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2,581 results for “amphibians”
Figure 7 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 7. Amphibians recorded at the Reserva Extrativista do Baixo Juruá. (A) Osteocephalus aff. leprieurii; (B) Osteocephalus taurinus; (C) Scarthyla goinorum; (D) Scinax ruber; (E) Trachycephalus typhonius; (F) Adenomera andreae; (G) Adenomera simonstuarti; (H) Edalorhina perezi. Photographs by LJCLM (A, B, G) andVTC (C-F, H).
Figure 11 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 11. Lizards recorded at Reserva Extrativista do Baixo Juruá. (A) Loxopholis snethlageae; (B) Iguana iguana; (C) Copeoglossum nigropunctatum (juvenile); (D) Gonatodes humeralis; (E) Crocodilurus amazonicus; (F) Kentropyx pelviceps; (G) Plica umbra ochrocollaris; (H) Uranoscodon superciliosus. Photographs by LJCLM (A, D) and VTC (B, C, E-H).
Figure 3 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 3. Extrapolated rarefaction curves showing variation in amphibian (A) and reptile (B) species richness in the Reserva Extrativista do Baixo Juruá in relation to our sampling effort. Observed data are in full lines and extrapolated in dashed lines. Shaded areas represent 95% confidence intervals (bootstrap with 1,000 replications).
Figure 1 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 1. Geographic location of the Reserva Extrativista (RESEX) do Baixo Juruá in relation to South America (A) and the Juruá River basin, in Brazilian Western Amazonia (B); upon an elevation background). In (B), protected areas and indigenous territories that cover this river basin are delimited in white and pink, respectively. The focal area is zoomed at (C), showing the eleven localities sampled for amphibians and reptiles (numbered white symbols; see Table 1), and the Juruá municipality. Background in (C) is from Google Earth (Map data ©2015 Google/Landsat/Copernicus).
Figure 4 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 4. Amphibians recorded at the Reserva Extrativista do Baixo Juruá. (A) Allobates femoralis; (B) Rhinella castaneotica; (C) Rhinella aff. margaritifera; (D) Rhinella exostosica; (E) Rhinella marina; (F) Ceratophrys cornuta; (G) Oreobates quixensis; (H) Pristimantis reichlei. Photographs by VTC (A, C, E, F, H) and LJCLM (B, D, G).
Figure 13 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 13. Snakes recorded at Reserva Extrativistado Baixo Juruá.(A) Drepanoidesanomalus; (B) Erythrolampruspygmaeus; (C)Erythrolamprusreginae; (D) Erythrolamprus typhlus; (E) Helicops angulatus; (F) Helicops polylepis; (G) Oxyrhopus melanogenys; (H) Oxyrhopus occipitalis. Photographs byVTC (A-E, G, H) and LJCLM (F).
Figure 2 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 2. Panoramic view of the white-water Juruá River at its lower course (A); some habitats recently sampled for amphibians and reptiles at the Reserva Extrativista do Baixo Juruá, state of Amazonas, Brazil: (B) seasonally flooded habitats at the confluence of the tributary Andirá River, and (C) non-flooded forest (paleovárzea); as well as different trap methods and setups used during sampling: (D, E) linear pitfall trap stations, with drift fences, (F) funnel traps, installed between the buckets of pitfall traps, (G) bucket part of a pitfall trap station in "Y″ without drift fences. Photographs by LJCLM (A-C) and VTC (D-G).
Figure 5 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 5. Amphibians recorded at the Reserva Extrativista do Baixo Juruá. (A) Strabomantis sulcatus; (B) Ameerega trivittata; (C) Phyzelaphryne nimio; (D) Boana boans; (E) Boana calcarata; (F) Boana cinerascens; (G) Boana geographica; (H) Boana lanciformis. Photographs by VTC (A, B, D, E, H) and LJCLM (C, F, G).
Figure 12 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 12. Snakes recorded at Reserva Extrativista do Baixo Juruá. (A) Anilius scytale; (B) Epicrates cenchria; (C) Chironius fuscus; (D) Drymoluber dichrous; (E) Atractus major; (F) Atractus poeppigi; (G) Atractus torquatus; (H) Dipsas catesbyi. Photographs by VTC.
