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133 results for “conservation models”
Fig. 3 in Modelling the change in the distribution of the black-shanked douc, Pygathrix nigripes (Milne-Edwards) in the context of climate change: Implications for conservation
Fig. 3. Response curve plots illustrate the dependence of predicted potential distribution on the three most important environmental variables for the black-shanked douc (P. nigripes). The curve shows the mean response of 10 replicates by MaxEnt (red line) and the standard deviation (blue band).
Fig. 1. The 472 in Modelling the change in the distribution of the black-shanked douc, Pygathrix nigripes (Milne-Edwards) in the context of climate change: Implications for conservation
Fig. 1. The 472 points recorded for the black-shanked douc (P. nigripes) that were used in this study. BGM = Bu Gia Map National Park; CYS = Chu Yang Sin National Park; CT = Cat Tien National Park; HB = Hon Ba Nature Reserve; KL-SM = Kalon-Song Mao Nature Reserve; KT = Krong Trai Nature Reserve; NK = Nam Ka Nature Reserve; NN = Nam Nung Nature Reserve; NC = Nui Chua National Park; NO = Nui Ong Nature Reserve; TK = Takou Nature Reserve; VC = Vinh Cuu Nature Reserve.
Using interview surveys and multispecies occupancy models to inform vertebrate conservation
<p>The Excel workbook WGAllSpeciesCov.xlsx contains detection histories of 30 species of vertebrates in 395 sites in the Western Ghats, India obtained from interviews with field staff of the Forest Department, people from local communities and formally trained people. The workbook also contains site level covariates or determinants of species occurrence. The associated README text file contains metadata to describe the data in the xlsx workbook. Complete R code to read in the data and run the model is provided in the R file: FP_MSp_SS_SpR_AllTraitGr.R and the JAGS code for the multispecies occupancy model is provided in the text file FP_MSp_SS_SpR_AllTraitGr_Exp_NoFP.txt</p>
Data from: Different strokes for different croaks: Using an African reed frog species complex as a model to understand idiosyncratic population requirements for conservation management
Open the record for dataset details and reuse information.
Data from: Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management
Open the record for dataset details and reuse information.
Data from: Evaluating population viability and efficacy of conservation management using integrated population models
Predicting population responses to environmental conditions or management scenarios is a fundamental challenge for conservation. Proper consideration of demographic, environmental and parameter uncertainties is essential for projecting population trends and optimal conservation strategies. We developed a coupled integrated population model-Bayesian population viability analysis to assess the (1) impact of demographic rates (survival, fecundity, immigration) on past population dynamics; (2) population viability 10 years into the future; and (3) efficacy of possible management strategies for the federally endangered Great Lakes piping plover Charadrius melodus population. Our model synthesizes long-term population survey, nest monitoring and mark–resight data, while accounting for multiple sources of uncertainty. We incorporated latent abundance of eastern North American merlins Falco columbarius, a primary predator of adult plovers, as a covariate on adult survival via a parallel state-space model, accounting for the influence of an imperfectly observed process (i.e. predation pressure) on population viability. Mean plover abundance increased from 18 pairs in 1993 to 75 pairs in 2016, but annual population growth (math formula) was projected to be 0.95 (95% CI 0.72–1.12), suggesting a potential decline to 67 pairs within 10 years. Without accounting for an expanding merlin population, we would have concluded that the plover population was projected to increase (math formula = 1.02; 95% CI 0.94–1.09) to 91 pairs by 2026. We compared four conservation scenarios: (1) no proposed management; (2) increased control of chick predators (e.g. Corvidae, Laridae, mammals); (3) increased merlin control; and (4) simultaneous chick predator and merlin control. Compared to the null scenario, chick predator control reduced quasi-extinction probability from 11.9% to 8.7%, merlin control more than halved (3.5%) the probability and simultaneous control reduced quasi-extinction probability to 2.6%. Synthesis and applications. Piping plover recovery actions should consider systematic predator control, rather than current ad hoc protocols, especially given the predicted increase in regional merlin abundance. This approach of combining integrated population models with Bayesian population viability analysis to identify limiting components of the population cycle and evaluate alternative management strategies for conservation decision-making shows great utility for aiding recovery of threatened populations.
Figure 4 in Conservation gaps identification through patterns of species richness established from species niche models of mammals in a sector of Chaco Seco ecoregion
Figure 4. Response graphs of habitat suitability (ordinate axis) according to the explanatory variables that intervened in the adjustment of the model for brown brocket deer (A, B, C). The temperature is expressed in degrees Celsius.Source of bioclimatic variables (bio), site https://www.worldclim.org/data/bioclim.html.
