Data from: Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians
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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| Downloaded | 185 times |
| Description | Matrix of 3309 amphibian species sampled for up to 12 genes (12809bp total) and one outgroup. |
| Download | Amphibia_2_9.phy (42.47 Mb) |
| Details | View File Details |
| Title | Amphibia_Models |
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| Downloaded | 81 times |
| Description | Model file for the Amphibia_2_9 matrix, describing the 12 genes and their partitions. |
| Download | Amphibia_Models.txt (1.046 Kb) |
| Details | View File Details |
| Title | amph_shl |
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| Downloaded | 152 times |
| Description | NNI-optimized ML tree resulting from Amphibia_2_9 matrix, with SHL support values. |
| Download | amph_shl.tre (218.4 Kb) |
| Details | View File Details |
| Title | amph_shl_dates |
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| Downloaded | 159 times |
| Description | Dated version of the NNI-optimized ML tree with SHL support values, used for biogeographic reconstructions. |
| Download | amph_shl_dates.tre (146.0 Kb) |
| Details | View File Details |
| Title | amph_clade_areas |
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| Downloaded | 122 times |
| Description | Data illustrated in Figure 1: clade names, clade ages, number of areas occupied, and number of species in clade. |
| Download | amph_clade_areas.csv (1.711 Kb) |
| Details | View File Details |
| Title | amph_ecoregions |
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| Downloaded | 98 times |
| Description | Taxonomic database listing 6576 species, their family, and regions of occurrence. |
| Download | amph_ecoregions.csv (257.5 Kb) |
| Details | View File Details |
| Title | amph_shl_dates_trim.tre |
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| Downloaded | 83 times |
| Description | MESQUITE-format NEXUS file containing the tree pruned to the 3126 species inhabiting one ecoregion, with Mk1 estimates of ancestral states (Appendix S5). |
| Download | amph_shl_dates_trim.tre.nex (386.2 Kb) |
| Details | View File Details |
| Title | caecilian_ecoregions |
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| Downloaded | 63 times |
| Description | Ecoregion data for BioGeoBEARS analysis of caecilian subtree. |
| Download | caecilian_ecoregions.data (1.705 Kb) |
| Details | View File Details |
| Title | caecilian_ecoregions |
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| Downloaded | 153 times |
| Description | R Code for BioGeoBEARS run on caecilian subtree (Figure 1). |
| Download | caecilian_ecoregions.R (12.67 Kb) |
| Details | View File Details |
| Title | amph_shl_dates_caecilians |
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| Downloaded | 44 times |
| Description | Caecilian subtree for BioGeoBEARS analysis (Figure 1). |
| Download | amph_shl_dates_caecilians.tre (2.515 Kb) |
| Details | View File Details |
| Title | caecilian_DEC_M0_unconstrained_v1 |
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| Downloaded | 35 times |
| Description | Output for DEC model from caecilian subtree analysis. |
| Download | caecilian_DEC_M0_unconstrained_v1.Rdata (64.59 Kb) |
| Details | View File Details |
| Title | caecilian_DECJ_M0_unconstrained_v1 |
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| Downloaded | 41 times |
| Description | Output for DECj model from caecilian subtree analysis. |
| Download | caecilian_DECJ_M0_unconstrained_v1.Rdata (64.71 Kb) |
| Details | View File Details |
| Title | salamander_ecoregions |
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| Downloaded | 50 times |
| Description | Salamander ecoregion data for 6-area BioGeoBEARS run. Code given below. |
| Download | salamander_ecoregions.data (13.79 Kb) |
| Details | View File Details |
| Title | salamander_ecoregions |
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| Downloaded | 53 times |
| Description | R Code for BioGeoBEARS analysis of salamander subtree with 6 areas. Data produced are given below. |
| Download | salamander_ecoregions.R (12.53 Kb) |
| Details | View File Details |
| Title | amph_shl_dates_salamanders |
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| Downloaded | 43 times |
| Description | Salamander subtree from NNI-optimized, SHL-supported ML tree. Used for 6-area salamander analysis in BioGeoBEARS. |
| Download | amph_shl_dates_salamanders.tre (20.62 Kb) |
| Details | View File Details |
| Title | salamander_DEC_M0_unconstrained_v1 |
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| Downloaded | 26 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. |
| Download | salamander_DEC_M0_unconstrained_v1.Rdata (525.7 Kb) |
| Details | View File Details |
| Title | salamander_DECJ_M0_unconstrained_v1 |
