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136 results for “trophic level”
Perry et al. (2025) Data Package: Effects of diluted bitumen and remediation methods on lower trophic levels within boreal lake enclosures. Data were collected during 2019 at the IISD Experimental Lakes Area in Northwestern Ontario.
This data package corresponds to a research study by Perry et al. (2025) titled "The effects of diluted bitumen, the shoreline cleaner Corexit EC9580A, and bio-stimulation on the lower food web of a boreal lake, with a focus on natural phytoplankton communities." The study examines the effect of controlled spills of diluted bitumen and two remediation methods on lower trophic levels (phytoplankton, periphyton, zooplankton). The study was undertaken within shoreline enclosures within Lake 260 at the IISD Experimental Lakes Area during 2019. In addition to primary oil recovery using sorbent pads, the two secondary remediation methods: 1) enhanced monitoring natural recovery (eMNR) that included the biostimulation of microbial communities via a slow release nutrient fertilizer, and 2) a shoreline washing agent (SWA or SCA; Corexit 9580) used to increase oil removal from affected shorelines. This data package includes the response of perphyton and zooplankton.
Stable isotope data of a community of mid‑trophic level epipelagic species in the North Atlantic
<p>A total of 495 individuals from a guild of 14 species (fishes, squids and crustaceans) were sampled along the west and south Iberia (Portuguese coast) aboard a research vessel during 2014, 2016 and 2017. Two seasonal oceanographic surveys were conducted each year to sample pelagic mid-trophic level species during spring and autumn. Specimens were captured with trawl hauls, and information on date, time, position of capture (latitude and longitude) and depth (m) were recorded. The body mass (g) and total length (in fishes; mm), mantle length (in squids; mm) or carapace width (in crustaceans; mm) were recorded for each individual. Stable isotopes of carbon (δ13C) and nitrogen (δ15N) were analysed in the muscle of each individual. Lipids were removed from samples by successive rinses in a 2:1 chloroform–methanol solution. More details of the methodology can be found in:</p> <p>Ceia FR, Cherel Y, Silva AV, Garrido S, Angélico MM, da Silva JM, Laranjeiro MI, Ramos JA (2023) Drivers of niche partitioning in a community of mid-trophic level epipelagic species in the North Atlantic. Hydrobiologia, 850: 1583–1599. (DOI:10.1007/s10750-023-05160-3).</p>
Consensus QSAR models estimating acute aquatic toxicity for three trophic levels organisms: Algae, Daphnia and Fish
<p>We report new consensus models estimating acute toxicity for algae, daphnia and fish endpoints. We assembled a large collection of 3680 public unique compounds annotated by, at least, one experimental value for the given endpoint. Support Vector Machine models were internally and externally validated following the OECD principles. Reasonable predictive performances were achieved (RMSE<sub>ext</sub> = 0.56 – 0.78) which are in line with those of state-of-the-art models. The known structural alerts are compared with analysis of the atomic contributions to these models obtained using the ISIDA/<em>ColorAtom</em> utility. A benchmarking against existing tools has been carried out on a set of compounds considered more representative and relevant for the chemical space of the current chemical industry. Our model scored one of the best accuracies and data coverage.</p> <p>Nevertheless, industrial data performances were noticeably lower than those on public data, indicating that existing models fail to meet the industrial needs. Thus, final models were updated with the inclusion of new industrial compounds, extending applicability domain and relevance for application in an industrial context. Generate models and collected public data are made freely available.</p> <p><strong>Available fields in the SDF file:</strong></p> <ul> <li>SMILES_Canonical: canonical SMILES code</li> <li>DB: source of the data, "Litterature set" means that the data is originated from an article (see the companion article of the dataset for details).</li> <li>endpoint: organism for which endpoint is available</li> <li>CASRN: CAS registration number</li> <li>98-81-7</li> <li>pEC50 - DAPHNIA: Daphnia, mortality, which is evaluated by the immobilization of the invertebrate is recorded at 48 hours and expressed as the log median effective concentration (pEC50)</li> <li>mg/L - DAPHNIA: Daphnia, mortality, which is evaluated by the immobilization of the invertebrate is recorded at 48 hours and expressed as the median effective concentration (EC50)</li> <li>pLC50 - FISH: Fish, the log median lethal concentration measured at 96 hours is considered (pLC50)</li> <li>mg/L - FISH: Fish, the log median lethal concentration measured at 96 hours is considered (LC50)</li> <li>pEC50 - ALGA: Algae, the purpose is to determine the substance’s growth inhibition effect, expressed as the log median effective concentration (pEC50) measured at 72 hours</li> <li>mg/L - ALGA: Algae, the purpose is to determine the substance’s growth inhibition effect, expressed as the median effective concentration (EC50) measured at 72 hours</li> </ul>
