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862 results for “marine fish”
Tracking long-distance migration of marine fishes using compound-specific stable isotope analysis of amino acids
The long-distance migrations by marine fishes are difficult to track by field observation. Here, we propose a new method to track such migrations using stable nitrogen isotopic composition at the base of the food web (<i>δ</i><sup>15</sup>N<sub>Base</sub>), which allows for direct comparison of isotope ratios between proxy organisms of the isoscape and the target migratory animal. We initially constructed a <i>δ</i><sup>15</sup>N<sub>Base</sub> isoscape in the North Pacific by bulk and compound-specific isotope analyses of copepods (<i>n</i> = 360 and 24, respectively). We then determined retrospective <i>δ</i><sup>15</sup>N<sub>Base</sub> values of spawning chum salmon (<i>Oncorhynchus keta</i>) from their vertebral centra (10 sections from each of two salmon), and estimated their migration routes by using a state-space model. Our isotope tracking method successfully reproduced a known chum salmon migration route between the Okhotsk and Bering seas, and our findings suggest the presence of a migration route to the Bering Sea Shelf during a later growth stage.
Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses.
Metabolic impacts of climate change on marine fish communities and fisheries - Dataset and figure plot script
<p>Here we provide the MATLAB functions, model forcing data (net primary production and temperature), and model output required to generate the figures and perform calculations from the manuscript "Metabolic impacts of climate change on marine fish communities and fisheries", which is currently in submission as a research article. The figures plot script (plot_figures_climate_fish_deconstruction.m) is written in MATLAB version R2012a.</p>
Productivity-Susceptibility Analysis for Top 250 Marine Aquarium Fish Supplemental Information
<p>Data storage for supplemental information, containting the full dataset, a summarized dataset, and comparing vulnerability scores between FishBase and our Productivity-Susceptibility Analysis. </p>
Individual variation in marine larval-fish swimming speed and the emergence of dispersal kernels
<p>Dispersal emerges as a consequence of how an individual's phenotype interacts with the environment. Not all dispersing individuals have the same phenotype, and variation among individuals can generate complex variation in the distribution of dispersal distances and directions. While active locomotion performance is an obvious candidate for a dispersal phenotype, its effects on dispersal are difficult to measure or predict, especially in small organisms dispersing in wind or currents. Therefore, we analyzed the effects of larval swimming on dispersal and settlement of coral-reef fish larvae using a high-resolution biophysical model. The model is, to date, the only biophysical model of marine larval dispersal that has been statistically validated against genetic parentage estimates of larval origin and destination, and incorporates empirically-estimated larval behaviors and their ontogeny. Larval swimming, in combination with depth, orientation, and navigation behaviors, actually reduced dispersal distances compared to those of passive larvae. Swimming had no consistent effects on long distance dispersal, but increased the spread of settlement locations. Swimming speed, in contrast, did not consistently affect median dispersal distances, but faster swimming larvae had greater mean and maximum dispersal distances than slower swimming larvae. Finally, faster larval swimming speeds consistently increased the probability of settlement. Our analysis shows how larval swimming differentially affects multiple properties of dispersal kernels. In doing so, it indicates how selection could favor faster larval swimming to increase settlement, which may actually result in longer dispersal distances as a by-product of larvae trying to locate habitat rather than to disperse greater distances.</p>
An updated life history scheme for marine fishes predicts recruitment variability and sensitivity to exploitation
