Inbreeding Coefficients.
Using the same SNP set (n = 5007 SNPs) as for pairwise relatedness, we calculated ‘internal relatedness’ (IR ) for each individual . This measure was chosen as it strongly correlates with standard measures of heterozygosity but incorporates further information about the frequency of the alleles in the individual’s genotype. As such, internal relatedness is a common measure of individual heterozygosity used to investigate inbreeding depression. When calculated over multiple loci, individuals’ internal relatedness values in a population are approximately normally distributed with negative values suggesting more ‘outbred’ individuals and positive values being suggestive of inbreeding. We used the GENHET v3.1 function in the R statistical environment to estimate IR as\(IR=\frac{\left(2\text{H\ }-\ \Sigma fi\right)}{(2N\ -\ \Sigma fi)}\), where H is the number of loci that are homozygous, N is the number of loci and \(fi\) is the frequency of the i th allele contained in the genotype.