Jacob McC. Overton

Predicting species spatial distributions using presence-only data: a case study of native New Zealand ferns

Abstract Identification of areas containing high biological diversity (‘hotspots’) from species presence-only data has become increasingly important in species and ecosystem management when presence/absence data is unavailable. However, as presence-only data sets lack any information on absences and as they suffer from many biases associated with the ad hoc or non-stratified sampling, they are often assumed problematic and inadequate for most statistical modeling methods. In this paper, this supposition is investigated by comparing generalized additive models (GAM) fitted with 43 native New Zealand fern species presence/absence data, obtained from a survey of 19 875 forested plots, to GAM models and ecological niche factor analysis (ENFA) models fitted with identical presence data and, in the case of GAM models, computer generated ‘pseudo’ absences. By using the same presence data for all models, absence data is isolated as the varying factor allowing different techniques for generating ‘pseudo’ absences used in the GAM models to be analyzed and compared over three principal levels of investigation. GAM models fitted with an environmentally weighted distribution of ‘pseudo’ absences and ENFA models selected environmental variables more similar to the GAM presence/absence models than did the GAM models fitted with randomly distributed ‘pseudo’ absences. Average contributions for the GAM presence/absence model showed mean annual temperature and mean annual solar radiation as the most important factors followed by lithology. Comparisons of prediction results show GAM models incorporating an environmentally weighted distribution of ‘pseudo’ absences to be more closely correlated to the GAM presence/absence models than either the GAM models fitted with randomly selected ‘pseudo’ absences or the ENFA models. ENFA models were found to be the least correlated to the GAM presence/absence models. These latter models were also shown to give the most optimistic predictions overall, however, as ENFA predicts habitat suitability rather than probability of presence this was expected. Summation of species predictions used as a measure of species potential biodiversity ‘hotspots’ also shows ENFA models to give the highest and largest distribution of potential biodiversity. Additionally, GAM models incorporating ‘pseudo’ absences were more highly correlated to the GAM presence/absence model than was ENFA. However, ENFA identified more areas of potential biodiversity ‘hotspots’ similar to the GAM presence/absence model, than either GAM model incorporating ‘pseudo’ absences.

GRASP: generalized regression analysis and spatial prediction

We present generalized regression analysis and spatial prediction (GRASP) conceptually as a method for producing spatial predictions using statistical models, and introduce and demonstrate a specific implementation in Splus that facilitates the process. We put forward GRASP as a new name encapsulating an existing concept that aims at making spatial predictions using generalized regression analysis. Regression modeling is used to establish relationships between a response variable and a set of spatial predictors. The regression relationships are then used to make spatial predictions of the response. The GRASP process requires point measurements of the response, as well as regional coverages of predictor variables that are statistically (and preferably causally) important in determining the patterns of the response. This approach to spatial prediction is becoming more commonplace, and it is useful to define it as a general concept. For instance, GRASP could use a survey of the abundance of a species (the response), and existing spatial coverages of environmental (e.g. climate, landform) variables (the predictors) for a region. A multiple regression can be used to establish the statistical relationship between the species abundance and the environmental variables. These regression relationships can then be used to predict the species abundance from the environmental surfaces. This process defines relationships in environmental space and uses these relationships to predict in geographic space. We introduce GRASP (the implementation) as an interface and collection of functions in Splus designed to facilitate modern regression analysis and the use of these regressions for making spatial predictions. GRASP standardizes the modeling process and makes it more reproducible and less subjective, while preserving analysis flexibility. The set of functions provides a toolbox that allows quick and easy data checking, model building and evaluation, and calculation of predictions. The current version uses generalized additive models (GAMs), a modern non-parametric regression technique the advantages of which are discussed. We demonstrate the use of the GRASP implementation to model and predict the natural distributions of two components of New Zealand fern biodiversity: (1) the natural distribution of an icon species, silver fern (Cyathea dealbata); and (2) the natural pattern of total fern species richness. Key steps are demonstrated, including data preparation, options setting, data exploration, model building, model validation and interpretation, and spatial prediction.

A global meta‐analysis of the relative extent of intraspecific trait variation in plant communities

Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, we conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the total trait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies.

Combining α - and β -diversity models to fill gaps in our knowledge of biodiversity.

For many taxonomic groups, sparse information on the spatial distribution of biodiversity limits our capacity to answer a variety of theoretical and applied ecological questions. Modelling community-level attributes (α- and β-diversity) over space can help overcome this shortfall in our knowledge, yet individually, predictions of α- or β-diversity have their limitations. In this study, we present a novel approach to combining models of α- and β-diversity, with sparse survey data, to predict the community composition for all sites in a region. We applied our new approach to predict land snail community composition across New Zealand. As we demonstrate, these predictions of metacommunity composition have diverse potential applications, including predicting γ-diversity for any set of sites, identifying target areas for conservation reserves, locating priority areas for future ecological surveys, generating realistic compositional data for metacommunity models and simultaneously predicting the distribution of all species in a taxon consistent with known community diversity patterns.

