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129 results for “ecological niche models”
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>
Modeling data and R code for Chrysodeixis chalcites ecological niche
<p>The golden twin-spot moth, <em>Chrysodeixis chalcites</em> Esper (Lepidoptera: Noctuidae), is a polyphagous, polyvoltine crop pest occurring natively from northern Europe to Mediterranean Africa and the Canary Islands. Larvae feed on a wide variety of naturally occurring plants as well as soybean and other legume crops, short staple cotton, tomato, potato, peppers, tobacco, and banana. <em>Chrysodeixis chalcites</em> has been recorded in agricultural lands in the Ontario peninsula in eastern Canada and in northern counties of Indiana, USA. Given the strong potential for <em>C. chalcites</em> to invade USA crop lands, it is important to identify environments most likely to sustain growing populations of this pest. Though <em>C.</em> chalcites is native to Europe and North Africa, it has invaded sub-Saharan Africa. Using occurrence data form the native and invaded ranges, and environmental predictors including bioclimatic conditions and human disturbance, we trained three ecological niche models to estimate an ensemble prediction of environmental suitability in the contiguous US. Because human impact is potentially a confounding predictor, models were trained both with and without it. High environmental suitability was projected for the Atlantic coast from New England to Florida, the Gulf coast, the lower Midwest, and the Pacific coast and Central Valley of California.</p>
Data from: Integrating ecological niche and hydrological connectivity models to assess the impacts of hydropower plants on an endemic and imperiled freshwater turtle
<p>We built this dataset to assess the impacts of hydropower plants on the distribution of an endemic and imperiled freshwater turtle with very unique ecological requirements, the Williams' side-necked turtle (<em>Phrynops</em> <em>williamsi</em>). To prevent and mitigate impacts, we prioritized sites for species conservation by classifying planned HPP locations according to their predicted adverse effects on species distribution. The dataset has two files: i) species occurrence records and ii) hydropower plant data. The first dataset was fully built by the authors and the second was modified from the Brazilian Electricity Regulatory Agency (ANEEL) georeferenced data system.</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
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Data from: Integrating ecological niche and hydrological connectivity models to assess the impacts of hydropower plants on an endemic and imperiled freshwater turtle
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Data from: A new null model approach to quantify performance and significance for ecological niche models of species distributions
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Modeling data and R code for Chrysodeixis chalcites ecological niche
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Underlying microevolutionary processes parallel macroevolutionary patterns in ancient Neotropical Mountains - Ecological Niche Modeling and Corridors files
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Paleobiogeographic insights gained from ecological niche models: progress and continued challenges
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Preservation biases in the fossil record distort species ecological niche and distribution models
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Data from: Is there a correlation between abundance and environmental suitability derived from ecological niche modelling? A meta-analysis
It is thought that species abundance is correlated with environmental suitability and that environmental variables, scale, and type of model fitting can confound this relationship. We performed a meta-analysis to (i) test whether species abundance is positively correlated with environmental suitability derived from correlative ecological niche models (ENM), (ii) test whether studies encompassing large areas within a species range (>50%) exhibited higher AS correlations than studies encompassing small areas within a species range (<50%), (iii) assess which modelling method provided higher AS correlation, and (iv) compare strength of the AS relationship between studies using only climatic variables and those that used both climatic and other environmental variables to derive suitability. We used correlation coefficients to measure the relationship between abundance and environmental suitability derived from ENM. Each correlation coefficient was considered an effect size in a random-effects multivariate meta-analysis. In all cases we found a significantly positive relationship between abundance and suitability. This relationship was consistent regardless of scale of study, ENM method, or set of variables used to derive suitability. There was no difference in strength of correlation between studies focusing on large or small areas within a species' range or among ENM methods. Studies using other variables in combination with climate exhibited higher AS correlations than studies using only climatic variables. We conclude that occurrence data can be a reasonable proxy for abundance, especially for vertebrates, and the use of local variables increases the strength of the AS relationship. Use of ENMs can significantly decrease survey costs and allow the study of large-scale abundance patterns using less information. Including only climatic variables in ENM may confound the relationship between abundance and suitability when compared to studies including variables taken locally. However, modelers and conservationists must be aware that high environmental suitability does not always indicate high abundance.
