Abstract
Previous efforts to uncover the genetic underpinnings of ongoing ecological speciation of the M and S forms of the African malaria vector Anopheles gambiae revealed two centromere‐proximal islands of genetic divergence on X and chromosome 2. Under the assumption of considerable ongoing gene flow between M and S, these persistently divergent genomic islands were widely considered to be ‘speciation islands’. In the course of microarray‐based divergence mapping, we discovered a third centromere‐associated island of divergence on chromosome 3, which was validated by targeted re‐sequencing. To test for genetic association between the divergence islands on all three chromosomes, SNP‐based assays were applied in four natural populations of M and S spanning West, Central and East Africa. Genotyping of 517 female M and S mosquitoes revealed nearly complete linkage disequilibrium between the centromeres of the three independently assorting chromosomes. These results suggest that despite the potential for inter‐form gene flow through hybridization, actual (realized) gene flow between M and S may be substantially less than commonly assumed and may not explain most shared variation. Moreover, the possibility of very low gene flow calls into question whether diverged pericentromeric regions—characterized by reduced levels of variation and recombination—are in fact instrumental rather than merely incidental to the speciation process.