Population structure and domestication history of the Javan banteng

The domestication of the banteng in Southeast Asia is one of the world's least known livestock domestications yet a vital component of the agricultural system in Indonesia and surrounding countries. Here, we generated the first reference genome of the banteng and used it to analyze a set of 78 resequenced wild and domesticated bantengs, including 19 newly generated whole-genome-sequenced samples, of which three are historical samples. We found low heterozygosity and significant differentiation, the latter primarily driven by recent genetic drift and inbreeding in two populations and clearly attributable to anthropogenically driven founder events or ex situ breeding. Population structure, when excluding these two populations, was limited, and we found that the evolutionary divergence between wild and domestic banteng was moderate (F_ST = 0.14), relatively young (10,356 years), and accompanied by post-divergence gene flow. We found only weak signals of a domestication bottleneck between ∼6,100 and 2,900 years ago, and genetic diversity was, on average, higher in domestic than in wild banteng. Despite the soft domestication history, we found 36 candidate genes potentially under selection during domestication, with the leptin receptor gene (LEPR) of particular interest due to the robust selection signal across methods and its known association with metabolism, obesity, and energy homeostasis. Finally, genetic load estimation revealed that Bali cattle in Australia have high realized load, whereas Bali cattle from Bali have high masked load. These findings provide the first genomic insights into an understudied bovine that is critically endangered in its wild form and agriculturally important in its domesticated form.