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31 results for “Temporal sampling”
Temporal and spatial changes of the abundance and species composition of phytoplankton in the California Current from samples collected aboard CalCOFI cruises from summer 1996 through 2022.
The abundances of 385 taxonomic categories of phytoplankton (species where possible) are presented for the 26.5 -year period beginning with summer, 1996 and concluding with autumn 2022. There were four cruises per year. Samples were water samples collected from the second depth, which was designed to sample the mixed layer when a mixed layer existed, generally between 5m - 15m. Before counting, samples from single stations were pooled into four regions: NE (northern inshore), SE (southern inshore), Alley (the region of the California Current) and Offshore (Central Pacific). Pooled samples were enumerated with an inverted microscope. The species data are presented by seven major taxonomic categories followed by the sums of those major taxa. The species codes are defined in the table metadata.
Peak Flow Event Durations in the Mississippi River Basin and Implications for Temporal Sampling of Rivers
<p><strong>Corresponding peer-reviewed publication</strong></p> <p>This repository corresponds to all the input and output files that were used in the study reported in:</p> <ul> <li>Cerbelaud, A., David, C. H., Biancamaria, S., Wade, J., Tom, M., Prata de Moraes Frasson, R., & Blumstein, D. (2024). Peak flow event durations in the Mississippi River basin and implications for temporal sampling of rivers. Geophysical Research Letters, 51, e2024GL109220. <a href="https://doi.org/10.1029/2024GL109220" target="_blank" rel="noopener">https://doi.org/10.1029/2024GL109220</a>.</li> </ul> <p>When making use of any of the output files of this dataset, please cite both the aforementioned article and the dataset herein. </p> <p><strong>Main goals of the publication</strong></p> <p>The corresponding work aims to quantify peak flow event durations at an hourly time scale and their impact on high-frequency river sampling requirements using sampling ratios. The analysis is performed over the Mississippi basin using hourly USGS gages over 2010-2022.</p> <p>The findings derived from these output files have direct implications for future satellite missions concerned with capturing high-frequency dynamics in rivers, including flood events.</p>
Spanning Scales: The Airborne Spatial and Temporal Sampling Design of the National Ecological Observatory Network
<p>Supporting information, datasets, and R and JavaScript code for the the National Ecological Observatory Network’s Airborne Observation Platform (AOP) sampling design and publication, <em>"Spanning Scales: The Airborne Spatial and Temporal Sampling Design of the National Ecological Observatory Network"</em></p>
single cell RNA seq data of 3 healthy sample from frontal lobe and temporal lobe
<p><span>Frontotemporal lobe abnormalities are linked to neuropsychiatric disorders and cognition, but the role of cellular heterogeneity between temporal lobe (TL) and frontal lobe (FL) in the vulnerability to genetic risk factors remains to be elucidated. We provided single-nucleus transcriptome analysis in “fresh” human FL and TL which are integrated with genetic susceptibility, gene dysregulation in neuropsychiatric disease, and psychoactive drug response data. We show how intrinsic differences between TL and FL contribute to the vulnerability of specific cell types to both genetic risk factors and psychoactive drugs. Neuronal populations, specifically PVALB-neurons, were most highly vulnerable to genetic risk factors for psychiatric disease. These psychiatric disease-associated genes were mostly upregulated in the TL, and dysregulated in the brain of patients with obsessive-compulsive disorder, bipolar disorder and schizophrenia. these data provide prefound insight into brain frontotemporal lobe.</span></p>
Sampling a pika’s pantry: Temporal shifts in nutritional quality & over-winter preservation of American pika food caches
Climate change is increasing temperature, decreasing precipitation, and increasing atmospheric CO2 concentrations in many ecosystems. As atmospheric carbon rises, plants may increase carbon-based defenses such as phenolics, thereby potentially affecting food quality, foraging habits, and habitat suitability for mammalian herbivores. In alpine habitats, the American pika (Ochotona princeps) is a model species for studying effects of changing plant chemistry on mammals. To survive between growing seasons, pikas cache “haypiles” of plants rich in phenolics. Although they are acutely toxic to pikas, phenolic compounds help plants retain biomass and nutrition during storage, and they break down over time. Alpine avens (Geum rossii, Rosales: Rosaceae) is a high-phenolic plant species that comprises up to 75% of pika winter diet in Colorado. Here, we tested the hypothesis that contemporary climate change has affected the nutritional value of Alpine avens to pikas in the last 30 years. Specifically, we compared phenolic activity, nutritional quality, and overwinter preservation of plants collected at Niwot Ridge, Colorado (USA) in 1992 to those collected between 2010 – 2018, spanning nearly three decades of climate change. Phenolic activity increased in alpine avens since 1992, while fiber and nitrogen content decreased. Importantly, overwinter preservation of plant biomass also increased, particularly on windblown slopes without long-lasting snow cover. Previous studies indicate that pikas at this site still depend on alpine avens in their winter food caches. Increasing phenolic content in alpine avens could therefore enhance the preservation of haypiles over winter; however, if pikas must further delay consuming these plants to avoid acute toxicity, then he nutritional gains from enhanced preservation may not be beneficial. This study provides important insights into how changing plant chemistry will affect mammalian herbivores in the future.
