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6,861 results for “Animation”
Data from: Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies
Background: Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information. Results: Here we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen. The apicomplexan sequences were extracted from the sequence assemblies using a newly developed bioinformatic pipeline (ContamFinder) and tentatively assigned to distinct taxa employing phylogenetic methods. We analysed 920 assemblies and found 20,907 contigs of apicomplexan origin in 51 of the datasets. The contaminating species were identified as members of the apicomplexan taxa Gregarinasina, Coccidia, Piroplasmida, and Haemosporida. For example, in the platypus genome assembly, we found a high number of contigs derived from a piroplasmid parasite (presumably Theileria ornithorhynchi). For most of the infecting parasite species, no molecular data had been available previously, and some of the datasets contain sequences representing large amounts of the parasite's gene repertoire. Conclusion: Our study suggests that parasite-derived contaminations represent a valuable source of information that can help to discover and identify new parasites, and provide information on previously unknown host-parasite interactions. We, therefore, argue that uncurated assembly data should routinely be made available in addition to the final assemblies.
Data from: Two-current choice flumes for testing avoidance and preference in aquatic animals
Aquatic chemical ecology is an important and growing field of research that involves understanding how organisms perceive and respond to chemical cues in their environment. Research assessing the preference or avoidance of a water source containing specific chemical cues has increased in popularity in recent years, and a variety of methods have been described in the scientific literature. Two-current choice flumes have seen the greatest increase in popularity, perhaps because of their potential to address the broadest range of research questions. Here, we review the literature on two-current choice flumes and show that there is a clear absence of standardized methodologies that make comparisons across studies difficult. Some of the main issues include turbulent flows that cause mixing of cues, inappropriate size of choice arenas for the animals, short experiments with stressed animals, failure to report how experiment and researcher biases were eliminated, general underreporting of methodological details, underutilization of collected data and inappropriate data analyses. In this review, we present best practice guidelines on how to build, test and use two-current choice flumes to measure the behavioural responses of aquatic animals to chemical cues, and provide blueprints for flume construction. The guidelines include steps that can be taken to avoid problems commonly encountered when using two-current choice flumes and analysing the resulting data. This review provides a set of standards that should be followed to ensure data quality, transparency and replicability in future studies in this field.
Data from: Odd couples: extraordinary differences between the sexes in the animal kingdom.
Introducing readers to important discoveries in animal behavior and evolution, Odd Couples explores some of the most extraordinary sexual differences in the animal world and shows how all can be understood through the common conceptual framework of evolutionary biology. The book uncovers the unique and bizarre characteristics—in size, behavior, ecology, and life history—that exist in these remarkable species and the special strategies they use to maximize reproductive success. Eight chapters highlight individual species with exceptional sexual dimorphisms, including elephant seals (Mirounga sp.), great bustards (Otis tarda), shell-carrying cichlids (Lamprologus callipterus), deep-sea anglerfishes (Ceratias holboelli), garden spiders (Argiope aurantia), bone-eating worms (Osedax sp.), blanket octopuses (Tremoctopus sp.) and burrowing barnacles (Trypetesa lampas). In addition, two synthesis chapters use data from all known animal phyla and classes to discern overall trends and patterns of sexual differences, providing the first broad-scale, quantitative analysis of sexual dimorphisms across the entire Animal Kingdom.
Data from: Molecular paleobiology of early-branching animals integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges
Reconciliation of paleontological and molecular phylogenetic evidence holds great promise for a better understanding of the temporal succession of cladogenesis and character evolution, especially for taxa with a fragmentary fossil record and uncertain classification. In zoology, studies of this kind have largely been restricted to Bilateria. Hexactinellids (glass sponges) readily lend themselves to test such an approach for early-branching (non-bilaterian) animals: they have a long and rich fossil record, but for certain taxa paleontological evidence is still scarce or ambiguous. Furthermore, there is a lack of consensus for taxonomic interpretations, and discrepancies exist between neontological and paleontological classification systems. Using conservative fossil calibration constraints and the largest molecular phylogenetic data set assembled for this group, we infer divergence times of crown-group Hexactinellida in a Bayesian relaxed molecular clock framework. With some notable exceptions, our results are largely congruent with interpretations of the hexactinellid fossil record, but also indicate long periods of undocumented evolution for several groups. This study illustrates the potential of an integrated molecular/paleobiological approach to reconstructing the evolution of challenging groups of organisms.
