A genome-wide departure from the standard neutral model in natural populations of Drosophila

We analyze nucleotide polymorphism data for a large number of loci in areas of normal to high recombination in Drosophila melanogaster and D. simulans (24 and 16 loci, respectively). We find a genome-wide, systematic departur e from the neutral expectation for a panmictic population at equilibrium in natural populations of both species. The distribution of sequence-based es timates of 2Nc across loci is inconsistent with the assumptions of the stan dard neutral theory, given the observed levels of nucleotide diversity and accepted values for recombination and mutation rates. Under these assumptio ns, most estimates of 2Nc are severalfold too low; in other words, both spe cies exhibit greater intralocus linkage disequilibrium than expected. Varia tion in recombination or mutation rates is not sufficient to account for th e excess of linkage disequilibrium. While an equilibrium island model does not seem to account for the data, more complicated forms of population stru cture may. A proper test of alternative demographic models will require loc i to be sampled in a more consistent fashion.