Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Significance The level of DNA sequence variation at a site in the genome is affected by selection acting on genetically linked sites. We have developed models of selection at linked sites to explain the observed negative relation between the level of nearly neutral variability in Drosophila genes and their protein sequence divergence from a related species. We use fits of these models to polymorphism and divergence data to show that selective sweeps are the main determinants of this pattern. We obtain estimates of the strengths of selection on advantageous mutations and the proportions of new mutations that are selectively advantageous. Gene conversion, a major source of genetic recombination within genes, has a large effect on these parameter estimates.