Figure 10 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 10. Lizards recorded at Reserva Extrativista do Baixo Juruá. (A) Alopoglossus atriventris; (B) Alopoglossus brevifrontalis; (C) Alopoglossus indigenorum; (D) Anolis punctatus; (E) Anolis transversalis; (F) Anolis tandai (male); (G) Anolis tandai (female); (H) Cercosaura argulus. Photographs by LJCLM (A, B, D) and VTC (C, E-H).
Figure 14 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 14. Snakes and chelonians recorded at Reserva Extrativista do Baixo Juruá. (A) Thamnodynastes pallidus; (B) Xenodon rabdocephalus; (C) Micrurus hemprichii ortoni; (D) Micrurus lemniscatus; (E) Bothrops atrox; (F) Bothrocophias hyoprora; (G) Platemys platycephala; (H) Chelonoidis denticulata. Photographs by VTC.
Figure 9 in Amphibians and reptiles from a protected area in western Brazilian Amazonia (Reserva Extrativista do Baixo Juruá)
Figure 9. Amphibians recorded at the Reserva Extrativista do Baixo Juruá. (A) Chiasmocleis bassleri; (B) Chiasmocleis hudsoni; (C) Chiasmocleis ventrimaculata; (D) Ctenophryne geayi; (E) Phyllomedusa vaillantii; (F) Pipa pipa; (G) Lithobates palmipes (metamorph);(H) Caecilia tentaculata. Photographs by LJCLM (A-E) andVTC (F-H).
Towards the generation of gnotobiotic larvae as a tool to investigate the influence of the microbiome on the development of the amphibian immune system
<div> <div> <div> <p>The immune equilibrium model suggests that exposure to microbes during early life primes immune responses for pathogen exposure later in life. While recent studies using a range of gnotobiotic (germ-free) model organisms offer support for this theory, we currently lack a tractable model system for investigating the influence of the microbiome on immune system development. Here, we used an amphibian species (<em>Xenopus laevis</em>) to investigate the importance of the microbiome in larval development and susceptibility to infectious disease later in life. We found that experimental reductions of the microbiome during embryonic and larval stages effectively reduced microbial richness, diversity, and altered community composition in tadpoles prior to metamorphosis. In addition, our antimicrobial treatments resulted in few negative effects on larval development, body condition, or survival to metamorphosis. However, contrary to our predictions, our antimicrobial treatments did not alter susceptibility to the lethal fungal pathogen <em>Batrachochytrium dendrobatidis</em> (<em>Bd</em>) in the adult life stage. While our treatments to reduce the microbiome during early development did not play a critical role in determining susceptibility to disease caused by <em>Bd</em> in <em>X</em>. <em>laevis</em>, they nevertheless indicate that developing a gnotobiotic amphibian model system may be highly useful for future immunological investigations.</p> </div> </div> </div>
Data from: Evidence for the Predator Attraction Hypothesis in an amphibian predator-prey system
<p>Many species possess damage-released chemical alarm cues that function in alerting nearby individuals to a predator attack. One hypothesis for the evolution and/or maintenance of such cues is the Predator Attraction Hypothesis, where predators, rather than prey, are the 'intended' recipients of these cues. If a predator attack attracts additional predators, these secondary predators might interfere with the predation event, providing the prey with a better chance to escape. In this study, we conducted two experiments to explore this hypothesis in an amphibian predator/prey system. In Experiment 1, we found that tiger salamanders (<em>Ambystoma</em> <em>mavortium</em>) showed a foraging attraction to chemical cues from wood frog (<em>Lithobates</em> <em>sylvaticus</em>) tadpoles. Salamanders that were experienced with tadpole prey, in particular, were strongly attracted to tadpole alarm cues. In Experiment 2, we observed experimental encounters between a tadpole and either one or two salamanders. The presence of the second predator caused salamanders to increase attack speed at the cost of decreased attack accuracy (i.e., increasing the probability that the tadpole would escape attacks). We also found that the mere presence of visual and chemical cues from a second predator did not affect this speed/accuracy trade-off but did cause enough of a distraction to increase tadpole survival. Thus, our findings are thus consistent with the Predator Attraction Hypothesis for the evolution and/or maintenance of alarm cues.</p>
Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians
<p><span>Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera <em>Discoglossus</em>, <em>Rana</em>, <em>Lissotriton</em> and <em>Triturus</em> using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.</span></p>
Developmental environment has lasting effects on amphibian behavior and thermal physiology