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| Downloaded | 26 times |
| Description | R data object from DECj analysis of 6-area salamander subtree in BioGeoBEARS. Load for ancestral-area estimates. |
| Download | salamander_DECJ_M0_unconstrained_v1.Rdata (495.9 Kb) |
| Details | View File Details |
| Title | frog_ecoregions_reduced |
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| Downloaded | 48 times |
| Description | Ecoregion data for 2875-taxon subtree analysis of frogs (Appendix S3). |
| Download | frog_ecoregions_reduced.data (86.07 Kb) |
| Details | View File Details |
| Title | frog_ecoregions_reduced |
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| Downloaded | 257 times |
| Description | R Code for frog subtree analysis using BioGeoBEARS (Appendix S3). |
| Download | frog_ecoregions_reduced.R (12.47 Kb) |
| Details | View File Details |
| Title | amph_shl_dates_frogs |
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| Downloaded | 117 times |
| Description | 2875-taxon subtree for frogs (Appendix S3). |
| Download | amph_shl_dates_frogs.tre (122.0 Kb) |
| Details | View File Details |
| Title | frog_DEC_M0_unconstrained_v1 |
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| Downloaded | 36 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). |
| Download | frog_DEC_M0_unconstrained_v1.Rdata (6.876 Mb) |
| Details | View File Details |
| Title | frog_DECJ_M0_unconstrained_v1 |
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| Downloaded | 26 times |
| Description | R Data object from DECj model of frog subtree. Load for ancestral-state estimates. |
| Download | frog_DECJ_M0_unconstrained_v1.Rdata (6.870 Mb) |
| Details | View File Details |
| Title | amph_ecoregions_reduced |
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| Downloaded | 34 times |
| Description | Ecoregion data for 3309-taxon whole-tree analysis of amphibians in BioGeoBEARS (Appendix S4). |
| Download | amph_ecoregions_reduced.data (102.5 Kb) |
| Details | View File Details |
| Title | amph_ecoregions_reduced |
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| Downloaded | 58 times |
| Description | R code for whole-tree analysis of amphibians (Appendix S4) in BioGeoBEARS. |
| Download | amph_ecoregions_reduced.R (12.73 Kb) |
| Details | View File Details |
| Title | amph_shl_dates_trim |
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| Downloaded | 62 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. |
| Download | amph_shl_dates_trim.tre (144.8 Kb) |
| Details | View File Details |
| Title | amph_DEC_M0_unconstrained_v1 |
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| Downloaded | 24 times |
| Description | R Data object from DEC analysis of amphibians (Appendix S4). |
| Download | amph_DEC_M0_unconstrained_v1.Rdata (8.161 Mb) |
| Details | View File Details |
| Title | amph_DECJ_M0_unconstrained_v1 |
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| Downloaded | 22 times |
| Description | R Data object for DECj analysis of amphibians as a whole (Appendix S4). Load for ancestral-state estimates. |
| Download | amph_DECJ_M0_unconstrained_v1.Rdata (8.151 Mb) |
| Details | View File Details |
| Title | New_Names |
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| Downloaded | 85 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. |
| Download | New_Names.csv (15.67 Kb) |
| Details | View File Details |
| Title | README |
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| Downloaded | 96 times |
| Description | Guide to the supplemental materials. |
| Download | README.txt (2.893 Kb) |
| Details | View File Details |
| Title | Pyron_Appendix_S1 |
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| Downloaded | 86 times |
| Description | Appendix S1: caecilian subtree (DEC/DECj). |
| Download | Pyron_Appendix_S1.pdf (413.9 Kb) |
| Details | View File Details |
| Title | Pyron_Appendix_S2 |
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| Downloaded | 115 times |
| Description | Appendix S2: salamander subtree (DEC/DECj). |
| Download | Pyron_Appendix_S2.pdf (3.367 Mb) |
| Details | View File Details |
| Title | Pyron_Appendix_S3 |
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| Downloaded | 229 times |
| Description | Appendix S3: frog subtree (DEC/DECj). |
| Download | Pyron_Appendix_S3.pdf (21.80 Mb) |
| Details | View File Details |
| Title | Pyron_Appendix_S4 |
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| Downloaded | 204 times |
| Description | Appendix S4: whole-tree analysis of amphibians (DEC/DECj). |
| Download | Pyron_Appendix_S4.pdf (25.38 Mb) |
| Details | View File Details |
| Title | Pyron_Appendix_S5 |
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| Downloaded | 185 times |
| Description | Appendix S5: whole-tree analysis of amphibians (Mk1: MESQUITE). |
| Download | Pyron_Appendix_S5.pdf (9.598 Mb) |
| Details | View File Details |
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