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1,157 results for “Limited data”
Data from: Seascape genomics of red abalone: Limited range-wide population structure and evidence for local adaptation
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Data for: Economic and biophysical limits to seaweed farming for climate change mitigation
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Data from: Predator life history and prey ontogeny limit natural selection on the major armour gene, Eda, in threespine stickleback
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Carbon decomposition data from oxygen-limited soils
To understand carbon (C) decomposition under cyclic, time-varying oxygen (O2) fluctuations, we incubated two disparate soils (Oxisol and Mollisol) under five fluctuating oxygen treatments (0, 2, 4, 8, or 12 days of anoxic conditions followed by 4 days of oxic conditions), and measured C decomposition as CO2 and CH4 (and their stable isotope compostion) at 2–4-day measurement timesteps for 384 days. We also used a process-based mechanistic model to test C decomposition in response to O2 fluctuations. This dataset supports the findings described in the associated manuscript by Huang et al. (2021).
Data supporting "Leaf carbon and water status control stomatal and non-stomatal limitations of photosynthesis in trees."
<p>Data supporting our New Phytologist publication: "Leaf carbon and water status control stomatal and non-stomatal limitations of photosynthesis in trees"</p> <p> </p>
Data corresponding to the publication "The limited predictive power of the Pauling Rules"
<p>This is the data set corrresponding to the publication "The limited predictive power of the Pauling rules" (see https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202000829). This data can be reproduced with the following code: https://doi.org/10.5281/zenodo.3654428.</p>
Data from: Tradeoffs with growth limit host range in complex life cycle helminths
Parasitic worms with complex life cycles have several developmental stages, with each stage creating opportunities to infect additional host species. Using a dataset for 973 species of trophically transmitted acanthocephalans, cestodes, and nematodes, we confirmed that worms with longer life cycles (i.e. more successive hosts) infect a greater diversity of host species and taxa (after controlling for study effort). Generalism at the stage level was highest for 'middle' life stages, the second and third intermediate hosts of long life cycles. By simulating life cycles in real food webs, we found that middle stages had more potential host species to infect, suggesting that opportunity constrains generalism. However, parasites usually infected fewer host species than expected from simulated cycles, suggesting generalism also has costs. There was no tradeoff in generalism from one stage to the next, but worms spent less time growing and developing in stages where they infected more taxonomically diverse hosts. Our results demonstrate that life cycle complexity favors high generalism, and host use across life stages is determined by both ecological opportunity and life history tradeoffs.
Data from: Pollen limitation in the endangered Chinese endemic species Sinocalycanthus chinensis
<p>Pollen limitation negatively impacts endangered and endemic plants with small fragmented populations, such as <i>S</i><i>inocalycanthus chinensis</i><i>, </i>an endangered plant endemic to China. In this study, we analyzed the pollen limitation of the <i>S. chinensis</i> Damingshan (DMS) population in 2006, 2009, and 2010, and crossed plants with mates separated by different distances, both within and between populations. The DMS population exhibited strong pollen limitation in fruit set, seed set, and seeds per fruit in 2006, 2009, and 2010. The average accumulated pollen limitation (for fruit set times seeds per fruit) was 0.510 ± 0.180. Progeny crossed with pollen from intermediate neighboring plants within the same population (separated by 30 – 50 m from pollen recipients) had the lowest fitness. No optimal outcrossing distance was found within the<i> </i>DMS population. Progeny from crosses with the SXW and DLS populations performed relatively better, while those from crosses with QLF and LXS populations performed worse. Compared with average reproductive success, outbreeding depression was found in progeny from crosses with the LXS and QLF populations. Reproductive success from pure self-pollination indicated <i>S. chinensis </i>is self-compatible. Geitonogamous selfing increased reproductive success. Based on geitonogamous selfing, the proportion of selfed offspring was relatively high. These results provide basic references for the conservation of this species.</p>
Data from: Phosphorus limitation does not drive loss of bony lateral plates in freshwater stickleback (Gasterosteus aculeatus)
Connecting the selective forces that drive the evolution of phenotypes to their underlying genotypes is key to understanding adaptation, but such connections are rarely tested experimentally. Threespine stickleback (<i>Gasterosteus aculeatus</i>) are a powerful model for such tests because genotypes that underlie putatively adaptive traits have been identified. For example, a regulatory mutation in the <i>Ectodysplasin</i> (<i>Eda</i>) gene causes a reduction in the number of bony armor plates, which occurs rapidly and repeatedly when marine sticklebacks invade freshwater. However, the source of selection on plate loss in freshwater is unknown. Here, we tested whether dietary reduction of phosphorus can account for selection on plate loss due to a growth advantage of low-plated fish in freshwater. We crossed marine fish heterozygous for the 16 kilobase freshwater <i>Eda</i> haplotype and compared the growth of offspring with different genotypes under contrasting levels of dietary phosphorus in both saltwater and freshwater. <i>Eda</i> genotype was not associated with growth differences in any treatment, or with mechanisms that could mitigate the impacts of phosphorus limitation, like differential phosphorus deposition, phosphorus excretion, or intestine length. This study highlights the importance of experimentally testing the putative selective forces acting on phenotypes and their underlying genotypes in the wild.
