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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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“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]
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.
In the citing paper
“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]
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 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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Cites
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InfluentialThe genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107
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Molecular archaeology and machine learning
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“Even-tually, a team at the German Max Planck Institute for Evolutionary Anthropology in Leipzig used baseline phenotypes collected from 112,000 individuals in the UK Biobank, which allowed them to expand on previous findings (Dannemann & Kelso, 2017).”
Brain Evolution: Mapping the Inner Neandertal
Sherwood, C. C., & Bradley, B. J. (2019) · Current Biology · doi:10.1016/j.cub.2018.12.024 · Cited by 3
Exploring your Inner Hades: DNA as Mortuary Archaeology
Booth, T. J. (2018) · AP Online Journal in Public Archaeology · doi:10.23914/ap.v8i2.160 · Cited by 3
“Genetic variants that modern populations have inherited from Neanderthals include ones linked to pigmentation, however these variants have been shown to contribute to both lighter and darker pigmentation (Dannemann and Kelso 2017).”
BackgroundThe repertoire of family A-peptide GPCRs in archaic hominins
Mata, X., Renaud, G., & Mollereau, C. (2019) · Peptides · doi:10.1016/j.peptides.2019.170154 · Cited by 3
“A part of these archaic traces contributes to an archaic phenotypic legacy in present-day genomes (19, 20) that shapes some human physical traits, behavior and physiological functions, and influences health and disease related to metabolism, immune system or brain functions (4, 21, 22).”
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Ackermann, R., Arnold, M., Baiz, M. D., Cahill, J. A., Cortés‐Ortiz, L., Evans, B. J., Grant, B. R., Grant, P. R., Hallgrímsson, B., Humphreys, R. A., et al. (2018) · AfricArXiv (OSF Preprints) · doi:10.31730/osf.io/y3bp7 · Cited by 5
The role of Neanderthal introgression in liver cancer
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“…Single Nucleotide Poly-morphisms (aSNPs) have for example been associated with several human traits, such as the genetic susceptibility of type 2 diabetes (T2D), obesity, age of menopause, neurological traits, morning preference, skin and hair morphology, immune response, and inflammation [7– 17].”
BackgroundSelf-citationChen, Y., Yu, X., Xu, S., Shi, X., Zhang, X., & Sun, C. (2023) · Annals of Human Genetics · doi:10.1111/ahg.12533 · Cited by 2
“It has been widely accepted that the genetic variants in noncoding region, including the introgressed ones, influence human diseases or phenotypes through altering gene expression (Dannemann et al., 2017; McCoy et al., 2017; Rinker et al., 2020; Silvert et al., 2019).”
BackgroundWlasnowolski, M., Kozlov, N., Wojcik, M. J., Jacobs, G. S., & Plewczyński, D. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1256 · Cited by 2
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“…immune system (e.g. SELP , OAS , genes coding HLA, Toll-like receptors – TLRs and linked to cytokines) may have archaic ancestry, including the ones connected with Crohn’s disease or coeliac disease (Dolgova and Lao, 2018), as well as those linked to chronotype ( ASB1 ) (Dannemann and Kelso, 2017).”
BackgroundInfluentialGroß, M. (2019) · Nachrichten aus der Chemie · doi:10.1002/nadc.20194089256 · Cited by 2
Recovering signatures of archaic introgression using ancestral recombination graphsPreprint
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The Neanderthal population history and the introgression landscape inferred from the UK BiobankPreprint
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“In addition, indirect reconstruction of surviving Neanderthal fragments within modern humans is mostly limited by analytical strategy that captured only a fraction of the Neanderthal variation segregating in present-day genomes ( 20 , 29 ).”
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“Both fi ndings are supported in prior research that found archaic loci associated with sleep duration and daytime napping behaviours 20,23 , however, our variantswerenotdescribedintheirdatasets,soitisunclearifthedirectionof the effect is the same.”
InfluentialHuman evolution, migration, and adaptation in the Last Glacial environments
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“[17] agreed that introgressed genomes provide genetic adaptation to new environments.”
