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108 results for “environmental monitoring”
Indigenous Peoples and environmental research and monitoring within the Laurentian Great Lakes Basin: A systematic map
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Environmental impact assessment for large carnivores: a methodological review of the wolf (Canis lupus) monitoring in Portugal
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Effects of soil preservation for biodiversity monitoring using environmental DNA
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Ruffed grouse (Bonasa umbellus) drumming surveys, 1987-2017, Adirondack Long-Term Ecological Monitoring Program Project No. 9 by Adirondack Ecological Center of the State University of New York College of Environmental Science and Forestry, Newcomb, New York. Environmental Data Initiative
The objective is to document long-term population trends of ruffed grouse in a northern hardwood ecosystem. The survey area is the Huntington Wildlife Forest, a 6,000 ha field station which receives no hunting pressure. Routes are surveyed starting an hour prior to sunrise on 2-5 mornings each year between April 14 and May 9 (occasionally later), on days when wind and rain are minimal to absent. Counts are standardized relative to weather conditions and timing. Observers count the number of individual ruffed grouse heard drumming (""drummers"") at 32-50 route stations during a 4-minute period. Trends at stations over time as well as overall drummer index are calculated and compared to independent datasets.
Seed Production Survey, 1988-2009, Adirondack Long-Term Ecological Monitoring Program Project No. 26 by Adirondack Ecological Center of the State University of New York College of Environmental Science and Forestry, Newcomb, New York, USA
The purpose of this project is to 1) estimate number of seeds per unit area in a mature northern hardwood/mixed conifer forest stand and 2) document changes over time in selected tree and shrub seed production. Permanent seed traps were established in 1988 in two forest types. Seed traps (13.9 L [5 gal] capacity buckets) are installed 0.5 m off the ground on two metal stakes in the center of each forested plot. Buckets are open to the tree canopy and have small (< 2cm) holes near the bottom edges for drainage. Fifty collection buckets are placed approximately 30 m (100 feet) apart and distributed along painted grid lines in the Huntington Wildlife Forest Natural Area. Twenty-five plots are northern hardwood upland forest (dominated by sugar maple, American beech and yellow birch with some conifers) and 25 plots are in the mixed hardwood/conifer lakeshore forest type (dominated by red maple, yellow birch, red spruce and eastern hemlock). Tree and shrub seeds are collected annually during two periods: July to November (Fall) and November to July (Spring). The spring and autumn collections are based on tree species’ seed phenology. If a bucket was tipped over due to disturbance by a bear or some other factor, it was censored from the survey for that year. Mice or other seed predators that were physically found/present in buckets also resulted in sample censoring. Animal scat or partly-consumed seeds are not censored, as these may have fallen from the tree canopy during seed predators’ normal activities.
White-tailed Deer Population Study, 1962-2008, Adirondack Long-Term Ecological Monitoring Program by Adirondack Ecological Center of the State University of New York College of Environmental Science and Forestry, Newcomb, New York, USA
From 1962-2008, White-tailed deer (Odocoileus virginianus) were studied at the SUNY ESF Huntington Wildlife Forest (HWF) and adjacent private and public lands in Essex and Hamilton Counties, New York, USA. Social group membership, migration and dispersal, reproductive biology, and many other objectives were studied over the course of the study period. Deer were captured, individually marked with ear tags or streamers, fitted with radio collars (later, GPS collars), and released to be tracked for a variety of research objectives. Deer were located by visual observation, recapture, and/or their location was estimated with ground, air or tower-based radio telemetry. Physical condition of deer was recorded at capture and at subsequent recapture or visual observation select variables were documented (e.g., deer group size; presence of fawns with does). Physiological, demographic, social organization, home range and behavior data were collected. HWF is a no-hunting area but deer could be harvested if they moved to huntable parts of the study area; there was a managed hunt on HWF in 1966-1970 and in 1984 to meet deer density and forest management objectives at that time. Unmarked deer were incorporated into the dataset if they were roadkilled, harvested or otherwise encountered during field activity; these deer did not receive individual identifications but may have been incorporated into select projects.
