Molecular variation at the In(2L)t proximal breakpoint site in natural populations of Drosophila melanogaster and D-simulans

A previous study of nucleotide polymorphism in a Costa Rican population of Drosophila melanogaster found evidence for a nonneutral deficiency in the n umber of haplotypes near the proximal breakpoint of In(2L)t, a common inver sion polymorphism in this species. Another striking feature of the data was a window of unusually high nucleotide diversity spanning the breakpoint si te. To distinguish between selective and neutral demographic explanations f or the observed patterns in the data, we sample alleles from three addition al populations of D. melanogaster and one population of D. simulans. We fin d that the strength of associations among sites found at the breakpoint var ies between populations of D. melanogaster. In D. simulans, analysis of the homologous region reveals unusually elevated levels of nucleotide polymorp hism spanning the breakpoint site.;ls with American populations of D. melan ogaster our D. simulans sample shows a marked reduction in the number of ha plotypes but not in nucleotide diversity. Haplotype tests reveal a signific ant deficiency in the number of haplotypes relative to the neutral expectat ion in the D. simulans sample and some populations of D, melanogaster At th e breakpoint site, the level of divergence between haplotype classes is com parable to interspecific divergence. The observation of interspecific polym orphisms that differentiate major haplotype classes in both species suggest s that haplotype classes at this locus are considerably old. When considere d in the context of other studies on patterns of variation within and betwe en populations of D. melanogaster and D. simulans, our data appear more con sistent with the operation of selection than with simple demographic explan ations.