Fig. S1 Proportions of O.  clarkii diagnostic and O.  mykiss diagnostic alleles observed in validation samples. Bars not summing to one indicate ‘no call’ individuals.

Table S1 Putative functions of loci containing SNPs and SNP location with respect to gene features. Superscripts indicate species in which the best Blast match was found: 1O.  mykiss; 2Salmo salar; 3Danio rerio; 4other. Only matches with an E-value ≤1e-15 are shown. Location abbreviations refer to the following: UTR: untranslated region; CDS: protein-coding sequence; ss: synonymous polymorphism; ns: nonsynonymous polymorphism. Amino acid codes show changes generated by nonsynonymous substitutions.

Table S2 SNP calls for all samples. C: homozygous O.  clarkii diagnostic; M: homozygous O.  mykiss diagnostic; H: heterozygote; NC: no call; nr: assay not run or failed over entire Fluidigm plate.

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