Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans

Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Dros ophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addit ion, while conservative, this assumption is made at the cost of a great los s in power. Perhaps as a result, tests of the frequency spectrum based on z ero recombination suggest an adequate fit of Drosophila polymorphism data t o the predictions of the standard neutral model. Here, we analyze the frequ ency spectrum of a large number of loci in Drosophila melanogaster and D. s imulans using two summary statistics. We use an estimate of the population recombination rate based on a laboratory estimate of the rate of crossing o ver per physical length and an estimate of the species' effective populatio n size. In contrast to previous studies, we find that roughly half of the l oci depart from the predictions of the standard neutral model. The extent o f the departure depends on the exact recombination rate, but the global pat tern that emerges is robust. Interestingly, these departures from neutral e xpectations are not unidirectional. The large variance in outcomes may be d ue to a complex demographic history and inconsistent sampling, or to the pe rvasive action of natural selection.