Continuous Forest Inventory (CFI), 1970-2017, Long-term Forest Property Monitoring by State University of New York College of Environmental Science and Forestry, New York, USA
SUNY College of Environmental Science and Forestry (ESF) based in Syracuse, New York, maintains a series of Continuous Forest Inventory (CFI) permanent plots on their Forest Properties. ESF has over 700 CFI plots located on 5 different properties, four properties in the Adirondack Mountains of northern New York and one property south of Syracuse. Plots cover northern hardwood species including sugar maple, red maple, yellow birch, beech, white ash, red oak, white pine, hemlock, red spruce, and pine/softwood plantations of various species. Data is collected at ten year intervals on each property starting from initial plot establishment. Plot information collected includes: location information, slope, aspect, forest type, cutting history, and photo of plot. Tree information/measurements include (in general, trees greater than 3.6 inches diameter at breast height): tree tag number, species, tree history, diameter at breast height, sawlog height, bole height, total height, crown vigor, crown class, tree location, and tree notes. Data is collected/field checked/edited according to detailed written procedures by ESF professional staff with assistance of students. Data is collected to monitor general forest health, growth rates, mortality, and overall forest metrics. Data is used to calculate standing volumes, stocking of forest trees, carbon stocking in addition to other information. ESF Forest Properties with CFI plots:
Figure 3 in Terrestrial isopods as bioindicators for environmental monitoring in olive groves and natural ecosystems
Figure 3. Activity density of isopods in olive grove management systems. Letters indicate homogeneous groups.
Data from: Development and testing of an environmental DNA (eDNA) assay for endangered Atlantic sturgeon to assess its potential as a monitoring and management tool
<p>Significant declines in Atlantic sturgeon (<i>Acipenser oxyrhynchus oxyrhynchus</i>) abundances along the US east coast have spurred major research efforts and management actions over the last 50 years, yet information on spawning stock abundances and habitat use is still lacking for many river systems, including in the Chesapeake Bay, USA. Here, we developed and tested a new quantitative PCR (qPCR) assay to detect Atlantic sturgeon environmental DNA (eDNA) in water samples with the goal of providing an alternative method to monitor presence and relative abundance. We also examined Atlantic sturgeon eDNA shedding rates in laboratory experiments. A qPCR-probe assay targeting Cytochrome-B was developed and showed no amplification of other related and co-occurring fishes. Pond trials at a density of ~0.2 g/L sturgeon produced relatively strong eDNA detections (~1,000-25,000 copies/L) in all seven water samples assayed. Water samples taken from two river systems in the Chesapeake Bay produced zero eDNA detections in the summer, while fall sampling during sturgeon spawning produced positive eDNA detections in 26% of samples, though at much lower concentrations (400-1,800 copies/L) compared with the pond (mesocosm) detections. Acoustic detections of sturgeon near river sampling sites were positively associated with eDNA detections. However, the eDNA assay failed to detect the presence of sturgeon in some samples when abundances were very low or when fish were in deep water. Finally, Atlantic sturgeon eDNA shedding rates were estimated to be on the order of estimates for other fish species, which suggests that relatively weak detections in the field are not necessarily driven by low rates of eDNA shedding. Overall, eDNA analysis represents a promising new monitoring tool for Atlantic sturgeon. Applying these methods in other rivers along the US east coast is an important next step in documenting Atlantic sturgeon distribution for management and conservation purposes.</p>
Data from: An environmental DNA-based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica)
Determining the timing and location of reproductive events is critical for efficient management of species. However, methods currently used for aquatic species are costly, time intensive, biased and often require destructive or injurious sampling. Hence, developing a non-invasive sampling method to accurately determine the timing and location of reproduction for aquatic species would be extremely valuable. We conducted an experimental and field study to determine the influence of spawning, and the mass release of spermatozoa in particular, on environmental DNA (eDNA) concentrations. Using a quantitative PCR approach we monitored changes in nuclear and mitochondrial eDNA concentrations over time. The data from the experimental study and the field survey supported our hypothesis that spawning events are characterized by higher concentrations of nuclear relative to mitochondrial eDNA. Outside of the reproductive period, we find that nuclear and mitochondrial DNA fragments are equally abundant in environmental water samples. We have shown that changes in the relative abundance of nuclear and mitochondrial eDNA can be used to monitor spawning activity of the endangered Macquarie perch. Our method is likely to be transferrable to other aquatic species and can be particularly useful to increase our understanding of the spawning biology of cryptic, rare or threatened species as well as design and evaluate environmental management actions and determine species establishment.
