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212 results for “fish ecology”
Data from: Ecological specialisation of reef fishes peaks in global biodiversity hotspots
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Data from: Dine and dash: How trophic ecology and migration shape functional locomotory traits in Clupeiform fishes
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Thermal history mediates the ecological role of body size in a freshwater fish
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Common barriers, but temporal dissonance: genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community
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The visual ecology of Holocentridae, a nocturnal coral reef fish family with a deep-sea-like multibank retina
<p>The visual systems of teleost fishes usually match their habitats and lifestyles. Since coral reefs are bright and colourful environments, the visual systems of their diurnal inhabitants have been more extensively studied than those of nocturnal species. In order to fill this knowledge gap, we conducted a detailed investigation of the visual system of the nocturnal reef fish family Holocentridae. Results showed that the visual system of holocentrids is well adapted to their nocturnal lifestyle with a rod-dominated retina. Surprisingly, rods in all species were arranged into 6-17 well-defined banks, a feature most commonly found in deep-sea fishes, that may increase the light sensitivity of the eye and/or allow colour discrimination in dim-light. Holocentrids also have the potential for dichromatic colour vision during the day with the presence of at least two spectrally different cone types: single cones expressing the blue-sensitive <i>SWS2A</i> gene, and double cones expressing one or two green-sensitive <i>RH2</i> genes. Some differences were observed between the two subfamilies, with Holocentrinae (squirrelfish) having a slightly more developed photopic visual system than Myripristinae (soldierfish). Moreover, retinal topography of both ganglion cells and cone photoreceptors showed specific patterns for each cell type, likely highlighting different visual demands at different times of the day, such as feeding. Overall, their well-developed scotopic visual systems and the ease of catching and maintaining holocentrids in aquaria, make them ideal models to investigate teleost dim-light vision and more particularly shed light on the function of the multibank retina and its potential for dim-light colour vision.</p>
Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic and environmental influences. We demonstrate how this may be done by comparing the ontogenetic scaling of resting metabolic rate among populations of the same species (the amphipod Gammarus minus) in mid-Appalachian freshwater springs with similar, relatively constant environmental conditions, except for the varying presence of the predatory fish Cottus cognatus. We found that populations of G. minus exhibit significantly lower metabolic scaling slopes (0.54 to 0.62) in three freshwater springs with C. cognatus than in two springs without these fish (0.76 to 0.77). We tested multiple hypothetical causes for these population differences. Our results best supported the hypothesis that metabolic scaling was influenced by the effects of size-selective predation on the ontogeny of growth, a metabolically expensive process. The body-size scaling of growth is significantly less steep in the populations inhabiting springs with versus without fish, thus paralleling the interpopulation differences in metabolic scaling. Prematurational growth of G. minus is as high or higher in the fish springs, whereas postmaturational growth is significantly lower, often approaching zero. Similarly the amphipods in the fish springs tend to have higher metabolic rates at small sizes, but lower metabolic rates at large sizes, compared to those in the fishless springs. Our results do not support other hypothetical causes of the interpopulation variation in metabolic scaling, including differential scaling of cell size or low-metabolism body components (fat and mineralized exoskeleton), or possible effects of other environmental factors associated with the presence of fish. However, fish-induced population differences in adult behavioral activity may influence metabolic scaling in G. minus, a possibility under current study. We conclude that ecological factors may significantly influence metabolic scaling, contrary to common belief.
Data from: Demographic plasticity facilitates ecological and economic resilience in a commercially important reef fish
1. Variation in life-history characteristics is evident within and across animal populations. Such variation is mediated by environmental gradients and reflects metabolic constraints or trade-offs that enhance reproductive outputs. While generalizations of life-history relationships across species provide a framework for predicting vulnerability to overexploitation, deciphering patterns of intraspecific variation may also enable recognition of peculiar features of populations that facilitate ecological resilience. 2. This study combines age-based biological data from geographically disparate populations of bluespine unicornfish (Naso unicornis)—the most commercially-valuable reef-associated species in the insular Indo-Pacific—to explore the magnitude and drivers of variation in life span and examine the mechanisms enabling peculiar mortality schedules. 3. Longevity and mortality schedules were investigated across eleven locations encompassing a range of latitudes and exploitation levels. The presence of different growth types was examined using back-calculated growth histories from otoliths. Growth-type dependent mortality (mortality rates associated with particular growth trajectories) was corroborated using population models that incorporated size-dependent competition. 4. We found a threefold geographic variation in life span that was strongly linked to temperature, but not to anthropogenic pressure or ocean productivity. All populations consistently displayed a two-phase mortality schedule, with higher than expected natural mortality rates in earlier stages of post-settlement life. Reconstructed growth histories and population models demonstrated that variable growth types within populations can yield this peculiar biphasic mortality schedule, where fast growers enjoy early reproductive outputs at the expense of greater mortality, and benefits for slow growers derive from extended reproductive outputs over a greater number of annual cycles. This promotes population resilience because individuals can take advantage of cycles of environmental change operating at both short and long-term scales. 5. Our results highlight a prevailing, fundamental misperception when comparing the life histories of long-lived tropical ectotherms: the seemingly incongruent combination of extended life spans with high mortality rates was enabled by coexistence of variable growth types in a population. Thus a demographic profile incorporating contrasting growth and mortality strategies obscures the demographic effects of harvest across space or time in N. unicornis and possibly other ectotherms with the combination of longevity and asymptotic growth.
Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g. dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an ANOVA-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within-populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.
Data from: Predicting ecological and phenotypic differentiation in the wild: a case of piscivorous fish in a fishless environment
Environmental variation drives ecological and phenotypic change. How predictable is differentiation in response to environmental change? Answering this question requires the development and testing of multifarious a priori predictions in natural systems. We employ this approach using Gobiomorus dormitor populations that have colonized inland blue holes differing in the availability of fish prey. We evaluated predictions of differences in demographics, habitat use, diet, locomotor and trophic morphology, and feeding kinematics and performance between G. dormitor populations inhabiting blue holes with and without fish prey. Populations of G. dormitor independently diverged between prey regimes, with broad agreement between observed differences and a priori predictions. For example, in populations lacking fish prey, we observed male-biased sex ratios, a greater use of shallow-water habitat, and larger population diet breadths as a result of greater individual diet specialization. Furthermore, we found predictable differences in body shape, mouth morphology, suction generation capacity, strike kinematics, and feeding performance on different prey types, consistent with the adaptation of G. dormitor to piscivory when coexisting with fish prey and to feeding on small invertebrates in their absence. The results of the present study suggest great potential in our ability to predict population responses to changing environments, which is an increasingly important capability in a human-dominated, ever-changing world.
Data from: Ecological change alters the evolutionary response to harvest in a freshwater fish
Harvesting can induce rapid evolution in animal populations, yet the role of ecological change in buffering or enhancing that response is poorly understood. Here, we developed an eco-genetic model to examine how ecological changes brought about by two notorious invasive species – zebra and quagga mussels– influence harvest-induced evolution and resilience in a freshwater fish. Our study focused on lake whitefish (Coregonus clupeaformis) in the Laurentian Great Lakes, where the species supports valuable commercial and subsistence fisheries, and where the invasion of dreissenid (zebra and quagga) mussels caused drastic shifts in ecosystem productivity. Using our model system, we predicted faster rates of evolution of maturation reaction norms in lake whitefish under pre-invasion ecosystem conditions when growth and recruitment of young to the population were high. Slower growth rates that occurred under post-invasion conditions delayed when fish became vulnerable to the fishery, thus decreasing selection pressure and lessening the evolutionary response to harvest. Fishing with gill nets and traps nets generally selected for early maturation at small sizes, except when fishing at low levels with small mesh gill nets under pre-invasion conditions; in this latter case, evolution of delayed maturation was predicted. Overall, the invasion of dreissenid mussels lessened the evolutionary response to harvest, while also reducing the productivity and commercial yield potential of the stock. These results demonstrate how ecological conditions shape evolutionary outcomes and how invasive species can have a direct effect on evolutionary responses to harvest and sustainability.
Data and code for: A sensory ecology of fear: Eye size predicts moonlight avoidance responses in Neotropical electric fishes
<p>Data in support of: Eye size predicts moonlight avoidance responses in Neotropical electric fishes</p>
FIGURE 3. FISH showing the chromosomes with 35S in Does Solidago litoralis (Asteraceae) merit specific rank? Insights from cytogenetic, molecular and ecological data
FIGURE 3. FISH showing the chromosomes with 35S (red) and 5S (green) signals. A. Partial metaphase of S. litoralis; B. Partial metaphase of S. virgaurea (Livorno); C. S. virgaurea (Monte Pisano); D. S. virgaurea (Tre Potenze). Scale bar: 10 μm.
