Genetic history of an archaic hominin group from Denisova Cave in Siberia
Open accessAbstract
Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans. Anatomically modern humans were in Africa from some point after 200,000 years ago and reached Eurasia rather later. Meanwhile, archaic hominins — including the Neanderthals — had been in Eurasia from at least 230,000 years ago and disappear from the fossil record only about 30,000 years ago. The genome of a female archaic hominin from Denisova Cave in southern Siberia has now been sequenced from DNA extracted from a finger bone. The group to which this 'Denisovan' individual belonged shares a common origin with Neanderthals and, although it was not involved in the putative gene flow from Neanderthals into Eurasians, it contributed 4–6% of the genomes of present-day Melanesians. In addition, the morphology of a tooth with a mitochondrial genome very similar to that of the finger bone suggests that these hominins are evolutionarily distinct from both Neanderthals and modern humans. Using DNA from a finger bone, the genome of an archaic hominin from southern Siberia has been sequenced to about 1.9-fold coverage. The group to which this individual belonged shares a common origin with Neanderthals, and although it was not involved in the putative gene flow from Neanderthals into Eurasians, it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. A tooth whose mitochondrial genome is very similar to that of the finger bone further suggests that these hominins are evolutionarily distinct from Neanderthals and modern humans.
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There is evidence for superarchaic gene flow into Denisovans, into Neanderthal-Denisovan ancestors, and into Africans.
“There is evidence for superarchaic gene flow into Denisovans 13,21,22 , into Neanderthal-Denisovan ancestors 27 , and into Africans 4 .”
From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [27]
Citation 13 is attached to the claim of superarchaic gene flow into Denisovans. The Discussion considers gene flow from a more diverged hominin as one possible explanation for Denisovan features, but explicitly says it could not be detected with the available DNA data. The paper therefore does not present evidence for that gene flow. (LLM, conf=0.88)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredEast Asian populations show evidence of introgression from Denisovans.
“EAS populations also show evidence of introgression from Denisovans [18, 19, 31].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [31]
The Discussion says Denisovan relatives contributed genes to present-day Melanesians but not to Han Chinese or Mongolians. The population-history model likewise places Denisovan admixture in the ancestors of Melanesians, not other non-African populations. These passages contradict the claim about East Asian populations. (LLM, conf=0.89)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredUnder model αβγδ, successive methodological improvements led to less and less plausible estimates of the separation time T XY between modern west Africans and Europeans.
“These results solve a puzzle: under model αβγδ 27 (Fig. 1), successive methodological improvements led to less and less plausible estimates of the separation time, T XY , between modern west Africans and Europeans.”
From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [27]
The ‘A model of population history’ section describes a parameterized model, which supports citing this paper for a population-history model. It does not report successive methodological improvements or a trend toward less plausible estimates of the separation time between west Africans and Europeans; that part of the attributed claim is unsupported by our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredMethods for quality control, calling ancestral alleles, and calibrating the molecular clock are as described by Rogers et al. 27.
“Methods for quality control, calling ancestral alleles, and calibrating the molecular clock are as described by Rogers et al. 27 .”
From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [27]
The DNA sequence determination section describes measures to reduce sequencing errors and mapping to an inferred ancestral genome; Ancestral features and duplications discusses identifying ancestral alleles. Relationship to Neanderthals and modern humans uses an assumed human–chimpanzee divergence time to date sequence divergence. These passages cover the three methodological topics, but the cited paper is by Reich et al., not Rogers et al., and our copy cannot establish that the citing authors used the same methods. (LLM, conf=0.78)
Experimental — accuracy not yet measuredNearly all Eurasians have ~2% Neanderthal ancestry resulting from interbreeding events that occurred shortly after their ancestors left Africa.
