Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers

The ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic basis of population-specific adaptations genome-wide. Here, we present the analysis of recent selective sweeps, specifically in the X chromosome, in human populations from the...

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Autores: Villegas-Mirón, Pablo, Acosta, Sandra, Nye, Jessica, Bertranpetit, Jaume, 1952-, Laayouni, Hafid
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Recursos:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/221210
Acesso em linha:https://hdl.handle.net/2445/221210
Access Level:acceso abierto
Palavra-chave:Genòmica
Cromosomes
Genètica de poblacions humanes
Genomics
Chromosomes
Human population genetics
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spelling Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancersVillegas-Mirón, PabloAcosta, SandraNye, JessicaBertranpetit, Jaume, 1952-Laayouni, HafidGenòmicaCromosomesGenètica de poblacions humanesGenomicsChromosomesHuman population geneticsThe ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic basis of population-specific adaptations genome-wide. Here, we present the analysis of recent selective sweeps, specifically in the X chromosome, in human populations from the third phase of the 1,000 Genomes Project using three different haplotype-based statistics. We describe instances of recent positive selection that fit the criteria of hard or soft sweeps, and detect a higher number of events among sub-Saharan Africans than non-Africans (Europe and East Asia). A global enrichment of neural-related processes is observed and numerous genes related to fertility appear among the top candidates, reflecting the importance of reproduction in human evolution. Commonalities with previously reported genes under positive selection are found, while particularly strong new signals are reported in specific populations or shared across different continental groups. We report an enrichment of signals in genes that escape X chromosome inactivation, which may contribute to the differentiation between sexes. We also provide evidence of a widespread presence of soft-sweep-like signatures across the chromosome and a global enrichment of highly scoring regions that overlap potential regulatory elements. Among these, enhancers-like signatures seem to present putative signals of positive selection which might be in concordance with selection in their target genes. Also, particularly strong signals appear in regulatory regions that show differential activities, which might point to population-specific regulatory adaptations.Frontiers Media2025202520212025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion11 p.application/pdfhttps://hdl.handle.net/2445/221210Articles publicats en revistes (Patologia i Terapèutica Experimental)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.3389/fgene.2021.714491Frontiers In Genetics, 2021, vol. 12https://doi.org/10.3389/fgene.2021.714491cc-by (c) Villegas-Mirón, Pablo et al., 2021http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/2212102026-05-29T05:05:01Z
dc.title.none.fl_str_mv Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
title Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
spellingShingle Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
Villegas-Mirón, Pablo
Genòmica
Cromosomes
Genètica de poblacions humanes
Genomics
Chromosomes
Human population genetics
title_short Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
title_full Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
title_fullStr Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
title_full_unstemmed Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
title_sort Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
dc.creator.none.fl_str_mv Villegas-Mirón, Pablo
Acosta, Sandra
Nye, Jessica
Bertranpetit, Jaume, 1952-
Laayouni, Hafid
author Villegas-Mirón, Pablo
author_facet Villegas-Mirón, Pablo
Acosta, Sandra
Nye, Jessica
Bertranpetit, Jaume, 1952-
Laayouni, Hafid
author_role author
author2 Acosta, Sandra
Nye, Jessica
Bertranpetit, Jaume, 1952-
Laayouni, Hafid
author2_role author
author
author
author
dc.subject.none.fl_str_mv Genòmica
Cromosomes
Genètica de poblacions humanes
Genomics
Chromosomes
Human population genetics
topic Genòmica
Cromosomes
Genètica de poblacions humanes
Genomics
Chromosomes
Human population genetics
description The ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic basis of population-specific adaptations genome-wide. Here, we present the analysis of recent selective sweeps, specifically in the X chromosome, in human populations from the third phase of the 1,000 Genomes Project using three different haplotype-based statistics. We describe instances of recent positive selection that fit the criteria of hard or soft sweeps, and detect a higher number of events among sub-Saharan Africans than non-Africans (Europe and East Asia). A global enrichment of neural-related processes is observed and numerous genes related to fertility appear among the top candidates, reflecting the importance of reproduction in human evolution. Commonalities with previously reported genes under positive selection are found, while particularly strong new signals are reported in specific populations or shared across different continental groups. We report an enrichment of signals in genes that escape X chromosome inactivation, which may contribute to the differentiation between sexes. We also provide evidence of a widespread presence of soft-sweep-like signatures across the chromosome and a global enrichment of highly scoring regions that overlap potential regulatory elements. Among these, enhancers-like signatures seem to present putative signals of positive selection which might be in concordance with selection in their target genes. Also, particularly strong signals appear in regulatory regions that show differential activities, which might point to population-specific regulatory adaptations.
publishDate 2021
dc.date.none.fl_str_mv 2021
2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/221210
url https://hdl.handle.net/2445/221210
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.3389/fgene.2021.714491
Frontiers In Genetics, 2021, vol. 12
https://doi.org/10.3389/fgene.2021.714491
dc.rights.none.fl_str_mv cc-by (c) Villegas-Mirón, Pablo et al., 2021
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Villegas-Mirón, Pablo et al., 2021
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 11 p.
application/pdf
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv Articles publicats en revistes (Patologia i Terapèutica Experimental)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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