Reduced variation at concertina, a heterochromatic locus in Drosophila

In Drosophila melanogaster and closely related species, polymorphism has been shown to be reduced at loci located in regions of low recombination on the X chromosome and on the fourth chromosome, which does not normally recombine. This positive correlation between nucleotide polymorphism level and recombination rate is not predicted by standard neutral theory and therefore must result from natural selection and genetic hitchhiking along the chromosomes. We report here the near-complete absence of variation at concertina (cta), a locus located in the beta-heterochromatic base of chromosome 2L, a region of strongly reduced recombination. A 1.2 kilobase region containing coding regions and introns was sequenced from each of nine lines of D. melanogaster and nine lines of D. simulans representing worldwide collections. Variation is significantly reduced in eta in both species compared with other available loci on the same chromosome. Two analyses of background selection demonstrate that the reduction in variation at cta. considered in combination with other loci on chromosome 2L or alone, is consistent with the background selection model.