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Anopheles gambiae, the primary mosquito vector of malaria in sub-Saharan Africa, is divided into 2 sympatric incipient species known as M form and S form. Recent genomic analysis of each form revealed that differentiation between forms is clustered into 3 unlinked regions of the genome. Here, we expand the investigation of these "genomic islands of speciation" to multiple populations, including all of the genes across one of the islands. Differentiation between the M and S forms in 2 of the islands is complete across all individuals in all populations, confirming that the M and S forms are reproductively isolated taxa. Differentiation at the third island (on chromosome 2R) is limited to Cameroon populations. There is reduced variation in the M form in Cameroon at this location and increased divergence to the outgroup Anopheles arabiensis, supporting an association of adaptation with reproductive isolation.

Locus- and Population-Specific Selection and Differentiation between Incipient Species of Anopheles gambiae