Figure 3:

The impact of assortative mating on the average squared effect size estimate in population and within-family GWASs. Same-trait assortative mating of strength ρ = 0.2 occurs in generations 0–19; mating is random before and after this period. Under random mating, the average squared effect size estimates exceed the true average squared effect size (yellow line) because random drift generates chance local LD with causal alleles that inflates the variance of effect size estimation (e.g. Bulik-Sullivan et al. 2015b). The magnitude of this variance inflation depends on the GWAS design and sample size, and the effect of assortative mating and its cessation should be judged in reference to it. To guide the eye in this judgment, the faint horizontal lines show the average squared effect size estimate in the last 20 generations of the initial burn-in period of random mating. Profiles are averages across 10,000 replicate simulation trials. Simulation details can be found in the Methods.