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Environmental and biological data associated with captive-reared Delta Smelt Study, Sacramento-San Joaquin Delta, CA, January-March 2019
The endangered Delta Smelt Hypomesus transpacificus is an osmerid fish endemic to the upper San Francisco Estuary. A captive breeding program for the species led by the Fish Culture and Conservation Laboratory (FCCL), University of California, Davis, began in 1996 to create a refuge population. In order to better understand how captive Delta Smelt would fare in conditions outside of the hatchery, we placed captive-reared fish in enclosures in the Sacramento San-Joaquin Delta, and evaluated their ability to survive, feed, and maintain condition. Fish were acclimated in the hatchery at FCCL, tagged, swabbed, weighed, measured, and transferred to enclosures in the field. There were three types of enclosures (n=2 for each type), varying in mesh size and wrap condition. In January 2019, 384 adult Delta Smelt (243 days post hatch) were transferred to enclosures in Rio Vista. In February 2019, 360 adult Delta Smelt (278 days post hatch) were transferred to enclosures in the Deepwater Shipping Channel. For each deployment, fish remained in enclosures for approximately one month, then were retrieved from enclosures, euthanized, identified, weighed and measured. A subset were also analyzed for diet contents. During the one-month long deployments, cages were checked for biofouling, damage, and dead fish, and water quality measurements and zooplankton samples were collected.
Data from: Flock size and structure influence reproductive success in four species of flamingo in 540 captive populations worldwide
<p><strong>Summary</strong></p> <p>This dataset accompanies the publication "<strong>Flock size and structure influence reproductive success in four species of flamingo in 540 captive populations worldwide</strong>" published in Zoo Biology. It contains anonymised data from 540 captive flamingo populations, and includes the four species: <em>Phoeniconaias minor, Phoenicopterus chilensis, Phoenicopterus roseus</em> and<em> Phoenicopterus ruber</em>. Data were sourced from the Zoological Information Management System (ZIMS), operated by Species360 (https://www.species360.org/). ZIMS is the largest real-time database of comprehensive and standardized information spanning more than 1,200 zoological collections globally, and provides the number of institutions currently managing each flamingo species and both their current and historic population sizes. These data were used to investigate the relationship between reproductive success and both flock size, and structure, on a global scale.</p> <p>This dataset also contains climatic data provided by WorldClim, which were used to assess the influence of climatic variables on captive flamingo reproductive success globally. The WorldClim database averages 19 different climatic variables derived from monthly temperature and rainfall values at a 1 km spatial resolution for the period 1970-2000. Using geographic coordinates (latitude and longitude) we calculated several climatic metrics for each institution. </p> <p> </p> <p><strong>Description of the Dataset</strong></p> <p>One file is provided for each species (<em>P. minor, P. chilensis, P. roseus </em>and <em>P. ruber</em>) as a csv file. Each file contains the following 15 columns:</p> <ul> <li><strong>Institution Code: </strong>An anonymous code used to identify individual zoological institutions. </li> <li><strong>Country: </strong>The country where the institution is located.</li> <li><strong>Year: </strong>Current year (<em>t</em>).</li> <li><strong>Flock Size:</strong> Flock size in year <em>t.</em></li> <li><strong>Males: </strong>The number of males in the flock in year <em>t.</em> </li> <li><strong>Females:</strong> The number of females in the flock in year <em>t.</em></li> <li><strong>Unsexed:</strong> The number of unsexed individuals in the flock in year <em>t.</em></li> <li><strong>Proportion of Females: </strong>The proportion of the flock made up of female individuals in year <em>t</em>. </li> <li><strong>Proportion of Unsexed:</strong> The proportion of the flock made up of unsexed individuals in year <em>t.</em></li> <li><strong>Hatches:</strong> Number of birds hatched in year <em>t.</em></li> <li><strong>Proportion of Additions:</strong> The proportion of the flock in year <em>t</em> made up of additions from year <em>t-1</em> (not including new birds hatched into the flock).</li> <li><strong>MAP: </strong>Mean annual precipitation (mm).</li> <li><strong>MAT: </strong>Mean annual temperature (°C).</li> <li><strong>MAP Var: </strong>Mean annual variation in precipitation (MAP coefficient of variation).