Abstract

The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture1. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.

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European Nucleotide Archive

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Acknowledgements

We gratefully acknowledge B. Schäfer for providing photographs of barley spikes and A. Fiebig for sequence data submission. This work was supported by a grant of the Israel Science Foundation (1179/13) to E.W., funding from the Endowed Chair in Molecular Genetics Applied to Crop Improvement at the University of Minnesota and the Triticeae Coordinated Agricultural Project, USDA-NIFA 2011-68002-30029 to G.J.M., and core funding of IPK Gatersleben to N.S. and M.M. R.W., J.R. and I.K.D. were supported by Research Programme funding from the Scottish government and the University of Dundee (R.W.). N.M. and U.D. acknowledge a grant from the Irene Levi Sela CARE Foundation.

Author information

Author notes

    • Martin Mascher
    • , Verena J Schuenemann
    •  & Benjamin Kilian

    Present address: Bayer CropScience, BCS Breeding and Trait Development, Zwijnaarde (Gent), Belgium.

Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.

    • Martin Mascher
    • , Axel Himmelbach
    • , Mona Schreiber
    • , Benjamin Kilian
    •  & Nils Stein
  2. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.

    • Martin Mascher
  3. Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.

    • Verena J Schuenemann
    • , Ella Reiter
    • , Simone Riehl
    •  & Johannes Krause
  4. Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany.

    • Verena J Schuenemann
    • , Simone Riehl
    •  & Johannes Krause
  5. Institute of Archaeology, Hebrew University, Jerusalem, Israel.

    • Uri Davidovich
  6. Laboratory of Archaeozoology, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel.

    • Nimrod Marom
  7. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.

    • Sariel Hübner
  8. Department of Biotechnology, Tel Hai College, Upper Galilee, Israel.

    • Sariel Hübner
  9. Institute of Evolution, University of Haifa, Haifa, Israel.

    • Abraham Korol
    •  & Tzion Fahima
  10. Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.

    • Abraham Korol
    •  & Tzion Fahima
  11. Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, Ramat-Gan, Israel.

    • Michal David
    •  & Ehud Weiss
  12. Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA.

    • Samuel H Vohr
    •  & Richard E Green
  13. Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK.

    • Ian K Dawson
    • , Joanne Russell
    •  & Robbie Waugh
  14. Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, USA.

    • Gary J Muehlbauer
  15. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA.

    • Gary J Muehlbauer
  16. Division of Plant Sciences, University of Dundee, Dundee, UK.

    • Robbie Waugh
  17. Max Planck Institute for the Science of Human History, Jena, Germany.

    • Johannes Krause

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Contributions

E.W., T.F., N.S. and J.K. conceived the study. E.W., T.F., N.S., J.K., V.J.S. and M.M. designed experiments. N.M., U.D., M.D., S.R. and E.W. performed excavations and archaeobotanical analyses. V.J.S., A.H. and E.R. performed the ancient DNA experiments. M.M., S.H., A.K., M.S., S.H.V. and R.E.G. analyzed data. J.R., M.M., I.K.D., B.K., G.J.M., N.S. and R.W. provided exome capture data. M.M., V.J.S., A.H., S.R., T.F., J.K., E.W. and N.S. wrote the manuscript with input from all co-authors. All authors read and approved the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Tzion Fahima or Johannes Krause or Ehud Weiss or Nils Stein.

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    Identity-by-state matrix.

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DOI

https://doi.org/10.1038/ng.3611

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