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72 results for “Biodiversity monitoring”
Analysis, camera, and image files for: ecoEye, embedded vision camera for biodiversity monitoring
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Data from: Using terrestrial haematophagous leeches to enhance tropical biodiversity monitoring programmes in Bangladesh
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Data from: The importance of standardization for biodiversity comparisons: a case study using Autonomous Reef Monitoring Structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French Polynesia
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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
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Data and code for: Leveraging long-term data to improve biodiversity monitoring with species distribution models
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King's College Cambridge wildflower meadow monitoring data: biodiversity, climate change and society
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Unionid Monitoring and Biodiversity Observation (UMBO): Monitoring data for freshwater mussels (Bivalvia: Unionidae) in seven southwestern Ontario, Canada watersheds (1999-2024)
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Monitoring vertebrate biodiversity of a protected coastal wetland using eDNA metabarcoding
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Data from: Addressing the challenges of managing and monitoring biodiversity in High Conservation Value areas and High Carbon Stock forests within oil palm landscapes
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Effects of soil preservation for biodiversity monitoring using environmental DNA
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Data from: Monitoring and predictive mapping of floristic biodiversity along a climatic gradient in ENSO's terrestrial core region, NW Peru
<p>This is the data from the publication "Monitoring and predictive mapping of floristic biodiversity along a climatic gradient in ENSO's terrestrial core region, NW Peru" (<a href="http://onlinelibrary.wiley.com/doi/10.1111/ecog.05091/abstract">http://onlinelibrary.wiley.com/doi/10.1111/ecog.05091/abstract</a>).</p> <p>The code (including figures, appendices and the manuscript) can be found directly in the <a href="https://github.com/jannes-m/2020-enso-tdf">GitHub repository</a>.</p> <p><strong>Data sources and description</strong></p> <p>Column descriptions for all tables can be found in <em>variable_description.ods. </em>Following tables are stored in <em>tables.gpkg</em>:</p> <ol> <li>plot_species_matrix_2011: Plot species matrix recorded in 2011</li> <li>plot_species_matrix_2012: Plot species matrix recorded in 2012.</li> <li>plot_species_matrix_2016: Plot species matrix recorded in 2016.</li> <li>plot_species_matrix_2017: Plot species matrix recorded in 2017.</li> <li>lifeform: Lifeforms of the recorded species</li> <li>plot_variables: Variables specific to the plots such as height of the first tree layer, cover of dead wood, etc.</li> <li>soil: Edaphic variables.</li> <li>topography: Topographic variables.</li> <li>streets: Streets and dirt tracks in the study area.</li> <li>towns: Polygons displaying the outline of the cities Paita, Piura and Chulucanas.</li> <li>rivers: Lines displaying the major rivers in the study area.</li> <li>study_area: Outline of the study area.</li> <li>peru: Outline of Peru.</li> <li>neighbors: Outline of Peru's neighbors (Bolivia, Brazil, Chile, Colombia, Ecuador).</li> <li>coast: Coastal strip of and close to the study area.</li> <li>precipitation: Precipitation measured at the three climatic stations (Paita, Piura, Chulucanas).</li> <li>experiment_count: species counted per visit (irrigation-fertilization experiment).</li> <li>experiment_irrigation: Rain input by time during the irrigation-fertilization experiment.</li> <li>experiment_cover: Cover of each plant species per visit and per experimental plot (irrigation-fertilization experiment).</li> </ol>
Up in the air: threats to Afromontane biodiversity from climate change and habitat loss revealed by genetic monitoring of the Ethiopian Highlands bat
<p>Whilst climate change is recognised as a major future threat to biodiversity, most species are currently threatened by extensive human-induced habitat loss, fragmentation and degradation. Tropical high altitude alpine and montane forest ecosystems and their biodiversity are particularly sensitive to temperature increases under climate change, but they are also subject to accelerated pressures from land conversion and degradation due to a growing human population. We studied the combined effects of anthropogenic land-use change, past and future climate changes and mountain range isolation on the endemic Ethiopian Highlands long-eared bat, <i>Plecotus balensis</i>, an understudied bat that is restricted to the remnant natural high altitude Afroalpine and Afromontane habitats. We integrated ecological niche modelling, landscape genetics and model-based inference to assess the genetic, geographic and demographic impacts of past and recent environmental changes. We show that mountain range isolation and historic climates shaped population structure and patterns of genetic variation, but recent anthropogenic land-use change and habitat degradation are associated with a severe population decline and loss of genetic diversity. Models predict that the suitable niche of this bat has been progressively shrinking since the last glaciation period. This study highlights threats to Afroalpine and Afromontane biodiversity, squeezed to higher altitudes under climate change while losing genetic diversity and suffering population declines due to anthropogenic land-use change. We conclude that the conservation of tropical montane biodiversity requires a holistic approach, using genetic, ecological and geographic information to understand the effects of environmental changes across temporal scales and simultaneously addressing the impacts of multiple threats.</p>
Data from: The use and utility of surrogates in biodiversity monitoring programmes
Monitoring programmes are intended to inform effective biodiversity conservation and management (Legge et al. 2018). Well‐designed programmes can establish baseline conditions, determine trends in threatened species populations, quantify the effects of management, and provide warning of ecosystem changes (Magurran et al. 2010). For these reasons, biodiversity monitoring underpins the activities of land management agencies worldwide. However, it is not always possible to directly monitor key variables at ideal spatio‐temporal resolutions, due to resourcing or logistic constraints. For example, direct monitoring of koalas (Phascolarctos cinereus) can be cost‐ and time‐intensive as koalas are cryptic, occur at low densities, and are difficult to reliably observe in dense forest canopies (McAlpine et al. 2006).
