The power of different types of markers to detect population structure
When comparing the relative performance of microsatellites and RADseq there was the expected discrepancy of higher heterozygosity values in the microsatellite compared to the RADseq data, which reflect the high mutational rate of microsatellites. Overall, both markers were able to uncover genetic structuring. Based on the small but widely geographically spread, number of sampling sites in the UK, both microsatellite and SNP data agree that there is a lack of deep phylogeographic structure within the wild British samples. Considering the larger distance between sampling sites compared to Greek sampling sites, for example, more than 500 km between Fife and Essex, this was unexpected. This result is suggestive of a large, homogenous population within the UK, but considering the low dispersal of grey partridge, this points towards large-scale human-mediated translocations. However, sampling from a much larger number of sites with known histories of management and partridge releasing are required to confirm this finding more generally. On the contrary, both molecular markers suggested similar trends concerning phylogeographic structure in Greek populations, with SNP data being somewhat more conclusive, although fewer individuals were included in the analysis. The most distinct was the population of Drama, followed by the population of Grevena while the other three populations (Kozani, Thessaloniki and Xanthi) revealed more mixed patterns and greater similarity with North Macedonia.
To be able to confidently assign individuals to either a Western or Eastern origin, a marker panel of 15 SNPs has been identified, based on the ddRAD libraries. Only wild individuals were used for this panel development, however not a single SNP was at fixation in both populations, i.e. only occurred in the Eastern individuals, while completely absent from the Western individuals (see Table S5_Appendix for a summary of the SNP frequencies). These may reflect either the recent divergence of the two lineages from the common ancestor or could be the result of past introduction events that affected the allele frequency. However, this panel of 15 SNPs could be combined with a mitochondrial DNA test for the identification of non-native stocks within Greece or within the UK.