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”
Amphibian species recorded within the Hubbard Brook Experimental Forest and vicinity (1963-2020; updated January 2021).
This dataset contains confirmed observations of amphibian species at the Hubbard Brook Experimental Forest and adjacent Mirror Lake. The original list was published in Holmes, R. T. and G. E. Likens. 1999. Organisms of the Hubbard Brook Valley, New Hampshire. USDA Forest Service, Northeastern Research Station, General Tech. Report NE-257. 32 pp. The list is updated here (January 2021) to include additional species observed since the original publication, update taxonomic classifications, and provide annotations on distribution.
Data from: Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees
<p>Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt <i>Calotriton asper </i>(Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.</p>
Data from: Telomere attrition with age in a wild amphibian population
<p>Telomere shortening with age has been documented in many organisms, but few studies have reported telomere length measurements in amphibians, and no information is available for growth after metamorphosis, nor in wild populations. We provide both cross-sectional and longitudinal evidence of net telomere attrition with age in a wild amphibian population of natterjack toads (<em>Epidalea calamita</em>). Based on age-estimation by skeletochronology and qPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recaptured males. Our results support that toads experience telomere attrition throughout<br> their ontogeny, and that most attrition occurs during the first 1–2 years.We did not find associations between telomere length and inbreeding or body condition. Our results on telomere length dynamics under natural conditions confirm telomere shortening with age in amphibians and provide quantification of wide telomere length variation within and among age-classes in a wild breeding population.</p>
Amphibian survey of riparian buffer zones at SAFE Project, Borneo
<b>Description: </b><p>Results from amphibian surveys carried out along riparian transect sites at SAFE project, Borneo</p><p><b>Project: </b>This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/152"><b>MRes Tropical Forest Ecology Field Course</b></a></p><p><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=3973551">here</a></p><p><b>Files: </b>This consists of 1 file: frogs_data_rob.xlsx</p><p><b>frogs_data_rob.xlsx</b></p><p>This file contains dataset metadata and 3 data tables:</p><ol><li><p><b>Stream Overview</b> (described in worksheet StreamMeasuresParent)</p><p>Description: Survey overview details</p><p>Number of fields: 16</p><p>Number of data rows: 12</p><p>Fields: </p><ul><li><b>ec5_uuid</b>: EpiCollect 5 code (Field type: id)</li><li><b>created_at</b>: Date and time of measurement (Field type: date)</li><li><b>created_by</b>: Researcher contact email (Field type: id)</li><li><b>title</b>: Survey location and visit (Field type: id)</li><li><b>2_Stream_ID</b>: Stream idenity code (Field type: location)</li><li><b>RiparianWidth</b>: Riparian buffer width (Field type: numeric)</li><li><b>lat_3_GPS_Location</b>: Latitude (Field type: numeric)</li><li><b>long_3_GPS_Location</b>: Longitude (Field type: numeric)</li><li><b>accuracy_3_GPS_Location</b>: Accuracy of GPS location data (Field type: numeric)</li><li><b>4_Visit</b>: Visit number (Field type: id)</li><li><b>5_Photo_of_stream_la</b>: File ID of photo of river (Field type: id)</li><li><b>7_Start_Time</b>: Time sampling started (Field type: time)</li><li><b>8_Date_ddMMYYYY</b>: Calendar date of sampling (Field type: date)</li><li><b>9_Comments_weather_e</b>: Weather conditions (Field type: comments)</li><li><b>11_Surveyors</b>: Identity of surveyors (Field type: id)</li><li><b>12_RAs</b>: Identity of research assistants (Field type: