Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
Open accessAbstract
Neanderthal ancestry remains across modern Eurasian genomes and introgressed sequences influence diverse phenotypes. Here, we demonstrate that introgressed sequences reintroduced thousands of ancestral alleles that were lost in Eurasian populations before introgression. Our simulations and variant effect predictions argue that these reintroduced alleles (RAs) are more likely to be tolerated by modern humans than are introgressed Neanderthal-derived alleles (NDAs) due to their distinct evolutionary histories. Consistent with this, we show enrichment for RAs and depletion for NDAs on introgressed haplotypes with expression quantitative trait loci (eQTL) and phenotype associations. Analysis of available cross-population eQTLs and massively parallel reporter assay data show that RAs commonly influence gene expression independent of linked NDAs. We further validate these independent effects for one RA in vitro. Finally, we demonstrate that NDAs are depleted for regulatory activity compared to RAs, while RAs have activity levels similar to non-introgressed variants. In summary, our study reveals that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated than NDAs. Thus, RAs and their distinct evolutionary histories must be considered when evaluating the effects of introgression.
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The depletion in cognitive traits suggests that the previously observed strong depletion for Neanderthal alleles in regulatory regions active in the brain may be due to effects on brain-related complex traits.
“The depletion in cognitive traits suggests that the previously observed strong depletion for Neanderthal alleles in regulatory regions active in the brain may be due to effects on brain-related complex traits5,28,29.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [5]
The Discussion (page not available) reports depletion of Neanderthal-derived alleles among introgressed brain eQTLs and discusses selection affecting regulatory regions. It does not report a depletion in cognitive traits or suggest that effects on brain-related complex traits explain the regulatory-region depletion. (LLM, conf=0.83)
Experimental — accuracy not yet measuredAnalyses of available genome-wide association studies and large-scale biobank data revealed that alleles of Neanderthal ancestry are associated with diverse traits in modern Eurasians.
“Analyses of available genome-wide association studies and large-scale biobank data revealed that alleles of Neanderthal ancestry are associated with diverse traits in modern Eurasians1,3–5.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [5]
The Results section ('RA-containing introgressed haplotypes are associated with anthropometric human traits and disease risk'; page not specified) reports GWAS Catalog associations between introgressed variants and diverse traits in Eurasians. The Methods section describes the GWAS Catalog analysis, but our copy does not establish that this paper analyzed large-scale biobank data. (LLM, conf=0.85)
Experimental — accuracy not yet measuredPrevious studies have not comprehensively characterized the genome-wide influence of Neanderthal introgression on modern human diseases and traits.
“previous studies have not comprehensively characterized the genome-wide influence of Neanderthal introgression on modern human diseases and traits.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [5]
In the introductory passage under “ONE SENTENCE SUMMARY” (page unavailable), the paper says most previous studies focused on Neanderthal-derived alleles and may have overlooked reintroduced ancestral alleles. This supports the idea that prior work left part of introgression’s effects uncharacterized, but it does not establish the broader claim that no previous study comprehensively characterized genome-wide effects on diseases and traits. (LLM, conf=0.78)
Experimental — accuracy not yet measuredThe remaining alleles of Neanderthal ancestry are predicted to be less likely to modify protein and regulatory functions than matched sets of alleles that arose on the human lineage.
“the remaining alleles of Neanderthal ancestry—i.e., introgressed alleles that were maintained by either selection or drift since admixture—are predicted to be less likely to modify protein and regulatory functions than matched sets of alleles that arose on the human lineage, suggesting that functional introgressed variants were less tolerated5,30.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [5]
The Results section, “RAs are more likely than NDAs to have gene regulatory activity” (page unavailable), reports that Neanderthal-derived alleles were less likely to show regulatory activity than non-introgressed variants, including after matching for allele frequency and linkage disequilibrium. The paper does not establish the claimed lower likelihood of modifying protein function relative to matched human-lineage alleles; its protein-effect predictions instead compare Neanderthal-derived alleles with reintroduced ancestral alleles. (LLM, conf=0.85)
Experimental — accuracy not yet measuredIntrogressed variants are depleted in regulatory elements and eQTL generally.
“Given the previously observed depletion for introgressed variants in regulatory elements and eQTL (Petr et al. 2019; Rinker et al. 2020; Telis et al. 2020)”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Rinker et al. 2020
The Results section (page unavailable) reports depletion of Neanderthal-derived alleles relative to reintroduced ancestral alleles among introgressed haplotypes with eQTL. The Discussion (page unavailable) also discusses depletion of Neanderthal-derived alleles in regulatory regions. These findings do not establish that introgressed variants as a whole are generally depleted in regulatory elements and eQTL. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Introgressed haplotypes carry alleles of different origins, including ancestral alleles lost in some modern Eurasian populations.
“Introgressed haplotypes carry alleles of different origins, including ancestral alleles lost in some modern Eurasian populations5.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [5]
The set of all introgressed variants includes not only high-confidence Neanderthal-origin introgressed variants, but also ancestral alleles lost in Africans that were reintroduced to Eurasians through archaic introgression, variants with origins in other archaic hominins such as Denisovans, and possibly variants tightly linked to introgressed haplotypes that arose in Eurasians shortly after introg
“This set includes not only high-confidence Neanderthal-origin introgressed variants, but also ancestral alleles lost in Africans that were reintroduced to Eurasians through archaic introgression5, variants with origins in other archaic hominins, such as Denisovans, and possibly variants tightly linked to introgressed haplotypes that arose in Eurasians shortly after introgression.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [5]
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Velazquez-Arcelay, K., Colbran, L. L., McArthur, E., Brand, C. M., Rinker, D. C., Siemann, J. K., McMahon, D. G., & Capra, J. A. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad203 · Cited by 18 · see citing works
Self-citationA signature of Neanderthal introgression on molecular mechanisms of environmental responses
Findley, A. S., Zhang, X., Boye, C., Lin, Y. L., Kalita, C. A., Barreiro, L., Lohmueller, K. E., Pique-Regi, R., & Luca, F. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009493 · Cited by 14 · see citing works
- Authors
- Rinker, D. C., Simonti, C. N., McArthur, E., Shaw, D., Hodges, E., & Capra, J. A.
- Affiliations
- Vanderbilt University (US)
- Georgia Institute of Technology (US)
- Corresponding author
- Capra, John A.
- Venue
- Nature Ecology & Evolution
- Published
- 2020-07-27
- Volume
- 4
- Issue
- 10
- Pages
- 1332-1341
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC7529911
- OpenAlex
- W3044115990
- Cited by
- 44
- References
- 66
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 3 · 2023: 7 · 2022: 10 · 2021: 11 · 2020: 5 · 2019: 1
- FWCI
- 31.08
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35GM127087, T32GM080178, T32GM007347)
- U.S. Department of Health & Human Services | NIH | National Eye Institute (T32EY021453)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (F30HG011200)
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (K22CA184308)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- Neanderthal introgression, Neanderthal ancestry, expression quantitative trait loci, massively parallel reporter assay, gene expression, modern human genomes
- MeSH terms
- Alleles, Animals, Haplotypes, Humans, Population, Hominidae, Neanderthals
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