DOI: 10.5281/zenodo.15876271
title: Dataset for "Paleo-biome dynamics shaped a large Gondwanan plant radiation"

description: Datasets associated with Skeels et al., 2025 "Paleo-biome dynamics shaped a large Gondwanan plant radiation". PNAS

Dataset S1. Phylogeny of Grevilleoideae and selected outgroups estimated using a concatenated super-matrix of 458 genomic loci with IQ-Tree (.TREE format).  

Dataset S2. Phylogeny of Grevilleoideae and selected outgroups estimated using a short-cut coalescent approach with ASTRAL-III based on 458 gene trees estimated across genomic loci with IQ-Tree (.TREE format).  

Dataset S3. Sheet 1. Sample IDs and herbarium accession numbers. Sheet 2. Fossil calibration table includes information on the fossil taxon name, locality, phylogenetic placement, age, stratigraphy, and associated references in support of each. We also estimate the best practice score. Sheet 3. Summary statistics for the amount of missing data, invariant sites, taxa sampled, parsimony informative sites, and also alignment length, coefficient of variation in the root-to-tip distance (cvr2t) derived from cleaned DNA alignments. Table also includes information on locus filtering for completeness, clock-likeness, protein coding information and whether the locus was used in the divergence dating analysis. Sheet 4. Number of outliers (“rogue taxa”) detected at each locus using TreeShrink and PhylteR algorithms. Sheet 5. Cleaned occurrence records for all species of Grevilleoideae used in this study. Data originally from the Atlas of Living Australia (ALA) and Global Biodiversity Information Facility (GBIF) and cleaned using the R package CoordinateCleaner. Sheet 6. Biome occupancy table for all Grevilleoideae species derived from occurrence records and modified Koppen-Geiger biome classification. Values refer to the proportion of unique cells (5-arcminute resolution) that occurrence records are found in each biome or region. Sheet 7. Scaled pairwise environmental distances between biomes. Values scaled between 0 and 10. A = tropical, b = subtropical and temperate, c = Mediterranean, d = semi-arid, e = arid, f = South America, g = Madagascar, h = Cape of South Africa, I = Tropical Asia, j = New Caledonia, k = New Zealand. Sheet 8. Time-stratified, pairwise geographic distances between biomes. Values scaled between 0 and 10. Times from top to bottom (20-0 Ma, 40-20 Ma, 60-40 Ma, 80-60 Ma, 100-80 Ma). A = tropical, b = subtropical and temperate, c = Mediterranean, d = semi-arid, e = arid, f = South America, g = Madagascar, h = Cape of South Africa, I = Tropical Asia, j = New Caledonia, k = New Zealand. Sheet 9. Time-stratified, pairwise connectivity between biomes. Values scaled between 0 and 10. Times from top to bottom (20-0 Ma, 40-20 Ma, 60-40 Ma, 80-60 Ma, 100-80 Ma). A = tropical, b = subtropical and temperate, c = Mediterranean, d = semi-arid, e = arid, f = South America, g = Madagascar, h = Cape of South Africa, I = Tropical Asia, j = New Caledonia, k = New Zealand. Sheet 10. Branch specific estimates of diversification rate from CLaDS, geographic states from BioGeoBEARS and predictor variables for the phylogenetic generalized linear mixed model (PGLMM) including biome area, time since first biome occupation, sympatric species richness, and biome shifting. Sheet 11. The age of the first appearance of climate variables and species richness in climate space based on a principal component analysis of mean annual temperature, mean annual precipitation, temperature seasonality, and precipitation seasonality, of paleo-temperature and paleo-precipitation (.xlsx format).

Dataset S4. Dated Phylogeny of Grevilleoideae and selected outgroups estimated using MCMCTree and the ASTRAL-III topology (.TREE format).  

Dataset S5. Dated Phylogeny of Grevilleoideae and selected outgroups estimated using MCMCTree and the IQ-Tree topology (.TREE format).  

Dataset S6. Modified Koppen-Geiger biomes estimated from monthly temperature and precipitation values at 10 Ma intervals from 130 Ma to 10 Ma (19). The interval for 10-0 is given by modified Koppen-Geiger biomes from the present-day (18). Values legend: 1 = tropical, 2 = subtropical and temperate, 3 = Mediterranean, 4 = semi-arid, 5 = arid, 6 = Polar (.ncf format).

Dataset S7. Raw assembled DNA alignments  from 458 Anchored Hybrid Enrichment loci for all samples of Grevilleoideae and selected outgroups used in this study (.fasta format).  

Dataset S8. Cleaned DNA alignments from 458 Anchored Hybrid Enrichment loci for all samples of Grevilleoideae and selected outgroups used in this study. Cleaning used a pipeline which removed sequences or sites with high missing data or potentially erroneous or misaligned locations using TAPER (.fasta format).  

Dataset S9. Gene tree phylogenies of Grevilleoideae and selected outgroups for 458 genomic loci with IQ-Tree (.TREE format).  

Dataset S10. Dated phylogeny of Grevilleoideae pruned to species level (.TREE format).  

Dataset S11. Stochastic maps from best-fitting dispersal-extirpation-cladogenesis (DEC) model from BioGeoBEARS software (DEC+w+n with alternated state-space based on paleobiome reconstruction) in simmap format from the R package phytools (.rds format).