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1,076 results for “Metabarcoding”
Environmental DNA Metabarcoding of Cephalopod Diversity in the Tyrrhenian Deep Sea
<p>This dataset contains the raw demultiplexed reads of the study "Environmental Metabarcoding of Cephalopod Diversity in the Tyrrhenian Deep Sea". eDNA was extracted from water (wat) and sediment (sed) matrices, amplified with Ceph18S primers that specifically target cephalopods (de Jonge et al. 2021), and sequenced on IonTorrent platform. The names of the files indicate the sampling station (ST1, ST4, ST5, ST6), the replicate number (R1, R2), and the environmental matrix (wat, sed). </p>
Screening of bacterial diversity by 16S rRNA metabarcoding in Orbicella faveolata healthy and with Black Band Disease
<p>Screening of bacterial diversity by 16S rRNA metabarcoding in Orbicella faveolata healthy and with Black Band Disease</p>
Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys
Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.
DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
<p>DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome <i>c</i> oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed "universal" markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macro-eukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image-based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multi-marker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.</p>
Diet DNA metabarcoding data from spiders (Heteropoda venatoria) from Palmyra Atoll (2015-2017) with both individual samples that have and have not been surface sterilized
<p>These are data and code from a study examining the potential for surface contamination to influence diet DNA metabarcoding datasets when DNA is sequenced from full body parts (in this case, the opisthosomas of spider individuals). These datasets include the raw sequencing data, all downstream datasets, and taxonomic assignments collected from database searches on BOLD and GenBank (accessed 2019). The code includes code to reproduce all bioinformatics (merge, filter, match to taxonomies, rarefy, sort) as well as all statistics and figures generated from analyses. Raw data are from DNA extractions of predator gut regions (opisthosomas) and amplification of the CO1 gene using PCR. The predator species is <em>Heteropoda venatoria </em>collected individually with sterilized implements and either the diet sequences from their natural diets were extracted or their diets following feeding spiders in a feeding trial. </p>
Data from: Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding
<p>Although environmental DNA (eDNA) metabarcoding has become widely applied to gauge ecosystems in a noninvasive and cost-efficient manner, false negatives can occur due to various factors in its inherent multistage workflow. It is therefore essential to deal with this kind of species detection errors in eDNA metabarcoding to achieve accurate assessment of species distribution and diversity. To address this issue, we proposed a variant of the multispecies site occupancy model for eDNA metabarcoding studies and applied it to an eDNA metabarcoding dataset of freshwater fish communities collected in the Kasumigaura watershed in Japan.</p> <ul> </ul>
Data from: The role of taxonomic expertise in interpretation of metabarcoding studies
<p>The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analyzed taxonomic assignment of metabarcoded samples using two genetic markers (COI, 18S V1-2), two types of clustering into molecular operational taxonomic units (OTUs, ZOTUs), and three methods for taxonomic assignment (RDP Classifier, BLASTn to GenBank, BLASTn to a local barcode database). The local database includes 1042 COI and 1108 18S (SSU) barcode sequences, and we added new high-quality sequences to GenBank for both markers, including 109 contributions at the species level. The number of phyla detected and the number of taxa identified to phylum varied between genetic marker and among the three methods used for taxonomic assignments. Blasting the metabarcodes to the local database generated multiple unique contributions to identify OTUs and ZOTUs. We argue that a multi-marker approach combined with taxonomic expertise to develop a curated, vouchered, local barcode database increases taxon detection with metabarcoding, and its potential as a tool for zooplankton biodiversity surveys.</p>
Data from: Fine-tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches
<p><span>Accurate quantification of biodiversity can be demanding and expensive. Although environmental DNA (eDNA) metabarcoding can facilitate biodiversity assessments through non-invasive, cost-efficient, and rapid surveys, the approach struggles to outperform traditional morphological approaches in providing reliable quantitative estimates for surveyed species (e.g., abundance and biomass).</span></p> <p><span>We present an integrated methodology for improving biodiversity surveys that pairs eDNA metabarcoding with morphological data, following a series of taxonomic and geographic filters. We demonstrate its power by applying it to a new spatiotemporal dataset generated on an Iberian-wide distributed aquatic mesocosm infrastructure that spans a wide biogeographic gradient.</span></p> <p><span>By building upon the strengths that these two approaches offer, our framework improved taxonomic resolution for 30% of the taxa and enabled species' traits (e.g., body-size) and abundance to be assigned to 85% of the taxa in hybrid datasets.</span></p> <p><span>These results indicate that eDNA-based assessments can complement, but not always replace, conventional approaches. Integrating conventional and modern eDNA metabarcoding approaches, already available in the ecologist's toolbox, will greatly enhance biodiversity assessments.</span></p>