Data from: Orientation to the sun by animals and its interaction with crypsis
1. Orientation with respect to the sun has been observed in a wide range of species and has generally been interpreted in terms of thermoregulation and/or ultraviolet (UV) protection. For countershaded animals, orientation with respect to the sun may also result from the pressure to exploit the gradient of coloration optimally to enhance crypsis. 2. Here, we use computational modelling to predict the optimal countershading pattern for an oriented body. We assess how camouflage performance declines as orientation varies using a computational model that incorporates realistic lighting environments. 3. Once an optimal countershading pattern for crypsis has been chosen, we determine separately how UV protection/irradiation and solar thermal inflow fluctuate with orientation. 4. We show that body orientations that could optimally use countershading to enhance crypsis are very similar to those that allow optimal solar heat inflow and UV protection. 5. Our findings suggest that crypsis has been overlooked as a selective pressure on orientation and that new experiments should be designed to tease apart the respective roles of these different selective pressures. We propose potential experiments that could achieve this.
Dataset for "Space use by animals on the urban fringe: interactive effects of sex and personality"
<p>Personality traits shape individual perceptions of risks and rewards, and so, should affect how animals value and use their environment. Evidence is emerging that personality affects foraging, space use and exploitation of novel environments such as urban habitat. But the influence of personality is also hypothesized to be sex-dependent when primary motivation for space use differs between sexes, as often occurs in polygynous species. We tested the influence of personality traits, interacting with sex, on space use by the polygynous common brushtail possum, <i>Trichosurus vulpecula</i>, in an urban-woodland boundary in Sydney, Australia. We quantified personality traits, including exploration, using behavioural assays in an artificial arena. We also GPS-tracked free-ranging individuals, and measured range size, core area: home range, and proportional urban range. We found that personality traits affected space use either as a main effect or, as predicted, an interaction with sex. More exploratory animals, regardless of sex, had higher core area: home range ratios and proportionally larger ranges within urban habitat. However, less exploratory females yet more exploratory males had larger ranges. Our findings provide new insight into movement ecology by demonstrating, for the first time, the sex-dependent influence of personality. The demonstrated influence of personality on urban use by possums also suggests a personality filter for wildlife, as populations transition into urban areas. Finally, as individuals at the interface between urban and natural habitat are also a conduit between the two, a corollary of our findings is that there may be personality-mediated spread of disease across this boundary.</p>
Data from: Predicting rates of isotopic turnover across the animal kingdom: a synthesis of existing data
The stable isotopes of carbon (13C /12C) and nitrogen (15N /14N) represent powerful tools in food-web ecology, providing a wide range of dietary information in animal consumers. However, identifying the temporal window over which a consumer's isotopic signature reflects its diet requires an understanding of elemental incorporation, a process that varies from days to years across species and tissue types. Though theory predicts body size and temperature are likely to control incorporation rates, this has not been tested empirically across a morphologically and phylogenetically diverse range of taxa. Readily available estimates of this relationship would, however, aid in the design of stable isotope food-web investigations and improve the interpretation of isotopic data collected from natural systems. Using literature-derived turnover estimates from animal species ranging in size from 1 mg to 2000 kg, we develop a predictive tool for stable isotope ecologists, allowing for estimation of incorporation rates in the structural tissues of entirely novel taxa. In keeping with metabolic scaling theory, we show that isotopic turnover rates of carbon and nitrogen in whole organisms and muscle tissue scale allometrically with body mass raised approximately to the power -0.19, an effect modulated by body temperature. This relationship did not, however, apply to incorporation rates in splanchnic tissues, which were instead dependent on the thermoregulation tactic employed by an organism, being considerably faster in endotherms than ectotherms. We believe the predictive turnover equations we provide can improve the design of experiments and interpretation of results obtained in future stable isotopic food-web studies.
3D photogrammetry as a low cost and noninvasive method for acoustic modeling of animal hearing
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Group F: Pendulum_Animation
<p>Group F's model of the pendulum animation in the Euler's model</p>
Data for: Simulating animal space use from fitted integrated Step-Selection Functions (iSSF)
Open the record for dataset details and reuse information.
Supplementary material 7 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Observation critical appraisal
Supplementary material 3 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Citation screening
Supplementary material 6 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Unobtainable articles at full-text screening
Supplementary material 9 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Additional bibliometric results and narrative synthesis
Supplementary material 4 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Citations excluded at full-text screening
Supplementary material 2 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Test list and comprehensiveness
Supplementary material 1 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
ROSES form
Supplementary material 5 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Citations with irretrievable abstracts
Supplementary material 8 from: Lafitte A, Sordello R, Legrand M, Nicolas V, Obein G, Reyjol Y (2023) Does a flashing artificial light have more or conversely less impacts on animals than a continuous one? A systematic review. Nature Conservation 54: 149-177. https://doi.org/10.3897/natureconservation.54.102614
Systematic review observation database
Animal population data complementing the European Union One Health 2022 Zoonoses Report
<p>This dataset includes animal population aggregated data under the framework of Directive 2003/99/EC.</p>
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.