Overlap of genomic divergence and association mapping
The range-wide F ST values that were mapped to the male Pacific lamprey genome were plotted by genomic position with the subset of SNPs used in the association testing for the two traits with consistent strong associations (i.e. adult total body length as measured at Bonneville Dam “T_BON” and female gonad size as measured at Willamette Falls “WFA♀”; Fig. 2a,b). For chromosomes 01 and 02, the adjusted -LOG10(P) values from the association tests were highly correlated with the genomic divergence as measured byF ST for the female gonad size and adult body size traits, respectively (Fig. 2a,b). We quantified the overlap of genomic divergence and trait association by regressing range-wideF ST and the adjusted -LOG10(P) values for the 302 SNPs in the GT-seq panel. These 302 SNPs show positive linear trends for both traits, but the linear trends with highest slope and R2 were observed for SNPs on chromosomes 01 and 02 for the gonad size and body length traits, respectively (Fig. S4). These results suggest that the high geographic divergence exhibited by SNPs on chromosomes 01 and 02 may be related to selection on the traits with which these same SNPs are highly associated.