Data from: Hurricanes overcome migration lag and shape intraspecific genetic variation beyond a poleward mangrove range limit
<p>Expansion of many tree species lags behind climate-change projections. Extreme storms can rapidly overcome this lag, especially for coastal species, but how will storm-driven expansion shape intraspecific genetic variation? Do storms provide recruits only from the nearest sources, or from more distant sources? Answers to these questions have ecological and evolutionary implications, but empirical evidence is absent from the literature. Hurricane Irma provided an opportunity to address this knowledge gap at the northern range limit of the neotropical black mangrove (<i>Avicennia germinans</i>) on the Atlantic coast of Florida, USA. We observed massive post-hurricane increases in beach-stranded <i>A. germinans</i> propagules at, and past, this species' present-day range margin when compared to a previously-surveyed, non-hurricane year. Yet, propagule dispersal does not guarantee subsequent establishment and reproductive success (i.e., effective dispersal). We also evaluated prior effective dispersal along this coastline with isolated <i>A. germinans</i> trees identified beyond the most northern established population. We used 12 nuclear microsatellite loci to genotype hurricane-driven drift propagules from nine sites (n = 896 propagules) and isolated trees from four sites (n = 10 trees), determined their sources of origin, and estimated dispersal distances. Almost all drift propagules and all isolated trees came from the nearest sources. This research suggests that hurricanes are a prerequisite for poleward range expansion of a coastal tree species and that storms can shape the expanding gene pool by providing almost exclusively range-margin genotypes. These insights and empirical estimates of hurricane-driven dispersal distances should improve our ability to forecast distributional shifts of coastal species.</p>
Data from: A resurrection study reveals limited evolution of thermal performance in response to recent climate change across the geographic range of the scarlet monkeyflower
<p>Evolutionary rescue can prevent populations from declining under climate change, and should be more likely at high-latitude, "leading" edges of species' ranges due to greater temperature anomalies and gene flow from warm-adapted populations. Using a resurrection study with seeds collected before and after a seven-year period of record warming, we tested for thermal adaptation in the scarlet monkeyflower <i>Mimulus</i> <i>cardinalis</i>. We grew ancestors and descendants from northern-edge, central, and southern-edge populations across eight temperatures. Despite recent climate anomalies, populations showed limited evolution of thermal performance curves. However, one southern population evolved a narrower thermal performance breadth by 1.31 °C, which matches the direction and magnitude of the average decrease in seasonality experienced. Consistent with the climate variability hypothesis, thermal performance breadth increased with temperature seasonality across the species' geographic range. Inconsistent with performance trade-offs between low and high temperatures across populations, we did not detect a positive relationship between thermal optimum and mean temperature. These findings fail to support the hypothesis that evolutionary response to climate change is greatest at the leading edge, and suggest that the evolution of thermal performance is unlikely to rescue most populations from the detrimental effects of rapidly changing climate.</p>
Data from: Inducing seed dispersal by generalist frugivores: A new technique to overcome dispersal limitation in restoration
<p><b>1.</b> Dispersal limitation severely impairs the trajectory of restoration, mainly due to the lack of seed vectors bringing seeds from nearby habitats; a role played by many frugivorous vertebrates that can be absent or reduced in restored or degraded sites.</p> <p><b>2.</b> Here we propose a new technique named Induced Seed Dispersal, that amplifies the role that many generalist frugivores have in seed dispersal. It consists in the offering of seeds embedded in the pulp of commercial fruits or whole native fleshy fruits in feeders to generalist frugivores, which ingest the seeds and defecate them elsewhere. We set feeders in a restored site and monitored the visiting pattern of these frugivores with cameras-traps. We also set seed traps to retrieve seeds dispersed by frugivores and offered around 1500 seeds of <i>Cecropia hololeuca</i> (Urticaceae) per week for one year.