Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans.
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Authors
Jagoda, Evelyn
Lawson, Daniel J
Wall, Jeffrey D
Lambert, David
Muller, Craig
Westaway, Michael
Leavesley, Matthew
Capellini, Terence D
Mirazón Lahr, Marta
Gerbault, Pascale
Thomas, Mark G
Migliano, Andrea Bamberg
Metspalu, Mait
Pagani, Luca
Publication Date
2018-03-01Journal Title
Mol Biol Evol
ISSN
0737-4038
Publisher
Oxford University Press (OUP)
Volume
35
Issue
3
Pages
623-630
Language
eng
Type
Article
Physical Medium
Print
Metadata
Show full item recordCitation
Jagoda, E., Lawson, D. J., Wall, J. D., Lambert, D., Muller, C., Westaway, M., Leavesley, M., et al. (2018). Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans.. Mol Biol Evol, 35 (3), 623-630. https://doi.org/10.1093/molbev/msx314
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 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.
Keywords
Neanderthal, adaptive introgression, archaic genomes, interferon, positive selection, toll-like receptor
Sponsorship
European Research Council (295907)
Identifiers
External DOI: https://doi.org/10.1093/molbev/msx314
This record's URL: https://www.repository.cam.ac.uk/handle/1810/279768
Rights
Attribution 4.0 International (CC BY 4.0)
Licence URL: https://creativecommons.org/licenses/by/4.0/
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