BackgroundFrom 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 FindingsThe 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/SignificanceWe 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.

For about 10 000 years, farmers have been managing cattle, sheep, and goats in a sustainable way, leading to animals that are well adapted to the local conditions. About 200 years ago, the situation started to change dramatically, with the rise of the concept of breed. All animals from the same breed began to be selected for the same phenotypic characteristics, and reproduction among breeds was seriously reduced. This corresponded to a strong fragmentation of the initial populations. A few decades ago, the selection pressures were increased again in order to further improve productivity, without enough emphasis on the preservation of the overall genetic diversity. The efficiency of modern selection methods successfully increased the production, but with a dramatic loss of genetic variability. Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50. With the development of these industrial breeds came economic pressure on farmers to abandon their traditional breeds, and many of these have recently become extinct as a result. This means that genetic resources in cattle, sheep, and goats are highly endangered, particularly in developed countries. It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources.

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.livestock origins ͉ Neolithic expansion ͉ phylogeography ͉ Middle East

The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species.

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Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.

Background: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA).

International audienceKnowledge about the phylogenetic history, genetic variation and ecological requirements of a species is important for its conservation and management. Unfortunately, for many species this information is lacking. Here we use multiple approaches (phylogenetics, population genetics and ecological modelling) to evaluate the evolutionary history and conservation status of Capra walie, an endangered flagship species of wild goat endemic to Ethiopia. The analysis of mitochondrial cytochrome b and Y-chromosome DNA sequences suggests that C. walie forms a monophyletic clade with Capra nubiana, but potentially has been isolated for up to 0.8 million years from this closely related species. Microsatellite DNA analyses show that C. walie has very low genetic variation (mean heterozygosity=0.35) compared with other endangered mammals. This reduced variation likely derives from a prolonged demographic decline and small effective population size. Ecological niche modelling using the bioclimatic features of habitats occupied by C. walie, suggests ecological differences between C. walie and C. nubiana, and identifies the areas most suitable for future reintroductions of C. walie. The genetic and bioclimatic data suggest that C. walie is distinct and requires immediate conservation actions including genetic monitoring and reintroductions to establish independent populations. This study illustrates how combining noninvasive sampling along with genetic and ecological (bioclimatic) approaches can help assess conservation status of poorly known species