Phylogenetic congruence, conflict and consilience between molecular and morphological data

Data for the paper Phylogenetic congruence, conflict and consilience between molecular and morphological data. This study is based on 32 total evidence datasets:

• Tetraodontiformes (Arcila, D., Pyron, R.A., et al. 2015)
• Ostariophysi (Near, T.J., Dornburg, A., et al. 2014)
• Mollusca (Vinther, J., Parry, L., et al. 2017)
• Mammalia (Lee, M.S. 2016)
• Lemuriformes (Herrera, J.P. and Dávalos, L.M. 2016)
• Sphenisciformes (Gavryushkina, A., Heath, T.A., et al. 2017)
• Hemiptera (Vea, I.M. and Grimaldi, D.A. 2016)
• Hymenoptera (Ronquist, F., Klopfstein, S., et al. 2012)
• Osteoglossiformes (Lavoué, S. 2016)
• Mysticeti (Marx, F.G. and Fordyce, R.E. 2015)
• Arthropoda (Lee, M.S., Soubrier, J., et al. 2013)
• Squamata (Wiens, J.J., Kuczynski, C.A., et al. 2010)
• Serpentes (Harrington, S.M. and Reeder, T.W. 2017)
• Palpimanoidea (Wood, H.M., Griswold, C.E., et al. 2012)
• Formicidae (Price, S.L., Etienne, R.S., et al. 2016)
• Opiliones (Garwood, R.J., Dunlop, J.A., et al. 2011)
• Cetecea (Geisler, J.H., McGowen, M.R., et al. 2011)
• Malacostraca (Jenner, R.A., Dhubhghaill, C.N., et al. 2009)
• Rhynchonellida (Bapst, D.W., Schreiber, H.A., et al. 2018)
• Fabriciidae (Huang, D., Fitzhugh, K., et al. 2011)
• Stygnopsidae (Cruz-López, J.A. and Francke, O.F. 2017)
• Chiroptera (Dávalos, L.M., Velazco, P.M., et al. 2014)
• Hydrophilidae (Short, A.E., Cole, J., et al. 2017)
• Tribelocephalinae (Forthman, M. and Weirauch, C. 2017)
• Apinae (Cameron, S.A. and Mardulyn, P. 2001)
• Biblidinae (Garzón‐Orduña, I.J., Marini‐Filho, O., et al. 2013)
• Caviidae (Pérez, M.E. and Pol, D. 2012)
• Abrotrichini (Teta, P., Cañón, C., et al. 2017)
• Hexactinellida (Dohrmann, M., Kelley, C., et al. 2017)
• Hydroptilidae (Santos, A.P., Nessimian, J.L., et al. 2016)
• Nephilidae (Kuntner, M., Arnedo, M.A., et al. 2013)
• Actinopterygii (Giles, S., Xu, G.-H., et al. 2017)

Each has its own folder. Inside each of these are four subfolders. These are:

• combined - contains the nexus file and mrbayes output files for the combined (morph + mol) analysis
• mol - contains the nexus file and mrbayes output files for the mol-only analysis 
• morph - contains the nexus file, mrbayes, equal weighting parsimony and implied weighting parsimony output files for the morph-only analysis.
• treespace - contains distance matrices, MDS coordinates and tabulated percentages of variance for the first 10 principal coordinates under both RF distance and quartet distance.
• linked - a stepping stone analysis with linked topology
• unlinked - a stepping stone analysis with unlinked topology

We also provide the following:

• create_empirical_plots.r = R script used to create the plots for the manuscript
• empirical_anova.R = R script for conducting anova tests on the data 
• empirical_treespace.r = R  script used for tree space analyses
• figs - a folder that contains plots used in the manuscript + supplementary plots. 
• Supplementary Information - supplementary plots, tables and associated captions.