Calculating Inbreeding Coefficients

SNP-based inbreeding coefficients were calculated using VCFTools.²⁷ VCFTools calculates the inbreeding coefficient F per individual using the equation F = (O−E)/(N−E), where O is the observed number of homozygotes, E is the expected number of homozygotes (given population allele frequency), and N is the total number of genotyped loci.

Pedigree-based inbreeding coefficients were computed using the R package kinship2.³⁵