Figure 4. Linkage disequilibrium (LD) for combined H. m. aglaope and H. m. amaryllis populations.

Pairwise LD between sites across the genomic region is shown as a heatmap, with greyscale indicating estimated r² values. Darker colours indicate a stronger correlation between SNP variants at the two sites, across the individuals sampled. The highest LD estimates are all within gene regions, or between closely linked loci. The largest block of LD is across the region with strong genotype-by-phenotype association in the HmB region, across the Slu7, Kinesin and GPCR genes (A, lower left). Comparisons are shown for a) all sites, b) sites associated with phenotype in the HmB locus, and c) sites associated with phenotype in the HmYb locus.