Replication data and scripts for - Mitochondrial variation in Anopheles gambiae and Anopheles coluzzii: phylogeographic legacy and mito-nuclear associations with metabolic resistance to pathogens and insecticides

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Supporting data and scripts related to the study: Romero, J. E. A., Chenal, C., Chehida, Y. B., Miles, A., Clarkson, C. S., Pedergnana, V., Wertheim, B., & Fontaine, M. C. (2024). Mitochondrial variation in Anopheles gambiae and Anopheles coluzzii: phylogeographic legacy and mito-nuclear associations with metabolic resistance to pathogens and insecticides. Accepted in the journal Genome Biology & Evolution (Oxford University Press). (biorXiv preprint: https://doi.org/10.1101/2023.07.18.549472) Content summary - Multiple alignments of DNA sequences of mitogenomes generated in the present study. - Input data, scripts, and metadata required to replicate the Analysis of Molecular Variance (AMOVA). - Codes and scripts are available via GitHub (https://github.com/jorgeamaya/automatic_genome_assembly and https://github.com/jorgeamaya/malaria_mitogenome). Research 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 Anopheles gambiae and Anopheles coluzzii, in relation 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 previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three salt-water tolerant species (Anopheles merus, Anopheles melas, Anopheles 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 structure, but not with the rare 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 potential mito-nuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.