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

Evelyn Jagoda, Daniel J Lawson, Jeffrey D Wall, David Lambert, Craig Muller, Michael Westaway, Matthew Leavesley, Terence D Capellini, Marta Mirazón Lahr, Pascale Gerbault, Mark G Thomas, Andrea Bamberg Migliano, Eske Willerslev, Mait Metspalu, Luca Pagani

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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.

Original languageEnglish
JournalMolecular Biology and Evolution
Early online date6 Dec 2017
DOIs
Publication statusE-pub ahead of print - 6 Dec 2017

Keywords

  • Journal Article

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    Jagoda, E., Lawson, D. J., Wall, J. D., Lambert, D., Muller, C., Westaway, M., Leavesley, M., Capellini, T. D., Mirazón Lahr, M., Gerbault, P., Thomas, M. G., Migliano, A. B., Willerslev, E., Metspalu, M., & Pagani, L. (2017). Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msx314