Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,581
datasets available to search
ShareScore release 0.7.1
Dataset results
2,581 results for “amphibians”
Data-set of studies on mortality, sub-lethal and reproductive effect on amphibians and reptiles
<p>Amphibians and reptiles have not been considered in environmental risk assessments of chemicals, which has generated some debate about whether risk posed by some pollutants like pesticides on these animals are covered by surrogates in the groups of fish, mammals and birds. In order to develop a scientifically sound and robust risk assessment scheme it is necessary to have enough information available on the biological relevance of effects observed in laboratory studies in view of population level effects, to identify sensitive life stages and to compare sensitivity of our target study groups with that of their surrogates.</p> <p>With these objectives, a systematic review of toxicological literature on amphibians and reptiles a comprehensive search of relevant literature on toxicity data related to amphibians and reptiles was conducted, using the appropriate search strings and combinations, in six different source types: multidisciplinary databases of scientific literature (i.e. Web of Science and Scopus), literature included in general amphibian and reptile ecotoxicology compilations, literature compiled in technical reports previously prepared for EFSA, literature sources used for creating amphibian or reptile records in the ecotoxicological database created by De Zwart (see references for details), literature sources used for creating amphibian or reptile records in toxicological online databases (United States Environmental Protection Agency’s Ecotoxicology Knowledgebase–ECOTOX, and National Library of Medicine’s Hazardous Substances Data Bank–HSDB), and indexes of herpetological scientific journals of local scope not included in Web of Science or Scopus.</p> <p>Data extraction consisted of the retrieval of relevant information, including among other fields: species, age, sex, chemical substance, exposure route and duration, type of recorded endpoint, type of response, exposure concentration, mean effect value of the control and exposed groups and the reported variability measures of these mean effects, and statistical significance of the comparison.</p> <ul> <li>Data category 1: Reporting endpoints. Endpoints are defined here as benchmark values obtained from the integration of responses measured at different concentrations (e.g. LC<sub>50</sub>, EC<sub>50</sub>, NOEC, for which calculation it is necessary to make a regression with the percentage of effect at different exposure concentrations).</li> <li>Data category 2: Reporting responses for each tested level. These are studies in which different replicates of experimental units are exposed to different levels (doses, concentrations), including a control treatment, and a magnitude of effect is recorded at each level. For some of these studies it was possible to calculate an endpoint (e.g. LC<sub>50</sub>, EC<sub>50</sub>, NOEC) and for others it was not (e.g. if only one concentration was tested or if a statistically significant adjustment between exposure level and effect cannot be achieved).</li> </ul> <p> </p> <p>Three objectives corresponding to the review of the effects of chemicals on amphibians and reptiles, the main results of the study were:</p> <ol> <li>Identification of the most sensitive life stage.</li> <li>Extrapolation from laboratory data to mesocosm and field situations</li> <li>Comparison with surrogate taxa</li> </ol> <p>The review was conducted on 3642 full-text records for chemical exposure effects and 556 for life history traits, out of which 1332 and 204, respectively, were finally used for data extraction. The datasets comprised 23152 values corresponding to effects of chemicals and 1854 values corresponding to life history traits.</p>
VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data
<p><span>In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behavior of target species, which can be modeled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1,056 individuals of two anuran and three urodele species (1,732–3,913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework and combined this genetic data with information obtained in a previous two-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results suggest a significant influence of local population sizes on patterns of genetic connectivity at small spatial scales. In addition, m</span><span>ovement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with </span><span>genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level. </span></p>
Figure 3 in Amphibian Diversity: Where everything starts to flood, Cáceres Municipality, North Pantanal, Central-West Brazil
Figure 3. Geographic distribution map of Oreobates heterodactylus (circles), and Leptodactylus bufonius (squares) in the region of Cáceres (highlighted by a blue frame on the South America map), Mato Grosso, Brazil. References: Black circles (Pansonato et al., 2020), red circle (fieldwork – this study), black squares (Neves et al., 2020), and red square (Pansonato et al., 2011). Abbreviations: BOL = Bolivia, PAR = Paraguai, BRA = Brazil, MT = Mato Grosso State, and MS = Mato Grosso do Sul State. Background elevation ranges from 0 to 1,000 meters.
Figure 2 in Amphibian Diversity: Where everything starts to flood, Cáceres Municipality, North Pantanal, Central-West Brazil
Figure 2. Some of the anurans registered in the fieldwork, municipality of Cáceres, Mato Grosso, Brazil. A = Adenomera cf. diptyx, B = Dermatonotus muelleri, C = D. muelleri in amplexus, D = Elachistocleis bicolor, E = E. corumbaensis, F = Leptodactylus cf. brevipes, G = L. elenae, H = L. podicipinus, I = Oreobates heterodactylus, J = Rhinella diptycha, K = R. diptycha young and L = R. scitula. (Photo by D.J. Silva).