</li> <li><strong>MAT Var: </strong>Mean annual variation in temperature (MAT standard deviation).</li> </ul> <p>Note: Mean Annual Temperature (MAT) is provided by WorldClim as °C multiplied by 10, and similarly mean annual variation in temperature as MAT standard deviation multiplied by 100. In the corresponding publication, both were divided (by 10 and 100 respectively) prior to modelling to avoid confusion in the units used.</p> <p> </p> <p><strong>Acknowledgements</strong></p> <p>We acknowledge and thank all Species360 member institutions for their continued support and data input. The research which data refers to was funded by the Irish Research Council Laureate Awards 2017/2018 IRCLA/2017/60 to Y.M.B. Additionally, S.Q.S. received funding from the International Max Planck Research School for Organismal Biology. The Species360 Conservation Science Alliance would like to thank their sponsors: the World Association of Zoos and Aquariums, Wildlife Reserves of Singapore, and Copenhagen Zoo. </p> <p> </p> <p><strong>Disclaimer</strong></p> <p>Despite our best efforts at screening the data for errors and inconsistencies, some information could be erroneous. Similarly, data contained within ZIMS are based on submitted records from individual institutions, and are not subject to editorial verification, potentially permitting errors or failure to update species holdings etc. Despite this, ZIMS represents the only global database of zoo collection composition records, and as a result, is used by the IUCN, Convention on International Trade in Endangered Species (CITES), the Wildlife Trade Monitoring Network (TRAFFIC), United States Fish and Wildlife Service (USFWS) and Department for Environment, Food and Rural Affairs (DEFRA). </p> <p> </p> <p><strong>Credit</strong></p> <p>If you use this dataset, please cite the corresponding publication:</p> <p>Mooney, A., Teare, J. A., Staerk, J.,Smeele, S. Q., Rose, P., Edell, R. H., King, C. E., Conrad, L., & Buckley, Y. M. (2023). Flock size and structure influence reproductive success in four species of flamingo in 540 captive populations worldwide.<em> Zoo Biology</em>, 1–14. <a href="https://doi.org/10.1002/zoo.21753">https://doi.org/10.1002/zoo.21753</a></p> <p> </p> <p> </p>
Dataset: Auditory brainstem responses to varying stimulus presentation rates of 12 bat species in the wild and captivity
<p>Dataset for the Dataset Publication: Auditory brainstem responses to varying stimulus presentation rates of 12 bat species in the wild and captivity</p> <p>There are two datasets available: 1) the measured ABRs from Experiments 1 and 2 and 2) the extracted IOIs:</p> <ol> <li>ABR measurements:</li> </ol> <p>The filename of the ABR recordings from Experiment 1 include the species name, individual ID, sex, stimulus presentation rate (indicated as “modrate”) and recording day and time (yyyyddmm). Each recording file contains 256 measurements of the same stimulus and stimulus presentation rate in columns. An exemplary filename would be “Carollia_perspicillata_cp6male_modrate6_20190905T125903”, meaning that this is a recording of <em>Carollia perspicillata</em> individual cp6 of sex male, tested with a stimulus presentation rate of 6 Hz on the 09.05.2019, and the file was saved at 12:59:03 (the T between date and time stands for “Time”).</p> <p>The filename of the ABR recordings from Experiment 2 include the place of the Experiments (Bad Segeberg) and species name (<em>C. perspicillata</em>), individual ID, sex, stimulus presentation rate (indicated as “modrate”) and recording day and time (yyyymmdd; be aware, that the date format is different between Experiment 1 and 2). Each recording file contains 256 measurements of the same stimulus and stimulus presentation rate in columns. An exemplary filename would be “BadSegeberg_cper_1_male_modrate6_20200622T140952_stimulus_ST01_short ”, meaning that this is a recording of <em>Carollia perspicillata</em> individual cp6 of sex male, tested with a stimulus presentation rate of 6 Hz on the 09.05.2019, and the file was saved at 12:59:03 (the T between date and time stands for “Time”), the individual was presented with stimulus example 01 of the short stimuli.</p> <ol> <li>IOI recordings</li> </ol> <p>The recordings of Inter-Onset-Intervals are all in one single csv file and species and sequence ID is given per row, to be able to analyze the data further.</p> <p> </p>
Fig. 2 in Growth and reproduction in captivity unveils remarkable life-history plasticity in the smallnose fanskate, Sympterygia bonapartii (Chondrichthyes: Rajiformes)
Fig. 2. Egg cases and neonate of Sympterygia bonapartii born at Temaikèn Aquarium (Argentina). ah, anterior horns; mt, mucous tendrils; ph, posterior horns. Scale bar: 20 mm.
