Find research datasets worth reusing

Linked collectors and determiners for: Nocturnal Velvet Ants (Hymenoptera: Mutillidae) of Joshua Tree National Park, Riverside County, California with the description of three new species.

Natural history specimen data linked to collectors and determiners held within, "Nocturnal Velvet Ants (Hymenoptera: Mutillidae) of Joshua Tree National Park, Riverside County, California with the description of three new species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c7db5cdc-51c3-4c2d-be5d-a8c11f59c09a">https://bionomia.net/dataset/c7db5cdc-51c3-4c2d-be5d-a8c11f59c09a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c7db5cdc-51c3-4c2d-be5d-a8c11f59c09a">https://gbif.org/dataset/c7db5cdc-51c3-4c2d-be5d-a8c11f59c09a</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: A new Calliprora species mining lead trees in Florida (Lepidoptera: Gelechiidae).

Natural history specimen data linked to collectors and determiners held within, "A new Calliprora species mining lead trees in Florida (Lepidoptera: Gelechiidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/a0a76453-f5d6-4758-8545-7ce2a6e0b092">https://bionomia.net/dataset/a0a76453-f5d6-4758-8545-7ce2a6e0b092</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/a0a76453-f5d6-4758-8545-7ce2a6e0b092">https://gbif.org/dataset/a0a76453-f5d6-4758-8545-7ce2a6e0b092</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: A taxonomic revision of Melanoxerus (Rubiaceae), with descriptions of three new species of trees from Madagascar.

Natural history specimen data linked to collectors and determiners held within, "A taxonomic revision of Melanoxerus (Rubiaceae), with descriptions of three new species of trees from Madagascar". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/302813c6-fb6d-4142-b635-4d0a1e18fb27">https://bionomia.net/dataset/302813c6-fb6d-4142-b635-4d0a1e18fb27</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/302813c6-fb6d-4142-b635-4d0a1e18fb27">https://gbif.org/dataset/302813c6-fb6d-4142-b635-4d0a1e18fb27</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: The montane trees of the Cameroon Highlands, West-Central Africa, with Deinbollia onanae sp. nov. (Sapindaceae), a new primate-dispersed, Endangered species.

Natural history specimen data linked to collectors and determiners held within, "The montane trees of the Cameroon Highlands, West-Central Africa, with Deinbollia onanae sp. nov. (Sapindaceae), a new primate-dispersed, Endangered species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/ceb40045-70f8-4933-91a1-a696aea66ebe">https://bionomia.net/dataset/ceb40045-70f8-4933-91a1-a696aea66ebe</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ceb40045-70f8-4933-91a1-a696aea66ebe">https://gbif.org/dataset/ceb40045-70f8-4933-91a1-a696aea66ebe</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: Terminalia carinata Sabatier & J. Engel, sp. nov. (Combretaceae), a new large tree species from the Guiana shield revealed by re-examination of material previously identified as T. guyanensis Eichler.

Natural history specimen data linked to collectors and determiners held within, "Terminalia carinata Sabatier & J. Engel, sp. nov. (Combretaceae), a new large tree species from the Guiana shield revealed by re-examination of material previously identified as T. guyanensis Eichler". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9d5d9cb4-e64f-4402-981a-7844a361f562">https://bionomia.net/dataset/9d5d9cb4-e64f-4402-981a-7844a361f562</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9d5d9cb4-e64f-4402-981a-7844a361f562">https://gbif.org/dataset/9d5d9cb4-e64f-4402-981a-7844a361f562</a>. Formatted as a Frictionless Data package.

opencc-by-4.0Oct 2024View details →

TreeGOER Holdridge Life Zone Distributions: Observations for 48,129 tree species across 45 historical (1901-1920) and contemporary (1979-2013) terrestrial life zones

