ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions

Methods in Ecology and Evolution, Год журнала: 2021, Номер 12(9), С. 1602 - 1608

Опубликована: Май 14, 2021

Abstract Quantitative evaluations to optimize complexity have become standard for avoiding overfitting of ecological niche models (ENMs) that estimate species’ potential geographic distributions. ENMeval was the first R package make such (often termed model tuning) widely accessible Maxent algorithm. It also provided multiple methods partitioning occurrence data and reported various performance metrics. Requests by users, recent developments in field, needs software compatibility led a major redesign expansion. We additionally conducted literature review investigate trends use (2015–2019). 2.0 has new object‐oriented structure adding other algorithms, enables customizing algorithmic settings metrics, generates extensive metadata, implements null‐model approach quantify significance effect sizes, includes features increase breadth analyses visualizations. In our review, we found insufficient reporting parameterization, heavy reliance on selection with AICc low utilization spatial cross‐validation; explain how can help address these issues. This redesigned expanded version promote progress field improve information available decision‐making. ​

Язык: Английский

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Want to model a species niche? A step-by-step guideline on correlative ecological niche modelling

Ecological Modelling, Год журнала: 2021, Номер 456, С. 109671 - 109671

Опубликована: Июль 19, 2021

Язык: Английский

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Data integration enables global biodiversity synthesis

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(6)

Опубликована: Фев. 1, 2021

Significance As anthropogenic impacts to Earth systems accelerate, biodiversity knowledge integration is urgently required support responses underpin a sustainable future. Consolidating information from disparate sources (e.g., community science programs, museums) and data types environmental, biological) can connect the biological sciences across taxonomic, disciplinary, geographical, socioeconomic boundaries. In an analysis of research uses world’s largest cross-taxon network, we report emerging roles open-access aggregation in development increasingly diverse, global research. These results indicate new landscape centered on big integration, informing ongoing initiatives strategic prioritization diverse domains, including environmental policy, evolutionary biology, conservation, human health.

Язык: Английский

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Species distribution models rarely predict the biology of real populations

Ecography, Год журнала: 2021, Номер 2022(6)

Опубликована: Дек. 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.

Язык: Английский

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Assessing the reliability of species distribution projections in climate change research

Diversity and Distributions, Год журнала: 2021, Номер 27(6), С. 1035 - 1050

Опубликована: Фев. 19, 2021

Abstract Aim Forecasting changes in species distribution under future scenarios is one of the most prolific areas application for models (SDMs). However, no consensus yet exists on reliability such drawing conclusions species’ response to changing climate. In this study, we provide an overview common modelling practices field and assess model predictions using a virtual approach. Location Global. Methods We first review papers published between 2015 2019. Then, use approach three commonly applied SDM algorithms (GLM, MaxEnt random forest) estimated actual predictive performance parameterized with different settings violations assumptions. Results Most relied single (65%) small samples ( N < 50, 62%), used presence‐only data (85%), binarized models' output (74%) split‐sample validation (94%). Our simulation reveals that tends be over‐optimistic compared real performance, whereas spatial block provides more honest estimate, except when datasets are environmentally biased. The binarization predicted probabilities presence reduces models’ ability considerably. Sample size main predictors accuracy, but has little influence accuracy. Finally, inclusion ecologically irrelevant violation assumptions increases accuracy decreases projections, leading biased estimates range contraction expansion. Main predict low average, particularly binarized. A robust by spatially independent required, does not rule out inflation assumption violation. findings call caution interpretation projections climates.

Язык: Английский

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SDMtune: An R package to tune and evaluate species distribution models

Ecology and Evolution, Год журнала: 2020, Номер 10(20), С. 11488 - 11506

Опубликована: Сен. 30, 2020

Abstract Balancing model complexity is a key challenge of modern computational ecology, particularly so since the spread machine learning algorithms. Species distribution models are often implemented using wide variety algorithms that can be fine‐tuned to achieve best prediction while avoiding overfitting. We have released SDMtune , new R package aims facilitate training, tuning, and evaluation species in unified framework. The main innovations this its functions perform data‐driven variable selection, novel genetic algorithm tune hyperparameters. Real‐time interactive charts displayed during execution several help users understand effect removing or varying hyperparameters on performance. supports three different metrics evaluate performance: area under receiver operating characteristic curve, true skill statistic, Akaike's information criterion corrected for small sample sizes. It implements four statistical methods: artificial neural networks, boosted regression trees, maximum entropy modeling, random forest. Moreover, it includes display outputs create final report. therefore represents new, user‐friendly framework still‐growing field modeling.

