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419 results for “capture data”
Spatial capture-recapture data of the Darwin's frog
<p>These data and code are intentended to serve as complementary information to allow the full reproducibility of the results presented in the study "Natal dispersal is facilitated by routine movements integrated along a straight path in the Darwin’s frog" submitted to Ecography.</p> <p>The first file titled "data and code used to run the sCJS.rar" contains capture-recapture data from three populations of the Darwin's frog (<em>Rhinoderma darwinii</em>) collected between March 2014 and December 2016. The age of the individuals, population of origin, and x- and y-coordinates of each capture are provided. The x- and y-coordinates are in meters. The sampling design follows the Pollock's robust design. The capture-history matrices (one for the x-coordinates and another for the y-coordinates) contain 48 columns representing twelve evenly distributed primary capture periods, each one composed of four consecutive days of capture (secondary capture ocassions). The time-period between primary capture periods is 3 months. However, note that we did not visited the populations during all these periods, therefore, some of collumns contain only NA's. The rows of the capture-history matrices represent the different individuals that were captured across the study. There are 370 rows, but for seven of these individuals we don't have spatial data (these individuals are removed in the code). Then we provide the R code used to run the sCJS of Schaub and Royle (2014). This code is almost identical to the provided by these authors, but a few modifications were made in order to fit our study design. Results of the model are also provided.</p> <p>The second file "Data required to run the simulation model.rar" contains the data required to run the movement path simulation model presented in the Supplementary material, Appendix 2 of the paper. Further details about these files and model can be found in the article.</p> <p>Any question can be adressed to andresvalenzuela.zoo@gmail.com</p> <p>Enjoy it!</p>
Data for "Investigating temporary capture in the Sun-Jupiter three-body system via Lagrangian coherent structures"
<p>The supplementary online materials for the paper "Investigating temporary capture in the Sun-Jupiter three-body system via Lagrangian coherent structures" consist of two parts.</p> <h3>Part 1: Coordinates of the LCS Surfaces in Figure 8</h3> <p>This part contains the coordinates of the local maxima of FTLE (Finite-Time Lyapunov Exponent) values that compose the Lagrangian Coherent Structures (LCS) surface presented in Figure 8 of the paper. These coordinates are crucial for understanding the formation and characteristics of the LCS in the three-body system.</p> <h3>Part 2: Orbital States of Asteroid 2002 GV28 Based on the High-Fidelity Ephemeris Model from Section 2.2 of the Paper</h3> <p>This part includes the orbital states of asteroid 2002 GV28, propagated using a high-fidelity ephemeris model as described in Section 2.2 of the paper. The data provides information on the asteroid's state in two different coordinate systems:</p> <ol> <li> <p><strong>Heliocentric J2000.0 Ecliptic Coordinate System:</strong></p> <ul> <li>This dataset includes the position and velocity of the asteroid relative to the Sun at various time steps.</li> <li>The columns typically include: Time (Julian Date), X (km), Y (km), Z (km), Vx (km/s), Vy (km/s), Vz (km/s).</li> </ul> </li> <li> <p><strong>Sun-Jupiter Rotating Coordinate System:</strong></p> <ul> <li>This dataset provides the position and velocity of the asteroid relative to the Sun-Jupiter rotating frame.</li> <li>The columns typically include: Time (Julian Date), X (normlized), Y (normlized), Z (normlized), Vx (normlized), Vy (normlized), Vz (normlized).</li> </ul> </li> </ol> <p>Each entry in these datasets corresponds to specific time steps during the propagation, providing a comprehensive view of the asteroid's trajectory in both coordinate systems.</p>
Data for high-yield atmospheric water capture via bioinspired material segregation
<p>This dataset includes raw data logs of indoor and outdoor water capture tests. The dataset also includes Mathematica code to calculate and generate convection-limited water capture fluxes.</p> <p>The data logs are TSV text files where the columns correspond to time (seconds), wind tunnel temperature (C), wind tunnel humidity (%), humidity setpoint (%), liquid desiccant chamber temperature (C), liquid desiccant chamber humidity (%), measured volume (mL).</p> <p>Links to this data are included in our paper.</p> <div> <div> <div> <p>The Mathematica code relies on external datasets listed in the mapping_plots.nb file</p> </div> </div> </div> <div> <div></div> </div>
Data for "Platform Materials for Moisture-Swing Carbon Capture"
<div> <p>This repository contains data for the manuscript "Platform Materials for Moisture-Swing Carbon Capture" </p> <p> </p> </div>
Data from: Using spatial capture–recapture to elucidate population processes and space-use in herpetological studies
The cryptic behavior and ecology of herpetofauna make estimating the impacts of environmental change on demography difficult; yet, the ability to measure demographic relationships is essential for elucidating mechanisms leading to the population declines reported for herpetofauna worldwide. Recently developed spatial capture–recapture (SCR) methods are well suited to standard herpetofauna monitoring approaches. Individually identifying animals and their locations allows accurate estimates of population densities and survival. Spatial capture–recapture methods also allow estimation of parameters describing space-use and movement, which generally are expensive or difficult to obtain using other methods. In this paper, we discuss the basic components of SCR models, the available software for conducting analyses, and the experimental designs based on common herpetological survey methods. We then apply SCR models to Red-backed Salamander (Plethodon cinereus), to determine differences in density, survival, dispersal, and space-use between adult male and female salamanders. By highlighting the capabilities of SCR, and its advantages compared to traditional methods, we hope to give herpetologists the resource they need to apply SCR in their own systems.
