Positive selection in admixed populations from Ethiopia

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• dc.contributor.author Walsh Capdevila, Sandra, 1991-
• dc.contributor.author Pagani, Luca
• dc.contributor.author Xue, Yali
• dc.contributor.author Laayouni, Hafid, 1968-
• dc.contributor.author Tyler-Smith, Chris
• dc.contributor.author Bertranpetit, Jaume, 1952-
• dc.date.accessioned 2020-10-28T07:01:14Z
• dc.date.available 2020-10-28T07:01:14Z
• dc.date.issued 2020
• dc.description.abstract Background: In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history. Results: Here, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world. The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens. Conclusions: Signals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.
• dc.description.sponsorship This study has been possible thanks to the F.P.I. grant BES-2014-068994 to SW, and grant BFU2016–77961-P (AEI/FEDER, UE) both awarded by the Agencia Estatal de Investigación (MINECO, Spain) and with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 702). Part of the “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018–000792-M). YX and CTS are supported by Wellcome Trust (098051), LP is supported by the European Union through the European Regional Development Fund Project No. 2014–2020.4.01.16–0024, MOBTT53. Publication costs were funded by Wellcome (grant 098051). The funding body has not played any role in the design of the study and collection, analysis, and interpretation of data and in writing of the manuscript.
• dc.format.mimetype application/pdf
• dc.identifier.citation Walsh S, Pagani L, Xue Y, Laayouni H, Tyler-Smith C, Bertranpetit J. Positive selection in admixed populations from Ethiopia. BMC Genet. 2020; 21(Suppl 1):108. DOI: 10.1186/s12863-020-00908-5
• dc.identifier.doi http://dx.doi.org/10.1186/s12863-020-00908-5
• dc.identifier.issn 1471-2156
• dc.identifier.uri http://hdl.handle.net/10230/45592
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof BMC Genet. 2020; 21(Suppl 1):108
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016–77961-P
• dc.rights © The Author(s). 2020 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data ma
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Admixture
• dc.subject.keyword African populations
• dc.subject.keyword Ethiopia
• dc.subject.keyword Genomics
• dc.subject.keyword Human population genetics
• dc.subject.keyword Positive selection
• dc.subject.keyword Selective sweeps
• dc.subject.keyword West Asia
• dc.title Positive selection in admixed populations from Ethiopia
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion