Accounting for multi‐scale spatial autocorrelation improves performance of invasive species distribution modelling (iSDM)

Aim  Analyses of species distributions are complicated by various origins of spatial autocorrelation (SAC) in biogeographical data. SAC may be particularly important for invasive species distribution models (iSDMs) because biological invasions are strongly influenced by dispersal and colonization processes that typically create highly structured distribution patterns. We examined the efficacy of using a multi-scale framework to account for different origins of SAC, and compared non-spatial models with models that accounted for SAC at multiple levels. Location  We modelled the spatial distribution of an invasive forest pathogen, Phytophthora ramorum, in western USA. Methods  We applied one conventional statistical method (generalized linear model, GLM) and one nonparametric technique (maximum entropy, Maxent) to a large dataset on P. ramorum occurrence (n = 3787) to develop four types of model that included environmental variables and that either ignored spatial context or incorporated it at a broad scale using trend surface analysis, a local scale using autocovariates, or multiple scales using spatial eigenvector mapping. We evaluated model accuracies and amounts of explained spatial structure, and examined the changes in predictive power of the environmental and spatial variables. Results  Accounting for different scales of SAC significantly enhanced the predictive capability of iSDMs. Dramatic improvements were observed when fine-scale SAC was included, suggesting that local range-confining processes are important in P. ramorum spread. The importance of environmental variables was relatively consistent across all models, but the explanatory power decreased in spatial models for factors with strong spatial structure. While accounting for SAC reduced the amount of residual autocorrelation for GLM but not for Maxent, it still improved the performance of both approaches, supporting our hypothesis that dispersal and colonization processes are important factors to consider in distribution models of biological invasions. Main conclusions  Spatial autocorrelation has become a paradigm in biogeography and ecological modelling. In addition to avoiding the violation of statistical assumptions, accounting for spatial patterns at multiple scales can enhance our understanding of dynamic processes that explain ecological mechanisms of invasion and improve the predictive performance of static iSDMs.

[1]  C. Dormann Assessing the validity of autologistic regression , 2007 .

[2]  Trevor Hastie,et al.  Generalized linear and generalized additive models in studies of species distributions: setting the scene , 2002 .

[3]  Jennifer A. Miller,et al.  Mapping Species Distributions: Spatial Inference and Prediction , 2010 .

[4]  Stephen N. Matthews,et al.  Modeling the invasive emerald ash borer risk of spread using a spatially explicit cellular model , 2010, Landscape Ecology.

[5]  M. Hutchinson,et al.  The effect of species response form on species distribution model prediction and inference , 2009 .

[6]  F van Langevelde,et al.  Spatial autocorrelation and the scaling of species-environment relationships. , 2010, Ecology.

[7]  B. Ripley The Second-Order Analysis of Stationary Point Processes , 1976 .

[8]  David M. Rizzo,et al.  Sudden oak death: endangering California and Oregon forest ecosystems , 2003 .

[9]  W. D. Kissling,et al.  Spatial autocorrelation and the selection of simultaneous autoregressive models , 2007 .

[10]  T. Rangel,et al.  SAM: a comprehensive application for Spatial Analysis in Macroecology , 2010 .

[11]  Ross K. Meentemeyer,et al.  When is connectivity important? A case study of the spatial pattern of sudden oak death , 2010 .

[12]  R. Gil Pontius,et al.  Land-cover change model validation by an ROC method for the Ipswich watershed, Massachusetts, USA , 2001 .

[13]  Michael C. Wimberly,et al.  Mapping wildland fuels and forest structure for land management: a comparison of nearest neighbor imputation and other methods , 2009 .

[14]  R. Dubayah Modeling a solar radiation topoclimatology for the Rio Grande River Basin , 1994 .

[15]  Jennifer A. Miller,et al.  Incorporating spatial dependence in predictive vegetation models , 2007 .

[16]  Ross K. Meentemeyer,et al.  Epidemiological modeling of invasion in heterogeneous landscapes: spread of sudden oak death in California (1990–2030) , 2011 .

[17]  Janet L. Ohmann,et al.  Predictive mapping of forest composition and structure with direct gradient analysis and nearest- neighbor imputation in coastal Oregon, U.S.A. , 2002 .

[18]  J. Elith,et al.  Species Distribution Models: Ecological Explanation and Prediction Across Space and Time , 2009 .

