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441 results for “Environmental DNA”
Data from: environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: towards a baseline for biodiversity monitoring of unexplored marine habitats
<p>Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from nineteen genera of fish, six of these have also been observed on towed underwater videos, while thirteen were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.</p>
Oxford Nanopore sequencing for comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity
<p><span>The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes</span><span>,<span> or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, </span>and <span>for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here, we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative</span>,<span> and unbiased identification of most eukaryotic species. </span></span></p>
Detection of black rat inhabitation using environmental DNA
<p>The all raw data of this study including expeirment 1, 2 and primer specificitiy as well as LOD.</p> <p> </p> <p>Pest management is essential for safeguarding agricultural productivity, public health, and ecological balance, especially as the global demand for sustainable pest control strategies rises with population growth. Among emerging technologies, environmental DNA (eDNA) analysis has gained prominence as a powerful tool, enabling the detection of pest species by isolating their genetic material from environmental samples. This study explores the innovative application of eDNA analysis in black rat (<a name="_Hlk184139956"></a><em>Rattus</em><em> rattus</em>) management, utilizing wipe sampling to recover eDNA from the air. Key experiments were found to determine the minimum surface area (~5 inch area) required for effective eDNA collection and to analyze the temporal persistence of black rat eDNA over two months. Our findings demonstrate the potential of eDNA techniques to transform pest management strategies, offering a highly efficient, cost-effective, and environmentally sustainable approach to monitoring and controlling black rat populations. This work represents a significant advancement in integrating molecular tools into pest control practices.</p> <p> </p>
Data for Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach
<p>Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA.</p> <p>Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species.</p> <p>eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with distance between sites. The distance decay of similarity derived from eDN<span>A </span>was similar, and even more pronounced, than that obtained with capture-based methods (gil-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species.</p> <p>Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provide a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture based methods, which describes fish fauna over a few hundred metres.</p>
Supplementary Table S1 (raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA "
<p>Supplementary Table S1 (all raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA ". Each data of the validation experiment; Experiment 1-4 was located in different sheets..</p>
Data from: Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers
<p>The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as water filtration and DNA precipitation are time consuming, require difficult-to-handle equipment and partially integrate eDNA signals. To overcome these limitations, we created the first proof of concept of a passive, 3D-printed and easy-to-use eDNA sampler. We designed the samplers from hydroxyapatite (HAp samplers), a natural mineral with a high DNA adsorption capacity. The porous structure and shape of the samplers were designed to optimise DNA adsorption and facilitate their handling in the laboratory and in the field. Here we show that HAp samplers can efficiently collect genomic DNA in controlled set-ups, but can also collect animal eDNA under controlled and natural conditions with yields similar to conventional methods. However, we also observed large variations in the amount of DNA collected even under controlled conditions. A better understanding of the DNA-hydroxyapatite interactions on the surface of the samplers is now necessary to optimise the eDNA adsorption and to allow the development of a reliable, easy-to-use and reusable eDNA sampling tool.</p>
Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions
<p>Although the use and development of molecular biomonitoring tools based on environmental nucleic acids (eDNA and eRNA; collectively known as eNAs) have gained broad interest for the quantification of biodiversity in natural ecosystems, studies investigating the impact of site-specific physicochemical parameters on eNA-based detection methods (particularly eRNA) remain scarce. Here, we used a controlled laboratory microcosm experiment to comparatively assess the environmental degradation of eDNA and eRNA across an acid-base gradient following complete removal of the progenitor organism (<em>Daphnia pulex</em>). Using water samples collected over a 30-day period, eDNA and eRNA copy numbers were quantified using a droplet digital PCR (ddPCR) assay targeting the mitochondrial <em>cytochrome c oxidase</em> subunit I (COI) gene of <em>D. pulex</em>. We found that eRNA decayed more rapidly than eDNA at all pH conditions tested, with detectability—predicted by an exponential decay model—for up to 57 hours (eRNA; neutral pH) and 143 days (eDNA; acidic pH) post organismal removal. Decay rates for eDNA were significantly higher in neutral and alkaline conditions than in acidic conditions, while decay rates for eRNA did not differ significantly among pH levels. Collectively, our findings provide the basis for a predictive framework assessing the persistence and degradation dynamics of eRNA and eDNA across a range of ecologically relevant pH conditions, establish the potential for eRNA to be used in spatially and temporally sensitive biomonitoring studies (as it is detectable across a range of pH levels), and may be used to inform future sampling strategies in aquatic habitats.</p>
