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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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.
“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]
The Introduction (page unavailable) reports adaptive introgressed variants in immunity-related genes, which supports the general possibility of archaic contributions to immune adaptation. But the Discussion (page unavailable) describes this paper’s analysis as testing Neanderthal alleles in present-day Europeans; it does not establish a Denisovan contribution to immune phenotypes among early modern humans in the citing study’s region. (LLM, conf=0.82)
Experimental — accuracy not yet measuredFor 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 [4]
The Discussion reports that Neanderthal alleles contribute more variation to smoking status than comparable non-archaic alleles, supporting a broad connection with smoking. It does not establish an enrichment for tobacco use disorders or give the claimed 1.2-fold estimate and q-value. The searched passages also do not report depletion of personality-related functions or its 1.4-fold estimate and q-value. (LLM, conf=0.84)
Experimental — accuracy not yet measuredIntrogression 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 [16]
The Introduction states that Neanderthal interbreeding contributed DNA to present-day non-Africans, and the Discussion reports phenotypic variation linked to Neanderthal introgression. The paper does not establish the same claim for Denisovan introgression; Denisovan DNA appears in a cited study and a haplotype-tree method, not as a finding of this analysis. Page numbers were not provided in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredSignatures of archaic introgression have been reported in genes associated with hair and skin pigmentation, immunity, neoplasms and metabolic traits, and male sterility.
“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]
The Introduction (page unavailable) reports introgressed variants in genes related to immunity, skin and hair pigmentation, and metabolism. The Results (page unavailable) also identify Neanderthal haplotypes associated with pigmentation. The cited paper does not report neoplasms; male sterility is attributed to different citations in the citing sentence. (LLM, conf=0.86)
Experimental — accuracy not yet measuredSeveral studies have associated Neandertal-introgressed genetic variants with variability in phenotypes in modern humans, such as immunity, metabolism, adaptation to environmental conditions, and neurological and behavioral phenotypes related to depression and addiction.
“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]
The Introduction reports prior findings on introgressed variants related to immunity, metabolism, adaptation, and depression; the Discussion reports associations with mood and smoking status and suggests a link to sunlight exposure (pages unavailable). The paper does not establish an association with addiction specifically, and its sunlight-adaptation interpretation is speculative rather than a demonstrated response to environmental conditions such as temperature. (LLM, conf=0.84)
Experimental — accuracy not yet measured
In a second study among 136 diverse non-disease phenotypes tested in about 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.
“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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Experimental — accuracy not yet measuredArchaic 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.
“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
The Results (page unavailable) report associations of archaic alleles with skin-color traits and leg impedance, which the paper interprets as suggesting differences in body-fat composition. The Discussion mentions suggested effects of archaic ancestry on immune phenotypes, but the passages do not establish resistance to new pathogens. The cited paper also does not report the claimed hemoglobin difference in high-altitude Tibetans. (LLM, conf=0.87)
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 [16]
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 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 [4]
We recover previous links between Neanderthal introgression and chronotype surrounding ASB1 (overall r = −0.92).
“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]
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.
“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]
Previous studies showed that Neanderthal-introgressed loci are associated with immunological, neurological, psychiatric, metabolic, cardiovascular, and dermatological outcomes in EUR populations.
“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]
A phenome-wide association study in the UK Biobank found loci near ASB1 and EXOC6 with introgressed variants significantly associated with self-reported sleeping patterns.
“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
One of these alleles showed a significant association between frequency and latitude.
“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
An introgressed haplotype on chr2 is associated with chronotype and increases in frequency with latitude.
“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
Previous studies have identified two introgressed loci associated with sleep patterns.
“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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BackgroundThe influence of evolutionary history on human health and disease
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“A recent study of the genetic contribution of Neanderthals to phenotypic variation in modern humans has recognized the introgression of two BNC2 haplotypes, one associated with sun sensitivity and the other with darker skin pigmentation (36).”
