PT - JOURNAL ARTICLE AU - William Barendse AU - Sean McWilliam AU - Rowan J. Bunch AU - Blair E. Harrison TI - Adaptive divergence in the bovine genome AID - 10.1101/022764 DP - 2015 Jan 01 TA - bioRxiv PG - 022764 4099 - http://biorxiv.org/content/early/2015/07/17/022764.short 4100 - http://biorxiv.org/content/early/2015/07/17/022764.full AB - Cattle diverged during the Pleistocene into two subspecies, one in temperate and one in tropical environments. Here we have used next generation sequencing of the indicine subspecies of cattle and compared it to the taurine subspecies. Although 23.8 million single nucleotide polymorphisms (SNP) were found, the number of fixed amino acid substitutions between the taurine and indicine subspecies was low and consistent with the Haldane predictions for adaptive selection rather than with Neutral Theory. We noted 33 regions of enhanced divergence of nonsynonymous SNP between the subspecies, which included an increased rate of deleterious variants. Signals of positive selection were found for genes associated with immunity, including the Bovine Major Histocompatibility Complex, which also showed an increased rate of deleterious amino acid variants. The genes important in sensing the environment, especially the olfactory system, showed a network wide signal of positive selection.