Background: In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results: We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed f 4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.

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Several different phenotypes of the native Pramenka sheep have been developed in the Balkan region for different environmental and socio-cultural conditions. Animals from seven West Balkan Pramenka sheep types were analysed for 15 microsatellite markers and for mitochondrial DNA (mtDNA) and the results were used to assess genetic variation within and among the types and to infer the genetic population structure of the Pramenka sheep. Mean expected heterozygosity and allelic richness over the microsatellite loci and sheep types were 0.78 and 7.9, respectively. A Bayesian statistical method for estimating hidden genetic structure suggested that a core of the largest panmictic population was formed by Serbian, Kosovan, Bosnian, Montenegrin and Albanian types, while Croatian and Macedonian types comprised two other main populations, respectively. Mitochondrial DNA analysis revealed two mtDNA haplogroups in the Pramenka sheep, B and A, with a frequency of 93.7% and 6.3%, respectively. A total of 60 mtDNA haplotypes were found in 64 animals sequenced, and the mean nucleotide and haplotypic diversities over the types were 0.013 and 0.945, respectively. Molecular analysis suggests that the West Balkan Pramenka sheep types have their origins in two distinct maternal lineages of domestic sheep and different Pramenka phenotypes tend to form few panmictic populations. The Pramenka sheep represents a valuable resource of genetic diversity in sheep.

We estimated neutral diversity of 21 European cattle breeds with 105 microsatellites. Nine of them resembled unselected Balkan Buša strains with diffuse breeding barriers and the 12 others were strongly differentiated, isolated breeds. Because of the impact of neutral genetic diversity on long-term population adaptive capacity, we discuss the long-term outcome of different conservation priorities in a subdivided metapopulation of the investigated cattle breeds. The optimal contribution to a pool of total genetic diversity allocated more than 95% of long-term relevant neutral diversity to virtually unselected strains of the Balkan Buša, while the maximization of total variance preferred inbred breeds. Current artificial selection methods, such as genomic selection sped up and a recovery of underestimated traits becomes quickly impossible. We emphasize that currently neutral and even deleterious alleles might be required for future genotypes in sustainable and efficient livestock breeding and production systems of a 21st century. We provide cumulative evidences that long-term survival relies on genetic complexity and complexity relies on allelic diversity. Our results suggest that virtually unselected, nonuniform strains harbor a crucial proportion of neutral diversity and should be conserved with high global priority. As one example, we suggest a cooperative maintenance of the nondifferentiated, highly fragmented, and fast vanishing metapopulation of Balkan Buša.

For the purpose of the morphometric characterization and differentiation of local sheep breeds that belong to the group of breeds called Pramenka or Zackel, two Slovenian (Bela Krajina and Istrian Pramenka) and four Montenegrin sheep breeds (Bardoka, Sjenička, Pivska Pramenka, and Zeta Žuja) were studied. The variation of morphometric measures and nine morphometric indices were analysed. Principal component analysis (PCA) was applied in order to provide an easier description of body size and shape. Regarding body size, the Sjenička breed was one of the largest breeds (body weight 76.4 kg, wither height 72.7 cm, chest circumference 100.3 cm), while Zeta Žuja had the smallest body size (37.1 kg, 64.8, and 81.9 cm). On the other hand, Slovenian Istrian Pramenka had the largest body length, chest depth, chest width, and rump width among all included breeds (79.4, 33.6, 22.7, and 21.2 cm). Bela Krajina, Istrian Pramenka, and the Sjenička breed, according to the index of body frame (IBF) value (107–114), have a rectangular body frame, Bardoka and Pivska Pramenka have a square body frame (99.3–100), and Zeta Žuja has a short body frame (91.8). The PCA of all morphometric parameters extracted three components accounting for 96.6 % of the cumulative variance. An unweighted pair–group method with arithmetic mean (UPGMA) cluster analysis by Euclidian distance shows diversity among the studied breeds, through it grouped Pivska Pramenka with Sjenička and Istrian with Bela Krajina Pramenka in two clusters, while Bardoka and Zeta Žuja were clustered separately.