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238 results for “vulnerability data”
Data from: Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes
<p>Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However the diversity of such microbiomes is mostly described in a few coral species, and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species.</p> <p>Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic diversity was specific and not recovered in surrounding plankton.</p> <p>Estimate of the total diversity associated to coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.</p>
Supplementary data for Development of Indicators of Social Vulnerability and Fishing Reliance in English Coastal Communities
<p>Supplementary data for Development of Indicators of Social Vulnerability and Fishing Reliance in English Coastal Communities by Tom Gibson, Chloe Lucas and Angela Muench. Full details are available via the publication and details of folder and file structures are available in the ReadMe file. </p>
Thesis data: Enhancing Vulnerability Detection: A Comparative Study of Change Identification Methods Across Granularity Levels
<p>Starting dataset used within the thesis; Enhancing Vulnerability Detection: A Comparative Study of Change Identification Methods Across Granularity Levels.</p> <p>Results of manual annotation of and extract of nonPatchTaggedCommitLinks within the NVD CVE dataset.</p>
Data for NHESS manuscript by Biass et al. (2022): Insights into the vulnerability of vegetation to tephra fallouts from interpretable machine learning and big Earth observation data
<p>This repository contains the data produced in the context of the following paper:</p> <blockquote> <p>Biass S, Jenkins SF, Aberhard WH, Delmelle P, Wilson T (2022): Insights into the vulnerability of vegetation to tephra fallouts from interpretable machine learning and big Earth observation data, Accepted in NHESS</p> </blockquote> <p>Naming convention is: `run_date`_`landcover`_`impact_metrics`_`VI`_`anomaly`_test.pkl, where:</p> <ul> <li>Landcover is either crops, shrubs, herbaceous vegetation (grass), forests (trees) or all together</li> <li>Impact metrics is either minV (impact magnitude) or minT (impact duration)</li> <li>VI is the vegetation index (here, EVI)</li> <li>Anomaly is the impact indicator (here, cumulative difference index)</li> </ul> <p>Refer to the associated paper for more information on the methodology.</p> <p>Files are saved as .pkl and were generated by the <a href="https://explainerdashboard.readthedocs.io/en/latest/">explainerdashboard</a> library. They are the result of <a href="https://xgboost.readthedocs.io/en/stable/">XGBoost</a> runs that were optimised with <a href="https://optuna.org">Optuna</a> and analysed with the <a href="https://shap.readthedocs.io/en/latest/">SHAP</a> library. They contain:</p> <ol> <li>The explanatory variables and observed and computed target variables for all features</li> <li>The SHAP values</li> </ol> <p>To load the files, use <a href="https://explainerdashboard.readthedocs.io/en/latest/cli.html?highlight=load#explainerdashboard.explainers.BaseExplainer.from_file">this method</a>.</p> <p> </p>
Data for: Temperate and tropical lizards are vulnerable to climate warming due to increased water loss and heat stress
<p><span>Climate warming has imposed profound impacts on species globally. Understanding the vulnerabilities of species from different latitudinal regions to warming climates is critical for biological conservation. </span><span>Using five species of <em>Takydromus </em>lizards as a study system, we quantified physiological and life-history responses and geography range change across latitudes under climate warming. Using integrated biophysical models and hybrid species distribution models, w</span><span>e found: (1) thermal safety margin is larger at high latitudes, and is predicted to decrease under climate warming for lizards at all latitudes; (2) climate warming will speed up embryonic development and increase annual activity time of adult lizards, but will exacerbate water loss of adults across all latitudes; and (3) species across latitudes are predicted to experience habitat contraction under climate warming due to different limitations: tropical and subtropical species are vulnerable due to increased extremely high temperatures, whereas temperate species are vulnerable due to both extremely high temperatures and increased water loss. This study provides a comprehensive understanding of the vulnerability of species from different latitudinal regions to climate warming in ectotherms and also highlights the importance of integrating environmental factors, behavior, physiology, and life-history responses in predicting the risk of species to climate warming.</span></p>
Data for: Social-ecological vulnerability of fishing communities to climate change: a U.S. West Coast case study
