Data from: Mass turnover and recovery dynamics of a diverse Australian continental radiation

Brennan IG, Oliver PM

Date Published: February 7, 2017

DOI: http://dx.doi.org/10.5061/dryad.991p6

 

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Title BEAST nuclear only operator file (xml)
Downloaded 2 times
Description Operator xml file for our NUCLEAR ONLY analysis investigating divergence times of the Pygopodoidea. Run on CIPRES (phylo.org) using BEAST 1.8.3. Log files inspected using Tracer, and trees summarized using TreeAnnotator.
Download Pygopodoidea.nuclear.all.300mil.xml (761.0 Kb)
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Title BEAST nDNA + mtDNA operator file (xml)
Downloaded 2 times
Description Operator xml file for our NUCLEAR + MITOCHONDRIAL (total) analysis investigating divergence times of the Pygopodoidea. Run on CIPRES (phylo.org) using BEAST 1.8.3. Log files inspected using Tracer, and trees summarized using TreeAnnotator.
Download Pygopodoidea.total.300mil.xml (1.128 Mb)
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Title BEAST alternative fossil calibration schemes operator files (xml)
Downloaded 5 times
Description Operator xml files for our ALTERNATIVE FOSSIL CALIBRATION SCHEMES, used to test the robustness of fossil calibrations in our divergence time estimation of the Pygopodoidea. Run on CIPRES (phylo.org) using BEAST 1.8.3. Log files inspected using Tracer, and trees summarized using TreeAnnotator.
Download Alternative Fossil Calibration Schemes.zip (595.4 Kb)
Download README.txt (1.557 Kb)
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Title Alignments: mtDNA + nDNA COMBINED analyses
Downloaded 3 times
Description Alignments used in the mtDNA+nDNA COMBINED analyses (BEAST). Folder includes separate gene alignments, as well as an interleaved file of all genes.
Download mtDNA+nDNA.zip (212.0 Kb)
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Title Alignments: nDNA for NUCLEAR ONLY analyses
Downloaded 2 times
Description Alignments of NUCLEAR loci used for NUCLEAR ONLY analyses (BEAST). Folder includes individual locus alignments, as well as a single interleaved alignment file of all loci.
Download nDNA.zip (90.41 Kb)
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Title TESS: Mass Extinction Bayes factors GIF
Downloaded 8 times
Description GIF (open in internet browser) of support for and timing of a mass extinction event across 100 posterior BEAST trees.
Download Mass Extinction BF.gif (5.420 Mb)
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Title TESS.Analysis Loop (R code)
Downloaded 15 times
Description This R code provides the functions necessary to run a TESS analysis, investigating the timing and frequency of mass extinction and diversification shifts across a sample of trees, and then summarize the data. It also includes functions for model comparison among constant rate and variable rate models with and without mass extinction, using stepping stone sampling and Bayes factors for support.
Download DRYAD.TESS.Analysis Loop.R (24.03 Kb)
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Title TreePar R Code
Downloaded 13 times
Description This is R code to run the TreePar analysis (optimizing the likelihood on speciation/extinction shifts). Also included is a loop for comparing TreePar models across a set of trees.
Download DRYAD.Pygopodoidea.TreePar.R (4.048 Kb)
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Title BioGeoBEARS.Pygopodoidea
Downloaded 5 times
Description BioGeoBEARS distribution area matrix and MCC tree used.
Download DRYAD.BioGeoBEARS.Pygopodoidea.zip (6.546 Kb)
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Title GeoSSE (R code & files)
Downloaded 9 times
Description This folder includes the R code/functions to recreate our GeoSSE analyses on biome diversification/transition rates. Included are the 5 GeoSSE binary distribution coding files.
Download DRYAD.GeoSSE.files.zip (15.03 Kb)
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Title BEAST MCC tree Pygopodoidea
Downloaded 6 times
Description The MCC tree of the Pygopodoidea used for GeoSSE and BioGeoBEARS analyses.
Download Pygopodoidea.tre (6.33 Kb)
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When using this data, please cite the original publication:

Brennan IG, Oliver PM (2017) Mass turnover and recovery dynamics of a diverse Australian continental radiation. Evolution 71(5): 1352–1365. http://dx.doi.org/10.1111/evo.13207

Additionally, please cite the Dryad data package:

Brennan IG, Oliver PM (2017) Data from: Mass turnover and recovery dynamics of a diverse Australian continental radiation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.991p6
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