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403 results for “captivity”
Genetic diversity and the implications of captive rearing for a small population of Black‐tailed Godwits
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Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM)
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Dyadic distances in African savannah elephants as they transition from Semi-captivity to the wild in Okavango Delta, Botswana, 2021 to 2023
Data package contains a dataset of distances(m) of 15 dyads generated from GPS collar data of 6 female savannah elephants as they were being released from semi-captivity to the wild in Okavango Delta, Botswana from November 1st, 2021-November 29th,2023. The dataset is provided as part the manuscript `Dyadic distance in African savannah elephants (Loxotonda africana) increases during release from semi-captivity to the wild`.
Data & example videos: Exploring effects of sound on the time budget of fishes: an experimental approach with captive cod
<p>Data abstract:</p> <p>The daily proportions of time each individual fish spent foraging, swimming and being stationary, this data was used for the analysis in the reference below.</p> <p> </p> <p>Video abstract:</p> <p>Some example video clips from which the behavioural state of both individuals was scored.</p> <p> </p> <p>Conference proceeding abstract:</p> <p>To estimate population level effects of anthropogenic sound on fish, data on energy intake and expenditure is needed. We present an experimental design of a controlled behavioural experiment that allows to collect relatively long-term data on foraging and swimming behaviour of Atlantic cod during sound exposures. Data on such behavioural states can be used as proxies for energy intake and expenditure. The Atlantic cod exhibited natural foraging behaviour in the experimental basins and the design allowed for efficient scoring of the behaviour throughout the 6-day trials. We conducted a pilot of three trials and share the experimental design to encourage other researchers to collect data on (proxies for) energy intake and expenditure to aid estimation of population level effects of sound exposures.</p> <p> </p> <p>Reference:</p> <p>Hubert, J., Wille, D.A., Slabbekoorn, H. (2020) Exploring effects of sound on the time budget of fishes: an experimental approach with captive cod. Proceedings of Meetings on Acoustics. 37 (1). 010012. DOI:10.1121/2.0001253.</p>
Captive-bred populations of a partially migratory salmonid fish are unlikely to maintain migratory polymorphism in natural habitats
Supplementation of wild populations with captive-bred individuals is often ineffective for boosting long-term productivity of wild populations. On the other hand, it remains unknown whether supplementation can act to maintain life-history variation in natural habitats, which is also important for the long-term persistence of populations and species. Partial migration, in which both migratory and resident individuals are maintained in a population, is commonly found across animal taxa. However, human-induced habitat fragmentation continues to cause rapid decline in a migratory phenotype among many natural populations. By using field and hatchery experiments, we here demonstrated that while migrants and residents could be maintained in captive environments, few fish became migrants in natural streams in red-spotted masu salmon Oncorhynchus masou ishikawae. Released captive-bred fish rarely reached the threshold body size necessary to become migrants in natural streams, presumably due to lower growth condition in natural than in captive environments. The decision to migrate is often considered a threshold trait in salmonids and other animal taxa. Our findings highlight the need for supplementation programs to acknowledge environmentally induced changes in life-history decisions for partially migratory species.
Mapping the geographic origin of captive and confiscated Hermann's tortoises: a genetic toolkit for conservation and forensic analyses
<p>The illegal trade has been threatening tortoise populations worldwide for decades. Nowadays, however, DNA typing and forensic genetic approaches allow us to investigate the geographic origin of confiscated animals and to relocate them into the wild, providing that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise <em>Testudo hermanni hermanni</em>. Specific allelic ladders were created for each locus and tested on several reference samples. We used the microsatellite panel to (i) increase our understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70% of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origins of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show that the microsatellite panel and the reference dataset can play a beneficial role in reintroduction and repatriation projects when confiscated individuals need to be re-assigned to their respective macro-area of origin before release, and can assist future forensic genetic applications in detecting the illegal trade and possession of <em>Testudo hermanni</em> individuals.</p>
Data from: Genetic wealth, population health: major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta)
Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur (Lemur catta) as a model, we compared two populations under long-term study: a relatively "open," wild population (n = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003–2013) and a "closed," captive population (n = 121) derived from the Duke Lemur Center (DLC, 1980–2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.
Data from: Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity
Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas, across 18 time points, four probiotic treatments, and two exposures to the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) in captivity, and compared these to 33 samples collected from wild populations at the same life stage. As the amphibians in captivity lost the Bd-inhibitory bacteria through time, the proportion of individuals exposed to Bd that became infected rose from 33% to 100% in subsequent exposures. Inoculations of the Bd-inhibitory probiotic Janthinobacterium lividum resulted in a 40% increase in survival during the second Bd challenge, indicating that the effect of microbiome depletion was reversible by restoring Bd-inhibitory bacteria. Taken together, this study highlights the functional role of ongoing environmental inputs of skin-associated bacteria in mitigating a devastating amphibian pathogen, and that long-term captivity decreases this defensive function.
