DOI: 10.5281/zenodo.14586022
title: Dataset for "Paleo-biome dynamics shaped a large Gondwanan plant radiation"

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

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

Dataset S2 (separate file). 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 (separate file). Sheet 1. Sample IDs and herbarium accession numbers. Sheet 2. Fossil calibration table including 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 (.csv format). 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. 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 7. Biome occupancy table for all Grevilleoideae species derived from occurrence records and modified Koppen-Geiger biome classification (.csv format). Values refer to the proportion of unique cells (0.1 x 0.1 degree) that occurrence records are found in each biome or region. Sheet 8. 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 Caledoina, k = New Zealand. Sheet 9. 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 Caledoina, k = New Zealand. Sheet 10. 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 Caledoina, k = New Zealand. Sheet 11. Branch specific estimates of diversification rate from CLaDS, geographic states from BioGeoBEARS and predictor variables for the phylogenetic generlised linear mixed model (PGLMM) including biome area, time since first biome occupation, standing biome diversity, and biome shifting. Sheet 12. The age of the first appearance of climate variables in climate space based on a principal component analysis of mean annual temperature, mean annual precipitation, temperature seasonality, and precipitation seasonality, of paleotemperature and precipitation from Valdes et al. (2019). (.xlsx format).

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

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

Dataset S6 (separate file). Modified Koppen-Geiger biomes estimated from monthly temperature and precipitation values at 20 Ma intervals from 120 Ma to 20 Ma. The interval for 20-0 is given by modified Koppen-Geiger biomes from the present-day (.ncf format). Values legend: 1 = tropical, 2 = subtropical and temperate, 3 = Mediterranean, 4 = semi-arid, 5 = arid, 6 = Polar.

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

Dataset S8 (separate file). Cleaned DNA alignments (.fasta format) from 458 Anchored Hybrid Enrichment loci for all samples of Grevilleoidaee 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.  

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

Dataset S10 (separate file). Dated phylogeny of Grevilleoideae pruned to species level (.TRE format).  

Dataset S11 (separate file). 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). 

Dataset S12 (separate file). Monthly temperature and precipitation values at 20 Ma intervals from 120 Ma to 0 Ma from Valdes et al. 2019 (.nc format).