Data from: Combined analysis of extant Rhynchonellida (Brachiopoda) using morphological and molecular data

Bapst D, Schreiber H, Carlson S

Date Published: May 12, 2017

DOI: http://dx.doi.org/10.5061/dryad.31048.2

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title README
Downloaded 12 times
Description README file describes the file type and contents of all files in this data repository.
Download README.txt (5.313 Kb)
Details View File Details
Title runScripts.zip
Downloaded 10 times
Description Zip file containing a necessary directory for recreating analyses
Download runScripts.zip (69.17 Kb)
Details View File Details
Title datafiles.zip
Downloaded 10 times
Description Zip file containing a necessary directory for recreating analyses
Download datafiles.zip (2.087 Kb)
Details View File Details
Title make_runI_06-29-15
Downloaded 6 times
Description R Script for creating MrBayes script for simulation-based sensitivity analyses
Download make_runI_06-29-15.R (4.709 Kb)
Details View File Details
Title rhynchComb_07-25-16
Downloaded 6 times
Description Rmarkdown script containing all topological comparison analyses
Download rhynchComb_07-25-16.Rmd (34.85 Kb)
Details View File Details
Title rhynchComb_07-25-16
Downloaded 55 times
Description PDF generated from knitting Rmarkdown script containing all topological comparison analyses
Download rhynchComb_07-25-16.pdf (658.5 Kb)
Details View File Details
Title rhynchComb_workspace_07-25-2016.Rdata
Downloaded 4 times
Description Saved R Workspace from running Rmarkdown script containing all topological comparison analyses
Download rhynchComb_workspace_07-25-2016.Rdata (60.94 Kb)
Details View File Details
Title figures_rhynchComb_08-03-16
Downloaded 4 times
Description R script for generating all figures in manuscript from provided R workspace file
Download figures_rhynchComb_08-03-16.R (10.78 Kb)
Details View File Details
Title figures_for_EvolTalk_06-20-16
Downloaded 3 times
Description R script for generating all figures in associated Evolution 2016 from provided R workspace file
Download figures_for_EvolTalk_06-20-16.R (1.551 Kb)
Details View File Details
Title SuppTable1_contraTable
Downloaded 13 times
Description Supplemental Table 1 as a PDF, reporting pair-wise CDs between considered summary topologies.
Download SuppTable1_contraTable.pdf (31.66 Kb)
Details View File Details
Title SuppMat_allTreesPlotted_suppFigures
Downloaded 49 times
Description PDF Supplementary Material containing plots of all summary trees considered in this paper, with associated support values.
Download SuppMat_allTreesPlotted_suppFigures.pdf (46.42 Kb)
Details View File Details
Title test_which_parsimony_informative_01-16-17
Downloaded 3 times
Description Revised script for testing whether characters are parsimony informative.
Download test_which_parsimony_informative_01-16-17.R (1.141 Kb)
Details View File Details
Title write_simple_sumt_01-16-17
Downloaded 5 times
Description Revised script for obtaining the simple summary tree files from MrBayes
Download write_simple_sumt_01-16-17.R (2.104 Kb)
Details View File Details
Title runFiles.zip
Downloaded 6 times
Description Zipped directory containing output from phylogenetic analyses, necessary for use with analyses in Rmd file. All tree files are contained in this zipped directory.
Download runFiles.zip (236.6 Mb)
Details View File Details
Title run_coding_12-15-16a.pdf
Downloaded 20 times
Description PDF 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.
Download run_coding_12-15-16a.pdf (137.7 Kb)
Details View File Details
Title raw_morphMat_MrBayes_04-21-17.nex
Downloaded 7 times
Description The raw morphological matrix, as used in the Bayesian analyses, as a Nexus-formatted text file.
Download raw_morphMat_MrBayes_04-21-17.nex (2.562 Kb)
Details View File Details
Title Appendix_1_05-11-17
Downloaded 9 times
Description List of 66 morphological characters used, revised from Schreiber et al. (2013).
Download Appendix_1_05-11-17.docx (15.05 Kb)
Details View File Details
Title Appendix_2_05-11-17
Downloaded 9 times
Description Morphological 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).
Download Appendix_2_05-11-17.docx (13.44 Kb)
Details View File Details
Title Appendix_3_05-11-17
Downloaded 7 times
Description Information on DNA specimens used in Cohen and Bitner (2013) and their respective Genbank accession numbers, taken from their Table 1.
Download Appendix_3_05-11-17.docx (13.88 Kb)
Details View File Details
Title Appendix_4_05-11-17
Downloaded 6 times
Description Table giving the number of taxa having each character state (or coded as missing) for each morphological character in the revised matrix.
Download Appendix_4_05-11-17.docx (17.31 Kb)
Details View File Details
Title Appendix_5_05-11-17
Downloaded 7 times
Description List of the 40 extant rhynchonellide species (modified from Logan 2007; Bitner 2009).
Download Appendix_5_05-11-17.docx (20.46 Kb)
Details View File Details

When using this data, please cite the original publication:

Bapst DW, Schreiber HA, Carlson SJ (2017) Combined Analysis of Extant Rhynchonellida (Brachiopoda) Using Morphological and Molecular Data. Systematic Biology, online in advance of print. http://dx.doi.org/10.1093/sysbio/syx049

Additionally, please cite the Dryad data package:

Bapst D, Schreiber H, Carlson S (2017) Data from: Combined analysis of extant Rhynchonellida (Brachiopoda) using morphological and molecular data. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.31048.2
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Version History

Item Version Date Summary

* Selected Version

Search for data

Be part of Dryad

We encourage organizations to: