Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans (original) (raw)

Accession codes

Accessions

Gene Expression Omnibus

Sequence Read Archive

Data deposits

Sequence data for MA-1 and AG-2, produced in this study, are available for download through NCBI SRA accession number SRP029640. Data from the Illumina genotyping analysis generated in this study are available through GEO Series accession number GSE50727; PLINK files can be accessed from http://www.ebc.ee/free_data. In addition, the above data and alignments for the published modern genomes, Denisova genome, Tianyuan individual and the two ancient genomes are available at http://www.cbs.dtu.dk/suppl/malta. Raw reads and alignments for the four modern genomes sequenced in this study are available for demographic research under data access agreement with E.W.

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Acknowledgements

We thank the Hermitage State Museum for providing access to the Mal’ta and Afontova Gora-2 human remains. We also thank the Danish National High-Throughput DNA Sequencing Centre and T. Reisberg for technical assistance. This work was supported by the Danish National Research Foundation and the Lundbeck Foundation (E.W. and M.R.) and the Arctic Social Sciences Program, National Science Foundation (grant PLR-1003725 to K.E.G.). R.V., M.M., M.K., E.M., K.T., S.Ro. and R.M. were supported by the European Regional Development Fund (European Union) through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu and Estonian Basic Research grant SF0270177As08. M.M. thanks the Estonian Science Foundation grant no. 8973 and Baltic-American Freedom Foundation Research Scholarship program and M.I.V. thanks the Government of Russian Federation grant no. 14.B25.31.0033 (to E. I. Rogaev). M.D. was supported by the US National Science Foundation (grant DBI-1103639). Computational analyses were carried out at the High Performance Computing Center, University of Tartu, and the Swedish National Infrastructure for Computing (SNIC-UPPMAX, project b2012063).

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Author notes

1. Maanasa Raghavan and Pontus Skoglund: These authors contributed equally to this work.

Authors and Affiliations

1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark ,
   Maanasa Raghavan, Thomas W. Stafford Jr, Ludovic Orlando, Paula F. Campos & Eske Willerslev
2. Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden,
   Pontus Skoglund & Mattias Jakobsson
3. Center for the Study of the First Americans, Texas A&M University, TAMU-4352, College Station, Texas 77845-4352, USA ,
   Kelly E. Graf
4. Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia ,
   Mait Metspalu, Monika Karmin, Kristiina Tambets, Siiri Rootsi, Sergey Litvinov, Toomas Kivisild & Richard Villems
5. Department of Integrative Biology, University of California, Berkeley, 94720, California, USA
   Mait Metspalu, Michael DeGiorgio & Rasmus Nielsen
6. Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia,
   Mait Metspalu, Ene Metspalu, Monika Karmin & Richard Villems
7. Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark,
   Anders Albrechtsen & Ida Moltke
8. Department of Human Genetics, The University of Chicago, Chicago, 60637, Illinois, USA
   Ida Moltke
9. Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark ,
   Simon Rasmussen, Thomas Sicheritz-Ponten & Søren Brunak
10. Department of Physics and Astronomy, AMS 14C Dating Centre, University of Aarhus, Ny Munkegade 120, Aarhus DK-8000, Denmark,
    Thomas W. Stafford Jr
11. Estonian Genome Center, University of Tartu, Tartu 51010, Estonia ,
    Reedik Mägi
12. Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia ,
    Elena Balanovska & Oleg Balanovsky
13. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, Moscow 119991, Russia ,
    Oleg Balanovsky
14. Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia ,
    Elza Khusnutdinova & Sergey Litvinov
15. Biology Department, Bashkir State University, Ufa, Bashkorostan 450074, Russia,
    Elza Khusnutdinova
16. The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia ,
    Ludmila P. Osipova & Mikhail I. Voevoda
17. Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Sakha (Yakutia) 677010, Russia,
    Sardana A. Fedorova
18. Institute of Internal Medicine, Siberian Branch of the Russian Academy of Medical Sciences, Borisa Bogatkova 175/1, Novosibirsk 630089, Russia ,
    Mikhail I. Voevoda
19. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark ,
    Thomas Sicheritz-Ponten & Søren Brunak
20. The State Hermitage Museum, 2, Dvortsovaya Ploshchad, St. Petersberg 190000, Russia ,
    Svetlana Demeshchenko
21. Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK,
    Toomas Kivisild
22. Estonian Academy of Sciences, Tallinn 10130, Estonia ,
    Richard Villems
23. Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden ,
    Mattias Jakobsson

