Multiple genomic approaches reveal geographic structure and local selection signals in invasive Anopheles stephensi from the Horn of Africa and Yemen

Background Anopheles stephensi , an invasive malaria vector expanding across the Horn of Africa, poses a growing public health threat. We applied a multi-faceted genomic approach combining whole genome sequencing (WGS), double-digest restriction-site associated DNA sequencing (ddRAD), and mitochondrial data to resolve population structure and adaptive evolution among An. stephensi populations from Ethiopia, Somaliland and Yemen relative to Indian lab-reared colony. Results WGS revealed broad-scale differentiation across the autosomal chromosomes, while ddRAD with a larger number of samples ( n = 402) provided finer resolution of substructure within Ethiopia and Yemen, including sites where heightened malaria has been reported post invasion. Distinct genetic compositions in Sayhut, Yemen, indicate cryptic diversity within An. stephensi . WGS-based scans identified selective sweeps in Ethiopian populations at loci encoding homologs of esterases, serine proteases, and lipases, and in Yemeni populations at cytochrome P450 gene clusters. Conclusions These results provide insight into An. stephensi diversity, particularly for locations where heightened malaria has been reported post-invasion and demonstrate that a combined WGS and ddRAD approach can offer a cost-effective option to resolve population structure and identify adaptive loci in a vector invasion scenario. Integrating these genomic approaches enhances understanding of invasion dynamics, informing surveillance and targeted vector control in urbanizing regions.