<p>Environmental challenges early in development can result in complex phenotypic trade-offs and long-term effects on individual physiology, performance, and behavior, with implications for disease and predation risk. We examined the effects of simulated pond-drying and elevated water temperatures on development, growth, thermal physiology, and behavior in a widespread North American amphibian, the Southern leopard frog, <em>Rana sphenocephala</em>. Tadpoles were raised in outdoor mesocosms under warming and drying regimes based on projected climatic conditions in 2070. We predicted that amphibians experiencing the rapid pond drying and elevated pond temperatures associated with climate change would accelerate development, be smaller at metamorphosis and demonstrate long-term differences in physiology and exploratory behavior post-metamorphosis. While both drying and warming accelerated development and reduced survival to metamorphosis, only drying resulted in smaller animals at metamorphosis. At approximately one month post-metamorphosis, animals from the control (ambient no-drying) treatment jumped relatively farther at high temperatures in jumping trials. In addition, across all treatments, frogs with shorter larval periods had lower critical thermal minima and maxima. We also found evidence that developing under warming and drying resulted in a less exploratory behavioral phenotype, and that drying, but not warming, resulted in warmer thermal preferences. Furthermore, behavior predicted thermal preference, with less exploratory animals selecting higher temperatures. Our results underscore the multi-faceted effects of early developmental environments on behavioral and physiological phenotypes later in life. For example, thermal preferences can influence disease risk through behavioral thermoregulation, and exploratory behavior may increase risk of predation or pathogen encounter. By impacting thermal physiology, behavior, and various physiological traits, climatic stressors during development may mediate amphibian exposure and susceptibility to predators and pathogens into adulthood.</p>
The role of environmental variation in mediating fitness tradeoffs for an amphibian polyphenism
<p class="MsoNormal"><span>Fitness tradeoffs are a foundation of ecological and evolutionary theory because tradeoffs can explain life history variation, phenotypic plasticity, and the existence of polyphenisms. </span></p> <p class="MsoNormal"><span>Using a 32-year mark-recapture dataset on lifetime fitness for 1,093 adult Arizona tiger salamanders (<em>Ambystoma mavortium nebulosum</em>) from a high elevation, polyphenic population, we evaluated the extent to which two life history morphs (aquatic paedomorphs vs terrestrial metamorphs) exhibited fitness tradeoffs in breeding and body condition with respect to environmental variation (e.g., climate) and internal state-based variables (e.g., age). </span></p> <p class="MsoNormal"><span>Both morphs displayed a similar response to higher probabilities of breeding during years of high spring precipitation (i.e., not indicative of a morph-specific fitness tradeoff). There were likely no climate-induced fitness tradeoffs on breeding state for the two life history morphs because precipitation and water availability are vital to amphibian reproduction. </span></p> <p class="MsoNormal"><span>Body condition displayed a contrasting response for the two morphs that was indicative of a climate-induced fitness tradeoff. While metamorphs exhibited a positive relationship with summer snowpack conditions, paedomorphs were unaffected. Fitness tradeoffs from summer snowpack are likely due to extended hydroperiods in temporary ponds, where metamorphs gain a fitness advantage during the summer growing season by exploiting resources that are unavailable to paeodomorphs. However, paedomorphs appear to have the overwintering fitness advantage because they consistently had higher body condition than metamorphs at the start of the summer growing season. </span></p> <p class="MsoNormal"><span>Our results reveal that climate and habitat type (metamorphs as predominately terrestrial, paedomorphs as fully aquatic) interact to confer different advantages for each morph. These results advance our current understanding of fitness tradeoffs in this well-studied polyphenic amphibian by integrating climate-based mechanisms. Our conclusions prompt future studies to explore how climatic variation can maintain polyphenisms and promote life history diversity, as well as the implications of climate change for polyphenisms. </span></p>
Data from: Widespread amphibian Perkinsea infections associated with Ranidae hosts, cooler months, and Ranavirus co-infection