</p> <p><b>3</b>. We recorded at least 24 generalist frugivore species of terrestrial mammals, bats, and birds, which ingested/removed the seeds/fruits from the feeders. Seeds of <i>C. hololeuca</i> dispersed by marmosets were retrieved in the seed traps and germinated. We estimated a potential seed rain of more than 600 <i>C. hololeuca </i>seeds ha<sup>-1</sup> mo<sup>-1</sup>.</p> <p><b>4</b>. <i>Synthesis and applications</i>. Our study demonstrates that this new technique can make use of generalist frugivores to assist restoration or regeneration into sites where seed dispersal is compromised by the lack of dispersers or limited seed arrival. Inducing seed dispersal by generalist frugivores is a low-cost and easy-managed technique that can be applied year-round in restoration and forest enrichments at all scales.</p>
Common field data limitations can substantially bias sexual selection metrics
<p>Sexual selection studies widely estimate several metrics, but values may be inaccurate because standard field methods for studying wild populations produce limited data (e.g., incomplete sampling, inability to observe copulations directly). We compared four selection metrics (Bateman gradient, opportunity for sexual selection, opportunity for selection, and <em>s'<sub>max</sub></em>) estimated with simulated complete and simulated limited data for 15 socially monogamous songbird species with extra-pair paternity (4-54% extra-pair offspring). Inferring copulation success from offspring parentage creates non-independence between these variables and systematically underestimates copulation success. We found that this introduces substantial bias for the Bateman gradient, opportunity for sexual selection, and <em>s'<sub>max</sub></em>. Notably, 47.5% of detected Bateman gradients were significantly positive for females, suggesting selection on females to copulate with multiple males, though the true Bateman gradient was zero. Bias generally increased with the extent of other sources of data limitations tested (nest predation, male infertility, and unsampled floater males). Incomplete offspring sampling introduced bias for all metrics except the Bateman gradient, while incomplete sampling of extra-pair sires did not introduce additional bias when sires were a random subset of breeding males. Overall, our findings demonstrate how biases due to field data limitations can strongly impact the study of sexual selection.</p>
Data from: An approach to incorporating inferred connectivity of adult movement into marine protected area design with limited data
Marine protected areas (MPAs) are important conservation tools that can support the resilience of marine ecosystems. Many countries, including Canada, have committed to protecting at least 10% of their marine areas under the Convention on Biological Diversity's Aichi Target 11, which includes connectivity as a key aspect. Connectivity, the movement of individuals among habitats, can enhance population stability and resilience within and among MPAs. However, little is known about regional spatial patterns of marine ecological connectivity, particularly adult movement. We developed a method to assess and design MPA networks that maximize inferred connectivity within habitat types for adult movement when ecological data are limited. We used the Northern Shelf Bioregion in British Columbia, Canada, to explore two different approaches: 1) evaluating sites important for inferred regional connectivity (termed hotspots); and 2) assessing MPA network configurations based on their overlap with connectivity hotspots and interconnectedness between MPAs. To assess inferred connectivity via adult movement, we used two different threshold distances (15 km and 50 km) to capture moderate home ranges, which are most appropriate to consider in MPA design. We applied graph theory to assess inferred connectivity within sixteen habitat and depth categories (proxies for distinct ecological communities), and used novel multiplex network methodologies to perform an aggregated assessment of inferred connectivity. We evaluated inferred regional connectivity hotspots based on betweenness and eigenvector centrality metrics, finding that the existing MPA network overlapped a moderate proportion of these regional hotspots, and identified key areas to be considered as candidate MPAs. Network density among existing MPAs was low within the individual habitat networks, as well as the multiplex. This work informs an ongoing MPA planning process, and approaches for incorporating connectivity into MPA design when data are limited, with lessons for other contexts.
