Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories

Anopheles gambiae s.l. are important malaria vectors, but little is known about their genomic variation in the wild. Here we present inter- and intra- species analysis of genome-wide RADseq data, in three Anopheles gambiae s.l. species collected from East Africa. The mosquitoes fall into three genotypic clusters representing described species (An. gambiae, An. arabiensis, and An. merus) with no evidence of cryptic breeding units. An. merus is the most divergent of the three species, supporting a recent new phylogeny based on chromosomal inversions. Even though the species clusters are well separated, there is extensive shared polymorphism, particularly between An. gambiae and An. arabiensis. Divergence between An. gambiae and An. arabiensis does not vary across the autosomes, but is higher in X-linked inversions than elsewhere on X or on the autosomes, consistent with the suggestion that this inversion (or a gene within it) is important in reproductive isolation between the species. The...