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1,076 results for “Metabarcoding”
Data from: Floral resource partitioning by individuals within generalised hoverfly pollination networks revealed by DNA metabarcoding
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Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding
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Data from: Assessing strengths and weaknesses of DNA metabarcoding based macroinvertebrate identification for routine stream monitoring
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Revealing cryptic interactions between large mammalian herbivores and plant-dwelling arthropods via DNA metabarcoding
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Faecal metabarcoding reveals pervasive long-distance impacts of garden bird feeding
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Data from: The choice of universal primers and the characteristics of the species mixture determines when DNA metabarcoding can be quantitative.
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Data from: Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcoding
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Data from: Seasonal progression and differences in major floral resource use by bees and hoverflies in a diverse horticultural and agricultural landscape revealed by DNA metabarcoding
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DNA metabarcoding reveals broad woodpecker diets in fire-maintained forests
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The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding
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Multiple mitochondrial haplotypes within individual specimens affect biodiversity estimation by DNA metabarcoding
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Multi-species models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams
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Assessing environmental DNA metabarcoding and camera trap surveys as complementary tools for biomonitoring of remote desert water bodies
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DNA-metabarcoding reveals the importance of gelatinous zooplankton in the diet of Pandalus borealis, a keystone species in the Arctic
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Capabilities and limitations of using DNA metabarcoding to study plant-pollinator interactions
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MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes) supplemental materials
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eDNA metabarcoding as a biomonitoring tool for marine protected areas
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A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish
<p>Accurate assessments of fish species diversity and community composition are essential for understanding fish ecology and conservation management. Environmental DNA (eDNA) metabarcoding has become an integrated method for monitoring fish species. The accuracy and efficacy of eDNA metabarcoding relies heavily on the choice of primers used for PCR amplification. A wide selection of metabarcoding primers for fish has been developed; however, there exists no comprehensive and comparative evaluation of their amplification or taxonomic classification of a rich diversity of fish species, which hinders informed decisions regarding their suitability for different study systems.</p> <p>Here, we reviewed the literature and compiled a list of 22 primer sets for eDNA-based metabarcoding analysis of teleost fish, the performance of which was compared using <i>in silico</i> PCR, followed by <i>in vitro</i> metabarcoding analysis using eDNA from waterbodies in Beijing, which harbour a high number of freshwater fish species.</p> <p>We found that the primers showed considerable differences in the amplified taxonomic ranges and proportions, fish taxa richness, species discrimination power, and fish community compositions, both <i>in silico</i> and <i>in vitro</i>. The number of fish taxa detected from eDNA by the primer sets varied from 0 to 66. Primers targeting the 12S rRNA gene generally detected greater fish diversity than those targeting the 16S rRNA or COI genes, while primers targeting the cytochrome b gene amplified the fewest fish taxa <i>in vitro</i>. 4. Regarding target genes, 12S primers generally outperformed other primers in terms of amplified fish diversity. The results of <i>in silico</i> PCR and <i>in vitro</i> tests were not always in agreement, suggesting that primer choice for biodiversity surveys should not be based solely on <i>in silico</i> evaluation. The use of different primers can qualitatively and quantitatively affect the detected biodiversity and these effects should be considered in experimental design and data interpretation. These results will assist with primer selection for eDNA-based fish surveys, and consequently support conservation of freshwater biodiversity.</p>
Data from: DNA metabarcoding reveals diet overlap between the endangered Walia ibex and domestic goats - implications for conservation
Human population expansion and associated degradation of the habitat of many wildlife species cause loss of biodiversity and species extinctions. The small Simen Mountains National Park in Ethiopia is one of the last strongholds for the preservation of a number of afro-alpine mammals, plants and birds, and it is home to the rare endemic Walia ibex, Capra walie. The narrow distribution range of this species as well as potential competition for resources with livestock, especially with domestic goat, Capra hircus, may compromise its future survival. Based on a curated afro-alpine taxonomic reference library constructed for plant taxon identification, we investigated the diet of the Walia ibex and addressed the dietary overlap with domestic goat using DNA metabarcoding of faecal samples. Faeces of both species were collected from different localities in the National Park. We show that both species are browsers, with forbs, shrubs and trees comprising the largest proportion of their diet, supplemented by grasses. There was a considerable overlap in dietary preferences. Several of the preferred diet items of the Walia ibex (Alchemilla sp., Hypericum revolutum, Erica arborea and Rumex sp.) were also among the most preferred diet items of the domestic goat. These results indicate that there is potential for competition between the two species, especially during the dry season, when resources are limited. Our findings, in combination with the expected increase in domestic herbivores, suggest that management plans should consider the potential threat posed by domestic goats to ensure future survival of the endangered Walia ibex.
Data from: A broadly applicable COI primer pair and an efficient single‐tube amplicon library preparation protocol for metabarcoding
The nucleotide variation in the cytochrome c oxidase subunit I (COI) gene makes it ideal for assigning sequences to species. However, this variability also makes it difficult to design truly universal primers. Here, we present the forward primer "Sauron-S878", specifically designed to facilitate library preparation for metabarcoding. This primer is modified to improve the coverage of terrestrial species compared to the primer mCOIintF, optimized for aquatic systems, which raised the in-silico coverage from 74.4% to 98.3% of available NCBI sequences (perfect match in 3'-region, up to 3 mismatches in remaining primer). When paired with the reverse primer "jgHCO2198" (fragment length ~313 bp) these primers amplified 98.4% of 255 tested DNA extracts from various taxa, which is better than many other common COI barcoding primers. Furthermore, a single tube protocol was developed, wherein these primers amplify the target gene, and attach MIDs and Illumina sequencing adapters in one reaction. This eliminates the need for re-amplification or enzymatic ligation during library preparation while keeping the flexibility to modularly combine primers and MIDs. Using the single tube approach, three replicates of three mock samples were sequenced on a MiSeq platform with no adverse effects compared to commercial Nextera indexing kits. From this run 75% of all included taxa could be recovered, with no considerable bias among taxonomic groups. Despite the fact that 98.4% of the extracts were confirmed to amplify in-vitro, this number was lower than expected. A reason for this discrepancy was a clear link between the relative concentration of a specific DNA type in the template and the number of returned reads for this DNA. We would argue that such a bias may be especially problematic in metabarcoding where samples usually contain trace DNA in unknown amounts. However, how this affects the completeness of metabarcoding results has yet been poorly investigated.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.