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.

通过鉴定化石类群的年代地层学系统发育树，古生物学家得以估计重大分歧的时间节点和灭绝类群的定位，并检验宏观进化假说。近年来开发的贝叶斯‘端点时间鉴定’方法可同时推断并鉴定化石类群间的分支关系，以及推断潜在的祖先关系。利用先前发表的灭绝兽脚类恐龙数据集，本研究对比了通过多种端点时间鉴定方法推断的鉴定关系，并评估了其对系统发育比较方法潜在的影响。此外，本研究还将端点时间鉴定分析与其他后验方法（包括通过概率cal3方法进行时间尺度化的最大简约树）进行了比较。在端点时间鉴定分析中，尽管推断的祖先相似，但仍发现存在强烈支持的对立关系。总体而言，端点时间鉴定方法推断的分歧时间通常比该类群最早的地层学出现时间早数百万（或数千万）年。对体型演化模式的研究发现，从cal3和端点时间鉴定方法得到的树样本中，对进化模式的支持度可能存在差异。这些差异表明，在年代鉴定分析中，模型和软件的选择可能会对获得的年代系统发育树和更广泛的进化推断产生重大影响。

使用说明
README文件描述了本数据仓库中所有文件的类型和内容。
B2noSA_inputFile
BEAST2分析的无SA输入文件
B2noSA_majrule_burn03
无SA BEAST2分析的一半兼容性摘要
B2noSA_mcc_burn03
无SA BEAST2分析的最大似然树可信度摘要
B2noSA_treelog
BEAST2无SA分析的后验抽样树文件
B2SA_inputFile
BEAST2分析的SA输入文件
B2SA_majrule_burn03
SA BEAST2分析的一半兼容性摘要
B2SA_mcc_burn03
SA BEAST2分析的最大似然树可信度摘要
B2SA_treelog
BEAST2 SA分析的后验抽样树文件
birdtree_workspace_03-07-2016
执行RMarkdown脚本保存的R环境
birdtreecomparison_03-07-16
执行RMarkdown脚本创建的PDF文件
birdtreecomparison_03-07-16
包含所有后推断分析的RMarkDown脚本
figures_theropod_06-17-16
生成手稿和补充材料的所有图表的R脚本
makeBEAST2_majRule_02-05-16
从BEAST2树日志中获得后验概率边缘上的半兼容性树的R脚本，尽管不包含分支长度
mass_data_for_PCMs_BensonEtal14_10-27-14
从Benson等人（2014年）提供的数据集中获得的类群质量估计数据文件
MrBayesSA_100treeSample_burn03
MrBayes分析的后验树样本
MrBayesSA_input_script
MrBayes分析的NEXUS输入文件
MrBayesSA_majrule_burn03
MrBayes分析的一半兼容性摘要
MrBayesSA_mcc_burn03
MrBayes分析的最大似然树可信度摘要
theropod_tree_LeeWorthy2011_RAXML_02-01-16
包含与Lee & Worthy（2011年）中RAXML树相匹配的无尺度拓扑的NEXUS文件
theropod_tree_XuEtAll2011_FigS6_02-01-16
包含与Xu等人（2011年）图S6中树相匹配的无尺度拓扑的NEXUS文件
timeList_sorted_asIs_theropods_DWB_11-05-14
这些类群的时间列表对象，按必要结构化，用于描述它们的年代学范围在离散的区间内
TNT_most_parsimonious_trees
从我们的TNT分析中选取的100棵最简约树的样本。