Incorporating low-resolution historic species location data decreases performance of distribution models

Developing robust species distribution models is important as model outputs are increasingly being incorporated into conservation policy and management decisions. A largely overlooked component of model assessment and refinement is whether to include historic species occurrence data in distribution models to increase the data sample size. Data of different temporal provenance often differ in spatial accuracy and precision. We test the effect of inclusion of historic coarse-resolution occurrence data on distribution model outputs for 187 species of birds in Australian tropical savannas. Models using only recent (after 1990), fine-resolution data had significantly higher model performance scores measured with area under the receiver operating characteristic curve (AUC) than models incorporating both fine- and coarse-resolution data. The drop in AUC score is positively correlated with the total area predicted to be suitable for the species (R² = 0.163-0.187, depending on the environmental predictors in the model), as coarser data generally leads to greater predicted areas. The remaining unexplained variation is likely to be due to the covariate errors resulting from resolution mismatch between species records and environmental predictors. We conclude that decisions regarding data use in species distribution models must be conscious of the variation in predictions that mixed-scale datasets might cause.     

Species distribution modelling: Does one size fit all? A phytogeographic analysis of Salix in Ontario

Empirical models for predicting the distribution of organisms from environmental data have often focused on principles of ecological niche theory. However, even at large scales, there is little agreement over how to represent the dimensions of a species’ niche. The performance of such models is greatly affected by the nature of species distributional and environmental data. Regional scale distribution models were developed for 30 willow species in Ontario to examine (i) the predictive ability of logistic regression analysis, and (ii) the effects of using different distributional and environmental data sets. Two original measures of model accuracy and over-prediction were employed and evaluated using independent data. Models based on unique combinations of monthly climate data predicted distributions most accurately for all species. Models based on a fixed set of variables, while generating the highest average probabilities of occurrence for certain species with limited ranges, resulted in the greatest under- and over-estimates of willow distributions. Comparisons of models demonstrated climatic patterns among willows of differing habit and habitat. The distribution of dwarf willow species, present only in the Ontario arctic, followed gradients of summer maximum temperatures. The distribution of the tree species in the southerly portions of the province followed gradients of fall and winter minimum temperatures. Regardless of distributional and environmental data input, no algorithm maximized model performance for all species. Individual species models require individual approaches; i.e., the variable selection technique, the set of environmental factors used as predictors, and the nature of species distributional data must be carefully matched to the intended application. An understanding of evolutionary processes enhances the meaningful interpretation of individual species models. Unless sampling bias and species prevalence can be accounted for, models based on collection point data are best used to guide field surveys. While inferred range data may be better suited to determine potential ecological niches, overestimation of species prevalence and environmental tolerance must be recognized. A combination of available distributional data types is recommended to best determine species niches, an important step in developing conservation strategies.     

Predicting species distributions from samples collected along roadsides

Predictive models of species distributions are typically developed with data collected along roads. Roadside sampling may provide a biased (nonrandom) sample; however, it is currently unknown whether roadside sampling limits the accuracy of predictions generated by species distribution models. We tested whether roadside sampling affects the accuracy of predictions generated by species distribution models by using a prospective sampling strategy designed specifically to address this issue. We built models from roadside data and validated model predictions at paired locations on unpaved roads and 200 m away from roads (off road), spatially and temporally independent from the data used for model building. We predicted species distributions of 15 bird species on the basis of point-count data from a landbird monitoring program in Montana and Idaho (U.S.A.). We used hierarchical occupancy models to account for imperfect detection. We expected predictions of species distributions derived from roadside-sampling data would be less accurate when validated with data from off-road sampling than when it was validated with data from roadside sampling and that model accuracy would be differentially affected by whether species were generalists, associated with edges, or associated with interior forest. Model performance measures (kappa, area under the curve of a receiver operating characteristic plot, and true skill statistic) did not differ between model predictions of roadside and off-road distributions of species. Furthermore, performance measures did not differ among edge, generalist, and interior species, despite a difference in vegetation structure along roadsides and off road and that 2 of the 15 species were more likely to occur along roadsides. If the range of environmental gradients is surveyed in roadside-sampling efforts, our results suggest that surveys along unpaved roads can be a valuable, unbiased source of information for species distribution models.     

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.     

Building statistical models to analyze species distributions.

