2.5.1 Estimation of inbreeding
Inbreeding can be estimated from individual WGS as the fraction of the genome covered by ‘runs of homozygosity’ (ROH), and their length (LnROH; Gomez-Raya, Rodríguez, Barragán, & Silió, 2015; Kardos, Qvarnström, & Ellegren, 2017; Magi et al., 2014). We identified ROHs in each individual using the PLINK ‘–homozyg’ method v1.90b4.9 (Purcell et al., 2007), since that approach provides lower false-positives than other methods (Kancheva et al., 2015). Homozygosity was determined for 1,000 kb overlapping windows. As suggested for low coverage data like ours (Ceballos, Hazelhurst, & Ramsay, 2018), the minimum length of a ROH was set to 300 kb which must contain at least 50 SNPs, and a maximum of 3 heterozygous genotypes per window were allowed. For measuring LnROH, we categorized lengths of ROHs into three groups: between 300 and 500 kb, >500 kb but ≤1,000 kb, and >1,000 kb. The fraction of ROH (F ROH) for each individual was calculated as the total length of ROHs (including all three length groups) divided by the total length of the autosomal genome sequenced.