... As a result, red deer have been extensively managed, introduced, restocked, and selectively hunted throughout its history and distribution area (Frantz et al., 2006;Milner et al., 2006;Csányi and Lehoczki, 2010;Haanes et al., 2010;Zachos and Hartl, 2011;Carden et al., 2012;Stanton et al., 2016), and are farmed for meat and for antler products (Csányi and Lehoczki, 2010;Wada et al., 2010;Zachos and Hartl, 2011;Frank et al., 2016). The species has been the subject of several studies with a phylogeographic focus at local (Zachos et al., 2003;Feulner et al., 2004;Haanes et al., 2010;Carden et al., 2012;Fickel et al., 2012;Karaiskou et al., 2014;Krojerová-Prokešová et al., 2015;Markov et al., 2015;Borowski et al., 2016;Carranza et al., 2016;Stanton et al., 2016) as well as larger geographical scales (Ludt et al., 2004;Skog et al., 2009;Niedziałkowska et al., 2011;Meiri et al., 2013). Based on previous studies of mitochondrial DNA (mtDNA) sequences, three deeply divergent lineages of red deer are known within Europe, enabling classification of individuals into Iberian (termed haplogroup A sensuSkog et al., 2009), Balkan (haplogroup C) and Mediterranean (haplogroup B) groups, suggesting retraction into three separate refugia during the last glaciation, the Iberian Peninsula, the Balkans and the Italian Peninsula (Ludt et al., 2004;Skog et al., 2009;Meiri et al., 2013;Karaiskou et al., 2014;Carranza et al., 2016). ...