Figures, plotting scripts, and data for "Resolving non-uniform temperature distributions with single-beam absorption spectroscopy. Part I: Theoretical capabilities and limitations"
<p>This dataset contains the necessary materials to recreate the figures in "Resolving nonuniform temperature distributions with single-beam absorption spectroscopy: Part I: Theoretical capabilities and limitations."</p> <p>The code included in this dataset is released under the BSD 3-Clause License. The figures are shared under the Creative Commons Attribution 4.0 International License (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/).</p>
Data from: Minimum size limits and the reproductive value of numerous, young, mature female fish
<p>Fisheries management relies on various catch and effort controls to preserve spawning stock biomass and maximise sustainable yields while limiting fishery impacts on marine ecosystems. These include species-specific minimum or maximum size limits to protect either small non-reproductive sub-adults, a portion of reproductively mature adults, or large highly fecund individuals. Protecting size classes of mature fish is expected to yield a viable source of larvae for replenishing populations and reduce the risk of recruitment overfishing, yet size-specific recruitment contributions have rarely been assessed empirically. Here we apply genetic parentage analysis to measure the reproductive success of a size-structured population of a commercially important species of coral grouper (<i>Plectropomus</i> <i>maculatus </i>- Serranidae) in no-take marine reserves in the Great Barrier Reef Marine Park, Australia. Although the per-capita reproductive success of individual fish increases rapidly with body-length, the numerous young mature female fish (NYMFFs), below the minimum size limit (38 cm total length), were responsible for generating disproportionately large contributions (36%) towards larval replenishment of both fished and reserve reefs. Our findings indicate that minimum size limits are an effective harvest control measure to safeguard a portion of the spawning stock biomass for coral grouper and supplement recruitment subsidies assured from no-take marine reserves.</p>
Data from: Life-history theory provides a framework for detecting resource limitation: a test of the Nutritional Buffer Hypothesis
<p>For ungulates and other long-lived species, life-history theory predicts that nutritional reserves are allocated to reproduction in a state-dependent manner because survival is highly conserved. Further, as per-capita food abundance and nutritional reserves decline (i.e., density-dependence intensifies), reproduction and recruitment become increasingly sensitive to weather. Thus, the degree to which weather influences vital rates should be associated with proximity to nutritional carrying capacity—a notion that we refer to as the Nutritional Buffer Hypothesis. We tested the Nutritional Buffer Hypothesis using six moose (<i>Alces alces</i>) populations that varied in calf recruitment (33-69 calves/ 100 cows). We predicted that populations with high calf recruitment were nutritionally buffered against the effects of unfavorable weather, and thus were below nutritional carrying capacity. We applied a suite of tools to quantify habitat and nutritional condition of each population and found that increased browse condition, forage quality, and body fat were associated with increased pregnancy and calf recruitment, thereby providing multiple lines of evidence that declines in calf recruitment were underpinned by resource limitation. From 2001 to 2015, recruitment was more sensitive to interannual variation in weather (e.g., winter severity, drought) and plant phenology (e.g., duration of spring) for populations with reduced browse condition, forage quality, and body fat, suggesting these populations lacked the nutritional reserves necessary to buffer demographic performance against the effects of unfavorable weather. Further, average within-population calf recruitment was determined by regional climatic variation, suggesting that the pattern of reduced recruitment near the southern range boundary of moose stems from an interaction between climate and resource limitation. When coupled with information on habitat, nutrition, weather, and climate, life-history theory provides a framework to estimate nutritional limitation, proximity to nutritional carrying capacity, and impacts of climate change for ungulates.</p>
Data from: Pushing the limits of photoreception in twilight conditions: The rod-like cone retina of the deep-sea pearlsides
Most vertebrates have a duplex retina comprising two photoreceptor types, rods for dim-light (scotopic) vision and cones for bright-light (photopic) and color vision. However, deep-sea fishes are only active in dim-light conditions; hence, most species have lost their cones in favor of a simplex retina composed exclusively of rods. Although the pearlsides, Maurolicus spp., have such a pure rod retina, their behavior is at odds with this simplex visual system. Contrary to other deep-sea fishes, pearlsides are mostly active during dusk and dawn close to the surface, where light levels are intermediate (twilight or mesopic) and require the use of both rod and cone photoreceptors. This study elucidates this paradox by demonstrating that the pearlside retina does not have rod photoreceptors only; instead, it is composed almost exclusively of transmuted cone photoreceptors. These transmuted cells combine the morphological characteristics of a rod photoreceptor with a cone opsin and a cone phototransduction cascade to form a unique photoreceptor type, a rod-like cone, specifically tuned to the light conditions of the pearlsides' habitat (blue-shifted light at mesopic intensities). Combining properties of both rods and cones into a single cell type, instead of using two photoreceptor types that do not function at their full potential under mesopic conditions, is likely to be the most efficient and economical solution to optimize visual performance. These results challenge the standing paradigm of the function and evolution of the vertebrate duplex retina and emphasize the need for a more comprehensive evaluation of visual systems in general.
