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419 results for “capture data”
Data from: Applying the multistate capture-recapture robust design to characterize metapopulation structure
1. Population structure must be considered when developing mark-recapture (MR) study designs as the sampling of individuals from multiple populations (or subpopulations) may increase heterogeneity in individual capture probability. Conversely, the use of an appropriate MR study design which accommodates heterogeneity associated with capture-occasion varying covariates due to animals moving between 'states' (i.e. geographic sites) can provide insight into how animals are distributed in a particular environment and the status and connectivity of subpopulations. 2. The Multistate Closed Robust Design was chosen to investigate: 1) the demographic parameters of Indo-Pacific bottlenose dolphins (Tursiops aduncus) subpopulations in coastal and estuarine waters of Perth, Western Australia; and 2) how they are related to each other in a metapopulation. Using four years of year-round photo-identification surveys across three geographic sites, we accounted for heterogeneity of capture probability based on how individuals distributed themselves across geographic sites and characterized the status of subpopulations based on their abundance, survival and interconnection. 3. MSCRD models highlighted high heterogeneity in capture probabilities and demographic parameters between sites. High capture probabilities, high survival and constant abundances described a subpopulation with high fidelity in an estuary. In contrast, low captures, permanent and temporary emigration and fluctuating abundances suggested transient use and low fidelity in an open coastline site. 4. Estimates of transition probabilities also varied between sites, with estuarine dolphins visiting sheltered coastal embayments more regularly than coastal dolphins visited the estuary, highlighting some dynamics within the metapopulation. 6. Synthesis and applications. To date, bottlenose dolphin studies using mark-recapture approach have focussed on investigating single subpopulations. Here, in a heterogeneous coastal-estuarine environment, we demonstrated that spatially structured bottlenose dolphin subpopulations contained distinct suites of individuals and differed in size, demographics and connectivity. Such insights into the dynamics of a metapopulation can assist in local-scale species conservation. The MSCRD approach is applicable to species/populations consisting of recognizable individuals and is particularly useful for characterizing wildlife subpopulations that vary in their vulnerability to human activities, climate change or invasive species.
Data from: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis. - See more at: http://elifesciences.org/content/3/e03318#sthash.Yx6nSY4J.dpuf
Data from: Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data
The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.
Data from: Invasion of two tick-borne diseases across New England: harnessing human surveillance data to capture underlying ecological invasion processes
Modelling the spatial spread of vector-borne zoonotic pathogens maintained in enzootic transmission cycles remains a major challenge. The best available spatio-temporal data on pathogen spread often take the form of human disease surveillance data. By applying a classic ecological approach—occupancy modelling—to an epidemiological question of disease spread, we used surveillance data to examine the latent ecological invasion of tick-borne pathogens. Over the last half-century, previously undescribed tick-borne pathogens including the agents of Lyme disease and human babesiosis have rapidly spread across the northeast United States. Despite their epidemiological importance, the mechanisms of tick-borne pathogen invasion and drivers underlying the distinct invasion trajectories of the co-vectored pathogens remain unresolved. Our approach allowed us to estimate the unobserved ecological processes underlying pathogen spread while accounting for imperfect detection of human cases. Our model predicts that tick-borne diseases spread in a diffusion-like manner with occasional long-distance dispersal and that babesiosis spread exhibits strong dependence on Lyme disease.
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.
Data from: The effect of trap colour and trap-flower distance on prey and pollinator capture in carnivorous Drosera species
1. The functional features of carnivorous plants' traps have been mostly interpreted as adaptations to capture prey. Carnivorous plants that feed on insects, however, run the risk that increasing trapping effectiveness might in turn reduce reproductive success through capture of pollinators. Such a pollinator–prey conflict might play an important role in the evolution of trap features. In carnivorous plants with sticky leaves (e.g. Drosera, Pinguicula), both spatial distance between traps and flowers and their visual signals (e.g. colour, display size) likely play a role in attracting prey but it has also been suggested that they affect the risk of potential pollinators landing on a trap. It has been reported, for example, that red pigmentation in carnivorous plants may lure insect prey to traps. This idea remains controversial, however, because colour vision of most insects does not extend very far into the red part of the spectrum. 2. We tested an alternative hypothesis, namely that red pigmentation of the trapping leaves may reduce the risk of a pollinator–prey conflict. Experiments were conducted in a natural habitat of Drosera arcturi and D. spatulata in the Southern Alps of New Zealand. Using sticky model traps similar in shape to Drosera leaf traps and flowers, we investigated the effect of colour (green vs. red vs. white) and flower-trap distance (flower stalk length and leaf arrangement, that is upright as in D. arcturi vs. flat ground rosette as in D. spatulata) on composition and abundance of insects landing and being trapped. 3. Flower-trap distance had no significant effect on the risk of pollinators being trapped but model flowers higher above the ground received more pollinator landings. Across all model traps, the number of trapped potential pollinators was significantly lower in traps with red leaves compared to green ones. 4. The results suggest that the typical red pigmentation of the trapping leaves in Drosera may be a way to protect pollinators from being attracted and captured. However, our data also suggest that pollinator protection via red traps may come with a trade-off since total prey capture was also significantly reduced.
