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.
Maximum credibility BEAST tree
Maximum credibility tree from the BEAST analysis. Node values represent medians.
combined.median.maxcred.tre
Congruified 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.tre
Congruified 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.tre
treePL tree -- matched to environmental data
treePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with environmental data.
intree.dated.crossvalidated.occurrencematched.tre
treePL tree -- matched to trait data
treePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with trait data.
intree.dated.crossvalidated.traitmatched.tre
Niche phyloPCA PC1 -- BEAST congruified
First axis of phyloPCA of environmental data using BEAST congruified tree.
niche_phylopca_PC1.txt
Trait phyloMDS PC1 -- BEAST congruified
First axis of phyloMDS of trait data using BEAST congruified tree.
trait_phylomds_PC1.txt
Niche phyloPCA PC1 -- treePL
First axis of phyloPCA of environmental data using treePL tree.
niche_phylopca_PC1.txt
Trait phyloMDS PC1 -- treePL
First axis of phyloMDS of trait data using treePL tree.
trait_phylomds_PC1.txt
ExaML phylogenomic tree
ExaML topology from phylogenomic data, used as a constraint for the GenBank supermatrix tree search. Node labels represent bootstrap frequencies.
RAxML_bipartitions.bootstrap_besttree.tre
Concatenated matrix -- phylogenomic data
Concatenated matrix for phylogenomic data. The matrix has been rearranged so that codon positions are in consecutive partitions.
concatenated_protein_aware_90stripped.phy
Partition file for phylogenomic data
Partition file for phylogenomic data. Partitions represent consecutive codon positions.
partition.90stripped.txt
Concatenated supermatrix -- GenBank data
Concatenated GenBank data supermatrix.
FINAL_concatenation.curated.curated.namematched.phy
Partition file for GenBank supermatrix
Partition file for GenBank supermatrix. Partitions represent gene boundaries.
partition_file.txt
Mean latitudes per species
Species latitude data for trait-associated diversification analysis.
mean_latitudes.treematched.tsv
Biogeographic data
Biogeographic data for trait-associated diversification analysis.
biogeo_trait_oneregiononly_environment_matched.txt
Mean elevation per species
Species elevation data for trait-associated diversification analysis.
character21_runID-var_1.txt
Saxifragales floristic traits
Matrix with Saxifragales traits extracted from floras.
Saxifragales trait data sheet.xlsx
Extracted environmental data
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.
35_environmental_variables.zip
Guide to variable numerical coding
Guide to variable numerical coding.
saxifragales_variable_explain.xlsx
Gene tree alignments
Gene tree alignment files for phylogenomic data.
alignments_genetrees.zip
Gene tree alignment partition files
Gene tree alignment partition files for phylogenomic data. Partitions represent codon positions.
partition_files_genetrees.zip
Gene trees
Gene trees inferred in RAxML. Node labels represent bootstrap frequencies.
besttrees_bipartitionfrequencies_genetrees.zip
ASTRAL tree
Inferred coalescent tree. Gene trees only included taxa with at least 10% gene representation.
best_astral_tree.atleasttenpercenttaxa.tre
BAMM diversification edata object -- BEAST
BAMM edata object for diversification using the BEAST congruified tree. This is an Rdata file to be loaded in R.
edata_diversification_ladderized.Rdata
BAMM phenotype edata object -- BEAST: part A
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.
edata_phenotype_NEWrep4_75percentburnin_ladderized.Rdata.part_a
BAMM phenotype edata object -- BEAST: part B
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.
edata_phenotype_NEWrep4_75percentburnin_ladderized.Rdata.part_b
BAMM phenotype edata object -- BEAST: part C
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.
edata_phenotype_NEWrep4_75percentburnin_ladderized.Rdata.part_c
BAMM niche edata object -- BEAST
BAMM edata object for niche using the BEAST congruified tree. This is an Rdata file to be loaded in R.
edata_environment_ladderized.Rdata
BAMM diversification edata object -- treePL
BAMM edata object for diversification using the treePL tree. This is an Rdata file to be loaded in R.
edata_diversification_ladderized.Rdata
BAMM phenotype edata object -- treePL
BAMM edata object for phenotype using the treePL tree. This is an Rdata file to be loaded in R.
edata_phenotype_ladderized.Rdata
BAMM niche edata object -- treePL
BAMM edata object for niche using the treePL tree. This is an Rdata file to be loaded in R.
edata_environment_ladderized.Rdata
Supermatrix bootstrap trees -- BEAST
Saxifragales 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.zip
Supermatrix bootstrap trees -- treePL
Saxifragales supermatrix bootstrap trees with branch lengths, dated using the treePL approach. Used to assess the sensitivity of BAMM results to phylogenetic uncertainty.
bootstraps.forcedultra.zip
Occurrence records
A zip archive of all occurrence records used in this study in Maxent format, one file per species.
all_occurrences.zip