Understanding signatures of positive natural selection in human zinc transporter genes

Zinc is an essential micronutrient with a tightly regulated systemic and cellular homeostasis. In humans, some zinc transporter genes (ZTGs) have been previously reported as candidates for strong geographically restricted selective sweeps. However, since zinc homeostasis is maintained by the joint a...

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Autores: Roca-Umbert Würth, Ana, Caro Consuegra, Rocio, Londono-Correa, Diego, Rodriguez-Lozano, Gabriel Felipe, Vicente García, Rubén, 1978-, Bosch Fusté, Elena
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/52882
Acceso en línea:http://hdl.handle.net/10230/52882
http://dx.doi.org/10.1038/s41598-022-08439-y
Access Level:acceso abierto
Palabra clave:Evolution
Evolutionary biology
Evolutionary genetics
Genetic variation
Population genetics
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spelling Understanding signatures of positive natural selection in human zinc transporter genesRoca-Umbert Würth, AnaCaro Consuegra, RocioLondono-Correa, DiegoRodriguez-Lozano, Gabriel FelipeVicente García, Rubén, 1978-Bosch Fusté, ElenaEvolutionEvolutionary biologyEvolutionary geneticsGenetic variationPopulation geneticsZinc is an essential micronutrient with a tightly regulated systemic and cellular homeostasis. In humans, some zinc transporter genes (ZTGs) have been previously reported as candidates for strong geographically restricted selective sweeps. However, since zinc homeostasis is maintained by the joint action of 24 ZTGs, other more subtle modes of selection could have also facilitated human adaptation to zinc availability. Here, we studied whether the complete set of ZTGs are enriched for signals of positive selection in worldwide populations and population groups from South Asia. ZTGs showed higher levels of genetic differentiation between African and non-African populations than would be randomly expected, as well as other signals of polygenic selection outside Africa. Moreover, in several South Asian population groups, ZTGs were significantly enriched for SNPs with unusually extended haplotypes and displayed SNP genotype-environmental correlations when considering zinc deficiency levels in soil in that geographical area. Our study replicated some well-characterized targets for positive selection in East Asia and sub-Saharan Africa, and proposes new candidates for follow-up in South Asia (SLC39A5) and Africa (SLC39A7). Finally, we identified candidate variants for adaptation in ZTGs that could contribute to different disease susceptibilities and zinc-related human health traits.This work was supported by Agencia Estatal de Investigación (AEI) and Fondo Europeo de Desarrollo Regional (FEDER) (project Grants BFU2016-77961-P, PID2019-110933GB-I00/AEI/10.13039/501100011033, PID2019-106755RB-I00/AEI/10.13039/501100011033); Unidad de Excelencia María de Maeztu funded by the MCIN and the AEI (https://doi.org/10.13039/501100011033, Ref: CEX2018-000792-M); and by Direcció General de Recerca, Generalitat de Catalunya (2017SGR00702).Nature Research202220222022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/52882http://dx.doi.org/10.1038/s41598-022-08439-yreponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésSci Rep. 2022 Mar 12;12(1):4320info:eu-repo/grantAgreement/ES/1PE/BFU2016-77961-Pinfo:eu-repo/grantAgreement/ES/2PE/PID2019-110933GB-I00info:eu-repo/grantAgreement/ES/2PE/PID2019-106755RB-I00© The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/528822026-06-12T07:21:37Z
dc.title.none.fl_str_mv Understanding signatures of positive natural selection in human zinc transporter genes
title Understanding signatures of positive natural selection in human zinc transporter genes
spellingShingle Understanding signatures of positive natural selection in human zinc transporter genes
Roca-Umbert Würth, Ana
Evolution
Evolutionary biology
Evolutionary genetics
Genetic variation
Population genetics
title_short Understanding signatures of positive natural selection in human zinc transporter genes
title_full Understanding signatures of positive natural selection in human zinc transporter genes
title_fullStr Understanding signatures of positive natural selection in human zinc transporter genes
title_full_unstemmed Understanding signatures of positive natural selection in human zinc transporter genes
title_sort Understanding signatures of positive natural selection in human zinc transporter genes
dc.creator.none.fl_str_mv Roca-Umbert Würth, Ana
Caro Consuegra, Rocio
Londono-Correa, Diego
Rodriguez-Lozano, Gabriel Felipe
Vicente García, Rubén, 1978-
Bosch Fusté, Elena
author Roca-Umbert Würth, Ana
author_facet Roca-Umbert Würth, Ana
Caro Consuegra, Rocio
Londono-Correa, Diego
Rodriguez-Lozano, Gabriel Felipe
Vicente García, Rubén, 1978-
Bosch Fusté, Elena
author_role author
author2 Caro Consuegra, Rocio
Londono-Correa, Diego
Rodriguez-Lozano, Gabriel Felipe
Vicente García, Rubén, 1978-
Bosch Fusté, Elena
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Evolution
Evolutionary biology
Evolutionary genetics
Genetic variation
Population genetics
topic Evolution
Evolutionary biology
Evolutionary genetics
Genetic variation
Population genetics
description Zinc is an essential micronutrient with a tightly regulated systemic and cellular homeostasis. In humans, some zinc transporter genes (ZTGs) have been previously reported as candidates for strong geographically restricted selective sweeps. However, since zinc homeostasis is maintained by the joint action of 24 ZTGs, other more subtle modes of selection could have also facilitated human adaptation to zinc availability. Here, we studied whether the complete set of ZTGs are enriched for signals of positive selection in worldwide populations and population groups from South Asia. ZTGs showed higher levels of genetic differentiation between African and non-African populations than would be randomly expected, as well as other signals of polygenic selection outside Africa. Moreover, in several South Asian population groups, ZTGs were significantly enriched for SNPs with unusually extended haplotypes and displayed SNP genotype-environmental correlations when considering zinc deficiency levels in soil in that geographical area. Our study replicated some well-characterized targets for positive selection in East Asia and sub-Saharan Africa, and proposes new candidates for follow-up in South Asia (SLC39A5) and Africa (SLC39A7). Finally, we identified candidate variants for adaptation in ZTGs that could contribute to different disease susceptibilities and zinc-related human health traits.
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
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 http://hdl.handle.net/10230/52882
http://dx.doi.org/10.1038/s41598-022-08439-y
url http://hdl.handle.net/10230/52882
http://dx.doi.org/10.1038/s41598-022-08439-y
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Sci Rep. 2022 Mar 12;12(1):4320
info:eu-repo/grantAgreement/ES/1PE/BFU2016-77961-P
info:eu-repo/grantAgreement/ES/2PE/PID2019-110933GB-I00
info:eu-repo/grantAgreement/ES/2PE/PID2019-106755RB-I00
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Research
publisher.none.fl_str_mv Nature Research
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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