Data from: Mitochondrial capture by a transmissible cancer
Canine transmissible venereal tumor (CTVT) is an infectious cell line circulating in many feral dog populations. It originated once, about 10,000 years ago. Phylogenetic analyses of mitochondrial sequences from dogs, wolves, and a geographically diverse collection of CTVT samples indicate that the cancer has periodically acquired mitochondria from its host. We suggest that this may be because the cancer's own mitochondria have a tendency to degenerate, due to high mutation rates and relaxed selection, resulting in host mitochondria being more fit.
Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
Environmental DNA (eDNA) is used to detect biodiversity by the capture, extraction, and identification of DNA shed to the environment. However, eDNA capture and extraction protocols vary widely across studies. This use of different protocols potentially biases detection results and could significantly hinder a reliable use of eDNA to detect biodiversity. We tested whether choice of eDNA capture and extraction protocols significantly influenced biodiversity detection in aquatic systems. We sampled lake and river water, captured and extracted eDNA using six combinations of different protocols with replication, and tested for the detection of four macroinvertebrate species. Additionally, using the same lake water technical replicates, we compared the effect of capture and extraction protocols on metabarcode detections of biodiversity using 16S for eubacteria and cytochrome c oxidase I (COI) for eukaryotes. Protocol combinations for capture and extraction of eDNA significantly influenced DNA yield and number of sequences obtained from next generation sequencing. We found significantly different detection rates of species ranging from zero percent to thirty-three percent. Differences in which protocol combinations produced the highest metabarcoded biodiversity were detected and demonstrate that different protocols are required for different biodiversity targets. Our results highlight that the choice of molecular protocols used for capture and extraction of eDNA from water can strongly affect biodiversity detection. Consideration of biases caused by choice of protocols should lead to a more consistent and reliable molecular workflow for repeatable and increased detection of biodiversity in aquatic communities.
Data from: Survival estimates strongly depend on capture-recapture designs in a disturbed environment inducing dispersal
Capture‐Recapture (CR) approaches are extensively used to estimate demographic parameters. Their robustness relies on the selection of suitable statistical models, but also on the sampling design and effort deployed in the field. In colonial or territorial species showing breeding site fidelity, recurrent local perturbations, such as predation‐induced breeding failure, may lead individuals to disperse locally or regionally. This might induce heterogeneity in individual CR histories and biases in demographic parameter estimates. Here, we assessed the effect of buffer areas and multi‐site designs on annual survival estimate accuracy and precision. First, using simulated data with and without a multi‐site design, we compared survival estimates for different scenarios involving contrasted local and regional dispersal. Then, using data from a local multi‐site long‐term monitoring survey carried out in a colony of black‐legged kittiwakes, we tested the homogeneity of individual CR histories and compared survival estimates from three datasets including one or several breeding cliffs with or without buffer areas. Results from simulations highlighted that a single‐site design consistently led to underestimated or less precise survival values compared to a multi‐site design. Similarly, a multi‐site design allowed detecting significant temporal trends while a single‐site one did not. In the field‐based study, adding buffer areas reduced individual heterogeneity, but all three datasets suffered from strong trap‐dependence possibly due to individual breeding success affecting nest‐site fidelity. Implementing a multi‐site design significantly improved the accuracy and precision of annual survival estimates, regardless of CR models applied. Adapting the spatial scale of sampling design to the local environment and species behaviour is essential to provide robust parameters of key relevance for population monitoring and management. We show that implementing buffer areas and/or multi‐site designs may be especially beneficial for long‐lived species facing regular local perturbation events leading to local dispersal.