Periodical cicadas disrupt trophic dynamics via community-level shifts in Avian Foraging
<p>Once every 13 or 17 years within eastern North American deciduous forests, billions of periodical cicadas concurrently emerge from the soil and briefly satiate a diverse array of naive consumers, offering a rare opportunity to assess the cascading impacts of an ecosystem-wide resource pulse on a complex food web. Here, we quantify the effects of the 2021 Brood X emergence, and report that >80 bird species opportunistically switched their foraging to include cicadas, releasing herbivorous insects from predation, and essentially doubling both caterpillar densities and accumulated herbivory levels on host oak trees. These short-lived but massive emergence events help us to understand how resource pulses can rewire interaction webs and disrupt energy flows in ecosystems, with potentially long-lasting effects. </p> <p> </p>
Genetic architecture of adaptive radiation across two trophic levels
<p>Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20,000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology, and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed Quantitative Trait Locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.</p>
How nitrogen and phosphorus supply to nutrient-limited autotroph communities affects herbivore growth: testing stoichiometric and co-limitation theory across trophic levels
<p><span>Primary producer communities are often growth-limited by essential nutrients such as nitrogen (N) and phosphorus (P). The magnitude of </span><span>limitation and whether N, P, or both elements are limiting autotroph </span><span>growth depends on the supply and ratios of these essential nutrients. </span><span>Previous studies identified single, serial or co-limitation as predominant </span><span>limitation outcomes in autotroph communities by factorial nutrient </span><span>additions. Little is known about potential consequences of such scenarios </span><span>for herbivores and whether their growth is primarily affected by changes </span><span>in autotroph quantity or nutritional quality. We grew a community of </span><span>phytoplankton species differing in various food quality aspects in </span><span>experimental microcosms at varying N and P concentrations resulting in </span><span>three different N:P ratios. At carrying capacity, N, P, both nutrients or </span><span>none were added to reveal which nutrients were limiting. The nutrient supplied </span><span>communities were fed to the generalist herbivorous rotifer </span><span>Brachionus calyciflorus to investigate how changing phytoplankton </span><span>biomass and community composition affect herbivore abundance. We </span><span>found phytoplankton being growth-limited either by N alone (single </span><span>limitation) or serially, i.e. primarily by N and secondarily by P, altering </span><span>available food quantity for rotifers. Rotifer growth showed a different </span><span>response pattern compared to phytoplankton, suggesting that apart from </span><span>food quantity food quality aspects played a substantial role in the </span><span>transfer from primary to secondary production. The combined addition of </span><span>N and P to phytoplankton had generally a positive effect on herbivore </span><span>growth, whereas adding non-limiting nutrients had a rather detrimental </span><span>effect probably due to stoichiometrically imbalanced food in terms of </span><span>nutrient excess. Our experiment shows that adding various nutrients to </span><span>primary producer communities will not always lead to increased </span><span>autotroph and herbivore growth, and that differences between autotroph </span><span>and herbivore responses under co-limiting conditions can be partly well </span><span>explained by concepts of ecological stoichiometry theory.</span></p>
Plant-associate interactions and diversification across trophic levels
<p>Interactions between species are widely understood to have promoted the diversification of life on Earth, but how interactions spur the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled population genetic studies of host plants and intimately associated herbivores, parasites, and mutualists. We used Bayesian multiple regressions and the BEDASSLE modeling framework to test whether host and associate population structures were correlated over and above the potentially confounding effects of geography and shared environmental variation. We found that associates' population structure often paralleled their hosts' population structure, and that this effect is robust to accounting for geographic distance and climate. Associate genetic structure was significantly explained by plant genetic structure somewhat more often in antagonistic interactions than in mutualistic ones. This aligns with a key prediction of coevolutionary theory, that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions more often promote diversity via the effect of hosts' geographic distribution on mutualists' dispersal.</p>
Figure 1 in Tissue pH and gut ecomorphology in six freshwater teleosts occupying different trophic levels
Figure 1. The line of best fit showing the relationship between blood pH and muscle pH of the 6 freshwater fish species.
