Fig. 2

Genetic differentiation (F_ST) and outlier genes for the three pairwise comparisons. F_ST is plotted across the 90 assembled chromosomes for the comparison between Lake Michigan and Connecticut River (a) and the comparison between Lake Champlain and Connecticut River (b). All SNPs on neighboring outlier genes are indicated by points in alternating colors, blue and black, with SNPs causing nonsynonymous mutations in red. F_ST averaged across SNPs in 100 Kb windows is plotted for chromosomes 1–90 in alternating colors, purple and grey. The dashed line indicates a threshold Z(F_ST) of 5 for identifying outlier SNPs. While no outlier SNPs were detected in the comparison between Lake Michigan and Lake Champlain (c; LM vs. LC), 436 outlier SNPs, corresponding to 121 outlier genes, among which 14 contain outlier SNPs causing nonsynonymous substitutions, and 209 outlier SNPs, corresponding to 43 outlier genes, among which 6 contain outlier SNPs causing nonsynonymous substitutions, were detected between Lake Michigan and Connecticut River (d; LM vs. CT) and between Lake Champlain and Connecticut River (e; LC vs. CT)