Chromosome 2 inversion, Est-l and Est-2 haplotype frequencies were determined for 19 wild D. buzzatii collections from the known range of this species in Australia. Three different chromosome 2 sequences (ST, j, j z3) were polymorphic across the collections. They occurred at overall frequencies which approximated those in the ancestral New World and colonized Old World populations, which indicated that no radical genetic change was associated with the colonization of Australia by D. buzzatii. Linkage disequilibria of Est-l and Est-2 alleles with the inversions tended to be strong, and consistent in direction, in almost all collections. The distributions of conditional allele frequencies within the different inversions were consistent with stochastic historical explanations for the linkage disequilibria. Significant linkage disequilibria between Est-l and Est-2 were evident after correcting for the inversions, but these disequilibria largely were restricted to southern (higher latitude) populations, and were inconsistent in direction among the collections. Hence, population bottlenecks may underlie these genic disequilibria.
A Genealogical Interpretation of Linkage Disequilibrium