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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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“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
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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“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]
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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“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]
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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“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]
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“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]
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“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 NPAS3 Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Meyer et al. 2012
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“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
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“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]
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“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]
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“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]
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“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]
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“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]
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“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
In the citing paper
“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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Metadata
- 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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