Abstract
Ongoing speciation in most African malaria vectors gives rise to cryptic species that differ remarkably in their behaviour, ecology and capacity to vector malaria parasites. Any vector control measure can be undermined if cryptic populations exist and are mistargeted within vector species. To examine population structure and the potential impacts of recent large-scale control programs, we have investigated genomic patterns of differentiation in mosquitoes belonging to a large taxonomic group that diverged ~3-Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high FST values between multiple divergent populations. Delineating cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA and SNP markers consistent with incomplete lineage sorting and/or gene flow. Throughout the genome, a very high proportion of loci are fixed (FST = 1) within putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.