Figure 8 in Conservation gaps identification through patterns of species richness established from species niche models of mammals in a sector of Chaco Seco ecoregion
Figure 8. Species richness maps obtained using three algorithms, (A) "fuzzy union″, (B) "species richness″ and (C) "total beta″.
Figure 7 in Conservation gaps identification through patterns of species richness established from species niche models of mammals in a sector of Chaco Seco ecoregion
Figure 7. Response graphs of habitat suitability (ordinate axis) according to the explanatory variables that intervened in theadjustment of themodel for collared peccary (A,B, C).Temperature is expressed in degrees Celsius and altitude in meters.Source of bioclimatic variables (bio), site https://www.worldclim.org/data/bioclim.html.
Data from: Statistical stream temperature modelling with SSN and INLA: an introduction for conservation practitioners
<p>Statistical stream temperature models can predict the fine-scale spatial distribution of water temperatures and guide species recovery and habitat restoration efforts. However, stream temperature modelling is complicated by spatial autocorrelation arising from non-independence data collected within dendritic networks. We used data from miniature sensors deployed in Canadian Rocky Mountain streams to develop and validate two statistical stream temperature modelling techniques that account for spatial autocorrelation. The first was based on spatial steam network models (SSNs) specifically developed to account for spatial autocorrelation in dendritic stream networks. The second used integrated nested Laplace approximation (INLA) that accounts for spatial autocorrelation but was not designed to address anisotropic stream network data. We evaluated the best-fitted SSN and INLA models using leave-one-out cross validation from the data collected along the stream network. Both modelling techniques had similar RMSE and MAE (near 1<sup>o</sup>C) and r<sup>2</sup> (> 0.6) values, and proved flexible with respect to implementation; however, the SSN models required more preprocessing steps before incorporating spatially correlated random errors. We provide practical advice and open-access data and r-script to help non-experts develop statistical stream temperature models of their own.</p>
Targeting fin whale conservation in the North-Western Mediterranean Sea: Insights on movements and behaviour from biologging and habitat modelling
<p>Biologging and habitat modelling are key tools supporting the development of conservation measures and mitigating the effects of anthropogenic pressures on marine species. Here, we analysed satellite telemetry data and foraging habitat preferences in relation to chlorophyll-a productivity fronts to understand the movements and behaviour of endangered Mediterranean fin whales (<em>Balaenoptera physalus)</em> during their spring-summer feeding aggregation in the North-Western Mediterranean Sea. Eleven individuals were equipped with Argos satellite transmitters across three years, with transmissions averaging 23.5 ± 11.3 days. Hidden Markov Models were used to identify foraging behaviour, revealing how individuals showed consistency in their use of seasonal core feeding grounds; this was supported by the distribution of potential foraging habitat. Importantly, tracked whales spent most of their time in areas with no explicit protected status within the study region. This highlights the need for enhanced time- and place-based conservation actions to mitigate the effects of anthropogenic impacts for this species, notably ship strike risk and noise disturbance in an area of exceptionally high maritime traffic levels. These findings strengthen the need to further assess critical habitats and Important Marine Mammal Areas that are crucial for focussed conservation, management, and mitigation efforts.</p>
Final products from "3D MODELING AS A CONSERVATION TOOL TO CHARACTERIZE ENDANGERED SEASONALLY FLOODED ECOSYSTEMS IN THE VOLTA GRANDE DO XINGU, AMAZON FOREST, PARÁ, BRAZIL"
<p>In these .zip folders, you will find the products generated from flight missions carried out between November 7th to 14th, 2021, in the Volta Grande do Xingu, Pará, Brazil. <br>These results are presented as an integral part of the article titled '3D MODELING AS A CONSERVATION TOOL TO CHARACTERIZE ENDANGERED SEASONALLY FLOODED ECOSYSTEMS IN THE VOLTA GRANDE DO XINGU, AMAZON FOREST, PARÁ, BRAZIL' published on the doctoral thesis "Characterization and monitoring of the flooding dynamics and seasonally flooded environments of the Volta Grande do Xingu through remote sensing", available at <a href="https://doi.org/10.11606/T.106.2023.tde-02022024-211517">https://doi.org/10.11606/T.106.2023.tde-02022024-211517</a>. To understand the data processing methodology that led to these results, please refer to the thesis.<br>Each folder represents a flight mission. They are named by date and flight number (DD_MM_YYYY_FLIGHT#).<br>Within each folder, there are six files resulting from the processed flights: The georeferenced orthophoto and Digital Surface Model, which are raster files (.TIFs), the dense point cloud (.las), and the files composing the 3D Model generated by Agisoft Metashape (extensions .OBJ, .MTL, and .JPEG).<br>The .OBJ file is the primary file for visualizing the model, including the three-dimensional mesh formed by the points of the point cloud and containing geometry, texture, and color information. <br>The .MTL file contains the material description associated with the OBJ file and includes information about the visual properties of the model, such as texture, reflections, and materials. <br>The .JPEG files are the texture images used on the Digital Surface Model to generate the 3D model. This information provides the model with its realistic properties.<br>The .OBJ, .MTL and .JPEG files need to be together in the same folder for a complete 3D Model visualization (i.e., shape, color, and texture).<br>When using this data, please cite Affonso, A. A. (2023). <em>Caracterização e monitoramento da dinâmica de alagamento e dos ambientes sazonalmente alagáveis da Volta Grande do Xingu através de sensoriamento remoto</em>. Tese de Doutorado, Instituto de Energia e Ambiente, Universidade de São Paulo, São Paulo. doi:10.11606/T.106.2023.tde-02022024-211517. Recuperado em 2024-04-14, de www.teses.usp.br</p>
