Genetic isolation drives divergent insecticide resistance between coastal and western Kenya Anopheles funestus populations

Escalating levels of insecticide resistance and adaptive changes in mosquito populations threaten recent gains in malaria control. Understanding the molecular, ecological, and evolutionary processes driving these transformations is important for extending the effectiveness of current insecticides and informing the development of effective strategies and tools for vector control and insecticide resistance management. This study analyzed 103 whole-genome sequences from Anopheles funestus s.s. mosquitoes collected before the implementation of non-pyrethroid-based vector control tools in Kenya in 2017. Mosquito samples were collected from the western Kenya region (Bungoma, Migori and Kisumu Counties), the region with the highest malaria prevalence and the coastal region (Kilifi County), which has the second-highest malaria prevalence in Kenya. The study determined the population structure, evaluated the presence of insecticide-resistant alleles associated with pyrethroid insecticides and identified patterns of gene flow. Based on our results, Anopheles funestus s.s. from the western Kenya region were highly differentiated from the coastal population with a mean F_ST of 0.117 (P = 0.002). Genetic differentiation between the western and coastal regions is likely attributed to ecological and geographic barriers such as the Great Rift Valley, which may limit gene flow. The presence of selection signals at insecticide resistance loci and high frequencies of key cytochrome P450 genes, particularly at the Cyp6p rp1 locus and Cyp9k1, are major contributors to metabolic resistance to pyrethroids. Populations of An. funestus s.s. from western Kenya shared selection signals at the CYP6p rp1 on chromosome 2 and at the Cyp9k1 on the X chromosome, which were absent in the coastal region (Kilifi) samples. Anopheles funestus s.s. populations from coastal Kenya are genetically distinct from those in western Kenya, suggesting diverse bionomics and the critical need for region-specific vector control strategies. Increased pyrethroid resistance and negative Tajima's D indicate a selective sweep, further highlighting the potential for vector resurgence. These findings emphasize the value of integrating genomics into routine An. funestus surveillance in Kenya.