A new method for broad-scale modeling and projection of plant assemblages under climatic,biotic, and environmental cofiltering

There is increasing interestin broad-scale analysis, modeling, and prediction of the distribution and composition of plant species assemblages under climatic, environmental, and biotic change, particularly for conservation purposes. We devised a method to reliably predict the impact of climate change on large assemblages of plant communities, while also considering competing biotic and environmental factors. To this purpose, we first used multilabel algorithms in order to convert the task of explaining a large assemblage of plant communities into a classification framework able to capture with high cross-validated accuracy the pattern of species distributions under a composite set of biotic and abiotic factors. We applied our model to a large set of plant communities in the Swiss Alps. Our model explained presences and absences of 175 plant species in 608 plots with >87% cross-validated accuracy, predicted decreases in α, β, and γ diversity by 2040 under both moderate and extreme climate scenarios, and identified likely advantaged and disadvantaged plant species under climate change. Multilabel variable selection revealed the overriding importance of topography, soils, and temperature extremes (rather than averages) in determining the distribution of plant species in the study area and their response to climate change. Our method addressed a number of challenging research problems, such as scaling to large numbers of species, considering species relationships and rarity, and addressing an overwhelming proportion of absences in presence–absence matrices. By handling hundreds to thousands of plants and plots simultaneously over large areas, our method can inform broad-scale conservation of plant species under climate change because it allows species that require urgent conservation action (assisted migration, seed conservation, and ex situ conservation) to be detected and prioritized. Our method also increases the practicality of assisted colonization of plant species by helping to prevent ill-advised introduction of plant species with limited future survival probability.     

Assessing the effects of pseudo-absences on predictive distribution model performance

Modelling species distributions with presence data from atlases, museum collections and databases is challenging. In this paper, we compare seven procedures to generate pseudo-absence data, which in turn are used to generate GLM-logistic regressed models when reliable absence data are not available. We use pseudo-absences selected randomly or by means of presence-only methods (ENFA and MDE) to model the distribution of a threatened endemic Iberian moth species (Graellsia isabelae). The results show that the pseudo-absence selection method greatly influences the percentage of explained variability, the scores of the accuracy measures and, most importantly, the degree of constraint in the distribution estimated. As we extract pseudo-absences from environmental regions further from the optimum established by presence data, the models generated obtain better accuracy scores, and over-prediction increases. When variables other than environmental ones influence the distribution of the species (i.e., non-equilibrium state) and precise information on absences is non-existent, the random selection of pseudo-absences or their selection from environmental localities similar to those of species presence data generates the most constrained predictive distribution maps, because pseudo-absences can be located within environmentally suitable areas. This study shows that if we do not have reliable absence data, the method of pseudo-absence selection strongly conditions the obtained model, generating different model predictions in the gradient between potential and realized distributions.     

Using habitat suitability index and particle dispersion models for early detection of marine invaders.

Eradication and control of invasive species are often possible only if populations are detected when they are small and localized. To be efficient, detection surveys should be targeted at locations where there is the greatest risk of incursions. We examine the utility of habitat suitability index (HSI) and particle dispersion models for targeting sampling for marine pests. Habitat suitability index models are a simple way to identify suitable habitat when species distribution data are lacking. We compared the performance of HSI models with statistical models derived from independent data from New Zealand on the distribution of two nonindigenous bivalves: Theora lubrica and Musculista senhousia. Logistic regression models developed using the HSI scores as predictors of the presence/absence of Theora and Musculista explained 26.7% and 6.2% of the deviance in the data, respectively. Odds ratios for the HSI scores were greater than unity, indicating that they were genuine predictors of the presence/ absence of each species. The fit and predictive accuracy of each logistic model were improved when simulated patterns of dispersion from the nearest port were added as a predictor variable. Nevertheless, the combined model explained, at best, 46.5% of the deviance in the distribution of Theora and correctly predicted 56% of true presences and 50% of all cases. Omission errors were between 6% and 16%. Although statistical distribution models built directly from environmental predictors always outperformed the equivalent HSI models, the gain in model fit and accuracy was modest. High residual deviance in both types of model suggests that the distributions realized by Theora and Musculista in the field data were influenced by factors not explicitly modeled as explanatory variables and by error in the environmental data used to project suitable habitat for the species. Our results highlight the difficulty of accurately predicting the distribution of invasive marine species that exhibit low habitat occupancy and patchy distributions in time and space. Although the HSI and statistical models had utility as predictors of the likely distribution of nonindigenous marine species, the level of spatial accuracy achieved with them may be well below expectations for sensitive surveillance programs.     