Data from: Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation
Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-year) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We have used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporate repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites shows evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) have reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 years of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River shows no trends in species persistence, colonization or occupancy. None of the tested covariates show strong effects on persistence or colonization rates in either river. Previous studies and observations identify contaminants, nutrient loading, or changes in benthic habitat as possible causes for fish species declines in the Conasauga River. Our analysis provides baseline information that could be used to assess effectiveness of future management actions in the Conasauga or Etowah rivers, and illustrates the use of dynamic occupancy models to evaluate evidence of faunal decline from time-series data.
Data from: AudioMoth: evaluation of a smart open acoustic device for monitoring biodiversity and the environment
1. The cost, usability and power efficiency of available wildlife monitoring equipment currently inhibits full ground-level coverage of many natural systems. Developments over the last decade in technology, open science, and the sharing economy promise to bring global access to more versatile and more affordable monitoring tools, to improve coverage for conservation researchers and managers. 2. Here we describe the development and proof-of-concept of a low-cost, small-sized and low-energy acoustic detector: 'AudioMoth'. The device is open-source and programmable, with diverse applications for recording animal calls or human activity at sample rates of up to 384kHz. We briefly outline two ongoing real-world case studies of large-scale, long-term monitoring for biodiversity and exploitation of natural resources. These studies demonstrate the potential for AudioMoth to enable a substantial shift away from passive continuous recording by individual devices, towards smart detection by networks of devices flooding large and inaccessible ecosystems. 3. The case studies demonstrate one of the smart capabilities of AudioMoth, to trigger event logging on the basis of classification algorithms that identify specific acoustic events. An algorithm to trigger recordings of the New Forest cicada (Cicadetta montana) demonstrates the potential for AudioMoth to vastly improve the spatial and temporal coverage of surveys for the presence of cryptic animals. An algorithm for logging gunshot events has potential to identify a shotgun blast in tropical rainforest at distances of up to 500 m, extending to 1km with continuous recording. 4. AudioMoth is more energy efficient than currently available passive acoustic monitoring (PAM) devices, giving it considerably greater portability and longevity in the field with smaller batteries. At a build cost of ~US$43 per unit, AudioMoth has potential for varied applications in large-scale, long-term acoustic surveys. With continuing developments in smart, energy-efficient algorithms and diminishing component costs, we are approaching the milestone of local communities being able to afford to remotely monitor their own natural resources.
Data from: Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.
Data from: Scat DNA provides important data for effective monitoring of mammal and bird biodiversity
<p>Fauna has long been neglected in the monitoring of ecological restoration, despite the key role they play in ecosystem function. Vertebrate surveys can be time consuming and costly, often requiring multiple methodologies and taxonomic expertise, making comprehensive monitoring cost prohibitive. Here we evaluate a new method of assessing mammal and bird diversity through the genetic identification of scat collections. Using DNA metabarcoding of scat collections from three bioregions we generated bird and mammalian assemblage data and distinguished between sites with different restoration histories. However, scat detectability was affected by environmental conditions (e.g. rainfall and soil), suggesting that our approach is most applicable at certain times of year or in arid (or semi-arid) environments with rocky soils, where conditions are favourable for scat preservation. Taken together these data provide a pathway to: plan, monitor and establish best-practice when restoring landscapes and add to the growing body of literature on the value of DNA metabarcoding in biomonitoring applications.</p>
Supplementary material 1 from: Zapponi L, Mazza G, Farina A, Fedrigoli L, Mazzocchi F, Roversi PF, Sabbatini Peverieri G, Mason F (2017) The role of monumental trees for the preservation of saproxylic biodiversity: re-thinking their management in cultural landscapes. In: Campanaro A, Hardersen S, Sabbatini Peverieri G, Carpaneto GM (Eds) Monitoring of saproxylic beetles and other insects protected in the European Union. Nature Conservation 19: 231-243. https://doi.org/10.3897/natureconservation.19.12464
List of recorded species : Explanation note: The supplementary material contains the list of species recorded during the 1982 and 2017 inventories, showing for each species: number of individuals, average circunference and average height.
Data from: How much would it cost to monitor farmland biodiversity in Europe?
To evaluate progress on political biodiversity objectives, biodiversity monitoring provides information on whether intended results are being achieved. Despite scientific proof that monitoring and evaluation increase the (cost) efficiency of policy measures, cost estimates for monitoring schemes are seldom available, hampering their inclusion in policy programme budgets. Empirical data collected from 12 case studies across Europe were used in a power analysis to estimate the number of farms that would need to be sampled per major farm type to detect changes in species richness over time for four taxa (vascular plants, earthworms, spiders and bees). A sampling design was developed to allocate spatially, across Europe, the farms that should be sampled. Cost estimates are provided for nine monitoring scenarios with differing robustness for detecting temporal changes in species numbers. These cost estimates are compared with the Common Agricultural Policy (CAP) budget (2014–2020) to determine the budget allocation required for the proposed farmland biodiversity monitoring. Results show that the bee indicator requires the highest number of farms to be sampled and the vascular plant indicator the lowest. The costs for the nine farmland biodiversity monitoring scenarios corresponded to 0·01%–0·74% of the total CAP budget and to 0·04%–2·48% of the CAP budget specifically allocated to environmental targets. Synthesis and applications. The results of the cost scenarios demonstrate that, based on the taxa and methods used in this study, a Europe-wide farmland biodiversity monitoring scheme would require a modest share of the Common Agricultural Policy budget. The monitoring scenarios are flexible and can be adapted or complemented with alternate data collection options (e.g. at national scale or voluntary efforts), data mobilization, data integration or modelling efforts.
Data from: Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present into the environment. In this study, we tested if an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro, and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) versus 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.
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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.