Figure 2. The relationship between relative gut length and trophic position for the 6 in Tissue pH and gut ecomorphology in six freshwater teleosts occupying different trophic levels
Figure 2. The relationship between relative gut length and trophic position for the 6 freshwater fish species. (a) Relative gut length is presented in percent of body length; (b) Relative gut length is presented in percent of total length. Averaged values of trophic position (TP) from the study by Zhang et al. (2013). Grey and black circle dots correspond to TP for stable isotope analysis (SIA) and for gut content analysis (GCA), respectively. Dashed line represents the linear fitting of relative gut length and TP for SIA, while solid line represents the linear fitting of relative gut length and TP for GCA.
Fig. 2 in Habitat complexity does not influence prey consumption in an experimental three-level trophic chain
Fig. 2. Percentage of Chironomidae larvae consumed by Moenkhausia forestii Benine, Mariguela & C. de Oliveira, 2009 in low, intermediate and high habitat complexities in the presence and in the absence of the piscivore Hoplerythrinus unitaeniatus (Spix & Agassiz 1829).
Fig. 4 in Habitat complexity does not influence prey consumption in an experimental three-level trophic chain
Fig. 4. Correlation between the percentages of Chironomidae larvae consumed by Moenkhausia forestii Benine, Mariguela & C. de Oliveira, 2009 and the percentage of individuals of M. forestii consumed by Hoplerythrinus unitaeniatus (Spix & Agassiz 1829) in the all levels of habitat complexity.
Fig. 5 in Habitat complexity does not influence prey consumption in an experimental three-level trophic chain
Fig. 5. Conceptual scheme describing prey consumption by Hoplerythrinus unitaeniatus (Spix & Agassiz 1829) and Moenkhausi forestii Benine, Mariguela & C. de Oliveira, 2009 reported in this experimental study. Bold solid arrows represent trophic interactions and thin solid arrows represent direct effects. Dashed arrow represents indirect effects. Habitat complexity, represented by macrophytes density, affects prey capture strategy of H. unitaeniatus and indirectly affects invertivore foraging.
Fig. 1 in Habitat complexity does not influence prey consumption in an experimental three-level trophic chain
Fig. 1. The experimental design. The (A) axis represents habitat complexity [(a) low, (b) intermediate and (c) high] and the (B) axis represents the piscivore [(d) absence and (e) presence]. Numbers in the aquaria represent the number of replicates for each treatment combination.
Fig. 3 in Habitat complexity does not influence prey consumption in an experimental three-level trophic chain
Fig. 3. Percentage of Moenkhausia forestii Benine, Mariguela & C. de Oliveira, 2009 individuals consumed by Hoplerythrinus unitaeniatus (Spix & Agassiz 1829) in low, intermediate and high habitat complexities.
Fig. 3 in Mercury distribution in different tissues and trophic levels of fish from a tropical reservoir, Brazil
Fig. 3. Mean concentrations and ratios of mercury in different tissues of omnivorous (a), carnivorous (b), and detritivorous fishes (c) collected from Vigário Reservoir. Error bars represent one standard deviation of the mean.
Fig. 1 in Mercury distribution in different tissues and trophic levels of fish from a tropical reservoir, Brazil
Fig. 1. Map of Vigário reservoir, showing its drainage basin (Piraí river, Paraíba do Sul river and Santana reservoir). Black arrows indicate the water flow. (Source: Gomes et al., 2008).
Fig. 2 in Mercury distribution in different tissues and trophic levels of fish from a tropical reservoir, Brazil
Fig. 2. Mean concentrations and ratios of mercury in muscle of fish collected from Vigário reservoir. Different letters indicate significant difference between groups: inorganic (ab) and organic mercury concentrations (xyz), and ratios of organic mercury (αβγ). Error bars represent the standard deviation of the mean.
Dead or alive; or does it really matter? Level of congruency between trophic modes in total and active fungal communities in High Arctic soil.
