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).