<p><b>Aim:</b> Patterns of population renewal in marine fishes are often irregular and lead to volatile fluctuations in abundance that challenge management and conservation efforts. Here, we examine the relationship between life history strategies and recruitment variability in exploited marine fish species using a macroecological approach. <b>Location:</b> Global ocean.</p> <p><b>Time period:</b> 1950-2018.</p> <p><b>Major taxa studied:</b> Bony and cartilaginous fish.</p> <p><b>Methods:</b> Based on trait data for 244 marine fish species, we objectively extend the established Equilibrium-Periodic-Opportunistic (<i>E-P-O</i>) life history classification scheme to include two additional emergent life history strategies: "Bet-hedgers" (<i>B</i>) and Salmonic (<i>S</i>) strategists. <i>B</i> strategists include Rockfishes and other species inhabiting patchy benthic habitats with life histories that blend characteristics of <i>E</i> and <i>P</i> species; they combine very long lifespans with elevated investments in both parental care and fecundity. <i>S</i> strategists are comprised of mostly salmonids that share life history characteristics with <i>E</i> and <i>O</i> species: elevated investments in parental care reminiscent of <i>E</i> strategists, but with reduced fecundity and short lifespans characteristic of <i>O</i> species. We analyzed how the <i>E-B-P-O-S</i> life history classification mapped onto patterns of recruitment variability observed in population time series data (n = 156 species).</p> <p><b>Results:</b> Generalized linear models suggest that life history strategy explains a modest, yet significant amount of recruitment variability across species. Greater predictive power arose after controlling for increased recruitment variance associated with variable fishing pressure, with <i>O</i> strategists showing the strongest sensitivity. <i>B</i> strategists were similarly susceptible to exploitation as <i>P</i> stocks, but their longer times to maturity make them particularly vulnerable to overfishing. <b>Main conclusions:</b> A broader recognition of the distinct ecology of Salmonic and Bet-hedger groups is important when studying life history strategies in marine fish. More generally, our results stress the importance of considering life history strategies for understanding patterns of recruitment variability across fish stocks.</p>
Does genome size increase with water depth in marine fishes?
<p><span>A growing body of research suggests that genome size in animals can be affected by ecological factors. Half a century ago, Ebeling et al. (1971; EEA71) proposed that genome size increases with depth in some teleost fish groups and discussed a number of biological mechanisms that may explain this pattern (e.g., passive accumulation, adaptive acclimation). Using phylogenetic comparative approaches, we revisit this hypothesis based on genome size and ecological data from up to 708 marine fish species in combination with a set of large-scale phylogenies, including a newly inferred tree. We also conduct modelling approaches of trait evolution and implement a variety of regression analyses to assess the relationship between genome size and depth. Our reanalysis of the EEA71 dataset shows a weak association between these variables, but the overall pattern in their data is driven by a single clade. While analyses based on the new dataset resulted in positive correlations, providing some evidence that genome size evolves adaptively as a function of depth, only a fraction of individual subclade analyses yielded statistically significant results. By contrast, negative correlations are rare and largely non-significant. All in all, we find modest evidence for an increase in genome size along the depth axis in marine fishes. We discuss some mechanistic explanations for the observed trends.</span></p>
Data from: Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary
The Cretaceous–Palaeogene (K–Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K–Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic. Recent multilocus studies have provided the first resolved phylogenetic backbone for acanthomorphs and suggested novel relationships among major lineages. However, these new relationships and associated timescales have not been interrogated using phylogenomic approaches. Here, we use targeted enrichment of >1,000 ultraconserved elements in conjunction with a divergence time analysis to resolve relationships among 120 major acanthomorph lineages and provide a new timescale for acanthomorph radiation. Our results include a well-supported topology that strongly resolves relationships along the acanthomorph backbone and the recovery of several new relationships within six major percomorph subclades. Divergence time analyses also reveal that crown ages for five of these subclades, and for the bulk of the species diversity in the sixth, coincide with the K–Pg boundary, with divergences between anatomically and ecologically distinctive suprafamilial clades concentrated in the first 10 million years of the Cenozoic.
Data and R script: Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era
<p>Raw data and R code necessary to reproduce the results of the paper entitled "Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era" published in Frontiers in Ecology and the Environment.</p> <p> </p>
Marine fishes of Belize list.docx: a species list of shorefishes from Belize by Marine Fish of Belize (Anon. 2008).
