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Ghost lineages can invalidate or even reverse findings regarding gene flow
Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch leng...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9473628/ https://www.ncbi.nlm.nih.gov/pubmed/36103518 http://dx.doi.org/10.1371/journal.pbio.3001776 |
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author | Tricou, Théo Tannier, Eric de Vienne, Damien M. |
author_facet | Tricou, Théo Tannier, Eric de Vienne, Damien M. |
author_sort | Tricou, Théo |
collection | PubMed |
description | Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies. |
format | Online Article Text |
id | pubmed-9473628 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-94736282022-09-15 Ghost lineages can invalidate or even reverse findings regarding gene flow Tricou, Théo Tannier, Eric de Vienne, Damien M. PLoS Biol Discovery Report Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies. Public Library of Science 2022-09-14 /pmc/articles/PMC9473628/ /pubmed/36103518 http://dx.doi.org/10.1371/journal.pbio.3001776 Text en © 2022 Tricou et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Discovery Report Tricou, Théo Tannier, Eric de Vienne, Damien M. Ghost lineages can invalidate or even reverse findings regarding gene flow |
title | Ghost lineages can invalidate or even reverse findings regarding gene flow |
title_full | Ghost lineages can invalidate or even reverse findings regarding gene flow |
title_fullStr | Ghost lineages can invalidate or even reverse findings regarding gene flow |
title_full_unstemmed | Ghost lineages can invalidate or even reverse findings regarding gene flow |
title_short | Ghost lineages can invalidate or even reverse findings regarding gene flow |
title_sort | ghost lineages can invalidate or even reverse findings regarding gene flow |
topic | Discovery Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9473628/ https://www.ncbi.nlm.nih.gov/pubmed/36103518 http://dx.doi.org/10.1371/journal.pbio.3001776 |
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