Systematic review and meta-analysis: water type and temperature affect environmental DNA decay metadata
<p>Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at present it is difficult to disentangle study-specific effects from factors that universally affect eDNA degradation. To address this, a systematic review and meta-analysis was conducted on aquatic eDNA studies. Analysis revealed eDNA decayed faster at higher temperatures and in marine environments (as opposed to freshwater). DNA type (mitochondrial or nuclear) and fragment length did not affect eDNA decay rate, although a preference for < 200 bp sequences in the available literature means this relationship was not assessed with longer sequences (<em>e.g.</em> > 800 bp). At present, factors such as ultraviolet light, pH, and microbial load lacked sufficient studies to feature in the meta-analysis. Moving forward, we advocate researching these factors to further refine our understanding of eDNA decay in aquatic environments. This dryad entry contains the metadata which formed the basis for the meta-analysis.</p>
Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies
<p>Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large – volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle <em>Mesobot</em> in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40 – 60 liters) samples collected by <em>Mesobot</em> with small volume (~2 liters) samples collected using the conventional CTD rosette – mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume <em>Mesobot</em> and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not – although the number of unique taxa associated with the <em>Mesobot</em> samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.</p>
Marine biodiversity patterns in coastal Australian waters revealed by a three-year environmental DNA survey
<p><strong>Aim</strong></p> <p>To test the capacity of eDNA to characterise the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme.</p> <p><strong>Location</strong></p> <p>Samples were sourced seasonally for three years from nine Pan-Australian marine sites (n=90).</p> <p><strong>Methods</strong></p> <p>Here we apply a multi-assay metabarcoding approach to environmental DNA extracted from a rare long-term collection of bulk plankton samples. Six assays (targeting both the 16SrRNA and COI genes) were used to amplify and sequence the zooplankton diversity found within each sample. The data generated from each assay was filtered and clustered into OTUs prior to analysis. Abiotic IMOS data collected alongside the plankton collection enabled us to explore the physical and chemical drivers of community composition.</p> <p><strong>Results</strong></p> <p>The eDNA metabarcoding generated over 25 million sequences, identified in excess of 500 distinct taxa and detected clear spatial differences in marine metazoan communities. We found that site and sea surface temperature are the most consistent predictors of differences between zooplankton communities. We detected endangered and invasive species such as the bryozoan Membranipora membranace and the mollusc Maoricolpus roseus, and seasonal occurrences of species such as humpback whales (Megaptera novaeangliae). We also estimated the number of samples required to ensure robust marine eDNA metabarcoding biomonitoring programs into the future.</p> <p><strong>Main Conclusion</strong></p> <p>Our results demonstrate the ability of eDNA to capture and map zooplankton community changes in response to seasonal and spatial stressors and provide vital evidence to environmental stakeholders. We confirm that eDNA offers a practical opportunity for an ecosystem-wide approach to the long-term biomonitoring and understanding marine biomes where a morphological approach is not feasible.</p>
Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination
<p>Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (<em>Alligator mississippiensis</em>), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and 4 test samples) and past incubation temperature with a mean absolute error of 1.2˚C (in 4 test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity. </p>
Data from: Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates
<p>Invasive species are of concern due to their impacts on ecosystems and economies, but they pose significant control challenges. Environmental DNA (eDNA) is a powerful tool in the detection of aquatic organisms at low densities due to high sensitivity and ease of collection. Aquatic eDNA analyses have increased worldwide and are generally either applied to a few target species (quantitative PCR) or for broad taxonomic applications (metabarcoding). Here we describe the development and testing of a hybrid approach that utilized high sensitivity PCR primer sets and high-throughput sequencing (HTS), referred to as <em>targeted metabarcoding</em>, to detect 69 fishes and invertebrates. We identified target species based on reports of globally important invasive species and developed two independent PCR primers for each species (CO1 and a second mtDNA region). We assessed sensitivity and eDNA interference for all 138 primers (2 per species, 69 species) using standard end-point PCR and tested them on 10 eDNA samples spiked with various amounts of one or more of the target species' DNA. The sensitivity of the 138 primer sets ranged between 1.5×10<sup>-5</sup> and 2.64 ng template DNA (mean = 0.069 ng). Primers were also tested for interference effects using plankton eDNA to simulate field conditions. The inclusion of interfering plankton DNA reduced the sensitivity for most primer sets by one or more orders of magnitude (range 0 to 3). Overall, our targeted metabarcoding resulted in the detection of ~ 98% of species in the DNA spiked samples, and, perhaps more importantly, the HTS read count was positively related to the quantity of spiked DNA (P < 0.002). We envision this technique being particularly useful for the early detection of species at low population densities; however, there are diverse applications of targeted metabarcoding for monitoring aquatic community composition and quantifying ecosystem change and health.</p>
