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Data for: Hematology and biochemistry of critically endangered radiated tortoises (Astrochelys radiata): reference intervals in previously confiscated subadults and variability based on common techniques
<p>Dataset for: Brenn-White M, Raphael BL, Rakotoarisoa NAT, Deem SL. 2022. Hematology and biochemistry of critically endangered radiated tortoises (<em>Astrochelys radiata</em>): reference intervals in previously confiscated subadults and variability based on common techniques. PLOS One.</p> <p>Dataset is contained in a.radiata_bloodwork.csv. Metadata and data definitions are contained in a.radiate_bloodwork_readme.txt.</p> <p>Dataset contains hematology and biochemistry values of 120 previously confiscated, clinically healthy subadult radiated tortoises living under human care within their native habitat at the Tortoise Conservation Center (TCC), Madagascar. To evaluate the effects of different commonly used techniques on these parameters, we compared results between two venipuncture sites (subcarapacial sinus and brachial vein) and three different WBC quantification methods (Natt and Herrick, Leukopet<sup>TM</sup>, and slide estimate). Data from tortoises removed from the final analyses due to sample quality issues are also included as frequency of sample quality issues varied by venipuncture site. See associated publication for detailed methods. </p> <p> </p>
Figure 3 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 3 Dorsal and ventral photos of glassfrogs in life. (A) Male of Hyalinobatrachium mashpi sp. nov., CJ11642 (holotype). (B) Gravid female of H. mashpi sp. nov., Mashpi Reserve, Ecuador. (C) Male of H. nouns sp. nov., ZSFQ0537. (D) Male of H. nouns sp. nov., MZUTI3299 (holotype). (E) Male of H. aureoguttatum, Ecuador. (F) Gravid female of H. aureoguttatum, Ecuador. Photos by Jaime Culebras (A, B, D, E, F) and Ross Maynard (C). Full-size DOI: 10.7717/peerj.13109/fig-3
Figure 7 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 7 Discriminant analysis of principal components (DAPC) of glassfrog species' calls. Variables analyzed include: peak frequency, maximum frequency, minimum frequency, call duration, and inter-call duration. Sample size as follows: H. adespinosai one individual, 10 calls; H. aureoguttatum six individuals, 24 calls; H. mashpi sp. nov. two individuals, 12 calls; H. pellucidum one individual, 41 calls; H. tatayoi four individuals, 26 calls; H. valerioi three individuals, 70 calls. Full-size DOI: 10.7717/peerj.13109/fig-7
Figure 10 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 10 Distribution of Hyalinobatrachium mashpi sp. nov. and H. nouns sp. nov. in Ecuador. Note that localities of the two new taxa are separated by the Intag-Guayllabamba valley. Full-size DOI: 10.7717/peerj.13109/fig-10
Figure 2 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 2 Phylogenetic position of Hyalinobatrachium mashpi sp. nov. and H. nouns sp. nov. Phy- logenetic relationships of Hyalinobatrachium inferred from the 16S mitochondrial gene under ML cri- terion. All sequences were downloaded from GenBank, except those in red (Material S2). Genbank codes are listed next to each terminal. Associated locality data is available at Genbank, as well as in Guayasamin et al. (2008, 2020), Castroviejo-Fisher et al. (2014), and Twomey, Delia & Castroviejo-Fisher (2014). Full-size DOI: 10.7717/peerj.13109/fig-2
Figure 6 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 6 Visual representation of Hyalinobatrachium mashpi sp. nov. advertisement call, with comparisons of two similar species, H. aureoguttatum and H. valerioi. The call of each species is depicted in three forms: (Top) oscillograms, waveforms representing amplitude changes over time; (Middle) spectrograms, plots of frequency over time, with higher amplitudes represented by brighter colors; and (Bottom) power spectra, representing the relative amplitude of each frequency. Full-size DOI: 10.7717/peerj.13109/fig-6
Figure 9 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 9 Habitat of Hyalinobatrachium mashpi sp. nov. (A) Tributary of the Mashpi River, Tayra Reserve, Pichincha Province, Ecuador. (B) Mashpi Reserve, Pichincha Province, Ecuador. (C) Tayra Reserve, Pichincha Province, Ecuador. (D) Habitat loss in the vicinity of Tayra Reserve, Pichincha Province, Ecuador. Photos by Jaime Culebras. Full-size DOI: 10.7717/peerj.13109/fig-9
