To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia.

A N Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia

Bureau of Wildlife Biology Bavaria Rottach Egern Germany

Centre for Agricultural Genomics and Biotechnology Faculty of Agricultural and Food Sciences and Environmental Management University of Debrecen Debrecen Hungary

Department of Anesthesiology University of Virginia Health System Charlottesville Virginia USA

Department of Biology and Ecology Faculty of Sciences University of Novi Sad Novi Sad Republic of Serbia

Department of Biology Vytautas Magnus University Kaunas Lithuania

Department of Fisheries Apiculture Wildlife Management and Special Zoology Faculty of Agriculture University of Zagreb Zagreb Croatia

Department of Forest Ecology Faculty of Forestry and Wood Technology Mendel University in Brno Brno Czech Republic

Department of Forest Ecology Slovenian Forestry Institute Ljubljana Slovenia

Department of Forest Protection and Wildlife Management Mendel University in Brno Brno Czech Republic

Department of Geography Tourism and Hotel Management Faculty of Sciences University of Novi Sad Novi Sad Serbia

Department of Phytology Technical University in Zvolen Zvolen Slovak Republic

Department of Wildlife Monitoring Estonian Environment Agency Tallin Estonia

Department of Zoology Musée National d'Histoire Naturelle Luxembourg City Luxembourg

Faculty of Biology University of Warsaw Warszawa Poland

Faculty of Environmental Protection Velenje Slovenia

Faculty of Forestry Stefan cel Mare University of Suceava Suceava Romania

Faculty of Forestry University of Belgrade Belgrade Serbia

Faculty of Natural Sciences and Mathematics University of Banja Luka Banja Luka Bosnia and Herzegovina

Grigore Antipa National Museum of Natural History Bucharest Romania

Institute of Marine Biology Biotechnology and Aquaculture Hellenic Centre for Marine Research Heraklion Crete Greece

Kyiv Zoological Park of National Importance Kyiv Ukraine

Lammi Biological Station University of Helsinki Lammi Finland

Mammal Research Institute Polish Academy of Sciences Białowieża Poland

Natural Resources Institute Finland Helsinki Finland

Research Institute of Wildlife Ecology University of Veterinary Medicine Vienna Vienna Austria

State National Park Belovezhskaya Pushcha Kamenyuki Republic of Belarus

Wildlife Management Department University of Forestry Sofia Bulgaria

Working Group for Wildlife Research at Clinic for Birds Reptiles Amphibians and Fish Justus Liebig University Giessen Gießen Germany

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