Figure 1.

Overview of selection models examined in this study. (A) Hitchhiking models (either hard or soft sweeps) in which there is a recent sweep in the center of the simulated region (blue site), and the recomb rate is flat but varies across simulated replicates. (B) The central BGS model in which mutations in the central ∼10% of the region can be deleterious, but all other mutations are neutral. (C) The real BGS model, in which for each rep both the recombination map and the locations of sites experiencing negative selection (red regions) are drawn from a randomly selected region in the genome, but all selected sites have the same DFE. (D) The real BGS model with weak selection on CNEs, which is the same as the real BGS model but mutations at CNEs (purple) have 10-fold lower s than those within exons (red) on avg. avg, average; BGS, background selection; CNE, conserved noncoding element; DFE, distribution of fitness effects; recomb rate, recombination rate; rep, replicate.