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14 results for “large-scale monitoring”
Data for: Zebra finch song ecology: monitoring of breeding, observational transects, focal and year-round acoustic recordings, and a large-scale simultaneous playback experiment
<p class="MsoNormal">Male songbirds sing to establish territories and to attract mates. However, increasing reports of singing in non-reproductive contexts and by females show that song use is more diverse than previously considered. Therefore, alternative functions of song, such as social cohesion and synchronisation of breeding, by and large were overlooked even in such well-studied species as the zebra finch (<em>Taeniopygia guttata</em>). In these social songbirds only the males sing and pairs breed synchronously in loose colonies following aseasonal rain events in their arid habitat. As males are not territorial, and pairs form long-term monogamous bonds early in life, conventional theory predicts that zebra finches should not sing much at all; yet they do and their song is the focus of hundreds of lab-based studies. We hypothesise that zebra finch song functions to maintain social cohesion and to synchronise breeding. Here we test this idea using data from five years of field studies, including observational transects, focal and year-round audio recordings, and a large-scale playback experiment. We show that zebra finches frequently sing while in groups, that breeding status influences song output at the nest and at aggregations, that they sing year-round, and that they predominantly sing when with their partner, suggesting that song remains important after pair formation. Our playback reveals that song actively features in social aggregations as it attracts conspecifics. Together, these results demonstrate that birdsong has important functions beyond territoriality and mate choice, illustrating its importance in coordination and cohesion of social units within larger societies.</p>
Data for: Large-scale long-term passive-acoustic monitoring reveals spatiotemporal activity patterns of boreal bats
<p class="MsoNormal"><span>The distribution ranges and spatio-temporal patterns in the occurrence and activity of boreal bats are yet largely unknown due to their cryptic lifestyle and lack of suitable and efficient study methods. We approached the issue by establishing a permanent passive-acoustic sampling setup spanning the area of Finland to gain an understanding on how latitude affects bat species composition and activity patterns in northern Europe. The recorded bat calls were semi-automatically identified for three target taxa; <em>Myotis</em> spp., <em>Eptesicus nilssonii</em> or <em>Pipistrellus nathusii</em> and the seasonal activity patterns were modeled for each taxa across the seven sampling years (2015–2021). We found an increase in activity since 2015 for <em>E. nilssonii</em> and <em>Myotis </em>spp. For <em>E. nilssonii</em> and <em>Myotis</em> spp. we found significant latitude -dependent seasonal activity patterns, where seasonal variation in patterns appeared stronger in the north. Over the years, activity of <em>P. nathusii</em> increased during activity peak in June and late season but decreased in mid season. We found the passive-acoustic monitoring </span><span>network to be an effective and cost-efficient method for gathering b</span><span>at activity data to analyze spatio-temporal patterns. Long-term data on the composition and dynamics of bat communities facilitates better estimates of abundances and population trend directions for conservation purposes and predicting the effects of cli</span><span>mate change.</span></p>
Data for: Large-scale long-term passive-acoustic monitoring reveals spatiotemporal activity patterns of boreal bats
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Data for: Zebra finch song ecology: monitoring of breeding, observational transects, focal and year-round acoustic recordings, and a large-scale simultaneous playback experiment
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Monitoring of large-scale archaeological excavations using photogrammetric techniques - Nea Paphos case study
<p>Photogrammetric data (images) for five contexts from a single archaeological trench from the Paphos Agora Project (Excavations conducted in Nea Paphos Archaeological Site by Jagiellonian Unversity in Krakow - under the direction of Prof. Ewdoksia Papuci-Władyka). Images for photogrammetric modelling of all contexts were taken in 2015 with the NIKON D7100 camera (24 Mpx resolution), with the number of images per model varying from 25 to 41. For photogrammetric processing, the Agisoft PhotoScan and Reality Capture were used. </p><p>The data (images) were uploaded together with project files from Agisoft Metashape and RealityCapture, exported results (3D models, orthoimages and DEMs) and reference data - point clouds from terrestrial laser scanner measurements are available as supplementary material for the article in Journal of Archaeological Science: Reports. Also, data for one layer below and above, which do not include reference point clouds, have been added.</p>
