The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression

Data sets include a total of 233 new genomes, out of which 179 whole genomes are of Indonesian cattle breeds, including Aceh, Pesisir, Pasundan, Jabres, Madura and Sumba Ongole; 51 whole genomes are of Bali cattle from Bali, Kupang and the feral population in Australia; and three captive Javan bantengs from Texas, US. The study aim is to understand the population structure, genetic diversity, admixture, to investigate the detailed genomic landscape of ancestry in the admixed breeds, and ultimately to obtain an understanding of the origin and history of cross-breeding of Indonesian cattle. The study provide a detailed insight into a unique and globally important admixture system of cattle, and addresses fundamental questions regarding the evolutionary forces acting on introgressing genetic elements.