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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. 2. — Veredatrypa rosai n. gen., n in New Brazilian Tafaliscina increase the diversity of this Neotropical cricket clade (Orthoptera: Grylloidea: Gryllidae: Oecanthinae: Paroecanthini)
FIG. 2. — Veredatrypa rosai n. gen., n. sp. male: A, dorsal habitus; B, lateral habitus; C, frontal head; D, right FW, dorsal field; E, metanotum, dorsal; F, supra anal plate; G, subgenital plate; H, hind tibia, inner face; I, hind tibia, outer face. Female: J, dorsal habitus; K, supra anal plate and ovipositor, dorsal; L, subgenital plate and ovipositor, ventral. Scale bars: A, B, K, 2 mm; C-J, L, M, 1 mm.
FIG. 8. — Veredatrypa fusca n. gen., n in New Brazilian Tafaliscina increase the diversity of this Neotropical cricket clade (Orthoptera: Grylloidea: Gryllidae: Oecanthinae: Paroecanthini)
FIG. 8. — Veredatrypa fusca n. gen., n. sp. male: A, dorsal habitus; B, lateral habitus; C, frontal head; D, right FW, dorsal field; E, metanotum, dorsal; F, supra anal plate; G, subgenital plate. Female: H, dorsal habitus; I, supra anal plate and ovipositor, dorsal; J, subgenital plate and ovipositor, ventral. Scale bars: A, B, H, 2 mm; C-G, I, J, 1 mm.
Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla)
<p>The stipple-throated antwrens of the genus <i>Epinecrophylla</i> (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of <i>Epinecrophylla</i> antwrens and the first population-level genetic analyses for most species in the genus. Most of our results are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to fully resolve the relationships between some western Amazonian species in the <i>haematonota </i>group. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in the <i>ornata </i>group that are currently regarded as species, and in the <i>haematonota </i>and <i>leucophthalma</i> groups we found paraphyly at the species and subspecies levels, respectively. As has been found in many Amazonian taxa, our phylogenetic results show that the major river systems of the Amazon Basin appear to have an effect on the genetic structure and range limits within <i>Epinecrophylla</i>. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group and suggest areas for further study.</p>
Fig. 3 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 3. Phylogenetic positioning of T. rotundus in the clade T. cruzi. ML phylogenetic analysis based on the concatenated sequences of V7V8 SSU rRNA and gGAPDH genes (1.690 characters, –Ln = 8768.346166) from ten isolates of T. rotundus, other 29 bat trypanosomes, and 21 trypanosomes from other mammals. T. lewisi was used as outgroup. The numbers at the nodes correspond respectively to P, ML (500 replicates) and BI support values.
Fig. 2 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 2. Barcoding (V7-V8 SSU rRNA sequences) of T. rotundus from cultures and bat blood samples, and its related species of the clade T. cruzi. Phylogenetic tree inferred by Parsimony using 93 (∼800 bp) of V7-V8 SSU rRNA sequences. The node numbers are bootstrap values derived from 500 replicates.
Fig. 1 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 1. Geographical origin of Trypanosoma rotundus n. sp. isolates obtained by hemoculturing and archived blood samples from Desmodus rotundus captured in the following Brazilian states: PA, Pará; MG, Minas Gerais; ES, Espírito Santo; RJ, Rio de Janeiro; SP, São Paulo and SC, Santa Catarina.
Fig. 4 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 4. Photomicrographs illustrative of the morphological diversity of culture forms of T. madeirae (isolate M3-209). (a) rosetes of epimastigotes, (b-d) flagellates resembling promastigotes forms, (d-h) epimastigotes (7 days), (i-k) large epimastigote forms under division, (l-m), large trypomastigotes, and (n) slender trypomastigotes (10 days). Giemsa stained. 1000x. K, kinetoplast, N, nucleus, F, flagellum. The scale bar indicates 10 μm.
FIGURE 43 in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 43. Centruroides yucatanensis, sp. nov., ♀ (CNAN T01417), habitus. A. Dorsal aspect. B. Ventral aspect. Scale bars = 10 mm.
