The African Anopheles gambiae complex of six sibling species has many
polymorphic and fixed paracentric inversions detectable in polytene ch
romosomes. These have been used to infer phylogenetic relationships as
classically done with Drosophila. Two species, A. gambiae and A. meru
s, were thought to be sister taxa based on a shared X inversion design
ated X(ag). Recent DNA data have conflicted with this phylogenetic inf
erence as they have supported a sister taxa relationship of A. gambiae
and A. arabiensis. A possible explanation is that the X(ag) is not mo
nophyletic. Here we present data from a gene (soluble guanylate cyclas
e) within the X(ag) that strongly supports the monophyly of the X(ag).
We conjecture that introgression may be occurring between the widely
sympatric species A. gambiae and A. arabiensis and that the previous D
NA phylogenies have been detecting the introgression. Evidently, intro
gression is not uniform across the genome, and species-specific region
s, like the X-chromosome inversions, do not introgress probably due to
selective elimination in hybrids and backcrosses.