Data from: Large-scale bioacoustic monitoring to elucidate the distribution of a non-native katydid
<p>For animals that produce species-specific audible sounds, environmental recordings combined with automated acoustic monitoring software (passive acoustic monitoring, PAM) may be an effective monitoring tool because it allows audio data from many, widely distributed autonomous recording units (ARUs) to be processed in a relatively short period of time. Males of many insect species produce loud, species-specific mating songs, yet acoustic insects have received less attention from PAM relative to vertebrates.</p> <p>We evaluated the use of PAM to monitor, <em>Roeseliana roeselii</em> (Orthoptera, Tettigoniidae), an acoustic insect that has expanded its range to Alberta, Canada far outside its naturalized North American range. We analyzed environmental recordings from ARUs: 1) at two control sites known to be occupied by <em>R. roeselii</em>, and 2) across Alberta established by the Alberta Biodiversity Monitoring Institute (ABMI) to search for new populations.</p> <p>PAM successfully detected <em>R. roeselii</em> at the two control sites, but not at any of the 74 ABMI sites that we analyzed. Despite the failure to detect new locations of <em>R. roeselii</em>, our analysis of ABMI environmental recordings detected several other species of acoustic insects, including <em>Orchelimum gladiator</em>, <em>Gryllus</em> sp. and <em>Allonemobius</em> spp.</p> <p>Our results add to the growing body of work showing the feasibility of using PAM for acoustic insects. We make suggestions for how to maximize the effectiveness of this monitoring tool for the conservation and management of singing insects in North America.</p>
Script and data from: The best of two worlds: toward large-scale monitoring of biodiversity combining metabarcoding and optimised parataxonomic validation.
<h2>Description</h2> <div> <p>Zenodo linked to : Penel, B., Meynard, C.N., Benoit, L., Bourdonné, A., Clamens, A., Soldati, L., Migeon, A., Chapuis, M.-P., Piry, S., Kergoat, G. and Haran, J. (2025), The best of two worlds: toward large-scale monitoring of biodiversity combining COI metabarcoding and optimized parataxonomic validation. Ecography, 2025: e07699. <a href="https://doi.org/10.1111/ecog.07699">https://doi.org/10.1111/ecog.07699</a></p> <div> <div> <div> <div> <p><strong>Publication abstract </strong></p> </div> </div> </div> <p>In a context of unprecedented insect decline, it is critical to have reliable monitoring tools to measure species diversity and their dynamic at large-scales. High-throughput DNA-based identification methods, and particularly metabarcoding, were proposed as an effective way to reach this aim. However, these identification methods are subject to multiple technical limitations, resulting in unavoidable false-positive and false-negative species detection. Moreover, metabarcoding does not allow a reliable estimation of species abundance in a given sample, which is key to document and detect population declines or range shifts at large scales. To overcome these obstacles, we propose here a Human-Assisted Molecular Identification (HAMI) approach, a framework based on a combination of metabarcoding and image-based parataxonomic validation of outputs and recording of abundance. We assessed the advantages of using HAMI over the exclusive use of a metabarcoding approach by examining 492 mixed beetle samples from a biodiversity monitoring initiative conducted throughout France. On average, 23% of the species are missed when relying exclusively on metabarcoding, this percent being consistently higher in species-rich samples. Importantly, on average, 20% of the species identified by molecular-only approaches correspond to false positives linked to cross-sample contaminations or mis-identified barcode sequences in databases. The combination of molecular methodologies and parataxonomic validation in HAMI significantly reduces the intrinsic biases of metabarcoding and recovers reliable abundance data. This approach also enables users to engage in a virtuous circle of database improvement through the identification of specimens associated with missing or incorrectly assigned barcodes. As such, HAMI fills an important gap in the toolbox available for fast and reliable biodiversity monitoring at large scales.</p> <div> <h4><strong>File description: </strong></h4> <h4>MiSeq raw sequences of the COI barcode from 492 Coleoptera field samples :</h4> <div>The Raw_sequencage_data ZIP directory contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Coleoptera field samples in duplicate using the MiSeq platform GenSeq (ISEM - University of Montpellier)</div> <div> </div> <div>The HAMI_data_script_results_R zip directory contains Rmarkdown script files (.Rmd and .html) and associated data used to analyse the systemic errors of the metabarcoding approach (N= 492 Coleoptera field samples).