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9,302 results for “DETECT”
Data from: Interspecies interference and monitoring duration affect detection rates in chew cards
Pest monitoring methods should provide unbiased accurate estimates of pest densities and locations, while also minimizing time-in-field and costs. Recent pest mammal monitoring studies have found that chew cards are more effective than conventional mammal monitoring methods, but little experimental work has been done to determine optimal experimental duration or quantify the risks of saturation by one species biasing detections of other species. Here, we used chew cards in three sites within Awarua wetland (Southland, New Zealand) to investigate the optimal amount of time required to detect targeted pest species (rats, possums and mice), and to examine the potential of rats and possums to bias detection rates of other species. We found depressed detections of possums and rats where a contraspecific had been detected on a card, which is consistent with previous studies of a similar duration on interspecies interference. This experiment is the first to analyse the rates at which species detections accrue over the course of a survey, and we found rat detections lagged behind possums for the first four nights. We modelled the effect of survey duration and relative rat abundance on the likelihood of further possum detections. Duration and rat abundance interacted, meaning there are trade-offs to be considered with regard to duration: shorter durations may avoid the risk of saturation in areas of high pest density, but risk not sampling sparse or neophobic populations. Our data suggest that chew cards remain one of the most sensitive pest monitoring tools for rats and possums, compared to conventional methods such as tracking tunnels and wax tags. In areas of moderate pest densities, we suggest that a duration of five nights is optimal for detecting pests. However, in areas of high pest density the sensitivity of chew cards may render them unsuitable because of saturation and interspecies interference effects.
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: Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears
Background <p>Detecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community‐level analyses due to their use of species‐specific (presence/absence) 'barcodes'. Metabarcoding methods provide information on entire communities based on sequencing of all taxon‐specific barcodes within an eDNA sample.</p> Aims <p>Evaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience.</p> Materials and Methods <p>In 2016, eight limnologically diverse lakes (surface area range: 13 – 1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish‐specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List.</p> Results <p>Analysis of species accumulation curves indicated multi‐locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 – 62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples.</p> Discussion <p>Results reported here are, in part, driven by the lack of species‐selectivity during eDNA sampling events. Given the efficacy of eDNA assays, we suggest multi‐locus eDNA metabarcoding assays be implemented in early detection efforts.</p>
Data from: Effects of distance on detectability of Arctic waterfowl using double-observer sampling during helicopter surveys
Aerial survey is an important, widely employed approach for estimating free‐ranging wildlife over large or inaccessible study areas. We studied how a distance covariate influenced probability of double‐observer detections for birds counted during a helicopter survey in Canada's central Arctic. Two observers, one behind the other but visually obscured from each other, counted birds in an incompletely shared field of view to a distance of 200 m. Each observer assigned detections to one of five 40‐m distance bins, guided by semi‐transparent marks on aircraft windows. Detections were recorded with distance bin, taxonomic group, wing‐flapping behavior, and group size. We compared two general model‐based estimation approaches pertinent to sampling wildlife under such situations. One was based on double‐observer methods without distance information, that provide sampling analogous to that required for mark–recapture (MR) estimation of detection probability, urn:x-wiley:20457758:media:ece34824:ece34824-math-0001, and group abundance, urn:x-wiley:20457758:media:ece34824:ece34824-math-0002, along a fixed‐width strip transect. The other method incorporated double‐observer MR with a categorical distance covariate (MRD). A priori, we were concerned that estimators from MR models were compromised by heterogeneity in urn:x-wiley:20457758:media:ece34824:ece34824-math-0003 due to un‐modeled distance information; that is, more distant birds are less likely to be detected by both observers, with the predicted effect that urn:x-wiley:20457758:media:ece34824:ece34824-math-0004 would be biased high, and urn:x-wiley:20457758:media:ece34824:ece34824-math-0005 biased low. We found that, despite increased complexity, MRD models (ΔAICc range: 0–16) fit data far better than MR models (ΔAICc range: 204–258). However, contrary to expectation, the more naïve MR estimators of urn:x-wiley:20457758:media:ece34824:ece34824-math-0006 were biased low in all cases, but only by 2%–5% in most cases. We suspect that this apparently anomalous finding was the result of specific limitations to, and trade‐offs in, visibility by observers on the survey platform used. While MR models provided acceptable point estimates of group abundance, their far higher stranded errors (0%–40%) compared to MRD estimates would compromise ability to detect temporal or spatial differences in abundance. Given improved precision of MRD models relative to MR models, and the possibility of bias when using MR methods from other survey platforms, we recommend avian ecologists use MRD protocols and estimation procedures when surveying Arctic bird populations.
Data from: Detection of outlier loci and their utility for fisheries management
Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific ("outlier") effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide ("neutral") effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments, however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier-based approach to fisheries management by screening >11,000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype-level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Results were robust among-sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.