<p>Marine fishes of Belize list.docx: a species list of shorefishes from Belize by Marine Fish of Belize (Anon. 2008).<br> </p> <p>data from Starck, W.A., Estapé C.J. & Morgan Estapé, A. (2017) The fishes of Alligator Reef and environs in the<br> Florida Keys: a half-century update. Journal of the Ocean Science Foundation, 27, 74–117.</p>
Long-term changes in taxonomic and functional composition of European marine fish communities
<p>Evidence of large-scale biodiversity degradation in marine ecosystems has been reported worldwide, yet most research has focused on few species of interest or on limited spatiotemporal scales. Here we assessed the spatial and temporal changes in the taxonomic and functional composition of fish communities in European seas over the last 25 years (1994-2019). We then explored how these community changes were linked to environmental gradients and fishing pressure. We show that the spatial variation in fish species composition is more than two times higher than the temporal variation, with a marked spatial continuum in taxonomic composition and a more homogenous pattern in functional composition. The regions warming the fastest are experiencing an increasing dominance and total abundance of r-strategy fish species (lower age of maturity). Conversely, regions warming more slowly show an increasing dominance and total abundance of K-strategy species (high trophic level and late reproduction). Among the considered environmental variables, sea surface temperature, surface salinity, and chlorophyll-a most consistently influenced communities' spatial patterns, while bottom temperature and oxygen had the most consistent influence on temporal patterns. Changes in communities' functional composition were more closely related to environmental conditions than taxonomic changes. Our study demonstrates the importance of integrating community-level species traits across multi-decadal scales and across a large region to better capture and understand ecosystem-wide responses and provides a different lens on community dynamics that could be used to support sustainable fisheries management.</p>
Fig. 9 a–e N. exocoeti Pillai 1954 in Nerocila species (Crustacea, Isopoda, Cymothoidae) from Indian marine fishes
Fig. 9 a–e N. exocoeti Pillai 1954, ovigerous female (MNHN-IU-2009-1936): a–e, pleopods 1–5
Fig. 1 in Nerocila species (Crustacea, Isopoda, Cymothoidae) from Indian marine fishes
Fig. 1 Map showing the sampling area
Fig. 2 in First report on the occurrence of two marine ornamental fishes (Acanthuriformes) from Northern part of the Bay of Bengal, India
Fig. 2 — Zanclus cornutus (Linnaeus, 1758)
Fig. 1 in First report on the occurrence of two marine ornamental fishes (Acanthuriformes) from Northern part of the Bay of Bengal, India
Fig. 1 — Acanthurus xanthopterus Valenciennes, 1835
Fig. 2 in It is recreational but profitability also matters: A cost-effective economic approach to marine recreational fishing in Spain Abstract
Fig. 2: Summary diagram of the cost-effectiveness indicator calculation process.
Data from: Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance
<p>The separation of closely-related terrestrial or freshwater species by vast marine barriers represents a biogeographic riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographic ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here we present a new total-evidence hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographic pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.</p>
Fig. 1 in Assessment of coastal fish assemblages before the establishment of a new marine protected area in the central Mediterranean: its role in formulating a zoning proposal Abstract
Fig. 1: Map of the study area with indication of sampling sectors around the promontory of Milazzo.
Fig. 4. Transversotrema licinum MANTER, 1970 from Diplodus noct. Ventral view. Scale 1.00 in Digenetic Trematodes From Marine Fishes Off The Coast Of Kuwait, Arabian Gulf: Fellodistomidae And Some Smaller Families, New Host And Geographic Records
Fig. 4. Transversotrema licinum MANTER, 1970 from Diplodus noct. Ventral view. Scale 1.00 mm
Fig. 5. Treptodemus latus MANTER, 1961 from Hemiramphus marginatus. Ventral view. Scale 1.00 in Digenetic Trematodes From Marine Fishes Off The Coast Of Kuwait, Arabian Gulf: Fellodistomidae And Some Smaller Families, New Host And Geographic Records
Fig. 5. Treptodemus latus MANTER, 1961 from Hemiramphus marginatus. Ventral view. Scale 1.00 mm
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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)
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.