Maternal and genetic correlations between morphology and physical performance traits in a small captive primate, Microcebus murinus
<p>Physical performance traits are key components of fitness and direct targets of selection. Maternal effects are important components of integrated phenotypes in a variety of species. Yet their contribution to variation in performance, and phenotypes closely associated with performance, remains poorly understood. We used an animal model approach to quantify the contribution of maternal effects to performance trait variation (in bite force and pull strength) and the relationships between performance and the relevant underlying morphology in <i>Microcebus murinus</i>. We show that bite force is heritable (h<sup>2</sup>~0.23), and that maternal effects are also important source of variation, resulting in a medium inclusive heritability (IH<sup>2</sup>~0.47). Grip strength presented a rather low and non-significant narrow-sense heritability suggesting a higher selective pressure on this trait. Genetic correlations between performance traits and their associated morphometric traits were significant and high (0.47 bite force-head width; 0.48 grip strength-radius length), as was the maternal correlation for bite force-head width (0.75). Further studies evaluating the heritability of performance for other taxa and the role of maternal effects are badly needed to better understand the drivers of variation in performance ultimately allowing for a better understanding of the importance of these types of traits in an evolutionary context.</p>
Fig. 3 in A case of intersex occurrence in Steindachneridion parahybae (Steindachner, 1877) (Siluriformes: Pimelodidae) under captivity condition: a cytogenetic and morphological study
Fig. 3. Micrographs of the ovotestes of Steindachneridion parahybae juveniles in captivity showing the different germ cell types. a) unrestricted spermatogonial testes with anastomosing tubular type, composed by numerous tubules (arrowhead); b) many spermatozoa inside the tubular lumen (arrowhead), separated by interstitial tissue (asterisk); c) gonads section showing perinucleolar oocyte (arrow) close to testicular tissue (arrowhead), containing spermatozoa inside the duct and many intratubular cists; d) ovotestes showing perinucleolar oocyte (arrow) close to spermatozoa inside the duct (arrowhead). Periodic-Acid-Schiff (PAS)/Weigert's Haematoxylin/Metanil Yellow staining. Scale bars: 74 µm (a); 19 µm (b, d); 37 µm (c).
Fig. 4 in A case of intersex occurrence in Steindachneridion parahybae (Steindachner, 1877) (Siluriformes: Pimelodidae) under captivity condition: a cytogenetic and morphological study
Fig. 4. Karyotype in Giemsa in male (a), detail in (b), in female (c), detail in (d) and in intersex animal (e), detail in (f) of Steindachneridion parahybae from Unidade de Hidrobiologia e Aquicultura, Companhia Energética de São Paulo. See the text for more information about karyotype characteristics. Scale bars: 37 μm (a,c,e); 7,4 μm (b,d,f).