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The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2225-9 · Cited by 145 · see citing works
Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity
Gunz, P., Tilot, A. K., Wittfeld, K., Teumer, A., Shapland, C. Y., van Erp, T. G. M., Dannemann, M., Vernot, B., Neubauer, S., Guadalupe, T., et al. (2019) · Current Biology · doi:10.1016/j.cub.2018.10.065 · Cited by 117 · see citing works
Self-citationHuman Disease Variation in the Light of Population Genomics
Prohaska, A., Racimo, F., Schork, A. J., Sikora, M., Stern, A. J., Ilardo, M. A., Allentoft, M. E., Folkersen, L., Buil, A., Moreno-Mayar, J. V., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.052 · Cited by 108 · see citing works
“While the overall amount of introgressed sequences is low, multiple lines of evidence nevertheless suggest that archaic DNAplays an important role in human phenotypic diversity and adaptation (Dannemann and Kelso, 2017; Huerta-Sánchez et al., 2014; Quach et al., 2016; Racimo et al., 2017).”
BackgroundAncient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites
Platt, R. N., McDew‐White, M., Clecʼh, W. L., Chevalier, F. D., Allan, F., Emery, A. M., Garba, A., Hamidou, A. A., Ame, S. M., Webster, J. P., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz154 · Cited by 98 · see citing works
“Genes involved in immune response (AbiRached et al. 2011), pathogen defense (Enard and Petrov 2018), and protection from sun exposure (Dannemann and Kelso 2017) have introgressed from archaic humans as a result of these ancient hybridization events.”
BackgroundHybridization in human evolution: Insights from other organisms
Ackermann, R., Arnold, M. L., 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. (2019) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21787 · Cited by 101 · see citing works
Archaic hominin introgression into modern human genomes
Gökçümen, Ö. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23951 · Cited by 91 · see citing works
Something old, something borrowed: admixture and adaptation in human evolution
Dannemann, M., & Racimo, F. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.05.009 · Cited by 87 · see citing works
Self-citationThe history and evolution of the Denisovan- <i>EPAS1</i> haplotype in Tibetans
Zhang, X., Witt, K. E., Bañuelos, M. M., Ko, A., Yuan, K., Xu, S., Nielsen, R., & Huerta-Sanchez, E. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2020803118 · Cited by 105 · see citing works
“Discussion Previous studies have shown that archaic introgression contributed to a range of phenotypic variation in modern humans (5, 57, 58), and that a number of introgressed genes were plausibly subject to positive selection (17, 18).”
BackgroundQuantifying the contribution of Neanderthal introgression to the heritability of complex traits
McArthur, E., Rinker, D. C., & Capra, J. A. (2021) · Nature Communications · doi:10.1038/s41467-021-24582-y · Cited by 71 · see citing works
The contribution of Neanderthal introgression to modern human traits
Reilly, P. F., Tjahjadi, A., Miller, S. L., Akey, J. M., & Tucci, S. (2022) · Current Biology · doi:10.1016/j.cub.2022.08.027 · Cited by 80 · see citing works
Outstanding questions in the study of archaic hominin admixture
Wolf, A. B., & Akey, J. M. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007349 · Cited by 66 · see citing works
Gouy, A., & Excoffier, L. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz306 · Cited by 63 · see citing works
More than a decade of genetic research on the Denisovans
Peyrégne, S., Slon, V., & Kelso, J. F. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00643-4 · Cited by 66 · see citing works
“The Denisovan DNA that ‘lives on’ in the genomes of present-day people offers an opportunity to indirectly investigate the Denisovan phenotype by identifying associations between introgressed Denisovan genetic variants and particular phenotypes in people living today 128–130 .”
Self-citationInferred divergent gene regulation in archaic hominins reveals potential phenotypic differences
Colbran, L. L., Gamazon, E. R., Zhou, D., Evans, P., Cox, N. J., & Capra, J. A. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0996-x · Cited by 50 · see citing works
Silvert, M., Quintana-Murci, L., & Rotival, M. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.04.016 · Cited by 58 · see citing works
How Natural Genetic Variation Shapes Behavior
Niepoth, N., & Bendesky, A. (2020) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111219-080427 · Cited by 60 · see citing works
Recent evolution of the human skin barrier
Brettmann, E. A., & Strong, C. D. G. (2018) · Experimental Dermatology · doi:10.1111/exd.13689 · Cited by 57 · see citing works
The lingering effects of Neanderthal introgression on human complex traits
Wei, X., Robles, C. R., Pazokitoroudi, A., Ganna, A., Gusev, A., Durvasula, A., Gazal, S., Loh, P.-R., Reich, D., & Sankararaman, S. (2023) · eLife · doi:10.7554/elife.80757 · Cited by 43 · see citing works
“Previously, (Dannemann and Kelso, 2017) showed that some Neanderthal introgressed variants are significantly associated with traits such as skin tone, hair color, and height based on genome- wide association studies (GWAS) in British samples.”
