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GeoVectors-Africa-tags (v1.0)
<p><strong>Description</strong></p> <p>The GeoVectors corpus is a comprehensive large-scale linked open corpus of OpenStreetMap (https://www.openstreetmap.org/) entity embeddings that provides latent representations of over 980 million entities. The GeoVectors capture the semantic and geographic similarities of OpenStreetMap entities and make them directly accessible to machine learning applications. The "-tags" datasets provide embeddings that capture the semantic similarities of OpenStreetMap entities. The "-location" datasets provide the geographic similarities.</p> <p><strong>Contents</strong></p> <p>This dataset was derived from an OpenStreetMap snapshot that was taken on November 10, 2020 (© OpenStreetMap contributors).</p> <p>We provide the GeoVectors in region-specific subsets. This subset contains tag-embeddings for the region "Africa" including the following countries:</p> <ul> <li>Algeria</li> <li>Angola</li> <li>Benin</li> <li>Botswana</li> <li>Burkina-Faso</li> <li>Burundi</li> <li>Cameroon</li> <li>Canary-Islands</li> <li>Cape-Verde</li> <li>Central-African-Republic</li> <li>Chad</li> <li>Comores</li> <li>Congo-Brazzaville</li> <li>Congo-Democratic-Republic</li> <li>Djibouti</li> <li>Egypt</li> <li>Equatorial-Guinea</li> <li>Eritrea</li> <li>Ethiopia</li> <li>Gabon</li> <li>Ghana</li> <li>Guinea</li> <li>Guinea-Bissau</li> <li>Ivory-Coast</li> <li>Kenya</li> <li>Lesotho</li> <li>Liberia</li> <li>Libya</li> <li>Madagascar</li> <li>Malawi</li> <li>Mali</li> <li>Mauritania</li> <li>Mauritius</li> <li>Morocco</li> <li>Mozambique</li> <li>Namibia</li> <li>Niger</li> <li>Nigeria</li> <li>Rwanda</li> <li>Saint-Helena-Ascension-and-Tristan-Da-Cunha</li> <li>Sao-Tome-and-Principe</li> <li>Senegal-and-Gambia</li> <li>Seychelles</li> <li>Sierra-Leone</li> <li>Somalia</li> <li>South-Africa</li> <li>South-Sudan</li> <li>Sudan</li> <li>Swaziland</li> <li>Tanzania</li> <li>Togo</li> <li>Tunisia</li> <li>Uganda</li> <li>Zambia</li> <li>Zimbabwe</li> </ul> <p><strong>File format</strong></p> <p>The embeddings are provided in the tab-separated values (tsv) format. Each row contains the embedding of a single OpenStreetMap entity. The first column contains the OpenStreetMap type and the second column contains the OpenStreetMap id of the respective entity. The type can either be node (n), way (w), or relation (r). The remaining columns represent the dimensions of the embedding space. (See also header.tsv)</p> <p><strong>Further information:</strong></p> <p>For further information, please visit <a href="http://geovectors.l3s.uni-hannover.de">http://geovectors.l3s.uni-hannover.de</a></p> <p><strong>Funding</strong>:</p> <p>This work was partially funded by DFG, German Research Foundation (“WorldKG", DE 2299/2-1), the Federal Ministry of Education and Research (BMBF), Germany (“Simple-ML", 01IS18054), the Federal Ministry for Economic Affairs and Energy (BMWi), Germany (“d-E-mand", 01ME19009B), and the European Commission (EU H2020, “smashHit", grant-ID 871477).</p>
GeoVectors-US-Other-tags (v1.0)
<p><strong>Description</strong></p> <p>The GeoVectors corpus is a comprehensive large-scale linked open corpus of OpenStreetMap (https://www.openstreetmap.org/) entity embeddings that provides latent representations of over 980 million entities. The GeoVectors capture the semantic and geographic similarities of OpenStreetMap entities and make them directly accessible to machine learning applications. The "-tags" datasets provide embeddings that capture the semantic similarities of OpenStreetMap entities. The "-location" datasets provide the geographic similarities.</p> <p><strong>Contents</strong></p> <p>This dataset was derived from an OpenStreetMap snapshot that was taken on November 10, 2020 (© OpenStreetMap contributors).</p> <p>We provide the GeoVectors in region-specific subsets. This subset contains tag-embeddings for the region "US-Other" including the following countries:</p> <ul> <li>US-Midwest</li> <li>US-Northeast</li> <li>US-Pacific</li> </ul> <p><strong>File format</strong></p> <p>The embeddings are provided in the tab-separated values (tsv) format. Each row contains the embedding of a single OpenStreetMap entity. The first column contains the OpenStreetMap type and the second column contains the OpenStreetMap id of the respective entity. The type can either be node (n), way (w), or relation (r). The remaining columns represent the dimensions of the embedding space. (See also header.tsv)</p> <p><strong>Further information:</strong></p> <p>For further information, please visit <a href="http://geovectors.l3s.uni-hannover.de">http://geovectors.l3s.uni-hannover.de</a></p> <p><strong>Funding</strong>:</p> <p>This work was partially funded by DFG, German Research Foundation (“WorldKG", DE 2299/2-1), the Federal Ministry of Education and Research (BMBF), Germany (“Simple-ML", 01IS18054), the Federal Ministry for Economic Affairs and Energy (BMWi), Germany (“d-E-mand", 01ME19009B), and the European Commission (EU H2020, “smashHit", grant-ID 871477).</p>
