Archaeological evidence showed that two main colonization routes took place in Europe after the initial domestication events in the Fertile Crescent: the Mediterranean route and the Danubian route. Cañon et al. [18
], using microsatellites, report a decrease in genetic diversity as well as an increase in the level of differentiation at the breed level from south-east to north-west in European goat breeds, supporting the hypothesis of migration of domestic livestock from the Middle East towards western and northern Europe.
Our results indicate that a highly significant correlation between genetic and geographic distance exists. The presence of a geographic component in genetic diversity was already reported in breeds of Northern and Southern Italy in a previous study using SNPs [43
] and it is confirmed here in a larger area. Such a geographic component is generally not observed when using mitochondrial markers. As reported by Luikart et al. [11
] only 10% of the variance assessed by mtDNA is partitioned among continents. This could be due to the nature of the markers used for the analysis, as suggested by Naderi et al. [44
]. In fact, mtDNA informativeness is limited because it does not detect male-mediated gene flow and does not predict the nuclear genomic diversity [45
]. In the paper by Naderi et al. [44
] the breeds cannot be distinguished on the basis of mtDNA, even if authors report that more than 77% of the mtDNA variation is found within breeds, while there is a low regional differentiations of haplotypes. At a regional scale, the lack of geographic structure has been reported using mtDNA in different regions [16
] with the exception of one paper [24
From PCA analysis the breeds appear well differentiated with 52% of the variance explained by the first two principal components. There is also a good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances identified by the Mantel test. PCA indicates a westward route to southern Italy through Greece, that may suggest contacts between Albania and Italian peninsula and between Greece and Italian Islands (Sardinia and Sicily). In post-Neolithic times, some colonists may have improved local livestock as well as importing stock from overseas. The transport of animals made by sea has been already proposed for cattle [14
] and goats [15
]. The role of the Mediterranean Sea as a natural corridor connecting the Italian peninsula to the Near East, North Africa, and southern Europe is particularly plausible for small sized species, as sheep and goats species adaptable to various environments and easy to transport during human migration and commercial trade [4
The Greek Skopelos breed results the most distant one, reflecting the fact that it has been raised only in a island and on the mainland of Magnisia. The distance is not due to inbreeding as FIS
= 0.122, not the highest value in our breeds (max FIS
= 0.197 in Capore), but to the lack of admixture with other populations since long time and possibly a natural selection versus local environment. The Skopelos breed is largely differentiated from the other goat populations in Greece, both morphologically and in terms of performance. According to the inhabitants of the Skopelos island, the goat used to live in an uninhabited small island of Northern Sporades, and it was recently domesticated. The breed is also said to have some relationship with the wild goat of the Gioura island, originated from the homonymous island [46
]. Breeders, due to the favourable characteristics of the breed (high prolificacy and high milk production), established a breeders association and applied a genetic improvement programme since 1981. Also the Orobica is very far apart from the other breeds. Again the distance is not attributable to inbreeding (FIS
= 0.030), but to isolation of this breed in a very secluded valley of Italian Alps.
Among the Italian southern breeds, it is interesting that the lowest distance is seen between Argentata dell'Etna, from Sicily, and Sarda, original from Sardinia. The two islands, although quite far apart, were important trade posts of Phoenician, Punic and Roman traders.
The analysis carried so far excluded SNPs that were proven under selection [40
]. If we include these SNPs (CSN1S1_1, CSN1S1_2 and LIPE, [39
]) we find that the overall distance pattern remains unchanged but for two breeds of Northern Italy, Bionda and particularly Valdostana, that become closer to Orobica (Figure ). This is due to casein and LIPE allele frequency that are almost fixed in these breeds for the same allele, while the average allele frequency for the other breeds is 50% (Additional file 1
). Caseins have been the first genes to be associated to milk production, characteristics and curding properties [47
]. It is noteworthy that milk production and cheese making is a primary agricultural activity in North Italy since historical times as demonstrated by the high frequency of lactase persistence in humans [50
]. We hypothesize that converged selection for caseins and LIPE (an enzyme important for cheese making as well [51
]) occurred in Orobica, Valdostana and Bionda dell'Adamello breeds making them "similar" for what concerns their exploitation objectives.
Figure 2 Principal component analysis (PCA) of allele frequencies from twenty six SNP loci genotyped in the sixteen goat breeds. Projection on axis 1 and axis 2, which cumulatively explained 56.8% of the total inertia contained in the data set. Breeds acronyms (more ...)