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Dataset results
213 results for “species monitoring”
Supplementary Files: "Improved baited remote underwater video (BRUV) for 24h re-al-time monitoring of surface and deep-sea marine species"
<p>In the supplementary material you will find: Figure S1: Photographs of the different parts of the innovative BRUV design; Video S1: Video footage of a bluntnose sixgill shark; Video S2: Types of markings in blue sharks bodies to identify individuals; Video S3: Other marine pelagic species.</p>
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: Multi-tool marine metabarcoding bioassessment for baselining and monitoring species and communities in kelp habitats
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Data from: Predicting bushmeat biomass from species composition captured by camera traps: implications for locally-based wildlife monitoring
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Data and code for: Leveraging long-term data to improve biodiversity monitoring with species distribution models
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Data and code for: Acoustic monitoring enables multi-taxa conservation assessment and prioritisation over large scales and for rare and cryptic species
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Data from: Facebook groups as citizen science tools for plant species monitoring
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Data and code from: Integrating genomics, collections, and community science to delimit species clarifies the taxonomy of a variable monitor lizard (<em>Varanus tristis</em>)
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Improving citizen science data for long-term monitoring of plant species
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Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards
Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene dataset, we estimated phylogeny and used multilocus genetic networks, analysis of population structure, and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages, and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g., morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists, and conservationists.
Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK
<p>One of the most foundational aspects of ecological studies and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype-based identification. The CRISPR-Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR-Cas13a platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of proof of principle experiments to characterize SHERLOCK's ability to accurately, sensitively, and rapidly distinguished three fish species (two with protected status and one non-native) co-occurring in the San Francisco Estuary which are easily misidentified in the field. We improved SHERLOCK's ease of field deployment by combining its rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction-free DNA collection protocol as well as the option of instrument-free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.</p>
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: Have Welsh agri-environment schemes delivered for focal species? Results from a comprehensive monitoring programme
1. Agri-environment schemes (AES) have been criticised for being inadequately monitored and for not delivering the expected benefits to nature. Consequently, the Welsh Government funded a comprehensive programme of monitoring of Welsh AES, which took place between 2009 and 2012. The AES assessment focused primarily on Tir Gofal (which translates as "Land in Care"), but also included the Organic Farming Scheme, and monitoring focused on a range of taxa of conservation importance: arable plants, grassland fungi, bats (six species), butterflies (three species), birds (five species), water vole and brown hare. 2. Field work was undertaken to survey these taxa on matched farms and fields within and outside of AES. Response variables consisted of spatial trends of abundance, occurrence and species richness, which were modelled against AES status. Existing data were also available for two bird species. 3. Few differences were observed between AES and non-AES farms and fields. Those that were observed were for species that use arable habitats (which are uncommon in Wales): arable plants, yellowhammers, and brown hares. The lack of differences in non-arable habitats may reflect the smaller contrast between AES and non-AES management in these habitats. It may also reflect the original condition of habitat entered into AES prescriptions, as most non-arable prescriptions were defined by mandatory management of existing habitats, rather than optional habitat creation or restoration, which is the case for most arable prescriptions. 4. Despite the lack of differences observed, AES may help to maintain populations of species, making it more likely that they will persist in the landscape. There is evidence, from this monitoring programme and elsewhere, that AES can increase the populations of species, when well targeted and implemented. 5. Policy applications. The results indicate that Welsh AES have been only partly successful in achieving their stated aim of "maintaining and enhancing species abundance." These results can be used to improve AES design and management, both in Wales and more widely, by identifying and promoting effective management interventions, and by identifying ineffective management interventions and seeking alternatives. In particular, we highlight the importance of comprehensive monitoring of AES, and we recommend that this be combined with specific targets regarding the expected outcomes of AES management. This is essential to determine whether AES are providing value for money.28-Nov-2018
