SUPPLEMENTARY APPENDIX 7

Results of analyses of data sets from Scenario I. (a) Species delimitations estimated by the Bayesian coalescent method in BPP. Boxplots are shown for posterior probabilities of the one-species delimitation model (P1), across every 10 replicates under each set of conditions. Fifteen combinations of sample size n and population size N are shown along the top. The x-axis represents the number of loci. Probabilities are given on the y-axis. (b) Species delimitation estimated by the generalized mixed Yule-coalescent (GMYC) and the Poisson tree processes (PTP) methods. Stacked rows are shown for GMYC, Bayesian PTP heuristic (bPTP-h), Bayesian PTP maximum likelihood (bPTP-ML), and PTP heuristic (PTP-h), respectively. Twelve combinations of sample size n and population size N are along the top of the panels. The x-axis represents the number of loci. The y-axis represents the number of cases classified by false positive (dark blue) and not available (grey) among every 10 replicates under each set of conditions.