Data from: Experimental assessment of downstream environmental DNA patterns under variable fish biomass and river discharge rates
<p><span>The development of environmental DNA (eDNA) methods towards implementation as a cost-effective, nonlethal tool for fish biomonitoring in lotic environments requires insights on the temporal and spatial distribution of eDNA in river systems. Yet, little is known on how downstream eDNA dispersal is affected by the combination of river discharge and source biomass effects. In this study, we aimed at unravelling the effect of source- and system-specific processes on the stream reach of eDNA. We used a longitudinal cage study in two river sections characterized by a significantly different discharge rate, where two invasive and two native fish species were introduced under two contrasting biomass treatments. Using droplet digital PCR (ddPCR) analyses, we found that eDNA concentrations become strongly reduced 2 km downstream from the source, an effect that is strengthened with increasing river discharge and coinciding dilution effects. Higher discharge rates resulted in equal or even higher detection probabilities at increasing distance from the source. The introduction of high fish stock biomass resulted in an increase of eDNA concentrations, as well as detection probabilities and in parallel reduced the stochasticity of the measurements. A peak in eDNA concentrations at a downstream distance ranging between 300 m and 2 km confirms the complexity of plume-shaped downstream eDNA patterns. Our results showed interspecific variation in eDNA emission and suggest species-specific differences in eDNA persistence. This study underlines the impact of both river discharge rate and source biomass on downstream eDNA detection and dispersal patterns. </span></p>
Estimation of species abundance based on the number of segregating sites using environmental DNA (eDNA)
<p>The advancement of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. While most studies focus on detecting species presence or absence, recent research has explored using eDNA data to quantify species abundance. This estimation usually is based on the concentration of targeted eDNA. However, eDNA concentration can be influenced by various factors, both biotic and abiotic, which can obscure the relationship between concentration and species abundance. In this study, we suggest using the number of segregating sites as a proxy for estimating species abundance. We investigated this relationship in silico, in vitro, and in situ (mesocosm experiments) using two brackish goby species, <em>Acanthogobius hasta</em> and <em>Tridentiger bifasciatus</em>. Analysis of simulated and in vitro data, where DNA was mixed from a known number of individuals, revealed a strong correlation between the number of segregating sites and species abundance (R<sup>2</sup> > 0.9; P < 0.01). Results from the mesocosm experiment confirmed this correlation (R<sup>2</sup> = 0.70, P < 0.01). This correlation remained consistent despite biotic factors such as body size and feeding behavior of the fish (P > 0.05). Cross-validation tests demonstrated that the number of segregating sites predicts species abundance more accurately and reliably than eDNA concentration. In conclusion, the number of segregating sites is a precise and robust indicator of species abundance compared to eDNA concentration, offering a significant enhancement to the quantitative capabilities of eDNA technology.</p>
Data for: Environmental DNA storage and extraction method affects detectability for multiple aquatic invasive species
<p>Environmental DNA (eDNA) refers to genetic material released by organisms into their surrounding environment. Collecting and identifying eDNA has gained popularity for monitoring and surveillance of aquatic invasive species. Invasive species management is most successful when an invasion is identified early while population size is likely to be low, highlighting the importance of eDNA detection sensitivity. Various factors influence DNA yield recovered from environmental samples. Environmental DNA storage and extraction methods, for example, can be adjusted to maximize DNA yield, thereby improving detectability. In this study, we compared the performance of two eDNA storage and extraction methods in detecting three common aquatic invasive species (<em>Bythotrephes longimanus</em>, <em>Dreissena polymorpha</em>, and <em>Faxonius rusticus</em>) across five natural ecosystems of Minnesota, United States. One method involved storing filters in 95% ethanol (EtOH) and extracting DNA using a DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany), whereas the other method used cetyl trimethylammonium bromide (CTAB) for storage and a phenol–chloroform–isoamyl (PCI) procedure for DNA extraction. We also investigated the effect of DNA extract volume (1 μL relative to 3 μL) in qPCR reactions on eDNA detections for the commercial kit method. The CTAB‐PCI method yielded significantly more positive detections, across all three species, compared to the EtOH‐Qiagen method. Moreover, we found that using 1 μL of DNA extract in qPCR reactions was equally effective as using 3 μL. To improve detections of aquatic invasive species, we recommend that researchers store eDNA sample filters in CTAB or a similar lysis buffer such as Longmire's solution and extract with PCI when feasible, but note that lower extract volumes might be used without negative effect when either increasing technical replicates or repurposing samples for the detection of multiple species.</p>
Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga
<p>Early detection of nuisance species is crucial for the conservation and management of threatened ecosystems, reducing the risk of widespread establishment. Environmental DNA (eDNA) data can increase the sensitivity of biomonitoring programs, oftentimes with minimal cost and effort. However, eDNA analyses have inherent errors that can complicate the integration of molecular survey methods into existing management frameworks. Therefore, it is crucial for eDNA studies to consider imperfect detections and estimate error rates accordingly. Detecting nuisance species in low abundance with minimal uncertainty is vital to increase the chance of containment and eradication. We developed a novel eDNA assay to detect a nuisance marine macroalga across its colonization front using surface seawater samples from Papahānaumokuākea Marine National Monument (PMNM), one of the world's largest marine reserves. <em>Chondria tumulosa</em>, a cryptogenic red alga with invasive characteristics, has been documented forming dense mats that overgrow coral reefs and smother native flora and fauna in PMNM. We verified the eDNA assay using site-occupancy detection modeling from quantification polymerase chain reaction (qPCR) data, calibrated with visual estimates of benthic cover of <em>C. tumulosa </em>that ranged from < 1% to 95%. Results were subsequently validated with high-throughput sequencing of amplified eDNA and negative control samples. Overall, the probability of detecting <em>C. tumulosa </em>at occupied sites was at least 92% when multiple qPCR replicates were positive. Modeled false-positive inferences were 3% or less and false-negative errors were 11% or less. The developed assay is suitable for routine monitoring at shallow sites (less than 10 m), even when <em>C. tumulosa </em>abundance was less than 1%. Successful implementation of eDNA tools in conservation decision-making relies on balancing uncertainties in both visual and molecular detection methods. Our results and modeling demonstrated the assay's sensitivity to <em>C. tumulosa</em>, and we outline the necessary steps to infer ecological presence-absence from molecular detection data. By providing a reliable, cost-effective tool for detecting low-abundance species, eDNA analyses have the potential to enhance the surveillance of nuisance species and inform timely management interventions.</p>
Data from: Environmental DNA particle size distribution and quantity differ across taxa and organelles
Open the record for dataset details and reuse information.
Data from: Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary
<p>Estuarine ecosystems face increasing anthropogenic pressures, necessitating effective monitoring methods to mitigate their impacts on the biodiversity they harbour. The use of environmental DNA (eDNA) based detection methods is increasingly recognized as a promising tool to complement other, potentially invasive monitoring techniques. Integrating such eDNA analyses into monitoring frameworks for large spatial ecosystems is still challenging and requires a deeper understanding of the scale and resolution at which eDNA patterns may offer insights in species presence and community composition space and time. The Scheldt estuary, characterized by its diverse habitats and complex currents, is one of the largest Western European tidal river systems. Until now, it remains challenging to obtain accurate information on fish communities living in and migrating through this large ecosystem, consequently confining our knowledge to specific locations. To explore the potential of eDNA-based monitoring, we simultaneously combine stow net fishing with eDNA metabarcoding, to assess the Scheldt estuary's fish communities in space and time. In total, we detected 71 fish species in the estuary using eDNA metabarcoding, partly overlapping with historic fish community data gathered at the different study locations and in contrast to only 42 species using stow net fishing during the same survey period. Community compositions found by both detection methods varied amongst sampling locations, driven by a clear correlation to the salinity gradient. Limited effects of sampling depth and tide were observed on the eDNA metabarcoding data, allowing a significant reduction of the eDNA sampling effort for future eDNA fish monitoring campaigns in this study system. Our results further demonstrate that seasonal shifts in fish species occurrence can be detected using eDNA metabarcoding. Combining eDNA metabarcoding and stow net fishing further enhances our understanding of this vital waterway's diverse fish populations, allowing a higher resolution and more efficient monitoring strategy.</p>
Assessing Patterns of Metazoans in the Global Ocean using Environmental DNA
<p>Data for the above publication which is in RSOS. Code is available here, https://github.com/ngeraldi/Global_ocean_genome_analysis. The 5 files include the amplicon data (Malaspina and Tara) and all metagenome data is in DMAP_biomass_apr19 (it is not biomass, it is metagenome data). Global layers contain the metadata- april18 is amplicon data and genome is the metagenome data.</p> <p>Abstract:</p> <p>Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, <em>Tara </em>Oceans<em> </em>and <em>Malaspina</em>, that circumnavigated the oceans, and sampled down to 4000 meters to assess metazoans from eDNA extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer relative abundance of phyla using metagenome datasets, and relate these data with environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related with metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean’s surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.</p>
Inventory of ancient environmental DNA from sedimentary archives: locations, methods, and target taxa
<p>Locations of sampling sites from sedimentary ancient environmental DNA (aeDNA) studies. aeDNA is DNA that has degraded into short fragments, exhibits post-mortem damage signatures, and is recovered from a non-living tissue, organism, or environmental sample. Here we focus on sedimentary archives with contiguous records such as lake and marine sediments, permafrost, middens, cave sediments, soils, and incidental associated surface sediment samples used to interpret sedimentary archives. Studies span historic and ancient time periods using a variety of DNA-based methods (i.e., metabarcoding, shotgun sequencing, target capture, qPCR, ddPCR, and others) to study taxa from microorganisms to plants and mammals.</p>
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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)
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.