This is actually a spin-off from the last post [see: Demic Diffusion" Dynastic models: R.I.P], where the issue of cattle domestication came up. Being that it appears to be a subject that deserves to be the center of attention in its own right, the following presents an opportunity to dig further into the matter; here Achilli et al.'s piece, as a recent publication (2008), will be dissected and compared against findings of other researchers, to examine if any lingering "concerns" about an independent cattle domestication cannot be "ironed out", so to speak.
The following study by Ascunce et al. 2007 for one seems to address issues raised in Achilli et al.'s 2008 publication [excerpt provided below], for Achilli et al. say:
The phylogeny (Figure 1 and Supplemental data) allows one also to evaluate the possibility that T1 and T4 were domesticated independently from aurochs populations living in Africa and East Asia, respectively  and . The ancestor of T1 differs by only one mutation (16113) from the ancestor of T1’2’3 and by only two mutations (16113 and 16255) from the ancestor of T3, therefore a domestication of T1 in Africa would require that the B. primigenius populations of North Africa had accumulated no sequence variation in their entire mtDNA (except the T1 marker 16113) relative to the Near Eastern stocks — an unlikely scenario. - Achilli et al. 2008, Mitochondrial genomes of extinct aurochs survive in domestic cattle
They admit the well known fact about lineage differentiations between African domesticates and the so-called Near Eastern bunch, as that begrudgingly tossed out [highlighted] word "except" underlies, and go onto speak of a so-called "unlikely scenario", but to the contrary, it is likely, for we are told here how so...
An unusual pattern of ancient mitochondrial DNA haplogroups in Northern African cattle. Zoological Studies 46(1): 123-125. In this note, we report on a newly acquired ancient DNA sequence of the mitochondrial control region for cattle (Bos taurus), as obtained from a 900-yr-old archaeological sample from Eritrea, Northeastern Africa. In combination with 4 other ancient DNA sequences from Mali, Northwestern Africa, we hypothesize that Northern African cattle were more polymorphic, ca. 900-2000 yr ago, because of the greater frequency of a mitochondrial DNA haplogroup (T/T3) that is presently rare in Africa but otherwise common throughout the greater Mediterranean region - Abstract ends
For the greater Mediterranean area, these analyses have shown that the mitochondrial control region haplotypes for modern cattle (i.e., Bos taurus) belong to one of 4 sequence clusters or haplogroups (Fig. 1). Most (94%) modern cattle populations from Northern Africa carry haplogroup T1, which is rarely found outside of Africa (6% in the Near East and absent elsewhere). In contrast, modern populations from mainland Europe carry 2 very similar haplogroups, T and T3 (94%), which decrease in the Middle East (65%-74%) and almost completely disappearing Africa (6%). Haplogroup T2 makes up the remainder of this mtDNA diversity and is present at 6% in Europe and 21%-27% in the Near East, but is absent from Africa. These haplogroup distributions have been interpreted as indicating a Near East origin for European B. taurus and the independent domestication of cattle in Africa (Bradley et al. 1996, Troy et al. 2001, Hanotte et al. 2002).
In this note, we report on the analysis of an ancient mtDNA (control region) sequence as obtained from a bovine skeletal sample from a nearly, first millennium, archaeological site near the community of Adi Nefas, Eritrea in Northeastern Africa (900 yr before the present; YBP; Schmidt and Curtis 2001) (Fig. 1). This newly acquired ancient DNA sequence is combined with data for the same mitochondrial control region as determined for 4 specimens from Mali, Northwestern Africa (ca. 900-2200 YBR; Edwards et al. 2004).In concert with the modern mtDNA data, these 5 ancient DNA sequences raise the possibility that the mtDNA gene pool for Northern African cattle was more diverse ca. 900-2000 yr ago...
In conclusion, our results raise the possibility that the mtDNA gene pool for Northern African cattle ca. 900-2000 yr ago was more polymorphic in terms of the frequencies of the T1 and T/T3 haplogroups that currently predominate in African and European populations, respectively. This older polymorphism in Northern African cattle may reflect a transition from an even more diverse ancestral gene pool (as characteristic of its Near East progenitor) and/or the later secondary introduction of T/T3 haplotypes into this region by the immigration of European cattle (Hanotte et al.2002, Bruford et al. 2003). Concomitantly, selective pressures from domestication and breeding efforts and/or genetic drift may have then led to the final homogenization of this older polymorphism into the current situation of essentially only the T1 haplogroup occurring in Northern Africa. These possibilities reemphasize the fact that both ancient and modern DNA data are of value in the ultimate resolution of the complex history of African cattle (Edwards et al. 2004). - Ascunce et al. 2007, An Unusual Pattern of Ancient Mitochondrial DNA Haplogroups in Northern African Cattle
While African specimens may have by default, been included in a pre-existing database used by Achilli et al., the African cattle gene pool doesn't appear to have been the primary center of investigation in their study, as opposed to being primarily geared towards those of European and Near Eastern specimens. Considerations for the African cattle gene seems to be a secondary one, to help explain the Near Eastern and European ones...
Fifty-six mitochondrial genomes from autochthonous taurine breeds across Southern Europe and the Near East were sequenced and compared with 50 sequences available in GenBank (Supplemental data). - Achilli et al. 2008, Mitochondrial genomes of extinct aurochs survive in domestic cattle
In contrast, Honotte et al. seems to have specifically made African cattle populations a primary centre of investigation...
Hanotte et al. used allele frequencies from 50 populations of modern cattle across the African continent to examine genetic variation. Their results reveal three ancient genetic signatures and each signature’s center of origin or region of entry. The native African taurine breed was independently domesticated in northeastern Africa, perhaps the eastern Sahara, and later migrated with pastoralist or crop-livestock farmers west and south. Asian zebu cattle were introduced along the east coast of Africa and in Madagascar and were most likely transported along a marine route from the Indian subcontinent. Finally, Near Eastern and European taurine cattle were primarily introduced along the shores of North Africa during the colonial period. These findings provide a genetic record of African cattle origins and migrations that have far-reaching implications for human migrations and the adaptive strategies used by African populations. They also require us to reexamine the models of domestication more broadly. - M. A. Kennedy
The observations above is not necessarily inconsistent with findings produced in the later aforementioned study of Ascunce et al. 2007.
In summation, Achilli et al. 2008 don't really break ground, in so far as what comes to mind upon having read their piece, in terms of what African, Near Eastern and European cattle domesticate lineage patterns implicate respectively, in consideration of DNA alone. Of course, linguistic reconstructions and archaeology are only reaffirmed by these DNA distribution patterns.
*May be subject to modification as updating takes place.