Fig. S2.

Averaged SEs of ID estimates from 1,000 simulated datasets. Datasets were simulated assuming a true ID parameter $b=-3$ (horizontal gray line) phenotypic SD for complete inbreeding. In scenario 1 the $m$ = 1,000 causal variants were randomly sampled from all observed SNPs, whereas in scenarios 2 and 3 they were respectively sampled from low- and high-LD regions of the genome. In A the expectation of the dominance effects (${\delta }_j$ for the $j$th causal variant) is constant (neutral model) whereas in B ${\delta }_j$ is inversely proportional to the variance of the minor allele count at each causal variant. $F_{\mathrm{HOM}}$, excess homozygosity inbreeding measure; $F_{\mathrm{ROH}}^{(1)}$ and $F_{\mathrm{ROH}}^{(2)}$, runs of homozygosity-based inbreeding measures; $F_{\mathrm{UNI}}$, measure of inbreeding based on correlation between uniting gametes; LDMS, LD and MAF stratified inference.