Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
31
datasets available to search
ShareScore release 0.9.0
Dataset results
31 results for “Neotropical fungi”
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>
Figure 15a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 15a. - Neoempheriapuncticoxa Edwards, 1940.Figure 15a.Female pupal exuvia (lateral).Figure 15b.Larva intersegmental areas with creeping welts bearing rows of denticles. <br> Female pupal exuvia (lateral).
Figure 15b. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 15b. - Neoempheriapuncticoxa Edwards, 1940.Figure 15a.Female pupal exuvia (lateral).Figure 15b.Larva intersegmental areas with creeping welts bearing rows of denticles. <br> Larva intersegmental areas with creeping welts bearing rows of denticles.
Figure 13. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 13. - Neoempheriapuncticoxa Edwards, 1940. Female pupa hanging in its own silk (ventrolateral).
Figure 14a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 14a. - Neoempheriapuncticoxa Edwards, 1940.Figure 14a.Male pupal exuvia (ventral).Figure 14b.Male imago (dorsolateral). <br> Male pupal exuvia (ventral).
Figure 12c. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 12c. - Neoempheriapuncticoxa Edwards, 1940 prepupal larva.Figure 12a.Larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12b.Detail of larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12c.Larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12d.Detail of larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. <br> Larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. Substrate upside down.
Figure 14b. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 14b. - Neoempheriapuncticoxa Edwards, 1940.Figure 14a.Male pupal exuvia (ventral).Figure 14b.Male imago (dorsolateral). <br> Male imago (dorsolateral).
Figure 12b. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 12b. - Neoempheriapuncticoxa Edwards, 1940 prepupal larva.Figure 12a.Larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12b.Detail of larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12c.Larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12d.Detail of larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. <br> Detail of larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.
Figure 12a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 12a. - Neoempheriapuncticoxa Edwards, 1940 prepupal larva.Figure 12a.Larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12b.Detail of larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12c.Larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12d.Detail of larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. <br> Larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.
Figure 11b. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 11b. - Neoempheriapuncticoxa Edwards, 1940 larvae.Figure 11a.Larvae on ventral face of Goiás fungus, showing webs and slime trails produced by the larvae.Figure 11b.Detail of larvae on ventral face of Goiás fungus, showing webs and slime trails produced by the larvae. <br> Detail of larvae on ventral face of Goiás fungus, showing webs and slime trails produced by the larvae.
Figure 10b. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 10b. - Neoempheriapuncticoxa Edwards, 1940 host fungus.Figure 10a.Sparassis sp., (Polyporales: Sparassidaceae) fruiting body that larvae of N.puncticoxa were found on in São Paulo.Figure 10b.Ventral view of fruiting body of Polyporaceae where larvae of N.puncticoxa were found in Goiás. <br> Ventral view of fruiting body of Polyporaceae where larvae of N.puncticoxa were found in Goiás.
Figure 11a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 11a. - Neoempheriapuncticoxa Edwards, 1940 larvae.Figure 11a.Larvae on ventral face of Goiás fungus, showing webs and slime trails produced by the larvae.Figure 11b.Detail of larvae on ventral face of Goiás fungus, showing webs and slime trails produced by the larvae. <br> Larvae on ventral face of Goiás fungus, showing webs and slime trails produced by the larvae.
Figure 12d. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 12d. - Neoempheriapuncticoxa Edwards, 1940 prepupal larva.Figure 12a.Larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12b.Detail of larva (pre-pupa), ventral view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12c.Larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. Substrate upside down.Figure 12d.Detail of larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation. <br> Detail of larva (pre-pupa), frontal view, hanging in its own silk in preparation for pupation.
Figure 10a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 10a. - Neoempheriapuncticoxa Edwards, 1940 host fungus.Figure 10a.Sparassis sp., (Polyporales: Sparassidaceae) fruiting body that larvae of N.puncticoxa were found on in São Paulo.Figure 10b.Ventral view of fruiting body of Polyporaceae where larvae of N.puncticoxa were found in Goiás. <br> Sparassis sp., (Polyporales: Sparassidaceae) fruiting body that larvae of N.puncticoxa were found on in São Paulo.
Figure 8b. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 8b. - Neoempheriapuncticoxa Edwards, 1940 larval head capsule.Figure 8a.Ventral view.Figure 8b.Ventral view. <br> Ventral view.
Figure 9. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 9. - Neoempheriapuncticoxa Edwards, 1940 larval head capsule. Ventral view, without the mandible; e – eye; lb – labrum; lp – lateral plate; mp – maxillar papilla; mpl – medium plate; mx – maxilla; mxp – maxillary plate; of – occipital foramen; pmd – premandible.
Figure 8a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 8a. - Neoempheriapuncticoxa Edwards, 1940 larval head capsule.Figure 8a.Ventral view.Figure 8b.Ventral view. <br> Ventral view.
Figure 5. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 5. - Neoempheriapuncticoxa Edwards, 1940 adult. Male thorax; Ab – abdomen, anp – anepisternum, bas - basisternum, cxI-III – fore-, mid-, and hindcoxae, ha – haltere, ktp – katepisternum, ltg – laterotergite, anp – anepimeron, mep – mesepimeron, mes – metepisternum, mtg – mediotergite, pem – proepimeron, pes – proepisternum, pnt – pronotum, sc – scutum, sctl – scutellum.
Figure 1b. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 1b. - Neoempheriapuncticoxa Edwards, 1940. Male adultFigure 1a.Dorsal view.Figure 1b.Ventral view. <br> Ventral view.
Figure 7a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 7a. - Neoempheriapuncticoxa Edwards, 1940 larval head capsule.Figure 7a.Ventrolateral view.Figure 7b.Ventrolateral view. <br> Ventrolateral view.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.