The Five Goats of Eve: The Impact of Domestication on the Goat Mitogenome Variability

Domestic goat (Capra hircus) is among the most important and diffused livestock species, whose mitochondrial gene pool was dramatically shaped during the first phases of domestication. So far, the analysis of goat control region sequences identified 6 different haplogroups and highlighted a lower geographic structuring of diversity compared to other livestock species. Here, we present the first extensive survey of goat mitochondrial variability based on 84 complete mitogenomes of 79 C. hircus and 5 Capra aegagrus individuals. Phylogenetic analyses dated the most recent common ancestor to ~460 kya and revealed five distinctive domestic haplogroups (A, B1, C1a, D1 and G), clearly nested within wild goat branches. These five clades almost simultaneously diverged at the interface between the Epipaleolithic and early Neolithic periods and dramatically expanded ~12-10 ka ago. Thus, similarly to cattle and other livestock, it is conceivable that also in goat only few female founder lineages underwent domestication after surviving the last glacial maximum in the Near Eastern refugia. Zooarchaelogical and ancient DNA data indicate Southeastern Anatolia as the most likely center of this primary domestication and confirm that the C. hircus populations brought by the first Neolithic migration waves into the Mediterranean were already characterized by at least two ancestral A and C variants. Actually, the ancient phylogenetic separation of C branch (~130 ka ago) points to a genetically distinct population that could have been involved in a secondary domestication event in Western Iran where haplogroup C is still common among bezoars.