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Data, scripts, and R Notebook for Carneiro et al 2023. Flight performance and wing morphology in the bat Carollia perspicillata: biophysical models and energetics. Integrative Zoology DOI:10.1111/1749-4877.12707
<p>Files provided as supporting information for the paper by Carneiro et al. 2023. Flight performance and wing morphology in the bat <em>Carollia perspicillata</em>: biophysical models and energetics. Integrative Zoology. DOI:10.1111/1749-4877.12707</p> <p>File descriptions</p> <p>ArmTA.txt - Temperature and surface areas for arms of <em>C. perspicillata</em> after flight experiment<br> BodyTA.txt - Temperature and surface areas for body of <em>C. perspicillata</em> after flight experiment<br> HeadTA.txt - Temperature and surface areas for head of <em>C. perspicillata</em> after flight experiment<br> WingTA.txt - Temperature and surface areas for wings (patagium) of <em>C. perspicillata</em> after flight experiment<br> WingMorph.txt - Morphological variables measured in the body and wings of <em>C. perspicillata</em><br> HeatLoss.R - Function to estimate heat loss (Qt)<br> PowFlight.R - Function to estimate minimum power required to fly<br> Script-HeatLoss-FlightPerformance.R - R script with set of analyses performed<br> SupportingInformationFile.docx - R notebook with set of analyses performed, word format<br> SupportingInformationFile.nb.html - R notebook with set of analyses performed, html format<br> SupportingInformationFile.Rmd - R notebook with set of analyses performed (R markdown)</p> <p>For the R scripts (Script-HeatLoss-FlightPerformance.R) and notebook (<br> SupportingInformationFile.Rmd) to work and be compiled, all files need to be copied to the same folder.</p>
Brazilian Zoology Group 2023
<p>This list provides information on <strong>all</strong> the <strong>authors and coordinators of taxa of the Taxonomic Catalog of the Brazilian Fauna (TCBF), active between 2013-2023.</strong> </p> <p>Furthermore, all Authors/Coordinators have been invited (via Google Forms) to serve as authors of the manuscript entitled <strong>Catálogo Taxonômico da Fauna do Brasil</strong><strong>: setting the baseline knowledge on the animal diversity in Brazil, </strong>authored by: Walter A Boeger, Michel P Valim, Hussam Zaher, José Albertino Rafael, Rafaela Campostrini Forzza, Alexandre R Percequillo, Cristiana S Serejo, and Brazilian Zoology Group 2023 (BZG 2023) submitted to Zoologia and the answer is presented in <strong>column G ("AUTHOR MANUSCRIPT?")</strong>. While the majority accepted authorship of the manuscript, few answered negatively and others did not reply (and, hence, were not included in the authorship of the manuscript). We provide available inidividual ORCID, Institution, Country, Function, and taxon of responsability.</p> <p>The TCFB is the product of the effort of more than 800 zoologists, experts in many different groups of animals with species that inhabit the Brazilian territory. Since the start of the Project, the Taxonomic Catalog of the Brazilian Fauna (TCBF) team has been working in an integrated manner to generate the first list of valid species found in the country. So far, our list accounts for more species than ever reported for the Brazilian territory, and for the first time we have a robust estimate of the richness of animals in the country! The work of our experts was extensive and this list would not have been possible without them. Visit the "tabs" and learn a little more about the members of our team, coordinators, authors, and institutions involved.<br><br>The list is available for consultation by anyone, but we must emphasize that due to the narrow time, not all data on each species (eg. distribution, the habit of life, environment) were introduced into the system. The system is dynamic and allows additions and corrections in real-time, rapid inclusion of newly discovered species, corrections associated with nomenclatural decisions, and distribution expansion, among others. Hopefully, soon, this site will provide also tools that will present much more information on Brazilian animals.</p> <p>The updated database of the TCBF can be obtained through the website (<a href="http://fauna.jbrj.gov.br/fauna" target="_blank" rel="noopener">http://fauna.jbrj.gov.br/fauna</a>), <a href="https://dspace.jbrj.gov.br/jspui/bitstream/doc/124/1/Web%20Service%20Cat%c3%a1logo%20Taxon%c3%b4mico%20da%20Fauna%20do%20Brasil.pdf" target="_blank" rel="noopener">API-REST</a>, and monthly versions of the list through <a href="https://ipt.jbrj.gov.br/jbrj/resource?r=catalogo_taxonomico_da_fauna_do_brasil" target="_blank" rel="noopener">IPT</a>. </p> <p><em>Catálogo Taxonômico da Fauna do Brasil</em> (<em>CTFB</em>) - link: http://fauna.jbrj.gov.br/fauna</p>
MALDI-TOF-MS spectra of historical whale skeletons from the Museum of Zoology, Strasbourg
<p>Spectra data from historical whale skeletons from the Museum. Samples were acid demineralized followed by gelatinization, digestion with trypsin, and peptide purification on C18 filters. They were run on on Bruker autoflex MALDI-TOF-MS. Mzml file formats for the raw data are provided here along with a file information csv file which provides the identification of the samples.<br> <br> For more information see the associated publciation.</p>
UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC) Data Archive and Biodiversity Dataset Graph hash://md5/10663911550bb52a0f5741993f82db9d hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c
<p>A biodiversity dataset graph: UCSB-IZC</p> <p>The intended use of this archive is to facilitate (meta-)analysis of the UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC). UCSB-IZC is a natural history collection of invertebrate zoology at Cheadle Center of Biodiversity and Ecological Restoration, University of California Santa Barbara.</p> <p>This dataset provides versioned snapshots of the UCSB-IZC network as tracked by Preston [2,3] between 2021-10-08 and 2021-11-04 using [preston track "https://api.gbif.org/v1/occurrence/search/?datasetKey=d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0"].</p> <p>This archive contains 14349 images related to 32533 occurrence/specimen records. See included sample-image.jpg and their associated meta-data sample-image.json [4].</p> <p>The images were counted using:</p> <p>$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\<br> | grep -o -P ".*depict"\<br> | sort\<br> | uniq\<br> | wc -l</p> <p>And the occurrences were counted using:</p> <p>$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\<br> | grep -o -P "occurrence/([0-9])+"\<br> | sort\<br> | uniq\<br> | wc -l</p> <p>The archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance files and data files. Only two index and provenance files are included and have been individually included in this dataset publication. Index files provide a way to links provenance files in time to establish a versioning mechanism.</p> <p>To retrieve and verify the downloaded UCSB-IZC biodiversity dataset graph, first download preston-*.tar.gz. Then, extract the archives into a "data" folder. Alternatively, you can use the Preston [2,3] command-line tool to "clone" this dataset using:</p> <p>$ java -jar preston.jar clone --remote https://archive.org/download/preston-ucsb-izc/data.zip/,https://zenodo.org/record/5557670/files,https://zenodo.org/record/5660088/files/</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br> <urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .<br> <hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c> <http://purl.org/pav/previousVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .</p> <p>To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br> hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c file:/home/jhpoelen/ucsb-izc/data/ce/1d/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c OK CONTENT_PRESENT_VALID_HASH 66438 hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c<br> hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 file:/home/jhpoelen/ucsb-izc/data/f6/8d/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 OK CONTENT_PRESENT_VALID_HASH 4093 hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844<br> hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef file:/home/jhpoelen/ucsb-izc/data/3e/70/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef OK CONTENT_PRESENT_VALID_HASH 5746 hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef<br> hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b file:/home/jhpoelen/ucsb-izc/data/99/58/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b OK CONTENT_PRESENT_VALID_HASH 6147 hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b</p> <p>Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".</p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br> README</p> <p>-- executable java jar containing preston [2,3] v0.3.1. --<br> preston.jar</p> <p>-- preston archive containing UCSB-IZC (meta-)data/image files, associated provenance logs and a provenance index --<br> preston-[00-ff].tar.gz</p> <p>-- individual provenance index files --<br> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a</p> <p>-- example image and meta-data --<br> sample-image.jpg (with hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c)<br> sample-image.json (with hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844)</p> <p>--- end of file descriptions ---</p> <p><br> References</p> <p>[1] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-11-04 as indexed by the Global Biodiversity Informatics Facility (GBIF) with provenance hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36 hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c.<br> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .<br> [3] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132<br> [4] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-10-08. https://www.gbif.org/occurrence/3323647301 . hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c</p>
Figure 3 in Changes in a soil microarthropod community in the vicinity of dominant tree species under trampling management at the Safari Zoological Center, Israel
Figure 3 The taxon richness, Shannon index, Simpson index, and Evenness index (mean ± SD) of soil Acari at different treatment sites at the Safari Zoological Center, Israel, December 2013. OE = open places under enclosure, OT = open places under trampling; EE = E. camaldulensis canopy habitat under enclosure, ET =E. camaldulensis canopy habitat under trampling, TE =T. aphylla canopy habitat under enclosure, TT =T. aphylla canopy habitat under trampling, CE =C. sempervirens canopy habitat under enclosure, CT =C. sempervirens canopy habitat under trampling. Different letters represent significance at p<0.05.
