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1,157 results for “Limited data”
Learning to learn ecosystems from limited data
<p>Learning to learn ecosystems from limited data - a meta-learning approach.</p> <p>Food-chain, Hastings, and Lotka systems are ecological models used for predictive purposes. Learning other systems using meta-learning methods can enhance predictions on eological systems, even when only limited data is available.</p> <p>Codes: https://github.com/Zheng-Meng/Meta-learning-Ecosystems.</p> <p>Zhai, Zheng-Meng, Bryan Glaz, Mulugeta Haile, and Ying-Cheng Lai. "Learning to learn ecosystems from limited data--a meta-learning approach." <em>arXiv preprint arXiv:2410.07368</em> (2024).</p>
Data from: Does pollen limitation limit plant ranges? Evidence and implications
<p>Sexual reproduction often declines towards range edges, reducing fitness, dispersal, and adaptive potential at range edges. For plants, sexual reproduction is frequently limited by inadequate pollination. While case studies show that pollen limitation can limit plant distributions, the extent to which pollination commonly declines toward plant range edges is unknown. Here, we leverage global databases of pollen-supplementation experiments and plant occurrence data to test whether pollen limitation increases toward plant range edges, using a phylogenetically controlled meta-analysis. While there was significant pollen limitation across studies, we found little evidence that pollen limitation increases toward plant range edges. Pollen limitation was not stronger toward the tropics, nor at species' equatorward vs poleward range limits. Meta-analysis results are consistent with results from targeted experiments, in which pollen limitation increased significantly toward only 14% of 14 plant range edges, suggesting that pollination contributes to range limits less often than do other interactions. Together, these results suggest pollination is one of the rich variety of potential ecological factors that can contribute to range limits, rather than a generally important constraint on plant distributions.</p>
Data for: Warming temperatures limit the maximum body length of teleost fishes across a latitudinal gradient in Norwegian waters
<p>As the majority of marine organisms are water-breathing ectotherms, temperature and dissolved oxygen are key environmental variables that influence their fitness and geographic distribution. In line with the gill-oxygen limitation theory (GOLT), the maximum asymptotic body size of water-breathing ectotherms is limited by an insufficient amount of oxygen that is supplied to meet metabolic demand once a threshold of gill surface area to body weight ratio is surpassed. Here we employed generalised additive models (GAMs) to investigate the relative influence of temperature, regional variation in dissolved oxygen, and geographic location (that encompasses multiple latent variables) on the maximum body length of ten teleost fish species, as well to predict their maximum body length, across a large temperature, depth and latitudinal gradient throughout Norwegian waters. As dissolved oxygen levels were near saturation across the study area, we conclude that the predicted maximum lengths of our study species were not limited by oxygen availability. Conversely, the majority of study species display a clear relationship in that their predicted maximum length is either decreasing, asymptotic or parabolic across their observed temperature range. We also observed smaller maximum body lengths for multiple species within the coldest extent of their temperature range, which may be explained by increases in basal metabolism via cold denaturation. Overall, our results suggest that the maximum lengths of our study species are influenced by temperature, thus supporting the tenants of the GOLT.</p>
Data from: Loss of fungal symbionts at the arid limit of the distribution range in a native Patagonian grass – resource ecophysiological relations
<p>1. Crucial to our understanding of plant ecology is the consideration of the eco-physiological responses and constraints of plant-fungal symbioses throughout the native distribution range of their host.</p> <p>2. We examined key eco-physiological roles of two co-occurring fungal symbionts [Epichloë endophytes and arbuscular mycorrhizal fungi (AMF)] in the endemic grass Hordeum comosum across a wide bioclimatic gradient and contrasting grazing severity. We sampled H. comosum plants along four humid-to-arid transects in Patagonia, Argentina, covering its entire distribution range and determined Epichloë presence, AMF root colonization, nitrogen and phosphorus concentration, intrinsic water use-efficiency (iWUE, the ratio of photosynthesis to stomatal conductance) and 18O-enrichment of cellulose in shoots.</p> <p>3. Root colonization by AMF increased with Epichloë-presence. All plants hosted Epichloë in the humid range of the gradient, but symbioses occurrence decreased towards arid sites which also displayed severe grazing symptoms at site level.</p> <p>4. Symbiosis with Epichloë correlated positively with shoot nitrogen concentration in the centre of the distribution range, and with shoot phosphorus concentration across the entire distribution range.</p> <p>5. The site-level relationship of AMF colonization with 18O-enrichment and iWUE suggested that mycorrhiza boosted stomatal conductance in humid environments but curbed it in arid environments.</p> <p>6. While the interpretation of interactions and potential causalities from observational studies should be done with caution, this study demonstrates distinct correlations between plant-fungal symbiont associations and key resource parameters (phosphorus, nitrogen, and iWUE vs 18O-enrichment). Such correlations may suggest particular functional roles for these symbionts in the ecology of their host plant.</p>
