Population genomics of nicotinic acetylcholine receptors in Anopheles funestus reveals rapid evolution of the α9 and β2 subunits within a constrained gene family

The deployment of clothianidin-based insecticide formulations in malaria vector control has highlighted the capacity of Anopheles funestus to displace more susceptible mosquito species in treated areas and to rapidly evolve resistance under selection pressure. Metabolic detoxification, together with structural and genetic changes in nicotinic acetylcholine receptors (nAChRs), the primary molecular targets of neonicotinoids, can reduce insecticide efficacy. Here, we characterized amino acid substitutions across all 11 nAChR subunits in An. funestus to assess standing variation that may facilitate adaptive responses to chemical exposure. Using whole-genome sequencing data from 656 mosquitoes sampled in 13 African countries, we found marked contrasts in the distribution of nonsynonymous variants among nAChR subunits. Most subunits are strongly constrained and carry no missense variants, whereas two loci (3 and 7) display three geographically widespread amino acid substitutions across the continent. In contrast, 9 and {beta}2 accumulate dozens of nonsynonymous mutations occurring at intermediate to high frequencies, including within domains involved in orthosteric ligand binding and channel gating. Genetic differentiation at nAChR loci among populations from different countries is low to moderate, although several nonsynonymous mutations display high FST values consistent with geographic structuring. These results highlight relaxed constraint on two subunits that may provide opportunities for evolutionary diversification within a conserved family of multimeric receptor assemblies. Such diversification has not been observed in vector species displaced by An. funestus in indoor residual spraying areas, and the potential implications for reduced sensitivity to neonicotinoids are discussed.