Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens
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Abstract
Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.
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- Authors
- Gouy, A., & Excoffier, L.
- Affiliations
- University of Bern (CH)
- Corresponding author
- Gouy, Alexandre
- Excoffier, Laurent
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-01-14
- Volume
- 37
- Issue
- 5
- Pages
- 1420-1433
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2999381098
- Cited by
- 63
- References
- 64
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 12 · 2023: 8 · 2022: 9 · 2021: 15 · 2020: 8
- FWCI
- 36.64
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Swiss National Science Foundation (310030B-166605)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- adaptive introgression, polygenic adaptation, epistatic selection, gene networks, functional enrichment, immune response to pathogens, local adaptation, Out of Africa, human evolution
- MeSH terms
- Genetic Introgression, Adaptation, Biological, Humans, Melanesia, Selection, Genetic, Multifactorial Inheritance, Host-Pathogen Interactions
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