ntbox: An r package with graphical user interface for modelling and evaluating multidimensional ecological niches

Methods in Ecology and Evolution, Journal Year: 2020, Volume and Issue: 11(10), P. 1199 - 1206

Published: July 17, 2020

Abstract Biodiversity studies rely heavily on estimates of species' distributions often obtained through ecological niche modelling. Numerous software packages exist that allow users to model niches using machine learning and statistical methods. However, no existing package with a graphical user interface allows perform calibration selection based convex forms such as ellipsoids, which may match fundamental shapes better, incorporating tools for exploring, modelling, evaluating are intuitive both novice proficient users. Here we describe an r package, N iche T ool B ox ( ntbox ), conduct all processing steps involved in modelling: downloading curating occurrence data, obtaining transforming environmental data layers, selecting variables, exploring relationships between geographic spaces, calibrating ellipsoid models, models binomial partial ROC tests, assessing extrapolation risk, performing information system operations via interface. A summary the entire workflow is produced use stand‐alone algorithm or part research reports. The method explained detail tested modelling threatened feline species Leopardus wiedii . Georeferenced this queried display point occurrences IUCN extent polygon (IUCN, 2007). This used illustrate available accessing, biodiversity (e.g. number chronology collecting) PCA 19 bioclimatic layers). Visualizations three‐dimensional modelled minimum volume ellipsoids developed ancillary statistics. then projected space, represent corresponding potential suitability map. Using fast straightforward means by retrieve manipulate can be implemented calibration, projection evaluation space their combinations.

Language: Английский

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Species distribution models rarely predict the biology of real populations

Ecography, Journal Year: 2021, Volume and Issue: 2022(6)

Published: Dec. 21, 2021

Species distribution models (SDMs) are widely used in ecology. In theory, SDMs capture (at least part of) species' ecological niches and can be to make inferences about the of suitable habitat for species interest. Because suitability is expected influence population demography, have been estimate a variety parameters, from occurrence genetic diversity. However, critical look at ability predict independent data across different aspects biology lacking. Here, we systematically reviewed literature, retrieving 201 studies that tested predictions against assessments occurrence, abundance, performance, Although there some support (~53% depending on how was assessed), predictive performance these declines progressively mean fitness, At same time, observed higher success among evaluated single versus multiple species, pointing possible publication bias. Thus, limited accuracy reported here may reflect best‐case scenario. We discuss limitations provide specific recommendations their use applications going forward. emphasize SDMs, especially when inform conservation decisions, should treated as hypotheses with rather than stand‐ins parameters seek know.

Language: Английский

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A quantitative review of abundance‐based species distribution models

Ecography, Journal Year: 2021, Volume and Issue: 2022(1)

Published: Dec. 15, 2021

The contributions of species to ecosystem functions or services depend not only on their presence but also local abundance. Progress in predictive spatial modelling has largely focused occurrence rather than As such, limited guidance exists the most reliable methods explain and predict variation We analysed performance 68 abundance‐based distribution models fitted 800 000 standardised abundance records for more terrestrial bird reef fish species. found a large amount models. While many performed poorly, subset consistently reconstructed range‐wide patterns. best predictions were obtained using random forests frequently encountered abundant within same environmental domain as model calibration. Extending outside conditions used training generated poor predictions. Thus, interpolation abundances between observations can help improve understanding patterns, our results indicate extrapolated under changing climate have much greater uncertainty. Our synthesis provides road map key property distributions that underpins theoretical applied questions ecology conservation.

Language: Английский

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A simulation-based method for selecting calibration areas for ecological niche models and species distribution models

Frontiers of Biogeography, Journal Year: 2021, Volume and Issue: 13(4)

Published: Aug. 16, 2021

Ecological niche models and species distribution (ENM SDM, respectively) are tools that have seen massive use considerable improvement during the last twenty years. The choice of calibration areas for such has strong effects on model outcomes interpretation, as well transfer to distinct environmental settings. However, approaches selecting these remain simple and/or unlinked biological concepts. Such should be calibrated within interest explored throughout its recent history, accessible area (M). In this paper, we provide a simulation approach estimating species’ M considering processes dispersal, colonization, extinction in constant current climate or glacial-interglacial change frameworks, implemented new R package developed called grinnell. Using avian genus Aphelocoma, different parameterizations our simulation, compared them selection, terms performance risk extrapolation using algorithm Maxent mobility-oriented parity analyses. Model exercises from all resulted at least one meeting optimal criteria each species; however, noted high variability among taxa selection methods. More importantly, hypotheses derived directly simulations key processes, rather than being based proxies those better suited erecting biologically appropriate contrasts calibration, characterizing potential more rigorously. Major factors were layer resolution, dispersal kernel characteristics, inclusion changing framework climatic conditions. This contribution represents first simulation-based method ENM offering quantitative estimate while ability, along with patterns suitability across space time.

