DOI: 10.5061/dryad.n715n
title: Data from: Posterior predictive checks of coalescent models: P2C2M, an R package

description: Bayesian inference operates under the assumption that the empirical data
 are a good statistical fit to the analytical model, but this assumption
 can be challenging to evaluate. Here, we introduce a novel r package that
 utilizes posterior predictive simulation to evaluate the fit of the
 multispecies coalescent model used to estimate species trees. We conduct a
 simulation study to evaluate the consistency of different summary
 statistics in comparing posterior and posterior predictive distributions,
 the use of simulation replication in reducing error rates and the utility
 of parallel process invocation towards improving computation times. We
 also test P2C2M on two empirical data sets in which hybridization and gene
 flow are suspected of contributing to shared polymorphism, which is in
 violation with the coalescent model: Tamias chipmunks and Myotis bats. Our
 results indicate that (i) probability-based summary statistics display the
 lowest error rates, (ii) the implementation of simulation replication
 decreases the rate of type II errors, and (iii) our r package displays
 improved statistical power compared to previous implementations of this
 approach. When probabilistic summary statistics are used, P2C2M
 corroborates the assumption that genealogies collected from Tamias and
 Myotis are not a good fit to the multispecies coalescent model. Taken as a
 whole, our findings argue that an assessment of the fit of the
 multispecies coalescent model should accompany any phylogenetic analysis
 that estimates a species tree.
description: Figure 2a - Results of
 sim. 1 - subst. rate s1Complete file set of
 data set 1 that was simulated under the multispecies coalescent model and
 under substitution rate s1. The uncompressed folder constitutes the input
 for the R package P2C2M to generate the first column of columnspace s1 of
 Figure 2a.Fig2a_Rate.s1_Sim.001.tar.gzFigure 2a - Results of sim. 1 - subst. rate s2Complete file set of data set 1 that was simulated under the multispecies coalescent model and under substitution rate s2. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s2 of Figure 2a.Fig2a_Rate.s2_Sim.001.tar.gzFigure 2b - Results of sim. 1 - subst. rate s1Complete file set of data set 1 that was simulated in the presence of migration between species and under substitution rate s1. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s1 of Figure 2b.Fig2b_Rate.s1_Sim.001.tar.gzFigure 2b - Results of sim. 1 - subst. rate s2Complete file set of data set 1 that was simulated in the presence of migration between species and under substitution rate s2. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s2 of Figure 2b.Fig2b_Rate.s2_Sim.001.tar.gzSimulated Data behind Figure 2a - subst. rate s1Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model and substitution rate s1. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.SimulatedData_Fig2a_Rate.s1.tar.gzSimulated Data behind Figure 2a - subst. rate s2Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model and substitution rate s2. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.SimulatedData_Fig2a_Rate.s2.tar.gzSimulated Data behind Figure 2b - subst. rate s1Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated in the presence of migration between species and under substitution rate s1. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.SimulatedData_Fig2b_Rate.s1.tar.gzSimulated Data behind Figure 2b - subst. rate s2Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated in the presence of migration between species and under substitution rate s2. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.SimulatedData_Fig2b_Rate.s2.tar.gzFigure 3 - Loci 5 - Results of sim. 1Complete file set of data set 1 that comprises a total of five genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 5' of Figure 3.Fig3_Loci.5_Sim.01.tar.gzFigure 3 - Loci 10 - Results of sim. 1Complete file set of data set 1 that comprises a total of ten genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 10' of Figure 3.Fig3_Loci.10_Sim.01.tar.gzFigure 3 - Loci 15 - Results of sim. 1Complete file set of data set 1 that comprises a total of 15 genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 15' of Figure 3.Fig3_Loci.15_Sim.01.tar.gzFigure 3 - Loci 20 - Results of sim. 1Complete file set of data set 1 that comprises a total of 20 genes. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace 'N of loci: 20' of Figure 3.Fig3_Loci.20_Sim.01.tar.gzSimulated Data behind Figure 3 - Loci 5Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of five separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 5' of Figure 3.SimulatedData_Fig3_Loci.5.tar.gzSimulated Data behind Figure 3 - Loci 10Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of ten separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 10' of Figure 3.SimulatedData_Fig3_Loci.10.tar.gzSimulated Data behind Figure 3 - Loci 15Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of 15 separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 15' of Figure 3.SimulatedData_Fig3_Loci.15.tar.gzSimulated Data behind Figure 3 - Loci 20Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model using a total of 20 separate genes. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST. This set of data was used to generate columnspace 'N of loci: 20' of Figure 3.SimulatedData_Fig3_Loci.20.tar.gz