id)</li></ul></li><li><p><b>Stream characteristics</b> (described in worksheet StreamMeasures)</p><p>Description: Stream characteristics (dimensions, canopy cover and substrate)</p><p>Number of fields: 19</p><p>Number of data rows: 105</p><p>Fields: </p><ul><li><b>ec5_parent_uuid</b>: EpiCollect 5 code (Field type: id)</li><li><b>created_at</b>: Date and time of measurement (Field type: datetime)</li><li><b>created_by</b>: Researcher contact email (Field type: id)</li><li><b>StreamID</b>: Stream idenity code (Field type: location)</li><li><b>15_Marker_point</b>: Identity of marker point (Field type: id)</li><li><b>SiteCode</b>: Location code of site (Field type: location)</li><li><b>Width</b>: Width of stream bed (Field type: numeric)</li><li><b>17_Upstream_Canopy</b>: Percentage of canopy cover upstream from point (Field type: numeric)</li><li><b>18_Downstream_Canopy</b>: Percentage of canopy cover downstream from point (Field type: numeric)</li><li><b>19_Left_Canopy</b>: Percentage of canopy cover to left of point (Field type: numeric)</li><li><b>20_Right_Canopy</b>: Percentage of canopy cover to right of point (Field type: numeric)</li><li><b>20_Large_boulder__co</b>: Percentage coverage by large boulders (Field type: numeric)</li><li><b>21_Medium_rock__cove</b>: Percentage coverage by medium rocks (Field type: numeric)</li><li><b>22_Small_rock__cover</b>: Percentage coverage by small rocks (Field type: numeric)</li><li><b>23_Gravel__cover</b>: Percentage coverage by gravel (Field type: numeric)</li><li><b>24_Sand__cover</b>: Percentage coverage by sand (Field type: numeric)</li><li><b>25_MudGround__cover</b>: Percentage coverage by mud (Field type: numeric)</li><li><b>26_Substrate_cover_o</b>: Percentage coverage by other substrate type (Field type: categorical)</li><li><b>27_Water_flow_at_poi</b>: Water flow at point (Field type: categorical)</li></ul></li><li><p><b>Frog species </b> (described in worksheet FrogData)</p><p>Description: Recorded frog species and associated body measurements</p><p>Number of fields: 19</p><p>Number of data rows: 785</p><p>Fields: </p><ul><li><b>Stream_ID</b>: Stream identification code (Field type: location)</li><li><b>Date</b>: Date (Field type: date)</li><li><b>23_Closest_Marker</b>: Distance along transect at which frog was recorded (Field type: numeric)</li><li><b>SiteCode</b>: Location code of recorded frog (Field type: location)</li><li><b>24_Horizontal_Distan</b>: Approximate distance of recorded frog from stream bed (Field type: numeric)</li><li><b>25_Vertical_Distance</b>: Approximate distance of recorded frog above stream bed (Field type: numeric)</li><li><b>27_Substrate</b>: Substrate on which frog was recorded (Field type: categorical)</li><li><b>28_Substrate_if_othe</b>: Secondary substrate on which frog was recorded (Field type: categorical)</li><li><b>30_Dorsal</b>: EpiCollect 5 code for photograph (dorsal) of recorded frog species (Field type: id)</li><li><b>31_Ventral</b>: EpiCollect 5 code for photograph (ventral) of recorded frog species (Field type: id)</li><li><b>32_Left_side</b>: EpiCollect 5 code for photograph (left-side) of recorded frog species (Field type: id)</li><li><b>33_Right_side</b>: EpiCollect 5 code for photograph (right-side) of recorded frog species (Field type: id)</li><li><b>Species</b>: Species or Genus level identity (Field type: taxa)</li><li><b>36_Mass_of_frog_in_bag</b>: Combined mass of frog and bag (Field type: numeric)</li><li><b>38_Mass_of_empty_bag</b>: Mass of bag alone (Field type: numeric)</li><li><b>Mass_of_frog</b>: Mass of frog (Field type: numeric trait)</li><li><b>40_SnoutVent_Length</b>: Snout-vent length of frog (Field type: numeric trait)</li><li><b>Comment</b>: Comments on frog identity (Field type: comments)</li><li><b>Sex</b>: Sex of frog (Field type: categorical trait)</li></ul></li></ol><p><b>Date range: </b>2019-02-04 to 2019-02-13</p><p><b>Latitudinal extent: </b>4.6498 to 4.7273</p><p><b>Longitudinal extent: </b>117.5413 to 117.6414</p><p><b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.