<p>Amphibians suffer from large-scale population declines globally, and emerging infectious diseases contribute heavily to these declines. Amphibian Perkinsea (Pr) is a worldwide anuran pathogen associated with mass mortality events, yet little is known about its epidemiological patterns, especially in comparison to the body of literature on amphibian chytridiomycosis and ranavirosis. </p> <p>Here, we establish Pr infection patterns in natural anuran populations and identify important covariates including climate, host attributes, and co-infection with Ranavirus (Rv). </p> <p>We used quantitative (q)PCR to determine the presence and intensity of Pr and Rv across 1234 individuals sampled throughout central Florida in 2017-2019. We then implemented random forest ensemble learning models to predict infection with both pathogens based on physiological and environmental characteristics. </p> <p>Perkinsea infected 32% of all sampled anurans, and Pr prevalence was significantly elevated in Ranidae frogs, cooler months, metamorphosed individuals, and frogs co-infected with Rv, while Pr intensity was significantly higher in ranid frogs and individuals collected dead. Ranavirus prevalence was 17% overall and was significantly higher in Ranidae frogs, metamorphosed individuals, locations with higher average temperatures, and individuals co-infected with Pr. Perkinsea prevalence was significantly higher than Rv prevalence across months, regions, life stages, and species. Among locations, Pr prevalence was negatively associated with crayfish prevalence and positively associated with relative abundance of microhylids, but Rv prevalence did not associate with any tested co-variates. Co-infections were significantly more common than single infections for both pathogens, and we propose that Pr infections may propel Rv infections because seasonal Rv infection peaks followed Pr infection peaks and random forest models found Pr intensity was a leading factor explaining Rv infections. </p> <p>Our study elucidates epidemiological patterns of Pr in Florida and suggests that Pr may be under-recognized as a cause of anuran declines, especially in the context of pathogen co-infection.</p>
Amphibian imports into the United States from 1999 to 2021
<p>Shared here are data and code to support the manuscript: "Despite Lacey Act regulation, ongoing amphibian trade into the United States threatens salamanders with disease." A project overview is provided in the <a href="https://github.com/ecohealthalliance/amphibian_trade">GitHub repository</a>, but, in brief, this work required the compilation and cleaning of the United States Fish and Wildlife Service's Law Enforcement Management Information System (LEMIS) data in order to generate a complete time course of amphibian imports to the United States from 1999 to 2021. Others pursuing data reuse will most likely be interested in the full, cleaned amphibian import dataset (in CSV format) contained within these project files, which is named <strong>harmonized_amphibian_LEMIS_1999_to_2021.csv</strong>. Information regarding the LEMIS data, including detailed description of the data fields, can be found in <a href="https://www.nature.com/articles/s41597-020-0354-5">Eskew et al. 2020, "United States wildlife and wildlife product imports from 2000–2014"</a>.</p>
Multi‐species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds
<p>Aquatic environmental DNA is increasingly used for biodiversity monitoring, such as surveying threatened and invasive species. Mainstreaming these methods in practical applications, however, still requires significant standardisation and optimisation, namely regarding DNA capture methods. Here we evaluated how filter type (standard disc filters vs high-capacity capsules), number of sampling sites, volume of water filtered and environmental factors affected amphibian detection in Mediterranean temporary ponds. The study involved water filtering until clogging at one (capsules) and five (discs) sites from 16 small and shallow ponds, where three urodele and seven anuran species were recorded through sweep-netting and adult observations. Detection probabilities were estimated from site occupancy models based on replicate sampling and from an adaptation of time-to-detection models relating detection probability to volume of water filtered. Discs filtered relatively small volumes (15–1250 mL), with detection probabilities of the two abundant species (<em>Pelobates</em> <em>cultripes</em>, <em>Hyla</em> <em>meridionalis</em>) increasing rapidly with sample size and water volume, reaching almost perfect detection (0.95) at four and seven discs, and 420 mL and 1860 mL, respectively. However, reaching high detection probabilities for rare species (<em>Pelodytes</em> <em>atlanticus</em>, <em>Pleurodeles</em> <em>waltl</em>, <em>Triturus</em> <em>pygmaeus</em>) would require larger sampling effort than that used in our study. Despite filtering much larger volumes (600–5300 mL), filtering with capsules at a single site per pond provided lower detection probabilities for abundant species than filtering with discs at five sites. Rarer species showed no difference between methods, which may be due to small sample sizes and reduced statistical power for species with few detection. The effect of conductivity on species detectability was largely negative, while the influence of water clarity varied across species, and pH had no effects. Overall, our results suggest that eDNA amphibian surveys in Mediterranean temporary ponds need to consider filter clogging, heterogeneous DNA distribution, and highly conductive waters.</p>
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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
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.