BackgroundThe Neandertal Progesterone Receptor
Zeberg, H., Kelso, J. F., & Pääbo, S. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa119 · Cited by 48 · see citing works
Self-citationJagoda, E., Xue, J. R., Reilly, S. K., Dannemann, M., Racimo, F., Huerta-Sanchez, E., Sankararaman, S., Kelso, J., Pagani, L., Sabeti, P. C., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msab304 · Cited by 47 · see citing works
“Therefore, we included the 1,156 variants in the putatively adaptively introgressed variant set that were linked to one of the top 100 eQTLs (loci that affect gene expression) in any tissue (Dannemann et al. 2017).”
InfluentialSelf-citationDenisovan introgression has shaped the immune system of present-day Papuans
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F.-X., Cox, M. P., & Gallego Romero, I. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010470 · Cited by 46 · see citing works
“Several lines of evidence highlight associations between archaic DNA and risk for disease traits, including autoimmune diseases [12,13], or with traits of possible evolutionary advantage for early non-Africans [14,15].”
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
Rinker, D. C., Simonti, C. N., McArthur, E., Shaw, D., Hodges, E., & Capra, J. A. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1261-z · Cited by 44 · see citing works
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0
Yuan, K., Ni, X., Liu, C., Pan, Y., Deng, L., Zhang, R., Gao, Y., Ge, X., Liu, J., Ma, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26503-5 · Cited by 42 · see citing works
Human races are not like dog breeds: refuting a racist analogy
Norton, H., Quillen, E. E., Bigham, A. W., Pearson, L. N., & Dunsworth, H. M. (2019) · Evolution Education and Outreach · doi:10.1186/s12052-019-0109-y · Cited by 40 · see citing works
Zhang, X., Kim, B., Singh, A., Sankararaman, S., Durvasula, A., & Lohmueller, K. E. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad001 · Cited by 29 · see citing works
Natural Selection Has Differentiated the Progesterone Receptor among Human Populations
Li, J., Hong, X., Mesiano, S. A., Muglia, L. J., Wang, X., Snyder, M. P., Stevenson, D. K., & Shaw, G. M. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.05.009 · Cited by 36 · see citing works
“This notion is confirmed by the Neanderthal introgressionmap(55) as well as by amore recent study using rigorous criteria to identify alleles of Neanderthal origin in modern human’s genome.(56) We further investigated the sequence of the high-coverage Denisovan genome,(57) an extinct archaic human who lived 72,000 yea…”
ResultEvolutionary and medical consequences of archaic introgression into modern human genomes
Dolgova, O., & Lao, O. (2018) · Genes · doi:10.3390/genes9070358 · Cited by 34 · see citing works
New insights into human immunity from ancient genomics
Kerner, G., Patin, É., & Quintana‐Murci, L. (2021) · Current Opinion in Immunology · doi:10.1016/j.coi.2021.04.006 · Cited by 34 · see citing works
“The introgression of archaic material in humans has been also found to affect molecular phenotypes, such as gene expression [30,31].”
BackgroundThe Population-Specific Impact of Neandertal Introgression on Human Disease
Dannemann, M. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evaa250 · Cited by 33 · see citing works
Self-citationKoller, D., Wendt, F. R., Pathak, G. A., De Lillo, A., De Angelis, F., Cabrera-Mendoza, B., Tucci, S., & Polimanti, R. (2022) · BMC Biology · doi:10.1186/s12915-022-01449-2 · Cited by 27 · see citing works
“Introgression from Neanderthals and Denisovans, the only archaic humans sequenced to date, also contributes to the genetic pool of modern populations [13, 14] and consequently to the human phenotypic spectrum [15, 16].”