Fig. 2 in A case of intersex occurrence in Steindachneridion parahybae (Steindachner, 1877) (Siluriformes: Pimelodidae) under captivity condition: a cytogenetic and morphological study
Fig. 2. Micrographs of the testes of Steindachneridion parahybae juveniles in captivity showing the different germ cell types. a) unrestricted spermatogonial testes with anastomosing tubular type, composed by numerous tubules (arrowhead), which contained the germinal compartment (GC, indicate with arrow) and separated by interstitial tissue; b) isolated spermatogonia cell (arrow) surrounded by Sertoli cells (arrowhead), separated by interstitial tissue (asterisk); c) many spermatocytes and spermatids within the cysts (arrowhead), separated by interstitial tissue (asterisk); d) cysts of spermatocytes (arrowhead), separated by interstitial tissue (asterisk); e) cysts of spermatids (arrowhead), separated by interstitial tissue (asterisk); f) many spermatozoa inside the tubular lumen (arrowhead). Periodic-Acid-Schiff (PAS)/Weigert's Haematoxylin/Metanil Yellow staining. Scale bars: 74µm (a); 37 µm (f); 19 µm (c,e); 14 µm (b); 7.4 µm (d).
Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM)
<p>Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour, time, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (<em>Elephas maximus</em>). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, <em>RALYL</em> and <em>TET2,</em> were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.</p>
Fig. 1 in The identification of Theileria bicornis in captive rhinoceros in Australia
Fig. 1. Photomicrograph of Diff-Quik stained blood smear from black rhinoceros, Siabuwa infected with T. bicornis. The morphology of T. bicornis is not well-described in the literature. We observed comma-shaped piroplasms approximately 1.5 μm in length closely resembling T. orientalis. Ring forms were also occasionally observed (not shown). Bar = 5 μm.
Fig. 2 in The identification of Theileria bicornis in captive rhinoceros in Australia
Fig. 2. Molecular phylogenetic analysis of the piroplasm 18S rRNA gene, including the three rhinoceros samples (Aluka, Umfana and Siabuwa) used in this study. The 18S rRNA sequences were extracted from Genbank during BLAST analysis. The rooted phylogenetic tree was constructed using the neighbour-joining method with T. gondii forming the outgroup. Bootstrap percentages are represented on each node based on 1000 replicates. Phylogenetic analyses were conducted using the PHYLIP packages (Felsenstein, 2005). The haplotypes of the three T. bicornis sequences from this study are indicated at the end of the sequence label.
Fig. 3 in The identification of Theileria bicornis in captive rhinoceros in Australia
Fig. 3. Truncated alignment of the 18S rRNA T. bicornis haplotypes including the new haplotype H4 identified in this study. Geneious version (7.1.9) (Kearse et al., 2012) was used to generate alignments to highlight the differences between the four T. bicornis haplotypes. 18S rRNA sequences of the three previously described T. bicornis haplotypes H1 to H3 (accession numbers KC771140 to KC771142 respectively) were extracted from Genbank for this analysis. The new T. bicornis haplotype H4 was submitted to Genbank and assigned accession number MF567493.
Fig. 1 in Diversity of intestinal protozoa and clinical signs associated in wild-caught Phoneutria nigriventer kept in captivity for the anti-arachnid serum production
Fig. 1. Phoneutria nigriventer kept in glass containers with a humidified cotton ball and a cardboard substrate.
Fig. 2. – A and B in Diversity of intestinal protozoa and clinical signs associated in wild-caught Phoneutria nigriventer kept in captivity for the anti-arachnid serum production
Fig. 2. – A and B, Diarrheal stools, without differentiation of solid and liquid portion. C, Normal stools of Phoneutria nigriventer (red arrow). The white arrow indicates the urine portion, white in color due to urate. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Captive Rearing Success and Critical Thermal Maxima of Bombus griseocollis (Hymenoptera: Apidae): A Candidate for Commercialization?