TreeGOER (Tree Globally Observed Environmental Ranges) is a database that documents the environmental ranges (minimum, maximum, median, mean and 5%, 25%, 75% and 95% quantiles) for 48,129 tree species and for 51 environmental variables, including 38 bioclimatic variables, 8 soil variables and 3 topographic variables. TreeGOER is available from the following Zenodo archives: <a href="https://doi.org/10.5281/zenodo.7922927">https://doi.org/10.5281/zenodo.7922927.</a> The TreeGOER ranges were calculated after cleaning occurrence records and standardizing species names with the <a href="https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11388">WorldFlora</a> R package to <a href="https://onlinelibrary.wiley.com/doi/10.1002/tax.12373">World Flora Online</a> or the <a href="https://www.nature.com/articles/s41597-021-00997-6">World Checklist of Vascular Plants</a> for a global GBIF occurrence download of 44,267,164 occurrences (GBIF.org 2021 GBIF Occurrence Download <a href="https://doi.org/10.15468/dl.77gcvq">https://doi.org/10.15468/dl.77gcvq</a>). The process of compilation of TreeGOER with 30 arc-seconds global grid layers, two examples of BIOCLIM applications that investigated the effects of climate change on global tree diversity patterns and R scripts to repeat these analyses have been described by Kindt, R. (2023). TreeGOER: A database with globally observed environmental ranges for 48,129 tree species. Global Change Biology 29: 6303–6318. <a href="https://onlinelibrary.wiley.com/doi/10.1111/gcb.16914">https://onlinelibrary.wiley.com/doi/10.1111/gcb.16914</a>. This Zenodo archive documents the occurrence of the same previously compiled and cleaned observations for the TreeGOER across global raster layers that document the contemporary (1979-1920) and historical (1901-1920) distribution of 45 Terrestrial Life Zones. These global raster layers were created for the following article: <ul> <li>Elsen, P. R., Saxon, E. C., Simmons, B. A., Ward, M., Williams, B. A., Grantham, H. S., Kark, S., Levin, N., Perez-Hammerle, K.-V., Reside, A. E., & Watson, J. E. M. (2022). Accelerated shifts in terrestrial life zones under rapid climate change. Global Change Biology, 28, 918–935. <a href="https://doi.org/10.1111/gcb.15962">https://doi.org/10.1111/gcb.15962</a></li> </ul> and are <a href="https://datadryad.org/stash/dataset/doi:10.5061/dryad.41ns1rnff">available for download from DRYAD</a>: <ul> <li>Elsen, Paul R.; Saxon, Earl C.; Simmons, B. Alexander; Ward, Michelle; Williams, Brooke A.; Grantham, Hedley S.; Kark, Salit; Levin, Noam; Perez-Hammerle, Katharina-Victoria; Reside, April E.; Watson, James E. M.; Perez‐Hammerle, Katharina‐Victoria. 2021. Data from: Accelerated shifts in terrestrial life zones under rapid climate change. Nov 05 2021 version files. <a href="https://doi.org/10.5061/dryad.41ns1rnff">https://doi.org/10.5061/dryad.41ns1rnff</a></li> </ul> The raster layers were processed using R and Google Earth Engine following the methodology described in Elsen et al (<a href="https://doi.org/10.1111/gcb.15962">2022</a>). Documentation of the different zones are partially available from this README file: <a href="https://datadryad.org/stash/downloads/file_stream/1145694">https://datadryad.org/stash/downloads/file_stream/1145694</a> For each of the 48,129 tree species, the distribution is given for: <ul> <li>Contemporary climate: number of observations in life zones mapped by <a href="https://datadryad.org/stash/downloads/file_stream/1145680">https://datadryad.org/stash/downloads/file_stream/1145680</a></li> <li>Historical climate: number of observations in life zones mapped by <a href="https://datadryad.org/stash/downloads/file_stream/1145681">https://datadryad.org/stash/downloads/file_stream/1145681</a></li> <li>Mixed climate: number of observations for contemporary life zones if GBIF observations were from 1979 or later, and number of observations for historical life zones if GBIF observations were from before 1979</li> <li>Static climate: number of observations in the same zone in the contemporary and historical climate. The number of observations in areas where the life zone changed are listed in the variable of 'H-0'.</li> </ul> Observations outside the life zone maps are listed in the variable of 'H-1'.   The development of this data set archive supported by the Darwin Initiative to project DAREX001 of Developing a Global Biodiversity Standard certification for tree-planting and restoration, by Norway’s International Climate and Forest Initiative through the Royal Norwegian Embassy in Ethiopia to the Provision of Adequate Tree Seed Portfolio project in Ethiopia, by the Green Climate Fund through the IUCN-led Transforming the Eastern Province of Rwanda through Adaptation and through the Readiness proposal on Climate Appropriate Portfolios of Tree Diversity for Burkina Faso projects, by the Bezos Earth Fund to the Quality Tree Seed for Africa in Kenya and Rwanda project and by the German International Climate Initiative (IKI) to the regional tree seed programme on The Right Tree for the Right Place for the Right Purpose in Africa.

