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.