Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences

Abstract

The Afrotropical mosquito Anopheles gambiae sensu stricto, a major vector of malaria, is currently undergoing speciation into the M and S molecular forms. These forms have diverged in larval ecology and reproductive behavior through unknown genetic mechanisms, despite considerable levels of hybridization. Previous genome-wide scans using gene-based microarrays uncovered divergence between M and S that was largely confined to gene-poor pericentromeric regions, prompting a speciation-with-ongoing-gene-flow model that implicated only about 3% of the genome near centromeres in the speciation process. Here, based on the complete M and S genome sequences, we report widespread and heterogeneous genomic divergence inconsistent with appreciable levels of interform gene flow, suggesting a more advanced speciation process and greater challenges to identify genes critical to initiating that process.

Fig. 1

Sliding window analysis of polymorphism and divergence in M and S based on 250kb windows with 50kb steps. Approximate boundaries of chromosomal rearrangements differing between M and S colonies (2Rc and 2La) are indicated by solid black vertical lines. “Speciation islands” sensu (14, 15) are shaded in blue for reference. “F_ST” refers to the mean per-site estimate (19). Underneath the X axis, vertical black bars mark the approximate location of 1kb windows whose divergence values fall in the top percentile of the distribution across autosomes (or the X chromosome, calculated separately). For both 250kb and 1kb windows, only windows meeting coverage and quality restrictions (19) are plotted.