Figure 4.

LD patterns under different crossover models. Average values for 1000 simulations are shown. LD between each pair of windows along the sequence (D′) is coded with a number between 0 and 1 and represented with a color (from white to dark blue to light green). Three different IGC rates (0, 1, and 50) are represented in columns and three different crossover conditions are shown in rows: no crossover, SCC (R = 50), and WRC (R = 50). The red lines below the names identifying each block show regions undergoing crossover. In the first row, where no crossover is acting, a dark blue diagonal line appears when IGC is active (and increasing with IGC rate) representing LD between paralogous windows of duplicate blocks. LD within the duplicate region is high when no IGC is acting and when IGC is high (C = 50) but decreases with a medium IGC rate. LD between duplicates (dark blue diagonal line) decreases when crossover is active on the single-copy region (SCC model, row 2) and on the whole region (WRC model, row 3) with respect to R = 0. As expected, crossover breaks LD blocks in the regions where it is acting. IGC also breaks LD blocks within duplicates if crossover is active (both in the SCC model and in the WRC model).