10.5061/DRYAD.N2G80
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
Data from: Topology, divergence dates, and macroevolutionary inferences
vary between different tip-dating approaches applied to fossil theropods
(Dinosauria)
Dryad
dataset
2016
tip-dating
node dating
Maniraptora
Avialae
phylogenetic comparative methods
Theropoda
Dinosauria
cal3
time-scaling
2016-06-21T14:42:12Z
2016-06-21T14:42:12Z
en
https://doi.org/10.1098/rsbl.2016.0237
73559984 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.