Data from: Bias in phylogenetic measurements of extinction and a case study of end-Permian tetrapods

Soul LC, Friedman M

Date Published: January 30, 2017

DOI: http://dx.doi.org/10.5061/dryad.208b1

 

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Title Results
Description An R file containing all the results for the analysis of tetrapod data, including different timescaling methods and different length timeslices. Corresponds to plots shown in main manuscript and supplementary figures.
Download Results.RData (241.7 Kb)
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Title Tree Sets
Description R file containing sets of cladograms timescaled with different methods that were used in the analyses of tetrapods.
Download Tree Sets.RData (1.921 Mb)
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Title Supplementary data
Description Age data used to timescale cladograms, sources for cladogram topologies and dates of timeslices.
Download Supplementary data.txt (33.05 Kb)
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Title Supplementary Figure 1
Description Example timescaled topologies for each of the three focal clades, sauropsids, synapsids and temnospondyls.
Download Figure S1.pdf (1.287 Mb)
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Title Supplementary Figure 2
Description Measurement of D through time on three sets of 100 phylogenies timescaled using three different timescaling algorithms.
Download Figure S2.pdf (430.7 Kb)
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Title Supplementary Figure 3
Description Measurement of D and Moran's I through time on a set of 100 phylogenies timescaled using the Hedman method.
Download Figure S3.pdf (406.3 Kb)
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Title Supplementary Figure 4
Description Measurement of D through time on a set of 100 phylogenies timescaled using the Hedman method and divided into different time bin lengths.
Download Figure S4.pdf (399.2 Kb)
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Title Script to measure D
Description R code that takes as input a set of timescaled phylogenies with root ages and a matrix of time bins for analysis. Calculates D and associated p-values for each tree in each time bin.
Download Script to measure D (3.058 Kb)
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Title Simulation scripts
Description R code used to simulate phylogeny and measure D.
Download Simulation scripts (22.67 Kb)
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When using this data, please cite the original publication:

Soul LC, Friedman M (2017) Bias in phylogenetic measurements of extinction and a case study of end-Permian tetrapods. Palaeontology 60(2): 169-185. http://dx.doi.org/10.1111/pala.12274

Additionally, please cite the Dryad data package:

Soul LC, Friedman M (2017) Data from: Bias in phylogenetic measurements of extinction and a case study of end-Permian tetrapods. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.208b1
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