Fig. S1 Effect plots from all significant (i.e., 0.05 genome-wide level) two-way interactions are shown.

Fig. S2 A positive association is noted between relative pax3a transcript levels and xanthophore count in both LF and TRC.

Table S1 Various measures of genetic differentiation across SNPs derived from genotyping twenty wild caught LF and twenty wild caught TRC.

Table S2 Genetic linkage map for the LFxTRC F2 cross.

Table S3 Xanthophore-based color QTL interval for the pax3a locus on LG18.

Table S4 Dorsal fin melanocyte-based color QTL interval on LG18.

Table S5 Xanthophore-based flank color QTL interval on LG14.

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