Community science validates climate suitability projections from ecological niche modeling
<p><span>Climate change poses an intensifying threat to many bird species, and projections of future climate suitability provide insight into how species may shift their distributions in response. Climate suitability is characterized using ecological niche models (ENMs), which correlate species occurrence data with current environmental covariates and project future distributions using the modeled relationships together with climate predictions. Despite their widespread adoption, ENMs rely on several assumptions that are rarely validated <i>in situ </i>and can be highly sensitive to modeling decisions, precluding their reliability in conservation decision-making. Using data from a novel, large-scale community science program, we developed dynamic occupancy models to validate near-term climate suitability projections for bluebirds and nuthatches in summer and winter. We estimated occupancy, colonization, and extinction dynamics across species' ranges in the United States in relation to projected climate suitability in the 2020s, and used a Gibbs variable selection approach to quantify evidence of species-climate relationships. We also included a Bird Conservation Region strata-level random effect to examine among-strata variation in occupancy that may be attributable to land-use and ecoregional differences. Across species and seasons, we found strong evidence that initial occupancy and colonization were positively related to 2020 climate suitability, illustrating an independent validation of projections from ENMs across a large geographic area. </span><span>Random strata effects revealed that occupancy probabilities were generally higher than average in core areas and lower than average in peripheral areas of species' ranges, and served as a first step in identifying spatial patterns of occupancy from these community science data. </span><span>Our findings lend much-needed support to the use of ENM projections for addressing questions about potential climate-induced changes in species' occupancy dynamics. More broadly, </span>our work highlights the value of community scientist observations for ground-truthing projections from statistical models and for refining our understanding of the processes shaping species' distributions under a changing climate.</p>
Data from: Ecological niche modeling as a tool for prediction of the potential geographic distribution of Bacillus anthracis spores in Tanzania
Introduction: Anthrax is caused by the spore-forming, Gram-positive bacterium Bacillus anthracis. The aim of this study was to predict the potential distribution of B. anthracis in Tanzania and produce epidemiological evidence for the management of anthrax outbreaks in the country. Methods: The Maxent algorithm was used to predict areas at risk of anthrax outbreaks based on the occurrence and environmental data in Arusha and Kilimanjaro regions; the model was later transferred to predict the entire country. Seventy percent of the occurrence data were used to train the model, while 30% were used for model evaluation. Results: Four regions of northern Tanzania are predicted to have a high risk for anthrax outbreaks, while the southern and western regions had low-risk areas. Soil type (56.5%), soil pH (23.7%), and isothermally (10.4%) were the most important variables for the model prediction, and the most significant soil types were solonetz, fluvisols, and lithosols. Conclusions: A strong risk level across districts of the Tanzania mainland was identified in this study. A total of 18 districts in Tanzania Mainland are predicted to be at very high risk of an anthrax outbreak occurrence. These findings are important for policymakers to effectively mount targeted control measures for anthrax outbreaks in Tanzania.
Data from: An Appalachian population of neochoristoderes (Diapsida: Choristodera) elucidated through fossil evidence and ecological niche modeling
<p>Four neochoristoderan vertebral centra are described from the latest Cretaceous of New Jersey. One specimen was recovered from the basal transgressive lag of the Navesink Formation in the area of Holmdel Park, New Jersey, and two others were recovered nearby and likely were derived from the same horizon. The fourth was recovered from the Marshalltown sequence in the vicinity of the Ellisdale Dinosaur Site. These vertebrae expand the geographic range of Late Cretaceous neochoristoderes in North America by over 2000 km further east, and represent the first neochoristoderan remains from the Atlantic coastal plain. To discern whether neochoristodere remains are to be expected in New Jersey, and elucidate why neochoristoderes are apparently so rare in Appalachia, we implemented ecological niche modeling to predict the range of suitable habitat for <i>Champsosaurus</i>, the only known genus of Late Cretaceous neochoristoderes. We found that in Appalachia, the ideal habitat of <i>Champsosaurus</i> likely existed slightly further north and west than the Atlantic coastal plain, and New Jersey is likely on or near the margin of this suitable habitat space. These results suggest that the occurrence of neochoristoderes in New Jersey is consistent with the habitat requirements of known Late Cretaceous neochoristoderes. These vertebrae therefore may represent the southern margin of a population of neochoristoderes that lived further inland, where latest Cretaceous sediments are not preserved. The continued recovery of material from Late Cretaceous deposits along the Atlantic coast, and review of existing collections, is encouraged to clarify the true distribution of neochoristoderes in Appalachia.</p>
Do selfing species have greater niche breadth? Support from ecological niche modeling
<p>We explore the relationship between plant mating system (selfing or outcrossing) and niche breadth to gain new insights into processes that drive species distributions. Using a comparative approach with highly selfing versus highly outcrossing sister species, we test the extent to which: (1) species pairs have evolved significant niche divergence and less niche overlap, (2) selfers have wider niche breadths than outcrossers or vice versa, and (3) niches of selfers and outcrossers are defined by significant differences in environmental variables. We applied predictive ecological niche modeling approaches to estimate and contrast niche divergence, overlap and breadth, and to identify key environmental variables associated with each species' niche for seven sister species with divergent mating systems. Data from 4862 geo-referenced herbarium occurrence records were compiled for 14 species in Collinsia and Tonella (Plantaginaceae) and 19 environmental variables associated with each record. We found sister species display significant niche divergence, though not as a function of divergence time, and overall, selfers have significantly wider niche breadths compared to their outcrossing sisters. Our results suggest that a selfing mating system likely contributes to the greater capacity to reach, reproduce, establish, and adapt to new habitats, which increases niche breadth of selfers.</p>
