A haplotype-based evolutionary history of barley domestication
Barley is one of the oldest cultivated crops, with a complex evolutionary and domestication history<sup>1</sup>. Previous studies have rejected the idea of a single origin and instead support a model of mosaic genomic ancestry<sup>2,3</sup>. With increasingly comprehensive genome data, we now ask where the haplotypes - the building blocks of this mosaic - originate, and whether all domesticated barleys share the same wild progenitors or whether certain wild populations contribute more heavily to specific lineages. To address these questions, we apply a haplotype-based approach to investigate the genetic diversity and population structure of wild and domesticated barley. We analyse whole-genome sequences from 682 genebank accessions and 23 archaeological specimens, tracing the spatiotemporal origins of haplotypes and identifying wild contributors during domestication and later gene flow events. Ancient DNA supports our genome-wide findings from modern samples. Our results suggest that a founding domesticated population emerged in the Fertile Crescent during a prolonged period of pre-domestication cultivation. A key practical insight is that the high haplotype differentiation among barley populations - arising independently, or layered on top, of selection - poses challenges for mapping adaptive loci.
Authors
- Murukarthick Jayakodi (ORCID: https://orcid.org/0000-0003-2951-0541)
- Axel Himmelbach (ORCID: https://orcid.org/0000-0001-7338-0946)
- Michal David (ORCID: https://orcid.org/0000-0001-8622-0298)
- Erez Ben‐Yosef (ORCID: https://orcid.org/0000-0002-9483-3809)
- Martin Mascher (ORCID: https://orcid.org/0000-0001-6373-6013)
- Mordechai E. Kislev (ORCID: https://orcid.org/0009-0007-6237-3821)
- Ehud Weiss (ORCID: https://orcid.org/0000-0002-9730-4726)
- Verena J. Schuenemann
- Nils Stein (ORCID: https://orcid.org/0000-0003-3011-8731)
- Uri Davidovich (ORCID: https://orcid.org/0000-0001-5947-1534)
- Yu Guo (ORCID: https://orcid.org/0000-0002-5424-5797)
- Tzion Fahima (ORCID: https://orcid.org/0000-0001-5555-0040)
- Anat Hartmann-Shenkman
- Brian J. Steffenson (ORCID: https://orcid.org/0000-0001-7961-5363)
- Johannes Krause (ORCID: https://orcid.org/0000-0001-9144-3920)
- Ella Reiter (ORCID: https://orcid.org/0000-0001-7019-9383)
Institutions
- University of Minnesota (US)
- Bar-Ilan University (IL)
- Tel Aviv University (IL)
- University of Basel (CH)
- Hebrew University of Jerusalem (IL)
- University of Zurich (CH)
- German Centre for Integrative Biodiversity Research (DE)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE)
- Martin Luther University Halle-Wittenberg (DE)
- University of Tübingen (DE)
- University of Haifa (IL)
Publication Details
- Journal
- Nature
- Published
- 2025-09-24
- DOI
- https://doi.org/10.1038/s41586-025-09533-7
- Citations
- 8
- Primary Topic
- Wheat and Barley Genetics and Pathology
- Type
- article
- Field-Weighted Citation Impact
- 14.00