Cited by 64Pleistocene-Era Hominins and ArchaeologyForensic and Genetic ResearchEvolution and Genetic Dynamics

Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens

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Gouy, Alexandre, Excoffier, Laurent·2020·Molecular Biology and Evolution

Published version of a preprint

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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  1. Telis N, Aguilar R, Harris K. 2019. Selection against archaic DNA in hu- man regulatory regions. bioRxiv: 708230.

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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
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
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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