Individual-based simulations of genome evolution with ancestry: the GenomeAdmixR R package

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.

Genomic erosion in the assessment of species extinction risk and recovery potential

“…Unfortunately, these models very rarely take genetic information into account, and they are not designed to incorporate the effects of genomic erosion. A new generation of evolutionary genomics modelling tools 62,63,64,65 now enables construction of complex, genomic-scale models capable of incorporating demographic, ecological and evolutionary dynamics into a single framework (see below). The ongoing data generation from EBP projects can help assessing extinction risk and recovery potential for thousands of species: (c) Number of eukaryote species in millions and (d) log10-transformed that has beenand are projected to beassessed by the EBP (green) and the IUCN (red) in relation to the total number of eukaryote species (blue)).…”

“…Unfortunately, these models very rarely take genetic information into account, and they are not designed to incorporate the effects of genomic erosion. A new generation of evolutionary genomics modelling tools 62,63,64,65 now enables construction of complex, genomic-scale models capable of incorporating demographic, ecological and evolutionary dynamics into a single framework (see below).…”

Individual‐based simulations of genome evolution with ancestry: The GenomeAdmixR R package

“…The R package is available via CRAN on https://cran.r-proje ct.org/ packa ge=Genom eAdmixR. All code used for the paper has been deposited in the Dryad Digital Repository http://datad ryad.org/resou rce/doi:10.5061/dryad.sqv9s 4n3q (Janzen & Diaz, 2021).…”