Partial sweeping of variation at the Fbp2 locus in a west African population of Drosophila melanogaster.

Departure of molecular variation from neutral equilibrium was studied in a highly recombining region of the Drosophila genome. A 2.2-kb region including the Fbp2 locus was sequenced for 10 chromosomes from a D. melanogaster sample from West Africa and for the related species D. simulans. Of the 33 variable sites present in the 1.3-kb transcription unit, 32 made up a single haplotype present in half of the D. melanogaster sample. This pattern significantly departed from predictions of the neutral drift-mutation equilibrium model. The major haplotype presented a diagnostic restriction site which was investigated in 226 chromosomes from three distant European and African populations. It was found at a high frequency (31%) in the population from which the sequenced sample originated, but was nearly absent from the other two (below 4%), suggesting that the major haplotype frequency resulted from a local selective sweep event. Partial sweeping of variation in regions of high recombination rates has previously been found for American and European populations of D. melanogaster. Our study shows that this phenomenon also occurs in African populations, which are in the ancestral range of this species.