</p><div> -  Animalia <br> -  -  Chordata <br> -  -  -  Amphibia <br> -  -  -  -  Anura <br> -  -  -  -  -  [Other] <br> -  -  -  -  -  Bufonidae <br> -  -  -  -  -  -  <i>Ansonia</i> <br> -  -  -  -  -  -  -  <i>Ansonia spinulifer</i> <br> -  -  -  -  -  -  <i>Phrynoidis</i> <br> -  -  -  -  -  -  -  <i>Phrynoidis juxtaspera</i> <br> -  -  -  -  -  Dicroglossidae <br> -  -  -  -  -  -  <i>Limnonectes</i> <br> -  -  -  -  -  -  -  <i>Limnonectes finchi</i> <br> -  -  -  -  -  -  -  <i>Limnonectes kuhlii</i> <br> -  -  -  -  -  -  -  <i>Limnonectes leporinus</i> <br> -  -  -  -  -  -  -  <i>Limnonectes palavanensis</i> <br> -  -  -  -  -  -  <i>Ingerana</i> <br> -  -  -  -  -  -  -  <i>Ingerana baluensis</i> (as homotypic_synonym: <i>Occidozyga baluensis</i>)<br> -  -  -  -  -  -  <i>Fejervarya</i> <br> -  -  -  -  -  -  -  <i>Fejervarya limnocharis</i> <br> -  -  -  -  -  -  <i>Occidozyga</i> <br> -  -  -  -  -  -  -  <i>Occidozyga laevis</i> <br> -  -  -  -  -  Ranidae <br> -  -  -  -  -  -  <i>Chalcorana</i> <br> -  -  -  -  -  -  -  <i>Chalcorana megalonesa</i> <br> -  -  -  -  -  -  -  <i>Chalcorana raniceps</i> <br> -  -  -  -  -  -  <i>Meristogenys</i> <br> -  -  -  -  -  -  -  <i>Meristogenys orphnocnemis</i> <br> -  -  -  -  -  -  <i>Hylarana</i> <br> -  -  -  -  -  -  -  <i>Hylarana picturata</i> (as synonym: <i>Pulchrana picturata</i>)<br> -  -  -  -  -  -  <i>Staurois</i> <br> -  -  -  -  -  -  -  <i>Staurois guttatus</i> <br> -  -  -  -  -  -  -  <i>Staurois latopalmatus</i> <br> -  -  -  -  -  Megophryidae <br> -  -  -  -  -  -  <i>Leptolalax</i> <br> -  -  -  -  -  -  -  <i>Leptolalax fritinniens</i> <br> -  -  -  -  -  -  -  <i>Leptolalax gracilis</i> <br> -  -  -  -  -  -  <i>Leptobrachium</i> <br> -  -  -  -  -  -  -  <i>Leptobrachium abbotti</i> <br> -  -  -  -  -  Rhacophoridae <br> -  -  -  -  -  -  <i>Rhacophorus</i> <br> -  -  -  -  -  -  -  <i>Rhacophorus pardalis</i> <br> -  -  -  -  -  -  <i>Polypedates</i> <br> -  -  -  -  -  -  -  <i>Polypedates macrotis</i> <br></div><p></p>
Data from: Salinity stress increases the severity of ranavirus epidemics in amphibian populations
The stress-induced susceptibility hypothesis, which predicts chronic stress weakens immune defenses, was proposed to explain increasing infectious disease-related mass mortality and population declines. Previous work characterized wetland salinization as a chronic stressor to larval amphibian populations. Thus, we combined field observations with experimental exposures quantifying epidemiological parameters to test the role of salinity stress in the occurrence of ranavirus-associated mass mortality events. Despite ubiquitous pathogen presence (94%), populations exposed to salt runoff had slightly more frequent ranavirus related mass mortality events, more lethal infections, and 117-times greater pathogen environmental DNA. Experimental exposure to chronic elevated salinity (0.8-1.6 g/L Cl-) reduced tolerance to infection, causing greater mortality at lower doses. We found a strong negative relationship between splenocyte proliferation and corticosterone in ranavirus-infected larvae at a moderate elevation of salinity, supporting glucocorticoid-medicated immunosuppression, but not at high salinity. Salinity alone reduced proliferation further at similar corticosterone levels and infection intensities. Finally, larvae raised in elevated salinity had 10-times more intense infections and shed 5-times as much virus with similar viral decay rates, suggesting increased transmission. Our findings illustrate how a small change in habitat quality leads to more lethal infections and potentially greater transmission efficiency, increasing the severity of ranavirus epidemics.
