A high-coverage genome sequence from an archaic denisovan individual
Open accessAbstract
Ancient Genomics: The Denisovans were archaic humans closely related to Neandertals, whose populations overlapped with the ancestors of modern-day humans. Using a single-stranded library preparation method, Meyer et al. (p. 222 , published online 30 August) provide a detailed analysis of a high-quality Denisovan genome. The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size. The genome sequence also illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
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Some fossils can preserve relatively intact macromolecular organic material, as shown by recent discoveries in fossils and sub-fossils.
“However, recent discoveries of relatively intact macromolecular organic material in fossils and sub-fossils challenge this view.”
From Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities (2019) · cites this paper as Meyer et al., 2012
The Abstract reports a 30-fold-coverage genome reconstructed from DNA in a Denisovan bone, supporting the discovery of preserved organic material in a fossil. The “A single-stranded library preparation method” section describes that DNA as fragmented and chemically modified, so the paper does not establish that the macromolecules themselves were relatively intact. No page numbers are available in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe introgressing Neanderthals were probably from populations separated in time and space from the three high-coverage archaic individuals (DAV).
“Moreover, the introgressing Neanderthals were probably from populations that were separated both in time and space from the three archaic individuals who have so far been sequenced to high coverage-hereafter referred to as DAV (Denisovan, Altai Neanderthal and Vindija Neanderthal) 1,17,18 .”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [17]
The Abstract (page not provided) identifies this paper as reporting a high-coverage Denisovan genome, supporting its citation for the Denisovan member of DAV. It does not establish that the introgressing Neanderthals came from populations separated in time and space from all three named individuals. (LLM, conf=0.87)
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 [13]
The Abstract and “Denisovan and Neandertal gene flow” section report genetic contributions from both groups to present-day populations, with Denisovan ancestry concentrated in island Southeast Asia and Oceania. The paper does not establish that this introgression contributes to the phenotypic spectrum of modern humans; its discussion of phenotypes concerns other genomic differences and says their functional consequences are difficult to predict. No page numbers are available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredNeanderthal ancestry is relatively uniform among modern Eurasian populations but is approximately 8 to 24% higher in East Asia than in Europe.
“While NE ancestry is relatively uniform among modern Eurasian populations (1, 2), it is approximately 8 to 24% higher in East Asia than in Europe (5, 10, 12, 13).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [12]
In “Denisovan and Neandertal gene flow” (page not specified), the paper reports less Neandertal ancestry in Europe than in eastern Asia, supporting the direction of the comparison. It estimates that Europe’s proportion is 24% lower than eastern Asia’s (95% CI 12–36%); it does not give an 8–24% estimate for how much higher East Asia’s proportion is than Europe’s. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThis second range expansion is essential for explaining the pattern currently observed of lower Neanderthal ancestry in western Europe than in East Asia.
“This second range expansion is essential for explaining the pattern currently observed of lower NE ancestry in western Europe than in East Asia (5, 10, 12, 13).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [12]
The ‘Denisovan and Neandertal gene flow’ section estimates Neandertal ancestry in Europe to be 24% lower than in eastern Asia and South America. It offers later migration out of Africa as one possible explanation, alongside independent Neandertal gene-flow events; it does not say a second range expansion is essential. (LLM, conf=0.89)
Experimental — accuracy not yet measured
Non-African populations show 1% to 2% Neanderthal ancestry; Melanesians and East Asians display 3% and 0.2% Denisovan ancestry, respectively.
“In particular, non-African populations show 1% to 2% of Neanderthal ancestry in their genomes (Green et al. 2010; Prüfer et al. 2014) and Melanesians and East Asians display 3% and 0.2%, respectively, from Denisovans ancestry (Green et al. 2010; Meyer et al. 2012; Prüfer et al. 2014).”
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 Meyer et al. 2012
The “Denisovan and Neandertal gene flow” section supports Denisovan ancestry in Melanesians, but estimates 6.0% for present-day Papuans, not the cited 3%. It does not report 0.2% Denisovan ancestry in East Asians; for the Dai, it estimates less than 0.1%. The separate Neanderthal percentage is cited to other papers in the sentence. (LLM, conf=0.87)
Experimental — accuracy not yet measuredArchaic hominins diverged from AMHs around 700 ka.
“These archaic hominins diverged from AMHs around 700 ka (Meyer et al. 2012; Prüfer et al. 2014, 2017; Nielsen et al. 2017; Gómez-Robles 2019; Mafessoni et al. 2020)”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Meyer et al. 2012
In “Molecular estimates of divergence and fossil age” (page not supplied), Meyer et al. estimate the Denisovan–present-day human population divergence at 170,000–700,000 years. The claim treats 700 ka, the upper end of that range, as an approximate divergence date for archaic hominins generally; the paper does not establish that narrower date or broader scope. (LLM, conf=0.87)
Experimental — accuracy not yet measuredWest Eurasians harbour significantly less Neanderthal ancestry than East Asians.
“West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, which could be explained if West Eurasians (but not East Asians) have partial ancestry from a source diluting their Neanderthal inheritance22.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [20]
In “Denisovan and Neandertal gene flow,” the paper estimates 24% less Neandertal ancestry in Europe than in eastern Asia and South America (95% CI 12–36%), supporting a significant difference for the populations studied. Its European samples were French and Sardinian; it does not establish the claim for West Eurasians as a whole. (LLM, conf=0.83)
Experimental — accuracy not yet measuredThe mapping approaches employed in this study are consistent with those used in previous research.
