TY - JOUR T1 - Adaptive divergence in the bovine genome JF - bioRxiv DO - 10.1101/022764 SP - 022764 AU - William Barendse AU - Sean McWilliam AU - Rowan J. Bunch AU - Blair E. Harrison Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/07/17/022764.abstract N2 - 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. ER -