Genome positions found to show polymorphism within populations.

In our study, loci were considered to be polymorphic within a sample if they had coverage ≥ 30 and two or more alleles with a frequency of ≥ 25%. Any such loci occurring within the 16S rRNA or 23S rRNA genes were excluded from analysis, as we observed a relatively high level of contaminant reads mapping to these regions. Positions are shown relative to the GenBank reference sequences used for read mapping. For comparison, the results of Huang et al. [39] and Dainty et al. [40] are also shown. For Dainty et al. [40], multiple samples per population were analysed, with each sample containing a single individual—allele frequencies are reported as number individuals/total individuals per population. NR = not reported; not scored as polymorphic by the authors of the original study; in most cases these values are likely to be at or close to 100%. (XLSX)