Identity-by-descent calling in rhesus macaques

The most precise estimates of relatedness can be produced by quantifying the number and length of DNA segments that are identical-by-descent (IBD). We developed an IBD calling pipeline and applied it to primarily 4-6x coverage whole genome re-sequencing data (WGS) of 98 rhesus macaques, for which we have a long-term pedigree available. Our results reveal a considerable variation of relatedness within kin classes, leading to overlapping distributions between kin classes. Further, the new method allows us to identify cryptic relatives and measure the level of background relatedness in the population. Overall, this new method provides much more information than traditionally used methods to estimate relatedness, contributing to our understanding of a fundamental component of population structure in the wild.