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Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions
<p>## Metadata</p> <p>backbone_accessions.tsv - GenBank/INSDC accession numbers for LSU, rpb1 and rpb2 accessions used for the Russulaceae backbone tree including 472 taxa.</p> <p>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.</p> <p> </p> <p>## Sequences and alignments</p> <p>backbone_concat.fasta - Concatenated LSU-rpb1-rpb2 alignment for 372 backbone taxa.</p> <p>backbone_concat_part.txt - Gene partitions and substitution models applied to the backbone alignment.</p> <p>einsi_clade1_Russula_trimmed.fasta - Alignment of 2,279 representative ITS sequences in the Russula clade; alignment end columns with >90% missing data/gaps were trimmed.</p> <p>einsi_clade2_LactariusMultifurca_trimmed.fasta - Alignment of 621 representative ITS sequences in the Lactarius-Multifurca clade; alignment end columns with >90% missing data/gaps were trimmed.</p> <p>einsi_clade3_Lactifluus_trimmed.fasta - Alignment of 482 representative ITS sequences in the Lactifluus clade; alignment end columns with >90% missing data/gaps were trimmed.</p> <p> </p> <p>## Phylogenetic trees</p> <p>12_make_supertree.R - R script for grafting clade trees onto the backbone tree to produce a supertree.</p> <p>backbone_calibrated.nwk - Time-calibrated Russulaceae backbone phylogeny.</p> <p>backbone_TBE.raxml.support - Russulaceae backbone phylogeny annotated with transfer bootstrap expectation support values.</p> <p>clade1_Russula_TBE.raxml.support - Russula subclade ITS phylogeny (2,279 tips), annotated with transfer bootstrap expectation support values.</p> <p>clade2_LactariusMultifurca_TBE.raxml.support - Lactarius-Multifurca subclade ITS phylogeny (621 tips), annotated with transfer bootstrap expectation support values.</p> <p>clade3_Lactifluus_TBE.raxml.support - Lactifluus subclade ITS phylogeny (482 tips), annotated with transfer bootstrap expectation support values.</p> <p>supertree_calibrated.nwk - Combined Russulaceae supertree, time-calibrated (root age = 1).</p> <p>tree_calibrated_clade1_Russula.nwk - Russula subclade ITS backbone phylogeny, time-calibrated (root age = 1).</p> <p>tree_calibrated_clade2_LactariusMultifurca.nwk - Lactarius-Multifurca subclade ITS backbone phylogeny, time-calibrated (root age = 1).</p> <p>tree_calibrated_clade3_Lactifluus.nwk - Lactifluus subclade ITS backbone phylogeny, time-calibrated (root age = 1).</p> <p> </p> <p>## Biogeographic analysis</p> <p>3_disp_counts.R - R script to count dispersal events between biogeographic areas, based on stochastic mapping output.</p> <p>9_disp_count_time.R - R script to count dispersal events to and from each area through time, based on stochastic mapping output.</p> <p>area_codes.tab - Area letter coding and colours used for biogeographic analysis and plotting.</p> <p>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).</p> <p>areas_manually_zenodo.csv - Manual assignment of 800 ITS sequences to biogeographic areas based on associated literature records or metadata.</p> <p>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.</p> <p>disp_counts_focal.tab - Dispersal counts to and from each focal area through time, based on BioGeoBEARS stochastic mapping output.</p> <p>disp_counts_sam_afr.tab - Dispersal counts between Afrotopics and lowland tropical S. America through time, based on BioGeoBEARS stochastic mapping output.</p> <p>disp_matrix_025.txt - Dispersal rates between biogeographic areas (2.5% quantiles), based on stochastic mapping output.</p> <p>disp_matrix_975.txt - Dispersal rates between biogeographic areas (97.5% quantiles), based on stochastic mapping output.</p> <p>disp_matrix_median.txt - Dispersal rates between biogeographic areas (median values), based on stochastic mapping output.</p> <p> </p> <p>## Diversification analysis</p> <p>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.</p> <p>event_data.txt - Posterior samples of diversification rate regimes estimated with BAMM.</p> <p>div_rates_area_overall.txt - Overall diversification rates per biogeographic area, based on BAMM diversification rates and area stochastic mapping.</p> <p>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.</p> <p>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.</p> <p>div_rates_per_area_median.tsv - Diversification rates through time (means) partitioned by biogeographic area, based on BAMM diversification rates and area stochastic mapping.</p> <p>mcmc_out.txt - BAMM posterior sample characteristics.</p>
Fig. 27 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 27. Umbyquyra caxiuana gen. et sp. nov. A–C. Holotype, ♂, Floresta Nacional de Caxiuanã, Pará, Brazil (MPEG 0967). A. Palp, prolateral. B. retrolateral. C. Tibial apophysis, retrolateral. D. Paratype, ♀, same locality, spermathecae, dorsal (MPEG 0177).
