DOI: 10.5281/zenodo.5078087
title: Data for: Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, varies across neotropical regions

description: 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_concat.fasta - Concatenated ITS-LSU-rpb1-rpb2 alignment for 322 backbone taxa. backbone_concat_part.txt - Gene partitions and subsitution models applied to the backbone alignment. 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. einsi_clade1_Russula_trimmed.fasta - Alignment of 2,032 representative ITS sequences in the Russula clade; alignment end columns with &gt;90% missing data/gaps were trimmed.<br> einsi_clade2_LactariusMultifurca_trimmed.fasta - Alignment of 534 representative ITS sequences in the Lactarius-Multifurca clade; alignment end columns with &gt;90% missing data/gaps were trimmed.<br> einsi_clade3_Lactifluus_trimmed.fasta - Alignment of 451 representative ITS sequences in the Lactifluus clade; alignment end columns with &gt;90% missing data/gaps were trimmed. 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.