Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

Folk RA, Stubbs RL, Mort ME, Cellinese N, Allen JM, Soltis PS, Soltis DE, Guralnick RP

Date Published: May 14, 2019

DOI: https://doi.org/10.5061/dryad.cb8gd26

Files in this package

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 Maximum credibility BEAST tree
Downloaded 5 times
Description Maximum credibility tree from the BEAST analysis. Node values represent medians.
Download combined.median.maxcred.tre (98.97 Kb)
Details View File Details
Title Congruified BEAST tree -- matched to environmental data
Downloaded 1 time
Description "Congruified" BEAST tree. Result from treePL with BEAST dates used as node constraints. This tree contains taxa matched with environmental data.
Download intree.dated.crossvalidated.occurrencematched.tre (62.59 Kb)
Details View File Details
Title Congruified BEAST tree -- matched to trait data
Downloaded 1 time
Description "Congruified" BEAST tree. Result from treePL with BEAST dates used as node constraints. This tree contains taxa matched with trait data.
Download intree.dated.crossvalidated.traitmatched.tre (59.80 Kb)
Details View File Details
Title treePL tree -- matched to environmental data
Downloaded 2 times
Description treePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with environmental data.
Download intree.dated.crossvalidated.occurrencematched.tre (58.51 Kb)
Details View File Details
Title treePL tree -- matched to trait data
Downloaded 1 time
Description treePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with trait data.
Download intree.dated.crossvalidated.traitmatched.tre (55.81 Kb)
Details View File Details
Title Niche phyloPCA PC1 -- BEAST congruified
Downloaded 1 time
Description First axis of phyloPCA of environmental data using BEAST congruified tree.
Download niche_phylopca_PC1.txt (54.49 Kb)
Details View File Details
Title Trait phyloMDS PC1 -- BEAST congruified
Downloaded 1 time
Description First axis of phyloMDS of trait data using BEAST congruified tree.
Download trait_phylomds_PC1.txt (52.12 Kb)
Details View File Details
Title Niche phyloPCA PC1 -- treePL
Downloaded 1 time
Description First axis of phyloPCA of environmental data using treePL tree.
Download niche_phylopca_PC1.txt (57.36 Kb)
Details View File Details
Title Trait phyloMDS PC1 -- treePL
Downloaded 1 time
Description First axis of phyloMDS of trait data using treePL tree.
Download trait_phylomds_PC1.txt (55.70 Kb)
Details View File Details
Title ExaML phylogenomic tree
Downloaded 1 time
Description ExaML topology from phylogenomic data, used as a constraint for the GenBank supermatrix tree search. Node labels represent bootstrap frequencies.
Download RAxML_bipartitions.bootstrap_besttree.tre (43.98 Kb)
Details View File Details
Title Concatenated matrix -- phylogenomic data
Downloaded 1 time
Description Concatenated matrix for phylogenomic data. The matrix has been rearranged so that codon positions are in consecutive partitions.
Download concatenated_protein_aware_90stripped.phy (205.8 Mb)
Details View File Details
Title Partition file for phylogenomic data
Downloaded 1 time
Description Partition file for phylogenomic data. Partitions represent consecutive codon positions.
Download partition.90stripped.txt (67 bytes)
Details View File Details
Title Concatenated supermatrix -- GenBank data
Downloaded 2 times
Description Concatenated GenBank data supermatrix.
Download FINAL_concatenation.curated.curated.namem...ed.phy (74.03 Mb)
Details View File Details
Title Partition file for GenBank supermatrix
Downloaded 2 times
Description Partition file for GenBank supermatrix. Partitions represent gene boundaries.
Download partition_file.txt (590 bytes)
Details View File Details
Title Mean latitudes per species
Downloaded 1 time
Description Species latitude data for trait-associated diversification analysis.
Download mean_latitudes.treematched.tsv (40.92 Kb)
Details View File Details
Title Biogeographic data
Downloaded 1 time
Description Biogeographic data for trait-associated diversification analysis.
Download biogeo_trait_oneregiononly_environment_matched.txt (32.17 Kb)
Details View File Details
Title Mean elevation per species
Downloaded 1 time
Description Species elevation data for trait-associated diversification analysis.
Download character21_runID-var_1.txt (47.26 Kb)
Details View File Details
Title Saxifragales floristic traits
Downloaded 1 time
Description Matrix with Saxifragales traits extracted from floras.
Download Saxifragales trait data sheet.xlsx (419.1 Kb)
Details View File Details
Title Extracted environmental data
Downloaded 1 time
Description Extracted Saxifragales environmental data. Each variable is stored in a different file; for a guide to variable numbering see the excel sheet in this deposition.
Download 35_environmental_variables.zip (605.6 Kb)
Details View File Details
Title Guide to variable numerical coding
