BPEC: An R Package for Bayesian Phylogeographic and Ecological Clustering

Abstract

BPEC is an R package for Bayesian phylogeographic and ecological clustering which allows geographical, environmental and phenotypic measurements to be combined with deoxyribonucleic acid (DNA) sequences in order to reveal geographic structuring of DNA sequence clusters consistent with migration events. DNA sequences are modelled using a collapsed version of a simplified coalescent model projected onto haplotype trees, which subsequently give rise to constrained clusterings as migrations occur. Within each cluster, a multivariate Gaussian distribution of the covariates (geographical, environmental, phenotypic) is used. Inference follows tailored reversible jump Markov chain Monte Carlo sampling so that the number of clusters (i.e., migrations) does not need to be pre-specified. A number of output plots and visualizations are provided which reflect the posterior distribution of the parameters of interest. BPEC also includes functions that create output files which can be loaded into Google Earth. The package commands are illustrated through an example dataset of the polytypic Near Eastern brown frog Rana macrocnemis analyzed using BPEC.