DOI: 10.5061/dryad.n2g80
title: Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

description: 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.
description: 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.