[19]  A. Guisan,et al.  MigClim: Predicting plant distribution and dispersal in a changing climate , 2009 .

[20]  P. McCullagh,et al.  Generalized Linear Models , 1972, Predictive Analytics.

[21]  M. Tognelli,et al.  Analysis of determinants of mammalian species richness in South America using spatial autoregressive models , 2004 .

[22]  R. Meentemeyer,et al.  Predicting potential and actual distribution of sudden oak death in Oregon: prioritizing landscape contexts for early detection and eradication of disease outbreaks , 2010 .

[23]  Ingolf Kühn,et al.  Incorporating spatial autocorrelation may invert observed patterns , 2006 .

[24]  Faith R. Kearns,et al.  Geospatial Informatics for Management of a New Forest Disease: Sudden Oak Death , 2004 .

[25]  Omri Allouche,et al.  Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS) , 2006 .

[26]  José Alexandre Felizola Diniz-Filho,et al.  Modelling geographical patterns in species richness using eigenvector-based spatial filters , 2005 .

[27]  D. Elston,et al.  Red herrings remain in geographical ecology: a reply to Hawkins et al. (2007) , 2007 .

[28]  J. Franklin Moving beyond static species distribution models in support of conservation biogeography , 2010 .

[29]  David R. Anderson,et al.  Multimodel Inference , 2004 .

[30]  R. Peckham,et al.  Digital Terrain Modelling , 2007 .

[31]  D. Rizzo,et al.  AFLP and phylogenetic analyses of North American and European populations of Phytophthora ramorum. , 2004, Mycological research.

[32]  A. Hirzel,et al.  Evaluating the ability of habitat suitability models to predict species presences , 2006 .

[33]  Ross K. Meentemeyer,et al.  Mapping the risk of establishment and spread of sudden oak death in California , 2004 .

[34]  S. T. Buckland,et al.  An autologistic model for the spatial distribution of wildlife , 1996 .

[35]  S. Dark,et al.  The biogeography of invasive alien plants in California: an application of GIS and spatial regression analysis , 2004 .

[36]  M. Austin Spatial prediction of species distribution: an interface between ecological theory and statistical modelling , 2002 .

[37]  M. Austin Species distribution models and ecological theory: A critical assessment and some possible new approaches , 2007 .

[38]  I. Moore,et al.  Digital terrain modelling: A review of hydrological, geomorphological, and biological applications , 1991 .

[39]  R. G. Davies,et al.  Methods to account for spatial autocorrelation in the analysis of species distributional data : a review , 2007 .

[40]  D. Richardson,et al.  Inferring Process from Pattern in Plant Invasions: A Semimechanistic Model Incorporating Propagule Pressure and Environmental Factors , 2003, The American Naturalist.

[41]  Petr Pyšek,et al.  European map of alien plant invasions based on the quantitative assessment across habitats , 2009 .

[42]  P. Legendre Spatial Autocorrelation: Trouble or New Paradigm? , 1993 .

[43]  David M Rizzo,et al.  Transmission of Phytophthora ramorum in Mixed-Evergreen Forest in California. , 2005, Phytopathology.

[44]  Irene Casas,et al.  H.E.L.P: A GIS-based Health Exploratory AnaLysis Tool for Practitioners , 2011 .

[45]  Petr Pyšek,et al.  Traits Associated with Invasiveness in Alien Plants: Where Do we Stand? , 2008 .

[46]  P. McCullagh,et al.  Generalized Linear Models , 1992 .

[47]  Trevor Hastie,et al.  Making better biogeographical predictions of species’ distributions , 2006 .

[48]  George H. Taylor,et al.  High-quality spatial climate data sets for the United States and beyond , 2000 .

[49]  Richard Field,et al.  Coefficient shifts in geographical ecology: an empirical evaluation of spatial and non-spatial regression , 2009 .

[50]  Stéphane Dray,et al.  Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM) , 2006 .

[51]  A. Townsend Peterson,et al.  Transferability and model evaluation in ecological niche modeling: a comparison of GARP and Maxent , 2007 .

[52]  David Lonsdale,et al.  Tree diseases and landscape processes: the challenge of landscape pathology. , 2004, Trends in ecology & evolution.

[53]  R. Meentemeyer,et al.  Invasive species distribution modeling (iSDM): Are absence data and dispersal constraints needed to predict actual distributions? , 2009 .

