Species distributional or trait data based on range map (extent-of-occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species' distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing
BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships. BIOMOD includes the ability to model species distributions with several techniques, test models with a wide range of approaches, project species distributions into different environmental conditions (e.g. climate or land use change scenarios) and dispersal functions. It allows assessing species temporal turnover, plot species response curves, and test the strength of species interactions with predictor variables. BIOMOD is implemented in R and is a freeware, open source, package.Species distribution models (SDM, Guisan and Thuiller 2005) are being used in nearly all branches of life and environmental sciences. A quick search in ISI Web of Science (18/02/08) using ''species distribution models'' OR ''niche models'' OR ''habitat models'' OR ''bioclimatic models'' highlights 21 973 papers, 74% of which published in the past 10 yr, in fields as varied as environmental sciences (53% of the records), zoology (15%), marine and freshwater biology (15%), life sciences and biomedicine (9%), biodiversity and conservation (8%), evolutionary biology (8%), fisheries (6%), forestry (6%), oceanography (5%), genetics and heredity (5%), amongst others. Advancement of knowledge in these fields is now intertwined with technical innovation in species distribution modelling and dependent on the existence of suitable software for fitting models and examining results. One difficulty with the use of species distribution models is that the number of techniques available is large and is increasing steadily, making it difficult for ''non-aficionados'' to select the most appropriate methodology for their needs (Elith et al. 2006, Heikkinen et al. 2006. Recent analyses have also demonstrated that discrepancies between different techniques can be very large, making the choice of the appropriate model even more difficult. This is particularly true when models are used to project distributions of species into independent situations, which is the example of projections of species distributions under future climate change scenarios (Thuiller 2004, Pearson et al. 2006. A possible solution to account for this inter-model variability is to fit ensembles of forecasts by simulating across more than one set of initial conditions, model classes, model parameters, and boundary conditions (for a review see Araújo and New 2007) and analyse the resulting range of uncertainties with bounding box, consensus and probabilistic methodologies rather than lining up with a single modelling outcome New 2007, Thuiller 2007). BIOMOD offers such a platform for ensemble forecasting (Fig. 1) using freeware and open-source R software (R Development Core Team 2008). It overcomes some of the limitations of existing software (e.g. being able to fit and compare different models) and incorporates several features for testing models (e.g. k-fold cross validation) ...
Climate change has already triggered species distribution shifts in many parts of the world. Increasing impacts are expected for the future, yet few studies have aimed for a general understanding of the regional basis for species vulnerability. We projected late 21st century distributions for 1,350 European plants species under seven climate change scenarios. Application of the International Union for Conservation of Nature and Natural Resources Red List criteria to our projections shows that many European plant species could become severely threatened. More than half of the species we studied could be vulnerable or threatened by 2080. Expected species loss and turnover per pixel proved to be highly variable across scenarios (27-42% and 45-63% respectively, averaged over Europe) and across regions (2.5-86% and 17-86%, averaged over scenarios). Modeled species loss and turnover were found to depend strongly on the degree of change in just two climate variables describing temperature and moisture conditions. Despite the coarse scale of the analysis, species from mountains could be seen to be disproportionably sensitive to climate change (Ϸ60% species loss). The boreal region was projected to lose few species, although gaining many others from immigration. The greatest changes are expected in the transition between the Mediterranean and Euro-Siberian regions. We found that risks of extinction for European plants may be large, even in moderate scenarios of climate change and despite inter-model variability.Intergovernmental Panel on Climate Change storylines ͉ species extinction ͉ species turnover ͉ niche-based model
Distributions of Earth's species are changing at accelerating rates, increasingly driven by human-mediated climate change. Such changes are already altering the composition of ecological communities, but beyond conservation of natural systems, how and why does this matter? We review evidence that climate-driven species redistribution at regional to global scales affects ecosystem functioning, human well-being, and the dynamics of climate change itself. Production of natural resources required for food security, patterns of disease transmission, and processes of carbon sequestration are all altered by changes in species distribution. Consideration of these effects of biodiversity redistribution is critical yet lacking in most mitigation and adaptation strategies, including the United Nation's Sustainable Development Goals.
This chapter considers a concept of niche that emphasizes multidimensional spaces of scenopoetic variables and provides a natural connection to the study of geographic distributions of species. It first explains the relations between environmental and geographic spaces before discussing the use of equations to link spatially explicit population growth patterns to variation in the ecological characteristics of species. It then describes the BAM diagram, a Venn diagram that displays the joint fulfillment in geographic space of three sets of conditions that together determine species distribution: biotic conditions, abiotic conditions, and movement of the species. The chapter also explores the spatial resolution of scenopoetic variables, estimation of the fundamental and existing fundamental niches, the biotically reduced niche, and caveats about reducing Grinnellian niches and the Eltonian Noise Hypothesis. Finally, it shows how distributional areas and ecological niches can be estimated.
Species distribution modelling is central to both fundamental and applied research in biogeography. Despite widespread use of models, there are still important conceptual ambiguities as well as biotic and algorithmic uncertainties that need to be investigated in order to increase confidence in model results. We identify and discuss five areas of enquiry that are of high importance for species distribution modelling: (1) clarification of the niche concept; (2) improved designs for sampling data for building models; (3) improved parameterization; (4) improved model selection and predictor contribution; and (5) improved model evaluation. The challenges discussed in this essay do not preclude the need for developments of other areas of research in this field. However, they are critical for allowing the science of species distribution modelling to move forward.
Increasing concern over the implications of climate change for biodiversity has led to the use of species-climate envelope models to project species extinction risk under climatechange scenarios. However, recent studies have demonstrated significant variability in model predictions and there remains a pressing need to validate models and to reduce uncertainties. Model validation is problematic as predictions are made for events that have not yet occurred. Resubstituition and data partitioning of present-day data sets are, therefore, commonly used to test the predictive performance of models. However, these approaches suffer from the problems of spatial and temporal autocorrelation in the calibration and validation sets. Using observed distribution shifts among 116 British breeding-bird species over the past $ 20 years, we are able to provide a first independent validation of four envelope modelling techniques under climate change. Results showed good to fair predictive performance on independent validation, although rules used to assess model performance are difficult to interpret in a decision-planning context. We also showed that measures of performance on nonindependent data provided optimistic estimates of models' predictive ability on independent data. Artificial neural networks and generalized additive models provided generally more accurate predictions of species range shifts than generalized linear models or classification tree analysis. Data for independent model validation and replication of this study are rare and we argue that perfect validation may not in fact be conceptually possible. We also note that usefulness of models is contingent on both the questions being asked and the techniques used. Implementations of species-climate envelope models for testing hypotheses and predicting future events may prove wrong, while being potentially useful if put into appropriate context.
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