The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae)
The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty-five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype-based subspecies classification. These lineages diverged 2.32–5.23 million years ago, a timing that closely aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia.
Data from: Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians
Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation by distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distance (r = 0.057; p < 0.001); whereas, wood frogs exhibited a strongly non-linear and lower variance relationship (r = 0.429; p < 0.001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modelling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.
Multi-species occupancy modeling provides novel insights into amphibian metacommunity structure and wetland restoration
<p>A fundamental goal of community ecology is to understand species-habitat relationships and how they shape metacommunity structure. Recent advances in occupancy modeling enable habitat relationships to be assessed for both common and rare species within metacommunities using multi-species occupancy models (MSOM). These models account for imperfect species detection and offer considerable advantages over other analytical tools commonly used for community analyses under the elements of metacommunity structure (EMS) framework. Here, we demonstrate that MSOM can be used to infer habitat relationships and test metacommunity theory, using amphibians. Repeated frog surveys were undertaken at 55 wetland sites in eastern Australia. We detected 11 frog species from three families (Limnodynastidae, Myobatrachidae and Pelodryadidae). The rarest species was detected at only one site whereas the most common species was detected at 42 sites (naïve occupancy rate: 0.02 – 0.76). Two models were assessed representing two competing hypotheses; the best-supported model included the covariates distance to the nearest site (connectivity), wetland area, presence of the non-native eastern mosquitofish (<i>Gambusia holbrooki</i>), proportion cover of emergent vegetation, an interaction term between Gambusia and emergent vegetation cover, and the proportion canopy cover over a site. Hydroperiod played no detectable role in metacommunity structure. We found species-habitat relationships that fit with current metacommunity theory – occupancy increased with wetland area and connectivity. There was a strong negative relationship between occupancy and the presence of predatory Gambusia, and a positive interaction between Gambusia and emergent vegetation. The presence of canopy cover strongly increased occupancy for several tree frog species, highlighting the importance of terrestrial habitat for amphibian community structure. We demonstrated how responses by amphibians to environmental covariates at the species level can be linked to occupancy patterns at the metacommunity scale. Our results have clear management implications – wetland restoration projects for amphibians and likely other taxa should maximize wetland area and connectivity, establish partial canopy cover, and eradicate Gambusia or provide aquatic vegetation to mitigate the impact of this non-native fish. We strongly advocate the use of MSOM to elucidate the habitat drivers behind animal occupancy patterns and to derive unbiased occupancy estimates for monitoring programmes.</p>
Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data
<p>The growing availability of genetic datasets, in combination with machine learning frameworks, offer great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we analyzed repurposed data using machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this dataset, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contain lower genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful datasets with greater utility for understanding global biodiversity.</p>
Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians, and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in an enzootic disease state, and we address the hypothesis that such "persistent" populations are aided by mutualistic skin microbes. Our 16S rRNA metabarcoding data reveal that the skin microbiome of highly infected juvenile frogs is characterized by significantly reduced species richness and evenness, and by strikingly lower variation between individuals, compared to juveniles and adults with lower infection levels. Over 90% of DNA sequences from the skin microbiome of highly infected frogs were derived from bacteria in a single order, Burkholderiales, compared to just 54% in frogs with lower infection levels. In a culture-dependent Bd-inhibition assay, the bacterial metabolites we evaluated all inhibited the growth of Bd. Together, these results illustrate the disruptive effects of Bd infection on host skin microbial community structure and dynamics, and suggest possible avenues for the development of anti-Bd probiotic treatments.
