Signatures of adaptation at key insecticide resistance loci inAnopheles gambiaein Southern Ghana revealed by low-coverage WGS

Abstract

AbstractResistance to insecticides and adaptation to a diverse range of environments present challenges toAnopheles gambiae s.l.mosquito control efforts in sub-Saharan Africa. Whole-genome-sequencing is often employed for identifying the genomic basis underlying adaptation inAnopheles, but remains expensive for large-scale surveys. Low-coverage whole-genome-sequencing (lcWGS) can identify regions of the genome involved in adaptation at a lower cost, but is currently untested inAnophelesmosquitoes. Here, we use lcWGS to investigate population genetic structure and identify signatures of local adaptation inAnophelesmosquitoes across southern Ghana. In contrast to previous analyses, we find no structuring by ecoregion, withAnopheles coluzziiandAnopheles gambiaepopulations largely displaying the hallmarks of large, unstructured populations. However, we find signatures of selection at insecticide resistance (IR) loci that appear ubiquitous across ecoregions inAn. coluzzii,and strongest in forest ecoregions inAn. gambiae. In the IR geneCyp9k1, we find species-specific alleles under selection, suggesting interspecific variation in the precise mechanism of resistance conferred byCyp9k1. Our study highlights resistance candidate genes in this region, and validates lcWGS, potentially to very low coverage levels, for population genomics and exploratory surveys for adaptation inAnophelestaxa.