BackgroundAdmixture in Mammals and How to Understand Its Functional Implications
Fontsere, C., de Manuel, M., Marquès‐Bonet, T., & Kuhlwilm, M. (2019) · BioEssays · doi:10.1002/bies.201900123 · Cited by 32 · see citing works
Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture
Ahlquist, K. D., Bañuelos, M. M., Funk, A., Lai, J., Rong, S., Villanea, F. A., & Witt, K. E. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab115 · Cited by 33 · see citing works
“Some enhancer regions also show enrichment in Neanderthal alleles, such as adipose-related tissues and primary T cells (Dannemann et al. 2017; Petr et al. 2019; Silvert et al. 2019), but others, including brain and muscle-associated enhancers, show depletion (Telis et al. 2020).”
BackgroundInfluentialReticulate evolution: Detection and utility in the phylogenomics era
Bjornson, S., Verbruggen, H., Upham, N. S., & Steenwyk, J. L. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108197 · Cited by 34 · see citing works
An evolutionary compass for detecting signals of polygenic selection and mutational bias
Uricchio, L. H., Kitano, H. C., Gusev, A., & Zaitlen, N. (2019) · Evolution Letters · doi:10.1002/evl3.97 · Cited by 29 · see citing works
“…to the genetic variance in some traits (Simonti et al., 2016) and that some high frequency trait-associated alleles have Neanderthal origins (Dannemann and Kelso, 2017; Prüfer et al., 2017), we hypothesized that Neanderthal alleles for traits under selection might show distinct patterns…”
Dannemann, M., Milaneschi, Y., Yermakovich, D., Stiglbauer, V., Kariis, H. M., Krebs, K., Friese, M. A., Otte, C., Estonian Biobank Research Team, Esko, T., et al. (2022) · Translational Psychiatry · doi:10.1038/s41398-022-02196-2 · Cited by 23 · see citing works
“Testing for the proportional association strength to phenotypes In order to quantify the association strength of archaic variants, we compared their number of significantly associated tag aSNPs to the number of frequency-matched non-archaic tag SNPs following similar approaches that have previously been used for such…”
BackgroundResultSelf-citationCharacterizing the effect of background selection on the polygenicity of brain-related traits
Wendt, F. R., Pathak, G. A., Overstreet, C., Tylee, D. S., Gelernter, J., Atkinson, E. G., & Polimanti, R. (2021) · Genomics · doi:10.1016/j.ygeno.2020.11.032 · Cited by 27 · see citing works
Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees
Breyl, M. (2020) · Wiley Interdisciplinary Reviews Cognitive Science · doi:10.1002/wcs.1545 · Cited by 24 · see citing works
Rong, S., Neil, C. R., Welch, A., Duan, C., Maguire, S., Meremikwu, I. C., Meyerson, M., Evans, B. J., & Fairbrother, W. G. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218308120 · Cited by 24 · see citing works
“associated introgressed variants in modern human populations, such as those associated with complex traits (4, 24, 34-37), gene expression across tissues (38), or in response to infection (39-”
Liu, X., Koyama, S., Tomizuka, K., Takata, S., Ishikawa, Y., Ito, S., Kosugi, S., SUZUKI, K., Hikino, K., Koido, M., et al. (2024) · Science Advances · doi:10.1126/sciadv.adi8419 · Cited by 24 · see citing works
“However, beyond a few specific examples such as EPAS1 , the impacts of Denisovan introgression on human phenotypes remain less understood, particularly in comparison with introgression from Neanderthal ( 90 ).”
BackgroundQuantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?
Irving-Pease, E. K., Muktupavela, R., Dannemann, M., & Racimo, F. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.703541 · Cited by 24 · see citing works
Self-citationPredicting Archaic Hominin Phenotypes from Genomic Data
Brand, C. M., Colbran, L. L., & Capra, J. A. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111521-121903 · Cited by 23 · see citing works
“(104) and found associations with multiple phenotypes: chronotype, comparative height at 10 years of age, ease of skin tanning, hair color, impedance of right and left legs, incidence of childhood sunburn, narcolepsy, pulse rate, sitting height, and skin color (27).”
