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.
132
datasets available to search
ShareScore release 0.9.0
Dataset results
132 results for “environmental detection”
Supplementary data for: simultaneous species detection and discovery with environmental DNA metabarcoding: a freshwater mollusk case study
Open the record for dataset details and reuse information.
Data from: Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA
We developed and describe a qPCR assay for the detection of wood frogs (Rana sylvatica) using environmental DNA (eDNA) sampling. A single primer set was designed to amplify a 115-bp region of the wood frog cytochrome B gene and assessed for target specificity. There was no evidence of amplification in 11 non-target species. We evaluated the utility of the primer set in qPCR assay by conducting geo-referenced eDNA field surveys in Interior Alaska. Results indicate that the assay consistently detects wood frog DNA in the environment to 1.83 × 10−3 pg/μL. The assay provides a complement to traditional survey methods and can be readily applied in a wider conservation and management context.
Data from: Establishing detection thresholds for environmental DNA using receiver operator characteristic (ROC) curves
Environmental DNA (eDNA) detection is increasingly being used to assess the potential presence of aquatic species. Setting defensible thresholds for qPCR assays are necessary to differentiate "detection" from "non-detection", but threshold rationales are rarely reported in eDNA studies. Detection thresholds for data inclusion and exclusion have implications for downstream data analysis; uncritical acceptance could result in false positive results (Type I error), whereas overly conservative thresholds could result in high false negative interpretation (Type II error). We assessed the use of the receiver operator characteristics (ROC) framework to identify a detection threshold for balancing sensitivity and specificity of eDNA data. The ROC framework was tested using empirical eDNA data from redside dace (Clinostomus elongatus), an endangered freshwater fish in southwestern Ontario. Based on negative controls, positive controls, and quality assurance guidelines, a minimum concentration of 1 copy reaction−1 was identified as the most appropriate threshold for this study. Although optimal thresholds will likely vary between studies and labs based on empirical data, the ROC framework provides a statistical method for establishing defensible thresholds for data acceptance or rejection as well as tradeoffs between the sensitivity and specificity of eDNA data.
Data from: Detection of an endangered aquatic heteropteran using environmental DNA in a wetland ecosystem
The use of environmental DNA (eDNA) has recently been employed to evaluate the distribution of various aquatic macroorganisms. Although this technique has been applied to a broad range of taxa, from vertebrates to invertebrates, its application is limited for aquatic insects such as aquatic heteropterans. Nepa hoffmanni (Heteroptera: Nepidae) is a small (approx. 23 mm) aquatic heteropteran that inhabits wetlands, can be difficult to capture and is endangered in Japan. The molecular tool eDNA was used to evaluate the species distribution of N. hoffmanni in comparison to that determined using hand-capturing methods in two regions of Japan. The eDNA of N. hoffmanni was detected at nearly all sites (10 eDNA-detected sites out of 14 sites), including sites where N. hoffmanni was not captured by hand (five eDNA-detected sites out of six captured sites). Thus, this species-specific eDNA technique can be applied to detect small, sparsely distributed heteropterans in wetland ecosystems. In conclusion, eDNA could be a valuable technique for the detection of aquatic insects inhabiting wetland habitats, and could make a significant contribution to providing distribution data necessary to species conservation.
Data from: Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)
Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900 km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide polymorphisms (SNPs) using ddRAD sequencing. Despite high gene flow across sites (pairwise Fst = 0.0003-0.08), landscape genetic resistance modelling identified a positive non-linear effect of mean annual temperature on genetic connectivity. Urban areas and water bodies had a greater influence on genetic distance among sites than pasture, agricultural areas, and forest. Together, Fst outlier tests and Environmental Association Analysis (EAA) detected 242 unique SNPs under putative selection, with the highest numbers associated with latitude, mean annual temperature, and body size. A combination of landscape genetic connectivity analysis together with EAA identified mean annual temperature as a key driver of both neutral gene flow and environmental selection processes. Gene annotation of putatively adaptive SNPs matched with gene functions for olfaction, metabolic detoxification and ultra-violet light shielding. Our results imply that this widespread agricultural pest has the potential to spread and adapt under shifting temperature regimes and land cover change.
