DOI: 10.5061/dryad.739bs
title: Data from: Comparison of methods for molecular species delimitation across a range of speciation scenarios

description: Species are fundamental units in biological research and can be defined on
 the basis of various operational criteria. There has been growing use of
 molecular approaches for species delimitation. Among the most widely used
 methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree
 processes (PTP) were designed for the analysis of single-locus data but
 are often applied to concatenations of multilocus data. In contrast, the
 Bayesian multispecies coalescent approach in the software BPP explicitly
 models the evolution of multilocus data. In this study, we compare the
 performance of GMYC, PTP, and BPP using synthetic data generated by
 simulation under various speciation scenarios. We show that in the absence
 of gene flow, the main factor influencing the performance of these methods
 is the ratio of population size to divergence time, while number of loci
 and sample size per species have smaller effects. Given appropriate priors
 and correct guide trees, BPP shows lower rates of species overestimation
 and underestimation, and is generally robust to various potential
 confounding factors except high levels of gene flow. The single-threshold
 GMYC and the best strategy that we identified in PTP generally perform
 well for scenarios involving more than a single putative species when gene
 flow is absent, but PTP outperforms GMYC when fewer species are involved.
 Both methods are more sensitive than BPP to the effects of gene flow and
 potential confounding factors. Case studies of bears and bees further
 validate some of the findings from our simulation study, and reveal the
 importance of using an informed starting point for molecular species
 delimitation. Our results highlight the key factors affecting the
 performance of molecular species delimitation, with potential benefits for
 using these methods within an integrative taxonomic framework.
description: SUPPLEMENTARY APPENDIX
 1Original data files
 generated by simulation.supplementary appendix
 1.tar.gzSUPPLEMENTARY APPENDIX
 2Detailed methods and
 results of variations of Scenario II.supplementary appendix
 2.pdfSUPPLEMENTARY APPENDIX
 3Chronograms of the five
 species in Scenario IV, with speciation rate r as (a) 10e-5, (b) 10e-6,
 (c) 10e-7, and (d) 10e-8 speciation events per year. The timescale for
 each tree is indicated by the scale axis in time units of one million
 years before the present.supplementary appendix
 3.pdfSUPPLEMENTARY APPENDIX
 4Data
 files from the case study of bears.supplementary appendix
 4.tar.gzSUPPLEMENTARY APPENDIX
 5Data
 files from the case study of Apidae bees.supplementary appendix
 5.tar.gzSUPPLEMENTARY APPENDIX
 6Data
 files from the case study of Osmia bees.supplementary appendix
 6.tar.gzSUPPLEMENTARY APPENDIX
 7Results 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.supplementary appendix
 7.pdfSUPPLEMENTARY APPENDIX
 8Results of supplementary
 data sets to Scenario II.supplementary appendix
 8.xlsxSUPPLEMENTARY APPENDIX
 9Species delimitations
 estimated by PTP-h for data sets from Scenario II. Panels show nine
 combinations of population size N and divergence time t along the top, and
 four values of sample size n on the right. The x-axis represents the
 number of loci. The y-axis represents the number of cases classified by
 correct delimitation (dark green), false positive (dark blue), complex
 false positive (light blue), and not available (grey) among the 10
 replicates under each set of conditions.supplementary apppendix
 9.pdfSUPPLEMENTARY APPENDIX
 10Species delimitations
 estimated by bPTP-h for data sets from Scenario II. Panels show nine
 combinations of population size N and divergence time t along the top, and
 four values of sample size n on the right. The x-axis represents the
 number of loci. The y-axis represents the number of cases classified by
 correct delimitation (dark green), false positive (dark blue), complex
 false positive (light blue), and not available (grey) among the 10
 replicates under each set of conditions.supplementary appendix
 10.pdfSUPPLEMENTARY APPENDIX
 11Results of analyses of
 data sets from Scenario III.supplementary appendix
 11.xlsxSUPPLEMENTARY APPENDIX
 12Results of analyses of
 data sets from Scenario IV.supplementary appendix
 12.xlsxSUPPLEMENTARY APPENDIX
 13Results of analyses of
 full data sets from Scenario V.supplementary appendix
 13.xlsxSUPPLEMENTARY APPENDIX
 14Results of analyses of
 separate data sets from Scenario V.supplementary appendix
 14.xlsxSUPPLEMENTARY APPENDIX
 15Inferred species
 delimitations for Apidae bees.supplementary appendix
 15.xlsxSUPPLEMENTARY APPENDIX
 16Inferred species
 delimitations for Osmia bees.supplementary appendix
 16.xlsx