<p><span>Climate change is already impacting coastal communities, and ongoing and future </span><span>shifts in fisheries species productivity from climate change have implications for the </span><span>livelihoods and cultures of coastal communities. Harvested marine species in the </span><span>California Current Large Marine Ecosystem support U.S. West Coast communities </span><span>economically, socially, and culturally. Ecological vulnerability assessments exist for </span><span>individual species in the California Current but ecological and human vulnerability are </span><span>linked and vulnerability is expected to vary by community. Here, we present </span><span>automatable, reproducible methods for assessing the vulnerability of U.S. West Coast </span><span>fishing-dependent communities to climate change within a social-ecological </span><span>vulnerability framework. We first assessed the ecological risk of marine resources, on </span><span>which fishing communities rely, to 50 years of climate change projections. We then </span><span>combined this with the adaptive capacity of fishing communities, based on social </span><span>indicators, to assess the potential ability of communities to cope with future changes. </span><span>Specific communities (particularly in Washington state) were determined to be at risk to </span><span>climate change mainly due to economic reliance on at risk marine fisheries species, </span><span>like salmon, hake, or sea urchins. But, due to higher social adaptive capacity, these </span><span>communities were often not found to be the most vulnerable overall. Conversely, </span><span>certain communities that were not the most at risk, ecologically and economically, </span><span>ranked in the category of highly vulnerable communities due to low adaptive capacity </span><span>based on social indicators (particularly in Southern California). Certain communities </span><span>were both ecologically at risk due to catch composition and socially vulnerable (low </span><span>adaptive capacity) leading to the highest tier of vulnerability. The integration of climatic, </span><span>ecological, economic, and societal data reveals that factors underlying vulnerability are </span><span>variable across fishing communities on the U.S West Coast, and suggests the need to </span><span>develop a variety of well-aligned strategies to adapt to the ecological impacts of climate </span><span>change.</span></p>
Data from: Hindcast-validated species distribution models reveal future vulnerabilities of mangroves and salt marsh species
<p>Rapid climate change threatens biodiversity via habitat loss, range shifts, increases in invasive species, novel species interactions, and other unforeseen changes. Coastal and estuarine species are especially vulnerable to the impacts of climate change due to sea level rise and may be severely impacted in the next several decades. Species distribution modeling can project the potential future distributions of species under scenarios of climate change using bioclimatic data and georeferenced occurrence data. However, models projecting suitable habitat into the future are impossible to ground truth. One solution is to develop species distribution models for the present and project them to periods in the recent past where distributions are known to test model performance before making projections into the future. Here, we develop models using abiotic environmental variables to quantify the current suitable habitat available to eight Neotropical coastal species: four mangrove species and four salt marsh species. Using a novel model validation approach that leverages newly available monthly climatic data from 1960-2018, we project these niche models into two time periods in the recent past (i.e., within the past half-century) when either mangrove or salt marsh dominance was documented via other data sources. Models were hindcast-validated and then used to project the suitable habitat of all species at four time periods in the future under a model of climate change. For all future time periods, the projected suitable habitat of mangrove species decreased, and suitable habitat declined more severely in salt marsh species.</p>
Data from: Too much of a good thing? Supplementing current species observations with fossil data to assess climate change vulnerability via ecological niche models
<p>Ecological niche models (ENMs) are a powerful tool in ecological research and conservation planning. Since ENMs provide probability maps of suitable areas under environmental change, they may assist in designing conservation actions and addressing conservation priorities. However, ENMs are usually implemented by learning the species climatic preferences from their current geographic distribution, which leaves them vulnerable to the issue of niche truncation issues, as if comes with non-climatic limits to the current species distribution posed by e.g. anthropic activities and settlements, and is bound to assume that species are at equilibrium with their environments. These problems might be alleviated by the inclusion of fossil occurrences, which refer to moments during species evolution when such limits were absent, and a larger fraction of the species fundamental niche was probably explored. Here, we combined current and fossil occurrence data for 38 medium-large mammal species of conservation concern to assess the influence of the fossil record on ENM predictions under future climate change scenarios. We found that ignoring or including fossil data yields consistent trends in terms of predicted range increase/decrease. Yet, although adding fossil data invariably results in increased niche width, estimates of range change magnitude improved for just one half only of the species. These results suggest that most species might be in non-equilibrium with their environment, and that the inclusion of fossil data may be crucial to the better understanding of species climatic requirements, hence for designing effective conservation strategies. </p>
Data from: Evaluating the vulnerability of Tetracentron sinense habitats to climate-induced latitudinal shifts
<p><strong>Objective:</strong> Exploring the changing process of the geographical distribution pattern of <em>Tetracentron sinense</em> Oliv. and its main influencing factors since the last interglacial period can provide a scientific basis for the effective protection and management of the species.</p> <p><strong>Methods: </strong>The MaxEnt model was used to construct the potential distribution areas of <em>T. sinense</em> in different periods such as the last interglacial (LIG), the last glacial maximum (LGM), the Mid-Holocene (MID), the current and future (2050s, 2070s). On the premise of discussing the influence of dominant environmental factors on its distribution model, the suitable area changes of <em>T. sinense</em> under different ecological climate situations were quantitatively analyzed.</p> <p><strong>Results:</strong> (1) The AUC and TSS values predicted by the optimized model were 0.959 and 0.835, respectively, indicating a good predictive effect by the MaxEnt model; the potential suitable areas for <em>T. sinense</em> in the current period are mainly located in southwest China, which are wider compared to the actual habitats. (2) Jackknife testing showed that the lowest temperature in the coldest month (Bio6), elevation (Elev), seasonal variation coefficient of temperature (Bio4) and surface calcium carbonate content (T-CACO3) are the dominant environmental factors affecting the distribution of <em>T. sinense</em>. (3) From the last interglacial period to the current period, the total suitable area of <em>T. sinense</em> showed a decreasing trend; the distribution points of <em>T. sinense</em> populations in Mid-Holocene period may be the origin of the postglacial population, and Southwest China may be its glacial biological refuge. (4) Compared with the current period, the total suitable area ranges of <em>T. sinense</em> in China in the 2050s and 2070s decreased, and the centroid location of its total fitness area all migrated to the northwest, with the largest migration distance in 2070s under the SSPs 7.0 climate scenario.</p> <p><strong>Conclusion:</strong> Temperature was the principal factor influencing the geographical distribution of <em>T. sinense</em>. With the global warming, the range of <em>T. sinense</em> suitable areas will show a shrinking trend, with a shift towards higher-latitude regions. Ex-situ conservation measures could be taken to preserve its germplasm resources.</p>
Data from: Quantifying coextinctions and ecosystem service vulnerability in coastal ecosystems experiencing climate warming
<p>Climate change is negatively impacting ecosystems and their contributions to human well-being, known as ecosystem services. Previous research has mainly focused on the direct effects of climate change on species and ecosystem services, leaving a gap in understanding the indirect impacts resulting from changes in species interactions within complex ecosystems. This knowledge gap is significant because the loss of a species in a food web can lead to additional species losses or "co-extinctions," particularly when the species most impacted by climate change are also the species that play critical roles in food web persistence or provide ecosystem services. Here, we present a framework to investigate the relationships among species vulnerability to climate change, their roles within the food web, their contributions to ecosystem services, and the overall persistence of these systems and services in the face of climate-induced species losses. To do this, we assess the robustness of food webs and their associated ecosystem services to climate-driven species extinctions in eight empirical rocky intertidal food webs. Across food webs, we find that highly connected species are not the most vulnerable to climate change. However, we find species that directly provide ecosystem services are more vulnerable to climate change and more connected than species that do not directly provide services, which results in ecosystem service provision collapsing before food webs. Overall, we find that food webs are more robust to climate change than the ecosystem services they provide and show that combining species roles in food webs and services with their vulnerability to climate change offer predictions about the impacts of coextinctions for future food web and ecosystem service persistence. However, these conclusions are limited by data availability and quality, underscoring the need for more comprehensive data collection on linking species roles in interaction networks and their vulnerabilities to climate change.</p>