GeoVectors-Netherlands-tags (v1.0)
<p><strong>Description</strong></p> <p>The GeoVectors corpus is a comprehensive large-scale linked open corpus of OpenStreetMap (https://www.openstreetmap.org/) entity embeddings that provides latent representations of over 980 million entities. The GeoVectors capture the semantic and geographic similarities of OpenStreetMap entities and make them directly accessible to machine learning applications. The "-tags" datasets provide embeddings that capture the semantic similarities of OpenStreetMap entities. The "-location" datasets provide the geographic similarities.</p> <p><strong>Contents</strong></p> <p>This dataset was derived from an OpenStreetMap snapshot that was taken on November 10, 2020 (© OpenStreetMap contributors).</p> <p>We provide the GeoVectors in region-specific subsets. This subset contains tag-embeddings for the region "Netherlands" including the following countries:</p> <ul> <li>Netherlands</li> </ul> <p><strong>File format</strong></p> <p>The embeddings are provided in the tab-separated values (tsv) format. Each row contains the embedding of a single OpenStreetMap entity. The first column contains the OpenStreetMap type and the second column contains the OpenStreetMap id of the respective entity. The type can either be node (n), way (w), or relation (r). The remaining columns represent the dimensions of the embedding space. (See also header.tsv)</p> <p><strong>Further information:</strong></p> <p>For further information, please visit <a href="http://geovectors.l3s.uni-hannover.de">http://geovectors.l3s.uni-hannover.de</a></p> <p><strong>Funding</strong>:</p> <p>This work was partially funded by DFG, German Research Foundation (“WorldKG", DE 2299/2-1), the Federal Ministry of Education and Research (BMBF), Germany (“Simple-ML", 01IS18054), the Federal Ministry for Economic Affairs and Energy (BMWi), Germany (“d-E-mand", 01ME19009B), and the European Commission (EU H2020, “smashHit", grant-ID 871477).</p>
Data from: Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation
In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals from Atlantic origin including both wild and farmed individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analyzed loci showed deviations from Mendelian segregation after analysis of five full-sib families including ~92 individuals/family. The markers are used to consolidate the turbot genetic map and, since they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) at 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.
Data from: Discrimination of fast click series produced by tagged Risso's dolphins (Grampus griseus) for echolocation or communication
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two types of rapid click-series pulsed sounds, buzzes and burst pulses, were identified as produced by the tagged dolphins and classified using a Gaussian mixture model based on their duration, association with jerk (i.e., rapid change of acceleration), and temporal association with click trains. Buzzes followed regular echolocation clicks and coincided with a strong jerk signal from accelerometers on the tag. They consisted of series averaging 359 ± 210 (mean ± SD) clicks with an increasing repetition rate and relatively low amplitude. Burst pulses consisted of relatively short click series averaging 45 ± 54 clicks with decreasing repetition rate and longer inter-click interval that were less likely to be associated with regular echolocation and the jerk signal. These results suggest that the longer, relatively lower amplitude, jerk-associated buzzes are used in this species to capture prey, mostly during the bottom phase of foraging dives, as seen in other odontocetes. In contrast, the shorter, isolated burst pulses that are generally emitted by the dolphins while at or near the surface are used outside of a direct, known foraging context.
