The effect of linkage on the site frequency spectrum. The synonymous site frequency spectrum (top row) and the ratio of non-synonymous to synonymous frequency spectrum (bottom) is shown for β=0.25 with mutation rates u=10−6and 10−5. All curves are averaged over 500 replicates, under conditions of only negative selection (grey), and different conditions of positive selection (coloured lines). Black dashed lines show the expected behaviour of the neutral site frequency spectrum under independently segregating sites (θ/i) and black dotted lines indicate the leading order behaviour expected under constant adaptation (θ/i2). In the bottom panels, solid lines show the average non-synonymous to synonymous ratio for only negatively selected sites, whereas dashed lines show the ratio across both positively and negatively selected sites.