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Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans

Jagoda, E; Lawson, DJ; Wall, JD; Lambert, D; Muller, C; Westaway, M; Leavesley, M; ... Pagani, L; + view all (2018) Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans. Molecular Biology and Evolution , 35 (3) pp. 623-630. 10.1093/molbev/msx314. Green open access

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Abstract

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 post-introgression 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 dataset, we report novel cases of selection on introgressed variation in living humans and shortlisted 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 introgressed haplotypes 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.

Type: Article
Title: Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/molbev/msx314
Publisher version: http://doi.org/10.1093/molbev/msx314
Language: English
Additional information: © The Author(s) 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.
Keywords: adaptive introgression, Neanderthal, positive selection, archaic genomes, interferon, toll-like receptor
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
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
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 > UCL SLASH
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Dept of Anthropology
URI: https://discovery.ucl.ac.uk/id/eprint/10040195
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