Downloaded 1 time
Description Guide to variable numerical coding.
Download saxifragales_variable_explain.xlsx (33.32 Kb)
Details View File Details
Title Gene tree alignments
Downloaded 1 time
Description Gene tree alignment files for phylogenomic data.
Download alignments_genetrees.zip (11.21 Mb)
Details View File Details
Title Gene tree alignment partition files
Downloaded 1 time
Description Gene tree alignment partition files for phylogenomic data. Partitions represent codon positions.
Download partition_files_genetrees.zip (267.5 Kb)
Details View File Details
Title Gene trees
Downloaded 1 time
Description Gene trees inferred in RAxML. Node labels represent bootstrap frequencies.
Download besttrees_bipartitionfrequencies_genetrees.zip (2.509 Mb)
Details View File Details
Title ASTRAL tree
Downloaded 1 time
Description Inferred coalescent tree. Gene trees only included taxa with at least 10% gene representation.
Download best_astral_tree.atleasttenpercenttaxa.tre (25.70 Kb)
Details View File Details
Title BAMM diversification edata object -- BEAST
Downloaded 1 time
Description BAMM edata object for diversification using the BEAST congruified tree. This is an Rdata file to be loaded in R.
Download edata_diversification_ladderized.Rdata (70.38 Mb)
Details View File Details
Title BAMM phenotype edata object -- BEAST: part A
Downloaded 1 time
Description BAMM edata object for phenotype using the BEAST congruified tree. This is an Rdata file to be loaded in R that has been divided into three parts. Concatenate file parts A, B, and C before use.
Download edata_phenotype_NEWrep4_75percentburnin_la...art_a (629.1 Mb)
Details View File Details
Title BAMM phenotype edata object -- BEAST: part B
Downloaded 1 time
Description BAMM edata object for phenotype using the BEAST congruified tree. This is an Rdata file to be loaded in R that has been divided into three parts. Concatenate file parts A, B, and C before use.
Download edata_phenotype_NEWrep4_75percentburnin_la...art_b (629.1 Mb)
Details View File Details
Title BAMM phenotype edata object -- BEAST: part C
Downloaded 1 time
Description BAMM edata object for phenotype using the BEAST congruified tree. This is an Rdata file to be loaded in R that has been divided into three parts. Concatenate file parts A, B, and C before use.
Download edata_phenotype_NEWrep4_75percentburnin_la...art_c (263.2 Mb)
Details View File Details
Title BAMM niche edata object -- BEAST
Downloaded 1 time
Description BAMM edata object for niche using the BEAST congruified tree. This is an Rdata file to be loaded in R.
Download edata_environment_ladderized.Rdata (708.8 Mb)
Details View File Details
Title BAMM diversification edata object -- treePL
Downloaded 1 time
Description BAMM edata object for diversification using the treePL tree. This is an Rdata file to be loaded in R.
Download edata_diversification_ladderized.Rdata (131.6 Mb)
Details View File Details
Title BAMM phenotype edata object -- treePL
Downloaded 1 time
Description BAMM edata object for phenotype using the treePL tree. This is an Rdata file to be loaded in R.
Download edata_phenotype_ladderized.Rdata (258.2 Mb)
Details View File Details
Title BAMM niche edata object -- treePL
Downloaded 1 time
Description BAMM edata object for niche using the treePL tree. This is an Rdata file to be loaded in R.
Download edata_environment_ladderized.Rdata (699.6 Mb)
Details View File Details
Title Supermatrix bootstrap trees -- BEAST
Downloaded 1 time
Description Saxifragales supermatrix bootstrap trees with branch lengths, dated using the BEAST-congruified approach. Used to assess the sensitivity of BAMM results to phylogenetic uncertainty.
Download bootstraps.forcedultra.zip (1.211 Mb)
Details View File Details
Title Supermatrix bootstrap trees -- treePL
Downloaded 1 time
Description Saxifragales supermatrix bootstrap trees with branch lengths, dated using the treePL approach. Used to assess the sensitivity of BAMM results to phylogenetic uncertainty.
Download bootstraps.forcedultra.zip (1.220 Mb)
Details View File Details
Title Occurrence records
Downloaded 1 time
Description A zip archive of all occurrence records used in this study in Maxent format, one file per species.
Download all_occurrences.zip (5.871 Mb)
Details View File Details

When using this data, please cite the original publication:

Folk RA, Stubbs RL, Mort ME, Cellinese N, Allen JM, Soltis PS, Soltis DE, Guralnick RP (2019) Rates of niche and phenotype evolution lag behind diversification in a temperate radiation. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1817999116

Additionally, please cite the Dryad data package:

Folk RA, Stubbs RL, Mort ME, Cellinese N, Allen JM, Soltis PS, Soltis DE, Guralnick RP (2019) Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation. Dryad Digital Repository. https://doi.org/10.5061/dryad.cb8gd26
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: