Antagonistic host-parasite interactions can drive rapid adaptive evolution in 
genes of the immune system, and such arms races may be an important force 
shaping polymorphism in the genome. The RNA interference pathway gene 
Argonaute-2 (AGO2) is a key component of antiviral defense in Drosophila, and we 
have previously shown that genes in this pathway experience unusually high rates 
of adaptive substitution. Here we study patterns of genetic variation in a 
100-kbp region around AGO2 in three different species of Drosophila. Our data 
suggest that recent independent selective sweeps in AGO2 have reduced genetic 
variation across a region of more than 50 kbp in Drosophila melanogaster, D. 
simulans, and D. yakuba, and we estimate that selection has fixed adaptive 
substitutions in this gene every 30-100 thousand years. The strongest signal of 
recent selection is evident in D. simulans, where we estimate that the most 
recent selective sweep involved an allele with a selective advantage of the 
order of 0.5-1% and occurred roughly 13-60 Kya. To evaluate the potential 
consequences of the recent substitutions on the structure and function of AGO2, 
we used fold-recognition and homology-based modeling to derive a structural 
model for the Drosophila protein, and this suggests that recent substitutions in 
D. simulans are overrepresented at the protein surface. In summary, our results 
show that selection by parasites can consistently target the same genes in 
multiple species, resulting in areas of the genome that have markedly reduced 
genetic diversity.