Data from: Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems.
<p>The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow-legged frog (<i>Rana sierrae</i>) and the foothill yellow-legged frog (<i>R. boylii</i>). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2-9.19X) in our protocol, from a probability of 0.51 to 0.85 per technical replicate. Lake sample volumes were limited by filter clogging and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3 - 2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow-legged frog eDNA captured in streams between 100 and 200 m, indicating that sampling at close intervals is important.</p>
Data from: Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems
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Data from: Genetic analysis of museum samples suggests temporal stability in the Mexican nonbreeding distribution of a neotropical migrant
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Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling
We estimated the effective population sizes (Ne) and tested for short-term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro-endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D-loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean Ne estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake-level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro-endemics and populations in less favourable habitats have smaller Ne, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.
Data from: Multi-year stigmatic pollen-load sampling reveals temporal stability in interspecific pollination of flowers in a subalpine meadow
Co-flowering plants may commonly experience interspecific pollination. It remains unknown, however, whether interspecific pollination is a largely stochastic process or consistent enough over years to exert selection for traits that can reduce interspecific pollination or ameliorate its deleterious effects on reproduction. To assess the likelihood of this precondition being met, stigmatic pollen loads on 17 to 34 insect-pollinated plant species over 3 consecutive years were scored in a subalpine meadow in southwestern China. Plant species varied significantly in the amount and proportion of heterospecific pollen (HP) on stigmas. Both the number of HP species and the proportion of the pollen load that was HP for each recipient species correlated positively between years (reflected in pairwise correlations for all year-by-year combinations). Although inter-annual variation was smaller for conspecific pollen (CP) than for HP loads, species tended to experience either consistently high or consistently low HP proportions across years. We found that species with higher stigmatic HP proportions generally experienced lower proportional variation in stigmatic HP, an unexpected result if high HP loads are the result of rare stochastic events. The novel finding of between-year consistency in stigmatic loads of heterospecific pollen suggests that adaption to stigmatic loads of HP is possible, and two divergent strategies may have evolved: HP avoidance and HP tolerance. The observation of temporally consistent differences among species in levels of HP supports the idea that natural selection may be operating either to increase tolerance or to minimize arrival of heterospecific pollen on stigmas in co-flowering plants. Such adaptations may be important for the maintenance of high levels of local plant diversity in biodiversity hotspots such as our study area.
Data from: Examining temporal sample scale and model choice with spatial capture-recapture models in the common leopard Panthera pardus
Many large carnivores occupy a wide geographic distribution, and face threats from habitat loss and fragmentation, poaching, prey depletion, and human wildlife-conflicts. Conservation requires robust techniques for estimating population densities and trends, but the elusive nature and low densities of many large carnivores make them difficult to detect. Spatial capture-recapture (SCR) models provide a means for handling imperfect detectability, while linking population estimates to individual movement patterns to provide more accurate estimates than standard approaches. Within this framework, we investigate the effect of different sample interval lengths on density estimates, using simulations and a common leopard (Panthera pardus) model system. We apply Bayesian SCR methods to 89 simulated datasets and camera-trapping data from 22 leopards captured 82 times during winter 2010–2011 in Royal Manas National Park, Bhutan. We show that sample interval length from daily, weekly, monthly or quarterly periods did not appreciably affect median abundance or density, but did influence precision. We observed the largest gains in precision when moving from quarterly to shorter intervals. We therefore recommend daily sampling intervals for monitoring rare or elusive species where practicable, but note that monthly or quarterly sample periods can have similar informative value. We further develop a novel application of Bayes factors to select models where multiple ecological factors are integrated into density estimation. Our simulations demonstrate that these methods can help identify the "true" explanatory mechanisms underlying the data. Using this method, we found strong evidence for sex-specific movement distributions in leopards, suggesting that sexual patterns of space-use influence density. This model estimated a density of 10.0 leopards/100 km2 (95% credibility interval: 6.25–15.93), comparable to contemporary estimates in Asia. These SCR methods provide a guide to monitor and observe the effect of management interventions on leopards and other species of conservation interest.
