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52 results for “visual fish”
Ten years (2013-2023) of fish assemblage data collected seasonally with underwater visual surveys on paired artificial and natural reefs
<p>The study of assembly patterns and dynamics of organisms has long remained a foundational theme in ecology. Further, the relationship between assemblages and different habitats can provide important insight on ecological processes and guide management and conservation efforts (e.g., restoration, protected areas). We conducted underwater visual surveys of reef fish assemblages at 14 sites in the eastern Gulf of Mexico, including eight that were paired artificial and natural reefs. By using a paired design, we controlled biotic (e.g., larval supply), abiotic (e.g., depth), and socio variables (e.g., fishing access) to isolate the effect of reef type. Trained scientific SCUBA divers with extensive experience with reef fishes from the broader tropical western Atlantic region conducted two to four 10-minute stationary surveys on the paired reefs each season (i.e., calendar quarters) for 10 years from spring 2013 to spring 2023. We also surveyed six additional artificial reefs from winter 2020 to spring 2023 that lacked natural reef pairs. During each survey, the divers identified and estimated the total lengths of all taxa<strong> </strong>observed within an imaginary cylinder around them. The imaginary cylinders had a radius up to 7.5 meters (depending on horizontal visibility) and extended from the seafloor to the highest visible water above the diver. During the period of study, we conducted a total of 1,349 surveys and counted 544,736 fish that represented 171 taxa (most at the species level). Analyses of these data have revealed habitat-specific heterogeneity of the fish assemblages at both taxonomic and functional trait levels, the importance of herbivory in structuring the benthos, and socio-ecological interactions in the system, among other findings. These data may be useful for other researchers interested in patterns and dynamics of populations and communities, functional traits, taxa-habitat relationships, and for parameterizing statistical, joint distribution, metacommunity, and ecosystem models. In addition, because many of the observed taxa<strong> </strong>are of management concern, they may be useful for researchers interested in fisheries science. The data are free to use, are not copyright restricted, and we ask users to cite this data paper.</p>
Data accompanying the master thesis: A neuronal model for visually evoked startle responses in schooling fish
<p>This dataset contains data that was generated and analyzed for the master thesis "A neuronal model for visually evoked startle responses". All related material, including analysis code, of the master thesis can be found at https://github.com/awakenting/master-thesis.</p>
Figure S2 in Assessing structure and seasonal variations of a temperate shallow water fish assemblage through Snorkel Visual Census
Figure S2. – Diel variation in observation frequency of individual species. Gobiusculus flavescens and S. melops were both more frequent at daytime, while A. anguilla, M. scorpius, S. trutta, G. morhua, C. harengus and T.bubalis were, all more frequently encountered at night.
Figure S1 in Assessing structure and seasonal variations of a temperate shallow water fish assemblage through Snorkel Visual Census
Figure S1. – Diel variations in assemblage structure was significant (X2 P <0.05). Demersal fishes are most abundant at day, while benthic fishes are dominant at night. Abundance of pelagic fishes increase at night.
Figure 2. – Monthly average species richness observed during diurnal counts from June 2013 in Assessing structure and seasonal variations of a temperate shallow water fish assemblage through Snorkel Visual Census
Figure 2. – Monthly average species richness observed during diurnal counts from June 2013 to August 2014. Error bars represent ±SD. Number of counts per month are, indicated at column bases.
Figure 3 in Assessing structure and seasonal variations of a temperate shallow water fish assemblage through Snorkel Visual Census
Figure 3. – Correlation between temperature and species richness compared between diurnal and nocturnal counts. Dotted trendlines show the quadratic and linear relationships between species richness and temperature at diurnal and nocturnal counts respectively.
Fig. 2 in The almost invisible league: crypsis and association between minute fishes and shrimps as a possible defence against visually hunting predators
Fig. 2. Three members of the almost invisible league: Priocharax ariel (top centre), Palaemonetes carteri (bottom left), Microphilypnus amazonicus (bottom right) in aquarium under artificial light. Same specimens as in Fig. 1 except for M. amazonicus (17.8 mm SL, INPA 25244).
Fig. 5. A in The almost invisible league: crypsis and association between minute fishes and shrimps as a possible defence against visually hunting predators
Fig. 5. A juvenile Centropomus mexicanus (12.9 mm SL, ZUEC 6171) gorged with eleotrid fish prey, photographed in field aquarium under artificial light.
