The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

Abstract

The emergence of farming during the Neolithic transition, including the domestication of livestock, was a critical point in the evolution of human kind. The goat (Capra hircus) was one of the first domesticated ungulates. In this study, we compared the genetic diversity of domestic goats to that of the modern representatives of their wild ancestor, the bezoar, by analyzing 473 samples collected over the whole distribution range of the latter species. This partly confirms and significantly clarifies the goat domestication scenario already proposed by archaeological evidence. All of the mitochondrial DNA haplogroups found in current domestic goats have also been found in the bezoar. The geographic distribution of these haplogroups in the wild ancestor allowed the localization of the main domestication centers. We found no haplotype that could have been domesticated in the eastern half of the Iranian Plateau, nor further to the east. A signature of population expansion in bezoars of the C haplogroup suggests an early domestication center on the Central Iranian Plateau (Yazd and Kerman Provinces) and in the Southern Zagros (Fars Province), possibly corresponding to the management of wild flocks. However, the contribution of this center to the current domestic goat population is rather low (1.4%). We also found a second domestication center covering a large area in Eastern Anatolia, and possibly in Northern and Central Zagros. This last domestication center is the likely origin of almost all domestic goats today. This finding is consistent with archaeological data identifying Eastern Anatolia as an important domestication center.

Fig. 1.

Phylogenetic relationships of the 243 haplotypes from the 473 bezoars studied. This tree was obtained with the NJ method. To identify shared mtDNA haplogroups, 22 haplotypes chosen to represent the overall diversity of modern domestic goats (11) have also been included in the analysis (red). The scale represents the genetic distance. The different colors correspond to the haplotypes from the different mtDNA haplogroups found in domestic goat (A, green; B, dark blue; C, yellow; D, purple; F, light blue; G, orange). The other bezoar haplotypes are represented in white.

Fig. 2.

Phylogenetic tree (NJ) of the C haplogroup in both goats (red) and bezoar (yellow with black border from Eastern Turkey, yellow from other locations). The numbers represent the populations as in Fig. 3B and Table S1. The close relationships between bezoars from Eastern Turkey and goats suggest that the domestication of the C haplogroup occurred in this area.

Fig. 3.

Study area and geographic distribution of the mtDNA haplogroups in the bezoar. (A) Natural distribution of the bezoar according to Uerpmann (38). This distribution may not have changed since the beginning of goat management/domestication, and stops at the eastern limit of the map. The archaeological sites that give evidence of local pre-Neolithic goat domestication are represented in red. The sites that suggest either local goat domestication or early prepottery Neolithic transfer of domesticated goat are represented in orange. Finally, the sites that provide evidence of transfer of domestic goats out of the original geographic range of the bezoar before the middle of the 10th millennium cal. B.P. are represented in yellow (see Table S1). The northern Zagros comprises the Iranian Provinces of Azerbaijan Gharbi, Zanjan and Kurdistan; the Central Zagros comprises Kermanshah, Lorestan, Khuzestan, and Isfahan Provinces. The Southern Zagros mainly comprises the Fars Province. (B) Geographic distribution of the mtDNA haplogroups in the bezoar. The size of the circles is proportional to the number of individuals analyzed. The different bezoar haplogroups are color-coded as in Fig. 1. Different localities are identified by numbers, as in Table S1.

Fig. 4.

Comparison of the Bayesian skyline plots (15) for domestic goats from Iran and for three different categories of bezoars. The thick solid lines correspond to the median estimate of the effective population size (Ne) according to time. The blue lines show the 95% highest posterior densities limits. Ne is presented on a logarithmic scale. Time is plotted linearly, the scale corresponding to the number of mutations per nucleotide site. Both domestic goats from Iran and bezoars close-to-domestics of the C haplogroup show a strong population expansion, probably at the domestication time ≈10,000 years ago.