BackgroundMethodInfluentialComplex Phenotypes: Mechanisms Underlying Variation in Human Stature
Muthuirulan, P., & Capellini, T. D. (2019) · Current Osteoporosis Reports · doi:10.1007/s11914-019-00527-9 · Cited by 22 · see citing works
McArthur, E., Rinker, D. C., Cheng, Y., Wang, Q., Wang, J., Gilbertson, E. N., Fudenberg, G., Pittman, M., Keough, K. C., Yue, F., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.07.479462 · Cited by 22 · see citing works
Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions
Dannemann, M., He, Z., Heide, C., Vernot, B., Sidow, L., Kanton, S., Weigert, A., Treutlein, B., Pääbo, S., Kelso, J. F., et al. (2020) · Stem Cell Reports · doi:10.1016/j.stemcr.2020.05.018 · Cited by 22 · see citing works
“15 j 214–225 j July 14, 2020 j a 2020 This is an open access article under the CC BY-NC-ND license (http://creativ morphology, blood coagulation, sleep patterns, and mood disorders (Dannemann and Kelso, 2017; Dannemann et al., 2016; Gunz et al., 2019; Khrameeva et al., 2014; Quach et al., 2016; Sams et al., 2016; Sank…”
BackgroundInfluentialSelf-citationTracing the Evolution of Human Immunity Through Ancient DNA
Patin, É., & Quintana‐Murci, L. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-082323-024638 · Cited by 20 · see citing works
“Furthermore, Neanderthal introgression appears to have played a role in shaping ultimate organismal phenotypes, as suggested by reported overlaps between Neanderthal variants and associations with certain autoimmune and inflammatory conditions (85, 115, 116).”
The MUC19 gene: An evolutionary history of recurrent introgression and natural selection
Villanea, F. A., Peede, D., Kaufman, E. J., Añorve-Garibay, V., Chevy, E. T., Villa-Islas, V., Witt, K. E., Zeloni, R., Marnetto, D., Moorjani, P., et al. (2025) · Science · doi:10.1126/science.adl0882 · Cited by 21 · see citing works
Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia
Deng, L., Pan, Y., Wang, Y., Chen, H., Yuan, K., Chen, S., Lu, D., Lü, Y., Mokhtar, S. S., Rahman, T. H. A., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab361 · Cited by 20 · see citing works
“Evidenced by the adaptive introgressed haplotypes in MTHFD1 and RAD18, we established the genetic contribution of Neanderthals to the skin pigmentation in TIA populations, which was not recognized before despite that such connection was only identified in the light-skinned modern Eurasians (Dannemann and Kelso 2017; R…”
BackgroundMoving beyond the adaptationist paradigm for human evolution, and why it matters
Schroeder, L., & Ackermann, R. (2022) · Journal of Human Evolution · doi:10.1016/j.jhevol.2022.103296 · Cited by 17 · see citing works
Archaic Introgression Shaped Human Circadian Traits
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
“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).”
BackgroundInfluentialA 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
“Two independent studies used eQTL mapping and allele-specific expression analysis, respectively, to show that a substantial number of Neanderthal introgressed haplotypes harbor regulatory variants in the human genome [23,24].”
BackgroundZMAT2 in Humans and Other Primates: A Highly Conserved and Understudied Gene
Baral, K., & Rotwein, P. S. (2020) · Evolutionary Bioinformatics · doi:10.1177/1176934320941500 · Cited by 14 · see citing works
Reticulate evolution underlies synergistic trait formation in human communities
Gontier, N., & Sukhoverkhov, A. V. (2022) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21962 · Cited by 13 · see citing works
Rewriting Human History and Empowering Indigenous Communities with Genome Editing Tools
Fox, K., Rallapalli, K. L., & Komor, A. C. (2020) · Genes · doi:10.3390/genes11010088 · Cited by 13 · see citing works
Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations
Yermakovich, D., André, M., Brucato, N., Kariwiga, J., Leavesley, M., Pankratov, V., Mondal, M., Ricaut, F.-X., & Dannemann, M. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2405889121 · Cited by 12 · see citing works
Self-citationSecondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks
Feng, X., Merilä, J., & Löytynoja, A. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae031 · Cited by 12 · see citing works
“On the other hand, introgression is more likely to induce regulatory changes in gene expression than radical alterations in protein-coding genes (Gittelman et al. 2016; Dannemann et al. 2017; Dannemann and Kelso 2017; McCoy et al. 2017; but see Petr et al. (2019) and Telis et al. (2020)).”
