Fig 2. Genomic variation within and average differentiation between sampling sites.

(A) Principal component analysis: PC1 separates site S2 individuals from the rest, while PC2 separates S1 individuals from the rest. Fill colors indicate the habitat in which individuals were caught, four stream habitat sites (orange) and two lake shore sites (black). PC analysis is based on the 24,784 SNP allele dataset with minor allele frequency >1%. (B) F-statistics: between sampling sites pairwise weighted average F_ST and F_IT-statistics are shown below and above the diagonal respectively, F_IS for each sampling site on the diagonal. Stars indicate values significantly different from zero (permutation test, >16,000 permutations, p<0.001). F-statistics are based on the 34,756 SNP genotype dataset.