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Disentangling Signatures of Selection Before and After European Colonization in Latin Americans

Mendoza-Revilla, Javier; Chacon-Duque, Juan Camilo; Fuentes-Guajardo, Macarena; Ormond, Louise; Wang, Ke; Hurtado, Malena; Villegas, Valeria; ... Hellenthal, Garrett; + view all (2022) Disentangling Signatures of Selection Before and After European Colonization in Latin Americans. Molecular Biology and Evolution , 39 (4) , Article msac076. 10.1093/molbev/msac076. Green open access

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Abstract

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

Type: Article
Title: Disentangling Signatures of Selection Before and After European Colonization in Latin Americans
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/molbev/msac076
Publisher version: https://doi.org/10.1093/molbev/msac076
Language: English
Additional information: © 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 License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, Evolutionary Biology, Genetics & Heredity, natural selection, Latin Americans, Native Americans, admixture, GESTATIONAL DIABETES-MELLITUS, GENOME-WIDE ASSOCIATION, POSITIVE SELECTION, GENETIC SIGNATURES, NATURAL-SELECTION, ANCESTRY, ADMIXTURE, HKDC1, POPULATIONS, LOCI
UCL classification: UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10147867
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