Data for: Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, varies across neotropical regions

5_rates_through_time.R - R script to partition diversification rates through time by biogeographic area, based on BAMM diverstifcation rates and BioGeoBEARS stochastic mapping. 8_disp_rates.R - R script to calculate dispersal rates between biogeographic areas, based on BioGeoBEARS stochastic mapping output.<br> <br> 9_disp_count_time.R - R script to count dispersal events to and from each area through time, based on BioGeoBEARS stochastic mapping output. area_codes.tab - Area letter coding used for BioGeoBEARS biogeographic analysis. area_dissim_phylo.txt - Distance matrix: Host phylogenetic UniFrac similiarites between biogeographic areas (unscaled). area_dissim_phylo_scaled.txt - Distance matrix: Host phylogenetic UniFrac similiarites between biogeographic areas (scaled).<br> <br> area_dist_geog_raw.txt - Distance matrix: Great circle geographic centroid distance between biogeographic areas (in km).<br> <br> area_dist_geog_scaled.txt - Distance matrix: Great circle geographic centroid distance between biogeographic areas (scaled). area_shapes.zip - Shapefiles for the nine biogeographic areas defined, based on merged areas from Dinerstein et al. 2017, BioScience 67: 534-545. areas_manually.csv - Manual assignment of 590 GenBank/INSDC sequences to biogeographic areas based on associated literature records. backbone_all_accessions_sel.tsv - GenBank/INSDC accession numbers for LSU, rpb1 and rpb2 accessions used for the backbone tree including 322 taxa. backbone_calibrated.nwk - Time-calibrated Russulaceae backbone phylogeny. backbone_TBE.raxml.support - Russulaceae backbone phylogeny annotated with transfer bootstrap expectation. bgb_DEC.Rdata - R object containing inputs and outputs for DEC ancestral area estimation with BioGeoBEARS. bgb_DECw.Rdata - R object containing inputs and outputs for DEC+w ancestral area estimation with BioGeoBEARS.<br> <br> bgb_DECx.Rdata - R object containing inputs and outputs for DEC+x ancestral area estimation with BioGeoBEARS.<br> <br> bgb_DECxw.Rdata - R object containing inputs and outputs for DEC+x+w ancestral area estimation with BioGeoBEARS. clade1_Russula_TBE.raxml.support - Russula subclade ITS phylogeny, annotated with transfer bootstrap expectation. clade2_LactariusMultifurca_TBE.raxml.support - Lactarius-Multifurca subclade ITS phylogeny, annotated with transfer bootstrap expectation. clade3_Lactifluus_TBE.raxml.support - Lactifluus subclade ITS phylogeny, annotated with transfer bootstrap expectation. disp_counts_focal.tab - Dispersal counts to and from each focal area through time, based on BioGeoBEARS stochastic mapping output. disp_counts_sam_afr.tab - Dispersal counts between Afrotopics and lowland tropical S. America through time, based on BioGeoBEARS stochastic mapping output. disp_matrix_025.txt - Dispersal rates between biogeographic areas (2.5% quantiles), based on BioGeoBEARS stochastic mapping output. disp_matrix_975.txt - Dispersal rates between biogeographic areas (97.5% quantiles), based on BioGeoBEARS stochastic mapping output. disp_matrix_mean.txt - Dispersal rates between biogeographic areas (means), based on BioGeoBEARS stochastic mapping output. event_data_1.txt - Posterior samples of diversification rate regimes estimated with BAMM. div_rates_per_area_025.tsv - Diversification rates through time (2.5% quantiles) partitioned by biogeographic area, based on BAMM diversification rates and BioGeoBEARS stochastic mapping. div_rates_per_area_975.tsv - Diversification rates through time (97.5% quantiles) partitioned by biogeographic area, based on BAMM diversification rates and BioGeoBEARS stochastic mapping. div_rates_per_area_median.tsv - Diversification rates through time (means) partitioned by biogeographic area, based on BAMM diversification rates and BioGeoBEARS stochastic mapping. ITS_sequences_OTUs.tsv - Metadata for all 29,739 ITS sequences