Updating the RZooRoH package for the analysis of inbreeding, identity-by-descent and relatedness from genomic data

Abstract

The RZooRoH R package was implemented to characterize individual inbreeding levels. It identifies DNA segments inherited twice from a common ancestor through different paths, which are known as homozygous-by-descent (HBD) segments. The package accepts different data formats and provides multiple outputs: HBD segments, inbreeding rates and genome-wide and locus-specific HBD probabilities. In addition, it partitions HBD levels into multiple HBD classes. The length distribution varies between these classes, which therefore correspond to distinct groups of ancestors that can be traced back to different generations in the past. This provides information about mating structure and recent demographic history. The computational performance of the package has been substantially improved, enabling, for example, computing times to be reduced when working with whole-genome sequence data and more HBD classes to be fitted. It is now possible to fit one class per past generation, which facilitates interpretation of the results. Since we have previously demonstrated that the ZooRoH model can be used to characterize identity-by-descent (IBD) between haploid individuals or phased haplotypes, this option has been included in the new package version. Estimating kinship by characterizing IBD levels between the four possible pairs of haplotypes from two individuals is another feature we added to the package. Finally, new options allow models to be refined, for instance by defining HBD classes as intervals or constant inbreeding rates for neighboring classes. Overall, the new version of the package offers improved computational efficiency and interpretability when characterizing inbreeding, IBD and relatedness levels.