Niche‐based modelling as a tool for predicting the risk of alien plant invasions at a global scale
TL;DR: Cumulative probabilities of climatic suitability show that high-risk regions are spatially limited globally but that these closely match hotspots of plant biodiversity, emphasizing the pivotal role of climate in defining invasion potential.
Abstract: Predicting the probability of successful establishment of plant species by matching climatic variables has considerable potential for incorporation in early warning systems for the management of biological invasions. We select South Africa as a model source area of invasions worldwide because it is an important exporter of plant species to other parts of the world because of the huge international demand for indigenous flora from this biodiversity hotspot. We first mapped the five ecoregions that occur both in South Africa and other parts of the world, but the very coarse definition of the ecoregions led to unreliable results in terms of predicting invasible areas. We then determined the bioclimatic features of South Africa’s major terrestrial biomes and projected the potential distribution of analogous areas throughout the world. This approach is much more powerful, but depends strongly on how particular biomes are defined in donor countries. Finally, we developed bioclimatic niche models for 96 plant taxa (species and subspecies) endemic to South Africa and invasive elsewhere, and projected these globally after successfully evaluating model projections specifically for three wellknown invasive species (Carpobrotus edulis, Senecio glastifolius, Vellereophyton dealbatum) in different target areas. Cumulative probabilities of climatic suitability show that high-risk regions are spatially limited globally but that these closely match hotspots of plant biodiversity. These probabilities are significantly correlated with the number of recorded invasive species from South Africa in natural areas, emphasizing the pivotal role of climate in defining invasion potential. Accounting for potential transfer vectors (trade and tourism) significantly adds to the explanatory power of climate suitability as an index of invasibility. The close match that we found between the climatic component of the ecological habitat suitability and the current pattern of occurrence of South Africa alien species in other parts of the world is encouraging. If species’ distribution data in the donor country are available, climatic niche modelling offers a powerful tool for efficient and unbiased first-step screening. Given that eradication of an established invasive species is extremely difficult and expensive, areas identified as potential new sites should be monitored and quarantine measures should be adopted.
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AT&T1
TL;DR: This paper presents a tuning method that uses presence-only data for parameter tuning, and introduces several concepts that improve the predictive accuracy and running time of Maxent and describes a new logistic output format that gives an estimate of probability of presence.
Abstract: Accurate modeling of geographic distributions of species is crucial to various applications in ecology and conservation. The best performing techniques often require some parameter tuning, which may be prohibitively time-consuming to do separately for each species, or unreliable for small or biased datasets. Additionally, even with the abundance of good quality data, users interested in the application of species models need not have the statistical knowledge required for detailed tuning. In such cases, it is desirable to use "default settings", tuned and validated on diverse datasets. Maxent is a recently introduced modeling technique, achieving high predictive accuracy and enjoying several additional attractive properties. The performance of Maxent is influenced by a moderate number of parameters. The first contribution of this paper is the empirical tuning of these parameters. Since many datasets lack information about species absence, we present a tuning method that uses presence-only data. We evaluate our method on independently collected high-quality presence-absence data. In addition to tuning, we introduce several concepts that improve the predictive accuracy and running time of Maxent. We introduce "hinge features" that model more complex relationships in the training data; we describe a new logistic output format that gives an estimate of probability of presence; finally we explore "background sampling" strategies that cope with sample selection bias and decrease model-building time. Our evaluation, based on a diverse dataset of 226 species from 6 regions, shows: 1) default settings tuned on presence-only data achieve performance which is almost as good as if they had been tuned on the evaluation data itself; 2) hinge features substantially improve model performance; 3) logistic output improves model calibration, so that large differences in output values correspond better to large differences in suitability; 4) "target-group" background sampling can give much better predictive performance than random background sampling; 5) random background sampling results in a dramatic decrease in running time, with no decrease in model performance.
5,314 citations
Cites background from "Niche‐based modelling as a tool for..."
...For example, they have been applied to study spread of invasive species (Thuiller et al. 2005), impacts of climate change (Thomas et al. 2004), and spatial patterns of species diversity (Graham et al. 2006)....
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...Example applications include predicting the effect of climate change on species distributions (Thomas et al. 2004, Araujo et al. 2005) and predicting areas at risk for species invasions (Peterson et al. 2003, Thuiller et al. 2005)....
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TL;DR: Species distribution models (SDMs) as mentioned in this paper are numerical tools that combine observations of species occurrence or abundance with environmental estimates, and are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time.
Abstract: Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.
5,076 citations
Cites background from "Niche‐based modelling as a tool for..."
