popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator.

ABSTRACT

BACKGROUND: Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will allow more complex and fine-scale inferences about population history than ever before; however, new methods are needed to test complex hypotheses. RESULTS: This article presents popRange, a forward genetic simulator, which incorporates large-scale genetic data with stochastic spatially and temporally explicit demographic and selective models. Features such as spatially and temporally variable selection coefficients and demography are incorporated in a highly flexible manner. popRange is implemented as an R package and presented with an example simulation exploring a selected allele's trajectory in multiple subpopulations. CONCLUSIONS: popRange allows researchers to evaluate and test complex scenarios by simulating large-scale data with complicated demographic and selective features. popRange is available for download at http//cran.r-project.org/web/packages/popRange/index.html.