Models of the geographic distributions of species have wide application in ecology. But the nonspatial, single-level, regression models that ecologists have often employed do not deal with problems of irregular sampling intensity or spatial dependence, and do not adequately quantify uncertainty. We show here how to build statistical models that can handle these features of spatial prediction and provide richer, more powerful inference about species niche relations, distributions, and the effects of human disturbance. We begin with a familiar generalized linear model and build in additional features, including spatial random effects and hierarchical levels. Since these models are fully specified statistical models, we show that it is possible to add complexity without sacrificing interpretability. This step-by-step approach, together with attached code that implements a simple, spatially explicit, regression model, is structured to facilitate self-teaching. All models are developed in a Bayesian framework. We assess the performance of the models by using them to predict the distributions of two plant species (Proteaceae) from South Africa's Cape Floristic Region. We demonstrate that making distribution models spatially explicit can be essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results. Adding hierarchical levels to the models has further advantages in allowing human transformation of the landscape to be taken into account, as well as additional features of the sampling process.     

Use of Community‐Composition Data to Predict the Fecundity and Abundance of Species

Abstract: Species distribution models are critical tools for the prediction of invasive species spread and conservation of biodiversity. The majority of species distribution models have been built with environmental data. Community ecology theory suggests that species co‐occurrence data could also be used to predict current and potential distributions of species. Species assemblages are the products of biotic and environmental constraints on the distribution of individual species and as a result may contain valuable information for niche modeling. We compared the predictive ability of distribution models of annual grassland plants derived from either environmental or community‐composition data. Composition‐based models were built with the presence or absence of species at a site as predictors of site quality, whereas environment‐based models were built with soil chemistry, moisture content, above‐ground biomass, and solar radiation as predictors. The reproductive output of experimentally seeded individuals of 4 species and the abundance of 100 species were used to evaluate the resulting models. Community‐composition data were the best predictors of both the site‐specific reproductive output of sown individuals and the site‐specific abundance of existing populations. Successful community‐based models were robust to omission of data on the occurrence of rare species, which suggests that even very basic survey data on the occurrence of common species may be adequate for generating such models. Our results highlight the need for increased public availability of ecological survey data to facilitate community‐based modeling at scales relevant to conservation.     

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.     

Multi-model analysis of tree competition along environmental gradients in southern New England forests.

Robust predictions of competitive interactions among canopy trees and variation in tree growth along environmental gradients represent key challenges for the management of mixed-species, uneven-aged forests. We analyzed the effects of competition on tree growth along environmental gradients for eight of the most common tree species in southern New England and southeastern New York using forest inventory and analysis (FIA) data, information theoretic decision criteria, and multi-model inference to evaluate models. The suite of models estimated growth of individual trees as a species-specific function of average potential diameter growth, tree diameter at breast height, local environmental conditions, and crowding by neighboring trees. We used ordination based on the relative basal area of species to generate a measure of site conditions in each plot. Two ordination axes were consistent with variation in species abundance along moisture and fertility gradients. Estimated potential growth varied along at least one of these axes for six of the eight species; peak relative abundance of less shade-tolerant species was in all cases displaced away from sites where they showed maximum potential growth. Our crowding functions estimate the strength of competitive effects of neighbors; only one species showed support for the hypothesis that all species of competitors have equivalent effects on growth. The relative weight of evidence (Akaike weights) for the best models varied from a low of 0.207 for Fraxinus americana to 0.747 for Quercus rubra. In such cases, model averaging provides a more robust platform for prediction than that based solely on the best model. We show that predictions based on the selected best models dramatically overestimated differences between species relative to predictions based on the averaged set of models.     

The effect of species response form on species distribution model prediction and inference

Ecological theory and current evidence support the validity of various species response curves according to a variety of environmental gradients. Various methods have been developed for building species distribution models but it is not well known how these methods perform under various assumptions about the form of the underlying species response. It is also not well known how spatial correlation in species occurrence affects model performance. These effects were investigated by applying an environmental envelope method (BIOCLIM) and three regression-based methods: logistic regression (LR), generalized additive modelling (GAM), and classification and regression tree (CART) to simulated species occurrence data. Each simulated species was constructed as a sum of responses with varying weights. Three basic species response curves were assumed: Gaussian (bell-shaped), Beta (skew) and linear. The two non-linear responses conform to standard ecological niche theory. All three responses were applied in turn to three simulated environmental variables, each with varying degrees of spatial autocorrelation. GAM produced the most consistent model performance over all forms of simulated species response. BIOCLIM and CART were inclined to underrate the performance of variables with a linear response. BIOCLIM was less sensitive to data density. LR was susceptible to model misspecification. The use of a linear function in LR underestimated the performance of variables with non-linear species response and contributed to increased spatial autocorrelation in model residuals. Omission of important environmental variables with non-linear species response also contributed to increased spatial autocorrelation in model residuals. Adding a spatial autocovariate term to the LR model (autologistic model) reduced the spatial autocorrelation and improved model performance, but did not correct the misidentification of the dominant environmental determinant. This is to be expected since the autologistic approach was designed primarily for prediction and not for inference. Given that various forms of species response to environmental determinants arise commonly in nature: (1) higher order functions should always be tested when applying LR in modelling species distribution; (2) spatial autocorrelation in species distribution model residuals can indicate that environmental determinants with non-linear response are missing from the model; and (3) deficiencies in LR model performance due to model misspecification can be addressed by adding a spatial autocovariate to the model, but care should be taken when interpreting the coefficients of the model parameters.     

