Abstract

Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago1,2. Here we present the genome of ‘Denisova 11’, a bone fragment from Denisova Cave (Russia)3 and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave4,5,6. The mother came from a population more closely related to Neanderthals who lived later in Europe2,7 than to an earlier Neanderthal found in Denisova Cave8, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal–Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.

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Acknowledgements

We thank B. Schellbach and A. Weihmann for DNA sequencing; G. Renaud and U. Stenzel for data processing; F. Brock for the computed tomography scans; R. Barr, P. Korlević and C. Zickert for graphics; and M. Slatkin and L. Vigilant for comments on the manuscript. This work was funded by the Max Planck Society; the Max Planck Foundation (grant 31-12LMP Pääbo to S.Pä.); the European Research Council (grant agreements 694707 to S.Pä., 324139 (PalaeoChron) to T.H. and 715069 (FINDER) to K.D.); and the Russian Science Foundation (project no. 14-50-00036 to M.B.K., M.V.S. and A.P.D.).

Reviewer information

Nature thanks D. Lambert, R. Nielsen and C. Stringer for their contribution to the peer review of this work.

Author information

Author notes

  1. These authors contributed equally: Viviane Slon, Fabrizio Mafessoni, Benjamin Vernot

Affiliations

  1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    • Viviane Slon
    • , Fabrizio Mafessoni
    • , Benjamin Vernot
    • , Cesare de Filippo
    • , Steffi Grote
    • , Mateja Hajdinjak
    • , Stéphane Peyrégne
    • , Sarah Nagel
    • , Janet Kelso
    • , Matthias Meyer
    • , Kay Prüfer
    •  & Svante Pääbo
  2. Department of Anthropology, University of Toronto, Toronto, Ontario, Canada

    • Bence Viola
  3. Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia

    • Bence Viola
    • , Maxim B. Kozlikin
    • , Michael V. Shunkov
    •  & Anatoly P. Derevianko
  4. Max Planck Institute for the Science of Human History, Jena, Germany

    • Samantha Brown
    •  & Katerina Douka
  5. Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK

    • Katerina Douka
    •  & Tom Higham
  6. Novosibirsk State University, Novosibirsk, Russia

    • Michael V. Shunkov

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Contributions

V.S. and S.N. performed the laboratory work; V.S., F.M., B.Ve., C.d.F., S.G., M.H., S.Pe., J.K., M.M., K.P. and S.Pä. analysed the genetic data; B.Vi. carried out the morphological analysis; S.B., K.D., T.H., M.B.K., M.V.S. and A.P.D. discovered Denisova 11 and provided archaeological data; V.S., K.P. and S.Pä. wrote the manuscript with input from all authors.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Viviane Slon or Svante Pääbo.

Extended data figures and tables

  1. Extended Data Fig. 1 Comparison between cortical thickness of long bones from modern humans, Neanderthals and Denisova 11.

    Maximum cortical thickness of femora, tibiae, humeri, radii and ulnae from humans from the Bronze Age and two Neanderthals compared to the minimum thickness of Denisova 11 (dashed line).

  2. Extended Data Fig. 2 Comparison of the genome of Denisova 11 and simulated genomes.

    Percentage of sites at which Denisova 11 and genomes simulated under the demographic model described in Supplementary Information 6 carry two Neanderthal alleles (NN, blue), two Denisovan alleles (DD, red) or one allele of each type (ND, purple). a, Percentages calculated for two random DNA fragments from Denisova 11 and from simulated F1, F2, Neanderthal (NF0) or Denisovan (DF0) genomes. b, Proportions of sites for the simulated genotypes, before sampling two fragments.

  3. Extended Data Fig. 3 Neanderthal and Denisovan allele proportions from Denisova 11 in 1-Mb windows.

    The y axis shows −log(P) of the deviation of Neanderthal and Denisovan allele counts from the genome-wide average (χ2 test of goodness-of-fit; see Supplementary Information 7). The colour shows the proportion of alleles matching the Neanderthal state (%N) within each 1-Mb window (100-kb steps, n = 26,414 windows).

  4. Extended Data Table 1 DNA extracts and DNA libraries prepared from the Denisova 11 specimen

Supplementary information

  1. Supplementary Information

    This file contains Supplementary Information sections 1-8, including Supplementary Text, Figures and Tables and Supplementary References. See contents page for details.

  2. Reporting Summary

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DOI

https://doi.org/10.1038/s41586-018-0455-x

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