Ancient gene flow from early modern humans into Eastern Neanderthals

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It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

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Primary accessions

European Nucleotide Archive

Data deposits

Sequence data are available in the European Nucleotide Archive (ENA) under accession number PRJEB11828.


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Download references


We thank M. Slatkin, F. Racimo, J. Kelso, K. Prüfer, M. Stoneking and D. Reich for comments; the MPI-EVA sequencing group, B. Nickel and R. Schultz for technical support; A. Heinze, S. Sawyer and J. Dabney for sequencing library preparation; U. Stenzel and G. Renaud for help with sequence processing. M.J.H. was supported by the National Science Foundation Graduate Research Fellowship under grant DGE-1144153. Q.F. was funded in part by the Special Foundation of the President of the Chinese Academy of Sciences. T.M-B. was supported by ICREA, EMBO YIP 2013 and Fundació Barcelona Zoo. The Max Planck Society, the Krekeler Foundation, MINECO (grants BFU2014-55090-P FEDER, BFU2015-7116-ERC and BFU2015-6215-ERC to T.M-B. and BFU2012-34157 FEDER to C.L.-F.) and the US National Institutes of Health (grant GM102192 to A.S. and U01 MH106874 to T.M-B.) provided financial support.

Author information

Author notes

    • Martin Kuhlwilm
    •  & Ilan Gronau

    These authors contributed equally to this work.


  1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany

    • Martin Kuhlwilm
    • , Cesare de Filippo
    • , Martin Kircher
    • , Qiaomei Fu
    • , Hernán A. Burbano
    • , Aida M. Andrés
    • , Svante Pääbo
    • , Matthias Meyer
    •  & Sergi Castellano
  2. Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center (IDC), Herzliya 46150, Israel

    • Ilan Gronau
  3. Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA

    • Melissa J. Hubisz
    •  & Adam Siepel
  4. Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain

    • Javier Prado-Martinez
    • , Carles Lalueza-Fox
    •  & Tomas Marques-Bonet
  5. Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA

    • Martin Kircher
  6. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Qiaomei Fu
  7. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China

    • Qiaomei Fu
  8. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany

    • Hernán A. Burbano
  9. Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain

    • Marco de la Rasilla
  10. Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, 28006 Madrid, Spain

    • Antonio Rosas
  11. Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia

    • Pavao Rudan
    • , Željko Kucan
    •  & Ivan Gušic
  12. Croatian Academy of Sciences and Arts, Institute for Quaternary Paleontology and Geology, 10000 Zagreb, Croatia

    • Dejana Brajkovic
  13. Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain

    • Tomas Marques-Bonet
  14. Centro Nacional de Análisis Genómico (CRG-CNAG), 08028 Barcelona, Spain

    • Tomas Marques-Bonet
  15. Department of Anthropology, University of Toronto, Toronto, Ontario M5S 2S2, Canada

    • Bence Viola
  16. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany

    • Bence Viola
  17. Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA

    • Adam Siepel


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M.M. and Q.F. performed experiments; M.Ku., I.Gr., M.J.H., C.d.F., J.P.-M., M.Ki, Q.F., H.A.B., T.M.-B., A.M.A., S.P., M.M., A.S. and S.C. analysed genetic data; C.L.-F., M.d.l.R., A.R., P.R., D.B., Ž.,K., I.Gu. and B.V. analysed anthropological data; M.Ku., I.Gr., M.J.H., B.V., S.P., A.S. and S.C. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Adam Siepel or Sergi Castellano.

Extended data

Supplementary information

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  1. 1.

    Supplementary Information

    This file contains Supplementary Text 1-11, Supplementary Tables 1-19, Supplementary Figures 1-34 and additional references (see Contents).


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