Data from: Phylogenetic inference of reciprocal effects between geographic range evolution and diversification

Goldberg EE, Lancaster LT, Ree RH

Date Published: January 17, 2011

DOI: http://dx.doi.org/10.5061/dryad.8343

 

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Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title habitat character states for Arctostaphylos
Downloaded 122 times
Description 1 = chaparral, 2 = forest, 0 = both
Download arc-states.csv (1.088 Kb)
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Title habitat character states for Ceanothus
Downloaded 84 times
Description 1 = chaparral, 2 = forest, 0 = both
Download cea-states.csv (1.129 Kb)
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Title phylogenetic trees for Arctostaphylos
Downloaded 109 times
Description 1000 trees from the posterior set produced by BEAST
Download arc-trees.tre (2.037 Mb)
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Title phylogenetic trees for Ceanothus
Downloaded 81 times
Description 1000 trees from the posterior set produced by BEAST
Download cea-trees.tre (2.337 Mb)
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Title chaparral analysis script
Downloaded 202 times
Description Fitting the GeoSSE model with this script requires the R package diversitree, written by Rich FitzJohn. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (diversitreeGSE_0.4-5.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. This package is presently undergoing rapid development, so for any new applications, please use the current, improved version of the package, available from: http://cran.r-project.org/web/packages/diversitree/ and http://www.zoology.ubc.ca/prog/diversitree/.
Download chaparral-analysis.R (5.064 Kb)
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Title simulation analysis script
Downloaded 136 times
Description Simulating trees under the GeoSSE model requires the C program SimTreeSDD. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (SimTreeSDD-2009.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. Extensive further development is not planned, but the current version of the package is available from: http://tigger.uic.edu/~eeg/code/code.html. The R package diversitree is also required by this script. See Description for chaparral-analysis.R.
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Title alignment for Arctostaphylos
Downloaded 62 times
Description also contains habitat states and maximum clade credibility tree
Download Arctostaphylos.nex (28.35 Kb)
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Title alignment for Ceanothus
Downloaded 50 times
Description also contains habitat states and maximum clade credibility tree
Download Ceanothus.nex (28.31 Kb)
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Title BEAST input file for Arctostaphylos
Downloaded 63 times
Download ArctostaphylosBeastfile.xml (55.15 Kb)
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Title BEAST input file for Ceanothus
Downloaded 49 times
Download CeanothusBeastfile.xml (42.93 Kb)
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Title arc & cea supplementary table
Downloaded 97 times
Description GenBank accession numbers and habitat encoding notes and references
Download ArcCeaSupplementaryTable.xls (50.17 Kb)
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When using this data, please cite the original publication:

Goldberg EE, Lancaster LT, Ree RH (2011) Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Systematic Biology 60(4): 451-465. http://dx.doi.org/10.1093/sysbio/syr046

Additionally, please cite the Dryad data package:

Goldberg EE, Lancaster LT, Ree RH (2011) Data from: Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8343
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