Microsatellite analysis
In total, 106 grey partridge samples from the UK and 118 samples from
Greece/North Macedonia were used for microsatellite analysis at eight
loci. All samples that were successfully genotyped in more than six loci
were included in the global analysis. Thus, a dataset was created with
224 individuals, and they were split into five different groups for
further analysis: “UK Wild” including all individuals from Scotland
and England, “UK Captive”, “Greek/North Macedonia Wild”, “Greek
Captive” referring to Greek farmed individuals and “Hybrids” first
generation offspring of Greek captive individuals paired with wild
individuals. Eighty alleles were found across the eight microsatellite
loci. The most variable loci were MNT412 and MNT12 while the least
polymorphic were MNT404, MNT45 and Aru1A (Table S4_Appendix).
Genetic diversity indices were estimated for the five different groups
of samples (Table 2). Heterozygosity values were moderate for all groups
ranging from 0.438 to 0.631 with captive stocks as expected showing
higher inbreeding coefficient levels due to higher levels of inbreeding.
None of the populations met the criteria for HWE at a significance level
of P≤0.05. Further analysis revealed that most loci were out of HWE
probably due to null alleles (frequencies 15-20%). Pairwise
FST values range from 0.069 (UK Captive-Greek Captive)
to 0.2 (Hybrids-UK Wild).
Population genetic structure was investigated on the entire global
dataset and then separately for the wild birds in the UK, and Greece and
North Macedonia. In the global analysis, there was a clear separation
into two clusters, geographically into Western and Eastern lineages
(Figure 4). The wild birds of North Macedonia and Greece clearly cluster
separately from the wild birds of the UK. However, Greek captive stocks
are more closely aligned with the -UK-Wild birds than any of the wild
Greek birds. The microsatellites also reveal fine-scale information
compared to mitochondrial data, including the large number of
individuals within the captive UK stock as well as Greek stock that
appear to be descended from birds of both Western and Eastern origin,
but with a larger proportion of Western origins. Indeed, even in the
wild birds of both regions there is evidence of hybrid individuals, one
in the UK and approximate five in Greece/North Macedonia.
No genetic structure was found within the wild UK birds (Figure
S1_Appendix). Regarding the population structure of wild birds in
Greece and North Macedonia, three main geographical clusters were
revealed by the analysis (Figure S2_Appendix). One genetic cluster
consisted of the birds from Drama in north-eastern Greece, the second
genetic cluster included the birds within North Macedonia and the third
cluster including mostly birds from Grevena. Birds in Grevena and the
three remaining populations (Kozani, Thessaloniki and Xanthi) exhibited
a mix of the three genetic clusters, with the most south-westerly
population (Grevena) showing slight distinction, i.e. exhibiting less
genetic similarity to the birds from Drama than the other populations.