Forecasting the continued naturalization of widely planted alien conifers: On Sitka spruce (Picea sitchensis) in Norway

Imported plants frequently spread from where they are planted — forestry conifers being a prime example. A particular species may spread rapidly into many ecosystems across a large area, or its spread may be more gradual and confined. For species that have just begun to spread, it is crucial to know where they will move, and how fast. To make these forecasts, we can look at where the species occurs in its home range, and observe the early stages of naturalization in the introduced range. The home range reveals broad environmental constraints on the species’ spatial distribution, while the introduced range manifests the fine-scale processes underpinning the expansion. But the forecasts will only be good if the inferences are made carefully, this thesis finds. The thesis: (1) introduces software that isolates important environmental constraints from spurious ones, (2) presents a method to handle spatial bias in occurrence data, (3) quantifies spread into ecosystems with unequal levels of exposure, and (4) identifies current bottlenecks that could release populations from their observed trajectories. Sitka spruce in Norway serves as the motivating case throughout

The MIAmaxent R package: Variable transformation and model selection for species distribution models

The widely used “Maxent” software for modeling species distributions from presence‐only data (Phillips et al., Ecological Modelling, 190, 2006, 231) tends to produce models with high‐predictive performance but low‐ecological interpretability, and implications of Maxent's statistical approach to variable transformation, model fitting, and model selection remain underappreciated. In particular, Maxent's approach to model selection through lasso regularization has been shown to give less parsimonious distribution models—that is, models which are more complex but not necessarily predictively better—than subset selection. In this paper, we introduce the MIAmaxent R package, which provides a statistical approach to modeling species distributions similar to Maxent's, but with subset selection instead of lasso regularization. The simpler models typically produced by subset selection are ecologically more interpretable, and making distribution models more grounded in ecological theory is a fundamental motivation for using MIAmaxent. To that end, the package executes variable transformation based on expected occurrence–environment relationships and contains tools for exploring data and interrogating models in light of knowledge of the modeled system. Additionally, MIAmaxent implements two different kinds of model fitting: maximum entropy fitting for presence‐only data and logistic regression (GLM) for presence–absence data. Unlike Maxent, MIAmaxent decouples variable transformation, model fitting, and model selection, which facilitates methodological comparisons and gives the modeler greater flexibility when choosing a statistical approach to a given distribution modeling problem

Data from: Bunching up the background betters bias in species distribution models

Sets of presence records used to model species’ distributions typically consist of observations collected opportunistically rather than systematically. As a result, sampling probability is geographically uneven, which may confound the model’s characterization of the species’ distribution. Modelers frequently address sampling bias by manipulating training data: either subsampling presence data or creating a similar spatial bias in non-presence background data. We tested a new method, which we call “background thickening,” in the latter category. Background thickening entails concentrating background locations around presence locations in proportion to presence location density. We compared background thickening to two established sampling bias correction methods — target group background selection and presence thinning — using simulated data and data from a case study. In the case study, background thickening and presence thinning performed similarly well, both producing better model discrimination than target group background selection, and better model calibration than models without correction. In the simulation, background thickening performed better than presence thinning when the number of simulated presence locations was low, and vice versa. We discuss drawbacks to target group background selection, why background thickening and presence thinning are conservative but robust sampling bias correction methods, and why background thickening is better than presence thinning for small sample sizes. Particularly, background thickening is advantageous for treating sampling bias when data are scarce because it avoids discarding presence records

Zip file archive of code, data, and output

-2

Bunching up the background betters bias in species distribution models

Sets of presence records used to model species’ distributions typically consist of observations collected opportunistically rather than systematically. As a result, sampling probability is geographically uneven, which may confound the model's characterization of the species’ distribution. Modelers frequently address sampling bias by manipulating training data: either subsampling presence data or creating a similar spatial bias in non‐presence background data. We tested a new method, which we call ‘background thickening’, in the latter category. Background thickening entails concentrating background locations around presence locations in proportion to presence location density. We compared background thickening to two established sampling bias correction methods – target group background selection and presence thinning – using simulated data and data from a case study. In the case study, background thickening and presence thinning performed similarly well, both producing better model discrimination than target group background selection, and better model calibration than models without correction. In the simulation, background thickening performed better than presence thinning when the number of simulated presence locations was low, and vice versa. We discuss drawbacks to target group background selection, why background thickening and presence thinning are conservative but robust sampling bias correction methods, and why background thickening is better than presence thinning for small sample sizes. Particularly, background thickening is advantageous for treating sampling bias when data are scarce because it avoids discarding presence records

