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

Abstract

O_LIHybridization 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. C_LIO_LIHere, we present the R package GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR, which uses an individual-based model to simulate genomic patterns following admixture forward in time. GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR provides user-friendly functions to set up and analyze simulations under evolutionary scenarios with selection, linkage and migration. C_LIO_LIWe show the flexible functionality of the GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR workflow by demonstrating 1) how to design an E&R simulation using GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR and 2) how to use GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR to verify analytical expectations following from the theory of junctions. C_LIO_LIGO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR 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. C_LI