Data from: Sequential use of niche and occupancy models identifies conservation and research priority areas for two data-poor endemic birds from the Colombian Andes
<p>The lack of high-quality information on data-poor species can hinder efforts to inform conservation actions via spatial distribution modeling. This is particularly true for tropical birds of conservation concern, for which ecological studies and assessments of their conservation status have received limited funding. Here we use a cost- and time-efficient protocol for assessing the distribution of range-restricted taxa and to identify priority areas for their conservation based on a sequential application of Environmental Niche Models (ENMs) and Occupancy-Detection Models. This approach first uses available geographical information and niche-theory to prioritize potential study sites, which can later be surveyed to obtain high-quality presence-absence data to accurately model distributional ranges with limited resources. We apply this protocol to identify priority areas for two Neotropical birds of conservation concern endemic to the Colombian Andes: Yellow-headed Brush-finch (<i>Atlapetes flaviceps</i>) and Tolima Dove (<i>Leptotila conoveri</i>). We first fitted ENMs using spatially-filtered datasets containing all available records up to 2018. We then conducted field surveys across climatically suitable areas identified for both species, carrying out a total of 1750 counts to generate input data for the occupancy models. Overall, our results suggested more extended and more continuous distribution ranges for both species than previously reported, but also identified population strongholds that are not currently represented within the national protected areas system. Both species occupied a narrow elevational belt (~1300–2600) of the Central Andes of Colombia primarily on the slopes of the Magdalena River valley, with isolated populations in the Western and Eastern Andes; these areas have undergone some of the most marked landscape transformations in Colombia. This straightforward protocol maximizes available information and minimizes costs, while allowing for estimation of occurrence probabilities for range-restricted, data-poor taxa.</p>
Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci
<p>Understanding the genetic aetiology of loci associated with disease is crucial for developing preventative measures and effective treatments. Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, the utility of mouse models is limited by evolutionary divergence in transcription regulation for pathways of interest. Here, we summarise the conservation of genomic (exonic and multi-cell regulatory) features and complex disease associated variant sites between humans and mice. Our results highlight the importance of understanding evolutionary divergence in transcription regulation when interpreting functional studies using mice as models for human disease variants.</p>
Fig. 5 in Using Ecological Niche Modeling For Biodiversity Conservation Guidance In The Western Podillya (Ukraine): Amphibians
Fig. 5. Summarized species richness map (see text for explanation).
Random forest modelling of multi-scale, multi-species habitat associations within KAZA transfrontier conservation area using spoor data
<p>As landscape-scale conservation models grow in prominence, assessments of how wildlife utilise multiple-use landscapes are required to inform effective conservation and management planning. Such efforts should strive to incorporate multi-species perspectives to maximise value for conservation, and should account for scale to accurately capture species-environment relationships. We show that the random forest machine learning algorithm can be used to model large-scale sign-based data in a multi-scale framework. We used this method to investigate scale-dependent habitat associations for 16 mammal species of high conservation importance across the southern Kavango Zambezi (KAZA) Transfrontier Conservation Area in Botswana and Zimbabwe. Our findings revealed substantial variation in the factors shaping habitat use across species, and illustrate that different species often have divergent responses to the same environmental and anthropogenic factors, and differ in the scales at which they respond to them. For all variables across all species, scale optimisation most often selected our largest scale. Precipitation, soil nutrients, and vegetation appeared to be the most important factors determining mammal distributions, likely through their associations with food resources for herbivores and, in turn, prey availability for carnivores. Anthropogenic pressures also had an important influence on habitat use, with many species selecting against areas with high cattle density. The variety of relationships with human density indicated that species vary in their tolerance of humans. We found a consistent positive relationship with areas under high protection, and negative relationship with unprotected and less-strictly protected areas. Policy implications: This study highlights the importance of adopting a multi-scale, multi-species approach for critical decision-making processes that depend on understanding wildlife distributions and habitat associations, such as protected area, corridor, and buffer zone prioritisation. We use our findings to identify changing rainfall patterns and increasing livestock numbers as two emerging trends that may impact wildlife distributions, both within sub-Saharan Africa and on a global scale.</p>
