Data from: Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Paleogene boundary

 

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Title mammal_nexus
Downloaded 41 times
Description Nexus file containing molecular and morphological data for living and fossil Mammaliaformes, plus outgroups. Also contains MrBayes block with constraints, node calibrations, and tip ages
Download mammaliforme_combinded.nex (12.83 Mb)
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Title MCCT
Downloaded 22 times
Description Maximum clade credibility tree from simultaneous phylogenetic and dating analysis of living and fossil mammals. extant clade names reflect those in Meredith et al.
Download mammaliaforme_combinded.tre (358.4 Kb)
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Title body_mass
Downloaded 26 times
Description a csv file containing mean and standard errors for ln body mass in living and fossil mammals and mammaliaformes
Download mammal_mass.csv (8.881 Kb)
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Title fitContinuous_paleoModels
Downloaded 60 times
Description A corrected version of the functions used in Slater (2013) to fit mode shift models to phylogenetic data. This version uses direct conversion of the variance covariance matrix to fit OU models to non-ultrametric data.
Download fitContinuous_paleo_CORRECTED.R (24.55 Kb)
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Title mammaliaformes tree
Downloaded 18 times
Description The pruned, renamed tree used in model fitting
Download mammal.phy (7.97 Kb)
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Title fit_mammal_models
Downloaded 53 times
Description An R script that allows the user to repeat model fitting analyses performed in the manuscript using the pruned and renamed mammal tree.
Download fit_mammal_models.R (8.014 Kb)
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Title mammal_mass_posterior
Downloaded 14 times
Description mammaliaforme body mass data with row names corresponding to those in the posterior distribution of trees. Used when fitting models to posterior distribution.
Download mammal_mass_posterior.csv (8.929 Kb)
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Title pfile
Downloaded 18 times
Description parameter (.p) file from dating analysis of living and fossil mammals conducted in MrBayes. This file is required to rescale branch lengths in the posterior distribution of trees
Download pfile.txt (70.27 Mb)
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Title tfile
Downloaded 19 times
Description posterior distribution of time calibrated mammaliaforme trees from MrBayes analysis
Download tfile.nex (333.0 Mb)
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Title fit_models_posterior
Downloaded 20 times
Description R script to fit macroevolutionary models to trees from MrBayes Posterior distribution
Download fit_models_posterior.R (2.365 Kb)
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When using this data, please cite the original publication:

Slater GJ (2013) Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Paleogene boundary. Methods in Ecology and Evolution 4(8): 734-744. http://dx.doi.org/10.1111/2041-210X.12084

Additionally, please cite the Dryad data package:

Slater GJ (2013) Data from: Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Paleogene boundary. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1n14c.2
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