Язык: Английский

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Major restructuring of marine plankton assemblages under global warming

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Сен. 1, 2021

Marine phytoplankton and zooplankton form the basis of ocean's food-web, yet impacts climate change on their biodiversity are poorly understood. Here, we use an ensemble species distribution models for a total 336 524 to determine present future habitat suitability patterns. For end this century, under high emission scenario, find overall increase in plankton richness driven by ocean warming, poleward shift species' distributions at median speed 35 km/decade. Phytoplankton is projected more than 16% over most regions except Arctic Ocean. In contrast, slightly decline tropics, but strongly temperate subpolar latitudes. these latitudes, nearly 40% assemblages replaced shifting species. This implies that threatens contribution communities plankton-mediated ecosystem services such as biological carbon sequestration.

Язык: Английский

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Widespread homogenization of plant communities in the Anthropocene

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Дек. 6, 2021

Abstract Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait phylogenetic differences in assemblages between regions, thus diminishing regional distinctiveness biotas likely have negative impacts on key ecosystem functions. However, a global assessment this phenomenon is lacking. Here, using dataset >200,000 plant species, we demonstrate widespread temporal decreases turnover across grain sizes spatial extents. The extent within biomes pronounced overwhelmingly explained naturalizations. Asia North America sources species; however, they export tend to be phylogenetically close recipient floras. Australia, Pacific Europe, contrast, contribute fewer pool non-natives, but represent disproportionate amount diversity. timeline most naturalisations coincides with human migration last ~500 years, demonstrates profound influence humans exert beyond changes richness.

Язык: Английский

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Species distribution modelling supports the study of past, present and future biogeographies

Journal of Biogeography, Год журнала: 2023, Номер 50(9), С. 1533 - 1545

Опубликована: Апрель 10, 2023

Abstract Species distribution modelling (SDM), also called environmental or ecological niche modelling, has developed over the last 30 years as a widely used tool in core areas of biogeography including historical biogeography, studies diversity patterns, species ranges, ecoregional classification, conservation assessment and projecting future global change impacts. In 50th anniversary year Journal Biogeography , I reflect on developments illustrate how embedded methodology become all speculate directions field. Challenges to raised this journal 2006 have been addressed significant degree. Those challenges are clarification concept; improved sample design for occurrence data; model parameterization; predictor selection; assessing performance transferability; integrating correlative process models distributions. SDM is used, often conjunction with other evidence, understand past range dynamics, identify patterns drivers biological diversity, limits, define delineate ecoregions, estimate distributions biodiversity elements relation protected status prioritize action, forecast shifts response climate scenarios. Areas progress that may more accessible useful tools include genetically informed community models.

Язык: Английский

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wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions

Ecography, Год журнала: 2023, Номер 2023(3)

Опубликована: Янв. 16, 2023

Released 4 years ago, the Wallace EcoMod application (R package wallace ) provided an open‐source and interactive platform for modeling species niches distributions that served as a reproducible toolbox educational resource. harnesses R tools documented in literature makes them available via graphical user interface runs analyses returns code to document reproduce them. Since its release, feedback from users partners helped identify key areas advancement, leading development of 2. Following vision growth by community expansion, core team engaged with collaborators undertook major restructuring enable: simplified addition custom modules expand methodological options, multiple same session, improved metadata features, new database connections, saving/loading sessions. 2 features nine added functionalities facilitate data acquisition climate‐simulation, botanical paleontological databases; inputs; model tracking; citations packages used (to promote documentation give credit developers). Three these compose component environmental space (e.g., niche overlap). This expansion was paired outreach biogeography biodiversity communities, including international presentations workshops take advantage software's extensive guidance text. Additionally, advances extend accessibility cloud‐computing implementation include suite comprehensive unit tests. The greatly improve expandability, breadth analyses, reproducibility use emerging standards. architecture serves example other modular software, especially those developed using rapidly proliferating shiny , showcasing straightforward module ingestion testing. Importantly, sets stage future expansions, enabling estimation threat assessments conservation.

Язык: Английский

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