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.