Landscape-level impact of tropical forest loss and fragmentation on bird occurrence in eastern Guatemala

Tropical forest destruction and fragmentation of habitat patches may reduce population persistence at the landscape level. Given the complex nature of simultaneously evaluating the effects of these factors on biotic populations, statistical presence/absence modelling has become an important tool in conservation biology. This study uses logistic regression to evaluate the independent effects of tropical forest cover and fragmentation on bird occurrence in eastern Guatemala. Logistic regression models were constructed for 10 species with varying response to habitat alteration. Predictive variables quantified forest cover, fragmentation and their interaction at three different radii (200, 500 and 1000 m scales) of 112 points where presence of target species was determined. Most species elicited a response to the 1000 m scale, which was greater than most species’ reported territory size. Thus, their presence at the landscape scale is probably regulated by extra-territorial phenomena, such as dispersal. Although proportion of forest cover was the most important predictor of species’ presence, there was strong evidence of area-independent and -dependent fragmentation effects on species presence, results that contrast with other studies from northernmost latitudes. Species’ habitat breadth was positively correlated with AIC model values, indicating a better fit for species more restricted to tropical forest. Species with a narrower habitat breadth also elicited stronger negative responses to forest loss. Habitat breadth is thus a simple measure that can be directly related to species’ vulnerability to landscape modification. Model predictive accuracy was acceptable for 4 of 10 species, which were in turn those with narrower habitat breadths.     

Modelling species distributions with penalised logistic regressions: A comparison with maximum entropy models

An important aspect of species distribution modelling is the choice of the modelling method because a suboptimal method may have poor predictive performance. Previous comparisons have found that novel methods, such as Maxent models, outperform well-established modelling methods, such as the standard logistic regression. These comparisons used training samples with small numbers of occurrences per estimated model parameter, and this limited sample size may have caused poorer predictive performance due to overfitting. Our hypothesis is that Maxent models would outperform a standard logistic regression because Maxent models avoid overfitting by using regularisation techniques and a standard logistic regression does not. Regularisation can be applied to logistic regression models using penalised maximum likelihood estimation. This estimation procedure shrinks the regression coefficients towards zero, causing biased predictions if applied to the training sample but improving the accuracy of new predictions. We used Maxent and logistic regression (standard and penalised) to analyse presence/pseudo-absence data for 13 tree species and evaluated the predictive performance (discrimination) using presence-absence data. The penalised logistic regression outperformed standard logistic regression and equalled the performance of Maxent. The penalised logistic regression may be considered one of the best methods to develop species distribution models trained with presence/pseudo-absence data, as it is comparable to Maxent. Our results encourage further use of the penalised logistic regression for species distribution modelling, especially in those cases in which a complex model must be fitted to a sample with a limited size.     

Modelling skewed data with many zeros: A simple approach combining ordinary and logistic regression

We discuss a method for analyzing data that are positively skewed and contain a substantial proportion of zeros. Such data commonly arise in ecological applications, when the focus is on the abundance of a species. The form of the distribution is then due to the patchy nature of the environment and/or the inherent heterogeneity of the species. The method can be used whenever we wish to model the data as a response variable in terms of one or more explanatory variables. The analysis consists of three stages. The first involves creating two sets of data from the original: one shows whether or not the species is present; the other indicates the logarithm of the abundance when it is present. These are referred to as the presence data and the log-abundance data, respectively. The second stage involves modelling the presence data using logistic regression, and separately modelling the log-abundance data using ordinary regression. Finally, the third stage involves combining the two models in order to estimate the expected abundance for a specific set of values of the explanatory variables. A common approach to analyzing this sort of data is to use a ln (y+c) transformation, where c is some constant (usually one). The method we use here avoids the need for an arbitrary choice of the value of c, and allows the modelling to be carried out in a natural and straightforward manner, using well-known regression techniques. The approach we put forward is not original, having been used in both conservation biology and fisheries. Our objectives in this paper are to (a) promote the application of this approach in a wide range of settings and (b) suggest that parametric bootstrapping be used to provide confidence limits for the estimate of expected abundance.     

