Cited by 330Pleistocene-Era Hominins and ArchaeologyGenetic Associations and EpidemiologyForensic and Genetic Research

The phenotypic legacy of admixture between modern humans and Neandertals

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Simonti, Corinne N., Vernot, Benjamin, Bastarache, Lisa, Bottinger, Erwin, Carrell, David S., Chisholm, Rex L., Crosslin, David R., Hebbring, Scott J. +13 more·2016·Science

Abstract

The legacy of human-Neandertal interbreeding: Non-African humans are estimated to have inherited on average 1.5 to 4% of their genomes from Neandertals. However, how this genetic legacy affects human traits is unknown. Simonti et al. combined genotyping data with electronic health records. Individual Neandertal alleles were correlated with clinically relevant phenotypes in individuals of European descent. These archaic genetic variants were associated with medical conditions affecting the skin, the blood, and the risk of depression. Science , this issue p. 737

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Crossref · 10.1126/science.aad2149

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  • The majority of archaic alleles that are strongly associated with disease in single-locus tests are risk-increasing in the context of modern human populations.

    “the majority of archaic alleles that are strongly associated with disease in single-locus tests are risk-increasing in the context of modern human populations3.”

    From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]

    The paper’s single-locus PheWAS reports four strongly associated, replicated Neanderthal SNP–phenotype associations (passage labeled Abstract; page unavailable). It explicitly says the coagulation-associated allele increases risk and describes the malnutrition-associated allele as potentially harmful, but the available passages do not establish that a majority of the four alleles increase disease risk. Its separate combined-SNP analysis reports similar numbers of risk-increasing and risk-decreasing alleles; that analysis does not settle the single-locus claim. (LLM, conf=0.78)

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  • For psychiatric traits, tobacco use disorders trend towards enrichment (1.2-fold enriched, q = 0.23), while introgressed variants are depleted for contribution to personality-related functions (1.4-fold depleted, q = 0.07).

    “For psychiatric traits, tobacco use disorders trend towards enrichment (1.2-fold enriched, CI: 1.0-1.5, q = 0.23), consistent with previous observations, while introgressed variants are depleted for contribution to personality-related functions (1.4-fold depleted, CI: 1.1–1.8, q = 0.07, Fig. 2E)3,4.”

    From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]

    The paper reports a replicated association between a Neanderthal SNP and tobacco use disorder, and says Neanderthal SNPs were associated with more psychiatric phenotypes (main text, indexed as Abstract; page unavailable). It does not report the claimed 1.2-fold tobacco enrichment or 1.4-fold depletion for personality-related functions, or their q-values. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • This is consistent with previous hypotheses that genomic regions associated with skin traits tolerated introgression and with previous tests for genome-wide effects of Neanderthal ancestry on complex traits that found enrichment for traits related to skin and hair.

    “This is consistent with previous hypotheses that genomic regions associated with skin traits tolerated introgression and with previous tests for genome-wide effects of Neanderthal ancestry on complex traits that found enrichment for traits related to skin and hair3,19.”

    From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]

    Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

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  • In populations of European descent, a phenome-wide association study of Neanderthal-introgressed alleles showed a wide range of associations with physiological conditions related to the immune system, skin pigmentation, and metabolic pathways, and with pathological outcomes such as depression, actinic keratosis, hypercoagulation, and tobacco use.

    “In populations of European descent (EUR), a phenome-wide association study of Neanderthal-introgressed alleles showed a wide range of associations with physiological conditions related to the immune system, skin pigmentation, and metabolic pathways, and with pathological outcomes such as depression, actinic keratosis, hypercoagulation, and tobacco use [15].”

    From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]

    The paper’s Abstract (page unavailable in our copy) describes an analysis of about 28,000 adults of European ancestry and reports associations involving immune and skin phenotypes, metabolism, depression, actinic keratosis, hypercoagulation, and tobacco use. It discusses skin phenotypes and keratinocytes, but the passages do not establish an association with skin pigmentation specifically. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • Introgression from extinct Neanderthal and Denisovan human species contributes to the genetic pool of modern human populations and their phenotypic spectrum.

    “Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum.”

    From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]

    The opening passage (section labeled Abstract; page unavailable) reports interbreeding involving Neanderthals and Denisovans and identifies Neanderthal DNA in modern Eurasian genomes. The Abstract also reports associations between Neanderthal alleles and human phenotypes. It does not directly establish a Denisovan contribution to modern humans’ phenotypic variation, although it cites a study of Denisovan-like DNA and altitude adaptation. (LLM, conf=0.79)

    Experimental — accuracy not yet measured

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Authors
Simonti, C. N., Vernot, B., Bastarache, L., Bottinger, E., Carrell, D. S., Chisholm, R. L., Crosslin, D. R., Hebbring, S. J., Jarvik, G. P., Kullo, I. J., Li, R., Pathak, J., Ritchie, M. D., Roden, D. M., Verma, S. S., Tromp, G., Prato, J. D., Bush, W. S., Akey, J. M., Denny, J. C., & Capra, J. A.
Affiliations
  • Vanderbilt University (US)
  • University of Washington (US)
  • Mount Sinai School of Medicine, New York, NY, USA.
  • University of Washington Medical Center (US)
  • Northwestern University (US)
  • Marshfield Clinic (US)
  • Mayo Clinic (US)
  • National Institutes of Health (US)
  • Pennsylvania State University (US)
  • Stellenbosch University (ZA)
  • Case Western Reserve University (US)
Corresponding author
  • Pathak, Jyotishman
  • Akey, Joshua M.
  • Denny, Joshua C.
  • Capra, John A.
Venue
Science
Published
2016-02-12
Volume
351
Issue
6274
Pages
737-741
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W2279984879
Cited by
330
References
51
Citations by year
2026: 17 · 2025: 13 · 2024: 24 · 2023: 27 · 2022: 26 · 2021: 49 · 2020: 28 · 2019: 57 · 2018: 29 · 2017: 36 · 2016: 24
FWCI
190.29
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Johns Hopkins University (U01HG004438)
  • Group Health Cooperative and University of Washington, Seattle (U01HG004610, U01HG008657)
  • Marshfield Clinic (U01HG004608, 1K22LM011938)
  • Essentia Institute of Rural Health (U01HG006389)
  • Mayo Clinic (U01HG04599, U01HG006379)
  • Northwestern University (U01HG004609, U01HG006388)
  • Vanderbilt University (U01HG04603, U01HG006378)
  • Coordinating Center of the eMERGE Network (U01HG006385)
  • Geisinger Clinic (U01HG006382)
  • Mount Sinai School of Medicine (U01HG006380)
  • PheWAS (R01LM010685)
  • NIH (5T32EY021453, R01GM110068, 1R01GM114128)
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
electronic health records, depression, actinic keratosis, sun exposure, skin lesions, hypercoagulability, tobacco use, psychiatric phenotypes, neurological phenotype, immunological phenotype, European ancestry, disease risk
MeSH terms
Alleles, Animals, Depression, Disease, Haplotypes, Humans, Phenotype, Genetic Variation, Genome, Human, Evolution, Molecular, White People, Keratosis, Actinic, Neanderthals

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