Fig. 4: Parallel adaptation is associated with different signatures of selection on putative flatwing hotspot, scaffold 18404.

a Loci showing signatures of selective sweeps in wild Kauai flatwing males were identified by examining the distribution of fixation index (F_ST) and relative diversity (log₁₀[θ_{π,unselected_normal-wing}/θ_{π,selected_flatwing}]) between flatwing Kauai individuals and normal-wing Australian individuals. Datapoints represent 10 kb sliding windows calculated in 2.5 kb increments across the entire genome. Blue points and red points correspond to X chromosome and autosomal bins, respectively, showing the most significant selective-sweep signatures (top 5% of the empirical distribution). b Patterns of linkage disequilibrium (LD) along the flatwing-associated scaffold 18404. Top and bottom heatmaps show pairwise LD (r²) between SNPs (top—Kauai, bottom—Oahu), and SNPs were filtered as detailed in the ‘Method’ section to ensure LD is comparable between flatwing males from Kauai vs. Oahu. The colour scale refers to the value of r². Protein-coding genes and flatwing-associated SNPs are indicated by blocks and bars with different colours respectively (Prospero = brown, Doublesex = purple) in the middle panel. c–e, Signatures of selection on scaffold 18404 associated with parallel evolution in Hawaiian populations. Genes and flatwing-associated SNPs are shown in the top panel using the same scheme as in b. F_ST and π were calculated using sliding-window analyses with 10 kb windows for c Kauai and d Oahu. π_ratio = θ_{π,unselected_normal-wing}/θ_{π,selected_flatwing}. Horizontal dashed lines represent mean whole-genome value for the values shown in each panel, and dark red horizontal dashed lines in c and d represent the top 5% threshold values. e Tajima’s D for all wild-caught individuals. Kauai flatwing (purple), Oahu (blue, all samples combined), Hilo normal-wing (green), Australian normal-wing (orange). The dashed horizontal line indicates the Tajima’s D null hypothesis for neutrality.