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89 results for “Biomonitoring”
Getting to know our biomonitor neighbours: urban lichens and allied fungi of Edmonton, Alberta, Canada: Phylogenetic Datasets
<p>Here we provide one of the first detailed studies of lichen and allied fungi diversity in a continental North American city (Edmonton, Alberta, Canada), including an annotated checklist, images of all species, dichotomous keys, and local distribution maps. Edmonton is the northernmost city in North America with a population of over one million, and an industrial and transportation gateway for much of northern Canada. Lichen-based biomonitoring could be a tool to track airborne pollutants resulting from Edmonton's growing populace and industrial activity. The first step towards such a program is documenting the diversity and distribution of lichens in the city. To accomplish this, we conducted a city-wide, systematic survey of 191 sites focused on epiphytes growing on deciduous boulevard trees. We augmented that survey with surveys of rare trees, opportunistic collections from river valley and ravine habitats, herbarium collections, phylogenetic analyses of a subset of collections, and observations submitted to online nature-reporting applications. We present ITS sequence barcode data for 33 species, phylogenetic analyses for Candelariaceae<em>, Endocarpon, Flavopunctelia, </em>the <em>Lecanora dispersa</em> group, <em>Lecidella, Peltigera</em>, <em>Physconia</em>, and <em>Punctelia</em>, and detailed descriptions of 114 species in 47 genera and 23 families. Two species are hypothesized to be new to North America (<em>Endocarpon </em>aff. <em>unifoliatum, Lecidella albida</em>), twelve more are new to Alberta (<em>Amandinea dakotensis</em>, <em>Bacidia circumspecta</em>, <em>Candelaria pacifica</em>, <em>Candelariella antennaria, Heterodermia japonica</em>, <em>Lecania naegelii, Lecanora sambuci, Lecanora stanislai, Lecidea erythrophaea</em>, <em>Peltigera islandica, Phaeocalicium </em>aff. <em>tremulicola, </em>and the introduced <em>Xanthoria parietina</em>), and five are putative new species to science (<em>Physcia</em> aff. <em>dimidiata</em>, <em>Physcia</em> aff. <em>stellaris</em>, <em>Phaeocalicium</em> sp., <em>Phaeocalicium</em> aff. <em>tremulicola</em>, Lichenaceae sp.). Illustrations are provided for all species to aid in verification and public outreach. Species richness was highest in foliose lichens (48), followed by crustose and calicioid lichens and allied fungi (41), with the lowest richness in fruticose lichens (25). We did a preliminary assessment of the suitability of species for citizen-science biomonitoring by assessing their distribution across the city, perceptibility to the public, identification accuracy, and, for a subset, how consistently species were surveyed by trained novices. Compared to other urban areas where lichen diversity has been studied, Edmonton is relatively species-rich in calicioids and <em>Peltigera</em>. Promising bioindicators may be limited to chlorolichens, including <em>Caloplaca</em> spp., <em>Evernia mesomorpha</em>, <em>Flavopunctelia</em> spp., <em>Phaeophyscia orbicularis</em>, <em>Physcia adscendens</em>, <em>Physcia aipolia </em>group<em>, Physcia </em>aff. <em>stellaris</em>, <em>Usnea </em>spp., and <em>Xanthomendoza fallax</em>. Other genera that may be responsive to pollutants such as <em>Cladonia</em> and <em>Peltigera</em> were almost exclusively restricted to river valley and ravine ecosystems, limiting their application as bioindicators. Some species commonly used as biomonitors elsewhere were too rare, small, poorly developed, or obscured by more common species locally (e.g., <em>Candelaria concolor s.l.</em>, <em>Xanthomendoza hasseana</em>). The low overlap with lists of biomonitoring species from other regions of North America illustrates the necessity of grounding monitoring in knowledge of local diversity. Future augmentation of this list should focus on enhanced sampling of downed wood-, conifer-, and rock-dwelling lichens, particularly crustose species. The next step in developing a biomonitoring program will require modelling species' responses to known air quality and climatic gradients.</p>
Data supplementing the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal
<p>These data supplement the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal</p> <p>The directory contains the following files:</p> <p>1<strong>5 fastq files raw reads (5 mock communities, 3 replicates)</strong><strong>.rar </strong>- contains the 15 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>15 fastq files information.xlsx</strong> :</p> <p>- contains the information relative to the 15 fastq files corresponding to the PGM raw data of the 5 mock communities (sequenced with 3 replicates), including: the ID of the fastq files, the mock community name, the replicate number, the final sample Id and the number of raw reads per fastq file.</p> <p>- contains the information of the proportion of the 8 diatoms species (%) used to create the 5 mock communities (estimated from microscopy).</p>
Data supplementing the article "Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal
<p>These data supplement the article "Enhancing DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal</p> <p>The directory contains the following files:</p> <p><strong>278 (139 x 2 replicates) samples fastq files.rar </strong>- contains the 278 fastq files provided by the sequencing platform with demultiplexed and contig DNA reads corresponding to the 139 samples with 2 sequencing replicates (A and B).</p> <p><strong>Counts_diatoms.xlsx </strong>- contains the morphological inventories with species list (Omnidia code) and valve abundances for the 139 samples.</p> <p><strong>Sites_list.xlsx </strong>- contains information regarding the 139 samples, including: River name, GPS coordinates, code used for molecular analysis and corresponding to sequencing fastq names.</p>
Data supplementing the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal
<p>These data supplement the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal.</p> <p>The directory contains the following files:</p> <p><strong>464_samples_fastq_files_(mothur).rar </strong>- contains the 464 fastq files proceed together during the Mothur bioinformatics treatments to produce the OTUs and ISUs tables. As the contig and the demultiplexing steps were performed by the sequencing platform, there is 1 fastq file per sample. From this 464 samples OTU/ISU tables, only information regarding 76 samples were used in this study and are listed in the "<strong>76_samples_list_(mothur).xlsx" </strong>file<strong>.</strong></p> <p><strong>76_samples_list_(mothur).xlsx </strong>- contains the information regarding the 76 samples used to create the OTUs and ISUs tables presented in the paper.</p> <p><strong>76_samples_R1_R2_fastq_files(DADA2).rar - </strong>contains the raw demultiplexed fastq files (R1.fastq and R2.fastq) for each of the 76 samples used in this study to produce the ESVs table using the DADA2 bioinformatics pipeline.</p>
Figure 1 in Microtus guentheri (Danford & Alston, 1880) (Rodentia: Cricetidae) as a biomonitor for radionuclides in Mersin Province of Turkey
Figure 1. The localities of samples collected within Mersin Province.
Figure 8 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring
Figure 8 The final composite, sieved water mite sample ready for the picking process.
Mobile Device Biomonitoring to Prevent and Treat Obesity in Underserved Youth
ClinicalTrials.gov study NCT02017223. IPD Sharing: NO. Countries: 1. Publications: 6.
BioMonitor 2 In-Office Setting Insertion Safety and Feasibility Evaluation With Device Functionality Assessment
ClinicalTrials.gov study NCT02756338. IPD Sharing: NO. Countries: 1. Publications: 1.
A Personalized Biomonitoring and Report-back Intervention to Reduce Exposure to Endocrine Disrupting Chemicals
ClinicalTrials.gov study NCT06450951. IPD Sharing: YES. Countries: 1. Publications: 18.
Biomonitoring planktonic threats to salmon aquaculture: morphological and eDNA metabarcoding data
Open the record for dataset details and reuse information.
Sources of uncertainty in DNA metabarcoding of whole communities: implications for its use in biomonitoring
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Unveiling structure of tropical estuarine communities through eDNA and implications for biomonitoring
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Getting to know our biomonitor neighbours: urban lichens and allied fungi of Edmonton, Alberta, Canada: Phylogenetic Datasets
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Co-sampled fruticose and foliose epiphytic lichens as spatial biomonitors of airborne mercury and arsenic in a historical "Gold Rush" mining district
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A comparison of biomonitoring methodologies for surf zone fish communities
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Marine biomonitoring with eDNA: can metabarcoding of water samples cut it as a tool for surveying benthic communities?
