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47 results for “Biodiversity sampling”
Sampling metadata for the publication: "Deep-sea sponge derived environmental DNA analysis reveals demersal fish biodiversity of a remote Arctic ecosystem "
<p>Meta data of sampling location, time and depth of eDNA samples used in the study: "Deep-sea sponge derived environmental DNA analysis reveals demersal fish biodiversity of a remote Arctic ecosystem". As well as taxonomic identification of sponges, their microbial abundance and growth form.</p>
Fig. 9 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 9. Comparison between species frequency of museum collections (data from Frisone et al. 2016) and bulk sampling (this study). Error bars denote binomial standard errors of percentages.
Fig. 8 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 8. Distribution of sponge genera from museum collections (data from Frisone et al. 2016) and bulk sampling (this study). Error bars denote binomial standard errors of percentages.
Fig. 7 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 7. Families and relative abundances frequencies from museum collections (data from Frisone et al. 2016) and bulk sampling (this study). Error bars denote binomial standard errors of percentages.
Fig. 6 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 6. Comparison between frequency of museum collections (data from Frisone et al. 2016) and bulk field sampling (this study) at the ordinal level. Error bars denote binomial standard errors of percentages.
Fig. 5 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 5. Distribution of species richness (number of taxa) and species abundance (number of individuals per taxon) among classes.
Fig. 11 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 11. Rank-abundance distribution of bulk samples (A) and museum collection (Whittaker plots) (B). Y axis shows species abundance; X axis ranks each species in order from most to least abundant. Black dots represent species.
Fig. 2 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 2. Location (B) and geological map (A) of the study area (Verona and Vicenza provinces, Northern Italy), modified from http://gisgeologia.regione. veneto.it/, author: Regione Veneto, Sezione Geologia e Georisorse, and released under the Italian Open Data License 2.0 (https://www.dati.gov.it/content/ italian-open-data-license-v20). Outline of the Lessini Shelf during the Eocene modified from Bosellini (1989). The sponge-bearing outcrop is indicated by the white star near Chiampo. Cf, Castelvero fault; SVf, Schio-Vicenza fault; Pf, Pedemontana thrust fault.
Fig. 4 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 4. Rarefaction curve (line in the middle) of the Chiampo sponge fauna at Lovara. Grey area demarcate 95% confidence intervals of diversity estimates.
Fig. 12 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 12. In situ Eocene specimen of Laocoetis patula from Lovara Quarry, Italy; showing its characteristic morphology with canal openings in quadrate arrangement, indicated by the white arrow. Coin for scale is 22 mm in diameter.
Fig. 10 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 10. Percent similarity (A) and Jaccard similarity (B) measurements between bulk and museum collection material at different taxonomic levels.
Fig. 3 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 3. Bulk collection of Eocene sponges at Lovara Quarry. Some of the sponge specimens are indicated by white arrows.
Fig. 1 in Biodiversity of museum and bulk field samples compared: The Chiampo sponge fauna (Eocene, Lessini Mountains, Italy)
Fig. 1. Sponge fossils from the Eocene of Chiampo. A. The lyssacinosid Stauractinella eocenica Frisone, Pisera, and Preto, 2016. B. The lychniscosid Callicylix eocenicus Pisera and Busquets, 2002. C. The lithistid demosponge Platychonia sp. D. The hexactinosid Laocoetis patula Pomel, 1872. Scale bars 10 mm. Photos S. Castelli.
Figure 4. A in Avian biodiversity assessment studies in a Neotropical wetland - the combination of sampling methods makes the difference
Figure 4. A Song Meter (acoustic recorder, upper left, marked yellow) and a camera trap (photo and video recorder, lower left, marked green) were jointly applied to study the avian occurrence and behavior of ground-dwelling species, e.g., cracids and tinamous.
Figure 1 in Avian biodiversity assessment studies in a Neotropical wetland - the combination of sampling methods makes the difference
Figure 1. Number of individuals and species detected by three methodologies over the dry period of 2014 in areas of forest and savanna in the northeastern Pantanal, Mato Grosso, Brazil. MN = mist nets; PC = point counts; ARU = autonomous acoustic recording.
