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The genomic landscape of Neanderthal ancestry in present-day humans
Open accessAbstract
Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.
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“We found that East Asians have the greatest number of sites containing archaic alleles, followed by South Asians, while Europeans have the fewest (fig. 2A), as has been previously established (Sankararaman et al. 2014, 2016).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Sankararaman et al. 2014
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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“At the genomic level these introgressed archaic alleles are mostly observed outside protein-coding sequences, distributed over non-functional and regulatory regions [8, 9].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [8]
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
“Previous attempts to identify archaic fragments in contemporary humans have generally relied on existing archaic genomes [14][15][16] , which partially represent the haplotypic diversity of the archaic populations.”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · 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.
In the citing paper
“Humans in Central and East Asia are known to have elevated Neanderthal ancestry compared to other populations (22).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · 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.
In the citing paper
“This observation favors the hypothesis that the increased Neanderthal ancestry in these populations relative to others is due to weaker selection against alleles that may be mildly deleterious (32), made possible because of smaller historical population sizes in this part of Eurasia, rather than to additional admixture events (22).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [22]
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“First, previous studies of regions with Neanderthal ancestry found depletion for evidence of background selection and functional annotations, such as genes and gene regulatory elements active in specific tissues18,19,27,29.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [19]
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“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 [19]
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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 [17]
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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 [17]
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“These regions included previously recognized targets of adaptive introgression, such as SGCB and SPATA18 [13, 14, 17].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [13]
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“We began with a list of 95,462 SNPs that are likely to be Neanderthal-derived from Sankararaman et al., 2014.”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Sankararaman et al., 2014
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“beyond general agreement that introgressed archaic DNA has mainly been deleterious and actively removed from coding sequences and conserved non-coding elements [8, 12–14]”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [8]
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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 [17]
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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 [13]
The cited source says what the claim attributes to it.
In the citing paper
“On the other hand, many Neanderthal variants appear to have been deleterious in the modern human genetic background leading to a reduction in Neanderthal ancestry in conserved genomic regions (Sankararaman et al., 2014; Vernot and Akey, 2014; Harris and Nielsen, 2016; Juric et al., 2016; Petr et al., 2019).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Sankararaman et al., 2014
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In the citing paper
“First, Neanderthal ancestry is depleted in regions of the genome with strong background selection and evolutionary conservation18,19,27.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [19]
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In the citing paper
“archaic introgression tends to be rarer in gene-rich regions (15)”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [15]
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In the citing paper
“The X chromosome is particularly devoid of archaic introgression as previously reported 15 (Fig. 1d).”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [15]
The cited source says what the claim attributes to it.
In the citing paper
“We found that maps produced by SARGE are about as concordant with the published maps as the published maps are with each other (fig. S25).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [22]
The cited source says what the claim attributes to it.
In the citing paper
“Studies estimate that non-African populations have 1–4% Neanderthal admixture, with East Asian populations exhibiting more Neanderthal introgression than West Eurasian populations (Wall et al. 2013; Sankararaman et al. 2014), perhaps due to more archaic admixture events with ancestral East Asians, but other plausible scenarios have been proposed (Coll Macià et al. 2021; Witt et al. 2022).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Sankararaman et al. 2014
The cited source says what the claim attributes to it.
In the citing paper
“earlier studies found that on average, an EAS individual carries a higher percentage of Neanderthal genome DNA than a EUR individual (1.4% and 1.1%, respectively) [17].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [17]
The cited source says what the claim attributes to it.
In the citing paper
“However, most studies of archaic introgression have relied on the GRCh37 human reference genome [8, 10, 11, 13, 14, 20].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [13]
The cited source says what the claim attributes to it.
In the citing paper
“since prior work has shown that Neanderthal alleles tend to be distributed further away from regions of the genome under selective constraint (Sankararaman et al., 2014; Juric et al., 2016).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Sankararaman et al., 2014
The cited source says what the claim attributes to it.
