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233 results for “marine biodiversity”
Figure 31 in Biodiversity of marine planarians revisited (Platyhelminthes, Tricladida, Maricola)
Figure 31. Map of species richness on an equal area grid map from the Worldmap program. Maximum richness shown in black and minimum in light grey, with intermediate scores grouped into grey-scale classes of approximately equal numbers of grid cells. Numbers within cells denote number of species recorded within that grid cell.
Figures 2, 3 in Biodiversity of marine planarians revisited (Platyhelminthes, Tricladida, Maricola)
Figures 2, 3. Foviella affinis. (2) V.Pl. 948.3, sagittal section of the copulatory apparatus. (3) V.Pl. 948.3, sagittal section through eye cup with lens.
Figure 1 in Biodiversity of marine planarians revisited (Platyhelminthes, Tricladida, Maricola)
Figure 1. Foviella affinis, sagittal section through copulatory apparatus (from Sabussow 1900: pl. III, figure 34; labels adapted according to current terminology).
Figure 13 in Biodiversity of marine planarians revisited (Platyhelminthes, Tricladida, Maricola)
Figure 13. Geographic distribution of M. trifasciata, M. trifasciata?, P. asahinai and P. cervix in the Far East.
Figures 25–27 in Biodiversity of marine planarians revisited (Platyhelminthes, Tricladida, Maricola)
Figures 25–27. Procerodella cervix. (25) V.Pl. 953.3, sagittal reconstruction of the copulatory apparatus. (26) V.Pl. 953.6, sagittal reconstruction of the copulatory apparatus. (27) V.Pl. 953.1, sagittal reconstruction of the copulatory apparatus.
Data and R scrips for "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton"
<p>Research data and scripts associated with the article "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton" by Jönander et al.</p>
Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves
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Data from: A sedimentary eDNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem
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Scale-dependent effects of biodiversity and stability on marine ecosystem dynamics
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Testing biodiversity-ecosystem function relations in nearshore marine sediments
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Figure 5. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 5. - Kathy Omura holding whirl top bag containing sample which is ready to be filled with ethanol.
Figure 1. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 1. - Storage and shipping box also holds dive gear on small boats, large and small photographic trays, 10-12 liter [3 gallon] bucket with modified screw top lid and stainless steel carabiner, mesh dive sack, aquarium fish net, brass-framed mermaid's bra net (240 µm mesh or 63 µm for meiofauna), geology hammer, paint scraper, stainless steel spoon, dive sausage and reel. Photo credit: N. D. Pentcheff.
Figure 1. from Extending Marine Species Distribution Maps Using Non-Traditional Sources - Biodiversity Data Journal 3: e4900 (17 April 2015) https://doi.org/10.3897/BDJ.3.e4900
Figure 1. - The IUCN Red List Review Process (IUCN 2014a). Steps refer to the DOCUMENTATION STANDARDS AND CONSISTENCY CHECKS FOR IUCN RED LIST ASSESSMENTS AND SPECIES ACCOUNTS (IUCN 2013).
Figure 4. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 4. - N. Dean Pentcheff and Niel Bruce straining seawater containing isopods into mermaid's bra (netting). The bucket is swirled to suspend animals and quickly strained over the netting to retain them.
Figure 2. from Collecting and Preserving Marine and Freshwater Isopoda (Crustacea: Peracarida) - Biodiversity Data Journal 3: e4912 (12 May 2015) https://doi.org/10.3897/BDJ.3.e4912
Figure 2. - Plankton net (240 µm mesh), 25 x 25 cm [10 x 10 inches] 240 µm mesh plankton netting to use with funnel, numbered mesh draw-string collecting bags (28 x 46 cm [11 x 18 inches], 200 or 300 µm mesh, seams reinforced with sew-on edge binding), draw-string cotton sack 41 x 76 cm [16 x 30 inches] for larger bulkier samples, assorted screw-top vials and plastic eye dropper, stainless steel forceps (10 and 25 cm [6 and 10 inches] long), insect collecting forceps for picking up fast moving or fragile animals, leather garden gloves, Optivisor optical glass binocular magnifier (2 diopter, 1.5x), dive light, whirl top bags (2 sizes = 13 x 30 cm [5 x 12 inches] and 12 x 23 cm [4.5 x 9 inches]), fanny pack, and GPS. Photo credit: N. D. Pentcheff.