BackgroundYan, C.-C., 610065，中国, 四. 成., Zhang, X.-S., Zhou, L., Yang, Q. L., Zhou, M., Zhang, L.-W., Xing, J.-C., Yan, Z.-F., Price, M., et al. (2020) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2020.092 · Cited by 11 · see citing works
“The contribution of Neanderthals to phenotypic variation in modern humans.”
Long-range regulatory effects of Neandertal DNA in modern humans
Yermakovich, D., Pankratov, V., Võsa, U., Yunusbayev, B., Metspalu, A., Nelis, M., Milani, L. A., Mägi, R., Esko, T., & Dannemann, M. (2022) · Genetics · doi:10.1093/genetics/iyac188 · Cited by 11 · see citing works
“These observations might be helpful in the ongoing interpretation of both previous links between introgressed Neandertal DNA and behavioral phenotypes (Dannemann and Kelso, 2017; Simonti et al., 2016) and the extent of potential phenotypic differences between modern and archaic humans.”
BackgroundSelf-citationDiz, Á. P., & Skibinski, D. O. F. (2023) · Molecular Ecology · doi:10.1111/mec.17233 · Cited by 11 · see citing works
“For example, several percent of the genome of some modern humans derives through introgression from close relatives such as the Neanderthals and appears to have potential adaptive significance (Dannemann et al., 2017; Dannemann & Kelso, 2017).”
BackgroundNeanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneckPreprint
Rinker, D. C., Simonti, C., McArthur, E., Shaw, D. M., Hodges, E. C., & Capra, J. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/533257 · Cited by 11 · see citing works
Populations, Traits, and Their Spatial Structure in Humans
Sohail, M., Izarraras-Gomez, A., & Vecchyo, D. O. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab272 · Cited by 10 · see citing works
“Some of the introduced alleles from Neanderthals have been linked to particular phenotypes such as skin lesions, neurological disorders, and sleeping patterns (Simonti et al. 2016; Dannemann and Kelso 2017).”
BackgroundMethods for detecting introgressed archaic sequences
Sankararaman, S. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.026 · Cited by 10 · see citing works
Evolutionary genetics and acclimatization in nephrology
Adeyemo, A., Shriner, D., Bentley, A. R., Gbadegesin, R., & Rotimi, C. N. (2021) · Nature Reviews Nephrology · doi:10.1038/s41581-021-00483-7 · Cited by 10 · see citing works
Weasel, L. H. (2022) · The American Naturalist · doi:10.1086/720130 · Cited by 10 · see citing works
“…became a focus of introgression research, generating a proliferation of studies surrounding the purported selection of skin pigmentation alleles conferring lighter skin during the process of human evolution and Eurasian migrations (Gittelman et al. 2016; Dannemann and Kelso 2017; Deng and Xu 2018).”
BackgroundMedicine in the Light of Evolution
Dolgova, O., & Lao, Ó. (2018) · Genes · doi:10.3390/genes10010003 · Cited by 9 · see citing works
“Examples are skin pigmentation and hair color, height, sleeping patterns, mood, and smoking status in present-day Europeans [7] and hemoglobin concentration and response to hypoxia in Tibetans [8,9], associated with signatures of positive selection as evidence of their benefit for modern human survival in new territor…”
BackgroundGenetic legacy of ancient hunter-gatherer Jomon in Japanese populations
Yamamoto, K., Namba, S., Sonehara, K., Ken, S., Sakaue, S., Cooke, N. P., Higashiue, S., Kobayashi, S., Afuso, H., Matsuura, K., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54052-0 · Cited by 9 · see citing works
Variation in the repulsive guidance molecule family in human populations
Rotwein, P. S. (2019) · Physiological Reports · doi:10.14814/phy2.13959 · Cited by 7 · see citing works
Denisovan introgression has shaped the immune system of present-day PapuansPreprint
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F., Cox, M. P., & Romero, I. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.09.196444 · Cited by 8 · see citing works
Liang, S.-A., Ren, T., Zhang, J., He, J., Wang, X., Jiang, X., He, Y., McCoy, R. C., Fu, Q., Akey, J. M., et al. (2025) · Genome Biology · doi:10.1186/s13059-025-03502-z · Cited by 8 · see citing works
Ecological evaluation of the development of Neanderthal niche exploitation
