Disentangling immediate adaptive introgression from selection on standing introgressed variation in humans

Jagoda, Evelyn, Lawson, Daniel J., Wall, Jeffrey D., Lambert, David, Muller, Craig, Westaway, Michael, Leavesley, Matthew, Capellini, Terence D., Lahr, Marta Mirazon, Gerbault, Pascale, Thomas, Mark G., Migliano, Andrea Bamberg, Willerslev, Eske, Metspalu, Mait, and Pagani, Luca (2018) Disentangling immediate adaptive introgression from selection on standing introgressed variation in humans. Molecular Biology and Evolution, 35 (3). pp. 623-630.

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Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.

Item ID: 52914
Item Type: Article (Research - C1)
ISSN: 1537-1719
Keywords: adaptive introgression; Neanderthal; positive selection; archaic genomes; interferon; toll-like receptor
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© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Funders: European Union (EU), European Research Council (ERC), Australian Research Council (ARC)
Projects and Grants: EU European Regional Development Fund Project No. 2014-2020.4.01.16-0030, EU European Regional Development Fund Project No. 014-2020.4.01.15-0012, EU European Regional Development Fund Project No. 2014-2020.4.01.16-0024, EU European Regional Development Fund Project MOBTT53, ERC Award 295907, ARC Discovery Grant DP110102635, ARC Discovery grant DP140101405, ARC Linkage grant LP140100387, ARC Linkage grant LP120200144, ARC Linkage grant LP150100583
Date Deposited: 27 Mar 2018 02:45
FoR Codes: 43 HISTORY, HERITAGE AND ARCHAEOLOGY > 4301 Archaeology > 430101 Archaeological science @ 50%
44 HUMAN SOCIETY > 4401 Anthropology > 440103 Biological (physical) anthropology @ 50%
SEO Codes: 95 CULTURAL UNDERSTANDING > 9505 Understanding Past Societies > 950599 Understanding Past Societies not elsewhere classified @ 100%
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