Abstract
Here we illuminate the evolutionary trajectory of domesticated wheat through genomic analysis of 3,000-6,000-year-old grains excavated in the southern Levant. Our results identify these specimens as an early domesticated form closely related to wheat accessions from Ethiopia, the Arabian Peninsula and India. Genomic evidence supports a multi-stage domestication model centred on the non-shattering spike, requiring mutations in both TtBtr1-A and TtBtr1-B genes. These mutations probably arose independently in northern and southern wild populations, respectively. The foundational domestication event was hybridization of these populations, uniting the required mutations to create domesticated wheat. Remarkably, this hybridization occurred at least twice, producing distinct domesticated lineages. Following this, ancient grain lineages acquired advantageous traits through gene flow from local wild emmer populations. These findings redefine wheat domestication as a prolonged, dynamic and regionally interconnected process, characterized by repeated independent hybridization events that were later diversified through human-led dispersal and local adaptation.