Genus level DNA sequence data for three genes (matK, rbcL, trnH-psbA) for the paper: A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability
<p>This data file contains the consensus DNA sequences in fasta format, of 64 tree genera found in Mediterranean Europe, following the checklist of Médail et al. (2019). </p> <p>The data are used in a manuscript submitted for publication to Botany Letters and currently under revision. The manuscript is entitled: "<em>A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability</em>". Its authors are: Marwan Cheikh Albassatneh, Marcial Escudero, Loic Ponge<sup>*</sup>, Anne-Christine Monnet, Juan Arroyo, Toni Nikolic, Gianluigi Bacchetta, Francesca Bagnoli, Panayotis Dimopoulos, Agathe Leriche, Frédéric Médail, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Arndt Hampe, Bruno Fady.</p>
Data and code repository for the research "Assessing the use of Airborne Electromagnetic Data for nitrate vulnerability assessment in the Central Valley, California"
<p>Data and code for "Assessing the use of Airborne Electromagnetic Data for nitrate vulnerability assessment in the Central Valley, California". This repository contains the analysis and post-processing code for generating results and figures used in the manuscript.</p>
Data collection of article research tittle "Online GIS and Remote Sensing-Based Mapping of Flood Vulnerability in Samarinda Seberang Subdistrict"
<p>This dataset contains the definition and name of the data used in the study. It also contains rows of data for all flood parameters applied to the creation of flood vulnerability maps, namely rainfall data, landsat-8 files, DEM, DSMW and drainage survey data.</p>
Data testing of article research tittle "Online GIS and Remote Sensing-Based Mapping of Flood Vulnerability in Samarinda Seberang Subdistrict"
<p>This dataset explains validation testing in a study of the Samarinda Seberang flood vulnerability map. There are two test methods, namely the Kappa accuracy test and the 3D simulation visualization test. The Kappa accuracy test tab displays a table of Kappa calculation results, and the second tab contains a 3D simulation scenario image.</p>
Data from: Influences of fire–vegetation feedbacks and post-fire recovery rates on forest landscape vulnerability to altered fire regimes
1. In the context of on-going climatic warming, forest landscapes face increasing risk of conversion to non-forest vegetation through alteration of their fire regimes and their post-fire recovery dynamics. However, this pressure could be amplified or dampened, depending on how fire-driven changes to vegetation feed back to alter the extent or behavior of subsequent fires. 2. Here we develop a mathematical model to formalize understanding of how fire–vegetation feedbacks and the time to forest recovery following high-severity (i.e., stand-replacing) fire affect the extent and stability of forest cover across landscapes facing altered fire regimes. We evaluate responses to increasing burn rates while varying the direction (negative vs. positive) of fire–vegetation feedbacks under a continuum of values for feedback strength and post-fire recovery time to determine how interactions among these variables produce thresholds and tipping points in landscape responses to changing fire regimes. 3. Where the early-seral vegetation is less fire-prone than older forests, negative feedbacks limited the reductions in forest cover in response to increased fire frequency or slower forest recovery. By contrast, positive feedbacks (more flammable early-seral vegetation) produced a tipping point beyond which increased burn rates or slower forest recovery drove extensive forest loss. 4. With negative feedbacks, the rates of forest loss and expansion in response to variation in fire frequency were similar. However, where feedbacks are positive, the conversion from predominantly forested to non-forested conditions in response to increased fire frequency was faster than the re-expansion of forest cover following a return to the initial burn rate. Strengthening the positive feedbacks increased this asymmetry. 5. Synthesis. Our analyses elucidate how fire–vegetation feedbacks and post-fire recovery rates interact to affect the trajectories and rates of landscape response to altered fire regimes. We illustrate the vulnerability of ecosystems with positive fire–vegetation feedbacks to climate change-driven increases in fire activity, especially where post-fire recovery is slow. Although negative feedbacks initially provide resistance to forest loss with increasing burn rates, this resistance is eventually overwhelmed with sufficient increases to burn rates relative to recovery times.
