World-wide Patterns of Divergence, Migration and Admixture in Domesticated Cattle

Using genotypes from 43,043 autosomal single nucleotide polymorphism markers, we evaluate the population structure of 134 domesticated bovid breeds.  Irrespective of the analytical method or sample subset, three major groups are consistently observed, namely indicine, Eurasian taurine, and African taurine.  Patterns of geographic dispersal resulting from co-migration with human and exportation are recognizable in phylograms and phylogenetic networks calculated from F_ST values.  Hybridization occurring after exportation is evident from principal component and admixture analyses.  Using 19 breeds we map the cline of indicine introgression into Africa.  We detect previously undescribed exportation patterns in Asia and identify a cline of taurine/indicine hybridization in Asia.  Our analyses highlight the strong influence of Shorthorn and piebald cattle during breed formation in Europe.  Iberian and Italian cattle are shown to have introgression from African taurine.  American Criollo cattle are shown to be of Iberian, and not African, decent.  Florida Crackers are a unique American Criollo breed possessing both substantial British and Continental European coancestry. Using genotypes from over 2 million SNP markers, we apply demographic models to infer divergence times between indicine, Eurasian taurine, and African taurine cattle clades.  We argue that exportation and admixture have been important forces in shaping bovine genomic variation.