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.
README
README file describes the file type and contents of all files in this data repository.
B2noSA_inputFile
BEAST2 Input file for noSA analysis
B2noSA_majrule_burn03
Half-compatibility summary for noSA BEAST2 analysis
B2noSA_mcc_burn03
Maximum clade credibility summary for noSA BEAST2 analysis
B2noSA_treelog
Posterior sampled tree file from BEAST2 noSA analysis
B2SA_inputFile
BEAST2 Input file for SA analysis
B2SA_majrule_burn03
Half-compatibility summary for SA BEAST2 analysis
B2SA_mcc_burn03
Maximum clade credibility summary for SA BEAST2 analysis
B2SA_treelog
Posterior sampled tree file from BEAST2 SA analysis
birdtree_workspace_03-07-2016
Saved R Environment from executing RMarkdown script.
birdtreecomparison_03-07-16
PDF created by executing RMarkdown script.
birdtreecomparison_03-07-16
RMarkDown script containing all post-inference analyses.
figures_theropod_06-17-16
R script which, if executed from within the saved R environment, produces all figures in the manuscript and supplemental.
makeBEAST2_majRule_02-05-16
An 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_10-27-14
Datafile of mass estimates for taxa, as obtained from the dataset supplied by Benson et al., 2014.
MrBayesSA_100treeSample_burn03
The Posterior tree sample from MrBayes analysis.
MrBayesSA_input_script
NEXUS input with MrBayes block for our MrBayes analysis.
MrBayesSA_majrule_burn03
Half-compatibility summary for the MrBayes analysis
MrBayesSA_mcc_burn03
Maximum clade compatibility summary for the MrBayes analysis
theropod_tree_LeeWorthy2011_RAXML_02-01-16
NEXUS file containing an unscaled topology matching the RAXML tree presented in Lee & Worthy, 2011.
theropod_tree_XuEtAll2011_FigS6_02-01-16
NEXUS file containing an unscaled topology matching the tree presented in Figure S6 of Xu et al., 2011.
timeList_sorted_asIs_theropods_DWB_11-05-14
A timeList object for these taxa, structured as is necessary for use with paleotree, describing their stratigraphic ranges in discrete intervals.
TNT_most_parsimonious_trees
Sample of 100 most parsimonious trees taken from our TNT analysis.
