Additional informations These data provide additional information related to the manuscript. They include a supplementary material file containing supplementary figures (Fig. S1–S20) and tables (Table S1–S6) cited in the manuscript, as well as a supplementary text detailing aspects of the methodology and presenting additional findings. Furthermore, supplementary Table 7 reports genes overexpressed in a dose-response manner and associated with pyrethroid resistance escalation in Anopheles funestus in Southern Africa. Supplementary Table 8 lists non-synonymous polymorphisms linked to selective sweeps in An. funestus across Africa, while supplementary Table 9 highlights key structural variant-based duplications associated with selective sweeps in An. funestus across the continent.