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Mediterranean underwater fish visual census surveys data
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Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf
<p>Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf.</p> <p>Ludt, W.B., Jabado, R.W., Al Hameli, S.M., Freeman, L., Teruyama, G., Chakrabarty, P. & Al Dhaheri, S.S. (2020) Establishing a reference collection and DNA barcoding the coastal fishes of the United Arab Emirates. <em>Journal of the Ocean Science Foundation</em>, 35, 54–64.</p>
Multi-species models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams
Environmental DNA (eDNA) sampling can provide accurate, cost-effective, landscape-level data on species distributions. Previous studies have compared the sensitivity of eDNA sampling to traditional sampling methods for single species, but similar comparative studies on multi-species eDNA metabarcoding are rare. Using hierarchical species occupancy-detection models, we examined whether key choices associated with eDNA metabarcoding (primer selection, low-abundance read filtering, and the number of positive water samples used to classify a species as present at a site) affect the sensitivity of metabarcoding, relative to backpack electrofishing for fish in freshwater streams. Under all scenarios (teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering thresholds; 1 or 2 positive samples required to classify species as present), we found that eDNA metabarcoding is, on average, more sensitive than electrofishing. Combining vertebrate and teleostei markers resulted in higher detection probabilities relative to the use of either marker in isolation. Increasing the threshold used to filter low abundance reads decreased species detection probabilities but did not change our overall finding that eDNA metabarcoding was more sensitive than electrofishing. Using a threshold of two positive water samples (out of 5) to classify a species as present typically had negligible effects on detection probabilities compared to using one positive water sample. Our findings demonstrate that eDNA metabarcoding is generally more sensitive than electrofishing for conducting fish surveys in freshwater streams, and that this outcome is not sensitive to methodological decisions associated with metabarcoding.
Data from: A survey of digitized data from U.S. fish collections in the iDigBio data aggregator
Recent changes in institutional cyberinfrastructure and collections data storage methods have dramatically improved accessibility of specimen-based data through the use of digital databases and data aggregators. This analysis of digitized fish collections in the U.S. demonstrates how information from data aggregators, in this case iDigBio, can be extracted and analyzed. Data from U.S. institutional fish collections in iDigBio were explored through a strictly programmatic approach using the ridigbio package and fishfindR web application. iDigBio facilitates the aggregation of collections data on a purely voluntary fashion that requires collection staff to consent to sharing of their data. Not all collections are sharing their data with iDigBio, but the data harvested from 38 of the 143 known fish collections in the U.S. that are in iDigBio account for the majority of fish specimens housed in U.S. collections. In the 22 years since publication of the last survey providing information on these 38 collections, 1,219,168 specimen records (lots), 15,225,744 specimens, 3,192 primary types, and 32,868 records of secondary types have been added. This is an increase of 65.1% in the number of cataloged records and an increase of 56.1% in the number of specimens. In addition to providing specimen-based data for research, education, and various outreach activities, data that are accessible via data aggregators can be used to develop accurate, up-to-date reports of information on institutional collections. Such reports present collections data in an organized and accessible fashion and can guide targeted efforts by collections personnel to meet discipline-specific needs and make data more transparent to downstream users. Data from this survey will be updated and published regularly in a dynamic web application that will aid collections staff in communicating collections value while simultaneously giving stakeholders a way to explore collections holdings as they relate to the institutions in which they are housed. It is through this resource that collections will be able to leverage their data against those of similar collections to aid in the procurement of financial and institutional support.
FIGURE 11. Champsodon nudivittis, SMF 35063, 7.1 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 11. Champsodon nudivittis, SMF 35063, 7.1 cm SL, Jizan, Saudi Arabia.
FIGURE 13. Pseudorhombus arsius, SMF 35082, 18.3 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 13. Pseudorhombus arsius, SMF 35082, 18.3 cm SL, Jizan, Saudi Arabia.
FIGURE 9. Parastromateus niger, KAUMM 157, 15.8 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 9. Parastromateus niger, KAUMM 157, 15.8 cm FL, Jizan, Saudi Arabia.
FIGURE 12. Parapercis maculata, SMF 35064, 10.2 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 12. Parapercis maculata, SMF 35064, 10.2 cm SL, Jizan, Saudi Arabia.
FIGURE 10. Pomadasys maculatus, SMF 35117, 18.8 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 10. Pomadasys maculatus, SMF 35117, 18.8 cm SL, Jizan, Saudi Arabia.
FIGURE 8. Jaydia smithi, SMF 35013, 8.2 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 8. Jaydia smithi, SMF 35013, 8.2 cm SL, Jizan, Saudi Arabia.