Data from: Long-term environmental monitoring for assessment of change: measurement inconsistencies over time and potential solutions
The importance of long-term environmental monitoring and research for detecting and understanding changes in ecosystems and human impacts on natural systems is widely acknowledged. Over the last decades a number of critical components for successful long-term monitoring have been identified. One basic component is quality assurance/quality control protocols to ensure consistency and comparability of data. In Norway, the authorities require environmental monitoring of the impacts of the offshore petroleum industry on the Norwegian continental shelf, and in 1996 a large-scale regional environmental monitoring program was established. As a case study, we used a sub-set of data from this monitoring to explore concepts regarding best practices for long-term environmental monitoring. Specifically, we examined data from physical and chemical sediment samples and benthic macro-invertebrate assemblages from 11 stations from six sampling occasions during the period 1996-2011. Despite the established quality assessment and quality control protocols for this monitoring program, we identified several data challenges, such as, missing values and outliers, discrepancies in variable and station names, changes in procedures without calibration, and different taxonomic resolution. Furthermore, we show that the use of different laboratories over time makes it difficult to draw conclusions with regard to some of the observed changes. We offer recommendations to facilitate comparison of data over time. We also present a new procedure to handle different taxonomic resolution so valuable historical data is not discarded. These topics have a broader relevance and application than for our case study.
Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring
<div class="page"> <div class="section"> <p>Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016-0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.</p> </div> </div>
Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities
The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demands highly trained specialists and is extremely time-consuming and costly, what makes it unsuitable for large-scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next-generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and Redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for alpha diversity loss in strongly impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof-of-concept study, we conclude that NGS metabarcoding using foraminifera and other protists has considerable potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.
Data from: Weather conditions determine attenuation and speed of sound: environmental limitations for monitoring and analysing bat echolocation
Echolocating bats are regularly studied to investigate auditory-guided behaviours and as important bioindicators. Bioacoustic monitoring methods based on echolocation calls are increasingly used for risk assessment and to ultimately inform conservation strategies for bats. As echolocation calls transmit through the air at the speed of sound, they undergo changes due to atmospheric and geometric attenuation. Both the speed of sound and atmospheric attenuation, however, are variable and determined by weather conditions, particularly temperature and relative humidity. Changing weather conditions thus cause variation in analysed call parameters, limiting our ability to detect and correctly analyse bat calls. Here, I use real-world weather data to exemplify the effect of varying weather conditions on the acoustic properties of air. I then present atmospheric attenuation and speed of sound for the global range of weather conditions and bat call frequencies to show their relative effects. Atmospheric attenuation is a non-linear function of call frequency, temperature, relative humidity and atmospheric pressure. While atmospheric attenuation is strongly positively correlated with call frequency, it is also significantly influenced by temperature and relative humidity in a complex non-linear fashion. Variable weather conditions thus result in variable and unknown effects on the recorded call, affecting estimates of call frequency and intensity, particularly for high frequencies. Weather-induced variation in speed of sound reaches up to about ±3%, but is generally much smaller and only relevant for acoustic localisation methods of bats. The frequency- and weather-dependent variation in atmospheric attenuation has a three-fold effect on bioacoustic monitoring of bats: it limits our capability (1) to monitor bats equally across time, space, and species, (2) to correctly measure frequency parameters of bat echolocation calls, particularly for high-frequencies, and (3) to correctly identify bat species in species-rich assemblies or for sympatric species with similar call designs.
