a, Variation in black forewing patterning in the H. erato races. Black shading in the forewings highlights variation in melanin production in different parts of the forewing. Colour shading corresponds to shading in b and c. b, FST (lines; 20 kb window, 5 kb step size) and association (points) analysis at the peaks of divergence in chromosomes 10 and 13. Coloured points represent associations estimated from fixed SNPs. c, Phylogenetic weighting of phenotypic hypothesis consistent with the Sd, St, Ly and Ro elements. These weightings were obtained by summing weightings for topologies that were consistent with the hypothesized groupings presented in the phylogenies. Tree topologies consistent with a geographic grouping are represented negative in grey. Within the genomic regions with high phylogenetic weighting support for a particular phenotypic hypothesis, we defined the boundaries of the colour pattern intervals as position 4,634,972–4,641,535 for Sd, 4,657,452–4,658,207 for St, 4,666,909–4,670,474 for Ly1 and 4,700,932-4,708,441 for Ly2 on chromosome 10 and position 14,341,251–14,412,364 for Ro on chromosome 13. It is possible to further subdivide the Sd interval into two narrow intervals based on the phylogenetic weighting support and patterns of shared genotypes (position 4,637,657–4,637,727 for Sd1 and 4,639,853–4,641,535 for Sd2). See Supplementary Sections 4.1.2 and 4.2.2 for the full phylogenetic trees of the identified intervals including all H. erato samples and closely related outgroup species.