Figure 1 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 1 Morphological measurements as obtained in this study. Measurements are described in the text. SVL, Snout–vent length; HW, Head width; IOD, Interorbital distance. Ilustrations by Valentina Nieto Fernández. Full-size DOI: 10.7717/peerj.13109/fig-1
Figure 5 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 5 Dorsal patterns of glassfrogs in life. (A) Hyalinobatrachium mashpi sp. nov., CJ11642 (holotype). (B) H. nouns sp. nov., ZSFQ0537. (C) H. aureoguttatum, SC 435. (D) H. talamancae, Costa Rica. (E) H. vireovittatum, Costa Rica. (F) H. valerioi, Costa Rica.Photos by Jaime Culebras (A, D, E, F), Jose Vieira (B) and Luis Coloma (C). Full-size DOI: 10.7717/peerj.13109/fig-5
Figure 8 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 8 Parental care in Hyalinobatrachium mashpi sp. nov. (A) Male calling at San Vicente River, Mashpi Reserve, Pichincha Province, Ecuador. (B) Male at tributary of the Mashpi River, Tayra Reserve, Pichincha Province, Ecuador. Photos by Carlos Morochz (A) and Jaime Culebras (B). Full-size DOI: 10.7717/peerj.13109/fig-8
Figure 11 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 11 Habitat of Hyalinobatrachium nouns sp. nov. (A) Tributary of the Manduriacu River, Río Manduriacu Reserve, Imbabura Province, Ecuador. (B) Tributary of the Manduriacu River, Río Manduriacu Reserve, Imbabura Province, Ecuador. (C) Río Manduriacu Reserve, Imbabura Province, Ecuador. (D) Habitat loss in the vicinity of Los Cedros Reserve, Imbabura Province, Ecuador. Photos by Jaime Culebras. Full-size DOI: 10.7717/peerj.13109/fig-11
Figure 4 in Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
Figure 4 Dorsal and ventral photos of glassfrogs in life. (A, B) Male of Hyalinobatrachium vireovittatum, Costa Rica. (C, D) Male of H. talamancae, Costa Rica. (E, F) Male of H. valerioi, Costa Rica. Photos by Jaime Culebras (A, C, D, E, F) and Josué Alberto Vargas (B). Full-size DOI: 10.7717/peerj.13109/fig-4
Dataset for map in "Endangered languages in Brazil in 2021"
<p>Data set and R script used to produce the map of Brazilian indigenous languages in "Endangered languages in Brazil in 2021" by Sebastian Drude, Joshua Birchall, Ana Vilacy Galúcio, Denny Moore and Hein van der Voort. This is a chapter in the book <em>Endangered Languages in the 21<sup>st</sup> Century </em>edited by Eda Derhemi and Chris Moseley and to be published by Routledge in 2022.</p>
Predicting harvest impact and establishment success when translocating highly mobile and endangered species
<p>Harvesting individuals for translocations can negatively impact source populations, a critical challenge for species reduced to small populations. Consequently, translocation cohorts often remain small, reducing the establishment probability at the destination. Balancing the potential benefits and risks of such translocations is further complicated by philopatry and natural metapopulation dynamics if the target species is highly mobile. These challenges highlight the importance of translocation feasibility assessments, but such assessments often remain qualitative to date. The critically endangered Kuaka (Whenua Hou Diving Petrel; Pelecanoides whenuahouensis) is a philopatric, highly mobile seabird that could benefit from conservation translocations, but only one small population remains. Through expert elicitations with a user-friendly Shiny app, we developed a novel metapopulation extension to an integrated population model fitted to long-term data, allowing us to simultaneously project harvest impact on the source and establishment of destination populations under alternative translocation scenarios, while accounting for philopatry and metapopulation dynamics. Establishment of a destination population without excessive impact on the source was possible, but subject to uncertainty about philopatry and metapopulation dynamics. Accounting for juveniles returning to the source post-translocations reduced impact on the source, but also decreased establishment at the destination. Natural movements of adults and juveniles between source and destination populations were predicted to modulate effects of different harvest intensities. Synthesis and application: Using state-of-the art integrated population models and expert elicitations, we illustrate how translocation feasibility can be evaluated transparently and quantitatively, even when targeting endangered, philopatric, and highly mobile species. Our approach is a considerable improvement on current qualitative feasibility assessments. However, we also illustrate that, ultimately, the favoured translocation strategy depends on balancing biological and other fundamental objectives inherent to translocations. Therefore, the ideal strategy cannot be determined solely mathematically, and feasibility assessments should incorporate explicit value statements. Our methodology is applicable to any future translocation scenario.</p>