Data from: Large-scale recovery of an endangered amphibian despite ongoing exposure to multiple stressors
Amphibians are one of the most threatened animal groups, with 32% of species at risk for extinction. Given this imperiled status, is the disappearance of a large fraction of the Earth's amphibians inevitable, or are some declining species more resilient than is generally assumed? We address this question in a species that is emblematic of many declining amphibians, the endangered Sierra Nevada yellow-legged frog (Rana sierrae). Based on >7,000 frog surveys conducted across Yosemite National Park over a 20-y period, we show that, after decades of decline and despite ongoing exposure to multiple stressors, including introduced fish, the recently emerged disease chytridiomycosis, and pesticides, R. sierrae abundance increased sevenfold during the study and at a rate of 11% per year. These increases occurred in hundreds of populations throughout Yosemite, providing a rare example of amphibian recovery at an ecologically relevant spatial scale. Results from a laboratory experiment indicate that these increases may be in part because of reduced frog susceptibility to chytridiomycosis. The disappearance of nonnative fish from numerous water bodies after cessation of stocking also contributed to the recovery. The large-scale increases in R. sierrae abundance that we document suggest that, when habitats are relatively intact and stressors are reduced in their importance by active management or species' adaptive responses, declines of some amphibians may be partially reversible, at least at a regional scale. Other studies conducted over similarly large temporal and spatial scales are critically needed to provide insight and generality about the reversibility of amphibian declines at a global scale.
Data from: Serratia marcescens Shapes Cutaneous Bacterial Communities and Influences Survival of an Amphibian Host
A changing understanding of the functional interactions between microbial communities and their associated hosts is influencing how disease is perceived and ameliorated. Of the numerous host-microbiome-disease systems of study, the emergence of chytridiomycosis in anurans (caused by Batrachochytrium dendrobatidis, hereafter Bd), has been implicated in ongoing declines and extinction events of amphibians across the planet. Interestingly, there has been differential survival among amphibians in resisting Bd infection and subsequent disease. One factor thought to contribute to this resistance is the host-associated cutaneous microbiota. This has raised the possibility of utilizing genetically modified probiotics to restructure the host-associated microbiota for desired anti-fungal outcomes. Here, we utilize a previously described strain of Serratia marcescens (Sm) for manipulation of amphibian cutaneous microbiota. Sm was genetically altered to have a dysfunctional pathway for the production of the extracellular metabolite prodigiosin. This genetically altered strain (Δpig) and the functional prodigiosin producing strain (WT-pig) were compared for their microbial community and anti-Bd effects both in vitro and in vivo. In vitro, Bd growth was significantly repressed in the presence of prodigiosin. In vivo, the inoculation of both Sm strains was shown to significantly influence amphibian microbiota diversity with the Δpig-Sm treatment showing increasing α-diversity, and the WT-pig S. marcescens having no temporal effect on diversity. Differences were also seen in host mortality with Δpig-Sm exhibiting significantly decreased survival probability as compared to a no¬-Sm control in the presence of Bd. These results are important evidence for the potential of genetic-level manipulation of bacteria in a host microbial community, which may provide a way to alter disease outcomes and address critical frontiers in disease and microbial ecology.
Data from: Fast life history traits promote invasion success in amphibians and reptiles
Competing theoretical models make different predictions on which life history strategies facilitate growth of small populations. While 'fast' strategies allow for rapid increase in population size and limit vulnerability to stochastic events, 'slow' strategies and bet-hedging may reduce variance in vital rates in response to stochasticity. We test these predictions using biological invasions since founder alien populations start small, compiling the largest dataset yet of global herpetological introductions and life history traits. Using state-of-the-art phylogenetic comparative methods, we show that successful invaders have fast traits, such as large and frequent clutches, at both establishment and spread stages. These results, together with recent findings in mammals and plants, support 'fast advantage' models and the importance of high potential population growth rate. Conversely, successful alien birds are bet-hedgers. We propose that transient population dynamics and differences in longevity and behavioural flexibility can help reconcile apparently contrasting results across terrestrial vertebrate classes.
