Admixture and Selection after Initial Domestication of Cattle

Domestication is now appropriately viewed as a process and not an event. We used data from 134 breeds of cattle and the Illumina BovineSNP50 and BovineHD BeadChips to investigate the history of admixture and selection in cattle later in the process of domestication but prior to breed formation. From previous work, we hypothesized that the divergence of humpless African from Eurasian taurine cattle is due to admixture with the wild ancestor of cattle, the auroch, in Africa. We used weighted linkage disequilibrium decay curves as implemented in ALDER to further investigate this hypothesis. We also used the FLK statistic as implemented in hapFLK to investigate the history of selection. Using 780 samples from 11 breeds of indicine and taurine cattle, signatures of selection were found ubiquitously throughout the genome. For the loci with the most significant departures from drift, selection was inferred to occur on interior branches of the local phylogeny, suggesting that selection at these loci occurred prior to geographic isolation and breed formation. These loci are implicated in nervous system development, absorption and removal of bone mineral, feeding behavior, and coat color. These results clarify the processes that led to the diversity of modern cattle and the targets of selection prior to breed formation.