Genome sequence of a 45,000-year-old modern human from western Siberia (original) (raw)

Accession codes

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/).

References

1. Trinkaus, E. & Ruff, C. B. Diaphyseal cross-sectional geometry of Near Eastern Middle Paleolithic humans: the femur. J. Archaeol. Sci. 26, 409–424 (1999)
   Article Google Scholar
2. Brock, F. et al. Reliability of nitrogen content (%N) and carbon:nitrogen atomic ratios (C:N) as indicators of collagen preservation suitable for radiocarbon dating. Radiocarbon 54, 879–886 (2012)
   Article CAS Google Scholar
3. Richards, M. P. & Trinkaus, E. Out of Africa: modern human origins special feature: isotopic evidence for the diets of European Neanderthals and early modern humans. Proc. Natl Acad. Sci. USA 106, 16034–16039 (2009)
   Article CAS ADS Google Scholar
4. Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012)
   Article CAS ADS Google Scholar
5. Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013)
   Article CAS Google Scholar
6. The Y Chromosome Consortium A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12, 339–348 (2002)
   Article Google Scholar
7. Shapiro, B. et al. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol. Biol. Evol. 28, 879–887 (2011)
   Article CAS Google Scholar
8. Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012)
   Article Google Scholar
9. Olalde, I. et al. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225–228 (2014)
   Article CAS ADS Google Scholar
10. Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014)
    Article ADS Google Scholar
11. Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014)
    Article CAS ADS Google Scholar
12. Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014)
    Article ADS Google Scholar
13. Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011)
    Article CAS Google Scholar
14. Scally, A. & Durbin, R. Revising the human mutation rate: implications for understanding human evolution. Nature Rev. Genet. 13, 745–753 (2012)
    Article CAS Google Scholar
15. Kong, A. et al. Rate of de novo mutations and the importance of father’s age to disease risk. Nature 488, 471–475 (2012)
    Article CAS ADS Google Scholar
16. Langergraber, K. E. et al. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc. Natl Acad. Sci. USA 109, 15716–15721 (2012)
    Article CAS ADS Google Scholar
17. Prüfer, K. et al. The bonobo genome compared with the chimpanzee and human genomes. Nature 486, 527–531 (2012)
    Article ADS Google Scholar
18. Xue, Y. et al. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr. Biol. 19, 1453–1457 (2009)
    Article CAS Google Scholar
19. Kuroki, Y. et al. Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nature Genet. 38, 158–167 (2006)
    Article CAS Google Scholar
20. Wang, J., Fan, H. C., Behr, B. & Quake, S. R. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150, 402–412 (2012)
    Article CAS Google Scholar
21. Sankararaman, S., Patterson, N., Li, H., Pääbo, S. & Reich, D. The date of interbreeding between Neandertals and modern humans. PLoS Genet. 8, e1002947 (2012)
    Article CAS Google Scholar
22. Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010)
    Article CAS ADS Google Scholar
23. Reich, D. et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 89, 516–528 (2011)
    Article CAS Google Scholar
24. Skoglund, P. & Jakobsson, M. Archaic human ancestry in East Asia. Proc. Natl Acad. Sci. USA 108, 18301–18306 (2011)
    Article CAS ADS Google Scholar
25. Fenner, J. N. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am. J. Phys. Anthropol. 128, 415–423 (2005)
    Article Google Scholar
26. McCown, T. D. & Keith, A. The Stone Age of Mount Carmel Vol. 2 (Clarendon, Oxford, 1939)
    Google Scholar
27. Vandermeersch, B. Les Hommes Fossiles de Qafzeh (Israel) 319 (Éditions du CNRS, 1981)
    Google Scholar
28. Rasmussen, M. et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98 (2011)
    Article CAS ADS Google Scholar
29. Hublin, J. J. The earliest modern human colonization of Europe. Proc. Natl Acad. Sci. USA 109, 13471–13472 (2012)
    Article CAS ADS Google Scholar
30. Müller, U. C. et al. The role of climate in the spread of modern humans into Europe. Quat. Sci. Rev. 30, 273–279 (2011)
    Article ADS Google Scholar
31. Goebel, T. A., Derevianko, A. P. & Petrin, V. T. Dating the Middle to Upper Paleolithic transition at Kara-Bom. Curr. Anthropol. 34, 452–458 (1993)
    Article Google Scholar
32. Kuhn, S. L. & Zwyns, N. Rethinking the initial Upper Paleolithic. Quat. Int. http://dx.doi.org/10.1016/j.quaint.2014.05.040 (2014)
33. Bronk Ramsey, C., Scott, M. & van der Plicht, H. Calibration for archaeological and environmental terrestrial samples in the time range 26–50 ka cal bp. Radiocarbon. 55, 2021–2027 (2013)
    Article Google Scholar
34. Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 Years cal bp. Radiocarbon 55, 1869–1887 (2009)
    Article Google Scholar
35. Kircher, M., Stenzel, U. & Kelso, J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol. 10, R83 (2009)
    Article Google Scholar
36. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)
    Article CAS Google Scholar

Download references

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

Authors

1. Qiaomei Fu
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2. Heng Li
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3. Priya Moorjani
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4. Flora Jay
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5. Sergey M. Slepchenko
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6. Aleksei A. Bondarev
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7. Philip L. F. Johnson
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8. Ayinuer Aximu-Petri
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9. Kay Prüfer
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10. Cesare de Filippo
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11. Matthias Meyer
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12. Nicolas Zwyns
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13. Domingo C. Salazar-García
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14. Yaroslav V. Kuzmin
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15. Susan G. Keates
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16. Pavel A. Kosintsev
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17. Dmitry I. Razhev
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18. Michael P. Richards
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19. Nikolai V. Peristov
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20. Michael Lachmann
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21. Katerina Douka
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22. Thomas F. G. Higham
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23. Montgomery Slatkin
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24. Jean-Jacques Hublin
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25. David Reich
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26. Janet Kelso
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27. T. Bence Viola
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28. Svante Pääbo
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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 toQiaomei 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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• Received: 15 May 2014
• Accepted: 29 August 2014
• Published: 22 October 2014
• Issue Date: 23 October 2014
• DOI: https://doi.org/10.1038/nature13810