[54]  Jack J. Lennon,et al.  Red-shifts and red herrings in geographical ecology , 2000 .

[55]  Jennifer A. Miller,et al.  Modeling the distribution of four vegetation alliances using generalized linear models and classification trees with spatial dependence , 2002 .

[56]  J. Franklin Predictive vegetation mapping: geographic modelling of biospatial patterns in relation to environmental gradients , 1995 .

[57]  Ross K. Meentemeyer,et al.  Effects of landscape heterogeneity on the emerging forest disease sudden oak death , 2007 .

[58]  Steven J. Phillips Transferability, sample selection bias and background data in presence‐only modelling: a response to Peterson et al. (2007) , 2008 .

[59]  Jennifer A. Miller Incorporating Spatial Dependence in Predictive Vegetation Models: Residual Interpolation Methods , 2005 .

[60]  Kevin J. Gaston,et al.  Distribution patterns in butterflies and birds of the Czech Republic: separating effects of habitat and geographical position , 2003 .

[61]  Miroslav Dudík,et al.  Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation , 2008 .

[62]  David Rizzo,et al.  Detection and Quantification of Phytophthora ramorum from California Forests Using a Real-Time Polymerase Chain Reaction Assay. , 2004, Phytopathology.

[63]  J. Diniz‐Filho,et al.  Spatial autocorrelation and red herrings in geographical ecology , 2003 .

[64]  M. Araújo,et al.  Consequences of spatial autocorrelation for niche‐based models , 2006 .

[65]  Alberto Jiménez-Valverde,et al.  The uncertain nature of absences and their importance in species distribution modelling , 2010 .

[66]  Victor C. Mastro,et al.  Incorporating anthropogenic variables into a species distribution model to map gypsy moth risk , 2008 .

[67]  Antoine Guisan,et al.  Climatic extremes improve predictions of spatial patterns of tree species , 2009, Proceedings of the National Academy of Sciences.

[68]  C. Dormann Effects of incorporating spatial autocorrelation into the analysis of species distribution data , 2007 .

[69]  Robert P. Anderson,et al.  Maximum entropy modeling of species geographic distributions , 2006 .

[70]  M. Araújo,et al.  Five (or so) challenges for species distribution modelling , 2006 .

[71]  John Bell,et al.  A review of methods for the assessment of prediction errors in conservation presence/absence models , 1997, Environmental Conservation.

[72]  Steven J. Phillips,et al.  Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data. , 2009, Ecological applications : a publication of the Ecological Society of America.

[73]  Pierre Legendre,et al.  All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices , 2002 .

[74]  Mark W. Schwartz,et al.  How fast and far might tree species migrate in the eastern United States due to climate change , 2004 .

[75]  John Rogan,et al.  Identifying Trends in Land Use/Land Cover Changes in the Context of Post-Socialist Transformation in Central Europe: A Case Study of the Greater Olomouc Region, Czech Republic , 2009 .

[76]  Ross K Meentemeyer,et al.  Early detection of emerging forest disease using dispersal estimation and ecological niche modeling. , 2008, Ecological applications : a publication of the Ecological Society of America.

[77]  T. Simons,et al.  Spatial autocorrelation and autoregressive models in ecology , 2002 .

[78]  R. Real,et al.  AUC: a misleading measure of the performance of predictive distribution models , 2008 .

[79]  J. Diniz‐Filho,et al.  Spatial analysis improves species distribution modelling during range expansion , 2008, Biology Letters.

[80]  A. Lehmann,et al.  Improving generalized regression analysis for the spatial prediction of forest communities , 2006 .

[81]  Calvin A. Farris,et al.  Incorporating spatial non-stationarity of regression coefficients into predictive vegetation models , 2007, Landscape Ecology.

[82]  J. Webber,et al.  Plant pathology: Sudden larch death , 2010, Nature.

[83]  Gretchen G. Moisen,et al.  A comparison of the performance of threshold criteria for binary classification in terms of predicted prevalence and Kappa , 2008 .

[84]  Daniel A Griffith,et al.  Spatial modeling in ecology: the flexibility of eigenfunction spatial analyses. , 2006, Ecology.

[85]  Omri Allouche,et al.  Incorporating distance constraints into species distribution models , 2008 .