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The Contribution of Neanderthals to Phenotypic Variation in Modern Humans
Open accessAbstract
Assessing the genetic contribution of Neanderthals to non-disease phenotypes in modern humans has been difficult because of the absence of large cohorts for which common phenotype information is available. Using baseline phenotypes collected for 112,000 individuals by the UK Biobank, we can now elaborate on previous findings that identified associations between signatures of positive selection on Neanderthal DNA and various modern human traits but not any specific phenotypic consequences. Here, we show that Neanderthal DNA affects skin tone and hair color, height, sleeping patterns, mood, and smoking status in present-day Europeans. Interestingly, multiple Neanderthal alleles at different loci contribute to skin and hair color in present-day Europeans, and these Neanderthal alleles contribute to both lighter and darker skin tones and hair color, suggesting that Neanderthals themselves were most likely variable in these traits.
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![Figure 2 Archaic Haplotype Associated with Chronotype (A) The Neanderthal allele frequency in percentage (x axis) and the number of individuals in the UK Biobank cohort for the four reported chronotype phenotypes (y axis; from top to bottom: definitely an evening person, more an evening than a morning person, more a morning than an evening person, definitely a morning person) for the archaic tag SNP with the strongest association with chronotype (position chr2: 239,316,043 [rs75804782] near ASB1). (B) Worldwide frequency of the archaic allele (C, blue) and the modern human allele (T, orange) in the Simons Genome Diversity Panel populations. (C) The association p values (y axis; in the form of −log10(p)) with chronotype for all archaic and non-archaic SNPs (squares) genotyped by the UK Biobank study in the region of the inferred archaic haplotype at chr2: 239,316,043–239,470,654. The tag SNP at chr2: 239,316,043 (rs75804782) is shown in red, other aSNPs are shown in orange, and non-archaic SNPs are shown in black. The genome-wide significance cutoff of p = 1.0 × 10−8 and the extent of the inferred archaic haplotype are illustrated with dashed horizontal and vertical gray lines, respectively. At the top, we show all aSNPs that are within the inferred archaic haplotype and are present in any 1000 Genomes individual. The directly genotyped SNPs from the UK Biobank are illustrated as red (the archaic tag SNP) and orange bars. One archaic allele that leads to a missense mutation in ASB1 is marked as a green bar. (D) The cumulative density distribution of p values (zoom in for p < 0.01, x axis log scale) for associations between archaic alleles and chronotype (red line) and the 95% confidence interval region for 1,000 cumulative density distributions of associations between non-archaic alleles matched to the Neanderthal allele frequency and chronotype (gray shading).](/paper-figures/d81efe6b00614610801d7fba019d518c/the-contribution-of-neanderthals-to-phenotypic-variation-in-modern-humans-figure-2.jpg)
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“While further experimental validation of our observations is necessary in order to characterise the genome-wide impact of archaic introgression, the results presented in this study argue for a potential contribution of Denisovan variants to immune-related phenotypes amongst early modern humans in the region, potentially favouring adaptation to the local environment [15, 22].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [15]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“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 [4]
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“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 [16]
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“Additionally, signatures of archaic introgression have been reported in genes associated with hair and skin pigmentation, immunity [16, 17, 19, 20, 22], neoplasms and metabolic traits [19, 23, 24], and male sterility [17, 18].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [16]
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“Several studies have associated Neandertal-introgressed genetic variants with variability in phenotypes in modern humans, such as immunity, metabolism, and adaptation to environmental conditions, like temperature and sunlight, as well as neurological and behavioral phenotypes related to depression and addiction [17–20, 51].”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [51]
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“a second study has shown that among 136 diverse non-disease phenotypes, tested in ~122,000 individuals of the UK Biobank pilot release, Neandertal DNA was over-proportionally associated with two mood-related traits, sleeping patterns and smoking status [22].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [22]
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“For example, archaic alleles have been associated with differences in hemoglobin levels at higher altitude in Tibetans, immune resistance to new pathogens, levels of skin pigmentation, and fat composition (Huerta-Sánchez et al. 2014; Racimo et al. 2015; Racimo, Gokhman, et al. 2017; Dannemann and Kelso 2017; Racimo, Marnetto, and Huerta-Sánchez 2017; McArthur et al. 2021).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Dannemann and Kelso 2017
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“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 [16]
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“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 [4]
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“We also recover previous links between Neanderthal introgression and chronotype surrounding ASB1 (overall r = −0.92, Fig. S15)4.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [4]
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“Furthermore, the partitioned heritability method for identifying enrichment considers LD and the full distribution of variant effect sizes from a GWAS rather than selecting an ad hoc significance threshold and attempting to generate appropriate comparison sets of nonintrogressed alleles as in the analysis of 136 traits in an earlier release of the UK Biobank by Dannemann et al.4.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [4]
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“Previous studies showed that Neanderthal-introgressed loci are associated with immunological, neurological, psychiatric, metabolic, cardiovascular, and dermatological outcomes in EUR populations [10, 15–17].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [16]
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“First, a phenome-wide association study in the UK Biobank found loci near ASB1 and EXOC6 with introgressed variants that were significantly associated with self-reported sleeping patterns (Dannemann and Kelso 2017).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Dannemann and Kelso 2017
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“One of these alleles showed a significant association between frequency and latitude.”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Dannemann and Kelso 2017
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“Motivated by the previous discovery of an introgressed haplotype on chr2 that is associated with chronotype and increases in frequency with latitude (Dannemann and Kelso 2017; Putilov et al. 2019), we also tested each introgressed circadian variant for a correlation between allele frequency and latitude in modern non-African populations from the 1000 Genomes Project.”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Dannemann and Kelso 2017
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“previous studies have identified two introgressed loci associated with sleep patterns (Dannemann and Kelso 2017; Putilov et al. 2019).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Dannemann and Kelso 2017
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Metadata
- Authors
- Dannemann, M., & Kelso, J.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- Corresponding author
- Kelso, Janet
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2017-10
- Volume
- 101
- Issue
- 4
- Pages
- 578-589
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC5630192
- OpenAlex
- W2762049071
- Cited by
- 193
- References
- 38
- Citations by year
- 2026: 24 · 2025: 17 · 2024: 16 · 2023: 20 · 2022: 19 · 2021: 28 · 2020: 27 · 2019: 26 · 2018: 15 · 2017: 1
- FWCI
- 75.93
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Max-Planck-Gesellschaft
- 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
- Neanderthal DNA, Neanderthal introgression, skin color, hair color, height, sleep patterns, mood, smoking status, positive selection, UK Biobank, European populations, phenotypic variability
- MeSH terms
- Animals, Biological Evolution, Gene Frequency, Hair Color, Haplotypes, Humans, Phenotype, Phylogeny, Skin Pigmentation, Cohort Studies, Linkage Disequilibrium, Genome, Human, Polymorphism, Single Nucleotide, White People, Neanderthals
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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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