Inventory and Review of Quantitative Models for Spread of Plant Pests for Use in Pest Risk Assessment for the EU Territory1

EFSA supporting publication 2015:EN-795 EXTERNAL SCIENTIFIC REPORT Inventory and review of quantitative models for spread of plant pests for use in pest risk assessment for the EU territory1 NERC Centre for Ecology and Hydrology 2 Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK ABSTRACT This report considers the prospects for increasing the use of quantitative models for plant pest spread and dispersal in EFSA Plant Health risk assessments. The agreed major aims were to provide an overview of current modelling approaches and their strengths and weaknesses for risk assessment, and to develop and test a system for risk assessors to select appropriate models for application. First, we conducted an extensive literature review, based on protocols developed for systematic reviews. The review located 468 models for plant pest spread and dispersal and these were entered into a searchable and secure Electronic Model Inventory database. A cluster analysis on how these models were formulated allowed us to identify eight distinct major modelling strategies that were differentiated by the types of pests they were used for and the ways in which they were parameterised and analysed. These strategies varied in their strengths and weaknesses, meaning that no single approach was the most useful for all elements of risk assessment. Therefore we developed a Decision Support Scheme (DSS) to guide model selection. The DSS identifies the most appropriate strategies by weighing up the goals of risk assessment and constraints imposed by lack of data or expertise. Searching and filtering the Electronic Model Inventory then allows the assessor to locate specific models within those strategies that can be applied. This DSS was tested in seven case studies covering a range of risk assessment scenarios, pest types and dispersal mechanisms. These demonstrate the effectiveness of the DSS for selecting models that can be applied to contribute to EFSA Plant Health risk assessments. Therefore, quantitative spread and dispersal modelling has potential to improve current risk assessment protocols and contribute to reducing the serious impacts of plant pests in Europe. © NERC Centre for Ecology and Hydrology, 2015 KEY WORDS Plant pest, disease, invasion, dispersal, spread, model, simulation DISCLAIMER The present document has been produced and adopted by the bodies identified above as author(s). In accordance with Article 36 of Regulation (EC) No 178/2002, this task has been carried out exclusively by the author(s) in the context of a grant agreement between the European Food Safety Authority and the author(s). The present document is published complying with the transparency principle to which the Authority is subject. It cannot be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors. 1 Question No EFSA-Q-2012-00499 . 2 Daniel S. Chapman, Steven M. White, Danny A.P. Hooftman, James M. Bullock. Any enquiries related to this output should be addressed to [email protected] Suggested citation: Chapman, D.S., White, S.M., Hooftman, D.A.P. and Bullock, J.M. 2015. Inventory and review of quantitative models for spread of plant pests for use in pest risk assessment for the EU territory. EFSA supporting publication 2015:EN-795, 190 pp. Available online: www.efsa.europa.eu/publications © European Food Safety Authority, 2015 Inventory and review of quantitative models for spread of plant pests for use in pest risk assessment for the EU territory SUMMARY Pests of plants cause major economic losses to the production of agricultural, forestry and ornamental plants in Europe and globally. Risk assessment for plant pests can target resources efficiently at managing the spread of current and novel pests. Such efforts would be enhanced by quantitative models for pest spread and dispersal. In principle, spread and dispersal models are able to predict the areas at risk of future spread, provide insights into the biological and abiotic factors facilitating spread, estimate pest impacts and experiment with different management strategies. However, a large number of spread and dispersal models have been developed and published in the scientific literature. It is the wish of the EFSA Panel on Plant Health to make a better and more tailored use of spread models in risk assessments. Therefore it is necessary to survey the range of different modelling techniques and evaluate their relative usefulness and limitations. Furthermore, a system for selecting the most appropriate models for application in risk assessment is required to guide potential users through the wide variety of modelling approaches available. Here we report on such an evaluation, to provide EFSA with guidance and case studies for future risk assessment. The overall aims of this report are: 1. To conduct an extensive literature search of quantitative models of spread and dispersal of plant pests, and analyse the search results to identify distinct modelling strategies. 2. To produce a detailed electronic inventory of the spread and dispersal models located by the literature search. 3. To assess the fitness of different spread and dispersal model strategies for use in Plant Health risk assessment and develop a Decision Support Scheme (DSS) for choosing an appropriate model. 4. To present several risk assessment modelling case studies, including use of the DSS and practical application of the selected models. The extensive literature search was based upon protocols for Systematic Reviews and Systematic Mapping, in order to provide as comprehensive, unbiased and reproducible a search as is possible. We searched for relevant literature within Web of Knowledge, Scopus, Google Scholar, EFSA Journal and the MOPEST, PESTCAST and CAMASE model inventories. The search was designed to locate generic terms for pests and host plants, as well as the names of 2381 important pest organisms and 282 crop plants. The pest organisms included insects, invasive, weedy and parasitic plants, fungi, oomycetes, viruses, viroids, bacteria, phytoplasmas, nematodes and mites listed in EC Directive 2000/29/EC, the EPPO Plant Quarantine Data Retrieval System, Q-Bank database of regulated pests and EU Emergency Control Measures. The search yielded nearly 14000 articles. We established clear criteria by which irrelevant results were screened out and discarded based on sequential examination of their titles, abstracts and full texts. After this process the extensive literature search resulted in 468 eligible papers containing models of pest spread or dispersal. To identify the major modelling strategies, we performed a cluster analysis on the models located by the literature search. For clustering, we defined a set of 27 multiple-choice questions characterising the models’ representation of space and time (e.g. continuous or discrete, scales, numbers of dimensions, heterogeneity, etc.) and representation of the pest and host organisms (e.g. generality, number of species, stochasticity, dispersal mechanisms, evolutionary processes, etc.). To cluster the models, we applied two different clustering algorithms – co-clustering based on the Bernoulli Latent Block Model and model-based clustering using the Gaussian Finite Mixture Model. Both algorithms indicated that the optimal clustering of the models was into eight separate strategies. However, the model-based EFSA supporting publication 2015:EN-795 2 The present document has been produced and adopted by the bodies identified above as author(s). In accordance with Article 36 of Regulation (EC) No 178/2002, this task has been carried out exclusively by the author(s) in the context of a grant agreement between the European Food Safety Authority and the author(s). The present document is published complying with the transparency principle to which the Authority is subject. It cannot be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors. Inventory and review of quantitative models for spread of plant pests for use in pest risk assessment for the EU territory clustering gave a higher quality clustering than co-clustering, and so this model was retained for interpretation. Examination of the Clusters allowed us to identify the following major strategies: . Cluster A: Single-event pest dispersal, generally dispersal kernel or disease gradient models for a single pest spreading over a fixed time period. Cluster B: Large-scale simulation of pest dispersal events, generally wind dispersal of the pest simulated through Lagrangian atmospheric dispersion, advection-diffusion, or wind trajectory models. Cluster C: Pest spread or dispersal in continuous space and time, generally reaction-diffusion and diffusion models without explicit modelling of the host plant. Cluster D: Continuous-space pest spread in discrete time, generally integrodifference models for pest spread through a homogeneous landscape with no explicit host representation. Cluster E: Iterative colonisation of hosts at small scales, generally simulation of spatial susceptible-infected epidemic models and network contact spread models. Cluster F: Simulation of specific pest spread at large scales, generally cellular automata

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