Data from: Intersexual flower differences in an andromonoecious species: small pollen‐rich staminate flowers under resource limitation
<p>Data archived here were used for analyses in Murakami et al. "Intersexual flower differences in an andromonoecious species: small pollen‐rich staminate flowers under resource limitation." Data is in three worksheets.</p>
Data for: Warmer temperatures limit the effects of antidepressant pollution on life history traits
<p>Pharmaceutical pollutants pose a threat to aquatic ecosystems worldwide. Yet, few studies have considered the interaction between pharmaceuticals and other chronic stressors contemporaneously, even though the environmental challenges confronting animals in the wild seldom, if ever, occur in isolation. Thermal stress is one such environmental challenge that may modify the threat of pharmaceutical pollutants. Accordingly, we investigated how fluoxetine (Prozac), a common psychotherapeutic and widespread pollutant, interacts with temperature to affect life-history traits in the water flea, <i>Daphnia magna</i>. We chronically exposed two genotypes of <i>Daphnia</i> to two ecological relevant concentrations of fluoxetine (30ng/L and 300ng/L) and a concentration representing levels used in acute toxicity tests (3000ng/L), and quantified the change in phenotypic trajectories at two temperatures (20°C and 25°C). Across multiple life-history traits, we found that fluoxetine exposure impacted the fecundity, body size and intrinsic growth rate of <i>Daphnia</i> in a non-monotonic manner at 20°C, and often in genotypic-specific ways. At 25°C, however, the life-history phenotypes of individuals converged under the widely varying levels of fluoxetine, irrespective of genotype. Our study underscores the importance of considering the complexity of interactions that can occur in the wild when assessing the effects of chemical pollutants on life-history traits.</p>
Data set for "Intertwined spin, charge, and pair correlations in the two-dimensional Hubbard model in the thermodynamic limit"
<p>This data set is for the paper "Intertwined spin, charge, and pair correlations in the two-dimensional Hubbard model in the thermodynamic limit". It contains the raw DCA HD5 and DQMC plain text output files, as well as the scripts and final processed data used to generate figures 1-5 of the main text and supplementary figures 1-12. Copies of the figures and latex files are also included for completeness. </p>
Data for: Termites have wider thermal limits to cope with environmental conditions in savannas
<p>The most diverse and abundant family of termites, the Termitidae, evolved in African tropical forests. They have since colonised grassy biomes such as savannas. These open environments have more extreme conditions than tropical forests, notably wider extremes of temperature and lower precipitation levels and greater temporal fluctuations (both annual and diurnal variation). These conditions are challenging for soft-bodied ectotherms, such as termites, to survive in, let alone become as ecologically dominant as termites have.</p> <p>Here, we quantified termite thermal limits to test the hypothesis that these physiological limits have widened in savanna termite species to facilitate their existence in savanna environments.</p> <p>We sampled termites directly from mound structures, across an environmental gradient in Ghana, ranging from wet tropical forest through to savanna. At each location we quantified both Critical Thermal Maximum (CT<sub>max</sub>) and Critical Thermal Minimum (CT<sub>min</sub>) of all the most abundant mound-building Termitidae species in the study areas. We modelled the thermal limits in two separate mixed effects models against: canopy cover at the mound, temperature and rainfall, as fixed effects, with sampling location as a random intercept.</p> <p>For both CT<sub>max</sub> and CT<sub>min</sub> savanna species had significantly more extreme thermal limits than forest species. Between and within environments, areas with higher amounts of canopy cover were significantly associated with lower CT<sub>max</sub> values of the termite colonies. CT<sub>min</sub> was significantly positively correlated with rainfall. Temperature was retained in both models, however it did not have a significant relationship in either. Sampling location explained a large proportion of the residual variation, suggesting there are other environmental factors that could influence termite thermal limits.</p> <p>Our results suggest there has been a widening of the thermal limits in termite savanna species. These physiological differences, in conjunction with other behavioural adaptations, are likely to have enabled termites to cope with the more extreme environmental conditions found in savanna environments and facilitated their expansion into open tropical environments.</p>