Trájer, A. J. (2023) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2023.108127 · Cited by 7 · see citing works
Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men
Janivara, R., Hazra, U., Pfennig, A., Harlemon, M. S., Kim, M. S., Eaaswarkhanth, M., Chen, W. C., Ogunbiyi, A. O., Kachambwa, P., Petersen, L. N., et al. (2025) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2025.100428 · Cited by 7 · see citing works
“…previous studies have noted that Neanderthal introgression impacts genes that affect skin and hair morphology-related traits in European genomes, 29,65,66 none so far have tested for a direct association between in-trogressed alleles and MPB. Importantly, African genomes are largely free of…”
The Year In Genetic Anthropology: New Lands, New Technologies, New Questions
Gökçümen, Ö. (2018) · American Anthropologist · doi:10.1111/aman.13032 · Cited by 6 · see citing works
Campbell, M. C., Ashong, B., Teng, S., Harvey, J., & Cross, C. N. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1516-y · Cited by 7 · see citing works
David, J. R., Ferreira, E. A., Jabaud, L., Ogereau, D., Bastide, H., & Yassin, A. (2022) · Ecology and Evolution · doi:10.1002/ece3.8821 · Cited by 7 · see citing works
“…cases of cross-species adaptive introgression involve color variation, e.g., coat in wolves (Anderson et al. 2009), skin and hair colors in humans (Dannemann and Kelso 2017), wing patterns in mimetic butterflies (Edelman et al. 2019), winter-coats in hares (Giska et al. 2019), plumage in pigeons…”
BackgroundBrejcha, J., Kodejš, K., Benda, P., Jablonski, D., Holer, T., Chmelař, J., & Moravec, J. (2021) · Journal of Vertebrate Biology · doi:10.25225/jvb.21016 · Cited by 7 · see citing works
“The genetic toolkits responsible for the colour pattern of S. s. terrestris may be shared by genetic introgression from S. s. terrestris to Czech salamanders with the striped phenotype, which is a process known in other organisms (e.g. Zhang et al. 2016, Dannemann & Kelso 2017, Andrade et al. 2019).”
BackgroundQuaternary DNA: A Multidisciplinary Research Field
Parducci, L. (2019) · Quaternary · doi:10.3390/quat2040037 · Cited by 6 · see citing works
“Dannemann and Kelso combined modern data from living people by the UK Biobank with phenotypic and genomic data from Neanderthal individuals and showed that Neanderthal DNA in modern Europeans affects a large number of modern behavioral, metabolic, immune, and skin traits like skin tanning and burning, sleeping pattern…”
BackgroundDisentangling archaic introgression and genomic signatures of selection at human immunity genes
Urnikytė, A., Masiulyte, A., Pranckėnienė, L., & Kučinskas, V. (2023) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2023.105528 · Cited by 5 · see citing works
“Various genomic regions of adaptive introgression representing up to 64% of Neanderthal ancestry related to immunity, skin and hair pigmentation, and metabolism have been identified (Dannemann and Kelso, 2017; Sankararaman et al., 2014).”
A regulatory variant impacting TBX1 expression contributes to basicranial morphology in Homo sapiens
Funato, N., Heliövaara, A., & Boeckx, C. A. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.03.012 · Cited by 5 · see citing works
“67 To dissect ancestral alleles, the identification of the target genes of actual causal variants and their potential network is critical.”
Underrepresented Populations at the Archaic Introgression Frontier
Villanea, F. A., & Witt, K. E. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.821170 · Cited by 5 · see citing works
Wendt, F. R., Pathak, G. A., Overstreet, C. M., Tylee, D. S., Gelernter, J. E., Atkinson, E. G., & Polimanti, R. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.26.966531 · Cited by 5 · see citing works
Genetic-based signatures of the latitudinal differences in chronotype
Putilov, A. A., Dorokhov, V. B., Puchkova, A. N., Arsenyev, G. N., & Sveshnikov, D. S. (2019) · Biological Rhythm Research · doi:10.1080/09291016.2018.1465249 · Cited by 4 · see citing works
“These results on geographic variation in allele frequency of rs75804782 are complementary to the results previously reported in publication of Dannemann and Kelso (2017) who used frequencies of rs75804782 alleles provided by another data-set (the Simons Genome Diversity Panel).”