“The mapping approaches employed in this study are consistent with those used in previous research [2, 6].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [6]
Denisovans (and presumably Neandertals) shared the fused HSA2 with modern humans.
“These findings corroborated the theory that the Denisovans (and presumably also the Neandertals) had shared the fused HSA2 with modern humans.”
From Revised time estimation of the ancestral human chromosome 2 fusion (2022) · cites this paper as [17]
After modern humans left Africa more than 60,000 years ago, multiple admixture events around 55,000 years ago occurred between modern humans and now extinct archaic humans including Neandertals and Denisovans.
“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 [13]
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 [52]
Neanderthals, Denisovans and modern humans share an identical FOXP2 protein.
“Perhaps surprisingly, Neanderthals, Denisovans and modern humans share an identical FOXP2 protein (Meyer et al., 2012; Noonan et al., 2006).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Meyer et al., 2012
For the Neanderthal sequence, all sites with genotype quality < 40 and mapping quality < 30 were removed.
“For the Neanderthal sequence, we removed all sites with genotype quality < 40, and mapping quality < 30, as done previously 67 .”
From A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years (2015) · cites this paper as [67]
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Human-specific gene <i>ARHGAP11B</i> promotes basal progenitor amplification and neocortex expansion
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Self-citationHuman-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis
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Self-citationGenomic evidence for the Pleistocene and recent population history of Native Americans
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Self-citationCortical Evolution: Judge the Brain by Its Cover
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Self-citationAncient DNA DamagePreprint
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Self-citationSouthern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
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The prehistoric peopling of Southeast Asia
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Self-citationAccurate sex identification of ancient human remains using DNA shotgun sequencing
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Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture
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The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes
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Self-citationEarly human dispersals within the Americas
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Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest
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Self-citationGenome-Wide Comparison of Medieval and Modern Mycobacterium leprae
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Replication landscape of the human genome
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Targeted capture in evolutionary and ecological genomics
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The genetic prehistory of southern Africa
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Self-citationMultiple Deeply Divergent Denisovan Ancestries in Papuans
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Self-citationAncient genomes show social and reproductive behavior of early Upper Paleolithic foragers
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- Authors
- Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., Sudmant, P. H., Alkan, C., Fu, Q., Do, R., Rohland, N., Tandon, A., Siebauer, M., Green, R. E., Bryc, K., Briggs, A. W., Stenzel, U., Dabney, J., Shendure, J., Kitzman, J., Hammer, M. F., Shunkov, M. V., Derevianko, A. P., Patterson, N., Andrés, A. M., Eichler, E. E., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- Max Planck Society (DE)
- Broad Institute (US)
- University of California, Berkeley (US)
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
- University of Washington (US)
- Bilkent University (TR)
- Chinese Academy of Sciences (CN)
- University of California, Santa Cruz (US)
- Harvard University (US)
- University of Arizona (US)
- Russian Academy of Sciences (RU)
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia.
- Howard Hughes Medical Institute (US)
- Corresponding author
- Meyer, Matthias
- Kircher, Martin
- Reich, David
- Pääbo, Svante
- ORCID
- Meyer, Matthias
- Kircher, Martin
- Gansauge, Marie-Theres
- Li, Heng
- Racimo, Fernando
- Mallick, Swapan
- Schraiber, Joshua G.
- Jay, Flora
- Prüfer, Kay
- Sudmant, Peter H.
- Alkan, Can
- Fu, Qiaomei
- Do, Ron
- Rohland, Nadin
- Green, Richard E.
- Bryc, Katarzyna
- Briggs, Adrian W.
- Dabney, Jesse
- Shendure, Jay
- Kitzman, Jacob
- Hammer, Michael F.
- Shunkov, Michael V.
- Patterson, Nick
- Andrés, Aida M.
- Eichler, Evan E.
- Slatkin, Montgomery
- Reich, David
- Kelso, Janet
- Pääbo, Svante
- Venue
- Science
- Published
- 2012-10-12
- Volume
- 338
- Issue
- 6104
- Pages
- 222-226
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3617501
- OpenAlex
- W2038686775
- Semantic Scholar
- 914243876fdc3842f1f9e33432ada3dcf130ad10
- Cited by
- 1,967
- References
- 200
- Citations by year
- 2026: 97 · 2025: 104 · 2024: 113 · 2023: 138 · 2022: 115 · 2021: 179 · 2020: 161 · 2019: 146 · 2018: 158 · 2017: 146 · 2016: 166 · 2015: 145 · 2014: 164 · 2013: 118 · 2012: 14
- FWCI
- 658.14
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (R01GM040282, 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 › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Denisovans, archaic humans, DNA library preparation, heterozygosity, genetic diversity, Denisovan admixture, modern human populations, positive selection, human evolution
- MeSH terms
- Alleles, Animals, Base Sequence, Fossils, Heterozygote, Humans, Molecular Sequence Data, Genetic Variation, Gene Library, Genome, Human, Sequence Analysis, DNA, Gene Flow, Neanderthals
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