Raw data for Evaluating community-wide temporal sampling in passive acoustic monitoring: A comprehensive study of avian vocal patterns in subtropical montane forests
<p>This dataset, utilized in the research paper "<a href="https://doi.org/10.12688/f1000research.141951.1">Evaluating community-wide temporal sampling in passive acoustic monitoring: A comprehensive study of avian vocal patterns in subtropical montane forests</a>", comprises columns such as site_name, longitude (WGS84), latitude (WGS84), altitude (meters above sea level), vegetation types, date, hour, minute, julian_day, scientific_name, and Vocal Activity Rate per minute (VAR_m). It encompasses data gathered from twelve Passive Acoustic Monitoring (PAM) stations positioned within Yushan National Park (YSNP), Taiwan. The collection period spanned from March 1 to June 30, 2021. The dataset documents 8,202,731 vocalizations from twelve bird species, detected using an automated sound identification tool named SILIC (Sound Identification and Labeling Intelligence for Creatures). The vocalization data is aggregated by site, species, and time (down to the minute).</p>
Temporal validity of software datasets for code metrics: an empirical assessment of sampling strategies
<p>This is the repository for the scripts and data of the study "Building and updating software datasets: an empirical assessment".</p> <h2>Data collected</h2> <p>The data generated for the study it can be downloaded as a zip file. Each folder inside the file corresponds to one of the datasets of projects employed in the study (qualitas, currentSample and qualitasUpdated). Every dataset comprised three files "class.csv", "method.csv" and "sample.csv", with class metrics, method metrics and repository metadata of the projects respectively. Here is a description of the datasets:</p> <ul> <li>qualitas: includes code metrics and repository metrics from the projects in the release 20130901r of the Qualitas Corpus.</li> <li>currentSample: includes code metrics and repository metrics from a recent sample collected with our sampling procedure.</li> <li>qualitasUpdated: includes code metrics and repository metrics from an updated version of the Qualitas Corpus applying our maintenance procedure.</li> </ul> <h2>Plot graphics</h2> <p>To plot the results and graphics in the article there is a Jupyter Notebook "Experiment.ipynb". It is initially configured to use the data in "datasets" folder.</p> <h2>Replication Kit</h2> <p>For replication purposes, the datasets containing recent projects from Github can be re-generated. To do so, the virtual environment must have installed the dependencies in "requirements.txt" file, add Github's tokens in "./token" file, re-define or leave as is the paths declared in the constants (variables written in caps) in the main method, and finally run "main.py" script. The portable versions of the source code scanner <a href="https://sourcemeter.com/" target="_blank" rel="noopener">Sourcemeter</a> are located as zip files in "./Sourcemeter/tool" directory. To install Sourcemeter the appropriate zip file must be decompressed excluding the root folder "SourceMeter-10.2.0-x64-<OS>".</p> <p>The script comprise 5 steps:</p> <ol> <li>Project retrieval from Github: at first the sampling frame with projects complying with a specific quality criteria are retrieved from Github's API.</li> <li>Create samples: with the sampling frame retrieved, the current samples are selected (currentSample and qualitasUpdated). In the case of qualitasUpdated, it is important to have first the "sample.csv" file inside the qualitas folder of the dataset originally created for the study. This file contains the metadata of the projects in Qualitas Corpus.</li> <li>Project download and analysis: when all the samples are selected from the sampling frame (currentSample and qualitasUpdated), the repositories are downloaded and scanned with SourceMeter. In the cases in which the analysis is not possible, the projects are replaced with another one with similar size.</li> <li>Outlier detection: once the datasets are collected, it is necessary to manually look for possible outliers in the code metrics under study. In the notebook "Experiment.ipynb" there are specific sections dedicated for it ("Outlier detection (Section 4.2.2)").</li> <li>Outlier replacement: when the outliers are detected, in the same notebook there is also a section for outlier replacement ("Replace Outliers") where the outliers' url have to be listed to find the appropriate replacement.</li> </ol> <ul> <li>If it is required, the metrics from the Qualitas Corpus can also be re-generated. First, it is necessary to download the release 20130901r from its <a href="http://www.qualitascorpus.com/download/" target="_blank" rel="noopener">official webpage</a>. Second, decompress the .tar files downloaded. Third, make sure that the compressed files with source code from the projects (.java files) are placed in the "compressed" folder, in some cases it is necessary to read the "QC_README" file in the project's folder. Finally, run the original main script "Generate metrics for the Qualitas Corpus (QC) dataset" part of the code. </li> </ul>
Data from: Low-cost automated flight intercept trap for the temporal sub-sampling of flying insects attracted to artificial light at night
<p>Sampling methods are selected depending on the targeted species or the spatial and temporal requirements of the study. However, most methods for passive sampling of flying insects have poor temporal resolution because it is time consuming, costly and/or logistically difficult. Effective sampling of flying insects attracted to artificial light at night (ALAN) requires sampling at user-defined time points (nighttime only) across well-replicated sites resulting in major time and labor-intensive survey effort or expensive automated technologies. Described here is a low-cost automated intercept trap that requires no specialist equipment or skills to construct and operate, making it a viable option for studies that require temporal sub-sampling across multiple sites. The trap can be used to address a wide range of other ecological questions that require a greater temporal and spatial scale than is feasible with previous trap technology.</p>
Figure 1 in Comparative success of two sampling techniques for high-altitude Alpine grassland reptiles under different temporal designs
Figure 1. Schematic representation of the plots' setup in Paneveggio-Pale di San Martino Nature Park.
Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling
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Data from: Evaluating the sensitivity of process domains for logjams to spatial and temporal sample size in river networks of the Southern Rockies, USA
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Data from: Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes
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Data from: Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift
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Data from: Low-cost automated flight intercept trap for the temporal sub-sampling of flying insects attracted to artificial light at night
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