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Abstract

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14C years before present (bp) (13,000 to 12,600 calendar years bp)1,2. Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology3. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans2. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum4. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14C years bp (approximately 12,707–12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal’ta population5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.

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Accessions

GenBank/EMBL/DDBJ

Sequence Read Archive

Data deposits

Sequence data (fastq files) for Anzick-1 is available for download through NCBI SRA accession number SRX381032. Additionally, alignments and genotype calls are available for download at http://www.cbs.dtu.dk/suppl/clovis/. Raw reads (fastq files) and alignments (BAM files) for the two modern genomes sequenced in this study are available for demographic research under data access agreement with E.W. The Cervus elaphus sequences are available under GenBank accessions KF906070, KF906071 and KF906072.

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Acknowledgements

We thank the Danish National High-throughput DNA Sequencing Centre for help with sequencing, B. Henn and J. Kidd for assistance with Human Genome Diversity Project data, J. Keene for help with illustrations, M. Li, P. L. F. Johnson and M. Stoneking for help with the mtDNA analysis, L. A. Lahren for input to the site description and for establishing contact with the Native American groups, and J. E. Morrow, S. Fiedel and E. Lorenzen for comments on the manuscript. GeoGenetics were supported by the Lundbeck Foundation and the Danish National Research Foundation (DNRF94). M.D. was supported by the US National Science Foundation (grant DBI-1103639). A.-S.M. was supported by the Swiss National Science foundation. G.D.P. was supported by National Science Foundation (NSF) graduate research fellowship DGE-1147470. M.M., M.K., K.T. and L.S. were supported by the European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu, Estonian Basic Research (grant SF0270177As08) and Estonian Science Foundation (grant 8973). Computations in Uppsala were performed on resources provided by SNIC-UPPMAX (project b2012063) and in Tartu using the High Performance Computing Centre of the University of Tartu. A.E., V.M.W., M.C.L., F.B. and A.M. were supported by the Biotechnology and Biological Sciences Research Council (grant P25032 and BB/H005854/1). We thank the North Star Archaeological Research Program, Center for the Study of the First Americans, Texas A&M University, E. Hill, and Stafford Research, Inc. for funding some of the project.

Author information

Author notes

    • Morten Rasmussen
    •  & Sarah L. Anzick

    These authors contributed equally to this work.

    • Michael DeGiorgio
    •  & Ian Barnes

    Present addresses: Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK (I.B.); Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA (M.D.).

Affiliations

  1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark

    • Morten Rasmussen
    • , Thomas W. Stafford Jr
    • , Anna-Sapfo Malaspinas
    • , Morten E. Allentoft
    • , Thorfinn Sand Korneliussen
    • , Tracey L. Pierre
    • , Jesper Stenderup
    • , Ludovic Orlando
    •  & Eske Willerslev
  2. Anzick Family, 31 Old Clyde Park Road, Livingston, Montana 59047, USA

    • Sarah L. Anzick
  3. Center for the Study of the First Americans, Departments of Anthropology and Geography, Texas A&M University, 4352 TAMU, College Station, Texas 77843-4352, USA

    • Michael R. Waters
  4. Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden

    • Pontus Skoglund
    •  & Mattias Jakobsson
  5. Department of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, California 94720, USA

    • Michael DeGiorgio
    •  & Rasmus Nielsen
  6. AMS 14C Dating Centre, Department of Physics & Astronomy, University of Aarhus, Ny Munkegade 120, DK-8000 Aarhus C, Denmark

    • Thomas W. Stafford Jr
  7. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark

    • Simon Rasmussen
    • , Valborg Gudmundsdottir
    • , Rachita Yadav
    • , Søren Brunak
    • , Thomas Sicheritz-Ponten
    •  & Ramneek Gupta
  8. The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark

    • Ida Moltke
    •  & Anders Albrechtsen
  9. Department of Human Genetics, University of Chicago, 920 E. 58th Street, CLSC 4th floor, Chicago, Illinois 60637, USA

    • Ida Moltke
  10. Education Department, Montana State University, Box 5103, Bozeman, Montana 59717, USA

