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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...

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Autores principales: Tricou, Théo, Tannier, Eric, de Vienne, Damien M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
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.
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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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