<p>In the marine realm, biomonitoring using eDNA of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at distances from a few centimetres to 20 m from the benthic habitat. Using as marker a fragment of the Cytochrome c oxidase subunit I gene with universal primers, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs) from the samples. The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida Rhodophyta and Stramenopiles being the most diverse group in benthic samples, and HacrobiaAlveolata, Metazoa and Alveolata Rhizaria in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples, and of these 180 MOTUs (5.1%) were identified as benthic MOTUs that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased and The distribution of these benthic shared MOTUs showed a decrease both in number of MOTUs and in number of reads as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex benthic communities via metabarcoding.</p>
A molecular method for biomonitoring of an exotic plant-pest: leafmining for environmental DNA
<p><span>1. Understanding how invasive species respond to novel environments is limited by a lack of sensitivity and throughput in conventional biomonitoring methods.<i> </i>Arthropods in particular are often difficult to monitor due to their small size, rapid lifecycles, and/or visual similarities with co-occurring species<i>. </i>This is true for the agromyzid leafminer fly, <i>Liriomyza sativae</i>, a global pest of vegetable and nursery industries that has recently established in Australia. </span></p> <p><span>2. A robust method based on environmental DNA (eDNA) was developed exploiting traces of DNA left inside 'empty' leaf mines, which are straightforward to collect and persist longer in the environment than the fly. This extends the window of possible diagnosis to at least 28 days after a leaf mine becomes empty. The test allowed for visually indistinguishable leafmining damage caused by <i>L. sativae</i> to be genetically differentiated from that of other flies. </span></p> <p><span> 3. Field application resulted in the identification of new local plant hosts for <i>L. sativae</i>, including widely distributed weeds and common garden crops, which has important implications for the pest's ability to spread. Moreover, the test confirmed the presence of a previously unknown population of <i>L. sativae</i> on an island in the Torres Strait. </span></p> <p>4. The developed eDNA method is likely to become an important tool for <i>L. sativae</i> and other leafmining species of biosecurity significance, which, historically, have been difficult to detect, diagnose and monitor. More generally, eDNA is emerging as a highly sensitive and labour-efficient surveillance tool for difficult to survey species to improve outcomes for agricultural industries, global health, and the environment.</p>
Data from: Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.
Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates
Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass determined. DNA was extracted from all macroinvertebrate samples and HTS undertaken using the illumina miseq platform. Macroinvertebrate communities were characterized from sequence data using either six genes (three of the original nine were not used) or just the COI gene in isolation. The gene-enrichment method (all genes) detected the highest number of taxa and obtained the strongest Spearman rank correlations between the number of sequence reads, abundance and biomass in 67% of the samples. Median detection rates across rare (<1% of the total abundance or biomass), moderately abundant (1–5%) and highly abundant (>5%) taxa were highest using the gene-enrichment method (all genes). Our data indicated primer biases occurred during amplicon metabarcoding with greater than 80% of sequence reads originating from one taxon in several samples. The accuracy and sensitivity of both HTS methods would be improved with more comprehensive reference sequence databases. The data from this study illustrate the challenges of using PCR amplification-based methods for biomonitoring and highlight the potential benefits of using approaches, such as gene enrichment, which circumvent the need for an initial PCR step.
Data from: Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring
Diatoms include a great diversity of taxa and are recognized as powerful bioindicators in rivers. However using diatoms for monitoring programs is costly and time consuming because most of the methodologies necessitate species-level identification. This raises the question of the optimal tradeoff between taxonomic resolution and bioassessment quality. Phylogenetic tools may form the bases of new more efficient approaches for biomonitoring if relationships between ecology and phylogeny can be demonstrated. We estimated the ecological optima of 127 diatom species for 19 environmental parameters using count data from 2119 diatom communities sampled during 8 years in eastern France. Using uni- and multivariate analyses, we explored the relationships between freshwater diatom phylogeny and ecology (i.e. the phylogenetic signal). We found a significant phylogenetic signal for many of the ecological optima that were tested, but the strength of the signal varied significantly from one trait to another. Multivariate analysis also showed that the multidimensional ecological niche of diatoms can be strongly related to phylogeny. The presence of clades containing species that exhibit homogeneous ecology suggests that phylogenetic information can be useful for aquatic biomonitoring. This study highlights the presence of significant patterns of ecological optima for freshwater diatoms in relation to their phylogeny. These results suggest the presence of a signal above the species level, which is encouraging for the development of simplified methods for biomonitoring survey.
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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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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.
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