Dataset for "Paleo-biome dynamics shaped a large Gondwanan plant radiation"

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).本数据集关联Skeels等人已投稿待审的论文《古生物群动态塑造冈瓦纳植物大类辐射演化》（"Paleo-biome dynamics shaped a large Gondwanan plant radiation"）。 数据集S1（单独文件）：基于458个基因组位点的串联超级矩阵，使用IQ-Tree估算得到的银桦亚科（Grevilleoideae）及选定外类群的系统发育树（.TREE格式）。 数据集S2（单独文件）：基于IQ-Tree对458个基因组位点构建的基因树，采用ASTRAL-III的快捷溯祖分析法估算得到的银桦亚科及选定外类群的系统发育树（.TREE格式）。 数据集S3（单独文件）：共包含12个工作表： 工作表1：样本编号与标本馆馆藏号。 工作表2：化石校准表，包含化石类群名称、产地、系统发育位置、年代、地层学信息及对应支撑文献，同时估算最佳实践得分（.csv格式）。 工作表3：缺失数据、不变位点、采样类群、简约信息位点、比对序列长度及经清理的DNA比对序列的根到枝长距离变异系数（cvr2t）的汇总统计。该表格还包含位点过滤的相关信息，包括完整性、类钟性、蛋白编码信息以及该位点是否用于分化时间测年分析。 工作表4：使用TreeShrink与PhylteR算法在每个位点检测到的异常类群（rogue taxa）数量。 工作表5：本研究中使用的所有银桦亚科物种的清理后出现记录。数据最初来源于澳大利亚生物图集（Atlas of Living Australia，ALA）与全球生物多样性信息设施（Global Biodiversity Information Facility，GBIF），并使用R语言包CoordinateCleaner进行清理。 工作表6：同工作表5，为本研究中使用的所有银桦亚科物种的清理后出现记录。数据最初来源于澳大利亚生物图集（ALA）与全球生物多样性信息设施（GBIF），并使用R语言包CoordinateCleaner进行清理。 工作表7：基于出现记录并经修改的柯本-盖格尔（Koppen-Geiger）生物群分类系统得到的所有银桦亚科物种的生物群占用表（.csv格式）。数值代表出现记录在每个生物群或区域中所占的唯一栅格单元（0.1°×0.1°）比例。 工作表8：生物群间的标准化成对环境距离。数值范围为0至10，分类标签：A=热带，b=亚热带与温带，c=地中海型，d=半干旱，e=干旱，f=南美洲，g=马达加斯加，h=南非好望角，I=热带亚洲，j=新喀里多尼亚，k=新西兰。 工作表9：生物群间的时间分层成对地理距离。数值范围为0至10，时间层从顶部到底部分别为：20-0 Ma、40-20 Ma、60-40 Ma、80-60 Ma、100-80 Ma。分类标签同工作表8。 工作表10：生物群间的时间分层成对连通性。数值范围为0至10，时间层从顶部到底部分别为：20-0 Ma、40-20 Ma、60-40 Ma、80-60 Ma、100-80 Ma。分类标签同工作表8。 工作表11：来自CLaDS的分支特异性分化速率估计、来自BioGeoBEARS的地理状态信息，以及系统发育广义线性混合模型（PGLMM）的预测变量，包括生物群面积、首次占据生物群后的时间、现存生物群多样性以及生物群转移。 工作表12：基于Valdes等人（2019）的古温度与古降水数据，对年均温、年降水量、温度季节性和降水季节性进行主成分分析后得到的气候变量首次出现于气候空间的时间（.xlsx格式）。 数据集S4（单独文件）：基于MCMCTree与ASTRAL-III拓扑结构估算得到的银桦亚科及选定外类群的测年系统发育树（.TREE格式）。 数据集S5（单独文件）：基于MCMCTree与IQ-Tree拓扑结构估算得到的银桦亚科及选定外类群的测年系统发育树（.TREE格式）。 数据集S6（单独文件）：基于120 Ma至20 Ma期间每20 Ma间隔的月均温与月降水量估算得到的修改版柯本-盖格尔生物群。20-0 Ma间隔的生物群数据来自现代的修改版柯本-盖格尔生物群（.ncf格式）。数值图例：1=热带，2=亚热带与温带，3=地中海型，4=半干旱，5=干旱，6=极地。 数据集S7（单独文件）：本研究中使用的所有银桦亚科样本及选定外类群的458个锚定杂交富集位点的原始组装DNA比对序列（.fasta格式）。 数据集S8（单独文件）：本研究中使用的所有银桦亚科样本及选定外类群的458个锚定杂交富集位点的清理后DNA比对序列（.fasta格式）。清理流程使用TAPER工具移除了高缺失率的序列或位点，以及潜在的错误序列或比对错位区域。 数据集S9（单独文件）：基于IQ-Tree对458个基因组位点构建的银桦亚科及选定外类群的基因树系统发育树（.TREE格式）。 数据集S10（单独文件）：修剪至物种级别的银桦亚科测年系统发育树（.TRE格式）。 数据集S11（单独文件）：来自R语言包phytools的simmap格式随机映射图，基于BioGeoBEARS软件的最优拟合扩散-灭绝-分支演化（Dispersal-Extirpation-Cladogenesis，DEC）模型（DEC+w+n，基于古生物群重建的交替状态空间）。 数据集S12（单独文件）：来自Valdes等人2019年研究的120 Ma至0 Ma期间每20 Ma间隔的月均温与月降水量数据（.nc格式）。