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

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    Author(s)
    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
    Pagani, Luca
    Griffith University Author(s)
    Lambert, David M.
    Year published
    2018
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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 postintrogression population dynamics ofthese 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 ...
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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 ofthese 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.
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    Journal Title
    Molecular Biology and Evolution
    Volume
    35
    Issue
    3
    DOI
    https://doi.org/10.1093/molbev/msx314
    Copyright Statement
    © 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.
    Subject
    Biochemistry and cell biology
    Biochemistry and cell biology not elsewhere classified
    Evolutionary biology
    Genetics
    Publication URI
    http://hdl.handle.net/10072/376537
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    • Journal articles

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