Data from: Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data
The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward-tagged animals in a Brownie tag-recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging-to-harvest survival rates from >20 individuals with radio transmitters combined with 50–100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo, to estimate harvest rates, and data from white-tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known-fate tag-recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior.
Data from: Fine-scale movement responses of free-ranging harbour porpoises to capture, tagging, and short-term noise pulses from a single airgun
Knowledge about the impact of anthropogenic disturbances on the behavioural responses of cetaceans is constrained by lack of data on fine-scale movements of individuals. We equipped five free-ranging harbour porpoises (Phocoena phocoena) with high-resolution location and dive loggers and exposed them to a single 10 in3 underwater airgun producing high-intensity noise pulses (2−3 second intervals) for one minute. All five porpoises responded to capture and tagging with longer, faster and more directed movements as well as with shorter, shallower, less wiggly dives immediately after release, with natural behaviour resumed in ≤24 hours. When we exposed porpoises to airgun pulses at ranges of 420−690 m with noise level estimates of 135−147 dB re 1µPa2s (SEL), one individual displayed rapid and directed movements away from the exposure site and two individuals used shorter and shallower dives compared to natural behaviour immediately after exposure. Noise-induced movement typically lasted for ≤8 hours with an additional 24-hour recovery period until natural behaviour was resumed. The remaining individuals did not show any quantifiable responses to the noise exposure. Changes in natural behaviour following anthropogenic disturbances may reduce feeding opportunities and evaluating potential population-level consequences should be a priority research area.
Data from: Parallel tagged next-generation sequencing on pooled samples – a new approach for population genetics in ecology and conservation
Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches – parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.
Data from: Variation in migration pattern, broodstock origin, and family productivity of coho salmon hatchery populations in British Columbia, Canada derived from parentage-based tagging.
In salmonid parentage-based tagging (PBT) applications, entire hatchery broodstocks are genotyped, and subsequently progeny can be non-lethally sampled and assigned back to their parents using parentage analysis, thus identifying their hatchery of origin and brood year (i.e. age). Inter- and intra-population variability in migration patterns, life history traits, and fishery contributions can be determined from PBT analysis of samples derived from both fisheries and escapements (portion of a salmon population that does not get caught in fisheries and returns to its natal river to spawn). In the current study of southern British Columbia coho salmon (Oncorhynchus kisutch) populations, PBT analysis provided novel information on intra-population heterogeneity among males in the total number of progeny identified in fisheries and escapements, the proportion of progeny sampled from fisheries versus escapement, the proportion of two-year old progeny (jacks) produced, and the within-season return time of progeny. Fishery recoveries of coho salmon revealed heterogeneity in migration patterns among and within populations, with recoveries from north and central coast fisheries distinguishing 'northern migrating' from 'resident' populations. In northern-migrating populations, the mean distance between fishery captures of sibs (brothers and sisters) was significantly less than the mean distance between non-sibs, indicating the possible presence of intra-population genetic heterogeneity for migration pattern. Variation among populations in productivity and within populations in fish catchability indicated that population selection and broodstock management can be implemented to optimize harvest benefits from hatcheries. Application of PBT provided valuable information for assessment and management of hatchery-origin coho salmon in British Columbia.
