Abstract
Mitochondrial DNA (mtDNA) has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mtDNA variation in An. gambiae and An. coluzzii, in perspective with other species in the Anopheles gambiae complex (AGC), by assembling the mitogenomes of 1219 mosquitoes across Africa. The mtDNA phylogeny of the AGC was consistent with a previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, An. arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three salt-water tolerant species (An. merus, An. melas, An. bwambae) in the AGC also suggested that introgression and possibly selection shaped mtDNA evolution. MtDNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mtDNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African “far-west” exhibited divergence comparable to the inter-species divergence in the AGC, with a geographic distribution matching closely An. coluzzii’s geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structuration, but not with Wolbachia occurrence. The lineage was significantly associated with SNPs in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline the mito-nuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticide in Anopheles.