FIGURE 42 in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 42. Centruroides yucatanensis, sp. nov., ♂ (CNAN T01416), habitus. A. Dorsal aspect. B. Ventral aspect. Scale bars = 10 mm.
FIGURE 41 in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 41. Centruroides chanae, sp. nov., ♀ (CNAN T01405), habitus. A. Dorsal aspect. B. Ventral aspect. Scale bars = 5 mm.
. mm 5 = bars Scale. aspect Ventral. B. aspect Dorsal. A. habitus,) 01407 T CNAN (♂,. nov. sp, chanae Centruroides. 40 FIGURE in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
. mm 5 = bars Scale. aspect Ventral. B. aspect Dorsal. A. habitus,) 01407 T CNAN (♂,. nov. sp, chanae Centruroides. 40 FIGURE
FIGURE 37. Centruroides schmidti Sissom 1995 in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 37. Centruroides schmidti Sissom 1995, ♀ (CASENT 9073317), habitus. A. Dorsal aspect. B. Ventral aspect. Scale bars = 5 mm
FIGURE 35 in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 35. Centruroides berstoni, sp. nov., ♀ (CASENT 9073313), habitus. A. Dorsal aspect. B. Ventral aspect. Scale bars = 5 mm.
. mm 5 = bars Scale. aspect Ventral. B. aspect Dorsal. A. habitus,) 9073278 CASENT (♂, 1995 Sissom schmidti Centruroides. 36 FIGURE in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
. mm 5 = bars Scale. aspect Ventral. B. aspect Dorsal. A. habitus,) 9073278 CASENT (♂, 1995 Sissom schmidti Centruroides. 36 FIGURE
FIGURE 23. Centruroides Marx, 1890 in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 23. Centruroides Marx, 1890, telson, dorsal aspect. A, D. C. rileyi Sissom, 1995, A. ♂ (CNAN SC4002), D. ♀ (CNAN SC4003). B, E. C. hamadryas, sp. nov., B. holotype ♂ (CNAN T01408), E. paratype ♀ (CNAN T01415). C, F. C. hoffmanni Armas, 1996, C. ♂, F. ♀ (CNAN SC3996). G, J. C. cuauhmapan, sp. nov., G. holotype ♂ (CNAN T01396), J. paratype ♀ (CNAN T01399). H, K. C. berstoni, sp. nov., H. holotype ♂ (CASENT 9073325), K. paratype ♀ (CASENT 9073313). I, L. C. chanae, sp. nov., I. holotype ♂ (CNAN T01403), L. paratype ♀ (CNAN T01405). M, P. C. catemacoensis, sp. nov., M. holotype ♂ (CNAN T01424), P. paratype ♀ (CNAN T01423). N, Q. C. schmidti Sissom, 1995, N. ♂ (CASENT 9073316), Q. ♀ (CASENT 9073317). O, R. C. yucatanensis, sp. nov., O. holotype ♂ (CNAN T01416), R. paratype ♀ (CNAN T01418). Scale bars = 1 mm.
FIGURE 22. Centruroides Marx, 1890, metasomal segment V, lateral aspect. A, D. C. rileyi Sissom, 1995, A in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 22. Centruroides Marx, 1890, metasomal segment V, lateral aspect. A, D. C. rileyi Sissom, 1995, A. ♂ (CNAN SC4002), D. ♀ (CNAN SC4003). B, E. C. hamadryas, sp. nov., B. holotype ♂ (CNAN T01408), E. paratype ♀ (CNAN T01415). C, F. C. hoffmanni Armas, 1996, C. ♂, F. ♀ (CNAN SC3996). G, J. C. cuauhmapan, sp. nov., G. holotype ♂ (CNAN T01396), J. paratype ♀ (CNAN T01399). H, K. C. berstoni, sp. nov., H. holotype ♂ (CASENT 9073325), K. paratype ♀ (CASENT 9073313). I, L. C. chanae, sp. nov., I. holotype ♂ (CNAN T01403), L. paratype ♀ (CNAN T01405). M, P. C. catemacoensis, sp. nov., M. holotype ♂ (CNAN T01424), P. paratype ♀ (CNAN T01423). N, Q. C. schmidti Sissom, 1995, N. ♂ (CASENT 9073316), Q. ♀ (CASENT 9073317). O, R. C. yucatanensis, sp. nov., O. holotype ♂ (CNAN T01416), R. paratype ♀ (CNAN T01417). Scale bars = 2 mm.