Fig. 25 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 25. Umbyquyra tucurui gen. et sp. nov. A–C. Holotype, ♂, Tucuruí, Pará, Brazil (IBSP 104834). A. Palp, prolateral. B. Retrolateral. C. Tibial apophysis, ventral. D. Paratype, ♀, spermathecae, dorsal (IBSP 107431).
Fig. 26 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 26. Umbyquyra tucurui gen. et sp. nov., holotype, ♂, Tucuruí, Pará, Brazil (IBSP 104834). A. Palp, prolateral. B. Anterolateral. C. Retrolateral. D. Tibial apophysis, retrolateral. E. Stridulatory organ, trochanter. F. Trochanter I. Abbreviations: see Material and methods.
Fig. 23 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 23. Umbyquyra tapajos gen. et sp. nov., paratype, ♂, Flona do Tapajós, Belterra, Pará, Brazil (IBSP 161728). A. Palp, prolateral. B. Retrolateral. C. Anterolateral, distal area. D. Tibial apophysis, retrolateral. Abbreviations: see Material and methods.
Fig. 24 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 24. Umbyquyra tapajos gen. et sp. nov., paratype, ♂, Flona do Tapajós, Belterra, Pará, Brazil (IBSP 161728). A. Palp, prolateral. B. Retrolateral. C. Anterolateral. D. Tibial apophysis, retrolateral. E. Stridulatory organ, trochanter. F. Trochanter I.
Fig. 22 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 22. Umbyquyra belterra gen. et sp. nov., holotype, ♂, Flona do Tapajós, Belterra, Pará, Brazil (IBSP 167421). A. Palp, prolateral. B. Anterolateral. C. Retrolateral. D. Tibial apophysis, retrolateral. E. Stridulatory organ, trochanter. F. Trochanter I. Abbreviations: see Material and methods.
Fig. 20 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 20. Umbyquyra araguaia gen. et sp. nov., paratype, ♂, Serra do Lajeado, Tocantins, Brazil (IBSP 110473). A. Palp, prolateral. B. Anterolateral. C. Retrolateral. D. Tibial apophysis, retrolateral. E. Stridulatory organ, palp trochanter. F. Trochanter I. Abbreviations: see Material and methods.
Fig. 19 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 19. Umbyquyra araguaia gen. et sp. nov., paratype, ♂, Serra do Lajeado, Tocantins, Brazil (IBSP 110473). A. Palp, prolateral. B. Retrolateral. C. Tibial apophysis, retrolateral.
Fig. 18 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 18 (opposite page). A–B. Umbyquyra acuminata (Schmidt & Tesmoingt in Schmidt, 2005) gen. et comb. nov. Live specimen from Santa Cruz de la Sierra, Bolivia (photos by Cristian Grismado). C–F. Umbyquyra cuiaba gen. et sp. nov. C. Live specimen from Parque Nacional Chapada dos Guimarães, Mato Grosso, Brazil, dorsal. D. Defensive display. E. Inside burrow. F. Detail of burrow interior without web. G–H. Umbyquyra paranaiba gen. et sp. nov. G. Live specimen from São Paulo, São Paulo, Brazil, dorsal. H. Defensive display, frontal (C–H, photos by Rafael Indicatti).