Data from: Evolution of codfishes (Teleostei: Gadinae) in geographical and ecological space: evidence that physiological limits drove diversification of subarctic fishes
Aim: To develop a holistic biogeographical history of codfishes in the subfamily Gadinae based on historical relationships, ecological niche, and evolution of physiological tolerances. Two alternative diversification scenarios were tested in two co-distributed, Northern Hemisphere clades: (1) clade ancestors were temperate, and environmental niche has been conserved over evolutionary time, implying that speciation was driven by vicariance associated with ice sheet formation; and (2) clade ancestors were Arctic, and species convergently adapted to temperate environmental conditions, implying that speciation was driven by repeated adaption to temperate environments. Location: Northern Hemisphere Arctic and subarctic oceans. Methods: Fifty-five new sequences of four genes from 23 tissue samples were combined with 10 GenBank sequences to generate a time-calibrated phylogenetic hypothesis. Combining the phylogeny with information on species' ecological niche tolerances inferred from correlational models, I reconstructed ancestral environmental tolerances of each of the focal clades. These results were combined with Bayesian area-based biogeographical analysis and regional palaeoclimatic history to develop a holistic biogeographical history of Gadinae. Results: Of 18 environmental variables describing species' tolerances to salinity, temperature, sea ice concentration, and mixed layer depth, only mean, maximum and minimum sea bottom temperature, and mean and minimum sea surface temperature showed phylogenetic signal across Gadinae. Both ecological niche and geographical distributions of gadine fishes are largely conservative, but two clades contain both Pacific and Atlantic species. Focal clade divergence time estimates suggest a Pliocene origin for both, with further Pleistocene divergence. Main conclusions: Reconstructed ancestral environmental tolerances of crown cods and tomcods support a temperate origin of both groups. The timing of diversification of these two clades and the intolerance of temperate species to sea ice suggest that cyclical Arctic ice formation drove divergence. Future sea ice reduction may have dramatic consequences for distributions and persistence of commercially important species when currently allopatric temperate species come into secondary contact.
Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
Figure 1. A in The den ecology and the effects of fishing pressure on the distribution of Octopus cyanea (Octopodidae: Mollusca) in Rodrigues lagoon, Rodrigues, Mauritius
Figure 1. A map of the geographical location of the island of Rodrigues showing the four protected areas in the north and north west (solid lines) and the approximate area of Ile aux Fous (nonprotected, dotted line).
Figure 3. A in The den ecology and the effects of fishing pressure on the distribution of Octopus cyanea (Octopodidae: Mollusca) in Rodrigues lagoon, Rodrigues, Mauritius
Figure 3. A schematic diagram of a transect set-up and the search path that was used for recording the octopus dens and the invertebrate benthos. The blue circle indicates the position of the painted rock, a marker to allow a second transect within 100 m of the first one to be measured. The dashed lines show the position of the outer tape measures which marked out the sample area, the small arrows show the direction each surveyor looked either side of the inner belt transect (2 m either side), the red lines show the position of the inner three transects that were used for recording, the long arrows show the direction each surveyor swam along each transect and the small numbers show the distance along the bottom tape measure that the three inner transects were placed.
Figure 5 in The den ecology and the effects of fishing pressure on the distribution of Octopus cyanea (Octopodidae: Mollusca) in Rodrigues lagoon, Rodrigues, Mauritius
Figure 5. Figure with the average plus standard error of the number of counted holes per region for the first sampling occasion (a) and the second sampling occasion(b). White = Area 1 (Ile aux Fous), stripes = Area 2 (Anse aux Anglais), black = Area 3 (Grand Bassin).
Figure 2. A in The den ecology and the effects of fishing pressure on the distribution of Octopus cyanea (Octopodidae: Mollusca) in Rodrigues lagoon, Rodrigues, Mauritius
Figure 2. A map of the 12 survey locations within the Rodrigues lagoon, with labels for each station number (square = stations 1A-1D, stars = stations 2A-2D, triangles = stations 3A-3D). The grey dashed line shows the edge of the fringing lagoon. The sites were chosen based on specific coral biotopes as determined during ground-truthing surveys (Turner and Chapman 2004) The location of the Shoals Rodrigues base centre is shown to illustrate that the sites were also chosen because of proximity to the base.
Figure 4 in The den ecology and the effects of fishing pressure on the distribution of Octopus cyanea (Octopodidae: Mollusca) in Rodrigues lagoon, Rodrigues, Mauritius
Figure 4. The total number of octopus observed per station in the lagoon over the course of two different sampling periods with a 23-day gap between sampling; 1 = Ile aux Fous (moderate fishing pressure), 2 = Anse aux Anglais (high fishing pressure) and 3 = Grand Bassin (low fishing pressure).
Data from: Ecological release from aquatic predation is associated with the emergence of marine blenny fishes onto land
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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)
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DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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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.
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