Figure 1 in Amphibian Diversity: Where everything starts to flood, Cáceres Municipality, North Pantanal, Central-West Brazil
Figure 1. Sampling sites in the municipality of Cáceres, Mato Grosso, Brazil. Abbreviations: MT = Mato Grosso, MS = Mato Grosso do Sul, EESA = Estação Ecológica da Serra das Araras and EET = Estação Ecológica de Taiamã. Fieldwork (stars): 1 = Sepotuba river mouth, 2 = Jauru River mouth, 3 = Morrinhos Farm region and 4 = Estação Ecológica de Taiamã. Literature records (triangles): A = ICMBio (2016), B = Andrade et al. (2017), C = Faria & Mott (2011), D = Silva-Alves et al. (2020), and E = Pansonato et al. (2011).
Known distribution of Uruguayan amphibians and environmental predictors
<p>Fuzzy logic modeling was employed to assess the distribution of amphibians in Uruguay using both expert knowledge and observational records. Fuzzy logic allowed for the assignment of continuous values between 0 and 1 to propositions based on fuzzy logical assumptions about the relationship between species and their environment. Models based on expert knowledge and species records were compared and combined, focusing on threatened species, those considered ubiquitous, and non-threatened/non-ubiquitous species. Results demonstrated equal or superior performance for threatened species according to expert knowledge compared to models based on species records, even when both had to classify the same set of records. Expert models predicted more restrictive favorable territories for threatened species. On the other hand, models based on observed records yielded the best-fitted models for non-threatened non-ubiquitous species and ubiquitous species. In summary, fuzzy logic proved to be an effective tool for integrating expert knowledge and observational records in species distribution modeling.</p>
Amphibian Dvinosaurus primus skull
A cast of the amphibian *Dvinosaurus primus* Amalitzky, 1921 skull. The cast belongs to the collection of the Saint Petersburg State University. A 3D scan was performed by [Grigoriev Dmitry](https://www.facebook.com/dmitry.grigoriev.946/) using a structure light based 3D scanner [RangeVision Spectrum](http://rangevision.com/en/products/spectrum/). The cast of fossil skull (holotype) made in Paleontological laboratory in Warsaw (Poland) under the guidance of Vladimir Amalitzky in 1908-1914. It is currently held and exhibited at the [Paleontological museum](http://spbu.ru/universitet/ekspozicii-i-kollekcii-spbgu/paleontologicheskiy-muzey) of Saint Petersburg State University. In 2020 the paint surface of this cast was restored by Ekaterina Ageeva under the guidance of prof. Vladimir S. Torbik (chair of restavration of SPbU) and [Vadim Glinsky](https://www.facebook.com/vadim.glinskiy.5) (Paleontological museum of SPbU). Source: Objaverse 1.0 / Sketchfab
Supplementary material: Machine learning and phylogenetic models identify predictors of genetic variation in Neotropical amphibians
<p><strong>Aim: </strong>Intraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, dispersal, and life history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogenetic relatedness, climatic, and geographic characteristics can explain intraspecific genetic diversity.</p> <p><strong>Location:</strong> Neotropics.</p> <p><strong>Taxon:</strong> Amphibians.</p> <p><strong>Methods: </strong>We assembled datasets using open-access databases for natural history traits, genetic sequences, phylogenetic trees, climatic, and geographic data. For each species, we calculated overall nucleotide diversity (<em>π</em>) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors of <em>π</em>, IBD, and IBE using Random Forest (RF) regression or RF classification. We also fitted phylogenetic generalized linear mixed models (PGLMMs) to predict<em> π</em>, IBD, and IBE.</p> <p><strong>Results:</strong> We compiled 4,052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2,477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation (σ) as the most important predictors of <em>π</em>, influencing it positively. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD; most species without IBD tended to occur at higher elevations. Maximum latitude and precipitation (σ) were the best predictors of IBE, and most species without IBE occur at lower latitudes and in areas with more variable precipitation.</p> <p><strong>Main conclusions: </strong>This study identified predictors of genetic variation in Neotropical amphibians using both machine learning and phylogenetic methods. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes, and Atlantic Forest biogeographic units harbor high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.</p>
Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior
<p>Microorganisms colonize the gastrointestinal tract of animals and establish symbiotic host-associated microbial communities that influence vertebrate physiology. More specifically, these gut microbial communities influence neurodevelopment through the microbiota-gut-brain (MGB) axis. We tested the hypothesis that larval amphibian neurodevelopment is affected by the aquatic microbial community present in their housing water. Newly hatched Northern Leopard Frog (<em>Lithobates pipiens</em>) tadpoles were raised in pond water that was unmanipulated (natural) or autoclaved. Tadpoles raised in autoclaved pond water had a gut microbiota with reduced bacterial diversity and altered community composition, had decreased behavioral responses to sensory stimuli, were larger in overall body mass, had relatively heavier brains, and had altered brain shape when compared with tadpoles raised in natural pond water. Further, the diversity and composition of the gut microbiota was associated with tadpole behavioral responses and brain measurements. Our results suggest that aquatic microbial communities shape tadpole behavior and brain development, providing strong support for the occurrence of the MGB axis in amphibians. Lastly, the dramatic role played by aquatic microbial communities on vertebrate neurodevelopment and behavior should be considered in future wildlife conservation efforts.</p>
Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?