Data from: Joint effects of environmental filtering and dispersal limitation on species assemblage of the Tibetan Plateau
<p><strong>Aim</strong> Mountains harbour a rich and non-random cluster of species, yet knowledge on the species' biological attributes that support species coexistence in the montane community is limited. Here, we investigated the association of species occurrence on the Tibetan Plateau with species' morphological, ecological or evolutionary constraints.</p> <p><strong>Location</strong> Tibetan Plateau (TP)</p> <p><strong>Taxon</strong> Mammals and birds</p> <p><strong>Methods </strong>We tested whether species occurrence on the TP correlates with morphological, ecological, or evolutionary constraints using the spatial distribution, phylogeny, dispersal ability, and thermal niche property data for 1,353 terrestrial vertebrates (383 mammals and 970 birds). We used standard (non-phylogenetic) and phylogenetic logistic regressions to disentangle the relative contributions of these attributes of species in explaining the species occurrence on the TP. We assessed the geographical patterns of community structures on the TP and fit linear mixed models to explore the underlying eco-evolutionary forces.</p> <p><strong>Results</strong> The TP species exhibited a higher cold tolerance, wider thermal niche breadth, and higher rate of niche evolution than the non-TP species. We supported the assumption that the TP species was not a random subset from the species pool, but was structured jointly by environmental filtering and dispersal limitation. While dispersal and ecological processes underlying species assemblages varied spatially and among taxa, we found that species in stressful environments was limited by environmental filtering, whereas dispersal limitation was more pronounced under favourable climatic conditions.</p> <p><strong>Main conclusions</strong> Our study finds that environmental filtering and dispersal limitation jointly shape the species assemblage on the TP. These findings provide significant insights into community assembly processes on the TP and other montane ecosystems on Earth, especially those that are sensitive to global warming.</p>
Data from: Coastal darkening substantially limits the contribution of kelp to coastal carbon cycles
<p>Macroalgal-dominated habitats are rapidly gaining recognition as important contributors to marine carbon cycles and sequestration. Despite this recognition, relatively little is known about the production and fate of carbon originating from these highly productive ecosystems, or how anthropogenic and climate related stressors affect the role of macroalgae in marine carbon cycles. Here, we examine the impact of increasing turbidity on carbon storage, fixation and loss in southern hemisphere kelp forests. We quantified net primary production (NPP) and biomass accumulation (BA), and estimated carbon release via detritus and dissolved organic carbon (DOC) across a large-scale turbidity gradient. We show that increased turbidity, resulting in a 63 % reduction in light, can result in a 95 % reduction in kelp productivity. When averaged annually, estimates of NPP and BA per plant at high light sites were nearly 6 and 2 times greater than those at low light sites, respectively. Furthermore, the quantity of carbon fixed annually by kelp forests was up to 4.7 times greater than that stored as average annual standing stock. At low light sites, the majority of C goes directly into tissue growth and is subsequently eroded. In contrast, excess production at high light sites accounts for up to 39 % of the total carbon fixed and is likely released as DOC. Turbidity is expected to increase in response to climate change and our results suggest this will have significant impacts on the capacity of kelp forests to contribute to carbon sequestration pathways. In addition to demonstrating that turbidity significantly reduces the quantity of carbon fixed by kelp forests, and subsequently released as detritus, our results highlight the negative impacts of turbidity on a large source of previously unaccounted for carbon.</p>
Data from: Ancestral ecological regime shapes reaction to food limitation in the Least Killifish, Heterandria formosa
