Uncovering signals of positive selection in peruvian populations from three ecological regions

Peru hosts extremely diverse ecosystems which can be broadly classified into the following three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might ha...

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Autores: Caro Consuegra, Rocio, Nieves-Colón, Maria A., Rawls, Erin, Rubin-de-Celis, Verónica, Lizárraga, Beatriz, Vidaurre, Tatiana, Sandoval Mendoza, Karla, Fejerman, Laura, Stone, Anne C., Moreno Estrada, Andrés, Bosch Fusté, Elena
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución: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:10230/54062
Acceso en línea:http://hdl.handle.net/10230/54062
http://dx.doi.org/10.1093/molbev/msac158
Access Level:acceso abierto
Palabra clave:Peruvian populations
High-altitude adaptation
Human adaptation
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spelling Uncovering signals of positive selection in peruvian populations from three ecological regionsCaro Consuegra, RocioNieves-Colón, Maria A.Rawls, ErinRubin-de-Celis, VerónicaLizárraga, BeatrizVidaurre, TatianaSandoval Mendoza, KarlaFejerman, LauraStone, Anne C.Moreno Estrada, AndrésBosch Fusté, ElenaPeruvian populationsHigh-altitude adaptationHuman adaptationPeru hosts extremely diverse ecosystems which can be broadly classified into the following three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide single-nucleotide polymorphism-array data from 286 Peruvians living across the three ecoregions and analyzed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44, and ICAM1 in the coast; CBLB and PRDM1 in the rainforest; and BRD2, HLA-DOA, HLA-DPA1 regions in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.This work was supported by the Ministerio de Ciencia e Innovación and the Agencia Estatal de Investigación (AEI) (PID2019-110933GB-I00/AEI/10.13039/501100011033 to E.B.); the Unidad de Excelencia María de Maeztu funded by the Ministerio de Ciencia e Innovación and the Agencia Estatal de Investigación (DOI: 10.13039/501100011033; ref: CEX2018-000792-M to E.B. and R.C.-C.); the National Science Foundation (NSF) SBE (Postdoctoral Research Fellowship Award No. 1711982 to M.A.N.-C.), NSF-BCS (BCS-0242958 to A.C.S.) and NSF-Research Experience for Undergraduates (BCS-0242958 to A.C.S.); the Mexican National Council for Science and Technology (CONACYT) (FONCICYT/50/2016 to A.M.-E.); and the International Center for Genetic Engineering and Biotechnology (ICGEB, Italy) (CRP/MEX15-04_EC to A.M.-E.). The PEGEN-BC study was supported by the National Cancer Institute at the National Institutes of Health (R01CA204797 to L.F.) and the Instituto Nacional de Enfermedades Neoplásicas in Lima, Peru.Oxford University Press202220222022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/54062http://dx.doi.org/10.1093/molbev/msac158reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésMol Biol Evol. 2022 Aug 3;39(8):msac158info:eu-repo/grantAgreement/ES/2PE/PID2019-110933GB-I00© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. 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.comhttps://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/540622026-05-29T05:05:01Z
dc.title.none.fl_str_mv Uncovering signals of positive selection in peruvian populations from three ecological regions
title Uncovering signals of positive selection in peruvian populations from three ecological regions
spellingShingle Uncovering signals of positive selection in peruvian populations from three ecological regions
Caro Consuegra, Rocio
Peruvian populations
High-altitude adaptation
Human adaptation
title_short Uncovering signals of positive selection in peruvian populations from three ecological regions
title_full Uncovering signals of positive selection in peruvian populations from three ecological regions
title_fullStr Uncovering signals of positive selection in peruvian populations from three ecological regions
title_full_unstemmed Uncovering signals of positive selection in peruvian populations from three ecological regions
title_sort Uncovering signals of positive selection in peruvian populations from three ecological regions
dc.creator.none.fl_str_mv Caro Consuegra, Rocio
Nieves-Colón, Maria A.
Rawls, Erin
Rubin-de-Celis, Verónica
Lizárraga, Beatriz
Vidaurre, Tatiana
Sandoval Mendoza, Karla
Fejerman, Laura
Stone, Anne C.
Moreno Estrada, Andrés
Bosch Fusté, Elena
author Caro Consuegra, Rocio
author_facet Caro Consuegra, Rocio
Nieves-Colón, Maria A.
Rawls, Erin
Rubin-de-Celis, Verónica
Lizárraga, Beatriz
Vidaurre, Tatiana
Sandoval Mendoza, Karla
Fejerman, Laura
Stone, Anne C.
Moreno Estrada, Andrés
Bosch Fusté, Elena
author_role author
author2 Nieves-Colón, Maria A.
Rawls, Erin
Rubin-de-Celis, Verónica
Lizárraga, Beatriz
Vidaurre, Tatiana
Sandoval Mendoza, Karla
Fejerman, Laura
Stone, Anne C.
Moreno Estrada, Andrés
Bosch Fusté, Elena
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Peruvian populations
High-altitude adaptation
Human adaptation
topic Peruvian populations
High-altitude adaptation
Human adaptation
description Peru hosts extremely diverse ecosystems which can be broadly classified into the following three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide single-nucleotide polymorphism-array data from 286 Peruvians living across the three ecoregions and analyzed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44, and ICAM1 in the coast; CBLB and PRDM1 in the rainforest; and BRD2, HLA-DOA, HLA-DPA1 regions in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.
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/10230/54062
http://dx.doi.org/10.1093/molbev/msac158
url http://hdl.handle.net/10230/54062
http://dx.doi.org/10.1093/molbev/msac158
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Mol Biol Evol. 2022 Aug 3;39(8):msac158
info:eu-repo/grantAgreement/ES/2PE/PID2019-110933GB-I00
dc.rights.none.fl_str_mv https://creativecommons.org/licenses/by-nc/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv 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
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