Data from: Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis
Terrestrial predators on marine shores benefit from the inflow of organisms and matter from the marine ecosystem, often causing very high predator densities and indirectly affecting the abundance of other prey species on shores. This indirect effect may be particularly strong if predators shift diets between seasons. We therefore quantified the seasonal variation in diet of two wolf spider species that dominate the shoreline predator community, using molecular gut content analyses with general primers to detect the full prey range. Across the season, spider diets changed, with predominantly terrestrial prey from May until July and predominantly marine prey (mainly chironomids) from August until October. This pattern coincided with a change in the spider age and size structure, and prey abundance data and resource selection analyses suggest that the higher consumption of chironomids during autumn is due to an ontogenetic diet shift rather than to variation in prey abundance. The analyses suggested that small dipterans with a weak flight capacity, such as Chironomidae, Sphaeroceridae, Scatopsidae and Ephydridae, were overrepresented in the gut of small juvenile spiders during autumn, whereas larger, more robust prey, such as Lepidoptera, Anthomyidae and Dolichopodidae, were overrepresented in the diet of adult spiders during spring. The effect of this inflow may be that the survival and growth of juvenile spiders is higher in areas with high chironomid abundances, leading to higher densities of adult spiders and higher predation rates on the terrestrial prey next spring.
Data from: Detection of airborne genetically modified maize pollen by real-time PCR
The cultivation of genetically modified (GM) crops has raised in the European Union and other parts of the world numerous concerns about their environmental and economic impact. Especially outcrossing of genetically modified organisms (GMO) was from the beginning a critical issue as airborne pollen has been considered an important way of GMO dispersal. Here, we investigate the use of airborne pollen sampling combined with microscopic analysis and molecular PCR analysis as an approach to monitor GM maize cultivations in a specific area. Field trial experiments in the European Union and South America demonstrated the applicability of the approach under different climate conditions, in rural and semi-urban environment, even at very low levels of airborne pollen. The study documents in detail the sampling of GM pollen, sample DNA extraction and real-time PCR analysis. Our results suggest that this ''GM pollen monitoring by bioaerosol sampling and PCR screening" approach might represent an aid in managing the co-cultivation of GM and non-GM crops, especially in the surveillance of GM-free areas, centres of origin, and natural reserves.
Data from: Escaping blood-fed malaria mosquitoes minimize tactile detection without compromising on take-off speed
To escape after taking a blood meal, a mosquito must exert forces sufficiently high to take off when carrying a load roughly equal to its body weight, while simultaneously avoiding detection by minimizing tactile signals exerted on the host's skin. We studied this trade-off between escape speed and stealth in malaria mosquitoes, Anopheles coluzzii, using 3D motion analysis of high-speed stereoscopic videos of mosquito take-offs and aerodynamic modelling. We found that during the push-off phase, mosquitoes enhanced take-off speed by using aerodynamic forces generated by the beating wings in addition to leg-based push-off forces, whereby wing forces contributed 61% to the total push-off force. Exchanging leg-derived push-off forces for wing-derived aerodynamic forces allows the animal to reduce peak force production on the host's skin. By slowly extending their long legs throughout the push-off, mosquitoes spread push-off forces over a longer time window than insects with short legs, thereby further reducing peak leg forces. Using this specialized take-off behavior, mosquitoes are capable of reaching take-off speeds comparable to those of similarly-sized fruit flies, but with weight-normalized peak leg forces that were only 27% of those of the fruit flies. By limiting peak leg forces, mosquitoes possibly reduce the chance of being detected by the host. The resulting combination of high take-off speed and low tactile signals on the host might help increase the mosquito's success to escape from blood-hosts, which consequently also increases the chance that they transmit vector-borne diseases, such as malaria, to future hosts.
Twisting and tilting of a mechanosensitive molecular probe detects order in membranes
<p>Original data and procedures underlying Figures S11 and S12.</p> <p>Data can be viewed using freely distributed Origin Viewer (https://www.originlab.com/viewer/)</p>
UCE phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders
<p>The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus <i>Batrachuperus</i>, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six <i>Batrachuperus</i> species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern <i>B. karlschmidti</i> population has experienced admixture with <i>B. tibetanus</i>. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of <i>B. pinchonii</i> (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of <i>B. daochengensis</i> and <i>B. yenyuanensis</i> and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.</p>
FIGURE 4 in MIDTAL (Microarrays for the Detection of Toxic Algae)
FIGURE 4: Average RNA amounts (pg/cell) over a three-day period for three different strains of Prymnesium parvum N. Carter (1937: 40) cultures grown under three levels of four environmental stressors: light (top left), nutrients (top right), salinity (bottom left) and temperature (bottom right). In each treatment, the optimal value for the growth of P. parvum is shown in red and the stress conditions tested are in blue and green.