Figure 2 in Changes in a soil microarthropod community in the vicinity of dominant tree species under trampling management at the Safari Zoological Center, Israel
Figure 2 The abundance (individuals per 10 g dry soil substrate; mean ± SD) of soil microarthropod taxa extracted from core samples at different treatment sites at the Safari Zoological Center, Israel, December 2013. OE = open places under enclosure, OT = open places under trampling; EE =E. camaldulensis canopy habitat under enclosure, ET =E. camaldulensis canopy habitat under trampling, TE = T. aphylla canopy habitat under enclosure, TT =T. aphylla canopy habitat under trampling, CE = C. sempervirens canopy habitat under enclosure, CT =C. sempervirens canopy habitat under trampling. Different letters within the same group represent significance at p<0.05.
Figure 1 in Changes in a soil microarthropod community in the vicinity of dominant tree species under trampling management at the Safari Zoological Center, Israel
Figure 1 Location of study sites at the Safari Zoological Center, Israel. OE = open places under enclosure, OT = open places under trampling; EE =E. camaldulensis canopy habitat under enclosure, ET = E. camaldulensis canopy habitat under trampling, TE =T. aphylla canopy habitat under enclosure, TT = T. aphylla canopy habitat under trampling, CE =C. sempervirens canopy habitat under enclosure, CT = C. sempervirens canopy habitat under trampling.
Figs. 4 6 in Araneae Spider.- Zoological Survey of India
Figs. 4 6.: Oxyopes tikaderi sp. nov.: 4. Dorsal view of female, legs omitted. 5. Epigyne. 6. Internal genitalia.
Figs. 1 3 in Araneae Spider.- Zoological Survey of India
Figs. 1 3: Oedignatha shillongensis sp. nov.: 1. dorsal view of female, legs omitted. 2. Epigyne. 3. Internal genitalia
Fig. 4 in The Lampyridae of the Achille Costa's (1823-1898) collection, preserved at the Zoological Museum of Naples (Italy)
Fig. 4. Achille Costa Collection (Zoological Museum of Naples). A: Paralectotypi, habitus; B: Paralectotypus (card number: 18), original label.
Fig. 3 in The Lampyridae of the Achille Costa's (1823-1898) collection, preserved at the Zoological Museum of Naples (Italy)
Fig. 3. Achille Costa Collection (Zoological Museum of Naples). A: Paralectotypus, habitus; B: Paralectotypus, original label.
Fig. 1 in The Lampyridae of the Achille Costa's (1823-1898) collection, preserved at the Zoological Museum of Naples (Italy)
Fig. 1. Achille Costa Collection (Zoological Museum of Naples). A: label of the entomological box containing the Lampyridae; B: overview of the entomological box containing the Lampyridae; C: detail of the specimens of the family Lampyridae. (The numbers are progressive and do not correspond to the card numbers.)
Figure 2 in Archival sea turtles in National Zoological Collections of Zoological Survey of India
Figure 2. Representatives of the archival Sea turtle specimens (the Green Sea Turtle, Chelonia mydas) preserved in Zoological Survey of India, Kolkata. A. Hatchling of C. mydas, Reg. No. ZSI 14544 (dorsal view, wet collection). B. Hatchling of C. mydas, Reg. No. ZSI 14543 (ventral view, wet collection). C. Eggs of C. mydas (wet collection). D. Skull of C. mydas, Reg. No. ZSI 389 (1404) (lateral view, dry collection). E. Adult individuals of C. mydas, Reg. No. ZSI 22489 (lateral view, wet collection).
Figure 1 in Archival sea turtles in National Zoological Collections of Zoological Survey of India
Figure 1. Representatives of the archival Sea turtle specimens (the Hawksbill Sea Turtle, Eretmochelys imbricata) preserved in Amphibia and Reptilia gallery of Indian museum, Kolkata and morphometric measurements. HD= Head diameter, FL= Forelimb length, HL= Hindlimb length, CCL=Curved carapace length, CPL= Curved plastron length, CCW= Curved carapace width, CPW= Curved plastron width, TL= Total length.
Figs 49-52 in New and little known Epilamprinae (Dictyoptera: Blaberidae) from the collections of the Muséum d'histoire naturelle de Genève and the Zoological Institute of Saint Petersburg. Part 4
Figs 49-52. Notolampra gibba (Thunberg, 1826), female. (49) Abdominal apex, dorsal view. (50) Genital plate, ventral view. (51) Abdominal apex and right tergal processes, ventral view. (52) Ovipositor and adjacent structures, ventral view, basivalvula broken. Dotted areas show membranous parts, except for valves of ovipositor. Abbreviations: bsv., gg., Par., pl., teIX., v.I., v.II., v.III., vs. - see chapter "abbreviation used in figures", for details see text. Scale bars 1 mm: a (49), b (50), c (51), d (52).
