TY - JOUR T1 - The effects on neutral variability of recurrent selective sweeps and background selection JF - bioRxiv DO - 10.1101/358309 SP - 358309 AU - José Luis Campos AU - Brian Charlesworth Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/06/29/358309.abstract N2 - Levels of variability and rates of adaptive evolution can be affected by hitchhiking, the effect of selection on variants at linked sites. Hitchhiking can be caused either by selective sweeps or by background selection, involving the spread of new favorable alleles or the elimination of deleterious mutations, respectively. Recent analyses of population genomic data have fitted models where both these processes act simultaneously, in order to infer the parameters of selection. Here, we investigate the consequences of relaxing a key assumption of some of these studies – that neutral variability at a site affected by recurrent selective sweeps fully recovers between successive sweeps. We derive a simple expression for the expected level of neutral variability in the presence of recurrent selective sweeps and background selection. We also derive approximate integral expressions for the effects of recurrent selective sweeps on a given gene. The accuracy of the theoretical predictions was tested against multilocus simulations, using the software SLiM with selection, recombination and mutation parameters that are realistic for Drosophila melanogaster. We find good agreement between the simulation results and predictions from the integral approximations, except when rates of crossing over are close to zero. We show that the observed relations between the rate of crossing over and the level of synonymous site diversity and rate of adaptive evolution largely reflect background selection, whereas selective sweeps are needed to produce substantial distortions of the site frequency spectrum. ER -