Assessing changes in genomic divergence following a century of human mediated secondary contact among wild and captive-bred ducks
<p>Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used world-wide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary time scales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (<i>Anas platyrhynchos</i>) throughout North America, and two domestic mallard-types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (<i>A. rubripes</i>) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.</p>
Data from: Social stability via management of natal males in captive rhesus macaques (Macaca mulatta)
<p>Keystone individuals are expected to disproportionately contribute to group stability. For instance, rhesus macaques (<em>Macaca mulatta</em>) who police conflict contribute towards stability. Not all individuals' motivations align with mechanisms of group stability. In wild systems, males typically disperse at maturity and attempt to ascend via contest competition. In a captive system, dispersal is not naturally enabled – individuals attempt to ascend in their natal groups, which can be enabled by matrilineal kin potentially destabilizing group dynamics. We relocated select high-ranking natal males from five groups and assessed group stability before and after. We quantified hierarchical metrics at the individual and group level. After removal, we found significantly higher aggression against the established hierarchy (reversals), indicative of opportunistic attempts to change the hierarchy. Mixed-sex social signaling became more hierarchical, but the strength of this effect varied. Stable structure was not uniformly reached across the groups and alpha males did not all benefit. Indiscriminate natal male removal is an unreliable solution to group instability. Careful assessment of how natal males are embedded within their group is necessary to balance individual and group welfare.</p>
The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn
<p>Binned microsatelite data of the peninsular pronghorn subspecies (Antilocapra americana peninsularis). Data is organized in by year manner. Each population correspond to the year samples were collected from, for example Pop_09 corresponds to samples collected from year 2009, whereas Pop_21 corresponds to the samples collected from year 2021.</p> <p> </p>
Microsatellite genotypes for temporal monitoring of the Floreana Island Galapagos Giant Tortoise captive breeding program
<p><span>Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017 – 2020) of the genetically-informed captive breeding program for the Floreana Island Galapagos giant tortoise, </span><em><span>Chelonoidis niger</span></em><span>. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome </span><span>persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, <em>Chelonoidis becki</em>. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. </span><span>We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. </span><span>This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding. </span></p>
Figures 1-2 in First records of Icius subinermis (Araneae: Salticidae) in North America, with notes on the local establishment of this species and its behavior in captivity
Figures 1-2. Photographs of Icius subinermis taken in Philadelphia, Pennsylvania, on a fence beside the Delaware River Trail at Washington Avenue Green. 1, Female with captured midge, May 2020. 2, Male, June 2019.
Figure 3 in First records of Icius subinermis (Araneae: Salticidae) in North America, with notes on the local establishment of this species and its behavior in captivity
Figure 3. Fence at Washington Avenue Green, beside the Delaware River, from which specimens of Icius subinermis were collected in May 2020.
Figure 2 in A comparison between affiliative and agonistic behaviours in wild and captive Sapajus libidinosus (Spix, 1823) (Mammalia, Primates, Cebidae)
Figure 2. Relative frequencies of social activities presented by free-living (Grey) and captive individuals (Black): (A) Affiliative behaviours and (B) Agonistic behaviours. We observed 10 different types of social behaviour, which occurred under both captivity and free-living conditions.
Figure 4 in A comparison between affiliative and agonistic behaviours in wild and captive Sapajus libidinosus (Spix, 1823) (Mammalia, Primates, Cebidae)
Figure 4. Captivity reduces agonistic interactions and does not change affiliative interactions. (A) Median and quartiles of the frequency of affiliative (A) and agonistic (B) behaviours presented by captive and free-living groups of S. libidinosus, separated by sex.
Figure 3 in A comparison between affiliative and agonistic behaviours in wild and captive Sapajus libidinosus (Spix, 1823) (Mammalia, Primates, Cebidae)
Figure 3. Relative frequency of social behaviours for each of the ten studied groups (BG = Baixa Grande; JB = Jurubeba; PF = Pedra Furada; OT = Oitenta; GT = Gato; FJZB = Fundação Jardim Zoológico de Brasília; PEDI = Parque Estadual Dois Irmãos; PZT2 = Parque Zoobotânico deTeresina (ilha 2); PZT3 = Parque Zoobotânico de Teresina (ilha 3); PZT1 = Parque Zoobotânico de Teresina (ilha 1). Under free-living conditions, agonistic behaviours were proportionally more frequent than were affiliative behaviours.
Data from: Response to food restriction, but not social information use, varies seasonally in captive cardueline finches
<p>Temperate winters can impose severe conditions on songbirds that threaten survival, including shorter days and often lower temperature and food availability. One well-studied mechanism by which songbirds cope with such conditions is seasonal acclimatization of thermal metabolic traits, with strong evidence for both preparative and responsive changes in thermogenic capacity (i.e., the ability to generate heat) to low winter temperature. However, a bird's ability to cope with seasonal extremes or unpredictable events is likely dependent on a combination of behavioral and physiological traits that function to maintain allostatic balance. The ability to cope with reduced food availability may be an important component of organismal response to temperate winters in songbirds. Here we compare responses to experimentally reduced food availability at different times of year in captive red crossbills (<em>Loxia curvirostra</em>) and pine siskins (<em>Spinus pinus</em>) – two species that cope with variable food resources and live in cold places – to investigate seasonal changes in the organismal response to food availability. Further, red crossbills are known to use social information to improve response to reduced food availability, so we also examine whether use of social information in this context varies seasonally in this species. We find that pine siskins and red crossbills lose less body mass during time-restricted feedings in late winter compared to summer, and that red crossbills further benefit from social information gathered from observing other food-restricted red crossbills in both seasons. Observed changes in body mass were only partially explained by seasonal differences in food intake. Our results demonstrate seasonal acclimation to food stress and social information use across seasons in a controlled captive environment and highlight the importance of considering diverse physiological systems (e.g., thermogenic, metabolic, digestive, etc) to understand organismal responses to environmental challenges.</p>
Fig. 3 in Reproductive characteristics of the Burmese Narrow-headed Softshell Turtle, Chitra vandijki, in captivity
Fig. 3. Hatchling of Burmese Narrow-headed Softshell Turtle.
Fig. 1 in Reproductive behavior of the marine gastropod Charonia seguenzae (Aradas & Benoit, 1870) in captivity Abstract
Fig. 1: Engraved number (encircled area) used as identification mark on a Charonia seguenzae shell.
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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.