Estimating the abundance of the critically endangered Baltic Proper harbour porpoise (Phocoena phocoena) population using passive acoustic monitoring
<p>Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (<i>Phocoena phocoena</i>) has collapsed since the mid-20<sup>th</sup> century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN and HELCOM; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011-April 2013, calibrating the loggers' spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 71-1,105 individuals (95% CI, point estimate 491) during May-October within the population's proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighbouring Belt Sea population. Further, we offer evidence that design-based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales.</p>
Data from: A new population record of Critically Endangered Dipterocarpus bourdillonii Brandis from the Anamalai Tiger Reserve, Tamil Nadu
<p><strong>This dataset is based on the following manuscript/publication:</strong><br> Page, N., S. Kasinathan, K. Bhat, G. Moorthi, T. Sundarraj, Divya Mudappa, and T. R. S. Raman (2022). A new population record of Critically Endangered <em>Dipterocarpus bourdillonii</em> Brandis from the Anamalai Tiger Reserve, Tamil Nadu. <em>Journal of Threatened Taxa</em> 14(8): 21651–21659. https://doi.org/10.11609/jott.7860.14.8.21651-21659</p> <p>Please refer to the README.txt file included with the dataset for complete details and usage notes.</p> <p><strong>Geographic Coverage:</strong><br> Location/Study Area: Valparai Plateau, Tamil Nadu, India; Anamalai Tiger Reserve, Tamil Nadu, India<br> GPS coordinates: Valparai Plateau (0°15'- 10°22'N, 76°52'-76°59'E); Anamalai Tiger Reserve (10°12'-10°35'N, 76°49'-77°24'E)</p> <p><strong>Temporal Coverage:</strong><br> Begins: 2020-10-01 (Year, Month, Day)<br> Ends: 2022-05-31 (Year, Month, Day)</p> <p><strong>Funding:</strong><br> Fondation Franklinia<br> AMM Murugappa Chettiar Research Centre<br> Rohini Nilekani Philanthropies</p> <p><strong>Dataset:</strong></p> <p>The dataset includes 7 files: 1 text file (<strong>README.txt</strong>), 5 data files in comma-delimited format (CSV), and 1 KML file of seven survey routes. Details of content of each CSV data file are provided below. The following files are included:<br> <strong>README.txt:</strong> Usage notes and metadata related to the dataset<br> <strong>1_Surveys_ver2.csv:</strong> Details of trails covered where Dipterocarpus bourdillonii was recorded during the survey<br> <strong>2_Focal_tree_data_ver2.csv:</strong> Details of focal trees of Dipterocarpus bourdillonii<br> <strong>3_Tree_centred_PCQ_ver2.csv: </strong>Data from point-centred quarter (PCQ) plots sampled with focal trees at the centre<br> <strong>4_Plant_checklist_ver2.csv:</strong> Checklist of plants (mainly trees) recorded on survey trails<br> <strong>5_Seed_fruit_ver2.csv:</strong> Measurements of fruits and seeds of Dipterocarpus bourdillonii<br> <strong>06_Dipterocarpus_bourdillonii_survey_trails.kml:</strong> This file includes the GPS tracks of the seven survey trails in KML format.</p> <p>Details and data available in the columns in each of the above CSV files and the KML file are explained below.