Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments

Abstract

Genetic relatedness plays a central role in ecology and evolution, but estimating it with high accuracy remains challenging. We established and validated a software pipeline that produces precise relatedness estimates for low-depth sequencing data by measuring the identical stretches of DNA that two individuals inherited from a common ancestor (genome segments that are identical-by-descent or IBD). We applied this method on genomic data from a free-ranging rhesus macaque population, which enabled us to show that IBD calls result in more precise estimates of relatedness than pedigree or earlier genetic estimates. We demonstrated that IBD-based analysis provides a powerful tool to estimate the continuous distribution of relatedness in animal populations, importantly even for relatively low-depth sequencing data. Keywords: SNP-based relatedness, STR-based relatedness, nonhuman primates, deep pedigree, WGS-based relatedness