Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster

Restriction map studies previously revealed extensive linkage disequilibria in the transcriptional trait of the white locus in natural Drosophila melanogaster populations. To understand the causes of these disequilibria, we sequenced a 4722-bp region of the white gene from 15 lines of D. melanogaster and 1 line of Drosophila simulans. Statistical tests applied to the entire 4722-bp region do not reject neutrality. In contrast, a test for high-frequency haplotypes ('Haplotype test') revealed an 834-bp segment, encompassing the 3' end of intron 1 to the 3' end of intron 2, in which the structure of variation deviates significantly from the predictions of a neutral equilibrium model. The variants in this 834-bp segment segregate as single haplotype blocks. We propose that these unusually large haplotype blocks are due to positive selection on polymorphisms within the white gene, including a replacement polymorphism, Arg → Leu, within this segment.