used in the study. "accession": GenBank/INSDC or UNITE accession number; "specimen": specimen number, for newly generate sequences; "taxon": specimen identification; "New": whether ITS sequences was generated for the study (*); "OTU": name of cluster/OTU, if not the sequence accession itself (*); "In_tree": whether sequence is represented in the Russulaceae supertree after filtering steps; "area": biogeographic area assigned; "host": host lineage assigned. mcmc_out_1.txt - BAMM posterior sample characteristics. RES_ana_events_tables.Rdata - BioGeoBEARS DEC+x+w stochastic maps (anagenetic events). RES_clado_events_tables.Rdata - BioGeoBEARS DEC+x+w stochastic maps (cladogenetic events). supertree_calibrated.nwk - Combined Russulaceae supertree. tree_calibrated_clade1_Russula.nwk - Time-calibrated Russula subclade ITS backbone phylogeny. tree_calibrated_clade2_LactariusMultifurca.nwk - Time-calibrated Lactarius-Multifurca subclade ITS backbone phylogeny. tree_calibrated_clade3_Lactifluus.nwk - Time-calibrated Lactifluus subclade ITS backbone phylogeny.5_rates_through_time.R：用于按生物地理区域划分时间维度分化速率的R脚本，基于BAMM分化速率与BioGeoBEARS随机映射（BioGeoBEARS stochastic mapping）结果构建。 8_disp_rates.R：用于计算不同生物地理区域间扩散速率的R脚本，基于BioGeoBEARS随机映射输出结果生成。 9_disp_count_time.R：用于统计各区域间随时间变化的迁入与迁出扩散事件数量的R脚本，基于BioGeoBEARS随机映射输出结果生成。 area_codes.tab：BioGeoBEARS生物地理分析中使用的区域字母编码表。 area_dissim_phylo.txt：距离矩阵文件，记录各生物地理区域间的宿主系统发育UniFrac相似性（未标准化）。 area_dissim_phylo_scaled.txt：距离矩阵文件，记录各生物地理区域间的宿主系统发育UniFrac相似性（已标准化）。 area_dist_geog_raw.txt：距离矩阵文件，记录各生物地理区域间的地理质心大圆距离（单位：千米）。 area_dist_geog_scaled.txt：距离矩阵文件，记录各生物地理区域间的地理质心大圆距离（已标准化）。 area_shapes.zip：包含9个预设生物地理区域的矢量形状文件，基于Dinerstein等人2017年发表于《BioScience》第67卷534-545页的合并区域数据集。 areas_manually.csv：将590条GenBank/INSDC序列依据相关文献记录手动分配至对应生物地理区域的对照表。 backbone_all_accessions_sel.tsv：用于构建包含322个分类单元的主干系统发育树的LSU、rpb1及rpb2基因序列的GenBank/INSDC登录号列表。 backbone_calibrated.nwk：经时间校准的红菇科（Russulaceae）主干系统发育树。 backbone_TBE.raxml.support：带有转移Bootstrap期望（transfer bootstrap expectation, TBE）注释的红菇科主干系统发育树。 bgb_DEC.Rdata：包含BioGeoBEARS进行DEC祖先区域推断（DEC ancestral area estimation）的输入与输出结果的R数据对象。 bgb_DECw.Rdata：包含BioGeoBEARS进行DEC+w祖先区域推断的输入与输出结果的R数据对象。 bgb_DECx.Rdata：包含BioGeoBEARS进行DEC+x祖先区域推断的输入与输出结果的R数据对象。 bgb_DECxw.Rdata：包含BioGeoBEARS进行DEC+x+w祖先区域推断的输入与输出结果的R数据对象。 clade1_Russula_TBE.raxml.support：带有转移Bootstrap期望注释的红菇亚分支（Russula subclade）ITS（internal transcribed spacer）系统发育树。 clade2_LactariusMultifurca_TBE.raxml.support：带有转移Bootstrap期望注释的乳菇-多枝菇亚分支（Lactarius-Multifurca subclade）ITS系统发育树。 clade3_Lactifluus_TBE.raxml.support：带有转移Bootstrap期望注释的乳菇属（Lactifluus）亚分支ITS系统发育树。 disp_counts_focal.tab：基于BioGeoBEARS随机映射输出结果，统计各目标区域随时间变化的迁入与迁出扩散事件数量的对照表。 disp_counts_sam_afr.tab：基于BioGeoBEARS随机映射输出结果，统计非洲热带区与低地热带南美洲间随时间变化的扩散事件数量的对照表。 disp_matrix_025.txt：基于BioGeoBEARS随机映射输出结果，记录各生物地理区域间扩散速率（2.5%分位数）的矩阵文件。 disp_matrix_975.txt：基于BioGeoBEARS随机映射输出结果，记录各生物地理区域间扩散速率（97.5%分位数）的矩阵文件。 disp_matrix_mean.txt：基于BioGeoBEARS随机映射输出结果，记录各生物地理区域间扩散速率（均值）的矩阵文件。 event_data_1.txt：通过BAMM估计得到的分化速率制度的后验样本文件。 div_rates_per_area_025.tsv：基于BAMM分化速率与BioGeoBEARS随机映射结果，按生物地理区域划分的时间维度分化速率（2.5%分位数）文件。 div_rates_per_area_975.tsv：基于BAMM分化速率与BioGeoBEARS随机映射结果，按生物地理区域划分的时间维度分化速率（97.5%分位数）文件。 div_rates_per_area_median.tsv：基于BAMM分化速率与BioGeoBEARS随机映射结果，按生物地理区域划分的时间维度分化速率（均值）文件。 ITS_sequences_OTUs.tsv：本研究使用的全部29739条ITS序列的元数据文件，各字段说明如下： "accession"：GenBank/INSDC或UNITE序列登录号； "specimen"：标本编号，针对本研究新生成的序列； "taxon"：标本分类鉴定信息； "New"：是否为本次研究中新生成的ITS序列（*）； "OTU"：聚类簇/操作分类单元（operational taxonomic unit, OTU）名称，若序列本身并非OTU则填写此项（*）； "In_tree"：经过滤步骤后是否出现在红菇科超级系统发育树中； "area"：分配的生物地理区域； "host"：分配的宿主谱系信息。 mcmc_out_1.txt：BAMM后验样本特征文件。 RES_ana_events_tables.Rdata：包含BioGeoBEARS DEC+x+w随机映射（线系进化事件）结果的R数据对象。 RES_clado_events_tables.Rdata：包含BioGeoBEARS DEC+x+w随机映射（分支进化事件）结果的R数据对象。 supertree_calibrated.nwk：经时间校准的红菇科超级系统发育树。 tree_calibrated_clade1_Russula.nwk：经时间校准的红菇亚分支ITS主干系统发育树。 tree_calibrated_clade2_LactariusMultifurca.nwk：经时间校准的乳菇-多枝菇亚分支ITS主干系统发育树。 tree_calibrated_clade3_Lactifluus.nwk：经时间校准的乳菇属亚分支ITS主干系统发育树。