Capture data for American Robins (Turdus migratorius) at a fall migration banding station in Mid-Michigan from 2012 - 2019
<p>At the Burke Lake Banding Station in Bath, Michigan we captured American robins (Turdus migratorius) during fall migration from 2011 to 2019. The data shared consists of capture date and age. The data are used only for looking at the relative ratio of hatching year (HY) to after-hatching year (AHY) robins captured during fall migration. </p>
Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
Over the last decade, protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been widely developed. Their use is however limited to DNA of relatively high molecular weight. During the last year, several methods exploiting hybridization capture using probes based on RAD-sequencing loci have circumvented this limitation and opened avenues to the study of samples characterized by degraded DNA, such as historical specimens. Here, we present a major update to those methods, namely Hybridization capture from RAD-derived probes obtained from a reduced eXome template (hyRAD-X), a technique applying RAD-sequencing to messenger RNA from one or few fresh specimens to elaborate bench-top produced probes, i.e., a reduced representation of the exome, further used to capture homologous DNA from a samples set. In contrast to previous hybridization-capture methods, the reference catalog on which reads are aligned does not rely on de novo assembly of anonymous RAD-sequencing loci, but on an assembled transcriptome obtained from RNAseq data, thus increasing the accuracy of loci definition and Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically, expressed genes. Finally, the capture step of hyRAD-X relies on RNA probes, increasing stringency of hybridization, making it well suited for low-content DNA samples. As a proof of concept, we applied hyRAD-X to subfossil needles from the coniferous tree Abies alba, collected in lake sediments (Origlio, Switzerland) and dating back from 7200-5800 years before present (BP). More specifically we investigated genetic variation before, during, and after an anthropogenic perturbation that caused an abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X produced a matrix encompassing 524 exome-derived SNPs. Despite a lower observed heterozygosity was observed during the 6.500-6.200 years BP time slice, genetic composition was nearly identical before and after the perturbation, indicating that re-expansion of the population after the decline was driven by autochthonous specimens. To the best of our knowledge, this is the first time a population genomic study incorporating ancient DNA samples of tree subfossils is conducted at a moderate cost using reproducible exome-reduced complexity.
Data from: An exon-capture system for the entire class Ophiuroidea
Exon-capture studies have typically been restricted to relatively shallow phylogenetic scales due primarily to hybridisation constraints. Here, we present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures ~90% of the 1552 exon target, across all major lineages of the quarter-billion year old extant crown group. Key features of our system are: 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map or align, 2) use of multiple artificial representatives based on ancestral state reconstructions rather than exemplars to improve capture and mapping of the target, 3) mapping reads to a multi-reference alignment, and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences and sample contamination. The resulting data gives a well-resolved tree (currently standing at 417 samples, 275,352 sites, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.
Data from: Incorporating capture heterogeneity in the estimation of autoregressive coefficients of animal population dynamics using capture-recapture data
<p>Population dynamics models combine density-dependence and environmental effects. Ignoring sampling uncertainty might lead to biased estimation of the strength of density-dependence. This is typically addressed using state-space model approaches, which integrate sampling error and population process estimates. Such models seldom include an explicit link between the sampling procedures and the true abundance, which is common in capture-recapture settings. However, many of the models proposed to estimate abundance in the presence of capture heterogeneity lead to incomplete likelihood functions and cannot be straightforwardly included in state-space models.</p> <p>We assessed the importance of estimating sampling error explicitly by taking an intermediate approach between ignoring uncertainty in abundance estimates and fully specified state-space models for density-dependence estimation based on autoregressive processes. First, we estimated individual capture probabilities based on a heterogeneity model, using a conditional multinomial likelihood, followed by a Horvitz-Thompson estimate for abundance. Second, we estimated coefficients of autoregressive models for the log abundance. Inference was performed using the methodology of integrated nested Laplace approximation (INLA). We performed an extensive simulation study to compare our approach with estimates disregarding capture history information, and using R-package VGAM, for different parameter specifications. The methods were then applied to a real dataset of gray-sided voles <em>Myodes rufocanus</em>from Northern Norway.</p> <p>We found that density-dependence estimation was improved when explicitly modelling sampling error in scenarios with low process variances, in which differences in coverage reached up to 8% in estimating the coefficients of the autoregressive processes. In this case, the bias also increased assuming a Poisson distribution in the observational model. For high process variances, the differences between methods were small and it appeared less important to model heterogeneity.</p>
Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements
Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27–43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 106 bp (Arachnothera, modern samples) to 1.98 × 106 bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.
