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

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.

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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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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This file contains Supplementary Information Sections 1-18 – see Supplementary Contents for details (PDF 25041 kb)

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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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