<p>The intestinal microbiota, an invisible organ supporting a host's survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host's biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non-invasive, convenient, and allows for longitudinal sampling. Yet, it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In amphibians, research on sampling methodology is limited. In this study, we characterize and compare microbiota (small intestine, large intestine, feces) of two Hong Kong stream-dwelling frog species: Lesser Spiny Frog (<em>Quasipaa exilispinosa</em>), and Hong Kong Cascade Frog (<em>Amolops hongkongensis</em>). We found that both species have similar dominant phyla and families, but diverge in terms of the dominant genera. Next, we assess the performance of fecal microbiota in representing the intestinal microbiota in these two species. We found that (1) microbiota of small and large intestine differs significantly, (2) feces are not an appropriate proxy of both intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our cautions equating fecal and intestinal microbiota. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over-extrapolation and interpret results carefully.</p>
Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population
<p>Body size variation is central in the evolution of life history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (<em>Lissotriton graecus</em>). By combining a Genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness related traits in small data sets from natural populations in non-model species.</p>
The high cost of movement in an arid working landscape for an endangered amphibian
<p>Connectivity is essential for the maintenance of genetic diversity and stability of wildlife populations. Drought and changing precipitation regimes have caused natural aquatic amphibian breeding habitats to disappear or become isolated and have led to the replacement of natural surface water with artificial livestock water tanks. Terrestrial movement is the only means of responding to aquatic threats in arid landscapes and to allow population connectivity. Aridity may present an impenetrable barrier in hydrologically fragmented environments. We used a facultatively paedomorphic and federally endangered salamander to assess the challenges of movement across arid working lands. Sonoran tiger salamanders (<em>Ambystoma mavortium stebbinsi</em>) are endemic to the San Rafael Valley of southeastern Arizona, United States of America, where they depend on livestock water tanks as breeding habitat. The ecology of this species' metamorphs outside of stock tanks is virtually unknown. To assess survival on the landscape during terrestrial movement we used radio transmitters to track 78 adult metamorphosed salamanders over two years. Sonoran tiger salamanders moved up to 1 km from the tank edge, and average distances moved of over 400 m were higher than most <em>Ambystoma </em>species. However, during the study period, none reached neighboring stock tanks. We found high mortality due to predation and desiccation. Individuals that dispersed to terrestrial habitat in summer survived longer than individuals that dispersed in spring. High mortality suggests terrestrial movement is exceptionally risky and may contribute to isolated subpopulations and elevated levels of inbreeding. Conservation actions that improve and maintain artificial aquatic habitats as well as increase connectivity may improve long-term management for pond-breeding amphibians in arid regions.</p>
Fig. 3 in Helminth communities from amphibians inhabiting agroecosystems in the Pampean Region (Argentina)
Fig. 3. Similarity matrix and dendrogram.