Fig. 29 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 29. Geographic distribution records of species of Umbyquyra gen. nov.: U. belterra gen. et sp. nov., U. caxiuana gen. et sp. nov., U. tucurui gen. et sp. nov. and U. tapajos gen. et sp. nov.
Fig. 16 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 16. Umbyquyra cuiaba gen. et sp. nov. A–C. Holotype, ♂, Cuiabá, Mato Grosso, Brasil (IBSP 167423). A. Palp prolateral. B. Retrolateral. C. Tibial apophysis, retrolateral. D–F. Paratype, ♀, Canarana, Mato Grosso, Brazil (IBSP 108933). D. Spermathecae, dorsal. E. Eye tubercle, dorsal. F. Abdomen, dorsal.
Fig. 15 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 15. Umbyquyra acuminata (Schmidt & Tesmoingt in Schmidt, 2005) gen. et comb. nov. A–C. ♂, Santa Cruz de la Sierra, Bolivia (ZMB 47188). A. Palp, prolateral. B. Retrolateral. C. Tibial apophysis, retrolateral. D–E. ♀, same locality (ZMB 47189). D. Spermathecae, dorsal. E. Carapace, lateral. Abbreviations: see Material and methods.
Fig. 28 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 28. Umbyquyra caxiuana gen. et sp. nov., holotype, ♂, Floresta Nacional de Caxiuanã, Pará, Brazil (MPEG 0967). A. Palp, prolateral. B. Anterolateral. C. Retrolateral. D. Tibial apophysis, retrolateral. E. Stridulatory organ, trochanter. F. Same, trochanter I. Abbreviations: see Material and methods.
Fig. 11 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 11. Umbyquyra palmarum (Schiapelli & Gerschman, 1945) gen. et comb. nov. A–C. Holotype, ♂, Barão de Melgaço River, Rondônia, Brazil (MACN 832). A. Palp prolateral. B. Retrolateral. C. Tibial apophysis, retrolateral. D. ♀, Chapada dos Guimarães, Mato Grosso, Brazil (IBSP 107257), spermathecae, dorsal.
Fig. 10 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 10. Umbyquyra sapezal gen. et sp. nov., holotype, ♂, Sapezal, Mato Grosso (IBSP 113753). A. Palp prolateral. B. Anterolateral. C. Retrolateral. D. Tibial apophysis, retrolateral. E. Stridulatory organ, palp trochanter. F. Trochanter I. Abbreviations: see Material and methods.
Fig. 8 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 8. Umbyquyra paranaiba gen. et sp. nov. Holotype, ♂ (IBSP 107411). A–C. Palpal bulb. A. Prolateral. B. Anterolateral. C. Retrolateral. D. Tibial apophysis, retrolateral. E. Stridulatory organ, trochanter, male palp. F. Stridulatory organ, trochanter I (arrows in E–F pointed the stridulatory bristles). Abbreviations: see Material and methods.
Fig. 13 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 13. Umbyquyra schmidti (Rudloff, 1996) gen. et comb. nov. A–C. ♂, Cuiabá, Mato Grosso, Brazil (IBSP 110728). A. Palp prolateral. B. Retrolateral. C. Tibial apophysis, retrolateral. D. ♀, spermathecae, dorsal (IBSP 107159).
Fig. 5. Fovea, carapace. A in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 5. Fovea, carapace. A. Umbyquyra schimidti gen. et sp. nov. B. U. sapezal gen. et sp. nov. C. U. caxiuana gen. et sp. nov. D. U. cuiaba gen. et sp. nov. E. U. paranaiba gen. et sp. nov. F. U. belterra gen. et sp. nov.
Fig. 3. Longilyra johnlonghorni Gabriel, 2014 in Umbyquyra gen. nov., a new tarantula spider genus from the Neotropical region (Araneae, Mygalomorphae, Theraphosidae), with a description of eight new species
Fig. 3. Longilyra johnlonghorni Gabriel, 2014, ♀, Santa Ana, Laguna de Las Ninfas, El Salvador (SMF 8582/2). A. Palp, trochanter, stridulatory organ. B. Trochanter I, stridulatory organ. C. Spermathecae, dorsal. From Gabriel (2014: figs 1, 2, 5).
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