A marine heatwave changes the stabilizing effects of biodiversity in kelp forests
<p>The code and data are used in a preliminary manuscript, titled "A marine heatwave changes the stabilizing effects of biodiversity in kelp forests".</p>
Data from: environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: towards a baseline for biodiversity monitoring of unexplored marine habitats
<p>Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from nineteen genera of fish, six of these have also been observed on towed underwater videos, while thirteen were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.</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>
Marine biodiversity patterns in coastal Australian waters revealed by a three-year environmental DNA survey
<p><strong>Aim</strong></p> <p>To test the capacity of eDNA to characterise the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme.</p> <p><strong>Location</strong></p> <p>Samples were sourced seasonally for three years from nine Pan-Australian marine sites (n=90).</p> <p><strong>Methods</strong></p> <p>Here we apply a multi-assay metabarcoding approach to environmental DNA extracted from a rare long-term collection of bulk plankton samples. Six assays (targeting both the 16SrRNA and COI genes) were used to amplify and sequence the zooplankton diversity found within each sample. The data generated from each assay was filtered and clustered into OTUs prior to analysis. Abiotic IMOS data collected alongside the plankton collection enabled us to explore the physical and chemical drivers of community composition.</p> <p><strong>Results</strong></p> <p>The eDNA metabarcoding generated over 25 million sequences, identified in excess of 500 distinct taxa and detected clear spatial differences in marine metazoan communities. We found that site and sea surface temperature are the most consistent predictors of differences between zooplankton communities. We detected endangered and invasive species such as the bryozoan Membranipora membranace and the mollusc Maoricolpus roseus, and seasonal occurrences of species such as humpback whales (Megaptera novaeangliae). We also estimated the number of samples required to ensure robust marine eDNA metabarcoding biomonitoring programs into the future.</p> <p><strong>Main Conclusion</strong></p> <p>Our results demonstrate the ability of eDNA to capture and map zooplankton community changes in response to seasonal and spatial stressors and provide vital evidence to environmental stakeholders. We confirm that eDNA offers a practical opportunity for an ecosystem-wide approach to the long-term biomonitoring and understanding marine biomes where a morphological approach is not feasible.</p>
Nearshore marine biodiversity of Osa Peninsula, Costa Rica
<p>Osa Peninsula in remote southwest Costa Rica harbors 2.5% of global terrestrial biodiversity in only 1,200 km2 and has the largest remaining tract of Pacific lowland wet forest in Mesoamerica. However, little is known about the marine ecosystems of this diverse region. Much of the coastline consists of soft sediment exposed to strong wave action. Three major hard bottom habitat types define this region, including: 1) coral reefs around Isla del Caño Biological Reserve, a no-take marine protected area (MPA) of 52 km<sup>2</sup>, 2) coastal rocky reefs and islets along the peninsula, including Corcovado National Park, and 3) submerged pinnacles just outside the Isla del Caño MPA. Average coral cover at Isla del Caño was 21%, composed primarily of<em> Porites lobata</em> and <em>Pocillopora elegans</em>. In contrast, coastal rocky reefs were dominated by turf algae (39.8%) and macroalgae (20.7%) with low coral cover (1.1%). Submerged pinnacles were dominated by crustose coralline algae (33.3%) and erect coralline algae (25.7%). Fish assemblage characteristics (species richness, abundance, biomass) were significantly higher at the pinnacles compared to the other habitats and was dominated by schooling species such as Haemulon steindachneri, and the herbivores <em>Kyphosus ocyurus</em>, and <em>Acanthurus xanthopterus.</em> Top predators, primarily <em>Triaenodon obesus</em>, <em>Caranx sexfasciatus</em>, and <em>Lutjanus argentimaculatus</em>, were also most abundant at these pinnacles and accounted for the largest differences in fish trophic structure among habitats. Despite Isla del Caño being fully protected from fishing, biomass was similar to fished areas along the coast and lower than the adjacent submerged pinnacles outside the reserve. Similarly, Corcovado National Park includes 20.3 km<sup>2</sup> of no-take MPAs; however, there is limited enforcement, and we noted several instances of fishing within the park. The unique configuration of healthy offshore coral reefs and pinnacles connected to coastal habitats provides corridors for many species including large predators such as sharks and other marine megafauna, which warrants additional protection.</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.