A framework to identify priority wetland habitats and movement corridors for urban amphibian conservation
<p>Core corridors: derived from Circuitscape modeling results -top 50% of wood frog, boreal chorus frog and tiger salamander results converted to binary value and summed to produce core corridors (probable movement for 2-3 amphibian species). <br> <br> To derive core corridors, we summed connectivity models for three amphibian species. For each species we derived focal nodes from high habitat value (based on HSI modelling), used three resistance scenarios and summed the three scenarios for each species to represent probable movement pathways between focal nodes. Species connectivity models were then classified to top 50% of the model, and converted to a binary value of 0 to 1. The three species were summed where by values 0-3 represent number of amphibian species the corridor probably supports movement. </p>
A framework to identify priority wetland habitats and movement corridors for urban amphibian conservation - Raw Data
<p>Call of the Wetland Program observation data reported by citizen scientists at wetlands in the City of Calgary during three amphibian seasons from 2017 to 2019. Wetlands were surveyed up to 11 times per season and participants reported observations to a smartphone application – where they documented species, and type of observation (eggs, adult, juvenile, tadpole or call). Participants also recorded when they participated in a survey and there were no observations. Observations associated without a site ID represent opportunistic observations at non-survey wetlands. This data was used to validate habitat suitability models derived from the occupancy modeling results. <br> <br> Survey wetland location shapefile (centroid point of wetland) also included. </p>
Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat-specialization, Ascaphus truei, resolved using two types of genetic markers
<p>Reconstruction of historical relationships between geographic regions within a species' range can indicate dispersal patterns and help predict future responses to shifts in climate. <em>Ascaphus truei </em>(coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques — microsatellite and genotype-by-sequencing (GBS) — to compare the within region genetic diversity of populations near the northern extent of the species' range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving towards the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of <em>A. truei</em> to climate change.</p>
Amphibian diversity in the Amazonian floating meadows: a Hanski core-satellite species system (scripts and codes)
<p>The Amazon catchment is the largest river basin on earth, and up to 30% of its waters flow across floodplains. In its open waters, floating plants known as floating meadows abound. They can act as vectors of dispersal for their associated fauna and, therefore, can be important for the spatial structure of communities. Here, we focus on amphibian diversity in the Amazonian floating meadows over large spatial scales. We recorded 50 amphibian species over 57 sites, covering around 7,000 km along river courses. Using multi-site generalised dissimilarity modelling of zeta diversity, we tested Hanski's core-satellite (HCS) hypothesis and identified the existence of two functional groups of species operating under different ecological processes in the floating meadows. 'Core' species are associated with floating meadows, while 'satellite' species are associated with adjacent environments, being only occasional or accidental occupants of the floating vegetation. At large scales, amphibian diversity in floating meadows is mostly determined by stochastic processes, whereas at regional scales, climate and deterministic processes are central drivers. Compared with the turnover of 'core' species, the turnover of 'satellite' species increases much faster with distances and is also controlled by a wider range of climatic features. Distance is not a limiting factor for 'core' species, suggesting that they have a stronger dispersal ability even over large distances. This is probably related to the existence of passive long-distance dispersal of individuals along rivers via vegetation rafts. In this sense, Amazonian rivers can serve as corridors, facilitating dispersal especially for species associated with riverine habitats such as floating meadows.</p>
Synthesis of batrachochytrium dendrobatidis infection in South America: amphibian species under risk and areas to focus research and disease mitigation
<p>Amphibian chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), has been recognized as the infectious disease causing the most catastrophic loss of biodiversity known to science, with South America being the most impacted region. We tested whether Bd prevalence is distributed among host taxonomy, ecoregion, conservation status and habitat preference in South America. Here we provide a synthesis on the extent of Bd infection across South America based on 21,648 molecular diagnostic assays, roles of certain species in the epidemiology of Bd and explore its association with the reported amphibian catastrophic declines in the region. We show that Bd is widespread, with a continental prevalence of 23.2%. Its occurrence in the region shows a phylogenetic signal and the probability of infection is determined by ecoregion, preferred habitat, and extinction risk hosts' traits. The taxa exhibiting highest Bd occurrence, were mostly aquatic amphibians, including Ranidae, Telmatobiidae, Hylodidae, Calyptocephalellidae and Pipidae. Surprisingly, families exhibiting unusually low Bd prevalence included species in which lethal chytridiomycosis and population declines have been described (genus Atelopus, Rhinoderma and Eleutherodactylus). Higher than expected prevalence of Bd occurred mainly in amphibians living associated with mountain environments in the Andes and Atlantic forests, reflecting highly favourable Bd habitats in these areas. Invasive amphibian species (e.g. Lithobates catesbeianus and Xenopus laevis) exhibited high Bd prevalence, as thus we suggest using these as sentinels to understand their potential role as reservoirs, vectors or spreaders of Bd that can be subjected to management. Our results guide on the prioritization of conservation actions to prevent further biodiversity loss due to chytridiomycosis in the world's most amphibian diverse region.</p>
Fig. 2 in Mortality Of Amphibians On The Roads Of Lviv Region (Ukraine): Trend For The Last Decade
Fig. 2. Surveyed road sections of Lviv Region (open circles indicate sections with
Fig. 1 in Mortality Of Amphibians On The Roads Of Lviv Region (Ukraine): Trend For The Last Decade
Fig. 1. Investigated roads of Lviv Region.
ScienceDex guides
Understand access before you commit
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.