Vector population control using insecticides is a key element of current strategies to prevent
malaria transmission in Africa. The introduction of effective insecticides, such as the organophosphate
pirimiphos-methyl, is essential to overcome the recurrent emergence of resistance
driven by the highly diverse Anopheles genomes. Here, we use a population genomic
approach to investigate the basis of pirimiphos-methyl resistance in the major malaria vectors
Anopheles gambiae and A. coluzzii. A combination of copy number variation and a single
non-synonymous substitution in the acetylcholinesterase gene, Ace1, provides the key
resistance diagnostic in an A. coluzzii population from Coˆte d’Ivoire that we used for
sequence-based association mapping, with replication in other West African populations.
The Ace1 substitution and duplications occur on a unique resistance haplotype that evolved
in A. gambiae and introgressed into A. coluzzii, and is now common in West Africa primarily
due to selection imposed by other organophosphate or carbamate insecticides. Our findings
highlight the predictive value of this complex resistance haplotype for phenotypic resistance
and clarify its evolutionary history, providing tools to for molecular surveillance of the current
and future effectiveness of pirimiphos-methyl based interventions