Data from: Estimating age-dependent extinction: contrasting evidence from fossils and phylogenies

Hagen O, Andermann T, Quental TB, Antonelli A, Silvestro D

Date Published: October 17, 2017

DOI: https://doi.org/10.5061/dryad.r5f70

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Title Supplementary Material
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Description Supplementary Material including Figures and Table.
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Title Carnivora Fossil and Pylogenetic Empirical Data
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Description The folder “empirical_data” contains the empirical data used for estimating age-dependent extinction processes. The folder “fossil_ Pires_et_al_2015” stores fossil data of Carnivora from the Northern Hemisphere compiled and cleansed by Pires et al. (2015). Inside the folder, “all_carnivora_SpeciesList.txt” provides a species list with extinct or extant status. The file “all_carnivora.py” is a ready for PyRate input file of the fossil data set, for more information please refer to PyRate help literature provided at https://github.com/dsilvestro/PyRate/wiki. The files “all_carnivora_combined_10_files.log” and “all_carnivora_Neogene_combined_10_files.log” are the outputs from the PyRate runs of the 10 replicated data sets for the entire fossil data set and the data set for the fossils found during the Neogene (see Fig2 for a schematic workflow). The folder “phylogenetic_Nyakatura_Bininda-Emonds_2012” stores the dated phylogeny of 286 species extant carnivores, with crown age at about 65 Ma build by Nyakatura and Bininda-Emonds (2012) References - Pires M.M., Silvestro D., Quental T.B. 2015. Continental faunal exchange and the asymmetrical radiation of carnivores. Proc. R. Soc. Biol. Sci. Ser. B 282. - Nyakatura K., Bininda-Emonds O.R.P. 2012. Updating the evolutionary history of carnivora (mammalia): A new species-level supertree complete with divergence time estimates. Bmc Biol 10.
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Title Fossil Simulations
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Description The folder “fossil_simulations” contains the R and Python scripts used for the fossils simulation study. The folder “1.simulators” contains the R scripts adapted from (Hagen and Stadler 2014) used to simulate the initial complete phylogenies. “SimulatorScenarioIandII_ConstantOverTime.R” was used for simulating scenarios I and II, “SimulatorScenarioIII_2TimeBin.R” was used for simulating scenario III and “SimulatorScenarioIV_2TimeBin_BIGDROP.R” was used for simulating scenario IV. Please note that these files require the parameters given at “parametersage.csv” and generated by the scripts “Parametersage_Generator.R” found respectively inside each scenario folder. Please change the working directories before running the scripts. To generate fossil data from the phylogenies the script “2.FossilSamplerRunOverFolder.py” was run, evoking “fossil_sampler.py” for all fossils inside the respective scenario. The script “3.GetPyRateEstimatesRunOverFolders.py” automates a PyRate estimation while “4.PlottingScenarios.R” is used for visualizing the result. “SummarySimulations.RData” summarizes the results and analysis conducted. Each scenario folder also contains a “summary_ScenarioX.csv” file recording the number of: sampled species, singletons, simulated extinct species, simulated extant species, fossil occurrences and several other returned values from PyRate. References - Hagen O., Hartmann K., Steel M., Stadler T. 2015. Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies. Syst Biol. 64 (3): 432-440. doi: 10.1093/sysbio/syv001. - Hagen O., Stadler T. 2017. Treesimgm: Simulating phylogenetic trees under general bellman harris models with lineage-specific shifts of speciation and extinction in r. Methods Ecol. Evol. in press.
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Title Simulation of Morphospecies
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Description Script used to measure the effect of anagenesis on the estimation of true ADE shape parameter (Supplementary Material Fig. S6).
Download AnagenesisExperimentFigS6.R (3.477 Kb)
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When using this data, please cite the original publication:

Hagen O, Andermann T, Quental TB, Antonelli A, Silvestro D (2017) Estimating age-dependent extinction: contrasting evidence from fossils and phylogenies. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syx082

Additionally, please cite the Dryad data package:

Hagen O, Andermann T, Quental TB, Antonelli A, Silvestro D (2017) Data from: Estimating age-dependent extinction: contrasting evidence from fossils and phylogenies. Dryad Digital Repository. https://doi.org/10.5061/dryad.r5f70
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