FIGURE 17. Centruroides Marx, 1890, metasomal segments I and II, dorsal aspect. A, D. C. rileyi Sissom, 1995, A in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 17. Centruroides Marx, 1890, metasomal segments I and II, dorsal aspect. A, D. C. rileyi Sissom, 1995, A. ♂ (CNAN SC4002), D. ♀ (CNAN SC4003). B, E. C. hamadryas, sp. nov., B. holotype ♂ (CNAN T01408), E. paratype ♀ (CNAN T01415). C, F. C. hoffmanni Armas, 1996, C. ♂, F. ♀ (CNAN SC3996). G, J. C. cuauhmapan, sp. nov., G. holotype ♂ (CNAN T01396), J. paratype ♀ (CNAN T01399). H, K. C. berstoni, sp. nov., H. holotype ♂ (CASENT 9073325), K. paratype ♀ (CASENT 9073313). I, L. C. chanae, sp. nov., I. holotype ♂ (CNAN T01403), L. paratype ♀ (CNAN T01405). M, P. C. catemacoensis, sp. nov., M. holotype ♂ (CNAN T01424), P.paratype ♀ (CNAN T01423). N, Q. C. schmidti Sissom, 1995, N. ♂ (CASENT 9073316), Q. ♀ (CASENT 9073317). O, R. C. yucatanensis, sp. nov., O. holotype ♂ (CNAN T01416), R. paratype ♀ (CNAN T01417. Scale bars = 2 mm.
FIGURE 19. Centruroides Marx, 1890, metasomal segments I and II, lateral aspect. A, D. C. rileyi Sissom, 1995, A in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 19. Centruroides Marx, 1890, metasomal segments I and II, lateral aspect. A, D. C. rileyi Sissom, 1995, A. ♂ (CNAN SC4002), D. ♀ (CNAN SC4003). B, E. C. hamadryas, sp. nov., B. holotype ♂ (CNAN T01408), E. paratype ♀ (CNAN T01415). C, F. C. hoffmanni Armas, 1996, C. ♂, F. ♀ (CNAN SC3996). G, J. C. cuauhmapan, sp. nov., G. holotype ♂ (CNAN T01396), J. paratype ♀ (CNAN T01399). H, K. C. berstoni, sp. nov., H. holotype ♂ (CASENT 9073325), K. paratype ♀ (CASENT 9073313). I, L. C. chanae, sp. nov., I. holotype ♂ (CNAN T01403), L. paratype ♀ (CNAN T01405). M, P. C. catemacoensis, sp. nov., M. holotype ♂ (CNAN T01424), P. paratype ♀ (CNAN T01423). N, Q. C. schmidti Sissom, 1995, N. ♂ (CASENT 9073316), Q. ♀ (CASENT 9073317). O, R. C. yucatanensis, sp. nov., O. holotype ♂ (CNAN T01416), R. paratype ♀ (CNAN T01417). Scale bars = 2 mm.
FIGURE 13. Centruroides Marx, 1890 in Systematic Revision Of The Arboreal Neotropical "Thorellii" Clade Of Centruroides Marx, 1890, Bark Scorpions (Buthidae C.L. Koch, 1837) With Descriptions Of Six New Species
FIGURE 13. Centruroides Marx, 1890, pedipalp chela, retrolateral aspect. A. C. hamadryas, sp. nov., holotype ♂ (CNAN T01408). B. C. berstoni, sp. nov., holotype ♂ (CASENT 9073325). C. C. schmidti Sissom, 1995, ♂ (CASENT 9073316). Scale bars = 1 mm.
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