In the citing paper
“This model does not exclude the possibility that differences in population sizes (15) or in generation time (53) between eastern and western Asia may also have played a role in shaping NE ancestry patterns, but a modeling study focusing on these aspects would be”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [15]
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In the citing paper
“Introgressed fragments of Neandertal DNA can be reliably identified in modern humans and are estimated to account for 1%–2% of the genomes of non-African individuals, such that collectively ~40% of the Neandertal genome is represented in people living today [17–19].”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [17]
The cited source says what the claim attributes to it.
In the citing paper
“After modern humans left Africa more than 60,000 years ago, genetic evidence suggests multiple admixture events ~55,000 years [9] between modern humans and now extinct archaic humans including Neandertals [10–12] and Denisovans [13, 14].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
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In the citing paper
“previous studies have pointed out that Neandertal DNA shows a lower prevalence in regions that are associated with higher functional capacity in the human genome [12, 34].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
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In the citing paper
“Some of the remaining Neandertal variants have reached high frequencies in some present-day populations, suggesting that they might have conferred advantages at some point since admixture [12, 18, 19].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
The cited source says what the claim attributes to it.
In the citing paper
“However, given that previous analyses have demonstrated that Neandertal DNA is showing signals of depletion around functional gene groups [12, 34], makes our current setup rather conservative as it shouldn’t result in an artificial enrichment result due to functional genome context.”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
The cited source says what the claim attributes to it.
In the citing paper
“Recent data indicated that genomic regions experiencing strong levels of background selection are depleted in Neanderthal ancestry54.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [54]
In the citing paper
“Other examples include Neanderthal alleles that are enriched in genes affecting keratin filaments, which make up most of the outer layer of human skin and produce hair, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African cold environments [42].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
In the citing paper
“On the other hand, archaic admixture appears to have also introduced a few beneficial alleles, such as EPAS1.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
In the citing paper
“Indeed, strong purifying selection appears to have acted on the genome of modern humans to purge harmful archaic alleles.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
In the citing paper
“For example, genes that are highly expressed in testes have reduced Neanderthal ancestry [42].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
In the citing paper
“Some archaic alleles have been shown to confer an adaptive advantage for modern humans”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
In the citing paper
“the depletion of archaic ancestry around functional elements in the genomes of present-day people reflects widespread purifying selection against archaic variants [5–7]”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
In the citing paper
“a number of instances of adaptive introgression have been described, generally affecting systems that influence immune and metabolic phenotypes [1, 5, 10, 22, 40, 41].”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
In the citing paper
“Recent studies have shown that Neandertal alleles are depleted in more constrained, functional regions of the genome and that, on average, selection has acted to remove introgressed Neandertal alleles from the modern human population [5, 7, 39].”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
In the citing paper
“This is particularly the case near protein coding genes, and is consistent with negative selection on Neandertal DNA in modern humans [5, 6, 7, 39].”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
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Metadata
- Authors
- Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D.
- Affiliations
- Broad Institute (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Corresponding author
- Sankararaman, Sriram
- Reich, David
- ORCID
- Venue
- Nature
- Published
- 2014-01-29
- Volume
- 507
- Issue
- 7492
- Pages
- 354-357
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4072735
- OpenAlex
- W2009494639
- Cited by
- 1,107
- References
- 41
- Citations by year
- 2026: 49 · 2025: 93 · 2024: 131 · 2023: 69 · 2022: 58 · 2021: 110 · 2020: 81 · 2019: 80 · 2018: 98 · 2017: 96 · 2016: 108 · 2015: 66 · 2014: 65
- FWCI
- 535.37
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (R01HG006399)
- National Institute of General Medical Sciences (GM100233, R01GM100233)
- 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 ancestry, Neanderthal admixture, keratin genes, disease risk alleles, X chromosome, testis-expressed genes, male fertility, human evolution, modern human genomes, Neanderthal introgression
- MeSH terms
- Alleles, Animals, Female, Haplotypes, Humans, Hybridization, Genetic, Infertility, Male, Keratins, Male, Organ Specificity, Phylogeny, Selection, Genetic, Testis, X Chromosome, Genome, Human, Genetic Predisposition to Disease, Genomics, Gene Flow, Neanderthals
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