<p>Populations with different densities often show genetically-based differences in life histories. The divergent life histories could be driven by several agents of selection, one of which is variation in per-capita food levels. Its relationship with population density is complex, as it depends on overall food availability, individual metabolic demand, and food-independent factors potentially affecting density, such as predation intensity. Here we present a case study of two populations of a small live-bearing freshwater fish, one characterised by high density, low predation risk, low overall food availability, and presumably low per-capita food levels, and the other by low density, high predation risk, high overall food availability, and presumably high per-capita food levels. Using a laboratory experiment we examined whether fish from these populations respond differently to food limitation, and whether size at birth, a key trait with respect to density variation in this species, is associated with any such differential responses. While at the lower food level growth was slower, body size smaller, maturation delayed and survival reduced in both populations, these fitness costs were smaller in fish from the high-density population. At low food, only 15% of high-density fish died, compared to 75% of low-density fish. This difference was much smaller at high food (0% vs. 15% mortality). The increased survival of high-density fish may, at least partly, be due to their larger size at birth. Moreover, being larger at birth enabled fish to mature relatively early even at the lower food level. We demonstrate that sensitivities to food limitation differ between study populations, consistent with selection for a greater ability to tolerate low per-capita food availability in the high-density population. While we cannot preclude other agents of selection from operating in these populations simultaneously, our results suggest that variation in per-capita food levels is one of those agents.</p>
Data related to "Bilayer WSe2 as a natural platform for interlayer exciton condensates in the strong coupling limit"
<p>Data related to "Bilayer WSe2 as a natural platform for interlayer exciton condensates in the strong coupling limit"</p>
Raw data for the study titled "Fungal ectoparasites increase winter mortality of ladybird hosts despite limited effects on their immune system"
<p>Winter represents a challenging period for insects inhabiting temperate regions. A plethora of studies have investigated how abiotic environmental conditions such as temperature affect insect overwintering success. However, only a few studies have focused on biotic factors and the mechanisms affecting the overwintering performance of insects. Here, we investigated the effects of the parasitic fungus <em>Hesperomyces virescens</em> on the overwintering performance and immune system functioning of the invasive ladybird <em>Harmonia axyridis</em>. Winter survival was significantly lower for infected than for uninfected beetles. Body mass loss during overwintering tend to be higher for infected individuals compared to uninfected ones and for larger beetles. In addition, parasitic infection reduced post-winter longevity without food in male but not female ladybirds. Total haemocyte and protein concentration as well as antimicrobial activity against <em>Escherichia coli</em> significantly decreased during ladybird overwintering. However, haemolymph parameters were only poorly affected by <em>Hesperomyces</em> infection, with the exception of antimicrobial activity against <em>Escherichia coli</em> that tended to be higher in infected ladybirds. Interestingly, none of the pre-winter haemolymph parameters were good predictors of ladybird winter survival. Overall, our results indicate that energy exhaustion unrelated to immune system challenge is the most probable explanation for increased overwintering mortality in infected beetles.</p>
Modeling of protein conformational changes with Rosetta guided by limited experimental data
<p>Demos, models and files needed to reproduce results of the paper in the title</p>
Data from: Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates
<p><span><span><span><span>Antibiotic resistance spread via plasmids is a serious threat to successfully fight infections and makes understanding plasmid transfer in nature crucial to prevent the rise of antibiotic resistance. Studies addressing the dynamics of plasmid conjugation have yet neglected one omnipresent factor: prophages (viruses integrated into bacterial genomes), whose activation can kill host and surrounding bacterial cells. To investigate the impact of prophages on conjugation, we combined experiments and mathematical modelling. Using <em>E. coli</em>, prophage lambda and the multidrug-resistant plasmid RP4 we find that prophages can substantially limit the spread of conjugative plasmids. This inhibitory effect was strongly dependent on environmental conditions and bacterial genetic background. Our empirically parameterized model reproduced experimental dynamics of cells acquiring either the prophage or the plasmid well but failed to predict the number of cells acquiring both elements. This suggests more complex interactions between conjugative plasmids and prophages in sequential infections. Varying phage and plasmid infection parameters over empirically realistic ranges revealed that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid.</span></span></span></span></p>
