Brand, C. L.; Brown, N. J.; Dasgupta, A.; Buszczak, M.; Levine, M. T.

A fundamental driver of biological diversification is the evolution of reproductive barriers between species. Instability and mis-regulation of repetitive DNA underlie numerous post-zygotic reproductive barriers, yet the molecular mechanisms are unknown. A long-studied genetic incompatibility between Drosophila melanogaster and D. simulans arises from mis-segregation of the D. melanogaster-specific 359bp DNA satellite in hybrid embryos. Here we report that the D. simulans version of the essential enzyme Topoisomerase II/Top2 causes this lethal incompatibility. Combining interspecies gene swaps with cell biology and genetics revealed that D. simulans-specific adaptive divergence of Top2 DNA-interacting domains prevents the resolution of 359bp-induced topological stress. Our findings demonstrate that species-specific DNA satellite topology requires species-specific molecular machinery and that even vital housekeeping genes can underlie reproductive isolation between closely related species.