Chromosomal inversions largely inhibit recombination and may be associated with selective forces,
such as hitch-hiking effects: the effect of positive selection on linked loci. A West African
population of Drosophila melanogaster showed a high frequency (0·61) of the In(2L)t inversion.
Departure from neutrality statistically associated with the inversion polymorphism was previously
recorded at Su(H), a locus distant from the proximal breakpoint of the inversion. These results
were consistent with hitch-hiking effects with recombination. The present sequence polymorphism
survey involves a 1 kb fragment of the Vha68-1 locus located closer to the proximal breakpoint of
the inversion. It shows a significant deficit of polymorphism with respect to divergence when
compared with other loci studied in the same population, thus suggesting selective effects. Only 11
polymorphic sites are present in a sample of 20 chromosomes and these sites present a significant
excess of rare-frequency variants. The major haplotype shows an unexpectedly high frequency. Our
estimate of the background selection effect is not sufficient to account for the observed reduction
of polymorphism. Intraspecific variation is structured between inverted and standard
chromosomes; there are no shared polymorphisms but also no fixed differences between them. This
pattern, together with that found on other loci previously studied near this inversion breakpoint,
suggests hitch-hiking effects enhanced by the inversion.