Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.19.343491v1?rss=1 Authors: Janzen, T., Diaz, F. Abstract: Hybridization between populations or species results in a mosaic of the two parental genomes. Genome admixture has received increasing attention for its implications in speciation, human evolution, Evolve and Resequencing (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. Currently, there is no simulation framework that models whole-genome evolution of local ancestry following admixture. Here, we present the R package GENOMEADMIXR, which uses an individual-based model to simulate genomic patterns of local ancestry 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 2) how to use GENOMEADMIXR to verify analytical expectations following from the theory of junctions. GENOMEADMIXR provides a mechanistic approach to explore expected genome responses to realistic admixture scenarios. With this package, we aim to aid researchers in testing specific hypotheses based on empirical findings involving admixing populations. Copy rights belong to original authors. Visit the link for more info