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Behavioral Modernity, Evolutionary Synergies, and the Symbolic Species
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Sterner, E. A. (2023) · Science & Technology Libraries · doi:10.1080/0194262x.2022.2163451 · Cited by 1
“For example, using baseline phenotypes in the UK Biobank, Dannemann and Kelso (2017) suggested that variations in exposure to direct sunlight may have influenced Neandertal phenotypes and potential gene flow between Neandertals and modern humans. Sankararaman et al. (2014) demonstrated the absence of alleles”
MethodDid variants in inborn errors of immunity genes contribute to the extinction of Neanderthals?
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Adaptive Archaic Introgression
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Computational Genomics and Its Applications to Anthropological Questions
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“Many other examples have been identified, including genes related to skin pigmentation (Vernot and Akey 2014; Gittelman et al. 2016), ABO blood groups (Villanea et al. 2021), and immune function (Gittelman et al. 2016; Dannemann and Kelso 2017; and Villanea et al. 2023).”
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What have the revelations about Neanderthal DNA revealed about Homo sapiens?
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“Nevertheless, most of the research in human paleogenetic developed since the beginning of the 21st century reiterate the importance of interbreeding and hybridization (Green et al. 2010; Meyer et al. 2014; Prüfer et at. 2014; Sankararaman et al. 2014; Vernot and Akey 2014; Racimo et al. 2015; Fu et al. 2016; Gittelman…”
BackgroundInfluentialTraining im mittleren und höheren Lebensalter
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“…from archaic humans, and some studies suggested that introgressed genomic fragments are adaptive in certain environments (Sankararaman et al. 2014; Racimo et al. 2016; Sankararaman et al. 2016; Simonti et al. 2016; Dannemann and Kelso 2017; Enard and Petrov 2018)(rev., Dannemann and Racimo 2018).”
BackgroundThe Evolution of Systemic Approaches to Children and Adolescents
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A Neanderthal Origin of Genetic Variants Associated with AsthmaPreprint
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“To elevate the strength of the evidence for an origin in Neanderthals, we adopted a previously-used approach, most recently to demonstrate the link between COVID-19 genetic risk and Neanderthals (2, 4, 11).”
BackgroundMethodThe Emergence of Symbolically Mediated Behavior in Eastern Europe
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Effects of introgressed Neanderthal alleles on present-day brain morphology
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Reconstructing protein-coding sequences from ancient DNA
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Forschungsfeld Sprachevolution
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Population Variation of the Human Genome
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Predicting gene regulatory changes across human evolution using ancient DNA
Colbran, L. L. (2020)
The Negative Impact of the Hominin’s DPP4 Gene Inherited from Neanderthals to Pandemic of COVID-19
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Geny archaicznych ludzi w genomie człowieka współczesnego a pandemia COVID-19
Branicki, W., Marszałek, K., Herda, K., & Łabaj, P. P. (2021) · Kosmos · doi:10.36921/kos.2021_2816
THE NEGATIVE IMPACT OF The HOMININ’s DPP4 GENE INHERITED from NEANDERTHALS to PANDEMIC of COVID-19Preprint
Niknamian, S. (2021) · doi:10.31219/osf.io/6fhz9
The Evolution of Systemic Approaches to Children and Adolescents
Wampler, R. S. (2020) · Wiley eBooks · doi:10.1002/9781119788393.ch1
European light skin may have evolved as an adaptation to the Neolithic sedentary lifestylePreprint
Ferrando-Bernal, M. (2022) · doi:10.32942/osf.io/mpq7f
Комісаренко, С. В., & Романюк, С. И. (2022) · Visnik Nacional noi academii nauk Ukrai ni · doi:10.15407/visn2022.12.003
Fossil and genetic evidence for Neanderthal introgression
Herrera, R. J., & Garcia‐Bertrand, R. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-819086-9.00006-3
Комісаренко, С. В., & Романюк, С. И. (2023) · The Ukrainian Biochemical Journal · doi:10.15407/ubj95.01.103 · Cited by 1
Kang, J., Ramgolam, A. S., Vot, L. L., & Young, R. S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.26.538367
“The enrichments observed here for archaic variants confirm this, as Neanderthal DNA is enriched for European eQTLs (Fig.”
ResultInfluentialADN, histoire de nos différences
(2020) · Odile Jacob eBooks · doi:10.3917/oj.sablo.2020.01.0231
Towards a historical comparison framework
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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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