Data from: Environmental DNA (eDNA) detects the invasive rusty crayfish (Orconectes rusticus) at low abundances
Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types. We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus, and to reflect patterns of its relative abundance, in upper Midwest, USA inland lakes. We paired conventional baited trapping as a measure of crayfish relative abundance with water samples for eDNA, which were analysed in the laboratory with a qPCR assay. We modelled detection probability for O. rusticus eDNA using relative abundance and site characteristics as covariates, and also tested the relationship between eDNA copy number and O. rusticus relative abundance. We detected O. rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of O. rusticus eDNA was well-predicted by relative abundance of this species and lake water clarity. However there was poor correspondence between eDNA copy number and O. rusticus relative abundance estimated by trap catches. Synthesis and applications. Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperilled crayfishes and other benthic arthropods.
Data from: Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries
The extraction and characterization of DNA from aquatic environmental samples offers an alternative, non-invasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing ("metabarcoding"), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom designed group-specific primer set and next-generation sequencing for the detection of three species at risk; (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada; the Grand River and the Sydenham River. Out of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.
Data from: Detection of invasive mosquito vectors using environmental DNA (eDNA) from water samples
Repeated introductions and spread of invasive mosquito species (IMS) have been recorded on a large scale these last decades worldwide. In this context, members of the mosquito genus Aedes can present serious risks to public health as they have or may develop vector competence for various viral diseases. While the Tiger mosquito (Aedes albopictus) is a well-known vector for e.g. dengue and chikungunya viruses, the Asian bush mosquito (Ae. j. japonicus) and Ae. koreicus have shown vector competence in the field and the laboratory for a number of viruses including dengue, West Nile fever and Japanese encephalitis. Early detection and identification is therefore crucial for successful eradication or control strategies. Traditional specific identification and monitoring of different and/or cryptic life stages of the invasive Aedes species based on morphological grounds may lead to misidentifications, and are problematic when extensive surveillance is needed. In this study, we developed, tested and applied an environmental DNA (eDNA) approach for the detection of three IMS, based on water samples collected in the field in several European countries. We compared real-time quantitative PCR (qPCR) assays specific for these three species and an eDNA metabarcoding approach with traditional sampling, and discussed the advantages and limitations of these methods. Detection probabilities for eDNA-based approaches were in most of the specific comparisons higher than for traditional survey and the results were congruent between both molecular methods, confirming the reliability and efficiency of alternative eDNA-based techniques for the early and unambiguous detection and surveillance of invasive mosquito vectors. The ease of water sampling procedures in the eDNA approach tested here allows the development of large-scale monitoring and surveillance programs of IMS, especially using citizen science projects.
Data from: Development and validation of rapid environmental DNA (eDNA) detection methods for bog turtle (Glyptemys muhlenbergii)
Bog turtles Glyptemys muhlenbergii are listed as Species of Greatest Conservation Need (SGCN) for wildlife action plans in every state it occurs and multi-state efforts are underway to better characterize extant populations and prioritize restoration efforts. However, traditional sampling methods can be ineffective due to the turtle's wetland habitat, small size, and burrowing nature. Molecular methods, such as qPCR, provide the ability to overcome this challenge by effectively quantifying minute amounts of turtle DNA left behind in its environment (eDNA). Developing such methods for bog turtles has proved difficult partly because of the high sequence similarity between bog turtles and closely-related, cohabitating species, most often wood turtles ( Glyptemys insculpta ). Additionally, substrates containing bog turtle eDNA are often rich in organics or other substances that frequently inhibit both DNA extraction and qPCR amplification. Here, we describe the development and validation of a qPCR assay, BT3, targeting the mitochondrial cytochrome oxidase I gene that correctly identifies bog turtles with 100% specificity and sensitivity when tested on 201 blood samples collected from six species over a wide geographic range. We also developed a full-process internal control employing a genetically modified strain of Caenorhabditis elegans to improve DNA extraction methods, limit false negative results due to qPCR inhibition, and measure total DNA recovery from each sample. Using the internal control, we found that DNA recovery varied by over an order of magnitude between samples and likely explains the lack of bog turtle detection in some cases. Methods presented herein are highly-specific and may offer a more cost effective, non-invasive tool to supplement bog turtle population assessments in the eastern United States. Poor or differential DNA recovery, which remains unmeasured in the vast majority of eDNA studies, significantly reduced the ability to detect bog turtle in their natural environment.
