Extended Data Fig. 7: F_ST and genetic distances plotted against physical distance.

Physical distance is shown on the x axis; grey intervals are 1 Mb and black intervals are 5 Mb. Coloured bars show significant QTLs, with the QTL peak indicated by the triangle and the Bayesian credible intervals indicated by the length of the bar. Genetic distances are estimated using three crosses—within population (Heliconius elevatus; elev and Heliconius pardalinus; pard) and between population (F₂). Candidate inversions (CIs; indicated by black arrows) are regions that recombine within species but not in hybrids (see Methods). The largest CI we identified was around 1.4 Mb long at the distal end of chromosome 16. However, we identified no CIs greater than 870 kb within the credible intervals of QTLs, and only one instance of a CI that was coincident with a QTL peak (on chromosome 15). Nonetheless, some CIs outside of QTLs present compelling targets for future investigation. Notably, at the proximal end of chromosome 19 and the distal end of chromosome 16, two large CIs overlap regions with elevated F_ST in which phylogenies resolve species boundaries (see Fig. 3).