Complete mitochondrial genomes of <i>Bos taurus</i> and <i>Bos indicus</i> provide new insights into intra-species variation, taxonomy and domestication

Abstract

The taurine and zebuine cattle breeds comprise the majority of the world cattle population but their taxonomic status is still controversial. The two forms of cattle are currently classified as <i>Bos taurus </i>and <i>Bos indicus </i>species and are differentiated primarily by the presence or absence of a hump. However, these two species hybridize readily, producing fully fertile offspring. We have determined and analyzed complete <i>B. taurus </i>and <i>B. indicus </i>mitochondrial genome sequences to investigate the extent of sequence divergences and to study their taxonomic status by molecular dating. The sequences encompassed 16,338 and 16,339 nucleotides, respectively, and differed at 237 positions. Estimated divergence times indicated that the two cattle lineages separated 1.7–2.0 million years ago. Combined phylogenetic analyses of 18 new and 130 previously reported extant <i>B. taurus </i>and <i>B. indicus </i>control region sequences with data from 32 archaeological specimens of the extinct wild aurochs (<i>Bos primigenius</i>) identified four major maternal lineages. <i>B. primigenius </i>haplotypes were present in all but the <i>B. indicus </i>lineage, and one <i>B. taurus </i>sequence clustered with <i>B. primigenius </i>P haplotypes that were not previously linked with domestic cattle. The <i>B. indicus </i>cluster and a recently reported new <i>B. primigenius </i>haplotype that represents a new lineage were approximately equidistant from the <i>B. taurus </i>cluster. These data suggest domestications from several differentiated populations of <i>B. primigenius </i>and a subspecies status for taurine (<i>B. primigenius taurus</i>) and zebuine (<i>B. primigenius indicus</i>) cattle.