Cattle are my favorite comparative model for Pleistocene human evolution, not because I think we necessarily share the same pattern of species and subspecies interactions, but because interbreeding and introgression are so evident among populations that are separated by strong local adaptations. Greg Cochran and I went into some detail about recent cattle phylogeny in our 2006 PaleoAnthropology paper. So I try to follow current research into cattle phylogeography, to see what other interesting things turn up.
The current Current Biology has a brief paper by Alessandro Achilli and colleagues, who sampled complete mtDNA genomes from recent European and Near Eastern cattle:
Archaeological and genetic evidence suggest that modern cattle might result from two domestication events of aurochs (Bos primigenius) in southwest Asia, which gave rise to taurine (Bos taurus) and zebuine (Bos indicus) cattle, respectively ,  and . However, independent domestication in Africa  and  and East Asia  has also been postulated and ancient DNA data raise the possibility of local introgression from wild aurochs ,  and . Here, we show by sequencing entire mitochondrial genomes from modern cattle that extinct wild aurochsen from Europe occasionally transmitted their mitochondrial DNA (mtDNA) to domesticated taurine breeds. However, the vast majority of mtDNAs belong either to haplogroup I (B. indicus) or T (B. taurus). The sequence divergence within haplogroup T is extremely low (eight-fold less than in the human mtDNA phylogeny ), indicating a narrow bottleneck in the recent evolutionary history of B. taurus. MtDNAs of haplotype T fall into subclades whose ages support a single Neolithic domestication event for B. taurus in the Near East, 9-11 thousand years ago (kya).
It is somewhat hard to believe that the mtDNA would be selectively neutral in newly-domesticated cattle, considering their growth and metabolic requirements had radically changed. So I would hold out the possibility that the strong standardization on a single T haplogroup in West Asian cattle may be a direct consequence rather than a side effect of domestication.
The current locations of the introgressive mtDNAs were interesting:
However, the tree also reveals exceptions that radiate much earlier than the T node. MtDNAs #98 and #99 harbour identical sequences (both from the Cabannina - an endangered breed from Liguria, northern Italy) belonging to a novel haplogroup (Q) whose ML time estimate from the QT node is 52.2±8.0 kya. Sequence #100 radiates even earlier from the PQT node (74.4±9.7 kya) and was detected in one animal from Korea, generically classified as 'beef cattle'. Strikingly, the control region of this mtDNA harbours the mutational motif of haplogroup P -- the marker of the extinct aurochs of Northern and Central Europe .
Those "introgressive" haplotypes really are not very divergent from the main mtDNA variation of B. taurus -- for instance, European aurochsen would appear to have been relatively genetically homogeneous compared to human mtDNA.
Hawks J, Cochran G. 2006. Dynamics of adaptive introgression from archaic to modern humans. PaleoAnthropology 2006:101-115. Open Access (PDF)
Achilli A and 21 others. 2008. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Curr Biol 18:R157-R158. doi:10.1016/j.cub.2008.01.019