DOI: 10.5061/dryad.cb8gd26
title: Data from: Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

description: Environmental change can create opportunities for increased rates of
 lineage diversification, but continued species accumulation has been
 hypothesized to lead to slowdowns via competitive exclusion and niche
 partitioning. Such density-dependent models imply tight linkages between
 diversification and trait evolution, but there are plausible alternative
 models. Little is known about the association between diversification and
 key ecological and phenotypic traits at broad phylogenetic and spatial
 scales. Do trait evolutionary rates coincide with rates of
 diversification, are there lags among these rates, or is diversification
 niche-neutral? To address these questions, we combine a deeply sampled
 phylogeny for a major flowering plant clade-Saxifragales-with phenotype
 and niche data to examine temporal patterns of evolutionary rates. The
 considerable phenotypic and habitat diversity of Saxifragales is greatest
 in temperate biomes. Global expansion of these habitats since the
 mid-Miocene provided ecological opportunities that, with density-dependent
 adaptive radiation, should result in simultaneous rate increases for
 diversification, niche, and phenotype, followed by decreases with habitat
 saturation. Instead, these rates have significantly different timings,
 with increases in diversification occurring at the mid-Miocene Climatic
 Optimum (~15 mya), followed by increases in niche and phenotypic
 evolutionary rates by ~5 mya; all rates increase exponentially to the
 present. We attribute this surprising lack of temporal coincidence to
 initial niche-neutral diversification followed by ecological and
 phenotypic divergence coincident with more extreme cold and dry habitats
 that proliferated into the Pleistocene. A lack of density-dependence
 contrasts with investigations of other cosmopolitan lineages, suggesting
 alternative patterns may be common in the diversification of temperate
 lineages.
description: Maximum credibility
 BEAST treeMaximum credibility tree
 from the BEAST analysis. Node values represent medians.combined.median.maxcred.treCongruified BEAST tree -- matched to environmental data"Congruified" BEAST tree. Result from treePL with BEAST dates used as node constraints. This tree contains taxa matched with environmental data.intree.dated.crossvalidated.occurrencematched.treCongruified BEAST tree -- matched to trait data"Congruified" BEAST tree. Result from treePL with BEAST dates used as node constraints. This tree contains taxa matched with trait data.intree.dated.crossvalidated.traitmatched.tretreePL tree -- matched to environmental datatreePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with environmental data.intree.dated.crossvalidated.occurrencematched.tretreePL tree -- matched to trait datatreePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with trait data.intree.dated.crossvalidated.traitmatched.treNiche phyloPCA PC1 -- BEAST congruifiedFirst axis of phyloPCA of environmental data using BEAST congruified tree.niche_phylopca_PC1.txtTrait phyloMDS PC1 -- BEAST congruifiedFirst axis of phyloMDS of trait data using BEAST congruified tree.trait_phylomds_PC1.txtNiche phyloPCA PC1 -- treePLFirst axis of phyloPCA of environmental data using treePL tree.niche_phylopca_PC1.txtTrait phyloMDS PC1 -- treePLFirst axis of phyloMDS of trait data using treePL tree.trait_phylomds_PC1.txtExaML phylogenomic treeExaML topology from phylogenomic data, used as a constraint for the GenBank supermatrix tree search. Node labels represent bootstrap frequencies.RAxML_bipartitions.bootstrap_besttree.treConcatenated matrix -- phylogenomic dataConcatenated matrix for phylogenomic data. The matrix has been rearranged so that codon positions are in consecutive partitions.concatenated_protein_aware_90stripped.phyPartition file for phylogenomic dataPartition file for phylogenomic data. Partitions represent consecutive codon positions.partition.90stripped.txtConcatenated supermatrix -- GenBank dataConcatenated GenBank data supermatrix.FINAL_concatenation.curated.curated.namematched.phyPartition file for GenBank supermatrixPartition file for GenBank supermatrix. Partitions represent gene boundaries.partition_file.txtMean latitudes per speciesSpecies latitude data for trait-associated diversification analysis.mean_latitudes.treematched.tsvBiogeographic dataBiogeographic data for trait-associated diversification analysis.biogeo_trait_oneregiononly_environment_matched.txtMean elevation per speciesSpecies elevation data for trait-associated diversification analysis.character21_runID-var_1.txtSaxifragales floristic traitsMatrix with Saxifragales traits extracted from floras.Saxifragales trait data sheet.xlsxExtracted environmental dataExtracted Saxifragales environmental data. Each variable is stored in a different file; for a guide to variable numbering see the excel sheet in this deposition.35_environmental_variables.zipGuide to variable numerical codingGuide to variable numerical coding.saxifragales_variable_explain.xlsxGene tree alignmentsGene tree alignment files for phylogenomic data.alignments_genetrees.zipGene tree alignment partition filesGene tree alignment partition files for phylogenomic data. Partitions represent codon positions.partition_files_genetrees.zipGene treesGene trees inferred in RAxML. Node labels represent bootstrap frequencies.besttrees_bipartitionfrequencies_genetrees.zipASTRAL treeInferred coalescent tree. Gene trees only included taxa with at least 10% gene representation.best_astral_tree.atleasttenpercenttaxa.treBAMM diversification edata object -- BEASTBAMM edata object for diversification using the BEAST congruified tree. This is an Rdata file to be loaded in R.edata_diversification_ladderized.RdataBAMM phenotype edata object -- BEAST: part ABAMM 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.edata_phenotype_NEWrep4_75percentburnin_ladderized.Rdata.part_aBAMM phenotype edata object -- BEAST: part BBAMM 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.edata_phenotype_NEWrep4_75percentburnin_ladderized.Rdata.part_bBAMM phenotype edata object -- BEAST: part CBAMM 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.edata_phenotype_NEWrep4_75percentburnin_ladderized.Rdata.part_cBAMM niche edata object -- BEASTBAMM edata object for niche using the BEAST congruified tree. This is an Rdata file to be loaded in R.edata_environment_ladderized.RdataBAMM diversification edata object -- treePLBAMM edata object for diversification using the treePL tree. This is an Rdata file to be loaded in R.edata_diversification_ladderized.RdataBAMM phenotype edata object -- treePLBAMM edata object for phenotype using the treePL tree. This is an Rdata file to be loaded in R.edata_phenotype_ladderized.RdataBAMM niche edata object -- treePLBAMM edata object for niche using the treePL tree. This is an Rdata file to be loaded in R.edata_environment_ladderized.RdataSupermatrix bootstrap trees -- BEASTSaxifragales supermatrix bootstrap trees with branch lengths, dated using the BEAST-congruified approach. Used to assess the sensitivity of BAMM results to phylogenetic uncertainty.bootstraps.forcedultra.zipSupermatrix bootstrap trees -- treePLSaxifragales supermatrix bootstrap trees with branch lengths, dated using the treePL approach. Used to assess the sensitivity of BAMM results to phylogenetic uncertainty.bootstraps.forcedultra.zipOccurrence recordsA zip archive of all occurrence records used in this study in Maxent format, one file per species.all_occurrences.zip