Evaluating the ability of habitat suitability models to predict species presences

Models predicting species spatial distribution are increasingly applied to wildlife management issues, emphasising the need for reliable methods to evaluate the accuracy of their predictions. As many available datasets (e.g. museums, herbariums, atlas) do not provide reliable information about species absences, several presence-only based analyses have been developed. However, methods to evaluate the accuracy of their predictions are few and have never been validated. The aim of this paper is to compare existing and new presence-only evaluators to usual presence/absence measures.     

The derivation of species response curves with Gaussian logistic regression is sensitive to sampling intensity and curve characteristics

We investigated quantitatively the sensitivity of plant species response curves to sampling characteristics (number of plots, occurrence and frequency of species), along a simulated pH gradient. We defined 54 theoretical unimodal response curves, issued from combinations of six values for optimum (opt = 3, 4, …, 8), three values for tolerance (tol = 0.5, 1.0, and 1.5, sensu ter Braak and Looman [ter Braak, C.J.F., Looman, C.W.N., 1986. Weighted averaging, logistic regression and the Gaussian response model. Vegetatio 65, 3–11]), and three values for maximum probability of presence (p_max = 0.05, 0.20, and 0.50). For each of these 54 theoretical response curves, we built artificial binary data sets (presence/absence) to test the influence of species occurrence, frequency, or number of available plots. With real data extracted from EcoPlant, a phytoecological database for French forests [Gégout, J.-C., Coudun, Ch., Bailly, G., Jabiol, B., 2005. EcoPlant: a forest sites database linking floristic data with soil characteristics and climatic conditions. J. Veg. Sci. 16, 257–260], we compared the ecological response of 50 plant species to soil pH, based first on a small data set (100 randomly sampled plots), and then based on the whole data set available (3810 plots).     

Modeling and Predicting Species Occurrence Using Broad-Scale Environmental Variables: an Example with Butterflies of the Great Basin

Abstract: If occurrence of individual species can be modeled as a function of easily quantified environmental variables (e.g., derived from a geographic information system [GIS]) and the predictions of these models are demonstrably successful, then the scientific foundation for management planning will be strengthened. We used Bayesian logistic regression to develop predictive models for resident butterflies in the central Great Basin of western North America. Species inventory data and values for 14 environmental variables from 49 locations (segments of canyons) in the Toquima Range ( Nevada, U.S.A.) were used to build the models. Squares of the environmental variables were also used to accommodate possibly nonmonotonic responses. We obtained statistically significant models for 36 of 56 (64%) resident species of butterflies. The models explained 8–72% of the deviance in occurrence of those species. Each of the independent variables was significant in at least one model, and squared versions of five variables contributed to models. Elevation was included in more than half of the models. Models included one to four variables; only one variable was significant in about half the models. We conducted preliminary tests of two of our models by using an existing set of data on the occurrence of butterflies in the neighboring Toiyabe Range. We compared conventional logistic classification with posterior probability distributions derived from Bayesian modeling. For the latter, we restricted our predictions to locations with a high ( 70%) probability of predicted presence or absence. We will perform further tests after conducting inventories at new locations in the Toquima Range and nearby Shoshone Mountains, for which we have computed environmental variables by using remotely acquired topographic data, digital-terrain and microclimatic models, and GIS computation.     

Predicting tree distributions in an East African biodiversity hotspot: model selection, data bias and envelope uncertainty

The Eastern Arc Mountains (EAMs) of Tanzania and Kenya support some of the most ancient tropical rainforest on Earth. The forests are a global priority for biodiversity conservation and provide vital resources to the Tanzanian population. Here, we make a first attempt to predict the spatial distribution of 40 EAM tree species, using generalised additive models, plot data and environmental predictor maps at sub 1 km resolution. The results of three modelling experiments are presented, investigating predictions obtained by (1) two different procedures for the stepwise selection of predictors, (2) down-weighting absence data, and (3) incorporating an autocovariate term to describe fine-scale spatial aggregation. In response to recent concerns regarding the extrapolation of model predictions beyond the restricted environmental range of training data, we also demonstrate a novel graphical tool for quantifying envelope uncertainty in restricted range niche-based models (envelope uncertainty maps). We find that even for species with very few documented occurrences useful estimates of distribution can be achieved. Initiating selection with a null model is found to be useful for explanatory purposes, while beginning with a full predictor set can over-fit the data. We show that a simple multimodel average of these two best-model predictions yields a superior compromise between generality and precision (parsimony). Down-weighting absences shifts the balance of errors in favour of higher sensitivity, reducing the number of serious mistakes (i.e., falsely predicted absences); however, response functions are more complex, exacerbating uncertainty in larger models. Spatial autocovariates help describe fine-scale patterns of occurrence and significantly improve explained deviance, though if important environmental constraints are omitted then model stability and explanatory power can be compromised. We conclude that the best modelling practice is contingent both on the intentions of the analyst (explanation or prediction) and on the quality of distribution data; generalised additive models have potential to provide valuable information for conservation in the EAMs, but methods must be carefully considered, particularly if occurrence data are scarce. Full results and details of all species models are supplied in an online Appendix.     