Data from: Heat tolerance variation reveals vulnerability of tropical herbivore-parasitoid interactions to climate change
<p>Assessing the heat tolerance (CTmax) of organisms is central to understand the impact of climate change on biodiversity. While both environment and evolutionary history affect CTmax, it is unclear how these factors and their interplay influence ecological interactions, communities, and ecosystems under climate change. We collected and reared caterpillars and parasitoids from canopy and ground layers in different seasons in a tropical rainforest. We tested the CTmax and Thermal Safety Margins (TSM) of these food webs with implications for how species interactions could shift under climate change. We identified strong influence of phylogeny in herbivore-parasitoid community heat tolerance. The TSM of all insects were narrower in the canopy and parasitoids had lower heat tolerance compared to their hosts. Our CTmax-based simulation showed higher herbivore-parasitoid food web instability under climate change than previously assumed, highlighting the vulnerability of parasitoids and related herbivore control in tropical rainforests, particularly in the forest canopy.</p>
Data from: Relative brain size is associated with natal dispersal rate and species' vulnerability to climate change in seabirds
<p><span>The cognitive buffer hypothesis proposes that species with larger brains (relative to their body size) exhibit greater behavioural flexibility, conferring an advantage in unpredictable or novel environments. Therefore, behavioural flexibility – and relative brain size – are likely to be important predictors of a species' vulnerability to anthropogenic pressures and, ultimately, extinction risk. However, current evidence linking brain size to species vulnerability and extinction risk is inconclusive. Furthermore, studies examining the relationship between relative brain size and behavioural flexibility have mainly focused on foraging innovations, whilst other forms of behavioural flexibility remain unexplored. In this study, we collate species-specific information and examine links between relative brain size, rates of natal and adult dispersal (a measure of flexibility in breeding site fidelity), vulnerability to six anthropogenic threats and extinction risk for 131 species of seabird. We focused our study on seabirds, a highly threatened group that displays large variation in both relative brain size and dispersal behaviour. We found a significant positive relationship between relative brain size and natal dispersal rate, suggesting that relative brain size could enhance flexibility in breeding site choice in seabirds, consistent with the cognitive buffer hypothesis. However, this relationship does not persist when we consider adult dispersal, possibly reflecting constraints imposed by mate selection and knowledge transfer in seabirds. We also show that relative brain size is negatively associated with vulnerability to climate change. These findings have immediate application for predicting interspecific variation in species' vulnerability to climate change and identifying priority species for conservation.</span></p>
Multi-omic integration of DNA methylation and gene expression data reveals molecular vulnerabilities in glioblastoma (processed data)
<p>Glioblastoma multiforme (GBM) is one of the most aggressive types of cancer and exhibits profound genetic and epigenetic heterogeneity, making the development of an effective treatment a major challenge. The recent incorporation of molecular features into the diagnosis of GBM patients has led to an improved categorisation into various tumour subtypes with different prognoses and disease management. In this work, we have exploited the benefits of genome-wide multi-omic approaches to identify potential molecular vulnerabilities existing in GBM patients. Integration of gene expression and DNA methylation data from both bulk GBM and patient-derived GBM stem cell lines has revealed the presence of major sources of GBM variability, pinpointing subtype-specific tumour vulnerabilities amenable to pharmacological interventions. In this sense, inhibition of the AP1, SMAD3 and RUNX1 / RUNX2 pathways, in combination or not with the chemotherapeutic agent temozolomide, led to the subtype-specific impairment of tumour growth, particularly in the context of the aggressive, mesenchymal-like subtype. These results emphasize the involvement of these molecular pathways in the development of GBM and have potential implications for the development of personalized therapeutic approaches.</p>
Data from: Changing with the times: Seasonal environmental gradients unveil dynamic bat assemblages and vulnerability
<p>Uncovering the temporal and spatial dynamics of biological communities in response to biotic and abiotic drivers is essential to predict the effects of environmental change on biodiversity. Similarly, estimating species vulnerability in the face of such dynamics is crucial for implementing effective conservation actions. We explored how bat diversity changes over the year across an altitudinal gradient and identified the environmental drivers that shape bat communities. By analysing species' marginality within the biophysical niche space, we evaluated bats' vulnerability to foreseeable environmental changes. Our results suggest that altitude, the proportion of forest cover and shrubs cover are the main drivers shaping bat communities year-round. Additionally, while some bat species are restricted to a single ecological assemblage (or ecological preferences group), others show greater plasticity throughout the year. Importantly, we found that although bats associated with highland habitats and forests could be particularly vulnerable to environmental changes (in particular <em>Myotis mystacinus</em>), this vulnerability correlates poorly with their national conservation status. We suggest that species' ecological plasticity is critical for the resilience of biological communities exposed to environmental changes and should be considered when planning tailored conservation strategies.</p>
Data from: Hydraulic vulnerability of tropical forests is largely independent of water availability
<p>Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin, making these ecosystems vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site-level hydraulic diversity of leaf turgor loss point, resistance to embolism (P<sub>50</sub>), and hydraulic safety margins (HSMs) is high across tropical forests and largely independent of water availability. Species with high HSMs (>1 MPa) and low P<sub>50</sub> values (<-2 MPa) are common across the wet and dry tropics. This high site-level hydraulic diversity, largely decoupled from water stress, could influence which species are favored and become dominant under a drying climate. High hydraulic diversity could also make these ecosystems more resilient to variable rainfall regimes.</p>
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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.