FIGURE 6 in MIDTAL (Microarrays for the Detection of Toxic Algae)
FIGURE 6: Scan image of a portion of one of the grids (left panel, see also the lower panel in Fig. 2) in the first generation MIDTAL microarray after hybridization with Cy5-labelled RNA extracted from a field sample collected in the Skagerrak coast (Gullmarnfjord, Sweden) in the beginning of August 2009. An analysis of the hybridisation was performed with the PhyloChip program, and a portion of this analysis is presented in the histogram (right panel). Each cluster of four dots in the left panel represents the same probe spotted four times as shown in Fig. 2 lower panel. Fluorescence values in the right panel are arranged from lowest to highest signal strength. The red line across the intensity values marks the threshold over which a positive signal is recorded. Stars indicate a significant signal for species level probe of two toxic species Karenia brevis (Davis) G. Hansen et Moestrup in Daugbjerg et al. (2000: 308) (KB5) and Pseudo-nitzschia multistriata (Takano) Takano (1995: 73) (mD3) present in the sample, seen both with the microarray and traditional counts. Other high signals include the probes for the positive control Dunaliella and other higher group level probes, such as EUK1209, a probe for all eukaryotes and HETERO01, a probe for all heterokonts. Error bars represent duplicate hybridisation of the same field sample (two grids hybridised at the same time and signals averaged).
FIGURE 3 in MIDTAL (Microarrays for the Detection of Toxic Algae)
FIGURE 3: Hybridization of fragmented RNA to 16 probes (x axis) on the microarray with increasing hybridisation temperature as compared to non fragmented RNA hybridised at 37°C. Probes with low signals are enhanced by fragmentation. The signal to noise ratio values above the background cut-off of 1 are shown.
FIGURE 5 in MIDTAL (Microarrays for the Detection of Toxic Algae)
FIGURE 5: Comparison of RNA yields extracted from three filters of field material collected at eight stations in the Irish Sea at Galway, Ireland by PTR 5 NUIG with (av spiked = red) and without (av crudeblue = blue) the addition of cells of Dunaliella as the internal control prior to the extraction.
FIGURE 1 in MIDTAL (Microarrays for the Detection of Toxic Algae)
FIGURE 1: Scheme detailing the stress experiments performed on three strains of each species to obtain RNA for the calibration experiments using F/2 seawater media. N = nitrogen and P = phosphate.
FIGURE 2 in MIDTAL (Microarrays for the Detection of Toxic Algae)
FIGURE 2: Spotting scheme for the first generation MIDTAL microarray. In the upper panel the supergrid arrangement on each slide is shown. Each supergrid is composed of four grids. In the lower panel each grid is shown in more detail. Only two of the grids in each supergrid are hybridised in each experiment. Each probe is spotted four times, hence the four colors adjacent to one another. Each box in the cluster of four colors in the grid represents a spot of c. 50 µm in diameter where a given probe is immobilized. This generation of the microarray has 960 spots, covering 112 probes for toxic algal species and higher taxon levels, and various positive and negative control probes.
Data from: Genomics detects population structure within and between ocean basins in a circumpolar seabird: the white-chinned petrel
<p>The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (<i>Procellaria aequinoctialis</i>) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and 1st domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.</p>
Dataset for Crack Detection in Images of Masonry Using CNNs
<p>We trained a convolutional neural network (CNN) on images of brick walls built in a laboratory environment and test its ability to detect cracks in images of brick-and-mortar structures both in the laboratory and on real-world images taken from the internet. We also compared the performance of the CNN to a variety of simple classifiers operating on handcrafted features. This is the dataset used in that work.</p>
Probing DNA - transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices
<p>Readme.txt, 16.07.2021<br> Fontana et al.<br> “Probing DNA - transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices”</p> <p>pre-print: https://doi.org/10.1101/2021.05.12.443786 (BioRxiv)</p> <p>The repository contains the raw data ("*.tif") files, data from subsequent analysis steps performed in Matlab ("*.mat") and obtained histograms.</p> <p>For further information, please contact<br> dr. Johannes Hohlbein @ Wageningen University & Research<br> (johannes.hohlbein@wur.nl)</p>
Data from: Molecular detection of invertebrate prey in vertebrate diets: trophic ecology of Caribbean island lizards
Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for a common Caribbean lizard that has been intensively studied in the context of small island food webs: Anolis sagrei (a semi-arboreal 'trunk-ground' anole ecomorph). Novel PCR primers were identified in silico and tested in vitro. Illumina sequencing successfully characterized the arthropod component of 168 faecal DNA samples collected during three field trips spanning 12 months, revealing 217 molecular operational taxonomic units (mOTUs) from at least nine arthropod orders (including Araneae, Blattodea, Coleoptera, Hemiptera, Hymenoptera, Isoptera, Lepidoptera and Orthoptera). Three mOTUs (one beetle, one cockroach and one ant) were particularly frequent, occurring in ≥50% of samples, but the majority of mOTUs were infrequent (180, or 83%, occurred in ≤5% of samples). Species accumulation curves showed that dietary richness and composition were similar between size-dimorphic sexes; however, female lizards had greater per-sample dietary richness than males. Overall diet composition (but not richness) was significantly different across seasons, and we found more pronounced interindividual variation in December than in May. These methods will be generally useful in characterizing the diets of diverse insectivorous vertebrates.
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Allen Brain Atlas
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