Bunching up the background betters bias in species distribution models

Sets of presence records used to model species’ distributions typically consist of observations collected opportunistically rather than systematically. As a result, sampling probability is geographically uneven, which may confound the model's characterization of the species’ distribution. Modelers frequently address sampling bias by manipulating training data: either subsampling presence data or creating a similar spatial bias in non‐presence background data. We tested a new method, which we call ‘background thickening’, in the latter category. Background thickening entails concentrating background locations around presence locations in proportion to presence location density. We compared background thickening to two established sampling bias correction methods – target group background selection and presence thinning – using simulated data and data from a case study. In the case study, background thickening and presence thinning performed similarly well, both producing better model discrimination than target group background selection, and better model calibration than models without correction. In the simulation, background thickening performed better than presence thinning when the number of simulated presence locations was low, and vice versa. We discuss drawbacks to target group background selection, why background thickening and presence thinning are conservative but robust sampling bias correction methods, and why background thickening is better than presence thinning for small sample sizes. Particularly, background thickening is advantageous for treating sampling bias when data are scarce because it avoids discarding presence records

Composite landscape predictors improve distribution models of ecosystem types

Aim: Distribution modelling is a useful approach to obtain knowledge about the spatial distribution of biodiversity, required for, for example, red-list assessments. While distribution modelling methods have been applied mostly to single species, modelling of communities and ecosystems (EDM; ecosystem-level distribution modelling) produces results that are more directly relevant for management and decision-making. Although the choice of predictors is a pivotal part of the modelling process, few studies have compared the suitability of different sets of predictors for EDM. In this study, we compare the performance of 50 single environmental variables with that of 11 composite landscape gradients (CLGs) for prediction of ecosystem types. The CLGs represent gradients in landscape element composition derived from multivariate analyses, for example “inner-outer coast” and “land use intensity.” Location: Norway. Methods: We used data from field-based ecosystem-type mapping of nine ecosystem types, and environmental variables with a resolution of 100 × 100 m. We built nine models for each ecosystem type with variables from different predictor sets. Logistic regression with forward selection of variables was used for EDM. Models were evaluated with independently collected data. Results: Most ecosystem types could be predicted reliably, although model performance differed among ecosystem types. We identified significant differences in predictive power and model parsimony across models built from different predictor sets. Climatic variables alone performed poorly, indicating that the current climate alone is not sufficient to predict the current distribution of ecosystems. Used alone, the CLGs resulted in parsimonious models with relatively high predictive power. Used together with other variables, they consistently improved the models. Main conclusions: Our study highlights the importance of variable selection in EDM. We argue that the use of composite variables as proxies for complex environmental gradients has the potential to improve predictions from EDMs and thus to inform conservation planning as well as improve the precision and credibility of red lists and global change assessments.conservation planning, distribution modelling, ecosystem classification, ecosystem types, IUCN Red List of Ecosystems, landscape gradients, spatial prediction, species response curve

Composite landscape predictors improve distribution models of ecosystem types

Aim Distribution modelling is a useful approach to obtain knowledge about the spatial distribution of biodiversity, required for, for example, red‐list assessments. While distribution modelling methods have been applied mostly to single species, modelling of communities and ecosystems (EDM; ecosystem‐level distribution modelling) produces results that are more directly relevant for management and decision‐making. Although the choice of predictors is a pivotal part of the modelling process, few studies have compared the suitability of different sets of predictors for EDM. In this study, we compare the performance of 50 single environmental variables with that of 11 composite landscape gradients (CLGs) for prediction of ecosystem types. The CLGs represent gradients in landscape element composition derived from multivariate analyses, for example “inner‐outer coast” and “land use intensity.” Location Norway. Methods We used data from field‐based ecosystem‐type mapping of nine ecosystem types, and environmental variables with a resolution of 100 × 100 m. We built nine models for each ecosystem type with variables from different predictor sets. Logistic regression with forward selection of variables was used for EDM. Models were evaluated with independently collected data. Results Most ecosystem types could be predicted reliably, although model performance differed among ecosystem types. We identified significant differences in predictive power and model parsimony across models built from different predictor sets. Climatic variables alone performed poorly, indicating that the current climate alone is not sufficient to predict the current distribution of ecosystems. Used alone, the CLGs resulted in parsimonious models with relatively high predictive power. Used together with other variables, they consistently improved the models. Main conclusions Our study highlights the importance of variable selection in EDM. We argue that the use of composite variables as proxies for complex environmental gradients has the potential to improve predictions from EDMs and thus to inform conservation planning as well as improve the precision and credibility of red lists and global change assessments