Genomic response to selection:

We investigated if the phenotype-associated SNPs identified in our analyses showed signals of a response to selection and if those signals were replicated across ecomorph pairs. To test this, for each ecomorph pair we compared FST and DXY values for phenotype-associated SNPs to a random background subset of SNPs. This random subset was 100 SNPs randomly selected from the whole dataset and the mean FST and DXY values for those SNPs were calculated. This was repeated 10,000 times and the means for FST and DXY were taken across all permutations. These permuted values were then compared to the empirical mean FST and DXY values for the phenotype-associated SNPs using the t.test function in R.

Analyses of recombination rate variation:

To test the effect of the recombination landscape on phenotype-genotype association, we first estimated recombination rates using the published Arctic charr linkage map (N=3,636) using MareyMap v1.3.6 . RAD loci from the linkage map were aligned to the Salvelinus sp. reference genome with Bowtie2 using the -very-sensitive setting. Loci were kept if they uniquely mapped to one location, mapped to the same chromosome as all other loci on their linkage group, and followed the orientation of the linkage map (i.e., not reversed). The filtered dataset was used to estimate the recombination rate across each chromosome using a spline algorithm. Spar values were varied for each chromosome from 0.5 to 0.9, depending on chromosome size, to best fit the data . Subsequently, WindowScanR v0.1 (available at: https://github.com/tavareshugo/WindowScanR) was used to summarize recombination rate values in 1 MB windows along the genome. All SNPs were assigned to these windows using BEDtools . A random subset of 100 SNPs was then selected and the mean recombination rate for those SNPs was calculated based on their windows. This was repeated 10,000 times to generate a background mean recombination rate, which was then compared to the mean recombination rate of the phenotype-associated SNPs (based on their windows) using a t-test.