Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments
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As modern humans dispersed from Africa throughout the world, they encountered and interbred with archaic hominins, including Neanderthals and Denisovans [1, 2]. Although genome-scale maps of introgressed sequences have been constructed [3-6], considerable gaps in knowledge remain about the functional, phenotypic, and evolutionary significance of archaic hominin DNA that persists in present-day individuals. Here, we describe a comprehensive set of analyses that identified 126 high-frequency archaic haplotypes as putative targets of adaptive introgression in geographically diverse populations. These loci are enriched for immune-related genes (such as OAS1/2/3, TLR1/6/10, and TNFAIP3) and also encompass genes (including OCA2 and BNC2) that influence skin pigmentation phenotypes. Furthermore, we leveraged existing and novel large-scale gene expression datasets to show many positively selected archaic haplotypes act as expression quantitative trait loci (eQTLs), suggesting that modulation of transcript abundance was a common mechanism facilitating adaptive introgression. Our results demonstrate that hybridization between modern and archaic hominins provided an important reservoir of advantageous alleles that enabled adaptation to out-of-Africa environments.
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The regions of the novel T2T-CHM13 haplotypes included previously recognized targets of adaptive introgression, such as SGCB and SPATA18.
“These regions included previously recognized targets of adaptive introgression, such as SGCB and SPATA18 [13, 14, 17].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [17]
The Results and Discussion section on identifying adaptively introgressed loci says that seven high-frequency archaic haplotypes had previously been highlighted as putative targets of adaptive introgression. Our copy does not identify SGCB or SPATA18 as examples, and it does not address the novel T2T-CHM13 haplotypes (searched: SGCB, SPATA18). (LLM, conf=0.83)
Experimental — accuracy not yet measuredSome archaic alleles and haplotypes are adaptive and persist at high frequencies in human populations.
“For instance, substantial evidence suggests that some archaic alleles and haplotypes are adaptive and persist at high frequencies in human populations [10, 13–19].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [17]
The introgressed variants that remain in AMH genomes are the result of complex selective and demographic pressures following admixture.
“The introgressed variants that remain in AMH genomes are the result of complex selective and demographic pressures following admixture9,25,27.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [9]
Some remaining Neandertal variants have reached high frequencies in some present-day populations, suggesting they might have conferred advantages at some point since admixture.
“Some of the remaining Neandertal variants have reached high frequencies in some present-day populations, suggesting that they might have conferred advantages at some point since admixture [12, 18, 19].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [19]
Selected variants can exert their effect by modifying gene expression or by changing the amino acid sequence.
“Selected variants can exert their effect by modifying gene expression or by changing the amino acid sequence [8–12].”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [8]
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Self-citationEffects of introgressed Neanderthal alleles on present-day brain morphology
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“Although some examples of adaptive introgression from archaic humans have been identified 7–10 , most introgressed haplotypes are expected to be neutral, or even fitness-reducing due to a) critical demographic conditions of late Neanderthals leading to accumulation of deleterious variants 6,11 and…”
- Authors
- Gittelman, R. M., Schraiber, J. G., Vernot, B., Mikacenic, C., Wurfel, M. M., & Akey, J. M.
- Affiliations
- University of Washington (US)
- Corresponding author
- Akey, Joshua M.
- Venue
- Current Biology
- Publisher
- Elsevier BV
- Published
- 2016-12
- Volume
- 26
- Issue
- 24
- Pages
- 3375-3382
- ISSN
- 0960-9822 (ISSN-L)
- PMC
- PMC6764441
- OpenAlex
- W2550871030
- Cited by
- 181
- References
- 43
- Citations by year
- 2026: 12 · 2025: 11 · 2024: 17 · 2023: 20 · 2022: 16 · 2021: 28 · 2020: 27 · 2019: 22 · 2018: 18 · 2017: 10
- FWCI
- 65.17
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Current Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NIH (R01GM110068)
- 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 › Genetic Associations and Epidemiology
- Keywords
- adaptive introgression, Neanderthal DNA, Denisovan DNA, immune-related genes, A20, OCA2, BNC2, expression quantitative trait loci, positive selection, hybridization
- MeSH terms
- Adaptation, Physiological, Animals, Demography, DNA, Biological Evolution, Gene Expression Regulation, Haplotypes, Humans, Pigmentation, Genetic Variation, Genome, Human, Neanderthals
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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