</div> <div> </div> <div>The HAMI_pipeline zip directory contains all the codes associated with the HAMI pipeline, as well as a ReadMe file and a test data set.</div> <div> </div> <div>The Residual_chimera.zip directory contains lists of MOTUs associated to residual chimeric sequences that were not filtered using FROGS pipeline but secondarily detected with the <em>de novo</em> approach implemented in HAMI pipeline with ‘isBimeraDenovo’ R function from DADA2 v1.28.0. It contains two distinct files according to the two sequencing runs.</div> <div> </div> <div>The NUMTS_filtered.zip directory contains lists of MOTUs that were excluded of the final dataset according to the NUMTS filtering. File xxx_pseudogene_f1_deteled.csv corresponds to MOTUs that were excluded according to the first filtrering step based on DNA sequencing. File xxx_pseudogene_f2_deteled.csv corresponds to merged MOTUs that were excluded according to the second filter based on occurrence and percentage of identity. This folder contains files for the two sequencing runs.</div> </div> </div> </div>
Data from "Quantification of major particulate matter species from a single filter type using infrared spectroscopy – Application to a large-scale monitoring network"
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Data from: Large-scale bioacoustic monitoring to elucidate the distribution of a non-native katydid
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Using mobile device built-in microphones to monitor bats: A new opportunity for large-scale participatory science initiatives
<p>Here we present audio data collected in the study titled "Using mobile device built-in microphones to monitor bats: a new opportunity for large-scale participatory science initiatives", now accepted for publication in Biodiversity and Conservation (DOI: 10.1007/s10531-024-02818-9).</p> <p>Citizen science has become a crucial tool in biodiversity monitoring, often facilitated by the diffusion of mobile devices, such as smartphones and tablets. High costs of professional equipment often limit large-scale monitoring, particularly in bat monitoring programmes based on acoustic surveys. Here we present the potential of using mobile devices for bat monitoring, allowing for large-scale, volunteer-based monitoring programmes. We initially compared mobile devices' performance with a professional bat detector for recording low-frequency bat calls. We then conducted a citizen science pilot study to test the method's feasibility in a real-world setting, recording echolocation and social calls of nine European bat species. We found high similarity in spectrogram quality between calls recorded by mobile devices and professional bat detectors. However, differences in sound quality and effectiveness among mobile device brands and models were found. The citizen science pilot study tested 35 mobile device models, all of which effectively recorded bats. This study suggests that mobile devices could be an accessible, no-cost tool for large-scale bat monitoring. Incorporating mobile devices into existing monitoring networks or creating new dedicated programmes could not only enhance data collection, but also boost public knowledge and awareness about bats, ultimately promoting informed decision-making and better conservation strategies.</p> <p>To facilitate a comprehensive evaluation of the acoustic data quality achievable through the described method, we are providing access to all bat recordings collected via mobile devices during the study. These have been compiled into the compressed file named "mobile_device_recs.zip".</p> <p>For those seeking a quicker review, we recommend downloading the "Appendix_S6_recs.zip" file, which contains selected examples of echolocation or social calls from the nine bat species recorded during our research. Spectrograms of these example recordings are displayed in Appendix S6 of the published study.</p>
Data from: Potential for coupling the monitoring of bush-crickets with established large-scale acoustic monitoring of bats
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Using mobile device built-in microphones to monitor bats: A new opportunity for large-scale participatory science initiatives
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Data from: Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat
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Data from: Cost-effective large-scale occupancy–abundance monitoring of invasive brushtail possums (Trichosurus vulpecula) on New Zealand’s Public Conservation Land
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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
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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.