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 [Formula: see text] 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. CONCLUSIONS: Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.

AgResearch Invermay Agricultural Centre Mosgiel New Zealand

Biotechical Faculty Podgorica Montenegro

College of Animal Science and Technology China Agricultural University Beijing China

Department of Animal Production Faculty of Agriculture and Environment Agricultural University ofTirana Tirana Albania

Department of Animal Science Biotechnical Faculty University of Ljubljana Ljubljana Slovenia

Department of Animal Science University of Zagreb Zagreb Croatia

Department of Genetics Physical Anthropology and Animal Physiology University of Basque Country Leioa Spain

Department of Reproduction and Biomedicine Faculty of Veterinary Medicine Ss Cyril and Methodius University Skopje North Macedonia

Dipartamento Bioscienze Biotecnologie Biofarmaceutica Universita degli Studi di Bari Aldo Moro Bari Italy

Dipartamento Scienze Agroalimentari Ambientali e Animali Universita Udine Udine Italy

Dipartimento di Scienze Animali della Nutrizione e degli Alimenti Universita Cattolica del S Cuore di Piacenza Piacenza Italy

Dipartimento Scienze Agrarie Alimentari e Forestali Universita Studi di Palermo Palermo Italy

Estonian University of Life Sciences Tartu Estonia

Faculty of Agriculture and Natural Resources Arak University Arak Iran

Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands

Institute of Animal Husbandry Belgrade Zemun Belgrade Serbia

Roslin Institute and Royal School of Veterinary Studies University of Edinburgh Midlothian Scotland UK

State Veterinary Institute Jihlava Jihlava Czech Republic

Université de Limoges INRAE Pereine EA7500 USC1061 Gamaa 87000 Limoges France

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