Figure 8. Adults captured per hour averaged for the four central weeks, 22 March–18 April, from 1994–2017. Data were not available for 1997, 1999–2001 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 8. Adults captured per hour averaged for the four central weeks, 22 March–18 April, from 1994–2017. Data were not available for 1997, 1999–2001, and 2003–2004.
Capturing the dynamics of small populations: A retrospective assessment using long-term data for an island reintroduction
<p>1. The art of population modelling is to incorporate factors essential for capturing a population's dynamics while otherwise keeping the model as simple as possible. However, it is unclear how optimal model complexity should be assessed, and whether this optimal complexity has been affected by recent advances in modelling methodology. This issue is particularly relevant to small populations because they are subject to complex dynamics but inferences about those dynamics are often constrained by small sample sizes.</p> <p>2. We fitted Bayesian hierarchical models to long-term data on vital rates (survival and reproduction) for the toutouwai (Petroica longipes) population reintroduced to Tiritiri Matangi, a 220-ha New Zealand island, and quantified the performance of those models in terms of their likelihood of replicating the observed population dynamics. These dynamics consisted of overall growth from 33 (± 0.3) to 160 (± 6) birds from 1992–2018, including recoveries following five harvest events for further reintroductions to other sites.</p> <p>3. We initially included all factors found to affect vital rates, which included inbreeding, post-release effects, density-dependence, sex, age and random annual variation, then progressively removed these factors. We also compared performance of models where data analysis and simulations were done simultaneously to those produced with the traditional two-step approach, where vital rates are estimated first then fed into a separate simulation model. Parametric uncertainty and demographic stochasticity were incorporated in all projections.</p> <p>4. The essential factors for replicating the population's dynamics were density-dependence in juvenile survival and post-release effects, i.e. initial depression of survival and reproduction in translocated birds. Inclusion of other factors reduced the precision of projections, and therefore the likelihood of matching observed dynamics. However, this reduction was modest when the modelling was done in an integrated framework. In contrast, projections were much less precise when done with a two-step modelling approach, and the cost of additional parameters was much higher under the two-step approach.</p> <p>5. These results suggest that minimization of complexity may be less important than accounting for covariances in parameter estimates, which is facilitated by integrating data analysis and population projections using Bayesian methods. 13-Aug-2021 --</p>
Capture history data for: Sub-seasonal correlation between growth and survival in three sympatric aquatic ectotherms
<p><span>Animals experience seasonally changing conditions in temperate regions, thus population vital rates change seasonally. However, knowledge is lacking on patterns of seasonal correlation between growth and survival in sympatric ectotherms, and this knowledge gap limits our understanding of environmental change impacts on animal populations and communities. Here, we investigated sub-seasonal (2-month intervals) correlation between growth and survival in three stream fishes (bluehead chub <em>Nocomis leptocephalus</em>, creek chub <em>Semotilus atromaculatus</em>, and mottled sculpin <em>Cottus bairdii</em>) in South Carolina, USA, via a mark-recapture survey over 28 months. </span></p> <p><span><span>We found that </span></span><span><span><span>the patterns of temporal correlation between growth and survival differed among the sympatric species. G</span></span></span><span><span>rowth increased and survival decreased with water temperature in two eurythermal species (bluehead chub and creek chub), resulting in a negative correlation between growth and survival. Growth peaked in sub-seasons with an intermediate water temperature range in a third stenothermal species (mottled sculpin), while survival decreased with water temperature for this species too. Consequently, there was no significant negative or positive correlation between sub-seasonal growth and survival in the stenothermal species. </span></span></p> <p><span><span><span>Negative correlation among population vital rates stabilizes population size over time and buffers animal populations from environmental change because the vital rates are not affected simultaneously in the same direction, indicating some degree of resiliency in the face of climate changes in the two eurythermal species. However, such a demographic mechanism of resiliency could be maintained so long as climate warming does not exceed optimal growth temperature, above which a negative correlation between growth and survival may no longer be maintained.</span></span></span></p>
