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/).

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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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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 or David Reich or 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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