Individual-based simulations of genome evolution and ancestry: the GENOMEADMIXR R package

Hybridization between populations or species results in a mosaic of the two parental genomes. This and other types of genome admixture have received increasing attention for their implications in speciation, human evolution, Evolve and Resequence (E&R) and genetic mapping. However, a thorough understanding of how local ancestry changes after admixture, and how selection affects patterns of local ancestry remains elusive. The complexity of these questions limits analytical treatment, but these scenarios are specifically suitable for simulation. Here, we present the R package GenomeAdmixR, which uses an individual-based model to simulate genomic patterns following admixture forward in time. GenomeAdmixR provides user-friendly functions to set up and analyze simulations under evolutionary scenarios with selection, linkage and migration. We show the flexible functionality of the GenomeAdmixR workflow by demonstrating 1) how to design an E&R simulation using GenomeAdmixR and ...