<p>These are the rDNA and rRNA fragments of Internal transcribed spacer 2 (ITS2) extracted from snow fence experiment in Adventdalen, Svalbard. </p> <p>This is a dataset described in Wutkowska et al., (2019), 'Dead or alive; or does it really matter? Level of congruency between trophic modes in total and active fungal communities in High Arctic soil.', published in Frontiers in Microbiology</p> <p>All other corresponding data (for splitting libraries, environmental parameters etc.) can be found here: https://github.com/magdawutkowska/Dead_or_alive</p> <p> </p>
High trophic level feedbacks on global ocean carbon uptake and marine ecosystem dynamics under climate change (Dupont et al., GBC)
<p>Files used to make the analysis in the paper "High trophic level feedbacks on global ocean carbon uptake and marine ecosystem dynamics under climate change" (Dupont et al., accepted in GBC)</p> <p>- HTL_LTL_figures.ipynb is the python notebook in which are computed the different terms to make the figures of the paper </p> <p>- histrcp85.1-PISAPE-N-OW** and piCtrl2-PISAPE-N-OW** files contain the raw outputs of the one way (OW) simulation</p> <p>- histrcp85.1-PISAPE-N-TW* and piCtrl2-PISAPE-N-TW* files contain the raw outputs of the two way (TW) simulation</p> <p>- all files ending with *rmp_f.nc/ *regrid.nc/ *f20.nc are regridded files to make maps used in the paper. More details can be found in the python noteboook (briefly, dAT_* = change in active export, dDIC_*= change in dissolved inorganic carbon, dEPC200_* = change in carbon export at 200m depth, OW/TW_<a href="https://zenodo.org/api/files/cc2ae8cc-a150-4bc6-9125-04d9e3465859/TW_dBMapermp_f.nc">dBMape</a>* = OW/TW change in small high trophic levels biomass, OW/<a href="https://zenodo.org/api/files/cc2ae8cc-a150-4bc6-9125-04d9e3465859/TW_dBMapermp_f.nc">TW_dBM</a>meszo* = OW/TW change in mesozooplankton biomass)</p> <p>- <a href="https://zenodo.org/api/files/cc2ae8cc-a150-4bc6-9125-04d9e3465859/egestt2_2.nc">egestt2_2.nc</a>, excrett2_2.nc and graztt2_2.nc are the outputs of egestion, excretion and grazing terms used to compute the active export (AT). </p>
Meta-analysis and critical review of trophic discrimination factors (Δ13C and Δ15N): importance of tissue, trophic level, and diet source
<ol> <li>Robustly quantifying dietary resource use and trophic position using stable isotopes requires accurate trophic discrimination factors (TDF; Δ<sup>13</sup>C and Δ<sup>15</sup>N for carbon and nitrogen, respectively), defined as the isotopic difference between consumer and diet. Early TDF studies converged on values of around 1.0‰ for Δ<sup>13</sup>C and 3.4‰ for Δ<sup>15</sup>N, but more recent work indicates that TDF values may be more nuanced, depending on taxa, tissues, trophic level, and diets. Yet, the relative importance of these factors remains unclear.</li> <li>Focusing on vertebrates (birds, fish, herptiles, and mammals), we conducted a literature review of 279 studies that estimated TDF values and used a Bayesian framework to determine how tissue type, trophic level, and diet source influence variation in Δ<sup>13</sup>C and Δ<sup>15</sup>N. Additionally, we reviewed 358 trophic ecology studies to determine if studies accounted for these factors during their TDF selection process.</li> <li>For Δ<sup>13</sup>C, vertebrates showed consistent patterns among tissue types (likely influenced by amino acid composition) and between trophic levels and diet sources (likely a result of dietary protein content and metabolic routing). Comparatively, for Δ<sup>15</sup>N, vertebrates showed considerable variation among tissue types and trophic levels, likely due to differences in tissue synthesis and physiological capabilities. Overall, Δ<sup>13</sup>C ranged from -5.1‰ to 9.1‰ and Δ<sup>15</sup>N from -3.3‰ to 9.7‰, underscoring that 1.0‰ for Δ<sup>13</sup>C and 3.4‰ for Δ<sup>15</sup>N are not universally appropriate. Moreover, both Δ<sup>13</sup>C and Δ<sup>15</sup>N varied by more than 9‰ within a single species and tissue type, demonstrating that using TDF values from the same, or similar, species may not be appropriate if diet and trophic level are not considered.</li> <li>Despite the importance of diet source on TDF values, most trophic ecology studies did not account for it. Further, most fish studies relied on literature review values that failed to account for tissue type, trophic level, and diet source. To aid ecologists in diet and trophic assessments of vertebrates, we used our meta-analysis to model taxon-specific TDF estimates (mean ± SD) for each tissue type, trophic level, and diet source combination. These more refined TDF values should improve ecological assessments that use stable isotopes.</li> </ol>
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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 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.