Data for: Evolutionary history limits species' ability to match color sensitivity to available habitat light
<p>The spectrum of light that an animal sees – from ultraviolet to far red light – is governed by the number and wavelength sensitivity of a family of retinal proteins called opsins. It has been hypothesized that the spectrum of light available in an environment influences the range of colors that a species has evolved to see. However, invertebrates and vertebrates use phylogenetically distinct opsins in their retinae, and it remains unclear whether these distinct opsins influence what animals see, or how they adapt to their light environments. Systematically utilizing published visual sensitivity data from across animal phyla, we found that terrestrial animals are more sensitive to shorter and longer wavelengths of light than aquatic animals, and that invertebrates are more sensitive to shorter wavelengths of light than vertebrates. Controlling for phylogeny removes the effects of habitat and lineage on visual sensitivity. Closed and open habitat terrestrial species have similar spectral sensitivities when comparing across the Metazoa, and deep water animals are more sensitive to shorter wavelengths of light than shallow water animals. Our results suggest that animals do adapt to their light environment, however the invertebrate-vertebrate evolutionary divergence has limited the degree to which animals can perform visual tuning.</p>
Data from the parametric analysis of masonry buttressed arches with limit analysis subjected to vertical self-weight plus a proportional concentrated vertical live load applied at quarter-span
<p>For each one of the simulations performed from the parametric analysis of masonry buttressed arches with limit analysis subjected to vertical self-weight plus a proportional concentrated vertical live load applied at quarter-span, this database contains a .txt, a .vtk and a .png file. In the .txt file the elapsed time and the collapse multiplier of each simulation can be found. The .vtk file contains all the geometry and displacement values of every masonry buttressed arch. Finally, the .png file presents the collapse mechanism obtained. </p>
Data from: Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar
<p>With 178 species, the palm subtribe Dypsidinae is one of the largest plant radiations on Madagascar. A well-resolved species-level phylogeny is required not only to unpick the drivers of this spectacular radiation but also to define natural and useful generic limits in this taxonomically difficult group. The only recent taxonomic revision of Dypsidinae recognized just four genera, including the large genus <em>Dypsis</em> (currently with 172 species), which was considered impossible to divide further based on morphology alone. Here we describe the first comprehensively sampled species-level phylogeny of Dypsidinae, including 157 described species (88% of the subtribe) as well as 10 samples of uncertain taxonomic identity (potential new species). Our tree is based on target sequence capture data for 161 nuclear DNA loci. The phylogenetic relationships recovered render <em>Dypsis</em> s.l. paraphyletic, requiring the resurrection of two previously synonymised genera. In total, we recognize six genera in Dypsidinae (<em>Dypsis</em> Noronha ex Mart., <em>Chrysalidocarpus</em> H.Wendl., <em>Marojejya</em> Humbert, <em>Vonitra</em> Becc., <em>Lemurophoenix</em> J.Dransf., and <em>Masoala</em> Jum.), all of which are monophyletic and consistent with morphology.</p>
Fig. 9 in Corbiculate Bees (Hymenoptera: Apidae): Exploring the Limits of Morphological Data to Solve a Hard Phylogenetic Problem
Fig. 9. Micrographs of the meso/metafurca complex of female representatives of apine bees, dorsal view, anterior to the top. (a) Centris analis (Fabricius, 1804). (b) Euglossa cordata (Linnaeus, 1758). (c) Bombus pauloensis Friese, 1913. (d) Tetragonula carbonaria (Smith, 1854). (e) Apis mellifera Linnaeus, 1758. (f) Schematic representation depicting the general anatomy and relative positions of the elements of the internal morphology of mesosoma. Solid arrow indicates the meso/metafurca complex in dorsal view. Arrowheads indicate morphological conditions coded as character states. Scale bars: 0.2 mm.
Fig. 6 in Corbiculate Bees (Hymenoptera: Apidae): Exploring the Limits of Morphological Data to Solve a Hard Phylogenetic Problem
Fig. 6. Micrographs of the prosternum of female representatives of apine bees, dorsal view, anterior to the top. (a) Centris analis (Fabricius, 1804). (b) Euglossa cordata (Linnaeus, 1758). (c) Bombus pauloensis Friese, 1913. (d) Melipona scutellaris Latreille, 1811. (e) Apis mellifera Linnaeus, 1758. (f) Schematic representation depicting the general anatomy and relative positions of the elements of the complex of the propectus. Solid arrow indicates the prosternum in dorsal view. Arrowheads indicate morphological conditions coded as character states. Scale bars: 0.1 mm.
ScienceDex guides
Understand access before you commit
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.