    • Shane M. Doyle
  11. Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, California 94305, USA

    • G. David Poznik
  12. Anthropology Department, PhD Program, University of Montana, 4100 Mullan Road, no. 217, Missoula, Montana 59808, USA

    • Samuel Stockton White V
  13. School of Biological Sciences, Washington State University, PO Box 644236, Eastlick Hall 395, Pullman, Washington 99164, USA

    • Omar E. Cornejo
  14. Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, Riia 23b, 51010 Tartu, Estonia

    • Kristiina Tambets
    • , Monika Karmin
    • , Lauri Saag
    •  & Mait Metspalu
  15. Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK

    • Anders Eriksson
    • , Vera M. Warmuth
    •  & Andrea Manica
  16. Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia

    • Anders Eriksson
  17. School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK

    • Peter D. Heintzman
    •  & Ian Barnes
  18. Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA

    • David J. Meltzer
  19. Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK

    • Vera M. Warmuth
    •  & Margarida C. Lopes
  20. Department of Anthropology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, 209F Davenport Hall, 607 Matthews Avenue, Urbana, Illinois 61801, USA

    • Ripan S. Malhi
  21. BioArCh, Departments of Biology, Archaeology and Chemistry, University of York, Wentworth Way, York YO10 5DD, UK

    • Matthew Collins
  22. MRC Centre for Outbreak, Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, Imperial College Faculty of Medicine, London W2 1PG, UK

    • Francois Balloux
  23. Department of Genetics, School of Medicine, Stanford University, Littlefield Center, Stanford, California 94305, USA

    • Carlos D. Bustamante
  24. Center for Evolutionary and Human Genomics, Stanford University, Littlefield Center, Stanford, California 94305, USA

    • Carlos D. Bustamante
  25. Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden

    • Mattias Jakobsson

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Contributions

E.W., S.L.A., M.R.W. and T.W.S. conceived the project. E.W. headed the project. E.W. and M.R. designed the research project setup. R.N. supervised the bioinformatical and population genetic analyses with input from M.J. S.M.D., R.S.M. and T.L.P. helped with ethics and contact to local communities. S.L.A. and M.R.W. provided access to the Anzick-1 sample and the archaeological context, with input from S.S.W. and D.J.M. T.W.S. performed AMS 14C dating, stable isotope analyses and provided geochemical and geoarchaeological assessments. S.L.A. and J.S. performed initial mtDNA screening experiments. Elk extracts were processed by P.D.H. and I.B. Ancient DNA extractions and library constructs for shotgun sequencing and preparation for sequencing was done by M.R. O.E.C. prepared the two modern genomes. M.R. and S.R. did initial bioinformatics and mapping of the ancient sample. Mapping of modern samples, and genotype calls was done by S.R., with input from T.S.K., A.E., V.M.W. and M.C.L. S.R., T.S.-P. and S.B. provided super computing resources. O.E.C. and S.R. did phasing and ancestry painting, with input from A.E., V.M.W. and M.C.L. M.E.A. and M.C. did half-life estimates, with input on geology from T.W.S. DNA damage patterns were done by M.R. and L.O. mtDNA consensus and damage estimate was done by A.-S.M. I.M. and A.A. performed the X-chromosome contamination estimates, error rate estimates and D-statistic analyses on genomic sequence data. G.D.P. conducted Y-chromosome analysis with input from C.D.B. M.M. did ADMIXTURE analysis. K.T., M.K. and M.M. did mtDNA characterization. P.S. did f3-statistics on SNP array data and tested Native American population models using D-statistics. M.D. performed TreeMix analysis and genome-wide f3-statistics. R.N. and M.D. developed and implemented the ancestry test. M.R., S.L.A., M.R.W., P.S., M.D., R.N. and E.W. wrote most of the manuscript with input from T.W.S., M.E.A., A.-S.M., S.R., I.M., A.A., G.D.P., K.T., M.M., R.G., V.G., R.Y., P.D.H., O.E.C., M.C., F.B., A.M., L.S. and the remaining authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Eske Willerslev.

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https://doi.org/10.1038/nature13025

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