<p><em>Commercialized bumble bees (Bombus) are primary pollinators of several crops within open field and</em></p> <p><em>greenhouse settings. However, B. impatiens is the only species widely available for purchase in North</em></p> <p><em>America. As an eastern species, concerns have been expressed over their transportation outside of their</em></p> <p><em>native range. Therefore, there is a need to identify regionally appropriate candidates for commercial crop</em></p> <p><em>pollination services, especially in the western U.S.A. In this study, we evaluated the commercialization</em></p> <p><em>potential of B. griseocollis, a broadly distributed species throughout the U.S.A., by assessing nest initiation</em></p> <p><em>and establishment rates of colonies produced from wild-caught gynes, creating a timeline of colony</em></p> <p><em>development, and identifying lab-reared workers’ critical thermal maxima (CT</em><em>Max</em><em>) and lethal temperature</em></p> <p><em>(ecological death). From 2019 to 2021, 70.6% of the wild-caught B. griseocollis gynes produced brood in a</em></p> <p><em>laboratory setting. Of these successfully initiated nests, 74.8% successfully established a nest (produced a</em></p> <p><em>worker), providing guidance for future rearing efforts. Additionally, lab-reared workers produced from wildcaught</em></p> <p><em>B. griseocollis gynes had an average CT</em><em>Max </em><em>of 43.5°C and an average lethal temperature of 46.4°C,</em></p> <p><em>suggesting B. griseocollis can withstand temperatures well above those commonly found in open field</em></p> <p><em>and greenhouse settings. Overall, B. griseocollis should continue to be evaluated for commercial purposes</em></p> <p><em>throughout the U.S.A.</em></p>
Data and R code used for the GLMM and NBDA analyses in 'Captive Asian short-clawed otters (Aonyx cinereus) learn to exploit unfamiliar natural prey'
<p>Foraging plays a vital role in animal life histories, learning whether unfamiliar food items are palatable is a key part of this process. Animals that engage in extractive foraging must also learn how to overcome the protective measures of their prey. While otters (subfamily Lutrinae) are a taxon known for their extractive foraging behaviour, how they learn about prey palatability and acquire extractive foraging techniques remains poorly understood. Here we investigated: (i) how captive Asian short-clawed otters (<em>Aonyx cinereus</em>) learned to interact with, and extract meat from, unfamiliar natural prey, and (ii) how their exploitation of such prey compared to their ability to overcome artificial foraging tasks containing familiar food rewards. Network-based diffusion analysis showed that otters learned to interact with unfamiliar natural prey by observing their group mates. However, once interacting with the prey, they learned to extract the meat mainly asocially. In addition, otters took longer to overcome the protective measures of unfamiliar natural prey than those of extractive food puzzles. Asian short-clawed otter populations are declining in the wild. Increasing our understanding of how they learn to overcome novel foraging challenges could help develop pre-release training procedures as part of reintroduction programmes for otter conservation.</p>
Fig. 2 in Reproductive characteristics of the Burmese Narrow-headed Softshell Turtle, Chitra vandijki, in captivity
Fig. 2. Characteristics of Burmese Narrow-headed Softshell Turtles: (A) back; (B) head and neck, close-up; (C) male, ventral view; (D) female, ventral view.
Fig. 1 in Reproductive characteristics of the Burmese Narrow-headed Softshell Turtle, Chitra vandijki, in captivity
Fig. 1. Artificial rearing facility of Burmese Narrow-headed Softshell Turtles: (A) breeding pond, (B) nesting area, (C) incubation box, (D) rearing facilities.
Fig. 5 in Captive management, reproduction, and comparative larval development of Klappenbach's Red-bellied Frog, Melanophryniscus klappenbachi Prigioni and Langone, 2000
Fig. 5. Body size of different test groups. (A) Single tadpole, O‒1, and (B) five tadpoles per box, O‒5, in osmosis water. (C) Single tadpole, P‒1, and (D) five tadpoles per box, P‒5, in pond water.
Fig. 2. Keeping and rearing M in Captive management, reproduction, and comparative larval development of Klappenbach's Red-bellied Frog, Melanophryniscus klappenbachi Prigioni and Langone, 2000
Fig. 2. Keeping and rearing M. klappenbachi. (A) Terrarium of the adult group housing eight specimens. (B) Rearing of the tadpole test groups in a climate chamber.(C) Rearing containers for the young toadlets.
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)
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DANDI Archive for NWB datasets
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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.