</p> <p><strong>1_Surveys_ver2.csv</strong><br> Column: Description<br> Date: Date on which the survey was done<br> Place: Name of the place where the focal tree is located. e.g., Candura, Manamboli, Iyerpadi etc<br> Route_description:Description of place or route covered<br> Trail: Name of the tree survey trail<br> Trail_distance: Distance covered on the trail in kilometres (km)<br> Track_filename_kml: Name of the file with GPS track of survey trail/route, where available, in KML format<br> Observers: Names of observers who took measurements and filled datasheet during survey<br> Remarks: Notes and additional information</p> <p><strong>2_Focal_tree_data_ver2.csv</strong><br> Column: Description<br> FT_ID: Unique numeric linking ID of each focal tree (NA for 3 individuals found in plots around other focal trees)<br> Species: Focal tree species<br> Date: Date on which the survey was done<br> Place: Name of forest range (Manamboli)<br> Waypoint: Unique location waypoint number for the focal tree and GPS instrument used<br> Time: Time when the focal tree's data was collected<br> Location: Landmark where the focal tree is located (NA, if not available)<br> Latitude: Latitude of the focal tree (decimal degrees N)<br> Longitude: Longitude of the focal tree (decimal degrees E)<br> Elevation: Elevation of the focal tree from sea-level in metres<br> Slope: Slope at focal tree location assessed with Clinometer, categorised as Flat, Gentle, Moderate, or Steep (NA, if not available)<br> ID_Notes: Any obvious signs with which to identify focal tree (NA, if not available)<br> Phenophase: Phenophase of the focal tree viz. leaf flush, buds/flowers, fruits (NA, if not available)<br> GBH: Girth of the focal tree in cm, at 1.3m from ground; measured from the higher side if tree is on slope<br> Tree_ht: Focal tree's height in m (NA, if not available)<br> Canopy_ht: Height of canopy in m where the focal tree is located (NA, if not available)<br> Substrate: Substrate where focal tree is standing viz. Earth, Rock, Streamside, Other (NA, if not available)<br> Invasives: List of invasive plant species present within 5 m radius around the focal tree (NA, if not available)<br> Stature: Stature of the focal tree relative to its surroundings (NOT of the species in general) categorised as Understorey, Mid, Canopy, Emergent (NA, if not available)<br> Relatively: Relative height of focal tree in relation to other trees within 10 m radius categorised as Shorter than most, Taller than most, Same height as most (NA, if not available)<br> Deadwood: Estimated percentage of deadwood present on the tree in 4 classes of <25%, 26-50%, 51-75%, 76-100% (NA, if not available)<br> Damage: Observed damages such as Main trunk broken, Branches broken, Hollow at base, Gaping cavity, Infected, Dried leaves (as on a dead branch) (NA, if not available)<br> Shape: Canopy shape of the focal tree (not species in general) categorised as Spreading, Oval, Fan, Column, Cone (NA, if not available)<br> Closure: Canopy closure due to foliage visually estimated standing next to trunk of focal tree and looking up, categorised as 0% (only sky and leafless branches visible), 1-25%, 26-50%, 51-75%, 76-100% (NA, if not available)<br> Seedlings: Count of conspecific seedlings (stems of girth at breast height <10 cm) around the focal tree in a 5 m radius (NA, if not available)<br> Saplings: Count of conspecific saplings (stems of girth at breast height 10-30 cm) around the focal tree in a 5 m radius (NA, if not available)<br> Trees: Count of conspecific trees (stems of girth at breast height >30 cm) around the focal tree in a 5 m radius (NA, if not available)<br> Remarks: Notes and additional information (NA, if not available)</p> <p><strong>3_Tree_centred_PCQ_ver2.csv</strong><br> Column: Description<br> FT_ID: Unique numeric linking ID of each focal tree in point-centred quarter (PCQ) plot<br> Focal_tree: Scientific name of focal tree species at the centre of the PCQ plot<br> Species: Scientific name of tree species recorded in PCQ plot around focal tree<br> GBH (cm): Girth of PCQ tree in cm, at 1.3 m from ground; measured from the higher side if tree is on a slope. Main stem only.<br> Distance: Distance from focal tree, in m; measured from the approximate centre of bole to centre of bole and not bark to bark<br> Multistem: NA if single-stemmed; if multi-stemmed, then GBH of additional stems given as notes.