Comparative performance of generalized additive models and multivariate adaptive regression splines for statistical modelling of species distributions

Two statistical modelling techniques, generalized additive models (GAM) and multivariate adaptive regression splines (MARS), were used to analyse relationships between the distributions of 15 freshwater fish species and their environment. GAM and MARS models were fitted individually for each species, and a MARS multiresponse model was fitted in which the distributions of all species were analysed simultaneously. Model performance was evaluated using changes in deviance in the fitted models and the area under the receiver operating characteristic curve (ROC), calculated using a bootstrap assessment procedure that simulates predictive performance for independent data. Results indicate little difference between the performance of GAM and MARS models, even when MARS models included interaction terms between predictor variables. Results from MARS models are much more easily incorporated into other analyses than those from GAM models. The strong performance of a MARS multiresponse model, particularly for species of low prevalence, suggests that it may have distinct advantages for the analysis of large datasets. Its identification of a parsimonious set of environmental correlates of community composition, coupled with its ability to robustly model species distributions in relation to those variables, can be seen as converging strongly with the purposes of traditional ordination techniques.     

Predicting Bird Species Distributions in Reconstructed Landscapes

Abstract:  Landscape optimization for biodiversity requires prediction of species distributions under alternative revegetation scenarios. We used Bayesian model averaging with logistic regression to predict probabilities of occurrence for 61 species of birds within highly fragmented box–ironbark forests of central Victoria, Australia. We used topographic, edaphic, and climatic variables as predictors so that the models could be applied to areas where vegetation has been cleared but may be replanted. Models were evaluated with newly acquired, independent data collected in large blocks of remnant native vegetation. Successful predictions were obtained for 18 of 45 woodland species (40%). Model averaging produced more accurate predictions than "single best" models. Models were most successful for smaller-bodied species that probably depend on particular vegetation types. Predictions for larger, generalist species, and seasonal migrants were less successful, partly because of changes in species distributions between model building (1995–1997) and validation (2004–2005) surveys. We used validated models to project occurrence probabilities for individual species across a 12,000-km² region, assuming native vegetation was present. These predictions are intended to be used as inputs, along with landscape context and temporal dynamics, into optimization algorithms to prioritize revegetation. Longer-term data sets to accommodate temporal dynamics are needed to improve the predictive accuracy of models.     

Appreciating Ecological Complexity: Habitat Contours as a Conceptual Landscape Model

Abstract:  Organisms respond to their surroundings at multiple spatial scales, and different organisms respond differently to the same environment. Existing landscape models, such as the "fragmentation model" (or patch-matrix-corridor model) and the "variegation model," can be limited in their ability to explain complex patterns for different species and across multiple scales. An alternative approach is to conceptualize landscapes as overlaid species-specific habitat contour maps. Key characteristics of this approach are that different species may respond differently to the same environmental conditions and at different spatial scales. Although similar approaches are being used in ecological modeling, there is much room for habitat contours as a useful conceptual tool. By providing an alternative view of landscapes, a contour model may stimulate more field investigations stratified on the basis of ecological variables other than human-defined patches and patch boundaries. A conceptual model of habitat contours may also help to communicate ecological complexity to land managers. Finally, by incorporating additional ecological complexity, a conceptual model based on habitat contours may help to bridge the perceived gap between pattern and process in landscape ecology. Habitat contours do not preclude the use of existing landscape models and should be seen as a complementary approach most suited to heterogeneous human-modified landscapes.     

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.     

Variation partitioning of species data matrices: estimation and comparison of fractions

Establishing relationships between species distributions and environmental characteristics is a major goal in the search for forces driving species distributions. Canonical ordinations such as redundancy analysis and canonical correspondence analysis are invaluable tools for modeling communities through environmental predictors. They provide the means for conducting direct explanatory analysis in which the association among species can be studied according to their common and unique relationships with the environmental variables and other sets of predictors of interest, such as spatial variables. Variation partitioning can then be used to test and determine the likelihood of these sets of predictors in explaining patterns in community structure. Although variation partitioning in canonical analysis is routinely used in ecological analysis, no effort has been reported in the literature to consider appropriate estimators so that comparisons between fractions or, eventually, between different canonical models are meaningful. In this paper, we show that variation partitioning as currently applied in canonical analysis is biased. We present appropriate unbiased estimators. In addition, we outline a statistical test to compare fractions in canonical analysis. The question addressed by the test is whether two fractions of variation are significantly different from each other. Such assessment provides an important step toward attaining an understanding of the factors patterning community structure. The test is shown to have correct Type I. error rates and good power for both redundancy analysis and canonical correspondence analysis.     

