Data from: Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians

Pyron RA

Date Published: June 17, 2014

DOI: http://dx.doi.org/10.5061/dryad.jm453

 

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Title Amphibia_2_9
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Description Matrix of 3309 amphibian species sampled for up to 12 genes (12809bp total) and one outgroup.
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Title Amphibia_Models
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Description Model file for the Amphibia_2_9 matrix, describing the 12 genes and their partitions.
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Title amph_shl
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Description NNI-optimized ML tree resulting from Amphibia_2_9 matrix, with SHL support values.
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Title amph_shl_dates
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Description Dated version of the NNI-optimized ML tree with SHL support values, used for biogeographic reconstructions.
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Title amph_clade_areas
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Description Data illustrated in Figure 1: clade names, clade ages, number of areas occupied, and number of species in clade.
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Title amph_ecoregions
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Description Taxonomic database listing 6576 species, their family, and regions of occurrence.
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Title amph_shl_dates_trim.tre
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Description MESQUITE-format NEXUS file containing the tree pruned to the 3126 species inhabiting one ecoregion, with Mk1 estimates of ancestral states (Appendix S5).
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Title caecilian_ecoregions
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Description Ecoregion data for BioGeoBEARS analysis of caecilian subtree.
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Title caecilian_ecoregions
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Description R Code for BioGeoBEARS run on caecilian subtree (Figure 1).
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Title amph_shl_dates_caecilians
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Description Caecilian subtree for BioGeoBEARS analysis (Figure 1).
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Title caecilian_DEC_M0_unconstrained_v1
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Description Output for DEC model from caecilian subtree analysis.
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Title caecilian_DECJ_M0_unconstrained_v1
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Description Output for DECj model from caecilian subtree analysis.
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Title salamander_ecoregions
Downloaded 41 times
Description Salamander ecoregion data for 6-area BioGeoBEARS run. Code given below.
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Title salamander_ecoregions
Downloaded 44 times
Description R Code for BioGeoBEARS analysis of salamander subtree with 6 areas. Data produced are given below.
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Title amph_shl_dates_salamanders
Downloaded 34 times
Description Salamander subtree from NNI-optimized, SHL-supported ML tree. Used for 6-area salamander analysis in BioGeoBEARS.
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Title salamander_DEC_M0_unconstrained_v1
Downloaded 21 times
Description R data object produced by R code given above, from 6-area salamander-subtree analysis in BioGeoBEARS. Load to view ancestral area estimates.
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Title salamander_DECJ_M0_unconstrained_v1
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Description R data object from DECj analysis of 6-area salamander subtree in BioGeoBEARS. Load for ancestral-area estimates.
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Title frog_ecoregions_reduced
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Description Ecoregion data for 2875-taxon subtree analysis of frogs (Appendix S3).
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Title frog_ecoregions_reduced
Downloaded 224 times
Description R Code for frog subtree analysis using BioGeoBEARS (Appendix S3).
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Title amph_shl_dates_frogs
Downloaded 95 times
Description 2875-taxon subtree for frogs (Appendix S3).
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Title frog_DEC_M0_unconstrained_v1
Downloaded 22 times
Description R Data object containing results from DEC analysis of frog subtree in BioGeoBEARS (Appendix S3). Load this for ancestral-state estimates (see R code above).
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Title frog_DECJ_M0_unconstrained_v1
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Description R Data object from DECj model of frog subtree. Load for ancestral-state estimates.
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Title amph_ecoregions_reduced
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Description Ecoregion data for 3309-taxon whole-tree analysis of amphibians in BioGeoBEARS (Appendix S4).
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Title amph_ecoregions_reduced
Downloaded 53 times
Description R code for whole-tree analysis of amphibians (Appendix S4) in BioGeoBEARS.
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Title amph_shl_dates_trim
Downloaded 44 times
Description 3309-taxon amphibian tree for whole-tree analysis using BioGeoBEARS. This tree is "amph_shl_dates.tre" trimmed of the outgroup Homo_sapiens.
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Title amph_DEC_M0_unconstrained_v1
Downloaded 21 times
Description R Data object from DEC analysis of amphibians (Appendix S4).
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Title amph_DECJ_M0_unconstrained_v1
Downloaded 20 times
Description R Data object for DECj analysis of amphibians as a whole (Appendix S4). Load for ancestral-state estimates.
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Title New_Names
Downloaded 64 times
Description The taxonomic database used here is from the 2009 update of AmphibiaWeb (http://www.amphibiaweb.org/). The genus-level taxonomy of amphibians is in constant flux recently, and many genera have changed in the last few years. This document translates the taxon labels in the 3309-taxon matrix into the name appearing in a 2014 update of AmphibiaWeb. Notably, the genera _Rana_ and _Bufo_ were broken up by Frost et al. (2006) and others, and the monophyly of these groups is actually supported in the current tree using their names. Some other genera are still not monophyletic, even using recently updated names. However, for those wishing to use the trees presented here for comparative analyses, this chart shows the most recent "correct" names that should be used, and for which data may have been gathered.
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Title README
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Description Guide to the supplemental materials.
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Title Pyron_Appendix_S1
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Description Appendix S1: caecilian subtree (DEC/DECj).
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Title Pyron_Appendix_S2
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Description Appendix S2: salamander subtree (DEC/DECj).
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Title Pyron_Appendix_S3
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Description Appendix S3: frog subtree (DEC/DECj).
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Title Pyron_Appendix_S4
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Description Appendix S4: whole-tree analysis of amphibians (DEC/DECj).
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Title Pyron_Appendix_S5
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Description Appendix S5: whole-tree analysis of amphibians (Mk1: MESQUITE).
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When using this data, please cite the original publication:

Pyron RA (2014) Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians. Systematic Biology 63(5): 779-797. http://dx.doi.org/10.1093/sysbio/syu042

Additionally, please cite the Dryad data package:

Pyron RA (2014) Data from: Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.jm453
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