</p> <p><strong>4_Plant_checklist_ver2.csv</strong><br> Column: Description<br> Date: Date on which the survey was done<br> Place: Name of the place where the focal tree is located. e.g., Candura, Manamboli, Iyerpadi etc<br> Route: Route of the tree survey trail<br> Checklist_species: Scientific name of tree species observed as present along trail and within 10 m on either side<br> Remarks: Notes and additional information</p> <p><strong>5_Seed_Fruit_ver2.csv</strong><br> Column: Description<br> Sample: Serial number of sample of single winged fruit measured<br> Species: Scientific name of tree species<br> No_Seeds: Unit number of seed measured<br> Fresh_fruit_weight_g: Weight of each fruit measured on an Ohaus scale in grams<br> Nut_length_cm: Length of nut along the longitudinal axis in cm<br> Nut_width_1_cm: Width of nut in cm measured along axis perpendicular to nut length<br> Nut_width_2_cm: Width of nut in cm measured along axis perpendicular to nut length and nut width 1<br> Wing1_length_cm: Length of longer wing (sepal) in cm<br> Wing1_width_cm: Width of longer wing (sepal) in cm<br> Wing2_length_cm: Length of shorter wing (sepal) in cm<br> Wing2_width_cm: Width of shorter wing (sepal) in cm</p> <p><strong>06_Dipterocarpus_bourdillonii_survey_trails.kml</strong><br> This file includes the GPS tracks of the following seven trails in KML format:<br> 2021-01-30_Anali-Ayyankulam-Manamboli (Trail-2)<br> 2021-03-26_Ayyankulam (Trail-4)<br> 2021-04-10_Ayyankulam Parai (Trail-5)<br> 2022-03-07_Ayyankulam Parai to Ayyankulam_leftbank (Trail-8)<br> 2022-03-07_Ayyankulam Parai to Ayyankulam_rightbank (Trail-9)<br> 2022-03-09_Manamboli PH_leftbank (Trail-10)<br> 2022-03-09_Manamboli PH_rightbank (Trail-11)</p>
Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population
<p>Estimating the demographic parameters of contemporary populations is essential to the success of elasmobranch conservation programmes, and to understanding their recent evolutionary history. For benthic elasmobranchs such as skates, traditional fisheries-independent approaches are often unsuitable as the data may be subject to various sources of bias, whilst low recapture rates can render mark-recapture programmes ineffectual. Close-kin mark-recapture (CKMR), a novel demographic modelling approach based on the genetic identification of close relatives within a sample, represents a promising alternative approach as it does not require physical recaptures. We evaluated the suitability of CKMR as a demographic modelling tool for the critically endangered blue skate (<em>Dipturus batis</em>) in the Celtic Sea using samples collected during fisheries-dependent trammel-net surveys that ran from 2011 to 2017. We identified three full-sibling and 16 half-sibling pairs among 662 skates, which were genotyped across 6,291 genome-wide single nucleotide polymorphisms (SNPs), 15 of which were cross-cohort half-sibling pairs that were included in a CKMR model. Despite limitations owing to a lack of validated life-history trait parameters for the species, we produced the first estimates of adult breeding abundance, population growth rate, and annual adult survival rate for <em>D. batis</em> in the Celtic Sea. The results were compared to estimates of genetic diversity, effective population size (N<sub>e</sub>), and catch per unit effort (CPUE) estimates from the trammel-net survey. Although each method was characterised by wide uncertainty bounds, together they suggested a stable population size across the time-series. Recommendations for the implementation of CKMR as a conservation tool for data-limited elasmobranchs are discussed. In addition, the spatio-temporal distribution of the 19 sibling pairs revealed a pattern of site-fidelity in <em>D</em>. <em>batis</em>, and supported field observations suggesting an area of critical habitat that could qualify for protection might occur near the Isles of Scilly.</p>
Figure 6 in A New Coccidian (Apicomplexa: Eimeriidae) in the Critically Endangered Central American River Turtle (Dermatemys Mawii) in Belize
Figure 6. Evolutionary relationships of Eimeria grayi n. sp. inferred by Bayesian analysis of partial 18S rRNA sequences. Posterior probabilities are shown at branch points. Toxoplasma gondii (EF472967) was selected as the outgroup. Eimeria grayi n. sp. is bolded and underlined.
Figure 3 in A New Coccidian (Apicomplexa: Eimeriidae) in the Critically Endangered Central American River Turtle (Dermatemys Mawii) in Belize
Figure 3. Light microscopic photomicrograph of sporulated oocyst of Eimeria grayi n. sp. Oocyst showing 2 of 3 surface projections (arrows) at 1 pole and a broader-based projection (arrowhead) from the opposite pole.
Figure 2 in A New Coccidian (Apicomplexa: Eimeriidae) in the Critically Endangered Central American River Turtle (Dermatemys Mawii) in Belize
Figure 2. Light microscopic photomicrograph of sporulated oocyst of Eimeria grayi n. sp. Oocyst showing 3 surface projections (arrows) at 1 pole.
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.