Invasion, Disturbance, and Competition: Modeling the Fate of Coastal Plant Populations

Abstract:  Wetland habitats are besieged by biotic and abiotic disturbances such as invasive species, hurricanes, habitat fragmentation, and salinization. Predicting how these factors will alter local population dynamics and community structure is a monumental challenge. By examining ecologically similar congeners, such as Iris hexagona and I. pseudacorus (which reproduce clonally and sexually and tolerate a wide range of environmental conditions), one can identify life-history traits that are most influential to population growth and viability. We combined empirical data and stage-structured matrix models to investigate the demographic responses of native ( I. hexagona ) and invasive ( I. pseudacorus ) plant populations to hurricanes and salinity stress in freshwater and brackish wetlands. In our models I. hexagona and I. pseudacorus responded differently to salinity stress, and species coexistence was rare. In 82% of computer simulations of freshwater marsh, invasive iris populations excluded the native species within 50 years, whereas native populations excluded the invasive species in 99% of the simulations in brackish marsh. The occurrence of hurricanes allowed the species to coexist, and species persistence was determined by the length of time it took the ecosystem to recover. Rapid recovery (2 years) favored the invasive species, whereas gradual recovery (30 years) favored the native species. Little is known about the effects of hurricanes on competitive interactions between native and invasive plant species in marsh ecosystems. Our models contribute new insight into the relationship between environmental disturbance and invasion and demonstrate how influential abiotic factors such as climate change will be in determining interspecific interactions.     

New approaches to modelling fish-habitat relationships

Ecologists often develop models that describe the relationship between faunal communities and their habitat. Coral reef fishes have been the focus of numerous such studies, which have used a wide range of statistical tools to answer an equally wide range of questions. Here, we apply a series of both conventional statistical techniques (linear and generalized additive regression models) and novel machine-learning techniques (the support vector machine and three ensemble techniques used with regression trees) to predict fish species richness, biomass, and diversity from a range of habitat variables. We compare the techniques in terms of their predictive performance, and we compare a subset of the models in terms of the influence each habitat variable has for the predictions. Prediction errors are estimated by cross-validation, and variable importance is assessed using permutations of individual variable values. For predictions of species richness and diversity the tree-based models generally and the random forest model specifically are superior (produce the lowest errors). These model types are all able to model both nonlinear and interaction effects. The linear model, unable to model either effect type, performs the worst (produces the highest errors). For predictions of biomass, the generalized additive model is superior, and the support vector machine performs the worst. Depth range, the difference between maximum and minimum water depth at a given site, is identified as the most important variable in the majority of models predicting the three fish community variables. However, variable importance is highly dependent upon model type, which leads to questions regarding the interpretation of variable importance and its proper use as an indicator of causality. The representation of ecological relationships by tree-based ensemble learners will improve predictive performance, and provide a new avenue for exploring ecological relationships, both statistical and causal.     

Redesigning harvest strategies for sustainable fishery management in the face of extreme environmental variability

Short-lived, fast-growing species that contribute greatly to global capture fisheries are sensitive to fluctuations in the environment. Uncertainties in exact stock–environment relationships have meant that environmental variability and extremes have been difficult to integrate directly into fisheries management. We applied a management strategy evaluation approach for one of Australia's large prawn stocks to test the robustness of harvest control rules to environmental variability. The model ensemble included coupled environmental-population models and an alternative catchability scenario fitted to historical catch per unit effort data. We compared the efficacy of alternative management actions to conserve marine resources under a variable environment while accounting for fisher livelihoods. Model fits to catch per unit effort were reasonably good and similar across operating models (OMs). For models that were coupled to the environment, environmental parameters for El Niño years were estimated with good associated precision, and OM3 had a lower AIC score (77.61)  than the base model (OM1, 80.39), whereas OM2 (AIC 82.41) had a similar AIC score, suggesting the OMs were all plausible model alternatives. Our model testing resulted in a plausible subset of management options, and stakeholders selected a permanent closure of the first fishing season based on overall performance of this option; ability to reduce the risk of fishery closure and stock collapse; robustness to uncertainties; and ease of implementation. Our simulation approach enabled the selection of an optimal yet pragmatic solution for addressing economic and conservation objectives under a variable environment with extreme events.