Genome sequence of a 45,000-year-old modern human from western Siberia
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We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before-or simultaneously with-the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10(-9) to 0.6 × 10(-9) per site per year, a Y chromosomal mutation rate of 0.7 × 10(-9) to 0.9 × 10(-9) per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10(-8) to 3.2 × 10(-8) per site per year based on the age of the bone.
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Eurasians are estimated to trace around 2% of their genomes to introgression from archaic humans related to the Vindija Neanderthal.
“Eurasians are estimated to trace around 2% of their genomes to introgression from archaic humans 2 related to the Vindija Neanderthal 1 .”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [2]
The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans 50,000-60,000 years ago largely occurred after the splitting of the Basal Eurasians from other non-Africans.
“The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans 50,000-60,000 years ago11 largely occurred after the splitting of the Basal Eurasians from other non-Africans.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [11]
The dataset combines the newly reported ancient individuals with previously published ancient data to form a dataset of 281 ancient individuals.
“We combined our data with previously published ancient data7,8,9,10,8,10-15 to form a dataset of 281 ancient individuals.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [11]
The Ust'-Ishim genome shows genomic segments of Neanderthal ancestry that are ~1.8-4.2 times longer than those observed in present-day individuals.
“The genome sequence of a 45,000-year-old modern human male named Ust’-Ishim (after the region in Siberia where he was discovered), shows genomic segments of Neanderthal ancestry that are ~1.8–4.2 times longer than those observed in present-day individuals”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [17]
The Neanderthal gene flow occurred 232-430 generations before Ust'-Ishim lived, or approximately 50,000-60,000 ya.
“suggesting that the Neanderthal gene flow occurred 232–430 generations before Ust’-Ishim lived, or approximately 50,000–60,000 ya [17], narrowing the previous range.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [17]
The T maxD estimate for YRI compared to aEA was in good agreement with radiocarbon dating for this specimen.
“When YRI was compared to aEA, a similar decline of D aDNA,MHG was detected toward the more anciently dated signals, and T maxD was estimated to be 1,898 ga (47.5 kya, Chi-square test, P = 4.2 × 10 -5 , FDR permut = 0.02, Fig. 3c), which was in good agreement with the results of radiocarbon dating for this specimen 39 .”
From A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years (2015) · cites this paper as [39]
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Accurate detection of identity-by-descent segments in human ancient DNA
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Self-citationThe nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
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“99% of high-quality variants called de novo in Ust’Ishim chromosome 1 accessible regions are found in the 1000 Genomes Project variant set [36].”
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An evolutionary anthropological perspective on modern human origins.
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Detecting archaic introgression using an unadmixed outgroup
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Joint estimates of heterozygosity and runs of homozygosity for modern and ancient samples
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Human evolution: a tale from ancient genomes
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Testing for ancient selection using cross-population allele frequency differentiation
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Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia
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Detecting ancient positive selection in humans using extended lineage sorting
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Something old, something borrowed: admixture and adaptation in human evolution
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Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
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Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
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Evolution of language: Lessons from the genome
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ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
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Evolutionary and medical consequences of archaic introgression into modern human genomes
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A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years
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- Authors
- Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., Meyer, M., Zwyns, N., Salazar-García, D. C., Kuzmin, Y. V., Keates, S. G., Kosintsev, P. A., Razhev, D. I., Richards, M. P., Peristov, N. V., Lachmann, M., Douka, K., Higham, T. F. G., Slatkin, M., Hublin, J.-J., Reich, D., Kelso, J., Viola, T. B., & Pääbo, S.
- Affiliations
- Chinese Academy of Sciences (CN)
- Broad Institute (US)
- University of California, Berkeley (US)
- Siberian Branch of the Russian Academy of Sciences (RU)
- Ministry of Internal Affairs of the Russian Federation (RU)
- Emory University (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- V.S. Sobolev Institute of Geology and Mineralogy (RU)
- Institute of Plant and Animal Ecology (RU)
- University of British Columbia (CA)
- Santa Fe Institute (US)
- University of Oxford (GB)
- Corresponding author
- Fu, Qiaomei
- Reich, David
- Kelso, Janet
- ORCID
- Fu, Qiaomei
- Li, Heng
- Moorjani, Priya
- Jay, Flora
- Slepchenko, Sergey M.
- Prüfer, Kay
- Meyer, Matthias
- Zwyns, Nicolas
- Kuzmin, Yaroslav V.
- Kosintsev, Pavel A.
- Razhev, Dmitry I.
- Richards, Michael P.
- Lachmann, Michael
- Douka, Katerina
- Higham, Thomas F. G.
- Slatkin, Montgomery
- Hublin, Jean-Jacques
- Reich, David
- Kelso, Janet
- Pääbo, Svante
- Venue
- Nature
- Published
- 2014-10
- Volume
- 514
- Issue
- 7523
- Pages
- 445-449
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4753769
- OpenAlex
- W1975749505
- Cited by
- 1,023
- References
- 37
- Citations by year
- 2026: 46 · 2025: 97 · 2024: 63 · 2023: 68 · 2022: 67 · 2021: 93 · 2020: 82 · 2019: 84 · 2018: 116 · 2017: 113 · 2016: 109 · 2015: 80 · 2014: 5
- FWCI
- 490.62
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, cc-by-nc)
- Funders
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (R01GM040282, K99GM104158, GM100233, R01GM100233, R01‑GM40282, F32GM115006)
- 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
- Neanderthal ancestry, mutation rate estimation, mitochondrial mutation rate, Western Siberia, Denisovans
- MeSH terms
- Alleles, Animals, Chromosomes, Human, Pair 12, Diet, Fossils, Humans, Hybridization, Genetic, Male, Molecular Sequence Data, Phylogeny, Population Density, Population Dynamics, Siberia, Genome, Human, Sequence Analysis, DNA, Evolution, Molecular, Principal Component Analysis, Neanderthals, Mutation Rate
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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