...Models of the biotic repercussions of global warming and landuse changes require forecasting (Araújo & New 2007, Fitzpatrick et al. 2007, Thuiller et al. 2005), and hindcasting is used for exploring the effects of climate on evolutionary patterns (Kitchener & Dugmore 2000, Kozak et al. 2008, Ruegg…...
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TL;DR: In this article, the authors provide a theoretical explanation for the observed dependence of kappa on prevalence, and introduce an alternative measure of accuracy, the true skill statistic (TSS), which corrects for this dependence while still keeping all the advantages of Kappa.
Abstract: Summary
1In recent years the use of species distribution models by ecologists and conservation managers has increased considerably, along with an awareness of the need to provide accuracy assessment for predictions of such models. The kappa statistic is the most widely used measure for the performance of models generating presence–absence predictions, but several studies have criticized it for being inherently dependent on prevalence, and argued that this dependency introduces statistical artefacts to estimates of predictive accuracy. This criticism has been supported recently by computer simulations showing that kappa responds to the prevalence of the modelled species in a unimodal fashion.
2In this paper we provide a theoretical explanation for the observed dependence of kappa on prevalence, and introduce into ecology an alternative measure of accuracy, the true skill statistic (TSS), which corrects for this dependence while still keeping all the advantages of kappa. We also compare the responses of kappa and TSS to prevalence using empirical data, by modelling distribution patterns of 128 species of woody plant in Israel.
3The theoretical analysis shows that kappa responds in a unimodal fashion to variation in prevalence and that the level of prevalence that maximizes kappa depends on the ratio between sensitivity (the proportion of correctly predicted presences) and specificity (the proportion of correctly predicted absences). In contrast, TSS is independent of prevalence.
4When the two measures of accuracy were compared using empirical data, kappa showed a unimodal response to prevalence, in agreement with the theoretical analysis. TSS showed a decreasing linear response to prevalence, a result we interpret as reflecting true ecological phenomena rather than a statistical artefact. This interpretation is supported by the fact that a similar pattern was found for the area under the ROC curve, a measure known to be independent of prevalence.
5Synthesis and applications. Our results provide theoretical and empirical evidence that kappa, one of the most widely used measures of model performance in ecology, has serious limitations that make it unsuitable for such applications. The alternative we suggest, TSS, compensates for the shortcomings of kappa while keeping all of its advantages. We therefore recommend the TSS as a simple and intuitive measure for the performance of species distribution models when predictions are expressed as presence–absence maps.
3,518 citations
Cites background from "Niche‐based modelling as a tool for..."
...Distribution models are used to evaluate the spreading potential of invading species (Peterson & Robins 2003; Rouget et al . 2004; Thuiller et al . 2005b ), identify and manage threatened species (Engler, Guisan & Rechsteiner 2004; Norris 2004), prioritize places for biodiversity conservation (Araujo et al . 2004; Ortega-Huerta & Peterson 2004; Sanchez-Cordero et al . 2005) and evaluate the potential impact of climate change on ......
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TL;DR: A novel jackknife validation approach is developed and tested to assess the ability to predict species occurrence when fewer than 25 occurrence records are available and the minimum sample sizes required to yield useful predictions remain difficult to determine.
Abstract: Aim: Techniques that predict species potential distributions by combining observed occurrence records with environmental variables show much potential for application across a range of biogeographical analyses. Some of the most promising applications relate to species for which occurrence records are scarce, due to cryptic habits, locally restricted distributions or low sampling effort. However, the minimum sample sizes required to yield useful predictions remain difficult to determine. Here we developed and tested a novel jackknife validation approach to assess the ability to predict species occurrence when fewer than 25 occurrence records are available. Location: Madagascar. Methods: Models were developed and evaluated for 13 species of secretive leaf-tailed geckos (Uroplatus spp.) that are endemic to Madagascar, for which available sample sizes range from 4 to 23 occurrence localities (at 1 km2 grid resolution). Predictions were based on 20 environmental data layers and were generated using two modelling approaches: a method based on the principle of maximum entropy (Maxent) and a genetic algorithm (GARP). Results: We found high success rates and statistical significance in jackknife tests with sample sizes as low as five when the Maxent model was applied. Results for GARP at very low sample sizes (less than c. 10) were less good. When sample sizes were experimentally reduced for those species with the most records, variability among predictions using different combinations of localities demonstrated that models were greatly influenced by exactly which observations were included. Main conclusions: We emphasize that models developed using this approach with small sample sizes should be interpreted as identifying regions that have similar environmental conditions to where the species is known to occur, and not as predicting actual limits to the range of a species. The jackknife validation approach proposed here enables assessment of the predictive ability of models built using very small sample sizes, although use of this test with larger sample sizes may lead to overoptimistic estimates of predictive power. Our analyses demonstrate that geographical predictions developed from small numbers of occurrence records may be of great value, for example in targeting field surveys to accelerate the discovery of unknown populations and species. © 2007 The Authors.