Data from: A 2.6‐g sound and movement tag for studying the acoustic scene and kinematics of echolocating bats
1. To study sensorimotor behaviour in wild animals, it is necessary to synchronously record the sensory inputs available to the animal, and its movements. To do this, we have developed a biologging device that can record the primary sensory information and the associated movements during foraging and navigating in echolocating bats. 2. This 2.6 -gram tag records the sonar calls and echoes from an ultrasonic microphone, while simultaneously sampling fine-scale movement in three dimensions from wideband accelerometers and magnetometers. In this study, we tested the tag on an European noctula (Nyctalus noctula) during target approaches and on four big brown bats (Eptesicus fuscus) during prey interception in a flight room. 3. We show that the tag records both the outgoing calls and echoes returning from objects at biologically relevant distances. Inertial sensor data enables the detection of behavioural events such as flying, turning, and resting. In addition, individual wing-beats can be tracked and synchronized to the bat's sound emissions to study the coordination of different motor events. 4. By recording the primary acoustic flow of bats concomitant with associated behaviours on a very fine time-scale, this type of biologging method will foster a deeper understanding of how sensory inputs guide feeding behaviours in the wild.
Data from: Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing
The field of phylogenetics is changing rapidly with the application of high-throughput sequencing to non-model organisms. Cost-effective use of this technology for phylogenetic studies, which often include a relatively small portion of the genome but several taxa, requires strategies for genome partitioning and sequencing multiple individuals in parallel. In this study we estimated a multilocus phylogeny for the North American chorus frog genus Pseudacris using anonymous nuclear loci that were recently developed using a reduced representation library approach. We sequenced 27 nuclear loci and three mitochondrial loci for 44 individuals on 1/3 of an Illumina MiSeq run, obtaining 96.5% of the targeted amplicons at less than 20% of the cost of traditional Sanger sequencing. We found heterogeneity among gene trees, although four major clades (Trilling Frog, Fat Frog, crucifer, and West Coast) were consistently supported, and we resolved the relationships among these clades for the first time with strong support. We also found discordance between the mitochondrial and nuclear datasets that we attribute to mitochondrial introgression and a possible selective sweep. Bayesian concordance analysis in BUCKy and species tree analysis in *BEAST produced largely similar topologies, although we identify taxa that require additional investigation in order to clarify taxonomic and geographic range boundaries. Overall, we demonstrate the utility of a reduced representation library approach for marker development and parallel tagged sequencing on an Illumina MiSeq for phylogenetic studies of non-model organisms.
Data from: Long-term sound and movement recording tags to study natural behaviour and reaction to ship noise of seals
The impact of anthropogenic noise on marine fauna is of increasing conservation concern with vessel noise being one of the major contributors. Animals that rely on shallow coastal habitats may be especially vulnerable to this form of pollution. Very limited information is available on how much noise from ship traffic individual animals experience, and how they may react to it due to a lack of suitable methods. To address this, we developed long‐duration audio and 3D‐movement tags (DTAGs) and deployed them on three harbor seals and two gray seals in the North Sea during 2015–2016. These tags recorded sound, accelerometry, magnetometry, and pressure continuously for up to 21 days. GPS positions were also sampled for one seal continuously throughout the recording period. A separate tag, combining a camera and an accelerometer logger, was deployed on two harbor seals to visualize specific behaviors that helped interpret accelerometer signals in the DTAG data. Combining data from depth, accelerometer, and audio sensors, we found that animals spent 6.6%–42.3% of the time hauled out (either on land or partly submerged), and 5.3%–12.4% of their at‐sea time resting at the sea bottom, while the remaining time was used for traveling, resting at surface, and foraging. Animals were exposed to audible vessel noise 2.2%–20.5% of their time when in water, and we demonstrate that interruption of functional behaviors (e.g., resting) in some cases coincides with high‐level vessel noise. Two‐thirds of the ship noise events were traceable by the AIS vessel tracking system, while one‐third comprised vessels without AIS. This preliminary study demonstrates how concomitant long‐term continuous broadband on‐animal sound and movement recordings may be an important tool in future quantification of disturbance effects of anthropogenic activities at sea and assessment of long‐term population impacts on pinnipeds.