Data from: Climate limitation at the cold edge – contrasting perspectives from species distribution modelling and a transplant experiment
<p>The role of climate in determining range margins is often studied using species distribution models (SDMs), which are easily applied but have well-known limitations, e.g. due to their correlative nature and colonization and extinction time lags. Transplant experiments can give more direct information on environmental effects, but often cover small spatial and temporal scales. We simultaneously applied an SDM using high-resolution spatial predictors and an integral projection (demographic) model based on a transplant experiment at 58 sites to examine the effects of microclimate, light and soil conditions on the distribution and performance of a forest herb, <i>Lathyrus vernus</i>, at its cold range margin in central Sweden. In the SDM, occurrences were strongly associated with warmer climates. In contrast, only weak effects of climate were detected in the transplant experiment, whereas effects of soil conditions and light dominated. The higher contribution of climate in the SDM is likely a result from its correlation with soil quality, forest type, and potentially historic land use, which were unaccounted for in the model. Predicted habitat suitability and population growth rate, yielded by the two approaches, were not correlated across the transplant sites. We argue that the ranking of site habitat suitability is probably more reliable in the transplant experiment than in the SDM because predictors in the former better describe understory conditions, but that ranking might vary among years, e.g. due to differences in climate. Our results suggest that <i>L. vernus</i> is limited by soil and light rather than directly by climate at its northern range edge, where conifers dominate forests and create suboptimal conditions of soil and canopy-penetrating light. A general implication of our study is that to better understand how climate change influences range dynamics, we should not only strive to improve existing approaches but also to use multiple approaches in concert.</p>
Data from: Why time-limited individuals can make populations more vulnerable to disturbance
Individual variation in disturbance vulnerability (i.e. the likelihood that disturbance negatively affects an individual's fitness) can affect how disturbance impacts animal populations, as even at low disturbance levels some individuals could be severely affected and die. Individual variation in vulnerability can arise due to different responses to disturbance. We propose a new hypothesis that even when individuals respond similarly to disturbance, time-limited individuals are more at risk that their condition deteriorates since they have limited ability to extend their foraging time to compensate for disturbance. We investigate this 'time-limitation hypothesis' both empirically and mathematically by studying how individuals that differ in their average foraging time (presumably due to differences in foraging efficiency) are affected by disturbance. We used tracking data of 22 wintering Eurasian oystercatchers Haematopus ostralegus to compare time budgets between disturbed and undisturbed tidal periods. In three tidal periods with severe disturbance by transport airplane, more than a third of the variation in additional flight time and foraging time loss was explained by individual differences. Inefficient individuals that foraged longer in undisturbed tidal periods experienced higher costs in disturbed tidal periods, since they lost more foraging time. We next used an analytical energy balance model to study how time-limited individuals differed in their maximum disturbance thresholds. Both our theoretical model and empirical study suggest that inefficient individuals in a time-limited environment may be unable to increase their foraging time to compensate for the effects of disturbance. Consequently, the magnitude of individual variation in time budgets strongly determines what proportion of the population is at risk that their condition deteriorates due to disturbance. Our hypothesis implies that, when assessing disturbance effects on a population, it is not only important to consider individual variation in disturbance responses, but also variation in time budgets that determine the consequences of disturbance.
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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.