Data from: Using citizen science monitoring data in species distribution models to inform isotopic assignment of migratory connectivity in wetland birds
Stable isotopes have been used to estimate migratory connectivity in many species. Estimates are often greatly improved when coupled with species distribution models (SDMs), which temper estimates in relation to occurrence. SDMs can be constructed using from point locality data from a variety of sources including extensive monitoring data typically collected by citizen scientists. However, one potential issue with SDM is that these data oven have sampling bias. To avoid this potential bias, an approach using SDMs based on marsh bird monitoring program data collected by citizen scientists and other participants following protocols specifically designed to maximize detections of species of interest at locations representative of the species range. We then used the SDMs to refine isotopic assignments of breeding areas of autumn-migrating and wintering Sora (Porzana carolina), Virginia Rails (Rallus limicola), and Yellow Rails (Coturnicops noveboracensis) based on feathers collected from individuals caught at various locations in the United States from Minnesota south to Louisiana and South Carolina. Sora were assigned to an area that included much of the western U.S. and prairie Canada, covering parts of the Pacific, Central, and Mississippi Flyways. Yellow Rails were assigned to a broad area along Hudson and James Bay in northern Manitoba and Ontario, as well as smaller parts of Quebec, Minnesota, Wisconsin, and Michigan, including parts of the Mississippi and Atlantic Flyways. Virginia Rails were from several discrete areas, including parts of Colorado, New Mexico, the central valley of California, and southern Saskatchewan and Manitoba in the Pacific and Central Flyways. Our study demonstrates extensive data from organized citizen science monitoring programs are especially useful for improving isotopic assignments of migratory connectivity in birds, which can ultimately lead to better informed management decisions and conservation actions.
FIGURE 34 in Unravelling the underestimated diversity of Philippine water monitor lizards (Squamata: Varanus salvator complex), with the description of two new species and a new subspecies
FIGURE 34. Distribution ranges of the Philippine species of the V. s a l va t o r complex according to the morphological investigations presented here: V. marmoratus = red; V. nuchalis = blue; V. palawanensis sp. nov. = green; V. rasmusseni sp. nov. = black; V. c. cumingi = yellow; and V. c. s a m a re n s i s ssp. nov. = purple. Question marks denote the water monitor populations from Mindoro, Basilan, and northern Borneo of unknown taxonomic status. The grey shaded areas indicate the paleo-shorelines of several Pleistocene aggregate island complexes, which today, form biogeographic subregions of the Philippines: I = Greater Palawan; II = Greater Luzon; III = Greater Negros–Panay; IV = Greater Mindanao; and V = Greater Sulu. Map modified after Gaulke (in press).
FIGURE 23 in Unravelling the underestimated diversity of Philippine water monitor lizards (Squamata: Varanus salvator complex), with the description of two new species and a new subspecies
FIGURE 23. Ventral view of the juvenile paratype (ZFMK 89391) of V. rasmusseni sp. nov. Photo by André Koch.
FIGURE 26 in Unravelling the underestimated diversity of Philippine water monitor lizards (Squamata: Varanus salvator complex), with the description of two new species and a new subspecies
FIGURE 26. Ventral view of the holotype (SMF 73912) of V. palawanensis sp. nov. Photo by André Koch.
FIGURE 27 in Unravelling the underestimated diversity of Philippine water monitor lizards (Squamata: Varanus salvator complex), with the description of two new species and a new subspecies
FIGURE 27. Portrait of the holotype (SMF 73912) of V. palawanensis sp. nov. Note the ill-defined temporal stripe and the dark pigmentation on the dorsal and ventral side of the tongue. Photo by André Koch.
FIGURE 20 in Unravelling the underestimated diversity of Philippine water monitor lizards (Squamata: Varanus salvator complex), with the description of two new species and a new subspecies
FIGURE 20. Ventral view of the adult holotype (ZMUC R42151) of V. rasmusseni sp. nov. Photo by André Koch.
FIGURE 19 in Unravelling the underestimated diversity of Philippine water monitor lizards (Squamata: Varanus salvator complex), with the description of two new species and a new subspecies
FIGURE 19. Dorsal view of the adult holotype (ZMUC R42151) of V. rasmusseni sp. nov. Note the lack of colour pattern. Photo by André Koch.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.