Pigmentation genes
To find possible amino acid-changing variants that could explain phenotypical differences between G. lygdamus and G. xerces , we have identified and explored three well-known genes associated to colour patterns in butterflies: optix ,cortex and Wnt genes (19-23). We have first identified these genes in our annotation using a homology-based approach with BLAST algorithm tblastn (57). We used the homologs in the butterfly speciesPapilo machaon, Heliconius erato, Zerene cesonia, Danaus plexippus and Bombyx mori as proxies (63-66). We set an E-value lower than 0.001 and an Identity value above 60% for the tblastn results (Table S.3). Variants were then called at the gene coordinates using GATK v3.7 UnifiedGenotyper (67). We filtered the variants for indels and minimum Genotype Quality of 30 using vcftools v.1.14, but we kept them regardless of their coverage (45). A variant was considered as fixed in a species if it was covered in at least two individuals, did not present heterozygous genotypes, and if either Xerces Blue showed all their genotypes calls as homozygous for the derived allele while Silvery Blue being homozygous for the ancestral allele. Additionally, we assessed the coverage in the target genes using bedtools v2.2.2 (41) (Fig. S9).