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862 results for “marine fish”
Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
Data from: Persistence of marine fish environmental DNA and the influence of sunlight
Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.
Data from: Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish
Crude oil spills are a worldwide ocean conservation threat. Fish are particularly vulnerable to the oiling of spawning habitats, and crude oil causes severe abnormalities in embryos and larvae. However, the underlying mechanisms for these developmental defects are not well understood. Here, we explore the transcriptional basis for four discrete crude oil injury phenotypes in the early life stages of the commercially important Atlantic haddock (Melanogrammus aeglefinus). These include defects in (1) cardiac form and function, (2) craniofacial development, (3) ionoregulation and fluid balance, and (4) cholesterol synthesis and homeostasis. Our findings suggest a key role for intracellular calcium cycling and excitation-transcription coupling in the dysregulation of heart and jaw morphogenesis. Moreover, the disruption of ionoregulatory pathways sheds new light on buoyancy control in marine fish embryos. Overall, our chemical-genetic approach identifies initiating events for distinct adverse outcome pathways and novel roles for individual genes in fundamental developmental processes.
FIGURE 2. Comparison diagram for Rhipidocotyle danai n in Bucephalids (Digenea: Bucephalidae) from marine fishes off the south-western coast of Java, Indonesia, including the description of two new species of Rhipidocotyle and comments on the marine fish digenean fauna of Indonesia
FIGURE 2. Comparison diagram for Rhipidocotyle danai n. sp.
FIGURE 5. Comparison diagram for Rhipidocotyle jayai n in Bucephalids (Digenea: Bucephalidae) from marine fishes off the south-western coast of Java, Indonesia, including the description of two new species of Rhipidocotyle and comments on the marine fish digenean fauna of Indonesia
FIGURE 5. Comparison diagram for Rhipidocotyle jayai n. sp. (see text)
FIGURE 6 in Bucephalids (Digenea: Bucephalidae) from marine fishes off the south-western coast of Java, Indonesia, including the description of two new species of Rhipidocotyle and comments on the marine fish digenean fauna of Indonesia
FIGURE 6. Prosorhynchus platycephali (Yamaguti, 1934). Ventral view. Scale-bar = 500μm.
FIGURE 24 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 24. Siganus vulpinus (Siganidae), Madang Lagoon, St. PR 120, P. Laboute, 28 Nov. 2012.
FIGURE 35 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 35. Seaward barrier reef, Madang, St. PCT 22, S. Andréfouët, 1 Nov. 2012.
FIGURE 21 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 21. Ceratobregma helenae (Tripterygiidae), Madang Lagoon, St. PB 34, W.-J. Chen.
FIGURE 27 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 27. Sphyraena jello (Sphyraenidae), Madang Lagoon, St. PR 120, P. Laboute, 28 Nov. 2012.
FIGURE 15 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 15. Paracirrhites forsteri (Cirrhitidae), Madang Lagoon, St. CTR 16, M. Hamel, 30 Oct. 2012.
FIGURE 36 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 36. Soft bottom habitat, Madang, St. PCT 24, S. Andréfouët, 1 Nov. 2012.
FIGURE 9 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 9. Parupeneus barberinus (Mullidae), Madang Lagoon, P. Laboute, 10 Dec. 2012.
FIGURE 8 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 8. Anyperodon leucogrammicus (Serranidae), Madang Lagoon, St. CTR 32, M. Hamel, 6 Nov. 2012.
FIGURE 6 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 6. Dendrochirus zebra (Scorpaenidae), Madang Lagoon, P. Laboute, 3 Dec. 2012.
FIGURE 4 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 4. Saurida nebulosa (Synodontidae), Madang Lagoon, St. CTR 14, M. Hamel, 29 Oct. 2012.
FIGURE 3 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 3. Taeniura lymma (Dasyatidae), Madang Lagoon, P. Laboute, 11 Dec. 2012.
FIGURE 33 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 33. Fringing reef, Madang Lagoon, St. PCT 11, S. Andréfouët, 28 Oct. 2012.
FIGURE 22 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 22. Lobulogobius omanensis (Gobiidae), Madang Lagoon, Riwo waters, D Uyeno, 7 Dec. 2012.
FIGURE 5 in Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records
FIGURE 5. Solenostomus paradoxus (Solenostomidae), Madang Lagoon, P. Laboute, 4 Dec. 2012.
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)
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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.