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10 results for “natural tagging”
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>
The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)
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Data from: Long-term sound and movement recording tags to study natural behaviour and reaction to ship noise of seals
The impact of anthropogenic noise on marine fauna is of increasing conservation concern with vessel noise being one of the major contributors. Animals that rely on shallow coastal habitats may be especially vulnerable to this form of pollution. Very limited information is available on how much noise from ship traffic individual animals experience, and how they may react to it due to a lack of suitable methods. To address this, we developed long‐duration audio and 3D‐movement tags (DTAGs) and deployed them on three harbor seals and two gray seals in the North Sea during 2015–2016. These tags recorded sound, accelerometry, magnetometry, and pressure continuously for up to 21 days. GPS positions were also sampled for one seal continuously throughout the recording period. A separate tag, combining a camera and an accelerometer logger, was deployed on two harbor seals to visualize specific behaviors that helped interpret accelerometer signals in the DTAG data. Combining data from depth, accelerometer, and audio sensors, we found that animals spent 6.6%–42.3% of the time hauled out (either on land or partly submerged), and 5.3%–12.4% of their at‐sea time resting at the sea bottom, while the remaining time was used for traveling, resting at surface, and foraging. Animals were exposed to audible vessel noise 2.2%–20.5% of their time when in water, and we demonstrate that interruption of functional behaviors (e.g., resting) in some cases coincides with high‐level vessel noise. Two‐thirds of the ship noise events were traceable by the AIS vessel tracking system, while one‐third comprised vessels without AIS. This preliminary study demonstrates how concomitant long‐term continuous broadband on‐animal sound and movement recordings may be an important tool in future quantification of disturbance effects of anthropogenic activities at sea and assessment of long‐term population impacts on pinnipeds.
Supplementary material 3 from: Osawa T, Ueno Y, Nishida T, Nishihiro J (2020) Do both habitat and species diversity provide cultural ecosystem services? A trial using geo-tagged photos. Nature Conservation 38: 61-77. https://doi.org/10.3897/natureconservation.38.36166
: Explanation note: Table S1. All plants and main habitats in the study area. Table S2. All birds and main habitats in the study area. Table S3. All butterflies and main habitats in the study area. Table S4. All dragonflies and main habitats in the study area. Table S5. List of threatened plants in the study area. Table S6. Picture objects list which took in area with threatened species from spring to autumn.
Leafcutter ants of the genus Atta in the Insects Collection at the Field Museum of Natural History. The field data on the attached tags are transcribed for entry into databases such as AntWeb and the Global Biodiversity Information Facility. Photograph: Matthew Nelsen. in The Evolution of Natural History Collections
Leafcutter ants of the genus Atta in the Insects Collection at the Field Museum of Natural History. The field data on the attached tags are transcribed for entry into databases such as AntWeb and the Global Biodiversity Information Facility. Photograph: Matthew Nelsen.
Data from: Long-term sound and movement recording tags to study natural behaviour and reaction to ship noise of seals
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Supplementary material 1 from: Osawa T, Ueno Y, Nishida T, Nishihiro J (2020) Do both habitat and species diversity provide cultural ecosystem services? A trial using geo-tagged photos. Nature Conservation 38: 61-77. https://doi.org/10.3897/natureconservation.38.36166
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Supplementary material 2 from: Osawa T, Ueno Y, Nishida T, Nishihiro J (2020) Do both habitat and species diversity provide cultural ecosystem services? A trial using geo-tagged photos. Nature Conservation 38: 61-77. https://doi.org/10.3897/natureconservation.38.36166
: Explanation note: All objects were not the threaten species itself.
Data from: Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti
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In vivo G-CSF Treatment Activates GR-SOCS1 Axis Suppressing IFN-γ Secretion by Natural Killer Cells [CUT&TAG]
GEO Series GSE205824. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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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.