Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)
Bapst, David W., South Dakota School of Mines and Technology
Wright, April M., Iowa State University
Matzke, Nick J., Australian National University
Lloyd, Graeme T., Macquarie University
Published Jun 21, 2016 on Dryad.
Cite this dataset
Bapst, David W.; Wright, April M.; Matzke, Nick J.; Lloyd, Graeme T. (2016). Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria) [Dataset]. Dryad. https://doi.org/10.5061/dryad.n2g80
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 file describes the file type and contents of all files in this data repository.
BEAST2 Input file for noSA analysis
Half-compatibility summary for noSA BEAST2 analysis
Maximum clade credibility summary for noSA BEAST2 analysis
Posterior sampled tree file from BEAST2 noSA analysis
BEAST2 Input file for SA analysis
Half-compatibility summary for SA BEAST2 analysis
Maximum clade credibility summary for SA BEAST2 analysis
Posterior sampled tree file from BEAST2 SA analysis
Saved R Environment from executing RMarkdown script.
PDF created by executing RMarkdown script.
RMarkDown script containing all post-inference analyses.
R script which, if executed from within the saved R environment, produces all figures in the manuscript and supplemental.
An R script for obtaining half-compatibility trees with posterior probabilities on the edges from BEAST2 treelogs, albeit without branch lengths.
Datafile of mass estimates for taxa, as obtained from the dataset supplied by Benson et al., 2014.
The Posterior tree sample from MrBayes analysis.
NEXUS input with MrBayes block for our MrBayes analysis.
Half-compatibility summary for the MrBayes analysis
Maximum clade compatibility summary for the MrBayes analysis
NEXUS file containing an unscaled topology matching the RAXML tree presented in Lee & Worthy, 2011.
NEXUS file containing an unscaled topology matching the tree presented in Figure S6 of Xu et al., 2011.
A timeList object for these taxa, structured as is necessary for use with paleotree, describing their stratigraphic ranges in discrete intervals.
Sample of 100 most parsimonious trees taken from our TNT analysis.