DNA Sequence statistical analysis
A total of 224 sequences of the control region (CR) (Genbank Accession numbers: PQ431575 - PQ431798) and 228 sequences of the cytochrome B gene (cytb ) (Genbank Accession numbers: PQ295559 - PQ295786) were aligned using ClustalW (Clustal, 1994) and manually trimmed, to have the same size, considering the polymorphic sites detected, as well as the sequencing quality, using the Geneious R10 v10.2.3 software. Data from the present analysis were combined with sequences of P. perdix retrieved from GenBank. More specifically, sequences of the main eastern (AF115404) and western (AF115405) haplotype (Liukkonen-Anttila et al. , 2002), as well as 43 more sequences (PopSet: 51449199) of the sub-region CR1 (Liukkonen, 2006) were acquired. For the analysis ofcytb , the sequences AF02879 (Kimball and Braun, 2014), EU839466 and GU214276 (Bao et al. , 2010) were recovered.
A median-joining network (Bandelt, Forster and Röhl, 1999) was constructed using the software Network 5.0.0 and the frequencies of the sequences (Fluxus Technology) assuming equal weights for all mutations and setting the genetic distance parameter e to zero to restrict the choice of feasible links in the final network.
Genetic variability indices of grey partridge populations, i.e. the number of distinct haplotypes (h), haplotype diversity (Hd) and nucleotide diversity (π) values, were estimated using the combined data set of both CR and cytb with DnaSP 5 (Librado and Rozas, 2009) software.