In situ monitoring reveals cellular environmental instabilities in human pluripotent stem cell culture
<p>Mammalian cell cultures are a keystone resource in biomedical research, but the results of published experiments often suffer from reproducibility challenges. This has led to a focus on the influence of cell culture conditions on cellular responses and reproducibility of experimental findings. Here, we perform frequent in situ monitoring of dissolved O<sub>2</sub> and CO<sub>2</sub> with optical sensor spots and contemporaneous evaluation of cell proliferation and medium pH in standard batch cultures of three widely used human somatic and pluripotent stem cell lines. We collate data from the literature to demonstrate that standard cell cultures consistently exhibit environmental instability, indicating that this may be a pervasive issue affecting experimental findings. Our results show that <i>in vitro</i> cell cultures consistently undergo large departures of environmental parameters during standard batch culture. These findings should catalyze further efforts to increase the relevance of experimental results to the in vivo physiology and enhance reproducibility.</p>
The Bug in a teacup – Monitoring arthropod-plant associations with environmental DNA from dried plant material
<p class="MsoNormal">Environmental DNA analysis has revolutionized the field of biomonitoring in the past years. Various sources have been shown to contain eDNA of diverse organisms, for example water, soil, gut content and plant surfaces. Here we show that dried plant material is a highly promising source for arthropod community eDNA. We designed a metabarcoding assay to enrich diverse arthropod communities, while preventing amplification of plant DNA. Using this assay, we analyzed various commercially produced teas and herbs. These samples recovered ecologically and taxonomically diverse arthropod communities, a total of over a thousand species in more than 20 orders, many of them specific to their host plant and its geographic origin. Atypically for eDNA, arthropod DNA in dried plants shows a very high temporal stability, opening up plant archives as a source for historical arthropod eDNA. Considering these results, dried plant material appears excellently suited as a novel tool to monitor arthropods and arthropod-plant interactions, detect agricultural pests, and identify the geographic origin of imported plant material. The ability to detect highly diverse arthropod communities from all over the world in tea bags also highlights the utility of our approach for outreach purposes and to raise awareness about biodiversity.</p>
The use of environmental DNA to monitor impacted coastal estuaries
<p>Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon – one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with environmental parameters (sea surface temperature and freshwater input). Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.</p>
Spatiotemporal monitoring of the rare Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae): SNP genotyping and environmental niche modelling herbarium specimens
<p><strong>Aim: </strong>We have studied spatiotemporal genetic change in the Northern dragonhead, a plant species that has experienced a drastic population decline and habitat loss in Europe. We add a temporal perspective to the monitoring of dragonhead in Norway by genotyping herbarium specimens up to 200 years old. We also assess whether dragonhead has achieved its potential distribution in Norway. Location: Europe (mainly Norway)</p> <p><strong>Methods:</strong> We have applied a microfluidic array consisting of 96 SNP markers on 130 herbarium specimens collected from 1820 to 2008, mainly from Norway (83) but also beyond (47). We have compared our new genotype data with existing data from modern samples. We have modelled the species' environmental niche and potential distribution in Norway using sample metadata and observational records.</p> <p><strong>Results: </strong>The SNP array successfully genotyped all included herbarium specimens. The captured genetic diversity was negatively correlated with distance from Norway. The historical-modern comparison revealed similar genetic structure and diversity across space and limited genetic change through time in Norway. The ENM suggests that dragonhead is anchored in warmer and drier habitats.</p> <p><strong>Main conclusions: </strong>With appropriate design procedures, the SNP array technology is promising for genotyping old herbarium specimens. We found no signs of any regional bottleneck. The regional areas in Norway have remained genetically divergent, however, both from each other and more so from populations outside of Norway, rendering continued protection of the species in Norway relevant. The ENM suggests that dragonhead has not fully achieved its potential distribution in Norway.</p>
Monitoring Campaign of Environmental Data in Spotrs Centres of Catalonia, Spain
<p>The dataset contains the environmental data collected during a monitoring campaign between 2022 and 2023 in Catalonia, Spain. The work is further described in the research paper "Calculating comfort indexes and applying comfort models to predict thermal sensation vote in sports centres" published in Indoor Air by Hindawi-Wiley (<a href="https://doi.org/10.1155/1970/9142303">https://doi.org/10.1155/1970/9142303</a>).</p>
Supplementary material 9 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
Bland-Altman plots for the total fish eDNA (a), Japanese anchovy (Engraulis japonicus; b) and Japanese jack mackerel (Trachurus japonicus; c). Dashed lines indicate 95% uppper and lower limits and solid line indicates mean value.
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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.