Dataset: Habitat suitability models to make conservation decisions based on areas of high species richness and endemism
<p>This repository contains the files associated with the following article:</p> <p>Hernández-Quiroz NS, EI Badano, F Barragán-Torres, J Flores & C Pinedo-Álvarez. Habitat suitability models to make conservation decisions based on areas of high species richness and endemism. Biodiversity and Conservation, 27, pp. 3185-3200. <a href="https://doi.org/10.1007/s10531-018-1596-9">https://doi.org/10.1007/s10531-018-1596-9</a></p> <p>The Microsoft Excel file (SM 01-Oak occurrences.xlsx) contains the occurrence points used to calibrate the habitat suitability model of each oak species (59 species in total). This file indicates the name of the species (column A), latitude and longitude of each occurrence point (columns B and C; in geographic coordinates) and the full set of bioclimatic variables (columns D-V) and topographic variables (columns W-Z) associated to each point. These later data are provided as they were gathered from the bioclimatic layers of WorldClim and the topographic layers of the Mexican National Institute of Statistics and Geography. The repository also contains interactive maps indicating the predicted and observed distributions of the 59 Mexican oak species (SM 02-Estimated oak distribution ranges.kmz), and the probability-based and occurrence-based map of oak richness and endemic species (SM 03-Oak richness maps.kmz). These geographic projections are provided in KMZ format to make them easy to visualize in Google Earth (freely available at www.google.com/earth). Details about these KMZ files can be consulted by accessing the file properties after opening them in Google Earth.</p>
Fig. 1 in Modelling the distribution of the Ocellated Lizard in France: implications for conservation
Fig. 1. Timon lepidus, adult male, Hérault, France. Photo by Jean Nicolas.
Code and Data for Sturm and Silva (2024) A nudge to the truth: atom conservation as a hard constraint in models of atmospheric composition using an uncertainty-weighted correction
<p>This record contains the Julia photochemical model (https://doi.org/10.5281/zenodo.13385541) output in csv format used for training XGBoost in ProjectionConservationRF.py to emulate ozone photochemical formation. Nonphysical predictions that violate conservation of atoms are corrected using a closed-form, constrained least-squares approach that factors in uncertainty and scale using species-level weights. The file ozoneNOx_visualization.py contains an example and visualization for a smaller system, the primary photolytic cycle from which the Leighton relationship can be derived.</p> <p>The corresponding preprint is available here: <a href="https://doi.org/10.48550/arXiv.2408.16109">https://doi.org/10.48550/arXiv.2408.16109</a></p>
Multiple-model stock assessment frameworks for precautionary management and conservation on fishery-targeted coastal dolphin populations off Japan
<p>1. Stock assessment approaches are often oversimplified due to lack of biological knowledge and insufficient data. In spite of worldwide attention, fishery-targeted coastal dolphin species in Japan have lacked in-depth quantitative stock assessments because of limited time-series of population size and an absence of associated biological information. We consequently developed integrated population models that analyzed multiple sources of data simultaneously with published biological information within a Bayesian framework.<br> 2. We estimate population status and trends for three main species targeted by fisheries, bottlenose dolphins <em>Tursiops truncatus</em>, Risso's dolphins <em>Grampus griseus</em>, and short-finned pilot whales <em>Globicephala macrorhynchus</em>, using single-species age-aggregated and age-structured population dynamics models. Models were fit to absolute abundance estimates from systematic line-transect surveys, four series of abundance indices calculated from fisher's logbooks, and historical catch records. Published biological information was used to develop prior distributions for the biological parameters. We assessed the possible effects of ecological disturbance and competition using state-space and multispecies models.<br> 3. The multispecies model was selected by the model selection both for the age-aggregated and the age-structured approaches.<br> 4. Single-species assessments found that population size declined 4.2% (Risso's dolphin) to 8.0% (bottlenose dolphin) for three species since the late 1800s based on median posterior values, while the state-space and multispecies models found that environmental disturbance and an interaction among species could have reduced population size more substantially.<br> 5. '<em>Policy implications</em>' Simple single-species models are often used to provide conservation and management advice for wild animals but, in this case, results from such models are overly optimistic because they overlook important ecological process. In contrast, current population status could be less favorable if environmental disturbance and interspecific competition actually control population dynamics. Even if that is not the case, considering ecological process in the model will provide more precautionary ways. Our approach of combining multiple modelling frameworks is applicable to many other management systems, and offers increased confidence in estimated status and trends over assessments that consider only a single model.</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.