Trap success data for capturing hemlock woolly adelgid
<p><span>Hemlock woolly adelgid (HWA), <em>Adelges</em> <em>tsugae</em> Annand, threatens hemlock forests throughout eastern North America. Management efforts focus on early detection of HWA to ensure rapid management responses to control and stop the spread of this pest. This study's goal was to identify an affordable, efficient trap to aid with airborne environmental DNA (eDNA) sampling approaches as an early monitoring tool for HWA. We initially compared HWA detection success between a standard sticky trap, commonly used for HWA monitoring, and trap designs potentially compatible with eDNA protocols (i.e., passive trap, funnel trap, and motorized trap). Passive, funnel, and motorized traps' estimated capture success probabilities compared to sticky traps were 0.87, 0.8, and 0.4, respectively. A secondary evaluation of a modified version of the motorized trap further assessed trap performance and determined the number of traps needed in a set area to efficiently detect HWA. By modifying the original motorized trap design, its estimated capture success probability increased to 0.67 compared to a sticky trap. Overall, the cumulative capture success over the 16-week sampling period for the motorized trap was 94% and 99% for the sticky trap. The number of traps did impact capture success, and trap elevation and distance to infested hemlocks influenced the number of adelgids captured per trap. As environmental DNA (eDNA)-based monitoring approaches continue to become incorporated into invasive species surveying, further refinement with these types of traps can be useful as an additional tool in the manager's toolbox.</span></p>
Raw data for: Sublytic gasdermin-D pores captured in atomistic molecular simulations
<p>This archive contains data and code related to "Sublytic gasdermin-D pores captured in atomistic molecular simulations" by Schaefer & Hummer. Included are molecular dynamics parameter files, initial structures after system equilibration, final structures after production, subsampled production trajectories, and python scripts used for analysis. </p> <p>Publication doi: https://doi.org/10.7554/eLife.81432<br> <br> Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de</p>
HortiMED Data Capture System
<p>This video shows the functionalities of HortiMED Data Capture System (DCS). HortiMED DCS is in charge of collecting the data from the different demonstrative greenhouses, including both "manually collected data" and data from IoT sensors. A software platform has been deployed on the cloud to digitize the acquisition of “manually collected data” and relevant communication protocols have been implemeted to allow for the provision of near real time data between HortiMED greenhouses (IoT sensors) and the HortiMED cloud platform.</p>
Data for: Hunting behavior of a solitary sailfish Istiophorus platypterus and estimated energy gain after prey capture
<p>Foraging behavior and interaction with prey is an integral component of the niche of predators but is inherently difficult to observe for highly mobile animals in the marine environment. Billfish have been described as 'energy speculators', expending a large amount of energy foraging, expecting to offset high costs with periodic high energetic gain. Surface-based group feeding of sailfish, <em>Istiophorus</em> <em>platypterus</em>, is commonly observed, yet sailfish are believed to be solitary roaming predators with high metabolic requirements, suggesting that individual foraging also represents a major component of predator-prey interactions. Here, we use biologging data and video to examine daily activity levels and foraging behavior, estimate metabolic costs, and document a solitary predation event. We estimate a median active metabolic rate of 218.9 ± 70.5 mgO<sub>2</sub> kg<sup>-1</sup> h<sup>-1</sup> which increased to 518.8 ± 586.3 mgO<sub>2</sub> kg<sup>-1</sup> h<sup>-1</sup> during prey pursuit. Assuming a successful predation, we estimate a daily net energy gain of 2.4 MJ (5.1 MJ acquired, 2.7 MJ expended), supporting the energy speculator model. While group hunting may be a common activity used by sailfish to acquire energy, our calculations indicate that opportunistic individual foraging events offer a net energy return that contributes to the fitness of these highly mobile predators. </p>
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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
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.