opencc-by-4.0Feb 2023View details →

Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)

Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 individual gene trees obtained using RAxML. The node labels represent ASTRAL support values. Note that ASTRAL only calculates internal branch length and that tip lines are artificially fixed with the same length for all the specimens. Tip labels include the species names and the collector codes. Branch colors represent the traditional classification: Labramia (dark green), Manilkara (orange), Faucherea (yellow) and Labourdonnaisia (pink). The revised four major genetic clades are highlighted by a colored bar as follows: Labramia (dark green), Manilkara s.str. (orange), Faucherea and Labourdonnaisia (pink), and the Abebaia clade (blue). The main regions are indicated as follows: Afr: Africa; Ame: Americas; Com: Comoros; Ind: Indonesia; Mad: Madagascar; Msc: Mascarenes; Pac: Pacific Asia. RN: Réserves Naturelles; SF: Service Forestier.

opencc-by-4.0Jul 2021View details →

Fig. 1. Maximum likelihood tree inferred from the COI dataset with 1000 in Seven new giant pill-millipede species and numerous new records of the genus Zoosphaerium from Madagascar (Diplopoda, Sphaerotheriida, Arthrosphaeridae)

Fig. 1. Maximum likelihood tree inferred from the COI dataset with 1000 bootstrap pseudoreplicates implementing the GTR + I + G model. Colors representing newly described species of Zoosphaerium: orange = Z. nigrum sp. nov.; green = Z. silens sp. nov.; red = Z. ambatovaky sp. nov.; yellow = Z. beanka sp. nov.; purple = Z. voahangy sp. nov.; blue = Z. masoala sp. nov. Round-cornered rectangles indicate well-supported sister group relationships.

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Data for: PickMe: sample selection for species tree reconstruction using coalescent weighted quartets

After collecting large data sets of many genes for many species for phylogenomics studies, researchers may make ad hoc decisions about which genes or samples to include in a species tree reconstruction analysis based on various parameters, including the amount of missing data. Optimally, sampling would be maximized, but it can be difficult for empiricists to determine where to draw the line for sample inclusion when data sets are incomplete. Under the multispecies coalescent model, in which the dominant quartet topology displayed across gene trees matches the topology of that quartet on the species tree, we propose a Bayesian framework to select samples for which there is support for inclusion in a species tree analysis. Given a collection of gene trees, a posterior probability is assigned to each quartet topology, describing the likelihood that the species tree displays this topology. From this, individual samples are assigned reliability scores computed as the average of a rescaling of the posterior probabilities. These weights are used in a Bayesian framework in an algorithm called PickM}, which determines which individuals should be included in a species tree analysis. To illustrate the efficacy of this tool, PickMe is applied to gene trees generated from target capture data from milkweeds. PickMe indicates that more samples could have reliably been included in a previous milkweed phylogenomic analysis than the authors analyzed, without access to a formal decision-making procedure. Thus, PickMe will be a valuable addition to data analysis pipelines for phylogenomics studies.

opencc-zeroAug 2021View details →

opencc-by-4.0Oct 2017View details →

Figure 11. Neighbor joining tree for the 16 in Description of a new Nearctic species of Tragosoma Audinet-Serville (Coleoptera: Cerambycidae: Prioninae), with species validations, new synonymies and a lectotype designation

Figure 11. Neighbor joining tree for the 16 barcodes of Tragosoma included in the dataset; each record with province or state of origin, GenBank accession number, and sample ID. Full length sequences (658 base pairs) analyzed, unless otherwise indicated in parentheses.

opencc-by-4.0Aug 2021View details →

Pervasive selection biases inferences of the species tree

Supplementary files, scripts, and data of 'Pervasive selection biases inferences of the species tree' by Borges, Boussau, Szöllősi, and Kosiol

opencc-by-4.0Jun 2014View details →

FIG. 4 in Cryptosepalum korupense Burgt, sp. nov. (Leguminosae, Caesalpinioideae), a tree species from the Southwest Region in Cameroon