Data from: Ecological niche modelling for conservation planning of an endemic snail in the verge of becoming a pest in cardamom plantations in the Western Ghats biodiversity hotspot
Conservation managers and policy makers are often confronted with a challenging dilemma of devising suitable strategies to maintain agricultural productivity while conserving endemic species that at the early stages of becoming pests of agricultural crops. Identification of environmental factors conducive to species range expansion for forecasting species distribution patterns will play a central role in devising management strategies to minimize the conflict between the agricultural productivity and biodiversity conservation. Here, we present results of a study that predicts the distribution of Indrella ampulla, a snail endemic to the Western Ghats biodiversity hotspot, which is becoming a pest in cardamom (Ellettaria cardamomum) plantations. We determined the distribution patterns and niche overlap between I. ampulla and Ellettaria cardamomum using maximum entropy (MaxEnt) niche modeling techniques under current and future (2020–2080) climatic scenarios. The results showed that climatic (precipitation of coldest quarter and isothermality) and soil (cation exchange capacity of soil [CEC]) parameters are major factors that determine the distribution of I. ampulla in Western Ghats. The model predicted cardamom cultivation areas in southern Western Ghats are highly sensitive to invasion of I. ampulla under both present and future climatic conditions. While the land area in the central Western Ghats is predicted to become unsuitable for I. ampulla and Ellettaria cardamomum in future, we found 71% of the Western Ghats land area is suitable for Ellettaria cardamomum cultivation and 45% suitable for I. ampulla, with an overlap of 35% between two species. The resulting distribution maps are invaluable for policy makers and conservation managers to design and implement management strategies minimizing the conflicts to sustain agricultural productivity while maintaining biodiversity in the region.
Data from: Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account
The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.
Data from: Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawai'i
Under the threat of ongoing and projected climate change, communities in the Pacific Islands face challenges of adapting culture and lifestyle to accommodate a changing landscape. Few models can effectively predict how biocultural livelihoods might be impacted. Here, we examine how environmental and anthropogenic factors influence an ecological niche model (ENM) for the realized niche of cultivated taro (Colocasia esculenta) in Hawai'i. We created and tuned two sets of ENMs: one using only environmental variables, and one using both environmental and cultural characteristics of Hawa'i. These models were projected under two different Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCPs) for 2070. Models were selected and evaluated using average omission rate and area under the receiver operating characteristic curve (AUC). We compared optimal model predictions by comparing the percentage of taro plots predicted present and measured ENM overlap using Schoener's D-statistic. The model including only environmental variables consisted of 19 Worldclim bioclimatic variables, in addition to slope, altitude, distance to perennial streams, soil evaporation, and soil moisture. The optimal model with environmental variables plus anthropogenic features also included a road density variable (which we assumed as a proxy for urbanization) and a variable indicating agricultural lands of importance to the State of Hawai'i. The model including anthropogenic features performed better than the environment-only model based on omission rate, AUC, and review of spatial projections. The two models also differed in spatial projections for taro under anticipated future climate change. Our results demonstrate how ENMs including anthropogenic features can predict which areas might be best suited to plant cultivated species in the future, and how these areas could change under various climate projections. These predictions might inform biocultural conservation priorities and initiatives. In addition, we discuss the incongruences that arise when traditional ENM theory is applied to species whose distribution has been significantly impacted by human intervention, particularly at a local scale relevant to biocultural conservation initiatives.
Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)
The central-marginal hypothesis (CMH) predicts that population size, genetic diversity, and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size, and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean center on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core to edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.
Data from: Environmental filtering improves ecological niche models across multiple scales
1. A clear challenge for ecological niche modeling is determining how to best mitigate the effects of sampling bias from commonly collected biodiversity data. Recent approaches have focused on filtering occurrences in overrepresented regions based on geographic or environmental proximity. 2. We tested the efficacy of filtering in geographic and environmental space using occurrence data from four species. Our evaluation strategies examined 14 distance measures in geographic and environmental spaces and eight combinations of environmental variables and their ordinations. This resulted in 78 datasets for each species, which we evaluated using area under the curve (AUC), the difference between training and testing AUC, omission rate, the true skill statistic, and Schoener's D to examine the effects of different filtering schemes. 3. The degree of change produced by filtering on predicted suitability and evaluation statistics increased with increasing range size. Environmental filtering resulted in higher model fit at larger extents and retained more occurrences than geographic filtering. 4. Our results indicate that models should be evaluated using multiple evaluation statistics at multiple thresholds. The use of bin sizes when filtering in environmental space allows for simple comparison between species and filter types and makes for an easily reportable and repeatable distance metric. We specifically recommend that ecological niche models using natural history collection data filter in environmental space with variables derived from permutation importance or the first few axes of a principal components ordination.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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