Monitoring vertebrate biodiversity of a protected coastal wetland using eDNA metabarcoding
<p>Monitoring plans using environmental DNA have the potential to offer a standardized and cost-efficient method to survey biodiversity in aquatic ecosystems. Among these ecosystems, coastal wetlands are key elements that serve as transition zones between marine and freshwater ecosystems and are today the target of many conservation and restoration efforts. In this sense, eDNA monitoring could provide a rapid and efficient tool for studying and generating baseline biodiversity information to guide coastal wetland management programs. Here we test an eDNA metabarcoding assay as a tool to characterize vertebrate biodiversity in one of the largest coastal wetlands of Chile, the Rio Cruces Wetland, a Ramsar designated site since 1981. We sampled surface water from 49 sites along the entire wetland. Our eDNA approach detected 91 genera of vertebrates including amphibians, fishes, mammals, and birds, as well as identified several cryptic, exotic, and endangered species. Our results also indicated that the spatial distribution of eDNA from different species is spatially structured despite the complex hydrodynamics inherent in this wetland due to the influence of daily tidal regimes. For amphibians and fishes, the number of taxa detected with eDNA was higher in the periphery of the wetland, and increased with proximity to the ocean, a pattern consistent with small-scale spatial sensitivity for some species and eDNA accumulation downstream for others. Birds and mammals showed somewhat more idiosyncratic distributions. Taken together our results add to the growing body of evidence showing eDNA can serve as a rapid cost-effective tool to characterize vertebrate communities in protected coastal wetlands, where visual surveys are difficult and animal collections are often prohibited. The use of multiple primer sets is also recommended as it facilitates the detection of ephemeral terrestrial organisms and resident aquatic organisms that make use of these wetlands.</p>
Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR
<p>eDNA metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density / biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a qPCR approach to infer the absolute abundance of fish species. We carried out a 2,850 km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a non-linear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65.106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results show a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.</p>
The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)
<p>Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others – based on their unique combinations of tags – during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e. tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding datasets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3' tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our datasets – despite our use of methods suggested to minimize this error. We developed a topologic model to estimate the noise based on the counts in our blanks, which suggested that 40-80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses. </p>
Data from: DNA metabarcoding improves the taxonomical resolution of visually determined diet composition of beaked redfish (Sebastes sp.)
<p class="pf0"><span>Beaked r</span><span>edfish, dominated by <em>Sebastes mentella</em>, have recently reached record abundance levels in the Gulf of St. Lawrence (GSL) and knowledge of their diet composition is essential to understand the trophic role that these groundfish play in the ecosystem. The objective of the present study was to compare the performance of the visual examination and DNA metabarcoding of stomach contents of the same individual redfish caught in the estuary and northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial cytochrome c oxidase subunit I (COI) marker, a total of 27 taxonomic sequence matches, 16 at the species level considered as primary prey, were obtained from 185 stomachs with DNA metabarcoding and compared to </span><span>the</span> <span>26 prey types, 16 at genus or species level, obtained with stomach content analysis (SCA). While both techniques pointed to a similar definition of diet composition, our results</span><span> also revealed that the SCA and DNA metabarcoding perform differently among prey categories, both in terms of detectability and taxonomical resolution, as well as in estimated contribution to diet. </span><span>The use of DNA metabarcoding along with SCA improves the taxonomical resolution of visually determined prey,</span><span> which supports the concept that both techniques provide useful complementary information that is best used together to gain a maximum level of information on the predator's diet.</span></p>
Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding
<p>Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.</p>
Combining sampling gear to optimally inventory species highlights the efficiency of eDNA metabarcoding