Language: Английский

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Scale-sensitivity in the measurement and interpretation of environmental niches

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 38(6), P. 554 - 567

Published: Feb. 15, 2023

Species environmental niches are central to ecology, evolution, and global change research, but their characterization interpretation depend on the spatial scale (specifically, grain) of measurement. We find that grain niche measurement is usually uninformed by ecological processes varies orders magnitude. illustrate consequences this variation for volume, position, shape estimates, discuss how it interacts with geographic range size, habitat specialization, heterogeneity. Spatial significantly affects study breadth, suitability, tracking, climate effects. These other fields will benefit from a more mechanism-informed choice cross-grain evaluations integrate different data sources.

Language: Английский

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A species’ response to spatial climatic variation does not predict its response to climate change

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 121(1)

Published: Dec. 18, 2023

The dominant paradigm for assessing ecological responses to climate change assumes that future states of individuals and populations can be predicted by current, species-wide performance variation across spatial climatic gradients. However, if the fates systems are better past in situ through time, this current analytical may severely misleading. Empirically testing whether or temporal predict how species respond has been elusive, largely due restrictive data requirements. Here, we leverage a newly collected network ponderosa pine tree-ring time series test statistically inferred versus trees have responded recent change. When compared observed tree growth since 1980, predictions derived from were wrong both magnitude direction. This was not case which able replicate well. Future scenarios end 21st century exacerbated these disparities. These results suggest currently forecasting impacts based on misleading over decadal centennial timescales.

Language: Английский

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Ecological marginalization is widespread and increases extinction risk in mammals

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(3)

Published: Jan. 9, 2023

Human land-use results in widespread range change across taxa. Anthropogenic pressures can result species' realized niches expanding, shifting, or contracting. Marginalization occurs when contraction constrains species to the geographic ecological extremes of their historic niche. Using 4,785 terrestrial mammal species, we show that niche space and habitat diversity loss. Additionally, marginalization is a common consequence caused by human land use change. Remnant populations become located climatic topographic are more likely be at periphery greater distances from centroids. This associated with poor performance increased extinction risk independent Range loss may create "double whammy" vulnerable groups, such as large-bodied small geographical size. Our reveal hitherto unrecognized conservation threat vital incorporate into assessment management.

Language: Английский

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Climate change may reveal currently unavailable parts of species’ ecological niches

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(7), P. 1298 - 1310

Published: May 29, 2024

Language: Английский

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A grazer's niche edge is associated with increasing diet diversity and poor population performance

Ecology Letters, Journal Year: 2024, Volume and Issue: 27(1)

Published: Jan. 1, 2024

Abstract The core‐periphery hypothesis predicts niche cores should be associated with greater survivorship, reproductive output and population performance rates than marginal habitats at edges. However, there is very little empirical evidence of whether centrality influences trends in animals. Using the Cape mountain zebra ( Equus ) as a model system, we evaluated trends, resource availability diet across gradient. Population growth density progressively declined towards peripheries. Niche peripheries were resource‐poor consumed more phylogenetically diverse diets dominated by non‐grass families. In core they grass‐rich female success was higher. This combination spatial modelling functional ecology provides novel evaluation how bottom‐up limitation can shape species distributions, resilience range change guide conservation management.

Language: Английский

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Testing macroecological abundance patterns: The relationship between local abundance and range size, range position and climatic suitability among European vascular plants

Journal of Biogeography, Journal Year: 2020, Volume and Issue: 47(10), P. 2210 - 2222

Published: July 9, 2020

Abstract Aim A fundamental question in macroecology centres around understanding the relationship between species’ local abundance and their distribution geographical climatic space (i.e. multi‐dimensional or niche). Here, we tested three macroecological hypotheses that link to following range properties: (a) abundance–range size relationship, (b) centre (c) abundance–suitability relationship. Location Europe. Taxon Vascular plants. Methods Distribution maps were extracted from Chorological Database Halle derive information on niche sizes of 517 European vascular plant species. To estimate abundance, assessed samples 744,513 vegetation plots Vegetation Archive, where is available as cover per plot. We then calculated ‘centrality’, is, distance location observation each space. The suitability plot locations was estimated using coarse‐grain species models (SDMs). relationships centrality with linear quantile regression. summarized overall trend across regression slopes a meta‐analytical approach. Results did not detect any positive mean its niche. Contrasting yet significant correlations detected among Main conclusions Our results do provide unequivocal support for tested, demonstrating determining properties distributions at large grains extents might be limited use predicting including current SDM approaches. conclude environmental factors influencing individual performance are likely differ those driving coarse resolution broad extents.

Language: Английский

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