FIGURE 6. Dactyloptena gilberti, SMF 35003, 6.6 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 6. Dactyloptena gilberti, SMF 35003, 6.6 cm SL, anterior view, Jizan, Saudi Arabia.
FIGURE 4. Bregmaceros nectabanus, SMF 34987, 7.2 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 4. Bregmaceros nectabanus, SMF 34987, 7.2 cm SL, Jizan, Saudi Arabia.
FIGURE 3. Saurida longimanus, KAUMM 23, 14.2 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 3. Saurida longimanus, KAUMM 23, 14.2 cm SL, Jizan, Saudi Arabia.
FIGURE 14. Laeops sinusarabici, SMF 35091, 10.4 in Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea
FIGURE 14. Laeops sinusarabici, SMF 35091, 10.4 cm SL, Jizan, Saudi Arabia.
Reef Life Survey data (fish and mobile invertebrate counts) from Carrie Bow Cay, Belize, 2015-2019
<p><strong>Aim</strong></p> <p>Conservation efforts have traditionally addressed the threat of biodiversity loss by prioritizing regions and habitats with high endemic species richness. However, species-poor habitats often harbor distinct, valuable, and/or functionally unique species that contribute to regional diversity. In the tropical marine realm, the "mangrove-seagrass-coral reef continuum" has dominated both the scientific literature and marine spatial planning. Bare sediment habitats are also part of this continuum and often comprise the majority of bottom area, as they do in most regions worldwide, but are understudied and rarely considered in conservation. To address this information gap, we partition the relative contributions of five habitats in the coastal mosaic (forereefs, patch reefs, seagrass, mangroves, and bare sand) to fish diversity across a tropical seascape.</p> <p><strong>Location</strong></p> <p>Carrie Bow Cay, Belize Barrier Reef</p> <p><strong>Methods</strong></p> <p>Using diver visual censuses, we assessed fish community composition at three replicate sites from each of the five habitats annually for five years. We then partitioned diversity into within (α) and between (β) habitat contributions, and further partitioned β-diversity into components attributed to species replacement and richness difference. Finally, we determined the local contributions to β-diversity (LCBD) by each habitat and identified the key individual species behind these contributions.</p> <p class="MsoNormal"><strong>Main Results</strong><br>Tropical sand flats were unique habitats, contributing disproportionately to total fish species diversity across the seascape, despite having the fewest species overall. Sand flats also had higher-than-expected local contributions to β-diversity (LCBD) and had the highest percentage of species not found in other habitats.</p> <p><strong>Main Conclusions</strong></p> <p>Our results demonstrate that previously understudied sand habitats harbor a relatively unique assemblage of species compared with other nearby habitats. Marine spatial planning aimed at maximizing preservation of total biodiversity (including unique species) in the tropics should consider sand habitats.</p>
Fig. 1 in Coleoptera in Floods: Biotic Surveys, Fish Food, Adaptation, Reconstruction of Paleoenvironments, and Preconstruction of Neoenvironments
Fig. 1. "Beetles in a Flood" (from Lydekker 1896, facing page 128).
Supplementary material 1 from: Dou H, Wang M, Yin X, Feng L, Yang H (2023) Can the Eurasian otter (Lutra lutra) be used as an effective sampler of fish diversity? Using molecular assessment of otter diet to survey fish communities. Metabarcoding and Metagenomics 7: e96733. https://doi.org/10.3897/mbmg.7.96733
Bioinformatic processing
Supplementary material 2 from: Dou H, Wang M, Yin X, Feng L, Yang H (2023) Can the Eurasian otter (Lutra lutra) be used as an effective sampler of fish diversity? Using molecular assessment of otter diet to survey fish communities. Metabarcoding and Metagenomics 7: e96733. https://doi.org/10.3897/mbmg.7.96733
appendices S1–S4.2
Supplementary material 2 from: Nagy AA, Erős N, Imecs I, Bóné G, Fülöp A, Pap PL (2023) Distribution and diversity of fishes and lampreys in Transylvania (Romania): a complete survey and suggestions for new protected areas. ZooKeys 1166: 351-373. https://doi.org/10.3897/zookeys.1166.102854
Maps S1–S77
Supplementary material 1 from: Nagy AA, Erős N, Imecs I, Bóné G, Fülöp A, Pap PL (2023) Distribution and diversity of fishes and lampreys in Transylvania (Romania): a complete survey and suggestions for new protected areas. ZooKeys 1166: 351-373. https://doi.org/10.3897/zookeys.1166.102854
Raw data of sampling sites, fish and lamprey species and their numbers
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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.