Building phenological models from presence/absence data for a butterfly fauna.

Species phenology is increasingly being used to explore the effects of climate change and other environmental stressors. Long-term monitoring data sets are essential for understanding both patterns manifest by individual species and more complex patterns evident at the community level. This study used records of 78 butterfly species observed on 626 days across 27 years at a site in northern California, USA, to build quadratic logistic regression models of the observation probability of each species for each day of the year. Daily species probabilities were summed to develop a potential aggregate species richness (PASR) model, indicating expected daily species richness. Daily positive and negative contributions to PASR were calculated, which can be used to target optimum sampling time frames. Residuals to PASR indicate a rate of decline of 0.12 species per year over the course of the study. When PASR was calculated for wet and dry years, wet years were found to delay group phenology by up to 17 days and reduce the maximum annual expected species from 32.36 to 30. Three tests to determine how well the PASR model reflected the butterfly fauna dynamics were all positive: We correlated probabilities developed with species presence/absence data to observed abundance by species, tested species' predicted phenological patterns against known biological characteristics, and compared the PASR curve to a spline-fitted curve calculated from the original species richness observations. Modeling individual species' flight windows was possible from presence/absence data, an approach that could be used on other similar records for butterfly communities with seasonal phenologies, and for common species with far fewer dates than used here. It also provided a method to assess sample frequency guidelines for other butterfly monitoring programs.     

An improved approach for identifying suitable habitat of Sambar Deer (Cervus unicolor Kerr) using ecological niche analysis and environmental categorization: Case study at Phu-Khieo Wildlife Sanctuary,Thailand

To assess habitat suitability (HS) has become an increasingly important component of species/ecosystem management. HS assessment is usually based on presence/absence data related to environmental variables. An exception is Ecological Niche Factor Analysis (ENFA), which uses only presence data and which does not require absence data. Most HS modelling is based on input of all environmental parameters (EnvPs) without environmental categorization, and does not take into account species interaction and human intervention for an assessment of HS. In this study, the EnvPs are arranged into four features: geographical features, consumable features, human-factor features, and species–human interaction features. These features affect species with respect to movement, behavior and activity. The research presented here has used an already existing dataset of wildlife species and human activities/visitations, which was compiled during 2004–2006 in Phu-Khieo Wildlife Sanctuary (PKWS). Data from 2004 to 2005 were used to produce HS maps, while the data of 2006 were used for evaluating these maps. Sambar Deer (SD) was chosen to predict its own HS. Six HS maps of SD were analyzed using ENFA in the following manner: (1) inputting all EnvPs together, (2) inputting each feature, separately and (3) integrating the four resulting HS maps by model averaging. It was found that model averaging was capable of predicting the HS of SD more reliably than the model with all EnvPs put in together. Multiple linear regressions were computed between the HS map with all EnvPs and the HS maps with each feature. The results show that the HS map with only geographical features has the highest coefficient value (0.516) while the coefficient values of other HS maps with the above features are 0.296, 0.53 and −0.006, respectively. This indicates that the geographical features have an influence on the other features and that the predicting power is lower when all EnvPs are computed in the ENFA model. Therefore, in order to generate HS, each feature should at first be put into the model separately. Following that, the average of all features will be combined.     

