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441 results for “Environmental DNA”
Figure 2 in Assessing grass carp (Ctenopharyngodon idella) occupancy and detection probability within Lake Erie from environmental DNA
Figure 2. Mean posterior estimates of the probability of capturing grass carp eDNA from a site in a sample among sites (θ) from the model with the lowest WAIC score [ψ(Site)Θ(Site)p(.)]. Error bars represent 95% credible intervals. DR = Detroit River, HP = Hot Ponds, MB = Maumee Bay. All sites are located in western Lake Erie.
Figure 1 in Assessing grass carp (Ctenopharyngodon idella) occupancy and detection probability within Lake Erie from environmental DNA
Figure 1. Map denoting all monthly grass carp eDNA sampling events in 2018 (A–C) and 2019 (D–F) aggregated at each sampling location (Hot Ponds, Detroit River, and North Maumee Bay) and acoustic receiver locations (grey circles) in the western basin of Lake Erie. Positive and negative eDNA detections, defined as at least one positive qPCR detection on one replicate among all markers (GCTM10, GCTM22, GCTM32) are denoted by orange crosses and pink triangles, respectively. The 3 grass carp captured from conventional gear (total sampling events = 451) in the Detroit River (October 2018), Hot Pond (July 2019) and North Maumee Bay (July 2019) are denoted by a yellow hexagon.
Figure 2 in A workshop to advance invasive species early detection capacity of The Rapid Environmental DNA Assessment and Deployment Initiative & Network (READI-Net)
Figure 2. The Rapid Environmental (e)DNA Assessment and Deployment Initiative & Network (READI-Net) project components being developed to support molecular detection of invasive species. Molecular tools, like eDNA sampling, are sensitive and costeffective for early detection of invasive species and are one component of the National Early Detection Rapid Response framework.
Figure 1 in A workshop to advance invasive species early detection capacity of The Rapid Environmental DNA Assessment and Deployment Initiative & Network (READI-Net)
Figure 1. The National Early Detection Rapid Response framework developed by the U.S. Department of the Interior Invasive Species Task Force. Open circles represent the components to be enacted for effective early detection and rapid response of invasive species. The associated commentary reflects the primary questions, observations, and directives that the process from one component to the next. At the core of the process, are the informational inputs necessary for management decision-making.
Figure 2 in Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes
Figure 2. The mean number of cycles needed to detect DNA of zebra mussels from water samples collected at the surface, mid-column and bottom of Lake Minnetonka directly above a known zebra mussel population. A lower number of cycles indicates a greater amount of DNA. Bars represent the 95% confidence intervals.
Figure 3 in Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes
Figure 3. Structural Equation Model for zebra mussels in two lakes near Alexandria, Minnesota: Lake Le Homme Dieu (A) and Maple Lake (B). Nodes are environmental DNA copy numbers of zebra mussel DNA (eDNA), habitat, depth, lake and ash-free dry weight (AFDW). AFDW is log(AFDW + 0.1). eDNA is log(copy number eDNA + 0.1). Numbers next to a line between two nodes represents the correlation between the two nodes. The r2 values in boxes correspond % variance of dependent variable explained by the independent variable. Values with an asterisk (*) indicate significant correlation between nodes. Our significance level was established at α ≤ 0.05.
Data from: Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information
<p><span>Monitoring fish communities is central to the evaluation of ecological health of rivers. Not only presence/absence of species is important to assess, but also the species composition of local fish assemblages is a crucial parameter. Lotic fish communities are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. The use of environmental DNA-based analyses could serve as a non-destructive alternative, but this approach requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA fragments; as well as optimization of molecular detection in terms of predictive power and quality assurance. By introducing fifteen species known to occur in Belgian waters via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Introducing fish communities in two transects of a species poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable over a distance of 300 m up to 1 km downstream of the cages, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, can partly be attributed to variation in species-specific eDNA persistence. Our findings offer novel insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate snapshot of the total fish community composition occurring within an upstream perimeter ranging between 300 and 1000 meters. The potential application for other river systems is discussed in this study. </span></p>
Associated Dataset for Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes
<p>The dataset contains the final methylation call set (n=14,627,533), variant calling file for population genomics analyses, analysis codes/scripts, and other associated files related to the research (Constitutive and variable patterns of genome-wide DNA methylation in populations from spatial-environmental range extremes of the bumble bee <em>Bombus vosnesenskii)</em>. Raw WGBS reads generated in this study have been deposited and are currently available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under NCBI BioProject PRJNA956115.</p>
Environmental DNA-based detection of Batrachochytrium salamandrivorans in captive settings