Authors

1. Maanasa Raghavan
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2. Pontus Skoglund
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3. Kelly E. Graf
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4. Mait Metspalu
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5. Anders Albrechtsen
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6. Ida Moltke
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7. Simon Rasmussen
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8. Thomas W. Stafford Jr
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9. Ludovic Orlando
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10. Ene Metspalu
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11. Monika Karmin
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12. Kristiina Tambets
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13. Siiri Rootsi
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14. Reedik Mägi
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15. Paula F. Campos
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16. Elena Balanovska
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17. Oleg Balanovsky
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18. Elza Khusnutdinova
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19. Sergey Litvinov
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20. Ludmila P. Osipova
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21. Sardana A. Fedorova
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22. Mikhail I. Voevoda
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23. Michael DeGiorgio
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24. Thomas Sicheritz-Ponten
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25. Søren Brunak
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26. Svetlana Demeshchenko
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27. Toomas Kivisild
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28. Richard Villems
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29. Rasmus Nielsen
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30. Mattias Jakobsson
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31. Eske Willerslev
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Contributions

E.W. and K.E.G. conceived the project. E.W. headed the project. E.W. and M.R. designed the experimental research project setup. S.D. and K.E.G. provided access to the Mal’ta and Afontova Gora-2 samples, and K.E.G. provided archaeological context for the samples. T.W.S. Jr performed AMS dating. E.B. and O.B. (Tajik individual), E.K. and S.L. (Mari and Avar individuals) provided modern DNA extracts for complete genome sequencing. E.K. and S.L. (Kazakh, Kirghiz, Uzbek and Mari individuals), L.P.O. (Selkup individuals), S.A.F. (Even, Dolgan and Yakut individuals) and M.I.V. (Altai individuals) provided access to modern DNA extracts for genotyping. R.V. carried out Illumina chip analysis on modern samples. P.F.C. performed DNA extraction from the Indian individual. M.R. performed the ancient extractions and library constructions on the modern and ancient samples —the latter with input from L.O. M.R. coordinated the sequencing. M.R. and S.Ra. performed mapping of MA-1 and AG-2 data sets with input from L.O. S.Ra., T.S.-P. and S.B. provided super-computing resources, developed the next-generation sequencing pipeline and performed mapping and genotyping for all the modern genomes. M.R. performed DNA damage analysis with input from L.O. M.M. performed the admixture analysis. M.M., E.M., K.T. and R.V. performed the mtDNA analysis. M.M., M.K., S.Ro., T.K., R.V. and R.M. performed the Y-chromosome analysis. A.A. and I.M. performed the autosomal contamination estimates, error rate estimates, _D_-statistics tests based on sequence reads and ngsAdmix analyses. P.S. performed biological sexing, mtDNA contamination estimates, PCA, TreeMix, MixMapper, _D_-statistic tests based on allele frequencies, _f_3-statistics and phenotypic analyses, and analysis of AG-2 using nucleotide misincorporation patterns under the supervision of R.N. and M.J. M.R., P.S. and E.W. wrote the majority of the manuscript with critical input from R.N., M.J., M.M., K.E.G., A.A., I.M. and M.D. M.M., A.A. and I.M. contributed equally to this work.

Corresponding author

Correspondence toEske Willerslev.

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The authors declare no competing financial interests.

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Raghavan, M., Skoglund, P., Graf, K. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.Nature 505, 87–91 (2014). https://doi.org/10.1038/nature12736

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• Received: 14 July 2013
• Accepted: 04 October 2013
• Published: 20 November 2013
• Issue Date: 02 January 2014
• DOI: https://doi.org/10.1038/nature12736