Net Present Biodiversity Value and the Design of Biodiversity Offsets

There is an urgent need to develop sound theory and practice for biodiversity offsets to provide a better basis for offset multipliers, to improve accounting for time delays in offset repayments, and to develop a common framework for evaluating in-kind and out-of-kind offsets. Here, we apply concepts and measures from systematic conservation planning and financial accounting to provide a basis for determining equity across type (of biodiversity), space, and time. We introduce net present biodiversity value (NPBV) as a theoretical and practical measure for defining the offset required to achieve no-net-loss. For evaluating equity in type and space we use measures of biodiversity value from systematic conservation planning. Time discount rates are used to address risk of non-repayment, and loss of utility. We illustrate these concepts and measures with two examples of biodiversity impact–offset transactions. Considerable further work is required to understand the characteristics of these approaches.

Information pyramids for informed biodiversity conservation

We discuss a paradigm for informed ecosystem management that provides a quantitative and rigorous foundation for informing conservation decisions and sustainable ecosystem management. Information pyramids incorporate conceptual and technological advances in ecosystem depiction and provide a framework for the integration and generalization of raw data into forms that are spatially extensive and at the appropriate level of generalization for a particular use. The basic tenets of the pyramid are: (1) Higher levels of the pyramid are entirely derived from a foundation of underlying data. (2) The process of generalization and integration upward should be objective and explicit. (3) Pyramids for different purposes often overlap, with common data and common methods for integration. (4) All levels of the pyramid should be developed together, including base data, methods and kinds of integration, and algorithms for using the information for planning and decision-making. Information pyramids are a powerful approach to organizing research science, and provide a mechanism by which research, data collection, storage and generalization can be focused on conservation outcomes. Common data and methods lead to increased efficiency, while also allowing for separate disciplines and programs. A case study of an integrated pyramid from New Zealand is discussed, which illustrates the characteristics of information pyramids. Components of this pyramid are discussed that provide examples of integration and generalization at various levels of the pyramid, from base data, to derived data, to spatial predictions and classifications, to a method of integrating this information into conservation decisions.

Secondary woody vegetation patterns in New Zealand’s South Island dryland zone

Abstract Can New Zealand’s indigenous dryland ecosystems be rehabilitated by facilitating inherent successional tendencies to enhance development of indigenous-dominated and often woody communities in the long term? Here, we describe the geographic distribution of woody communities of New Zealand’s South Island drylands to generate hypotheses about successional trajectories to future vegetation states. Presences and absences of woody species in 3880 vegetation plots collated from past surveys were used to predict species potential distributions across drylands. Separate models and spatial predictions were built for each of four classes of woody richness, which were used as surrogates for successional stages. Woody species richness increased significantly from grassland to shrubland and from shrubland to forest cover, and trends in species traits also suggest richness class was related with successional stage. Indigenous woody species outnumbered exotic species in all richness classes. Assuming richness classes represent temporal progressions, our results suggest relatively homogeneous early-successional woody associations succeed to a divergent array of woody associations in different environments. Growth forms of species in our predicted associations suggest transitions from grassland to tall, tree-rich forests in northern and coastal drylands, and to liane-rich open or lightcanopied shrubland, woodland, or low forest in more severe inland environments. These putative communities are novel in species composition but physiognomically broadly similar to pre-settlement analogues. Especially in severe inland environments, unassisted transitions from grassland to indigenousdominated late-successional woody communities may depend on the exclusion of tall exotic trees, Scotch broom, and gorse in early succession.

Components of spatial patterning in a serpentine grassland

We analyzed the components of spatial patterning in species abundance in a diverse grassland dominated by early season, annual forbs. Species abundance, soil depth and gopher disturbances were measured by means of a nested spatial design on two 8 m × 20 m plots that differed in the amount of larger scale variability in soil depth. Species distributions at the scale of the 10 cm × 10 cm quadrat were highly clumped, with a decline in clumping with mean abundance. Even with the effect of abundance on clumping removed, species showed differences in the degree of clumping and these differences were consistent between the two plots. The abundance of the species and the frequency of disturbance correlated weakly to moderately with soil depth. Semivariance analyses indicated that the most common species all showed complex spatial patterning at a range of scales. Some of this variation corresponded to patterns of soil depth variation and patterns of gopher disturbance; however, a large amount of the spatial patterning in species abundance remains unexplained.

Land use effects on “spring annual” herbs in rare non‐forest ecosystems of New Zealand

Abstract We examined trends over six consecutive spring seasons in three “spring annual” herbs, Myosurus minimus subsp. novae‐zelandiae (Ranunculaceae), Ceratocephalapungens (Ranunculaceae), and Myosotis pygmaea var. minutiflora (Boraginaceae), in terms of their habitats and site land uses in several rare, non‐forest ecosystems. On dry hillslopes, saline soils, and turfs of ephemeral wetlands (including coastal turfs), Ceratocephala and Myosotis declined where sites were managed for conservation by removal of mammalian herbivores. Some populations of Myosurus declined only marginally or remained stable despite high cover of ruderal and weedy, herbaceous exotic plants. Loss of monitored populations during the study was offset by discoveries of additional populations of all three taxa. Statistical models of population trends suggest that in some instances spring annual populations benefit from farm animal and rabbit (Oryctolagus cuniculus cuniculus) disturbance of their habitats perhaps by 1) suppressing transitions to taller vegetation and retarding competition of invasive exotic plants and 2) maintaining nutrient supplementation from faeces lost with the extinction of ground‐dwelling birds. Frequent seeds of all three taxa preserved in moa coprolites from several sites in Central Otago point to 1) the herbs’ probable non‐rarity in pre‐human times and 2) dispersal mutualisms and mediation of community ground cover by extinct ratites.