Base frequencies for all identified ns-SNPs in the three AHR loci. Black dots above the frequency plots indicate ns-SNPs identified by more than one test for selected residues (see Figure 2). Sequence logos indicate the average base frequencies in populations classified as reference (left) and contaminated (right). Pie charts indicate the base frequencies in two focal populations in Massachusetts (Scorton Creek, a clean site, and New Bedford Harbor, a polluted site) for ns-SNPs identified in multiple selection tests as well as for two additional ns-SNPs in AHR1 (positions 2 and 3) and three in AHR2 (positions 2, 6, and 8). These later ns-SNPs were not identified in the multiple tests for selection but comparisons between these two sites showed strong divergence in base frequency between the SC and NBH populations.