Using PLINK software (Purcell et al. 2007), we quantified individuals' level of inbreeding by estimating the proportion of their genome that is in runs of homozygosity (ROH), by summing the total length of all their autosomal ROHs divided by the total SNP-mappable autosomal genome length (2.77*109). ROHs are homozygous stretches of DNA that can be observed in the offspring of even distant relatives (Howrigan et al. 2011; Keller et al. 2011b)). The Runs of Homozygosity program (PLINK; Purcell et al. 2007) slides a moving window of a specified number of SNPs across the genome in order to detect long runs of homozygous genotypes. Runs are flexibly definable in terms of the required number of homozygous SNPs spanning a certain distance.
