Data from: Integrating fossils with molecular phylogenies improves inference of trait evolution

 

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Title phylogeny of caniform carnivores
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Description A time-calibrated phylogeny of caniform carnivora used in the paper to estimate rates of body size evolution. The phylogeny is composed on individually inferred family level trees appended to a backbone from Eizirik et al. (2010: MPE). Full details of phylogeny reconstruction are provided in appendix 2 of the paper.
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Title caniform body mass data
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Description Natural log transformed body mass data for Caniformia used to fit models of evolution.
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Title caniform body size priors
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Description Informative prior distributions for nodes in the caniform phylogeny. Full details are provided in Appendix 2 of the paper.
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Title caniform analysis
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Description An R script containing code to perform the analyses done with the caniform carnivore dataset in the paper.
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Title simulation phylogeny
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Description A simulated, non-ultrametric phylogenetic tree generated using the birthdeath.tree function in the geiger package. This tree was used for simulation tests documented in the paper.
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Title fossils as tips addition
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Description R script for performing simulation tests where fossils are treated as tip taxa and models are fitted to data using Maximum likelihood. For space and clarity, simulations under different models have been added to a single script and commented out, such that individual models can be uncommented and run as required. It should also be noted that this script was written to be used on a cluster and thus to be distributed to many nodes at a single time. Users without access to a cluster may wish to loop this script multiple times if attempting to replicate results, but should take care not to overwrite previous results.
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Title fossils as tips swapping
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Description This script is identical to the fossils as tips addition script, except that here proportions of extant taxa are replaced with fossil taxa to test the signal contributed by fossils relative to extant taxa. See the description for the aforementioned script for further details/ warnings.
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Title fossils as nodes actual values
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Description This R script conducts MCMC analyses using informative node priors centered on the nodes' true values. The script was written to run multiple analyses simultaneously on a cluster. See fossils as tips description for more information.
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Title fossils as nodes fossil record
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Description This R script performs simulation tests using MCMC using a simulated fossil record to derive informative node priors for a comparative dataset. Results are those in Appendix 1.
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Title fitContinousMCMC
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Description An R script containing source code for functions related to fitContinuousMCMC. These are beta versions of the code that were used to conduct analyses in the manuscript. More user-friendly code with expanded options (different priors, for example) is available in a temporary package from http://www.webpages.uidaho.edu/~lukeh/software/index.html or from Graham Slater at gslater@ucla.edu
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When using this data, please cite the original publication:

Slater GJ, Harmon LJ, Alfaro ME (2012) Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66(12): 3931–3944. http://dx.doi.org/10.1111/j.1558-5646.2012.01723.x

Additionally, please cite the Dryad data package:

Slater GJ, Harmon LJ, Alfaro ME (2012) Data from: Integrating fossils with molecular phylogenies improves inference of trait evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.q96d7
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