Disequilibrium between linked inversions: an alternative hypothesis.

Data are presented which demonstrate a difference in the rate of recombination between cis and trans inversion double heterozygotes in Drosophila melanogaster. The corresponding two-locus theoretical model in which the double heterozygotes have different rates of recombination and no selection operates is analysed. We show that stable linkage disequilibrium can be maintained in this neutral situation. These results bear on the general observation in wild populations of several insect species that linked inversions manifest linkage disequilibrium.