Detection of Khapra Beetle environmental DNA using portable technologies in Australian biosecurity
<p>Khapra beetle, Trogoderma granarium Everts, 1898, is a serious pest of stored grain products globally. Environmental DNA (eDNA)-based methods offer sensitive detection tools used to inform biosecurity officers on the presence of high-risk pests. This study tested laboratory and portable molecular technologies to detect khapra beetle environmental DNA extracted from dust samples collected during biosecurity responses (Tuggeranong and Fyshwick) to khapra beetle incursions in Australia. Airborne and floor dust samples were collected opportunistically using handheld vacuum cleaners and eDNA was extracted using either field or laboratory-based extraction methods and analyzed using laboratory benchtop real time PCR machines and portable machines with two TaqMan and one LAMP-based assay. We successfully collected, extracted, and amplified khapra beetle eDNA from dust samples by qPCR, but failed to amplify T. granarium eDNA using LAMP. The Laboratory qPCR machine showed significantly higher mean Ct values (p &lt; 0.001) and significantly higher positive detections for both assays (p &lt; 0.001) compared to the portable thermocycler. DNA yield was significantly higher in samples extracted using laboratory-based kits compared to field kits (p &lt; 0.001) for both vacuumed and airborne samples (Mean DNA ± S.D. = 5.52 ± 4.45 and 4.77 ± 1.68 ng/μL, respectively), compared to field kits, (1.75 ± 1.17 and 1.36± 1.29 ng/μL for vacuumed and airborne samples, respectively). There were no significant differences in DNA yield between collection methods or differences in amplification associated to extraction or collection methods in either platform tested in this study. Portable technologies tested in this study (Franklin™ Real Time Thermocycler and Genie III) accurately amplified all tissue derived DNA during assay optimisation and field testing, highlighting the capacity of these technologies to complement biosecurity in confirming specimen ID. There was a high incidence of positive detections in field negative controls (Tuggeranong = 12.3 % and Fyshwick = 50 %), mostly attributed to the use of contaminated vacuum cleaners. We discuss suitable methods to minimize sample cross-contamination, the potential of portable molecular technologies as tools for biosecurity applications, and the suitability of eDNA-based molecular detection methods to complement global trade biosecurity for one of the most invasive and important grain pests worldwide.</p>
Sea lice (Lepeophtherius salmonis) detection and quantification around aquaculture installations using environmental DNA
<p>Here, we present supplementary material form our study<em> Sea lice (Lepeophtherius salmonis) detection and quantification around aquaculture installations using environmental DNA</em>. In our study, we developed and tested a new <em>L. salmonis</em> specific DNA-based assay (qPCR assay) for detection and quantification from seawater samples using an analytical pipeline compatible with the Environmental Sample Processor (ESP) for autonomous water sample analysis of gene targets.</p>
Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
Environmental DNA (eDNA) is used to detect biodiversity by the capture, extraction, and identification of DNA shed to the environment. However, eDNA capture and extraction protocols vary widely across studies. This use of different protocols potentially biases detection results and could significantly hinder a reliable use of eDNA to detect biodiversity. We tested whether choice of eDNA capture and extraction protocols significantly influenced biodiversity detection in aquatic systems. We sampled lake and river water, captured and extracted eDNA using six combinations of different protocols with replication, and tested for the detection of four macroinvertebrate species. Additionally, using the same lake water technical replicates, we compared the effect of capture and extraction protocols on metabarcode detections of biodiversity using 16S for eubacteria and cytochrome c oxidase I (COI) for eukaryotes. Protocol combinations for capture and extraction of eDNA significantly influenced DNA yield and number of sequences obtained from next generation sequencing. We found significantly different detection rates of species ranging from zero percent to thirty-three percent. Differences in which protocol combinations produced the highest metabarcoded biodiversity were detected and demonstrate that different protocols are required for different biodiversity targets. Our results highlight that the choice of molecular protocols used for capture and extraction of eDNA from water can strongly affect biodiversity detection. Consideration of biases caused by choice of protocols should lead to a more consistent and reliable molecular workflow for repeatable and increased detection of biodiversity in aquatic communities.
