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1,157 results for “Limited data”
Data from: Solving the paradox of stasis: squashed stabilizing selection and the limits of detection
Despite the potential for rapid evolution, stasis is commonly observed over geological timescales – the so-called "paradox of stasis." This paradox would be resolved if stabilizing selection were common, but stabilizing selection is infrequently detected in natural populations. We hypothesize a simple solution to this apparent disconnect: stabilizing selection is hard to detect empirically once populations have adapted to a fitness peak. To test this hypothesis, we developed an individual-based model of a population evolving under an invariant stabilizing fitness function. Stabilizing selection on the population was infrequently detected in an "empirical" sampling protocol, because (1) trait variation was low relative to the fitness peak breadth; (2) non-selective deaths masked selection; (3) populations wandered around the fitness peak; and (4) sample sizes were typically too small. Moreover, the addition of negative frequency-dependent selection further hindered detection by flattening or even dimpling the fitness peak, a phenomenon we term "squashed stabilizing selection". Our model demonstrates that stabilizing selection provides a plausible resolution to the paradox of stasis despite its infrequent detection in nature. The key reason is that selection "erases its traces": once populations have adapted to a fitness peak, they are no longer expected to exhibit detectable stabilizing selection.
Data from: Resource limitation prevents the emergence of drug resistance by intensifying within-host competition
Slowing the evolution of antimicrobial resistance is essential if we are to continue to successfully treat infectious diseases. Whether a drug-resistant mutant grows to high densities, and so sickens the patient and spreads to new hosts, is determined by the competitive interactions it has with drug-susceptible pathogens within the host. Competitive interactions thus represent a good target for resistance management strategies. Using an in vivo model of malaria infection, we show that limiting a resource that is disproportionately required by resistant parasites retards the evolution of drug resistance by intensifying competitive interactions between susceptible and resistant parasites. Resource limitation prevented resistance emergence regardless of whether resistant mutants arose de novo or were experimentally added before drug treatment. Our work provides proof of principle that chemotherapy paired with an "ecological" intervention can slow the evolution of resistance to antimicrobial drugs, even when resistant pathogens are present at high frequencies. It also suggests that a broad range of previously untapped compounds could be used for treating infectious diseases.
Data from: Defensive chemicals of neighboring plants limit visits of herbivorous insects: associational resistance within a plant population
Despite our understanding of chemical defenses and their consequences for plant performance and herbivores, we know little about whether defensive chemicals in plant tissues, such as alkaloids, and their spatial variation within a population play unappreciated and critical roles in plant-herbivore interactions. Neighboring plants can decrease or increase attractiveness of a plant to herbivores, an example of a neighborhood effect. Chemical defensive traits may contribute to neighborhood effects in plant-herbivore interactions. We examined the effects of nicotine in leaves (a non-emitted defense chemical) on plant-herbivore interactions in a spatial context, using two varieties of <i>Nicotiana tabacum</i> with different nicotine levels. A common garden experiment demonstrated that visits by grasshoppers decreased with increasing density of neighboring plants with a greater nicotine level. In contrast, visits of leaf caterpillars were not affected by neighbors, irrespective of nicotine levels. Thus, our results clearly highlighted that the neighborhood effect caused by the nicotine in leaves depended on the insect identity, and it was mediated by plant-herbivore interactions, rather than plant-plant interactions. This study demonstrates that understanding of effects of plant defensive traits on plant-herbivore interactions requires careful consideration of the spatial distribution of plant defenses, and provides support for the importance of spatial context to accurately capture the ecological and evolutionary consequences of plant-herbivore interactions.
Data from: Behavior influences range limits and patterns of coexistence across an elevational gradient in tropical birds
Does competition influence patterns of coexistence between closely related taxa? Here we address this question by analyzing patterns of range overlap between related species of birds ("sister pairs") co-occurring on a tropical elevational gradient. We explicitly contrast the behavioral dimension of interspecific competition (interference competition) with similarity in resource acquisition traits (exploitative competition). Specifically, we ask whether elevational range overlap in 118 sister pairs that live along the Manu Transect in southeastern Peru is predicted by proxies for competition (intraspecific territorial behavior) or niche divergence (beak divergence and divergence times, an estimate of evolutionary age). We find that close relatives that defend year-round territories tend to live in non-overlapping elevational distributions, while close relatives that do not defend territories tend to broadly overlap in elevational distribution. In contrast, neither beak divergence nor evolutionary age was associated with patterns of range limitation. We interpret these findings as evidence that behavioral interactions⎯particularly direct territorial aggression⎯can be important in setting elevational range limits and preventing coexistence of closely related species, though this depends upon the extent to which intraspecific territorial behavior can be extended to territorial interactions between species. Our results suggest that interference competition can be an important driver of species range limits in diverse assemblages, and thus highlight the importance of considering behavioral dimensions of the niche in macroecological studies.
Data for: Density dependence and spatial heterogeneity limit the population growth rate of invasive pines at the landscape scale
<p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>Determining population growth across large scales is difficult because it is often impractical to collect data at large scales and over long timespans. Instead, the growth of a population is often only measured at a small, plot-level scale and then extrapolated to derive a mean field estimate. However, this approach is prone to error since it simplifies spatial processes such as the neighbourhood effects of density and dispersal. We present a novel approach that estimates how spatial processes derived from the effects of density and dispersal affect population growth between plot scales and landscape scales. The method is based on a scale transition theory and calculates a transition term to measure the spatial scaling of population growth, which we extend to unstable, expanding populations in order to assess whether landscape-scale population dynamics are different from those estimated at smaller spatial scales. We illustrate this approach using aerial imagery of eight locations in New Zealand experiencing non-native pine invasions. Analyses examined the dynamics at a plot scale (1 hectare) and compared this to estimates across entire landscapes (between 24 and 1600 hectares), in several cases for more than one time period. We used a Bayesian spatial random effects model to examine population growth and to account for neighbourhood effects and dispersal between plots in a rapidly changing system. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>We found that the estimates of the scale transition term were typically 10-25% of the mean field estimates, which led to mean field estimates of population growth extrapolated from plots being considerably higher than landscape estimates. The approach we have developed will not only have applications for predicting the populations' growth of invasive species, but also for studies examining the scaling of landscape-scale phenomena.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations
Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.
Histopathology and Body weight data of 14 days limit test
Open the record for dataset details and reuse information.
Sample site coordinates, environmental data, number of copies of target DNA/ul for each sample and limit of detection plot
<p>Human activities in coastal areas are accelerating ecosystem changes at an unprecedented pace, resulting in habitat loss, hydrological modifications, and predatory species declines. Understanding how these changes potentially cascade across marine and freshwater ecosystems requires knowing how mobile euryhaline species link these seemingly-disparate systems. As upper trophic level predators, bull sharks (<i>Carcharhinus leucas</i>) play a crucial role in marine and freshwater ecosystem health. Telemetry studies in Mobile Bay, Alabama suggest that bull sharks extensively use the northern portions of the bay, an estuarine-freshwater interface known as the Mobile-Tensaw Delta. To assess whether bull sharks use freshwater habitats in this region, environmental DNA surveys were conducted during the dry summer and wet winter seasons in 2018. In each season, 5 x<span> 1</span> L water samples were collected at each of 21 sites: five sites in Mobile Bay, six sites in the Mobile-Tensaw Delta, and ten sites throughout the Mobile-Tombigbee and Tensaw-Alabama Rivers. Water samples were vacuum-filtered, DNA extractions were performed on the particulate, and DNA extracts were analyzed with Droplet Digital™ Polymerase Chain Reaction using species-specific primers and an internal probe to amplify a 237-base pair fragment of the mitochondrial NADH dehydrogenase subunit 2 gene in bull sharks. One water sample collected during the summer in the Alabama River met the criteria for a positive detection, thereby confirming the presence of bull shark DNA. While preliminary, this finding suggests that bull sharks use less urbanized, riverine habitats up to 120 km upriver during Alabama's dry summer season.</p>
Supplementary data to: Trapped in the morphospace: the trade-off between morphological integration and functional performance can limit adaptation
<p>The evolution of complex morphological structures can be seen as the result of interplay between different anatomical units evolving in a coordinated fashion. These can be influenced by genetic, developmental and/or functional integration in response to selective pressures. Using the highly derived humeral morphology of talpid moles as model, here we test whether functional specialization (measured as performance) can be linked to increased levels of morphological integration and, if so, what is the extent of the relationship. Combining 2D geometric morphometrics, phylogenetic comparative methods and functional landscape modelling, we demonstrate that the high biomechanical performance of subterranean moles was coupled with a high degree of integration, whereas less specialized taxa displayed intermediate or low magnitudes of integration. Theoretical morphs occurring in high-performance areas of the functional landscape not covered by any species showed a marked drop in covariation levels, suggesting the existence of a genuine tradeoff between integration and performance in the evolution of talpid moles. We argue that the remarkable stability of the subterranean environment may have helped constraining humeral morphology over a restricted area of the functional landscape, trapping subterranean moles in a narrow region of the landscape, impeding any attempt to reposition on a new ascending slope.</p>