Capturing Periodic I/O Using Frequency Techniques [Data Set]
<div>This file contains the data set from the paper: "Capturing Periodic I/O Using Frequency Techniques," which was accepted at the IPDPS 2024. <div>The Instructions are provided in the <a href="https://github.com/tuda-parallel/FTIO/tree/main/artifacts/ipdps24">FTIO GitHub</a>: https://github.com/tuda-parallel/FTIO/tree/main/artifacts/ipdps24</div> </div> <div> </div> <div>After extracting data.zip, the folder named <em>data</em> has the following structure:</div> <div> <pre>data ├── application_traces │ ├── HACC-IO │ ├── IOR │ ├── LAMMPS │ ├── NEK5000 │ └── README.md ├── exps_with_synthetic_traces ├── iosets_ftio_experiments └── README.md</pre> </div> <div><br>The folder iosets_ftio_experiments and exps_with_synthetic_traces in data.zip are snapshots from the repositories: <ul> <li><a href="https://gitlab.inria.fr/hpc_io/iosets-ftio-experiments">https://gitlab.inria.fr/hpc_io/iosets-ftio-experiments</a></li> <li><a href="https://gitlab.inria.fr/hpc_io/ftio_paper_exps_with_synthetic_traces">https://gitlab.inria.fr/hpc_io/ftio_paper_exps_with_synthetic_traces</a></li> </ul> </div>
Fig. 3 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 3. Likelihood phylogeny of concatenated supermatrix of Pogonolepis and outgroups. Numbers above branches indicate UltraFast Bootstrap values, gene Concordance Factors, and site Concordance Factors. The dashed branch was shortened for the figure. Western Australian specimens of P. muelleriana are marked with (WA), all others are from eastern states. A and B indicate informally named clades inside P. stricta.
Fig. 2 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 2. Geographic spread of the specimens of Pogonolepis at CANB sampled for molecular analysis (large, pale circles) and ranges of species according to the Australasian Virtual Herbarium (dots; see https://doi.org/10.26197/ala.6556e234- 7160-49de-bf63-5123af624e94, accessed 31 May 2022). Red: P. muelleriana; blue: P. stricta. Note that specimens of P. muel-leriana geocoded in Canberra and Hobart were likely cultivated.
Fig. 1 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 1. (a) Pogonolepis muelleriana, New South Wales, SchmidtLebuhn 1633 (CANB); (b) Pogonolepis stricta, Western Australia, Schmidt-Lebuhn 1474 (CANB).
Solid-state NMR data for the publication "Bonding of Polyethylenimine in Covalent Organic Frameworks for CO2 Capture from Air"
<p>This upload contains the solid-state NMR of COF-709 series obtained by using Bruker Avance IV NEO 400 MHz NMR instrument. The instrument used in this work was supported by the National Science Foundation under Grant No. 2018784. Per NSF requirements, the data will be publicly available at the time of publication. This dataset can be opened and processed by using MestreNova NMR or similar softwares.</p>
Popek, R., Roy, A., Mandal, M., et al. (2024) Enhancing Urban Sustainability: How Spatial and Height Var-iability of Roadside Plants Improves Pollution Capture for Greener Cities - DATA
Open the record for dataset details and reuse information.
LOPC (laser optical plankton counter) data captured during PolarFront 2024-01 cruise
<p>See the Cruise Report (Daase 2024) for details.</p> <p>Daase, M. (2024). PolarFront January 2024 Cruise Report. Zenodo. <a href="https://doi.org/10.5281/zenodo.10623810" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10623810</a></p>
Additional data, Table 2. — Forewing and proboscis lengths (cm) in Xanthopan praedicta stat. nov. – first 35 lines: MNHN specimens. – lines 36 (Ranomena) to 43 (Lakato): RCPB. – lines 44 (Ranomafana) to 47 (Amber Mountain): CJHL. – line 55 (female from Ranomafana) and last five lines: NHMUK. – last 30 lines: individuals captured and released by DCL, except for the six NHMUK specimens. in A new taxonomic status for Darwin's "predicted" pollinator: Xanthopan praedicta stat. nov. (Lepidoptera Sphingidae Sphinginae)
Additional data, Table 2. — Forewing and proboscis lengths (cm) in Xanthopan praedicta stat. nov. – first 35 lines: MNHN specimens. – lines 36 (Ranomena) to 43 (Lakato): RCPB. – lines 44 (Ranomafana) to 47 (Amber Mountain): CJHL. – line 55 (female from Ranomafana) and last five lines: NHMUK. – last 30 lines: individuals captured and released by DCL, except for the six NHMUK specimens.