ResultArchaic adaptive introgression in modern human reproductive genes
Kendall, C., Nooranikhojasteh, A., Parra, E. J., Schillaci, M. A., & Viola, B. (2025) · Communications Biology · doi:10.1038/s42003-025-08682-9 · Cited by 6 · see citing works
“These segments represent 37.88 Mb (million base pairs/megabases) of sequence data with at least one archaic variant in each segment surpassing a frequency of 40% (Supplementary Data 1), which is 20 times higher than the typical introgressing archaic DNA in modern humans 23 .”
InfluentialUne anthropologie biologique de la disparition de l’homme de Néandertal : données récentes
Charlier, P., Coppens, Y., Héry-Arnaud, G., & Hassin, J. (2018) · médecine/sciences · doi:10.1051/medsci/20183408024 · Cited by 4 · see citing works
Putilov, A. A. (2021) · Neuroscience and Behavioral Physiology · doi:10.1007/s11055-021-01187-y · Cited by 5 · see citing works
“Interbreeding between the two subspecies of Homo sapiens produced introgression of part of the genome belonging to a former root inhabitant of Eurasia [Dannemann and Kelso, 2017].”
BackgroundVoinescu, C., Mozere, M., Genovese, G., Downie, M. L., Gupta, S., Gale, D. P., Böckenhauer, D., Kleta, R., Arcos‐Burgos, M., & Stanescu, H. C. (2024) · Kidney International · doi:10.1016/j.kint.2024.01.017 · Cited by 4 · see citing works
Gouy, A., & Excoffier, L. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/732958 · Cited by 4 · see citing works
A genetic variant protective against severe COVID-19 is inherited from NeandertalsPreprint
Zeberg, H., & Pääbo, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.05.327197 · Cited by 4 · see citing works
“They have a biological impact on human physiology today through genetic contributions to modern human populations that occurred during the last tens of thousands of years of their existence (e.g., Simonti et al. 2016, Dannemann and Kelso 2017).”
BackgroundKoller, D., Wendt, F., Pathak, G., Lillo, A. D., Angelis, F. D., Cabrera-Mendoza, B., Tucci, S., & Polimanti, R. (2021) · bioRxiv · doi:10.1101/2021.08.12.456138 · Cited by 4 · see citing works
Amos, W., & Elhaik, E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.31.630954 · Cited by 4 · see citing works
“…to high altitude living in Tibetans (e.g., Huerta-Sánchez et al. 2014); anthropometric traits such as lip thickness (Bonfante et al. 2021) and sitting height (Dannemann and Kelso 2017); and immune-related phenotypes such as genetic risk factors for severe COVID-19 (Zeberg and Pääbo 2020).”
Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania
Reilly, P. F., Rong, S., Tejada-Martínez, D., Miller, S. L., Tjahjadi, A., Liu, C., Akers, J. F., Pomer, A., Prentice, M. E., Merriwether, D. A., et al. (2026) · Science · doi:10.1126/science.adr6749 · Cited by 3 · see citing works
Recovering signatures of archaic hominin introgression using ancestral recombination graphs
Zhang, Y., Biddanda, A., Johnson, S., O’Dushlaine, C., & Moorjani, P. (2026) · Science · doi:10.1126/science.aef8874 · Cited by 5 · see citing works
Aneli, S., Berti, C. C., Gilea, A. I., Birolo, G., Mutti, G., Pavesi, A., Baruffini, E., Goffrini, P., & Capelli, C. (2024) · Human Molecular Genetics · doi:10.1093/hmg/ddae057 · Cited by 3 · see citing works
“The combination of these dynamics, operating also on the direct ancestors of H. sapiens in Africa, has resulted in a number of genetic variants being differentially fixed in AMHs and archaic humans [14, 15].”
La paléogénétique en tant qu’approche archéométrique au cours des 30 dernières années
Geigl, E.-M. (2018) · ArchéoSciences · doi:10.4000/archeosciences.5575 · Cited by 3 · see citing works
- 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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