We performed forward genetic simulations in SLiM [version 2.4.2; (47)] under a divergence model with parameters estimated by Fan et al. (31). Each simulated individual consisted of a diploid 1-Mb genome, with a simple architecture of 1000 “genes” carried on 38 chromosomes proportional to chromosome lengths in the dog genome. Each gene consisted of a contiguous 1-kb sequence that accumulated mutations at a rate of 1 × 10−8 per site per generation. Selection coefficients for deleterious mutations were drawn from the distribution of fitness effects inferred from a large sample of humans by Kim et al. (66). Seventy percent of mutations were deleterious, and the remaining 30% were neutral (s = 0). Each simulation began with a burn-in period of 450,000 (10 × Ne) generations to allow the ancestral population to reach equilibrium. Recombination was permitted at single base positions between each gene at a rate of 1 × 10−3 per site per generation to simulate the effective rate of crossing over that would occur in 100-kb noncoding regions between each gene, assuming a recombination rate of 1 × 10−8 per site per generation. At the end of each simulation, the average number of alleles per individual and the average age of segregating mutations were calculated for weakly (0 < Nes ≤ 10), moderately (10 < Nes ≤ 100), and strongly (Nes > 100) deleterious and neutral (Nes = 0) mutations. We performed 100 replicates in which mutations were additive (h = 0.5) and 100 replicates in which mutations were completely recessive (h = 0.0) to examine the effects of dominance. Simulation scripts are available at https://doi.org/10.5281/zenodo.2666097.

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