Data from: Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears
Background <p>Detecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community‐level analyses due to their use of species‐specific (presence/absence) 'barcodes'. Metabarcoding methods provide information on entire communities based on sequencing of all taxon‐specific barcodes within an eDNA sample.</p> Aims <p>Evaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience.</p> Materials and Methods <p>In 2016, eight limnologically diverse lakes (surface area range: 13 – 1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish‐specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List.</p> Results <p>Analysis of species accumulation curves indicated multi‐locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 – 62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples.</p> Discussion <p>Results reported here are, in part, driven by the lack of species‐selectivity during eDNA sampling events. Given the efficacy of eDNA assays, we suggest multi‐locus eDNA metabarcoding assays be implemented in early detection efforts.</p>
Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea. Environmental DNA Metabarcoding DATASET
<p>Environmental DNA metabarcoding data set. Environmental samples were collected in 2018 (one sample replicate of 2L surface water) and 2019 (four replicates of 1 L surface water) from several Mediterranean ports and data were generated using 12S rRNA and mitochondrial COI. For each sampling campaign (2018 and 2019) and marker two sheets are presented (with the same numeration): the first one represents all the ASV/MOTUs after the bioinformatics pipelines; the second one shows the curated assignment. The last two sheets are the OTU tables (presence-absence).</p>
Rock pools as a source of environmental DNA for the detection of the threatened Pilbara olive python (Liasis olivaceus barroni)
<p>Environmental DNA (eDNA) research is transforming biomonitoring at a global scale, but applicability to reptiles has been restricted because of their presumed low shedding rate. Consequently, eDNA may have considerable limitations as a biomonitoring tool in Australia where 40% of the terrestrial vertebrates are reptiles. However, there is a need to evaluate if method improvements such as targeting certain substrates, improves the ability to detect reptile eDNA. The Pilbara olive python (<em>Liasis olivaceus barroni</em>) is an uncommon and elusive Australian top predator with a high conservation priority. Like many other snake species, Pilbara olive pythons are challenging to monitor with traditional survey methods, therefore exploring an eDNA-based approach is highly relevant. The pythons are known to occasionally reside in rock pools. Thus, development of a reliable eDNA-based approach to detect the pythons in water would provide a needed alternative method. Here we use a previously developed metabarcoding assay targeting reptiles, to sequence a total of 228 water samples collected from 40 rock pools from six broad locations across the Pilbara region of Western Australia, and we confirm the presence of Pilbara olive python eDNA in 37 samples from 12 of those pools at three of the six broad sampling locations. Other vertebrate taxa, including other reptiles, amphibians, mammals and birds were also detected. Our documented ability to detect Pilbara olive python eDNA from rock pool water samples represents an important step towards eDNA-based precision monitoring of this species.</p>
Monitoring the birds and the bees: Environmental DNA metabarcoding of flowers detects plant–animal interactions
<p>Animal pollinators are vital for the reproduction of ~90% of flowering plants. However, many of these pollinating species are experiencing declines globally, making effective pollinator monitoring methods more important than ever before. Pollinators can leave DNA on the flowers they visit, and metabarcoding of these environmental DNA (eDNA) traces provides an opportunity to detect the presence of flower visitors. Our study, collecting flowers from seven plant species with diverse floral morphologies, for eDNA metabarcoding analysis, illustrated the value of this novel survey tool. eDNA metabarcoding using three assays, including one developed in this study to target common bush birds, recorded more animal species visiting flowers than visual surveys conducted concurrently, including birds, bees, and other species. We also recorded the presence of a flower visit from a western pygmy possum; to our knowledge, this is the first eDNA metabarcoding study to simultaneously identify the interaction of insect, mammal, and bird species with flowers. The highest diversity of taxa was detected on large inflorescence flower types found on <em>Banksia arborea </em>and <em>Grevillea georgeana</em>. The study demonstrates that the ease of sample collection and the robustness of the metabarcoding methodology have profound implications for future management of biodiversity, allowing us to monitor both plants and their attendant cohort of potential pollinators. This opens avenues for rapid and efficient comparison of biodiversity and ecosystem health between different sites and may provide insights into surrogate pollinators in the event of pollinator declines.</p>
Data from: Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears
Open the record for dataset details and reuse information.
Data from: Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds
Open the record for dataset details and reuse information.
Data from: Detection of invasive mosquito vectors using environmental DNA (eDNA) from water samples
Open the record for dataset details and reuse information.
Data from: Establishing detection thresholds for environmental DNA using receiver operator characteristic (ROC) curves
Open the record for dataset details and reuse information.
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.