bGMYC4: Package Overview

Overview

The bGMYC4 package implements a Bayesian version of the General Mixed Yule-Coalescent model for species delimitation from single-locus phylogenetic data. It uses Markov Chain Monte Carlo simulation to evaluate the posterior distribution of species boundaries and supports flexible prior specification on model parameters.

Main functions

• bgmyc.singlephy() - Bayesian GMYC analysis for a single phylogeny
• bgmyc.multiphylo() - Analysis across multiple phylogenies
• bgmyc.dataprep() - Prepare data for analysis
• plot.singlebgmyc() - Visualize results for a single phylogeny
• plot.multibgmyc() - Visualize results across multiple phylogenies

Vignettes

• Interactive visualization with bGMYC4 (see bGMYC4-interactive.html)

References

Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D., and Vogler, A.P. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55(4), 595-609.

Reid, N.M. and Carstens, B.C. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology, 12, 196.