On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

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 diferentiation.

Results: We collected 50 K single nucleotide polymorphism (SNP) profles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from south‑
west-Asian, Mediterranean, central-European and north-European sheep and from Asian and European moufons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-inform‑
ative supervised principal component analysis (PCA), breed-specifc admixture analysis, across-breed f4 profles 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 moufon did not infuence the dif‑ferentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from
Iran where the moufons 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 moufon, 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.