Effect of BGS combined with bottlenecks and low X-linked mutation rate on diversity patterns. The models considered include the combination of a bottleneck model with 1 of 3 BGS models each combined with a lower X-linked mutation rate (µ_X/µ_A = 0.9, µ_X/µ_A = 0.75). For the BGS models, we varied the proportion of deleterious mutations (10, 50, and 80%) while the DFE for the deleterious selection coefficient (s_d) was gamma distributed with mean and shape parameter of −0.000133 and 0.35, respectively (Huber et al. 2017). The recombination rate was set to r = 5e⁻⁷ cM/bp across all simulations. Supplementary Fig. 8 shows the same corresponding plot for half the recombination rate (2.5e⁻⁷ cM/bp). The left column corresponds to a severe short bottleneck model and the right column to a shallow long bottleneck model (see Methods). For each model, we computed a) π_X/π_A across all models, where the red dashed line corresponds to the expected π_X/π_A = 0.75 value in the neutral model; b) π_X/π_X, _bottleneck where π_X, _bottleneck is the average π in the corresponding bottleneck model with no added biases and the solid gray line is 20% of π_X, _bottleneck; and c) haplotype homozygosity across all models and results from a 1-sided Wilcoxon rank-sum test for elevation of H in the bottleneck + BGS + low µ_X scenario compared to a neutral bottleneck model.