“nearly all Eurasians have ~2% Neanderthal ancestry resulting from interbreeding events that occurred shortly after their ancestors left Africa1,2.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [2]
The ‘Denisovan gene flow into the ancestors of Melanesians’ section (page not provided) estimates Neanderthal ancestry at 2.5 ± 0.6% in non-African populations. ‘A model of population history’ describes gene flow into the ancestors of all present-day non-Africans, but does not establish that it occurred shortly after they left Africa. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Past introgression events likely resulted in adaptive introgression, with selection favoring archaic variants to facilitate adaptation to novel environments in modern humans.
“In some cases, these past introgression events likely resulted in adaptive introgression (Bustamante and Henn 2010; Green et al. 2010; Reich et al. 2010)—selection favoring archaic variants to facilitate adaptation to novel environments in modern humans (Racimo et al. 2015).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Reich et al. 2010
The section “A model of population history” describes Neanderthal gene flow into ancestors of non-Africans and later Denisovan admixture with ancestors of Melanesians. It does not say that selection favored the introduced variants or that they helped modern humans adapt to new environments, so it supports the past-introgression premise but not the adaptive-introgression claim. (LLM, conf=0.86)
Experimental — accuracy not yet measuredArchaic and modern humans interbred, and numerous population replacement and admixture events occurred across Eurasia in the past, resulting in transmission of genes between previously geographically separated populations.
“For example, we now have evidence that archaic and modern humans interbred, and that numerous population replacement and admixture events occurred across Eurasia in the past, resulting in the transmission of genes between previously geographically separated populations (Bustamante and Henn 2010; Green et al. 2010; Reich et al. 2010).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Reich et al. 2010
In “A model of population history” (page not provided), the paper describes Neanderthal gene flow into ancestors of non-Africans and later Denisovan admixture with ancestors of Melanesians. This supports interbreeding and transmission of genes between populations, but the paper does not establish the claim of numerous population replacement events across Eurasia. (LLM, conf=0.85)
Experimental — accuracy not yet measuredPapuans and Indigenous Australians carry the largest amount of Denisovan introgression (~1% to 5%), followed by East and South Asians (~0.06% to 0.5%), and Indigenous Americans (~0.05% to 0.4%).
“It has been shown that Papuans and Indigenous Australians carry the largest amount of Denisovan introgression (∼1% to 5%), followed by East and South Asians (∼0.06% to 0.5%), and Indigenous Americans (∼0.05% to 0.4%) (Reich et al. 2010; Racimo et al. 2015; Mallick et al. 2016; Sankararaman et al. 2016; Browning et al. 2018).”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Reich et al. 2010
In “Denisovan gene flow into the ancestors of Melanesians” (page not available), the paper estimates that 4.8 ± 0.5% of Melanesian genomes derive from Denisovans and reports that Papuan and Bougainville populations stand out from other non-African populations. It does not provide the claimed estimates for Indigenous Australians, East and South Asians, or Indigenous Americans; its Discussion instead says Denisovan relatives do not seem to have contributed genes to present-day Han Chinese or Mongolians. (LLM, conf=0.91)
Experimental — accuracy not yet measuredApproximately 2% of the DNA of modern humans outside Africa is more similar to Neanderthal DNA than to DNA from sub-Saharan African populations.
“Sequencing of Neanderthal genomes has revealed that ~2% of the DNA of modern humans (MHs) outside of Africa is more similar to DNA from Neanderthals (NEs) than it is to DNA from sub-Saharan African populations (1, 2).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [2]
Model-averaged parameter estimates are in general agreement with previous work, with a few exceptions.
“Model-averaged parameter estimates (Fig. 4) are in general agreement with previous work 27 , but there are a few exceptions.”
From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [27]
Many modern humans show evidence of introgression from archaic humans like Neanderthals and Denisovans.
“Many modern humans also show evidence of introgression, or the incorporation of alleles from archaic humans like Neanderthals and Denisovans (Green et al. 2010; Reich et al. 2010).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Reich et al. 2010
Admixture with extinct hominins (Neanderthals and Denisovans) resulted in the introgression of archaic alleles into the human gene pool.