2,647 citations
Cites background from "Niche‐based modelling as a tool for..."
...…(Raxworthy et al., 2003; Bourg et al., 2005), projecting potential impacts of climate change (e.g. Iverson & Prasad, 1998; Thomas et al., 2004; Thuiller et al., 2005a), testing evolutionary hypotheses (e.g. Peterson et al., 1999; Graham et al., 2004b), predicting species invasions (e.g.…...
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...…Thomas et al., 2004; Thuiller et al., 2005a), testing evolutionary hypotheses (e.g. Peterson et al., 1999; Graham et al., 2004b), predicting species invasions (e.g. Peterson, 2003; Thuiller et al., 2005b) and supporting conservation planning (e.g. Araújo & Williams, 2000; Ferrier et al., 2002)....
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TL;DR: It is argued that increased awareness of the implications of spatial bias in surveys, and possible modeling remedies, will substantially improve predictions of species distributions and as large an effect on predictive performance as the choice of modeling method.
Abstract: Most methods for modeling species distributions from occurrence records require additional data representing the range of environmental conditions in the modeled region. These data, called background or pseudo-absence data, are usually drawn at random from the entire region, whereas occurrence collection is often spatially biased toward easily accessed areas. Since the spatial bias generally results in environmental bias, the difference between occurrence collection and background sampling may lead to inaccurate models. To correct the estimation, we propose choosing background data with the same bias as occurrence data. We investigate theoretical and practical implications of this approach. Accurate information about spatial bias is usually lacking, so explicit biased sampling of background sites may not be possible. However, it is likely that an entire target group of species observed by similar methods will share similar bias. We therefore explore the use of all occurrences within a target group as biased background data. We compare model performance using target-group background and randomly sampled background on a comprehensive collection of data for 226 species from diverse regions of the world. We find that target-group background improves average performance for all the modeling methods we consider, with the choice of background data having as large an effect on predictive performance as the choice of modeling method. The performance improvement due to target-group background is greatest when there is strong bias in the target-group presence records. Our approach applies to regression-based modeling methods that have been adapted for use with occurrence data, such as generalized linear or additive models and boosted regression trees, and to Maxent, a probability density estimation method. We argue that increased awareness of the implications of spatial bias in surveys, and possible modeling remedies, will substantially improve predictions of species distributions.
2,307 citations
Cites background from "Niche‐based modelling as a tool for..."
...Examples of such extrapolations involve future climate conditions (Thomas et al. 2004) or areas at risk for species invasions (Thuiller et al. 2005)....
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References
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TL;DR: In this article, a new estimate minimum information theoretical criterion estimate (MAICE) is introduced for the purpose of statistical identification, which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure.
Abstract: The history of the development of statistical hypothesis testing in time series analysis is reviewed briefly and it is pointed out that the hypothesis testing procedure is not adequately defined as the procedure for statistical model identification. The classical maximum likelihood estimation procedure is reviewed and a new estimate minimum information theoretical criterion (AIC) estimate (MAICE) which is designed for the purpose of statistical identification is introduced. When there are several competing models the MAICE is defined by the model and the maximum likelihood estimates of the parameters which give the minimum of AIC defined by AIC = (-2)log-(maximum likelihood) + 2(number of independently adjusted parameters within the model). MAICE provides a versatile procedure for statistical model identification which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure. The practical utility of MAICE in time series analysis is demonstrated with some numerical examples.
47,133 citations
"Niche‐based modelling as a tool for..." refers methods in this paper
...Generalized additive models (GAM, Hastie & Tibshirani, 1990) incorporated into the Splus-based BIOMOD application (Thuiller, 2003), relating the biome distributions to the four bioclimatic variables, were calibrated using a random sample of the data (70%) and a stepwise selection methodology, with the most parsimonious model being selected using the Akaike information criterion (AIC) (Akaike, 1974)....
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...%) and a stepwise selection methodology, with the most parsimonious model being selected using the Akaike information criterion (AIC) (Akaike, 1974)....
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Book•
01 Jan 1998
TL;DR: In this paper, an updated procedure for calculating reference and crop evapotranspiration from meteorological data and crop coefficients is presented, based on the FAO Penman-Monteith method.