<p>Biodiversity surveys may require the use of multiple types of sampling gear to maximize the efficiency of species detections, yet few studies have investigated how to optimally distribute effort among gear. In this study, we conducted eDNA metabarcoding and capture-based sampling surveys (electrofishing, fyke netting, gillnetting, and seining) to sample fish species richness in a large northern temperate lake. We evaluated the success of the sampling methods individually and in combination to determine the allocation of effort and cost across sampling gear that provides the optimal approach for lake-wide species inventories. We found that eDNA metabarcoding detected more species than any other sampling method, including 11 species that were not detected with any capture-based approach. Optimal gear combination analyses revealed that detected species richness is maximized when most of the effort or budget is allocated to eDNA metabarcoding, with smaller allocations to seining and fyke netting. eDNA metabarcoding and capture sampling gear showed similar patterns of spatial heterogeneity in the fish community across habitat types, with pelagic samples forming a group that was distinct from nearshore samples. Our results indicate that eDNA metabarcoding is a rapid and cost-efficient tool for biodiversity monitoring and that assessing the complementarity of multiple sampling types can inform the development of optimal approaches for measuring fish species richness.</p>
eDNA metabarcoding reveals high soil fungal diversity and variation in community composition among Spanish cliffs
<p><span>Environments characterized by physical extremes harbor unique species diversity with particular adaptations. Cliffs are harsh environments for organisms but host a great diversity of specialized plants with many endemics, rare and even endangered species. It is, however, less known which fungal diversity the cliff habitats contain and whether it differs among different cliff locations. We thus sampled soil from three separate cliff locations in the North, Centre and South of Spain and used eDNA metabarcoding to determine fungal diversity. To better understand whether cliff specialist plants may promote particular fungal communities, we have sampled soil from crevices with cliff specialist plants and no apparent plants as controls. Major lifestyles found in cliff soils were saprotrophs, and major fungal orders were Dothideomycetes, Sordariomycetes, and Eurotiomycetes, while the amount of symbiotrophic fungi was relatively low. We found no significant differences in fungal amplicon sequence variant (ASV) richness among the three sampled locations, but the sites were significantly different in their community composition and their main indicator species. Overall, there were no significant differences in fungal ASV richness or composition between soils from cliff specialist plants and soils without plants, suggesting a unique fungal diversity in cliff soils independent from specialized plants. However, preliminary findings on soils of the specialist cliff plant Sedum dasyphyllum against control soils suggest that the presence of a specialist plant may be a relevant factor affecting the specificity of the fungal community in cliff soils. Our results indicate the existence of particular cliff fungal communities in each location, and that, despite limited and poorly developed soils and harsh conditions, cliffs can harbor a great diversity of fungal species, comparable to other ecosystems of Spain. This study points out that some fungi may be cliff-specific, shaping particular communities that mediate plant adaptations to cliffs' extreme conditions.</span></p>
Data from: Two for the price of one: eDNA metabarcoding reveals temporal and spatial variability of mussel and fish co-distributions in Michigan riverine systems
<p>Freshwater mussels (family Unionidae) are among the world's most endangered taxa, with almost 75% of North American taxa classified as a species of concern, threatened, or endangered. Despite the critical importance of comprehensive distributional data for the conservation of unionids and fishes, these data are often lacking because of the labor and resources associated with traditional survey methods. During their larval stage, unionid mussels use various fish species as obligate hosts, making native fish species vital to unionid persistence and an understanding of host distribution similarly important. Here, we utilized an eDNA metabarcoding approach to evaluate patterns of co-distribution of unionid mussels and fishes along ~362 km of the densely sampled Grand River network as well as the outlets of 19 tributaries along the eastern shore of Lake Michigan, USA. We detected a total of 21 mussel and 40 fish taxa, with distinctive composition of both mussel and fish assemblages across tributaries and differences in fish taxa between sampling periods. Notably, we detected more mussel taxa within the Grand River watershed than at the outlets of all 20 rivers combined. Within the Grand River network, two fish taxa (<em>Pylodictus</em> <em>olivaris</em> and <em>Cyprinella</em>) were found more frequently in areas of high mussel diversity, and three fish taxa more frequently in areas of low mussel diversity (<em>Umbra</em>, Leuciscidae, and <em>Etheostoma</em>). There was little difference between eDNA detections of mussels from samples collected in June versus August, but we detected significantly more fish taxa in August compared to June. Taken together, our findings demonstrate the value of eDNA metabarcoding for evaluating co-distribution of ecologically connected taxa. The use of eDNA as a tool for determining distributions of mussels and their obligate hosts may facilitate conservation efforts for these imperiled taxa.</p>
Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands
<p>Ice-free areas are increasing worldwide due to the dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. Soils have a complex vertical structure. However, we know little about how microbial and animal communities differ across soil depths and development stages during the colonization of deglaciated terrains, how these differences evolve through time, and whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to describe how community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, Oligochaeta) differ between surface (0-5 cm) and relatively deep (7.5-20 cm) soils at different stages of development across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution; the pattern was consistent across different groups and soil depths. For Eukaryota, and particularly Mycota, alpha-diversity was generally the highest in soils close to the surface. Time since glacier retreat was a more important driver of community composition compared to soil depth; for nearly all the taxa, differences in community composition between surface and deep soils decreased with time since glacier retreat, suggesting that the development of soil and/or of vegetation tends to homogenize the first 20 cm of soil through time. Within both Bacteria and Mycota, several molecular operational taxonomic units were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes.</p>
Arctic nekton uncovered by eDNA metabarcoding: diversity, potential range expansions and benthopelagic coupling
<p><span>The Arctic Ocean is home to a unique fauna that is disproportionately affected by global warming but that remains under-studied</span><span>. Due to their high mobility and responsiveness to global warming, cephalopods and fishes are good indicators of the reshuffling of Arctic communities. Here, we established a nekton biodiversity baseline for the Fram Strait, the only deep connection between the North Atlantic and Arctic Ocean. Using universal primers for fishes (12S) and cephalopods (18S), we amplified environmental DNA (eDNA) from seawater (50–2700 m) and deep-sea sediment samples collected at the LTER HAUSGARTEN observatory. We detected twelve cephalopod and 31 fish taxa in the seawater and seven cephalopod and 28 fish taxa in the sediment,</span><span> including the elusive Greenland shark (</span><span><em>Somniosus</em> <em>microcephalus</em></span><span>)</span><span>. Our data suggest three fish (<em>Mallotus</em> <em>villosus</em>, <em>Thunnus</em> sp. and <em>Micromesistius</em> <em>poutassou</em>) and one squid (<em>Histioteuthis</em> sp.) range expansions. </span><span>The detection of eDNA of pelagic origin in the sediment also suggests that <em>M. villosus</em>, <em>Arctozenus</em> <em>risso</em> and <em>M. poutassou</em> as well as gonatid squids are potential contributors to the carbon flux. </span><span>Continuous nekton monitoring is needed to understand the ecosystem impacts of rapid warming in the Arctic and eDNA proves to be a suitable tool for this endeavor.</span></p>
Diet of a threatened rattlesnake (eastern massasauga) revealed by DNA metabarcoding
<p>Characterizing the diet of imperiled species using minimally invasive methods is crucial to understanding their ecology and conservation requirements. Here, we apply a DNA metabarcoding approach to study the diet of the eastern massasauga rattlesnake (<em>Sistrurus</em> <em>catenatus</em>), a Federally Threatened snake found throughout the Great Lakes region. Eighty-three fecal samples collected across 10 different massasauga populations located in Michigan, USA, were sequenced, with 70 samples containing prey DNA. We used universal metazoan primers and developed a host-specific oligonucleotide blocker to characterize their diet. We identified at least 12 different prey species, with eastern massasaugas exhibiting opportunistic feeding and a strong preference towards small mammals. Meadow voles (<em>Microtus</em> <em>pennsylvanicus</em>) were the most common prey item (70% of diet) followed by the northern short-tailed shrew (<em>Blarina</em> <em>brevicauda</em>) and masked shrew (<em>Sorex</em> <em>cinereus</em>; 15.7% of diet each), along with occasional bird and snake prey. Adult individuals exhibited a more generalized diet, consuming a larger number of prey taxa on average. Younger snakes consumed a smaller variety of prey items and tended to consume smaller-sized mammals such as masked shrews (<em>Sorex</em> <em>cinereus</em>) and northern short-tailed shrews (<em>Blarina</em> <em>brevicauda</em>). We conclude that small mammals are a crucial part of eastern massasauga rattlesnake diet and recommend this be taken into consideration when conservation strategies are developed. The methods developed in this study can be applied to other reptile species, providing an accurate, minimally invasive, and thorough diet assessment for at-risk reptile species.</p>
Data from: Environmental DNA metabarcoding revealed the impacts of anthropogenic activities on phytoplankton diversity in Dianchi Lake and its three inflow rivers
<p>Phytoplankton diversity is closely related to environmental variables and has been widely used in ecological health assessment of rivers and lakes. Combining the advantages of DNA-based identification and high-throughput sequencing technology, environmental DNA (eDNA) metabarcoding permits a new measurement for biodiversity monitoring in aquatic ecosystems. However, it had rarely been used to explore the variability and similarity of phytoplankton diversity between a lake and its inflow rivers and the effects of environmental variables on phytoplankton. This study utilized eDNA metabarcoding to investigate the spatial distribution of phytoplankton and the impacts of environmental variables on the phytoplankton diversity in Dianchi Lake (one of the most polluted urban lakes in China) and its main inflow rivers (Panlong River, Baoxiang River and Chai River). The OTU table is the original table about phytoplankton taxa. A total of 243 distinct phytoplankton taxa were detected, covering 9 phyla, 30 classes, 84 orders and 132 families, and the taxonomic richness of rivers was higher than that of Dianchi Lake.</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.