |
author_sort | Yan, Zhi |
collection | PubMed |
description | The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce the distance to the species tree. We investigate the performance of two representatives of these methods: TRACTION and TreeFix. We found that gene tree error correction frequently increases the level of error in gene tree topologies by “correcting” them to be closer to the species tree, even when the true gene and species trees are discordant. We confirm that full Bayesian inference of the gene trees under the multispecies coalescent model is more accurate than independent inference. Future gene tree correction approaches and methods should incorporate an adequately realistic model of evolution instead of relying on oversimplified heuristics. |
format | Online Article Text |
id | pubmed-10263008 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-102630082023-06-15 “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error Yan, Zhi Ogilvie, Huw A Nakhleh, Luay Genome Biol Evol Letter The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce the distance to the species tree. We investigate the performance of two representatives of these methods: TRACTION and TreeFix. We found that gene tree error correction frequently increases the level of error in gene tree topologies by “correcting” them to be closer to the species tree, even when the true gene and species trees are discordant. We confirm that full Bayesian inference of the gene trees under the multispecies coalescent model is more accurate than independent inference. Future gene tree correction approaches and methods should incorporate an adequately realistic model of evolution instead of relying on oversimplified heuristics. Oxford University Press 2023-05-27 /pmc/articles/PMC10263008/ /pubmed/37243541 http://dx.doi.org/10.1093/gbe/evad094 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Letter Yan, Zhi Ogilvie, Huw A Nakhleh, Luay “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error |
title | “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error |
title_full | “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error |
title_fullStr | “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error |
title_full_unstemmed | “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error |
title_short | “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error |
title_sort | “correcting” gene trees to be more like species trees frequently increases topological error |
topic | Letter |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10263008/ https://www.ncbi.nlm.nih.gov/pubmed/37243541 http://dx.doi.org/10.1093/gbe/evad094 |
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