Ancient and modern genomes elucidate the origins, spread and management practices underlying donkey domestication.

Donkeys transformed human history as beasts of burden for long-distance movement, connecting societies, especially across semi-arid and upland environments. They are globally expanding and provide key support to low-to-middle income communities. Donkeys remain, however, largely understudied at the genomic level, due to their generally depreciated status. To elucidate their origins, spread, and historical management practices, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, including 15 wild equids. The strong phylogeographic structure among modern subpopulations suggests that donkeys were domesticated once in Africa ~5,000BCE, before rapidly spreading and differentiating into Europe and Asia ~2,500BCE. We also uncover back migration into modern Nubia and Maghreb, secondary contacts with Europe impacting western Africa, a previously unknown divergent lineage in the Levant and a Roman mule breeding center. Donkey management involved wilf introgression and inbreeding for mule production. Our work reveals dramatically different domestication histories in horses and donkeys.