DOI: 10.5061/dryad.31048
title: Data from: Combined analysis of extant Rhynchonellida (Brachiopoda) using morphological and molecular data

description: Independent molecular and morphological phylogenetic analyses have often
 produced discordant results for certain groups which, for fossil-rich
 groups, raises the possibility that morphological data might mislead in
 those groups for which we depend upon morphology the most. Rhynchonellide
 brachiopods, with more than 500 extinct genera but only 19 extant genera
 represented today, provide an opportunity to explore the factors that
 produce contentious phylogenetic signal across datasets, as previous
 phylogenetic hypotheses generated from molecular sequence data bear little
 agreement with those constructed using morphological characters. Using a
 revised matrix of 66 morphological characters, and published ribosomal DNA
 sequences, we performed a series of combined phylogenetic analyses to
 identify conflicting phylogenetic signals. We completed a series of
 parsimony-based and Bayesian analyses, varying the data used, the taxa
 included, and the models used in the Bayesian analyses. We also performed
 simulation-based sensitivity analyses to assess whether the small size of
 the morphological data partition relative to the molecular data influenced
 the results of the combined analyses. In order to compare and contrast a
 large number of phylogenetic analyses and their resulting summary trees,
 we developed a measure for the incongruence between two topologies, and
 simultaneously ignore any differences in phylogenetic resolution.
 Phylogenetic hypotheses generated using only morphological characters
 differed amongst each other, and with previous analyses, while
 molecular-only and combined Bayesian analyses produced extremely similar
 topologies. Characters historically associated with traditional
 classification in the Rhynchonellida have very low consistency indices on
 the topology preferred by the combined Bayesian analyses. Overall, this
 casts doubt on the use of morphological systematics to resolve
 relationships among the crown rhynchonellide brachiopods. However,
 expanding our dataset to a larger number of extinct taxa with intermediate
 morphologies is necessary to exclude the possibility that the morphology
 of extant taxa is not dominated by convergence along long branches.
description: READMEREADME file describes
 the file type and contents of all files in this data
 repository.runScripts.zipZip file containing a necessary directory for recreating analysesdatafiles.zipZip file containing a necessary directory for recreating analysesmake_runI_06-29-15R Script for creating MrBayes script for simulation-based sensitivity analysesrhynchComb_07-25-16Rmarkdown script containing all topological comparison analysesrhynchComb_07-25-16PDF generated from knitting Rmarkdown script containing all topological comparison analysesrhynchComb_workspace_07-25-2016.RdataSaved R Workspace from running Rmarkdown script containing all topological comparison analysesfigures_rhynchComb_08-03-16R script for generating all figures in manuscript from provided R workspace filefigures_for_EvolTalk_06-20-16R script for generating all figures in associated Evolution 2016 from provided R workspace fileSuppTable1_contraTableSupplemental Table 1 as a PDF, reporting pair-wise CDs between considered summary topologies.SuppMat_allTreesPlotted_suppFiguresPDF Supplementary Material containing plots of all summary trees considered in this paper, with associated support values.test_which_parsimony_informative_01-16-17Revised script for testing whether characters are parsimony informative.write_simple_sumt_01-16-17Revised script for obtaining the simple summary tree files from MrBayesrunFiles.zipZipped directory containing output from phylogenetic analyses, necessary for use with analyses in Rmd file. All tree files are contained in this zipped directory.run_coding_12-15-16a.pdfPDF table explaining how the identifiers, labels and conditions of the different phylogenetic analyses as given in the main text and in the supplemental data materials relate.raw_morphMat_MrBayes_04-21-17.nexThe raw morphological matrix, as used in the Bayesian analyses, as a Nexus-formatted text file.Appendix_1_05-11-17List of 66 morphological characters used, revised from Schreiber et al. (2013).Appendix_2_05-11-17Morphological character matrix used for parsimony analyses, revised from Schreiber et al. (2013), for 25 genera and 66 characters (the codings for the two Basiliola species are not repeated).Appendix_3_05-11-17Information on DNA specimens used in Cohen and Bitner (2013) and their respective Genbank accession numbers, taken from their Table 1.Appendix_4_05-11-17Table giving the number of taxa having each character state (or coded as missing) for each morphological character in the revised matrix.Appendix_5_05-11-17List of the 40 extant rhynchonellide species (modified from Logan 2007; Bitner 2009).