FIG. 4. ― Distribution of 14 trees of Cryptosepalum korupense Burgt, sp. nov., in primary rainforest in Korup National Park. The size of a dot represents the trunk diameter at 1.3 m in three size classes: 10-30, 30-50 and 50-70 cm. The lines represent small streams. All trees grow on well-drained soil.

opencc-by-4.0Jun 2014View details →

FIG. 2 in Cryptosepalum korupense Burgt, sp. nov. (Leguminosae, Caesalpinioideae), a tree species from the Southwest Region in Cameroon

FIG. 2. ― Cryptosepalum korupense Burgt, sp. nov.: A, twig and infructescences with very young fruits; B, leaf upper surface; C, leaflet lower surface;D, stipule from upper part of twig (above) and lower part of twig (below);E, flower;F, adaxial petal; G, gynoecium;H, flower bract; J, hypanthium and sepals; K, infructescence with fruit; L, seeds.A, from van der Burgt 922; B-D, from van der Burgt 848; E-J, from Motoh 6; K, from van der Burgt 931; L, from Motoh 3. Scale bars:A, B, 2 cm; C, E, F, G, H, 2 mm; D, 5 mm; J, 1 mm; K, L, 2 cm. Drawn by Xander van der Burgt.

opencc-by-4.0Jun 2014View details →

FIG. 1 in Cryptosepalum korupense Burgt, sp. nov. (Leguminosae, Caesalpinioideae), a tree species from the Southwest Region in Cameroon

FIG. 1. ― Cryptosepalum korupense Burgt, sp. nov.: A, twigs and leaves; B, infructescence with two fruits; C, flushing leaves; D, trunk of a tree of 88 cm diameter at 1.3 m; A, C, from van der Burgt 848; B, from van der Burgt 931; D, from van der Burgt 941. Photos by Xander van der Burgt.

opencc-by-4.0Jan 2006View details →

Figure 2. Majority rule consensus tree for the 16S in Genus Baseodiscus (Nemertea: Heteronemertea): Molecular identification of a new species in a phylogenetic context

Figure 2. Majority rule consensus tree for the 16S rRNA data resulting from the Bayesian analysis (model GTR+G+I), 1,000,000 generations. Numbers refer to posterior probabilities.

opencc-by-4.0Dec 2010View details →

Figure 3 in Do male tree frogs feed during the breeding season? Stomach flushing of five syntopic hylid species in Rio Grande do Sul, Brazil

Figure 3. Relation between length of the reproductive period and food intake by 50 males per species.

Fig. 7 in A revision of the Asian tree toad complex Rentapia hosii (Anura: Bufonidae) with the description of a new species from Peninsular Malaysia

Fig. 7. Live photographs of: amplecting Rentapia flavomaculata, new species, displaying (A) normal and (B) stressed colouration; (C) female R. hosii s.s. from Sarawak (Photo by Alexander Haas); (D) female R. cf. hosii from Tawau, Sabah (Photo by Robert F. Inger; ©Field Museum of Natural History. FMNH 248199. Created by Field Museum of Natural History, Amphibian and Reptile Collection and licensed under CC-BY-SA 4.0); and (E) uncollected female from Tawau, Sabah (Photo by A. Haas).

Fig. 3 in A revision of the Asian tree toad complex Rentapia hosii (Anura: Bufonidae) with the description of a new species from Peninsular Malaysia

Fig. 3. Comparative spectrograms and corresponding oscillograms of a single call of the advertisement vocalisation of individuals of the Rentapia hosii complex from (A) Sarawak; (B) Brunei; and (C) Peninsular Malaysia.

Fig. 5 in A revision of the Asian tree toad complex Rentapia hosii (Anura: Bufonidae) with the description of a new species from Peninsular Malaysia

Fig. 5. Dorsal (A) and ventral (B) images of the adult female holotype (ZRC 1.13264) of Rentapia flavomaculata, new species, including close-ups of the head (C, D).

Fig. 4 in A revision of the Asian tree toad complex Rentapia hosii (Anura: Bufonidae) with the description of a new species from Peninsular Malaysia

Fig. 4. Dorsal and ventral representations of preserved adult female Rentapia hosii from Sarawak. A–C, FMNH 156354, 156344–45 respectively, from Bintulu; D, FMNH 119897 from Niah.