“Admixture with extinct hominins (Neanderthals and Denisovans) resulted in the introgression of archaic alleles into the human gene pool51–53.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [53]
Recent palaeo-genetic studies have hinted at a more explicit and active degree of social interaction between hominin species than was previously thought possible.
“Recent palaeo-genetic studies666768 have already hinted at a more explicit and active degree of social interaction between hominin species than was previously thought possible.”
From Assessing the calorific significance of episodes of human cannibalism in the Palaeolithic (2017) · cites this paper as [66]
The authors proposed that the second wave interbred with the Eurasian descendants of the first, during the δ episode of admixture.
“We proposed 27 that this second wave interbred with the Eurasian descendants of the first, during what we refer to as the δ episode of admixture.”
From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [27]
The “A model of population history” section describes Neanderthal gene flow into ancestors of present-day non-Africans, followed by Denisovan admixture with ancestors of Melanesians. It does not describe a second wave interbreeding with Eurasian descendants of a first wave or identify a δ episode (searched: “second wave,” “first wave,” and “δ episode”). Page numbers are unavailable in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredAnalyses of DNA from archaic humans showed strong evidence of a small amount of gene flow to modern humans, giving rise to a 'leaky replacement' model.
“Analyses of DNA from the archaic humans showed strong evidence of a small amount of gene flow to modern humans, giving rise to a ‘leaky replacement’ model.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [10]
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Orlando, L., Gilbert, M. T. P., & Willerslev, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3935 · Cited by 279 · see citing works
- Authors
- Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., Maricic, T., Good, J. M., Marques-Bonet, T., Alkan, C., Fu, Q., Mallick, S., Li, H., Meyer, M., Eichler, E. E., Stoneking, M., Richards, M., Talamo, S., Shunkov, M. V., Derevianko, A. P., Hublin, J.-J., Kelso, J., Slatkin, M., & Pääbo, S.
- Affiliations
- Harvard University (US)
- Max Planck Society (DE)
- Broad Institute (US)
- University of California, Berkeley (US)
- Emory University (US)
- Howard Hughes Medical Institute (US)
- University of British Columbia (CA)
- Russian Academy of Sciences (RU)
- Corresponding author
- Reich, David
- Viola, Bence
- Pääbo, Svante
- ORCID
- Reich, David
- Green, Richard E.
- Kircher, Martin
- Krause, Johannes
- Patterson, Nick
- Viola, Bence
- Briggs, Adrian W.
- Good, Jeffrey M.
- Alkan, Can
- Fu, Qiaomei
- Mallick, Swapan
- Li, Heng
- Meyer, Matthias
- Eichler, Evan E.
- Stoneking, Mark
- Richards, Michael
- Talamo, Sahra
- Shunkov, Michael V.
- Hublin, Jean-Jacques
- Kelso, Janet
- Slatkin, Montgomery
- Pääbo, Svante
- Venue
- Nature
- Published
- 2010-12
- Volume
- 468
- Issue
- 7327
- Pages
- 1053-1060
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4306417
- OpenAlex
- W1994263888
- Cited by
- 1,991
- References
- 37
- Citations by year
- 2026: 72 · 2025: 126 · 2024: 119 · 2023: 132 · 2022: 134 · 2021: 148 · 2020: 89 · 2019: 115 · 2018: 123 · 2017: 129 · 2016: 127 · 2015: 126 · 2014: 161 · 2013: 153 · 2012: 134
- FWCI
- 530.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by-nc-sa)
- Funders
- National Science Foundation (0754461, 1032255)
- Max-Planck-Gesellschaft
- Max-Planck-Institut für Evolutionäre Anthropologie
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM040282)
- Office of International Science and Engineering
- 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 › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Denisovans, Denisova Cave, archaic humans, Neanderthals, mitochondrial genome, human evolution, Neanderthal introgression, hominin phylogeny
- MeSH terms
- Animals, Asia, DNA, Mitochondrial, Europe, Fossils, Humans, Melanesia, Molecular Sequence Data, Phylogeny, Siberia, Tooth, Hominidae, Genome, Finger Phalanges, Gene Flow
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