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BPEC is an R package for Bayesian Phylogeographic and Ecological Clusteringwhich allows geographical, environmental and phenotypic measurements to becombined with DNA sequences in order to reveal clustered structure resultingfrom migration events. DNA sequences are modelled using a collapsed version ofa simplified coalescent model projected onto haplotype trees, whichsubsequently give rise to constrained clusterings as migrations occur. Withineach cluster, a multivariate Gaussian distribution of the covariates(geographical, environmental, phenotypic) is used. Inference follows tailoredReversible Jump Markov chain Monte Carlo sampling so that the number ofclusters (i.e., migrations) does not need to be pre-specified. A number ofoutput plots and visualizations are provided which reflect the posteriordistribution of the parameters of interest. BPEC also includes functions thatcreate output files which can be loaded into Google Earth. The package commandsare illustrated through an example dataset of the polytypic Near Eastern brownfrog Rana macrocnemis analysed using BPEC.

BPEC: An R Package for Bayesian Phylogeographic and Ecological Clustering