Relatedness assignment
We calculated pairwise relatedness estimates using the R packageRelated using the filtered set of 5007 SNPs, as per . Pairwise
relatedness across all pairs of individuals in our genetic dataset was
estimated using Queller and Goodnight’s relatedness estimator . Although
there are multiple relatedness estimates available, we selected to use
Queller and Goodnight’s because it has previously been found to be the
most accurate for this dataset in determining true pairwise
relationships. Briefly, using simulated genotypes of known
relationships, compared the accuracy of different estimates in correctly
determining relationships (i.e. parent-offspring or half-sibs), finding
that Queller and Goodnight’s estimate was the most accurate. Maternities
were identified through genetic parentage analyses, or, rarely, through
field observations. Materinity assignment was conducted using a reduced
panel of more stringently filtered SNPs (N = 427 SNPs, MAF
> 0.3, missingness < 1%, consistent marker
scores for technical replicate assay pairs of >99%),
linkage disequilibrium r2 < 0.4) in CERVUS 3.0.7 as per
.