Figure 3 in Avian biodiversity assessment studies in a Neotropical wetland - the combination of sampling methods makes the difference
Figure 3. Local contribution to beta diversity (LCBD) of avian taxa in the northeastern Pantanal, Mato Grosso, Brazil, in the dry period of 2014. The geographic positions of the savanna sites (orange) and forest sites (green) are shown. The relationship between the LCBD values and species richness is shown in A. The site contributions to beta diversity (i.e., the LCBD values) determined by each methodology were divided into two components: replacement B and nestedness C.
Figure 2 in Avian biodiversity assessment studies in a Neotropical wetland - the combination of sampling methods makes the difference
Figure 2. Number of species detected in each of the eight sampling sites using three methodologies over the dry period of 2014 in one region of the northeastern Pantanal, Mato Grosso, Brazil. MN = mist nets; PC = point counts; ARU = autonomous acoustic recording.
Leech-derived iDNA complements traditional surveying methods, enhancing species detections for rapid biodiversity sampling in the tropics
<p>Deforestation, exploitation, and other drivers of biodiversity loss in Madagascar leave its highly endangered and predominantly endemic wildlife at risk of extinction. Decreasing biodiversity threatens to compromise ecosystem functions and vital services provided to people. New, economical, and diverse methods of biodiversity monitoring can help to establish reliable baseline and long-term records of species richness. Metabarcoding with invertebrate-derived DNA (iDNA) has emerged as a promising new biosurveillance tool. An unexpected wet forest fragment tucked in the dry cliffs of Madagascar's southcentral plateau, the Ivohibory Protected Area (IPA), hosts a unique mosaic of species diversity, featuring both dry and wet forest species. Recently elevated to protected status, the IPA has been surveyed for flora and fauna with a range of inventory methods over three years and six expeditions (2016, 2017, & 2019). We collected 1,451 leeches over 12 days from the IPA to supplement known species richness and to compare results against current records. With iDNA, we pooled tissues, and isolated, and amplified bloodmeal DNA with five sets of primers. We detected 20 species of which four are species of frogs previously undetected and three of which are previously unknown to exist in this region. iDNA surveys can provide complementary data to traditional surveying methods like camera traps, line transects, and bioacoustic methods.</p>
Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies
<p>Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large – volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle <em>Mesobot</em> in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40 – 60 liters) samples collected by <em>Mesobot</em> with small volume (~2 liters) samples collected using the conventional CTD rosette – mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume <em>Mesobot</em> and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not – although the number of unique taxa associated with the <em>Mesobot</em> samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.</p>
Comparison of mosquitoes and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany
<p><span>The use of invertebrate-derived DNA (iDNA) is a promising non-invasive tool to monitor wildlife. While most studies have been carried out in dense tropical and sub-tropical forests and have focused on the use of a single category of invertebrates, this study compares the use of flies- and mosquito-derived DNA to assess vertebrate diversity in semi-urban environments. We conducted our sampling in four different forest plots in Berlin, Germany. Pools of flies and non-bloodfed mosquitoes were metabarcoded using 108 bp vertebrate-specific 12S rRNA (12S-V5) and 94 bp mammal-specific 16S rRNA (16Smam) mitochondrial markers, and individual bloodfed mosquitoes were sequenced using the 340 bp vertebrate-specific 12S rRNA fragment (Mam-12S-340). From the fly pools, we detected 10 mammal species using 16Smam, while 12S-V5 detected four bird, two amphibian and six mammal species. From the non-bloodfed mosquito pools, we only amplified putative contaminant DNA, indicating that mosquito females without visual signs of a blood meal carry no traces of vertebrate DNA. Finally, in the bloodfed mosquitoes, we identified four mammal and one bird species. Focusing on mammal species, we did not find significant differences in the proportion of species detected regarding the total available number of species between sampling localities. Fly samples were easier to obtain and more abundant over the sampled localities compared to mosquito samples. We conclude that, while there are a few advantages in using mosquito blood meals, the use of flies in the detection of wildlife in a suburban environment is more effective in terms of collection of samples and detection of vertebrates, although this technique is limited to few mammal species in the urban environment. </span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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.