The complete genome sequence of a Neanderthal from the Altai Mountains (original) (raw)

Accession codes

Accessions

European Nucleotide Archive

Data deposits

All sequence data have been submitted to the European Nucleotide Archive (ENA) and are available under the following accessions: Altai Neanderthal: ERP002097, Mezmaiskaya Neanderthal: ERP002447. The data from the 25 present-day human genomes and 13 experimentally phased present-day genomes are available as a public dataset from http://aws.amazon.com/datasets/ and from http://cdna.eva.mpg.de/neandertal/altai/.

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Acknowledgements

We thank M. Hammer, C. Winkler and W. Klitz for sharing DNA samples; W. Huttner and his group, B. Peter, J. G. Schraiber and M. A. Yang for helpful discussions; and A. Lewis and R. Qiu for technical assistance. N.P. and D.R. are grateful for the chance to discuss these results with Peter Waddell who independently found evidence of a deeply diverged hominin admixing into the Denisova genome. D.R. and E.E.E. are Howard Hughes Medical Institute Investigators. D.R. and N.P. were supported by NSF grant number 1032255 and NIH grant GM100233; E.E.E. by NIH grant HG002385; J.S. by grant HG006283 from the National Genome Research Institute (NHGRI); S.S. by a post-doctoral fellowship from the Harvard University Science of the Human Past Program; F.J. and M.S. in part by a grant from the NIH (R01-GM40282); P.H.S. by an HHMI International Student Fellowship. We thank the team at the NIH Intramural Sequencing Center and Alice Young in particular, for generating some of the sequence reported here. This research was supported in part by the Paul G. Allen Family Foundation. Major funding support came from the Presidential Innovation Fund of the Max Planck Society.

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Author notes

1. Ines Hellmann
   Present address: Present address: Ludwig-Maximilians-Universität München, Martinsried, 82152 Munich, Germany.,

Authors and Affiliations

1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,
   Kay Prüfer, Susanna Sawyer, Anja Heinze, Gabriel Renaud, Cesare de Filippo, Michael Dannemann, Qiaomei Fu, Martin Kircher, Martin Kuhlwilm, Michael Lachmann, Matthias Meyer, Matthias Ongyerth, Michael Siebauer, Christoph Theunert, Janet Kelso & Svante Pääbo
2. Department of Integrative Biology, University of California, Berkeley, 94720-3140, California, USA
   Fernando Racimo, Flora Jay & Montgomery Slatkin
3. Broad Institute of MIT and Harvard, Cambridge, 02142, Massachusetts, USA
   Nick Patterson, Sriram Sankararaman, Heng Li, Swapan Mallick, Arti Tandon & David Reich
4. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA
   Sriram Sankararaman, Swapan Mallick, Arti Tandon, Priya Moorjani, Joseph Pickrell & David Reich
5. Department of Genome Sciences, University of Washington, Seattle, 98195, Washington, USA
   Peter H. Sudmant, Martin Kircher, Jacob O. Kitzman, Jay Shendure & Evan E. Eichler
6. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
   Qiaomei Fu
7. Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA
   James C. Mullikin
8. Department of Biomolecular Engineering, University of California, Santa Cruz, 95064, California, USA
   Samuel H. Vohr & Richard E. Green
9. Max F. Perutz Laboratories, Mathematics and Bioscience Group, Campus Vienna Biocenter 5, Vienna 1030, Austria ,
   Ines Hellmann
10. Department of Biology, Emory University, Atlanta, 30322, Georgia, USA
    Philip L. F. Johnson
11. Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France ,
    Hélène Blanche & Howard Cann
12. Howard Hughes Medical Institute, Seattle, 98195, Washington, USA
    Evan E. Eichler
13. Allen Institute for Brain Science, Seattle, 98103, Washington, USA
    Ed S. Lein & Trygve E. Bakken
14. ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg 1990 34, Russia ,
    Liubov V. Golovanova & Vladimir B. Doronichev
15. Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia,
    Michael V. Shunkov & Anatoli P. Derevianko
16. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,
    Bence Viola
17. Howard Hughes Medical Institute, Harvard Medical School, Boston, 02115, Massachusetts, USA
    David Reich

Authors

1. Kay Prüfer
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2. Fernando Racimo
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3. Nick Patterson
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4. Flora Jay
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5. Sriram Sankararaman
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6. Susanna Sawyer
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7. Anja Heinze
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8. Gabriel Renaud
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9. Peter H. Sudmant
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10. Cesare de Filippo
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11. Heng Li
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12. Swapan Mallick
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13. Michael Dannemann
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14. Qiaomei Fu
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15. Martin Kircher
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16. Martin Kuhlwilm
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17. Michael Lachmann
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18. Matthias Meyer
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19. Matthias Ongyerth
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20. Michael Siebauer
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21. Christoph Theunert
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22. Arti Tandon
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23. Priya Moorjani
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24. Joseph Pickrell
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25. James C. Mullikin
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26. Samuel H. Vohr
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27. Richard E. Green
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28. Ines Hellmann
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29. Philip L. F. Johnson
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30. Hélène Blanche
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31. Howard Cann
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32. Jacob O. Kitzman
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33. Jay Shendure
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34. Evan E. Eichler
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35. Ed S. Lein
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36. Trygve E. Bakken
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37. Liubov V. Golovanova
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38. Vladimir B. Doronichev
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39. Michael V. Shunkov
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40. Anatoli P. Derevianko
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41. Bence Viola
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42. Montgomery Slatkin
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43. David Reich
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44. Janet Kelso
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45. Svante Pääbo
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Contributions

S.Saw., A.H. and Q.F. performed the experiments; K.P., F.R., N.P., F.J., S.San., S.Saw., A.H., G.R., P.H.S., C.d.F., M.D., Q.F., M.Ki., M.Ku., M.L., M.M., M.O., M.Si., C.T., H.L., S.M., A.T., P.M., J.P., J.C.M., S.H.V., R.E.G., I.H., P.L.F.J., J.O.K., J.S., E.E.E., E.S.L., T.E.B., M.Sl., D.R., J.K., and S.P. analysed genetic data; L.V.G., V.B.D., M.V.S., A.P.D. and B.V. analysed archaeological and anthropological data; H.B. and H.C. provided samples and reagents; K.P., J.K. and S.P. wrote and edited the manuscript with input from all authors.

Corresponding authors

Correspondence toMontgomery Slatkin, David Reich or Svante Pääbo.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 2 Neanderthal-introgressed loci in Denisova.

Divergence of the Altai Neanderthal to the most closely related Denisovan haplotype in windows of at least 200 kb on chromosome 6. Divergence is given as percentage of human–chimpanzee divergence and bars represent ± 1 standard error.

Extended Data Table 1 Neanderthal ancestry estimate

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Extended Data Table 2 Selected _D_-statistics supporting inferences about gene flows

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Extended Data Table 3 Lineage-specific segmental duplications along each of the terminal branches and genes encompassed

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Supplementary information

Supplementary Information

This file contains Supplementary Text, Tables and Figures – see contents page for details. (PDF 16537 kb)

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Prüfer, K., Racimo, F., Patterson, N. et al. The complete genome sequence of a Neanderthal from the Altai Mountains.Nature 505, 43–49 (2014). https://doi.org/10.1038/nature12886

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• Received: 05 September 2013
• Accepted: 15 November 2013
• Published: 18 December 2013
• Issue Date: 02 January 2014
• DOI: https://doi.org/10.1038/nature12886