Figs 25-35. Molytria vegranda Roth, 1999 in New and little known Epilamprinae (Dictyoptera: Blaberidae) from the collections of the Muséum d'histoire naturelle de Genève and the Zoological Institute of Saint Petersburg. Part 4
Figs 25-35. Molytria vegranda Roth, 1999, male. (25-26) Left hind tarsus, ventral (25) and inner (26) view. (27) Abdominal apex, dorsal view. (28) Hypandrium, ventral view. (29) Sclerites L2D, L4U and outlines of caudal part of hypandrium, dorsal view. (30-31) Right phallomere, ventral (30) and dorsal (31) view. (32) Apical part of sclerite L2D, dorsal view. (33) Sclerite L3. (34, 35) Apex of sclerite L3. Dotted areas show membranous parts. Abbreviations: a.s., b.L2D, b.L3, c.p.R1T, f.s., L4U, R2, R3, R4, R5, s.t., scl.a. - see chapter "abbreviation used in figures", for details see text. Scale bars 1 mm: a (24-25), b (27-29), c (30-31), d (32), e (33), f (34-35).
Figs 1-8 in New and little known Epilamprinae (Dictyoptera: Blaberidae) from the collections of the Muséum d'histoire naturelle de Genève and the Zoological Institute of Saint Petersburg. Part 4
Figs 1-8. Placoblatta semialata sp. nov., male holotype (1-5) and female paratype (6-8). (1) Facial part of head. (2, 6) Anterior part of body, dorsal view. (3) Right fore leg, ventral view. (4, 5) Right hind tarsus, ventral (4) and outer (5) view. (7-8) Abdominal apex, dorsal (7) and ventral (8) view. The black parallelogram in Fig. 5 is a pin. Abbreviations: a.s. - see chapter "abbreviation used in figures", for details see text. Not to scale.
Figs 36-48 in New and little known Epilamprinae (Dictyoptera: Blaberidae) from the collections of the Muséum d'histoire naturelle de Genève and the Zoological Institute of Saint Petersburg. Part 4
Figs 36-48. Notolampra gibba (Thunberg, 1826), male. (36) Facial part of head. (37) Head, pronotum and basal part of left tegmen, dorsal view. (38) Abdominal tergites VIII-IX, dorsal view. (39) Abdominal apex, dorsal view. (40) Paraprocts and adjacent structures, ventral view. (41) Hypandrium, ventral view. (42-43) Right phallomere, dorsal (42) and ventral (43) view. (44) Sclerite L2D, dorsal view. (45-46) Apical part of sclerite L2D, ventral (45) and dorsal (46) view. (47) Sclerite L3. (48) Apex of sclerite L3. Dotted areas show dark colour (37) or membranous parts (38-48). Abbreviations: ap.scl., b.L2D, b.L3, c.p.R1T, R2, R3, R4, R5, tr.l. - see chapter "abbreviation used in figures", for details see text. Scale bars 1 mm: a (36), b (37), c (38-39), d (40), e (41), f (42-43), g (44), h (45-46), i (47-48).
Data to "Evidence for the evolution of eusociality in stem ants and a systematic revision of †Gerontoformica (Hymenoptera: Formicidae)" published in Zoological Journal of the Linnean Society
<p>These are the µCT Datasets used in the study "Evidence for the evolution of eusociality in stem ants and a systematic revision of †<em>Gerontoformica</em> (Hymenoptera: Formicidae)" published in the Zoological Journal of the linnean society.<br> In the study, an amber piece containing 4 specimens of the stem ant genus †<em>Gerontoformica </em>was investigated, one of them being a pupa belonging to †<em>G. gracilis</em> (CASENT0741231), one adult belonging to †<em>G. gracilis</em> (CASENT0741232) and two adults of the newly described species †<em>G. sternorhabda</em> (CASENT0741233 and CASENT0741234). The adult specimen of †<em>G. gracilis</em> (CASENT0741232) had exception internal preservation, so higher magnification scans for anatomical details were performed. The dataset includes full body scans of all of these individuals, adjusted datasets in which the adult specimens were segmented out of the amber matrix (used for the volume renderings in the article) and the two head focused scans of †<em>G. gracilis</em> (CASENT0741232). The scanning parameters can be taken from the uploaded Scans Metadata Excel file, which is also part of the supplementary material of the related article. The two adult scans of †<em>G. sternorhabda</em> (CASENT0741233 and CASENT0741234) are in DICOM file format, all other data are in TIFF image format.</p>
Fig. 1 in Finding Of Two Species From The Tribe Synhimantea (Nematoda, Acuariidae) In The Kyiv Zoological Park
Fig. 1. De. sagitattus and Di. nasuta: 1 — anterior end of De. sagitattus; 2 — anterior end of Di. nasuta; 3 — anterior end of the larva Di. nasuta; 4 — posterior end of the larva Di. nasuta; pl — pseudolabia, bc — buccal capsule, cp — cervical papilla, nr — nerve ring, c — cordons, em — muscular esophagus, eg — glandural esophagus; a — anal pore. Scale bar 100 µm.
ScienceDex guides
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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.