<p>Detecting pathogens in the live animal trade is critical for tracking and preventing their movement, introduction, and spillover into susceptible fauna. However, the scale of the live animal trade makes individually testing animals infeasible for all but the most economically important taxa. For instance, while the fungal pathogen, <em>Batrachochytrium salamandrivorans</em> (<em>Bsal</em>), threatens amphibian, particularly caudate diversity, in Europe and the Americas, screening even a fraction of the millions of live amphibians imported into the United States, alone, is impractically laborious and expensive. A promising alternative to individual-level sampling (e.g., swabbing the skin of salamanders) is to instead collect DNA from the animals' environment (e.g., housing container or water) which allows us to screen a whole group of animals at a time. </p> <p>We used a series of experiments with <em>Bsal</em>-spiked water and substrates and experimentally infected rough-skinned newts (<em>Taricha granulosa</em>) to determine how best to collect <em>Bsal</em> environmental DNA (eDNA) samples, that is, which methods yield the greatest recovery of <em>Bsal</em> eDNA, and evaluate the capacity of these methods to detect <em>Bsal</em>-infected animals in conditions that might be found in captive settings and trade.</p> <p>We found that filtering water housing infected animals for even an hour can consistently recover detectable levels of <em>Bsal</em> eDNA, that there is little evidence of <em>Bsal </em>eDNA being clumped in housing containers or being swamped or inhibited under realistically dirty conditions, and that eDNA-based methods achieves an equivalent or higher chance of detecting <em>Bsal</em> infections in a group of co-housed newts with fewer samples than traditional methods of individually swabbing.</p> <p>By sampling the genetic materials shed or produced by a whole group of animals, eDNA-based methods are a powerful means of detecting pathogens, such as <em>Bsal,</em> in shipment and captive population. These methods bring routine pathogen surveillance into reach in many more contexts and can thus be an important tool in conservation and disease control.</p>
Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region
<p class="MsoNormal">Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to the coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of the coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine teleost and elasmobranch fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly lower during the sampled dry season. With the influx of freshwater and agricultural run-off during the wet season, teleost and elasmobranch taxa richness significantly decreased in all three estuaries, along with pronounced changes in fish community composition which were largely associated with environmental variables (particularly salinity). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Within the wet season, differing compositions of fish communities were observed among the four sampled locations, with this variation being significantly correlated with environmental variables (salinity, chlorophyll, DOC) and contaminants from agricultural run-off, i.e., nutrients (nitrogen and phosphorus) and pesticides. Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects (e.g., changes in salinity) play a key role in shaping the community structure of estuarine fish in this region, agricultural contaminants (nutrients and pesticides) are also important contributors in some systems.</p>
Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows
<p><span>Assessing biodiversity in marine nearshore ecosystems is crucial for effective management, especially in the context of climate change and overexploitation of marine resources. Conventional methods often fall short in providing comprehensive information for managing seagrass ecosystems. However, the emergence of environmental DNA (eDNA) techniques has transformed the field by enabling non-invasive surveys that are cost-effective and provide detailed information with high resolution. In this study, we utilized eDNA to assess fish diversity and compared its effectiveness to conventional techniques such as catch assessment surveys and underwater surveys. </span>We sampled three habitats (A: mangrove-seagrass, B: seagrass only, and C: coral-seagrass) with 4 replicates. Site A recorded 8 fish species, site B had 16 species, and site C, characterized by coral and seagrass habitats, exhibited the highest fish diversity with 45 species (mean H' index = 2.455), underscoring its ecological importance. To ensure accurate taxonomic identification, we utilized an updated MiFish reference database containing a larger number of fish species compared to the initial library. This expanded reference database with 9,569 fish species, facilitated more precise identification and enhanced the reliability of our findings. Notably, the eDNA technique outperformed conventional methods by detecting 23 additional fish species that went undetected using traditional surveys. Moreover, our study documented five fish species previously unknown to occur within the study region, further emphasizing the value of eDNA analysis in uncovering hidden biodiversity. These findings strongly advocate for integrating eDNA techniques into the monitoring and assessment of biodiversity in shallow tropical habitats of the Western Indian Ocean. By leveraging eDNA surveys, we can gain valuable insights into fish diversity, discover hidden species, and make informed decisions for the conservation and management of these ecologically significant areas.</p>
Data from: Holistic monitoring of aquatic and terrestrial vertebrates by camera trapping and aquatic environmental DNA
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Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves
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Data from: Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA (eDNA) metabarcoding
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Environmental DNA reveals fine-scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft and hard-bottom habitats
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Data from: Optimization of wetland environmental DNA metabarcoding protocols for Great Lakes region herpetofauna
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How, what, and where you sample environmental DNA affects diversity estimates and species detection
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Data for fitness analyses used in: Environmentally-induced DNA methylation is inherited across generations in water fleas (Daphnia magna)
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Environmental DNA data of aquatic insects for habitat suitability models
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Environmental DNA-based detection of Batrachochytrium salamandrivorans in captive settings
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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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.