DOI: 10.5281/zenodo.6941094
title: Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions

description: ## Metadata backbone_accessions.tsv - GenBank/INSDC accession numbers for LSU, rpb1 and rpb2 accessions used for the Russulaceae backbone tree including 472 taxa. ITS_sequences_OTUs.tsv - Metadata for all 34,624 ITS sequences used in the study. Columns: "accession": accession ID in analysis – GenBank/INSDC or UNITE accession number for compiled data, lab ID for newly generated data; "specimen": specimen/voucher number, for newly generated sequences; "INSDC_accession": INSDC/GenBank accession for new newly generated data; "taxon": specimen identification; "New": whether ITS sequences was generated in this 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 (*), "lb" long-branch accession removed during tree estimation, "ol" outlier removed during tree estimation; "area": biogeographic area assigned. ## Sequences and alignments backbone_concat.fasta - Concatenated LSU-rpb1-rpb2 alignment for 372 backbone taxa. backbone_concat_part.txt - Gene partitions and substitution models applied to the backbone alignment. einsi_clade1_Russula_trimmed.fasta - Alignment of 2,279 representative ITS sequences in the Russula clade; alignment end columns with &gt;90% missing data/gaps were trimmed. einsi_clade2_LactariusMultifurca_trimmed.fasta - Alignment of 621 representative ITS sequences in the Lactarius-Multifurca clade; alignment end columns with &gt;90% missing data/gaps were trimmed. einsi_clade3_Lactifluus_trimmed.fasta - Alignment of 482 representative ITS sequences in the Lactifluus clade; alignment end columns with &gt;90% missing data/gaps were trimmed. ## Phylogenetic trees 12_make_supertree.R - R script for grafting clade trees onto the backbone tree to produce a supertree. backbone_calibrated.nwk - Time-calibrated Russulaceae backbone phylogeny. backbone_TBE.raxml.support - Russulaceae backbone phylogeny annotated with transfer bootstrap expectation support values. clade1_Russula_TBE.raxml.support - Russula subclade ITS phylogeny (2,279 tips), annotated with transfer bootstrap expectation support values. clade2_LactariusMultifurca_TBE.raxml.support - Lactarius-Multifurca subclade ITS phylogeny (621 tips), annotated with transfer bootstrap expectation support values. clade3_Lactifluus_TBE.raxml.support - Lactifluus subclade ITS phylogeny (482 tips), annotated with transfer bootstrap expectation support values. supertree_calibrated.nwk - Combined Russulaceae supertree, time-calibrated (root age = 1). tree_calibrated_clade1_Russula.nwk - Russula subclade ITS backbone phylogeny, time-calibrated (root age = 1). tree_calibrated_clade2_LactariusMultifurca.nwk - Lactarius-Multifurca subclade ITS backbone phylogeny, time-calibrated (root age = 1). tree_calibrated_clade3_Lactifluus.nwk - Lactifluus subclade ITS backbone phylogeny, time-calibrated (root age = 1). ## Biogeographic analysis 3_disp_counts.R - R script to count dispersal events between biogeographic areas, based on stochastic mapping output. 9_disp_count_time.R - R script to count dispersal events to and from each area through time, based on stochastic mapping output. area_codes.tab - Area letter coding and colours used for biogeographic analysis and plotting. area_shapes.zip - Shapefiles for the nine biogeographic areas defined, based on merged areas from Dinerstein et al. 2017 (https://doi.org/10.1093/biosci/bix014) and Löwenberg-Neto (2014: https://doi.org/10.11646/zootaxa.3802.2.12; 2015: https://doi.org/10.11646/10.11646/zootaxa.3985.4.9). areas_manually_zenodo.csv - Manual assignment of 800 ITS sequences to biogeographic areas based on associated literature records or metadata. corHMM_ER.Rdata - R data archive with input data and results for the corHMM/Mv biogeographic area reconstruction.<br> <br> corHMM_ER_stoch_maps.Rdata - R data archive with results from the corHMM/Mv biogeographic stochastic mapping. 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 stochastic mapping output. disp_matrix_975.txt - Dispersal rates between biogeographic areas (97.5% quantiles), based on stochastic mapping output. disp_matrix_median.txt - Dispersal rates between biogeographic areas (median values), based on stochastic mapping output. ## Diversification analysis 5_rates_per_area.R - R script to partition diversification rates by biogeographic area, both overall and through time, based on BAMM diversification rates and area stochastic mapping. event_data.txt - Posterior samples of diversification rate regimes estimated with BAMM. div_rates_area_overall.txt - Overall diversification rates per biogeographic area, based on BAMM diversification rates and area stochastic mapping. div_rates_per_area_025.tsv - Diversification rates through time (2.5% quantiles) partitioned by biogeographic area, based on BAMM diversification rates and area 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 area stochastic mapping. div_rates_per_area_median.tsv - Diversification rates through time (means) partitioned by biogeographic area, based on BAMM diversification rates and area stochastic mapping. mcmc_out.txt - BAMM posterior sample characteristics.