Heaps' law and Heaps functions in tagged texts: Evidences of their linguistic relevance
<p>We study the relationship between vocabulary size and text length in a corpus of 75 literary works in English, authored by six writers, distinguishing between the contributions of three grammatical classes (or ``tags,'' namely, nouns, verbs, and others), and analyze the progressive appearance of new words of each tag along each individual text. We find that, as prescribed by Heaps' law, vocabulary sizes and text lengths follow a well-defined power-law relation. Meanwhile, the appearance of new words in each text does not obey a power law, and is on the whole well described by the average of random shufflings of the text. Deviations from this average, however, are statistically significant and show systematic trends across the corpus. Specifically, we find that the appearance of new words along each text is predominantly retarded with respect to the average of random shufflings. Moreover, different tags add systematically distinct contributions to this tendency, with verbs and others being respectively more and less retarded than the mean trend, and nouns following instead the overall mean. These statistical systematicities are likely to point to the existence of linguistically relevant information stored in the different variants of Heaps' law, a feature that is still in need of extensive assessment.</p>
Data from: Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach
In recent years, the explosion of affordable next generation sequencing technology has provided an unprecedented opportunity to conduct genome-wide studies of adaptive evolution in organisms previously lacking extensive genomic resources. Here, we characterise genome-wide patterns of variability and differentiation using pooled DNA from eight populations of the nine-spined stickleback (Pungitius pungitius L.) from marine, lake and pond environments. We developed a novel genome complexity reduction protocol, defined as paired-end double restriction-site associated DNA (PE dRAD), to maximise read coverage at sequenced locations. This allowed us to identify over 114,000 short consensus sequences and 15,000 SNPs throughout the genome. A total of 6,834 SNPs mapped to a single position on the related three-spined stickleback genome, allowing the detection of genomic regions affected by divergent and balancing selection, both between species and between freshwater and marine populations of the nine-spined stickleback. Gene ontology (GO) analysis revealed 15 genomic regions with elevated diversity, enriched for genes involved in functions including immunity, chemical stimulus response, lipid metabolism and signalling pathways. Comparisons of marine and freshwater populations identified nine regions with elevated differentiation related to kidney development, immunity and MAP kinase pathways. In addition, our analysis revealed that a large proportion of the identified SNPs mapping to LG XII are likely to represent alternative alleles from divergent X and Y chromosomes, rather than true autosomal markers following Mendelian segregation. Our work demonstrates how population-wide sequencing and combining inter- and intra-specific RAD analysis can uncover genome-wide patterns of differentiation and adaptations in a non-model species.
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans
Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions.
Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.
Data from: Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada
Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774–individual, 267–population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.
FIGURE 1 in First record of the genus Tag ali s Stål, 1860 (Hemiptera: Reduviidae: Saicinae) from Colombia with the description of two new species
FIGURE 1. Tagalis dichroa sp. nov. Male holotype. A. Habitus, dorsal view. B. Lateral view. C. Proleg, lateral view. D. Head and thorax, lateral view; arrow indicates pale coxal cavity. E. Meso- and metathorax showing mesoscutellar and metanotal spines; posterior metanotal spine is broken. F. Eight abdominal segment and pygophore. G. Tarsi of metaleg; arrow indicates the scopula.
FIGURE 3 in First record of the genus Tag ali s Stål, 1860 (Hemiptera: Reduviidae: Saicinae) from Colombia with the description of two new species
FIGURE 3. Tagalis albispina sp. nov. A. Head and prothorax, lateral view. B. Meso- and metathorax, dorsolateral view. C. Proepisternal process with anteroventrad spine, arrow points to the posteroventrad delicate seta. D. Right fore- and hindwing. E. Meso-, metathorax, and abdomen, ventral view; rectangle show detailed area. F. Detail of area indicated on E, sternite 7, gonocoxae and gonapophyses 8.
FIGURE 4 in First record of the genus Tag ali s Stål, 1860 (Hemiptera: Reduviidae: Saicinae) from Colombia with the description of two new species
FIGURE 4. Tagalis albispina sp. nov., female genitalia. A. Dorsal view. B. Lateral view. C. Ventral view. Abbreviations: bc, bursa copulatrix; gap8, gonapophysis eight; gcx8, gonocoxa eight; gpl, gonoplac; lbs, lateral lobes of the bursa; T9, tergite nine; vg, vermiform gland.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.