Data from: Landscape genetic inferences vary with sampling scenario for a pond breeding amphibian
A critical decision in landscape genetic studies is whether to use individuals or populations as the sampling unit. This decision affects the time and cost of sampling and may affect ecological inference. We analyzed 334 Columbia spotted frogs at 8 microsatellite loci across 40 sites in northern Idaho to determine how inferences from landscape genetic analyses would vary with sampling design. At all sites, we compared a proportion available sampling scheme (PASS), in which all samples were used, to resampled datasets of 2-11 individuals. Additionally, we compared a population sampling scheme (PSS) to an individual sampling scheme (ISS) at 18 sites with sufficient sample size. We applied an information theoretic approach with both restricted maximum likelihood and maximum likelihood estimation to evaluate competing landscape resistance hypotheses. We found that PSS supported a low-density forest model (0.87) and ISS supported this model as well as additional models when testing hypotheses of landcover types that create the greatest resistance to gene flow for Columbia spotted frogs. Increased sampling density and study extent, seen by comparing PSS to PASS, showed a change in model support from a model of only low-density forest to a model of only high-density forest. As number of individuals increased, model support converged at 7 individuals for ISS to PSS. ISS may be useful to increase study extent and sampling density, but may lack power to provide strong support for the correct model with microsatellite datasets. Our results highlight the importance of additional research on sampling design effects on landscape genetics inference.
Data from: Disease and climate effects on individuals drive post-reintroduction population dynamics of an endangered amphibian
The emergence of novel pathogens often has dramatic negative effects on previously unexposed host populations. Subsequent disease can drive populations and even species to extinction. After establishment in populations, pathogens can continue to affect host dynamics, influencing the success or failure of species recovery efforts. However, quantifying the effect of pathogens on host populations in the wild is challenging because individual hosts and their pathogens are difficult to observe. Here we use long-term mark-recapture data to describe the dynamics of reintroduced populations of an endangered amphibian (Rana sierrae) and evaluate the success of these recovery efforts in the presence of a recently-emerged pathogen, the amphibian chytrid fungus Batrachochytrium dendrobatidis. We find that high B. dendrobatidis infection intensities are associated with increases in frog detectability and reductions in survival. When average infection intensities are high, adults are more likely to gain infections and less likely to lose infections. We also find evidence for intensity-dependent survival, with heavily infected individuals suffering higher mortality. These results highlight the need in disease ecology for probabilistic approaches that account for uncertainty in infection intensity using imperfect observational data. Such approaches can advance the understanding of disease impacts on host population dynamics, and in the current study will improve the effectiveness of species conservation actions.
Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in non-laboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception amongst others. A large proportion of potential non-coding RNA transcripts present in our differentially expressed set provides first evidence of a possible role for long non-coding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from postitive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.
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.
Data from: Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life
<p>Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.</p>
Data from: Sexual dichromatism drives diversification within a major radiation of African amphibians
Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across both micro- and macroevolutionary timescales.
An invasive amphibian drives antipredator responses in two prey at different trophic positions
<p>Generalist invasive predators consume prey at different trophic levels and generate drastic changes in local communities. However, the long-term effects of predation may be reduced by eco-evolutionary responses of native populations. The capacity of prey species distributed across the trophic network to develop antipredator responses may determine the ecosystem potential to buffer against the invader. The African clawed frog is a major invader on several continents. Because of its large size, generalist diet, and aquatic lifestyle, we predicted the development of antipredator responses in prey species at different trophic levels. We tested for behavioral shifts between populations within and outside the invasive range in the herbivorous snail Physella acuta and the predatory heteropteran, the backswimmer Notonecta glauca. We detected antipredator responses in both prey species. In sympatry, P. acuta stayed higher in the water column, while N. glauca spent more time swimming underwater and less time surfacing when the predator cues were present. In allopatry, P. acuta dived deeper and N. glauca spent more time surfacing and stayed longer still underwater. In both species, sympatric populations showed evidence of olfactory recognition of the frog. Our results show that the introduction of a top predator like Xenopus laevis in the pond ecosystem drives behavioral antipredator responses in species across the trophic network. Eco-evolutionary processes may allow some degree of long-term resilience of pond communities to the invasion of X. laevis.</p>
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.