Fig. 1 in The almost invisible league: crypsis and association between minute fishes and shrimps as a possible defence against visually hunting predators
Fig. 1. The studied igapó habitat in Amazonia (top left) with leaf-litter debris on the bottom; the eleotrid fish Microphilypnus amazonicus camouflaged on a decomposing leaf (17.5 mm SL, INPA 25244, top right), the characid fish Priocharax ariel hovering in the water column close to a dead leaf (14.3 mm SL, INPA 25243, bottom left), and the palaemonid shrimp Palaemonetes carteri crawling on a dead leaf (23. 7 mm TL, INPA 1432, bottom right). The cryptic effect of each species' colour pattern is lessened under artificial light (photographed in aquarium).
Fig. 4. A in The almost invisible league: crypsis and association between minute fishes and shrimps as a possible defence against visually hunting predators
Fig. 4. A larval Eleotris pisonis (8.8 mm SL, ZUEC 6169, left) and a juvenile Eucinostomus melanopterus (11.3 mm SL, ZUEC 5378, right) photographed in field aquarium under artificial light.
Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika
<p>Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins – but not the rhodopsin – rank among the most differentially expressed genes in the retina, together with other vision-, circadian-rhythm-, and haemoglobin-related genes. We propose two new visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes.</p>
Data for: Coordination and persistence of aggressive visual communication in Siamese fighting fish
Open the record for dataset details and reuse information.
Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika
Open the record for dataset details and reuse information.
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Comparison of mono-, MiL- and CARD-FISH on LR-White embedded <em>Olavius algarvensis</em> cross sections A: Ethanol preserved specimen, cu = cuticle, sym = symbionts, sep = septum, epi = epidermis, mu = muscle, vbv = ventral blood vessel & nerve chord, chl = chloragogen tissue, grid square = example of region shown in images B, C, D and E.</p> <p>Probes for Gammaproteobacteria (Gam42a; green) and a subgroup of sulfate-reducing Deltaproteobacteria (DSS658; red) on B) mono-FISH on ethanol preserved specimen, 19 hour hybridisation. C) mono-FISH on ethanol preserved specimen, 3 hour hybridisation and D) CARD-FISH on Carnoy’s / PFA fixed specimen, 3-hour hybridisation. E) MiL-FISH on Carnoy’s / PFA fixed specimen, 3 hour hybridisation. Scale bar = 5 µm.</p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Sections of LR-White embedded <em>Olavius algarvensis </em>eggs. A) DAPI stained overview of egg after first cleavage, grid square = region in B, cle = cleavage. B) Gamma- (ii) and Delta- (i) proteobacteria hybridised with 4x labelled Gam42a & 4x labelled DSS658 probe respectively. Autofluorescence of egg yolk is overcome and bacteria are seen to closely associated with the developing embryo. y = egg yolk C) DAPI stained overview of juvenile worm in egg, grid square = region in D. D) Gamma 1 symbiont phylotype (iii) hybridised with 16S rRNA specific probe labelled with 2x FITC and 2x Cy3 to produce yellow in the overlay. Symbiont cells are incorporated between cuticle and epidermis and in close proximity to egg yolk. y = egg yolk, c = cuticle. Scale: A & C = 50 µm, B & D = 5 µm.</p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Epifluorescence images of MiL-FISH labelled microorganisms: A) <em>Beggiatoa sp. </em>hybridised with Gam42a, B) <em>Desulfococcus biacutus </em>with DSS658, C) <em>Roseobacter sp. </em>with Ros537, D) <em>Sulfurimonas denitrificans </em>with EPSY914, E) <em>Rhodopirellula sp. </em>SH1 T with PLA46, F) <em>Gramella forsetii </em>with CF319a, G) <em>Metallosphaera sedula </em>with Arch915, H) Composite image of all seven microbial partners in an artificial mix. Letters correlate to images of individual organisms A-G. Scale bar: A & H = 10 µm, B-G = 5 µm.</p> <p>From:</p> <p>Schimak MP, Kleiner M, Wetzel S, Liebeke M, Dubilier N, Fuchs BM. 2015. MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells. Applied and Environmental Microbiology. Accepted manuscript posted online. doi:10.1128/AEM.02776-15</p>
Data from: Dietary partitioning among three cryptobentic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis
<p>Understanding how mesopredators partition their diet and the identity of consumed prey can assist in understanding the ecological role predators and prey play in ecosystem trophodynamics. Here, we assessed the diet of three common coral reef mesopredators; <em>Pseudochromis flavivertex</em>, <em>Pseudochromis fridmani</em>, and <em>Pseudochromis olivaceus</em> from the family Pseudochromidae, commonly known as dottybacks, using a combination of i) visual stomach content analysis, ii) stomach content DNA metabarcoding (18S, COI), and iii) stable isotope analysis (δ<sup>15</sup>N, δ<sup>13</sup>C). In addition, <em>P. flavivertex</em> is found in two distinct color morphs in the Red Sea, providing an opportunity to analyze intra-morph differences. These techniques revealed partitioning in the dietary composition and resource use among species. Arthropods comprised the main dietary component of <em>P. flavivertex</em> (18S > 60%; COI > 10%), and <em>P. olivaceus</em> (18S = 57.2%) while <em>P. fridmani</em> ingested predominantly mollusks (18S = 51.3%, COI = 24.6%). Despite being small