Self-organized digging activity in ant colonies

Many ant species adjust the volume of their underground nest to the colony size. We studied whether the regulation of the volume of excavated sand could result from an interplay between recruitment processes and ant density. Experiments were performed with different group sizes of workers in the ant Messor sancta. When presented with a thin homogeneous sand disk, these groups excavated networks of galleries in less than 3 days. The excavation dynamics were logistic shaped, which suggests the existence of a double feedback system: a positive one resulting in an initial exponential growth phase, and a negative one leading the dynamics to a saturation phase. The total volume of excavated sand was almost proportional to the number of workers. We then developed a model in which we incorporated the quantitative behavioral rules of the workers digging activity. A positive feedback was introduced in the form of a recruitment process mediated by pheromones. The model predicts that the excavation dynamics should be logistic shaped and the excavation should almost stop despite the absence of any explicit negative feedback. Moreover, the model was able to reproduce the positive linear relationship between nest volume and colony size.Communicated by K. Ross     

Modeling and spatial prediction of pre-settlement patterns of forest distribution using witness tree data

At the time of European settlement, land surveys were conducted progressively westward throughout the United States. Outside of the original 13 colonies, surveys generally followed the Public Land Survey system in which trees, called witness trees, were regularly recorded at 1 mi by 1 mi grid intersections. This unintentional sampling provides insight into the composition and structure of pre-European settlement forests, which is used as baseline data to assess forest change following settlement. In this paper, a model for the Public Land Surveys of east central Alabama is developed. Assuming that the locations of trees of each species are realized from independent Poisson processes whose respective log intensities are linear functions of environmental covariates (i.e., elevation, landform, and physiographic province), the species observed at the survey grid intersections are independently sampled from a generalized logistic regression model. If all 68 species found in the survey were included, the model would be highly over-parameterized, so only the distribution of the most common taxon, pines, will be considered at this time. To assess the impact of environmental factors not included in the model, a hidden Gaussian random field shall be added as a random effect. A Markov Chain Monte Carlo algorithm is developed for Bayesian inference on model parameters, and for Bayes posterior prediction of the spatial distribution of pines in east central Alabama. Received: June 2004 / Revised: November 2004     

Modelling Ecological Presence–absence Data along an Environmental Gradient: Threshold Levels of the Environment

A methodology for estimating environmental thresholds of binary presence–absence data is presented where the level of the threshold is parameterised. Presence–absence data is fitted to three complementary different models: an independent null-model, a monotonically increasing or decreasing model, and an optimum model. The range of the three models is strictly between zero and one and the models are therefore well suited for modelling presence probabilities. The results of the three models may be combined by using Bayesian model selection methodologies. The proposed methodology is exemplified on observed binary presence–absence data of Bauera rubioides along an elevation gradient. Received: May 2005 / Revised: July 2005 An erratum to this article is available at.     

Efficient species-level monitoring at the landscape scale

Monitoring the population trends of multiple animal species at a landscape scale is prohibitively expensive. However, advances in survey design, statistical methods, and the ability to estimate species presence on the basis of detection-nondetection data have greatly increased the feasibility of species-level monitoring. For example, recent advances in monitoring make use of detection-nondetection data that are relatively inexpensive to acquire, historical survey data, and new techniques in genetic evaluation. The ability to use indirect measures of presence for some species greatly increases monitoring efficiency and reduces survey costs. After adjusting for false absences, the proportion of sample units in a landscape where a species is detected (occupancy) is a logical state variable to monitor. Occupancy monitoring can be based on real-time observation of a species at a survey site or on evidence that the species was at the survey location sometime in the recent past. Temporal and spatial patterns in occupancy data are related to changes in animal abundance and provide insights into the probability of a species' persistence. However, even with the efficiencies gained when occupancy is the monitored state variable, the task of species-level monitoring remains daunting due to the large number of species. We propose that a small number of species be monitored on the basis of specific management objectives, their functional role in an ecosystem, their sensitivity to environmental changes likely to occur in the area, or their conservation importance.     

The pattern of species turnover resulting from stochastic population dynamics: The model and field data

The model of random population dynamics in a sampling site returns geometric distribution of longevities of continuous presence (=persistence) and Poisson distribution of the presence–absence transitions. This discrete-time stochastic process describes the presence–absence pattern observed in the beetles surveyed 6 years on Mount Carmel, Israel. Homogeneous pools of species mostly on the Families rank, exhibit the predicted by the model patterns. Conformity to an ergodic hypothesis is the criterion of ecological homogeneity. This criterion assumes the equivalence of short-term behavior of entire pool and long-term behavior of any species from this pool. The pool of all 801 species of Order Coleoptera does not match the model. Thus a taxon of an arbitrary rank may not be considered a priory as a unit of ecological study. Determined from field data parameters of the model are biased and magnitude of the bias depends on longevity of the survey. Parameter of distribution depends also on species tolerance, which is the level adaptation of given species to given environment in given time interval. Random process of species turnover may be considered as a game of species to gain their presence against deteriorative fluctuations of environmental conditions.