We define ROHs following recommendations in Howrigan et al. (2011), in which simulations were used to determine the ROH definitions that yield the most power to detect distant inbreeding (i.e. within the last 50 generations). Accordingly, we define ROHs as stretches of at least 65 continuously homozygous SNPs, using lightly pruned SNP data (i.e. removing SNPs with a MAF<.05 and with a variance inflation factor [VIF] > 10 using PLINK (Purcell et al. 2007) (see Supplementary Table 2)). To minimise underestimation of the number of runs, three (~5%) missing genotypes within an otherwise unbroken homozygous segment were allowed in a run. Further details of the parameters used - based on recommendations from Howrigan et al. (2011) - can be found in Supplementary Information Table 3.