Abstract: (First edition: 1998, this reprint: 2004). This publication presents an updated procedure for calculating reference and crop evapotranspiration from meteorological data and crop coefficients. The procedure, first presented in FAO Irrigation and Drainage Paper No. 24, Crop water requirements, in 1977, allows estimation of the amount of water used by a crop, taking into account the effect of the climate and the crop characteristics. The publication incorporates advances in research and more accurate procedures for determining crop water use as recommended by a panel of high-level experts organised by FAO in May 1990. The first part of the guidelines includes procedures for determining reference crop evapotranspiration according to the FAO Penman-Monteith method. These are followed by updated procedures for estimating the evapotranspiration of different crops for different growth stages and ecological conditions.
21,958 citations
"Niche‐based modelling as a tool for..." refers methods in this paper
...Potential evapotranspiration estimates were calculated using the FAO 56 Penman Monteith combination equation (Allen et al., 1998), while actual evapotranspiration estimates were derived using the LPJ dynamic global vegetation model (Hickler et al., 2004)....
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...Potential evapotranspiration estimates were calculated using the FAO 56 Penman Monteith combination equation (Allen et al., 1998), while actual evapotranspiration estimates were derived using the LPJ dynamic global vegetation model (Hickler et al....
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TL;DR: For diagnostic systems used to distinguish between two classes of events, analysis in terms of the "relative operating characteristic" of signal detection theory provides a precise and valid measure of diagnostic accuracy.
Abstract: Diagnostic systems of several kinds are used to distinguish between two classes of events, essentially "signals" and "noise". For them, analysis in terms of the "relative operating characteristic" of signal detection theory provides a precise and valid measure of diagnostic accuracy. It is the only measure available that is uninfluenced by decision biases and prior probabilities, and it places the performances of diverse systems on a common, easily interpreted scale. Representative values of this measure are reported here for systems in medical imaging, materials testing, weather forecasting, information retrieval, polygraph lie detection, and aptitude testing. Though the measure itself is sound, the values obtained from tests of diagnostic systems often require qualification because the test data on which they are based are of unsure quality. A common set of problems in testing is faced in all fields. How well these problems are handled, or can be handled in a given field, determines the degree of confidence that can be placed in a measured value of accuracy. Some fields fare much better than others.
8,569 citations
"Niche‐based modelling as a tool for..." refers methods in this paper
...To validate our prediction in South Africa, the predictive power of each model was evaluated on the remaining 30% of the data using the values obtained for the area under the curve (AUC) of a receiver–operating characteristic (ROC) plot of sensitivity against (1 sensitivity) (Swets, 1988)....
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University of Buenos Aires1, University of Alaska Fairbanks2, University of Chile3, University of California, Berkeley4, Environmental Defense Fund5, National Autonomous University of Mexico6, Technische Universität München7, New Mexico State University8, Duke University9, Arizona State University10, University of Notre Dame11, Stanford University12, Colorado State University13, Commonwealth Scientific and Industrial Research Organisation14
TL;DR: This study identified a ranking of the importance of drivers of change, aranking of the biomes with respect to expected changes, and the major sources of uncertainties in projections of future biodiversity change.
Abstract: Scenarios of changes in biodiversity for the year 2100 can now be developed based on scenarios of changes in atmospheric carbon dioxide, climate, vegetation, and land use and the known sensitivity of biodiversity to these changes. This study identified a ranking of the importance of drivers of change, a ranking of the biomes with respect to expected changes, and the major sources of uncertainties. For terrestrial ecosystems, land-use change probably will have the largest effect, followed by climate change, nitrogen deposition, biotic exchange, and elevated carbon dioxide concentration. For freshwater ecosystems, biotic exchange is much more important. Mediterranean climate and grassland ecosystems likely will experience the greatest proportional change in biodiversity because of the substantial influence of all drivers of biodiversity change. Northern temperate ecosystems are estimated to experience the least biodiversity change because major land-use change has already occurred. Plausible changes in biodiversity in other biomes depend on interactions among the causes of biodiversity change. These interactions represent one of the largest uncertainties in projections of future biodiversity change.
8,401 citations
"Niche‐based modelling as a tool for..." refers background in this paper
...Because biological invasions are part of global change and as changes in species’ distributions alter global biodiversity (Vitousek et al., 1997; Chapin et al., 2000; Sala et al., 2000), procedures for identifying potential new areas for invaders must be incorporated into integrated strategies for reducing invasions....
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...…invasions are part of global change and as changes in species’ distributions alter global biodiversity (Vitousek et al., 1997; Chapin et al., 2000; Sala et al., 2000), procedures for identifying potential new areas for invaders must be incorporated into integrated strategies for reducing…...
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