Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.

Usage Notes
READMEREADME file describes the file type and contents of all files in this data repository.B2noSA_inputFileBEAST2 Input file for noSA analysisB2noSA_majrule_burn03Half-compatibility summary for noSA BEAST2 analysisB2noSA_mcc_burn03Maximum clade credibility summary for noSA BEAST2 analysisB2noSA_treelogPosterior sampled tree file from BEAST2 noSA analysisB2SA_inputFileBEAST2 Input file for SA analysisB2SA_majrule_burn03Half-compatibility summary for SA BEAST2 analysisB2SA_mcc_burn03Maximum clade credibility summary for SA BEAST2 analysisB2SA_treelogPosterior sampled tree file from BEAST2 SA analysisbirdtree_workspace_03-07-2016Saved R Environment from executing RMarkdown script.birdtreecomparison_03-07-16PDF created by executing RMarkdown script.birdtreecomparison_03-07-16RMarkDown script containing all post-inference analyses.figures_theropod_06-17-16R script which, if executed from within the saved R environment, produces all figures in the manuscript and supplemental.makeBEAST2_majRule_02-05-16An R script for obtaining half-compatibility trees with posterior probabilities on the edges from BEAST2 treelogs, albeit without branch lengths.mass_data_for_PCMs_BensonEtal14_10-27-14Datafile of mass estimates for taxa, as obtained from the dataset supplied by Benson et al., 2014.MrBayesSA_100treeSample_burn03The Posterior tree sample from MrBayes analysis.MrBayesSA_input_scriptNEXUS input with MrBayes block for our MrBayes analysis.MrBayesSA_majrule_burn03Half-compatibility summary for the MrBayes analysisMrBayesSA_mcc_burn03Maximum clade compatibility summary for the MrBayes analysistheropod_tree_LeeWorthy2011_RAXML_02-01-16NEXUS file containing an unscaled topology matching the RAXML tree presented in Lee & Worthy, 2011.theropod_tree_XuEtAll2011_FigS6_02-01-16NEXUS file containing an unscaled topology matching the tree presented in Figure S6 of Xu et al., 2011.timeList_sorted_asIs_theropods_DWB_11-05-14A timeList object for these taxa, structured as is necessary for use with paleotree, describing their stratigraphic ranges in discrete intervals.TNT_most_parsimonious_treesSample of 100 most parsimonious trees taken from our TNT analysis.