Variation in recombination rate across the X chromosome of Anopheles gambiae

The M and S molecular forms of Anopheles gambiae are considered to be incipient species, despite residual gene exchange. Of the three small genome regions that are strongly differentiated between the molecular forms ("speciation islands"), two are located near centromeres, on the left arm of chromosome 2 and the X chromosome. To test the prediction of reduced recombination in these islands, we estimated recombination rates between microsatellite loci on the X chromosome using two M-form strains. Across most of the chromosome, recombination occurred at approximately 1 centimorgan per megabase (cM Mb(-1)), a value closely matching the genome-wide average estimated for A. gambiae and for other eukaryotes. Recombination was much higher at the telomeric end, > 7 cM Mb(-1). In the speciation island at the centromeric end, recombination was sharply reduced to approximately 0.2 cM Mb(-1), consistent with a role for reduced recombination in maintaining differentiation between nascent species despite gene flow.