Insect cuticular hydrocarbon composition influences their interaction with spider capture threads - Raw data
<p>Raw data of the manuscript entitled "Insect cuticular hydrocarbon composition influences their interaction with spider capture threads", published in the Journal of Experimental Biology</p>
Subspecies and Distribution. H. uw. underwoodi Thomas, 1903 — disjunct from 8S Mexico (Veracruz) to E Guatemala, S Belize, and N & W Honduras, and from SE Nicaragua to W Panama. H. u. minor C. J. Phillips & J. K. Jones, 1971 — Pacific slope in Mexico, from Nayarit and Jalisco to S Oaxaca. A.p. discontinuous distribution with gap in Nicaragua might just reflect lack of data because Underwood's Long-tongued bat always occursat rather low densities and is therefore not very often captured. in Phyllostomidae
Subspecies and Distribution. H. uw. underwoodi Thomas, 1903 — disjunct from 8S Mexico (Veracruz) to E Guatemala, S Belize, and N & W Honduras, and from SE Nicaragua to W Panama. H. u. minor C. J. Phillips & J. K. Jones, 1971 — Pacific slope in Mexico, from Nayarit and Jalisco to S Oaxaca. A.p. discontinuous distribution with gap in Nicaragua might just reflect lack of data because Underwood's Long-tongued bat always occursat rather low densities and is therefore not very often captured.
Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture
The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for ~3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic dataset for cetaceans, spanning 6,527,596 aligned base pairs and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among ocean dolphins, especially the problematic subfamily Delphininae, which includes the common and bottlenose dolphins. We performed Bayesian estimation of species divergence times using MCMCtree, integrating recently described fossils as calibration points (e.g., Mystacodon selenensis) that have not been used before. Integration of new fossil dates in the context of autocorrelated rates indicate that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene.
Animation for "Capturing synoptic-scale variations in surface aerosol pollution using deep learning with meteorological data"
<p>Animation for "Capturing synoptic-scale variations in surface aerosol pollution using deep learning with meteorological data"</p>
Data from: Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks
<p>River otters (Lontra canadensis) were extirpated from New Mexico by the 1950s. A limited reintroduction occurred during 2008–2010 in which 33 otters sourced from Washington (WA) were translocated to the Upper Rio Grande Basin (URG) of New Mexico. We conducted a noninvasive genetic capture-recapture survey during the winter of 2018 by collecting fecal DNA samples from river otter scats found at latrines in the URG dendritic network of perennial waterways. Our objectives were to: 1) estimate genetic diversity and effective population size; 2) genetic divergence from the WA source population and potential connectivity with regionally proximal populations; 3) spatially explicit population density and size; and 4) population growth rate since the founder event. Between February and April 2018, we collected 1,184 fecal DNA samples from 622 individual scats at 20 latrines; genotyping was attempted at 10 otter-specific microsatellite loci for a subsample of 543 samples. A bottlenecking founder effect was strongly supported, which, combined with genetic drift, reduced genetic diversity and effective population size by 20–26% and 106–170%, respectively, compared with the WA source population. Estimated population density from spatial capture-recapture models was 0.23–0.28 otter/km of waterway, or 1 otter/3.57–4.35 km of waterway, corresponding to a total population size of 83–100 otters across 359 km of the perennial dendritic network from La Mesilla, New Mexico to Alamosa National Wildlife Refuge, Colorado. Estimated average annual population growth rate since the founder event was 1.12–1.15/year. Despite successful population establishment, the URG river otter population remains small, is genetically degraded, and does not yet meet the criteria for long-term reintroduction success. Projections suggested that the population could reach the recommended minimum viable population size of ≥400 otters by the years 2030–2033, though sufficient habitat may not exist in the URG Basin to support that many otters. </p>
(DATA) Exploring the potential of boron-nitride nanobelts in environmental applications: greenhouse gases capture
<ul> <li>Input structures.</li> <li>Scrip to run all the calculations.</li> <li>Output files from several calculations.</li> </ul>
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