predators, microplastics were found in the gut content of some of these fishes. Stable isotope analysis showed differences in species' isotopic niche breadth and trophic position. <em>Pseudochromis olivaceus</em> presented the largest isotopic niche (SEA<sub>C</sub> = 1.61‰<sup>2</sup>), while <em>P. fridmani</em> showed the smallest isotopic niche (SEA<sub>C</sub> = 0.45‰<sup>2</sup>) among species. Although the two techniques used for stomach content analysis did not show differences in the diet within color morphs of <em>P. flavivertex</em>, they differed in the isotopic niche and resource use. Despite our limited sampling, our findings provide evidence of species-specific differences in the trophic ecology of dottybacks and demonstrate their important role as predators of cryptic invertebrates and small fishes. This study highlights the importance of combining several approaches (short-term: visual analysis and DNA metabarcoding; and long-term: isotope analysis) when assessing the feeding habits of coral reef fish, as they provide complementary information necessary to delimit their niches and understand the role that small mesopredators play in coral reef ecosystems.</p>
Data for: Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes
<p>Coral reef fishes are diverse in ecology and behaviour and show remarkable colour variability. Investigating the visual pigment gene (opsin) expression in these fishes makes it possible to associate their visual genotype and phenotype (spectral sensitivities) to visual tasks, such as feeding strategy or conspecific detection. By studying all major damselfish clades (Pomacentridae) and representatives from five other coral reef fish families, we show that the long-wavelength-sensitive (<em>lws</em>) opsin is highly expressed in algivorous and less or not expressed in zooplanktivorous species. <em>Lws</em> is also upregulated in species with orange/red colours (reflectance >520 nm) and expression is highest in orange/red-coloured algivores. Visual models from the perspective of a typical damselfish indicate that sensitivity to longer wavelengths does enhance the ability to detect the red to far-red component of algae and orange/red-coloured conspecifics, possibly enabling social signalling. Character state reconstructions indicate that in the early evolutionary history of damselfishes, there was no <em>lws</em> expression and no orange/red coloration. Omnivory was most often the dominant state. Although herbivory was sometimes dominant, zooplanktivory was never dominant. Sensitivity to long wavelength (increased <em>lws</em> expression) only emerged in association with algivory but never with zooplanktivory. Higher <em>lws</em> expression is also exploited by social signalling in orange/red, which emerged after the transition to algivory. Although the relative timing of traits may deviate by different reconstructions and alternative explanations are possible, our results are consistent with sensory bias whereby social signals evolve as a correlated response to natural selection on sensory system properties in other contexts.</p>
The influence of food web structure and foraging behaviour on visual system traits in a predatory freshwater fish
<p>Dataset used in the manuscript titled "The influence of food web structure and foraging behaviour on visual system traits in a predatory freshwater fish" Dataset includes lake trout visual system traits, body size, and food web structural attributes sampled from four different lakes in Algonquin, ON, Canada.</p>
Data from: Navigating the scales of diversity in subtropical and coastal fish assemblages ascertained by eDNA and visual surveys
<p>Environmental DNA (eDNA) metabarcoding emerges as a powerful method, allowing a more exhaustive investigation of fish fauna than any other methods. Yet, the general use of eDNA as a replacement of traditional methods such as visual surveys or physical sampling remains debatable. Therefore, a prior understanding of eDNA's spatial resolution is necessary. This study aimed to compare the assessments of fish diversity at three spatial scales by eDNA, underwater visual census (UVC), and diver-operated video (DOV) surveys across 21 reef sites in northern Taiwan. The specific objectives were to explore the regional species pool (γ-diversity), reveal spatial patterns of fish assemblages (β-diversity), and disentangle the relationships between fish assemblages and benthic composition (α-diversity). At the γ-diversity level, a total of 438 marine fish species were detected across methods. eDNA exhibits an extraordinary power to explore the regional species pool given sufficient replication, a power which is unachievable by DOV and UVC. At the β-diversity level, all the methods successfully revealed the same spatial patterns of beta diversity and the distance decay of similarity in fish assemblages. At the α-diversity level, none of the methods is capable of investigating the entire resident fish fauna, but visual surveys are more suitable for scrutinizing interactions between fish and benthos. Instead of undiscriminatingly recommending a combination of eDNA with traditional survey methods, we suggest implementing specific surveys in accordance with the ecological questions of interest.</p>
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Allen Brain Atlas
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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.