Source code and data for Ou et al. (2021) Updates to Paris climate pledges improve chances of limiting global warming to well below 2°C
<p>There are two folders in this repository. The <strong>GCAM-model</strong> folder contains the version of GCAM5.3 used to estimate emission pathways for this analysis. The <strong>data</strong> folder contains source data for our main results. Please check readme.pdf and our original paper for details. </p> <p> </p> <p> </p>
Data from: Ephemeral forest regeneration limits carbon sequestration potential in the Brazilian Atlantic Forest
<p>This dataset contains native forest cover and planted forests data for 3014 municipalities in the Brazilian Atlantic Forest, Brazil, used in the paper: "Piffer, P.R., Calaboni, A., Rosa, M.R., Schwartz, N.B., Tambosi, L.R., & Uriarte, M. (2021) Ephemeral forest regeneration limits carbon sequestration potential in the Brazilian Atlantic Forest. Global Change Biology". The land cover data was obtained from the Mapbiomas Collection 5 products and is publicly available at <a href="https://mapbiomas.org/">https://mapbiomas.org/</a> for download. Socioeconomic data was obtained from the Brazilian Institute of Geography and Statistics, available at https://sidra.ibge.gov.br. More information on the dataset, analysis and results can be found in the associated manuscript referenced above.</p>
Data for: Modeling climate-driven range shifts in populations of two bird species limited by habitat independent of climate
<p>Ranges of species around the world are expected to contract in response to climate change. Species distribution models (SDMs) are a powerful tool for predicting changes in habitat availability, but the variables selected to create SDMs influence their performance. In addition to climate, habitat characteristics and species traits can play a role in predicted species distribution. In this paper, we consider how variable selection influences the accuracy of SDMs when applied to isolated subpopulations of two widely distributed bird species: the great gray owl (<em>Strix</em> <em>nebulosa</em>) and the willow flycatcher (<em>Empidonax</em> <em>traillii</em>). In the Sierra Nevada of California, these species are restricted largely to discrete patches of meadow habitat within a forest matrix, providing the potential to identify specific locations to target conservation efforts. We contrast predictions made by SDMs that consider climatic variables alone with those that incorporate both climate and geophysical variables. Adding geophysical variables resulted in differing model predictions. For willow flycatchers, adding geophysical variables improved predictive performance. In the case of great gray owls, models with and without geophysical variables had nearly identical performance under historical conditions but differed starkly in their predictions. The full model (climatic and geophysical variables) predicted habitat availability to decrease moderately, whereas the climate-only model predicted nearly complete loss of favorable habitat by 2099. The climate-only model is consistent with expectations based on previous SDMs of birds across North America, but previous studies also assume homogeneity in species traits and range-wide habitat requirements. The full model appears more consistent with recent trends in great gray owl numbers in the Sierra Nevada specifically, where the population has remained relatively stable over recent decades. Given contradictions in our model predictions, care should be taken when trying to apply similar SDM models to other systems.</p>
Supplementary material 6 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
PCA with Calomys terrer and C. expulsus : Data type: statistical data
Supplementary material 5 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
Tests for normality, hornoscedasticity and homogeneity : Data type: statistical data
Supplementary material 4 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
Protocol for testing error in the digitalization : Data type: statistical data
Supplementary material 3 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
Specimens of the wear category class 2 : Data type: species data
Supplementary material 2 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
Wear categories : Data type: measurement
Supplementary material 1 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
Alisphenoid strut : Data type: multimedia
Figure 3 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
Figure 3 - PCA showing the individual projections of Calomys sp., C. expulsus and C. tener in the two major axis (PC1 28.7%, PC2 12.3% of the variance). The wireframes illustrate shape differences between most different specimens: CE 09, CT 05, CT 02, and SP 11. Black circles: C. expulsus; Gray triangle: C. tener; Black square: Calomys sp. identified as C. expulsus; Gray square: Calomys sp. identified as C. tener; Gray triangle with black edge: specimen CT 02; Stars: mean shape for each species.
Figure 7 from: Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
Figure 7 - Pooled regression within the two species, between shape (dependent variable) and centroid size (independent variable). Black circles: C. expulsus; Gray triangle: C. tener; Black square: Calomys sp. identified as C. expulsus; Gray square: Calomys sp. identified as C. tener.
ScienceDex guides
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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.