Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity

Abstract

Background: From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species.

Methodology/principal findings: The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals.

Conclusions/significance: We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

Figure 1. Neighbor-joining trees of domestic goat based on 1540 mtDNA haplotypes (A) and on the 22 reference mtDNA haplotypes (B).

Distances were calculated using the Kimura 2-Parameter model with gamma correction (alpha = 0.28). On the (A) tree, the numbers on the branches represent bootstrap values out of 1000 replications, and the stars point out the position of reference individuals for each haplogroup used to construct the (B) tree (see Table 5).

Figure 2. Geographic distribution of domestic goat mtDNA haplogroups.

The size of each circle is proportional to the sample size and each specific haplotype is represented by a different colour.

Figure 3. Mismatch distributions for mtDNA haplogroups of domestic goats.

For the overall dataset, the distribution of pairwise differences were realized separately for comparisons between and within haplogroups.