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Genome sequence of a 45,000-year-old modern human from western Siberia

Nature volume 514, pages 445–449 (2014)Cite this article

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Abstract

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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Figure 1: Geographic location, morphology and dating.
Figure 2: Principal Components (PC) analysis exploring the relationship of Ust’-Ishim to present-day humans.
Figure 3: Statistics testing whether the Ust’-Ishim genome shares more derived alleles with one or the other of two modern human genomes (X, Y).
Figure 4: Inferred population size changes over time.
Figure 5: Regions of Neanderthal ancestry on chromosome 12 in the Ust’-Ishim individual and fifteen present-day non-Africans.
Figure 6: Dating the Neandertal admixture in Ust’-Ishim and present-day non-Africans.

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Primary accessions

European Nucleotide Archive

Data deposits

All sequence data have been submitted to the European Nucleotide Archive (ENA) and are available under the following Ust’-Ishim accession number: PRJEB6622. The data from the 25 present-day human genomes are available from (http://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project/) and from (http://cdna.eva.mpg.de/neandertal/altai/).

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Acknowledgements

We are grateful to P. Gunz, M. Kircher, A. I. Krivoshapkin, P. Nigst, M. Ongyerth, N. Patterson, G. Renaud, U. Stenzel, M. Stoneking and S. Talamo for valuable input, comments and help; T. Pfisterer and H. Temming for technical assistance. Q.F. is funded in part by the Chinese Academy of Sciences (XDA05130202) and the Ministry of Science and Technology of China (2007FY110200); P.A.K. by Urals Branch, Russian Academy of Sciences (12-C-4-1014) and Y.V.K. by the Russian Foundation for Basic Sciences (12-06-00045); F.J. and M.S. by the National Institutes of Health of the USA (R01-GM40282); P.J. by the NIH (K99-GM104158); and T.F.G.H. by ERC advanced grant 324139. D.R. is a Howard Hughes Medical Institute Investigator and supported by the National Science Foundation (1032255) and the NIH (GM100233). Major funding for this work was provided by the Presidential Innovation Fund of the Max Planck Society.

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Authors and Affiliations

  1. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China,

    Qiaomei Fu

  2. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany,

    Qiaomei Fu, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Michael Lachmann, Janet Kelso, T. Bence Viola & Svante Pääbo

  3. Broad Institute of MIT and Harvard, Cambridge, 02142, Massachusetts, USA

    Heng Li, Priya Moorjani & David Reich

  4. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Heng Li & David Reich

  5. Department of Biological Sciences, Columbia University, New York, 10027, New York, USA

    Priya Moorjani

  6. Department of Integrative Biology, University of California, Berkeley, 94720-3140, California, USA

    Flora Jay & Montgomery Slatkin

  7. Institute for Problems of the Development of the North, Siberian Branch of the Russian Academy of Sciences, Tyumen 625026, Russia,

    Sergey M. Slepchenko & Dmitry I. Razhev

  8. Omsk Division of the Ministry of Internal Affairs, Expert Criminalistics Center, Omsk 644007, Russia,

    Aleksei A. Bondarev

  9. Department of Biology, Emory University, Atlanta, 30322, Georgia, USA

    Philip L. F. Johnson

  10. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany,

    Nicolas Zwyns, Domingo C. Salazar-García, Michael P. Richards, Jean-Jacques Hublin & T. Bence Viola

  11. Department of Anthropology, University of California, Davis, 95616, California, USA

    Nicolas Zwyns

  12. Department of Archaeology, University of Cape Town, Cape Town 7701, South Africa,

    Domingo C. Salazar-García

  13. Departament de Prehistòria i Arqueologia, Universitat de València, Valencia 46010, Spain,

    Domingo C. Salazar-García

  14. Research Group on Plant Foods in Hominin Dietary Ecology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany,

    Domingo C. Salazar-García

  15. Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia,

    Yaroslav V. Kuzmin & Susan G. Keates

  16. Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg 620144, Russia,

    Pavel A. Kosintsev

  17. Department of Anthropology, Laboratory of Archaeology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada,

    Michael P. Richards

  18. Siberian Cultural Center, Omsk 644010, Russia,

    Nikolai V. Peristov

  19. Santa Fe Institute, Santa Fe, 87501, New Mexico, USA

    Michael Lachmann

  20. Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK,

    Katerina Douka & Thomas F. G. Higham

  21. Howard Hughes Medical Institute, Harvard Medical School, Boston, 02115, Massachusetts, USA

    David Reich

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Contributions

Q.F., S.M.S., A.A.B., Y.V.K., J.K., T.B.V. and S.P. designed the research. A.A.P. and Q.F. performed the experiments; Q.F., H.L., P.M., F.J., P.L.F.J., K.P., C.d.F., M.M., M.L., M.S., D.R., J.K. and S.P. analysed genetic data; K.D. and T.F.G.H. performed 14C dating; D.C.S.-G. and M.P.R. analysed stable isotope data; N.V.P., P.A.K. and D.I.R. contributed samples and data; S.M.S., A.A.B., N.Z., Y.V.K., S.G.K., J.-J.H. and T.B.V. analysed archaeological and anthropological data; Q.F., J.K., T.B.V. and S.P. wrote and edited the manuscript with input from all authors.

Corresponding authors

Correspondence to Qiaomei Fu, David Reich, Janet Kelso or T. Bence Viola.

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The authors declare no competing financial interests.

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Fu, Q., Li, H., Moorjani, P. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014). https://doi.org/10.1038/nature13810

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