**1. Introduction**

For our domesticated animals, their domestication history has long preoccupied professionals. Substantially earlier evolution of domesticated species is also an area of research.

In the case of the horse, from the *Phenacodus* onwards, the last 60 million years have been exceptionally well known through a chain of transitional species, sometimes separations.

The phylogeny of family *Bovidae* (e.g., cattle, sheep, and goats) is less resolved. Here, the *Hypertragulidae* appeared as the first identifiable primitive ancestor around 50 million years ago (Mya) in Southeast Asia [1]. The complex, functional stomach developed about 40 million years ago. The molecular dating applied to cytochrome b gene, which is located in mitogenome showed that the separation of the sub-family *Caprinae* occurred 6.2 ± 0.4 million years ago, but there are proposed earlier radiation from about 14 Mya [2]. The *Myotragus*, which is basal to the *Ovis* clade within sub-family *Caprinea* stood out 5.35 million years ago.

In regard of evolutionary questions, besides nuclear microsatellites [3], SNPs [4], retrovirus integrations [5], and Y chromosomal mutations [6] mitochondrial DNA (mtDNA) represents a very informative genomic element. At the same time, this part of the hereditary material can also be efficiently used to better understand domestication. Nowadays, the study of mtDNA plays a role in the genetic

characterization and differentiation of our animal species living with us. Looking to the future, we can believe that this will be essential for the conservation of genetic resources and preservation of endangered autochthonous animal breeds all over the world.
