Developing pragmatic maps of establishment likelihood for plant pests Technical Report for CEBRA project 170607 James Camac1, John Baumgartner1, Andrew Robinson1, Jane Elith1, and contributions from: Dr Ranjith Subasinghe2 Dr Mark Stanaway2 Dr Susie Collins2 Dr Anaís Gibert1 Dr Matthew Hill3 Dr Peter Caley3 Dr Simon Barry3 1The Centre of Excellence for Biosecurity Risk Analysis, The Univer- sity of Melbourne 2Department of Agriculture, Water and the Environment 3Data61, CSIRO November 3, 2020 Centre of Excellence for Biosecurity Risk Analysis Camac et al. 2020 Centre of Excellence for Biosecurity Risk Analysis How to cite: Camac, JS., Baumgartner, J., Robinson, A., Elith J (2020) Developing pragmatic maps of establishment likelihood for plant pests. Technical Report for CEBRA project 170607. i Contents 1 Executive summary 1 2 Introduction 3 3 Decision tree for invasive species distribution modelling 5 3.1 Guide for invasive species distribution modelling . 9 3.1.1 Step 1: Data Sourcing . 11 3.1.1.1 Pest biology . 11 3.1.1.2 Occurrence data . 12 3.1.1.3 Climatic data . 13 3.1.1.4 Non-climatic data . 13 3.1.1.5 Alternatives for data-poor species . 13 3.1.2 Step 2: Data Cleaning . 14 3.1.2.1 Physiological data . 14 3.1.2.2 Occurrence data . 16 3.1.3 Step 3: Model Development . 17 3.1.3.1 Process-based models . 18 3.1.3.2 Correlative models . 18 3.1.3.3 Model settings & complexity . 20 3.1.3.4 Sampling background & dealing with survey bias . 22 3.1.3.5 Covariate uncertainty . 24 3.1.4 Step 4: Model Validation . 24 3.1.5 Step 5: Model Utility . 27 4 Framework for mapping establishment likelihoods for plant pests 32 4.1 Identifying high risk pathways . 34 4.2 Pathways . 35 4.2.1 Pathway: Air passengers . 35 4.2.1.1 International tourists . 35 4.2.1.2 Returning residents . 41 4.2.1.3 Torres Strait visitors (Fruit fly specific) . 43 4.2.2 Pathway: Mail . 45 4.2.3 Pathway: Imported fertiliser . 45 4.2.4 Pathway: International Containers . 48 4.2.5 Pathway: Vessels . 50 4.2.6 Pathway: Imported Machinery . 51 4.2.7 Pathway: Imported nursery stock . 52 4.2.8 Pathway: Imported plant-based food . 52 4.3 Expected number of pest arrivals . 53 4.4 Abiotic suitability . 53 4.5 Biotic suitability . 54 Camac et al. 2020 Centre of Excellence for Biosecurity Risk Analysis 4.6 Estimating establishment likelihoods . 56 5 Case study 1: Oriental fruit fly 57 5.1 Background . 58 5.2 High risk pathways . 58 5.3 Abiotic suitability . 59 5.4 Biotic suitability . 65 5.5 Establishment likelihoods . 69 6 Case study 2: Khapra beetle 80 6.1 Background . 81 6.2 High risk pathways . 81 6.3 Abiotic suitability . 83 6.4 Biotic suitability . 83 6.5 Establishment likelihoods . 86 7 Case study 3: Brown marmorated stink bug (BMSB) 96 7.1 Background . 97 7.2 High risk pathways . 97 7.3 Abiotic suitability . 99 7.4 Biotic suitability . 106 7.5 Establishment likelihoods . 109 8 Case study 4: Gypsy moth 120 8.1 Background . 121 8.2 High risk pathways . 121 8.3 Abiotic suitability . 123 8.4 Biotic suitability . 128 8.5 Establishment likelihoods . 133 9 Informing biosecurity decisions 145 9.1 Utility 1: Informing where to conduct surveillance for early detection . 146 9.2 Utility 2: Surveillance coverage relative to total establishment likelihood 147 9.3 Utility 3: Informing likelihoods of area freedom . 149 9.4 Utility 4: Informing seeds in pest/disease spread modelling . 152 9.5 Utility 5: Developing true risk maps . 153 10 Future research needs and extensions 154 10.1 Major review of RRRA . 154 10.2 Collecting empirical data for pathway post-border movements . 154 10.3 Accounting for uncertainty . 156 10.4 Aggregating maps . 156 10.5 Predicting future establishment likelihoods . 157 10.6 Virtual analytics platform . 157 Bibliography 158 A Spatial heterogeneity in pest risk assessments: a review of risk maps 167 B Workshop 212 iii Camac et al. 2020 Centre of Excellence for Biosecurity Risk Analysis C Dealing with uncertainty in predictor selection 228 D edmaps: an R package for creating maps for early detection 259 D.1 Software requirements . 259 D.1.1 Minimum system requirements . 259 D.1.1.1 Operating system specific requirements . 260 D.1.2 Required R packages .......................... 261 D.1.3 Data directory . 261 D.2 Parametrising edmaps . ............................ 264 D.3 Running edmaps . ............................... 268 D.3.1 Using edmaps with Docker (recommended) . 269 D.3.2 Using edmaps with renv . ...................... 270 D.3.3 Using edmaps by itself . 270 E Reference manual for edmaps R package 271 iv List of Figures 3.1 Guide for developing scientifically robust species distribution models for invasive pests. For further details please see text in sections 3.1.1 to 3.1.5......................................... 10 3.2 Distribution and intensity of Global Biodiversity Information Facility (GBIF) occurrence records. Lighter colours equal higher intensity. Sourced from https://www.gbif.org on 09/01/2019. 12 3.3 An output from the web interface Climate Matcher........... 26 4.1 Polynomial relationship between the number of accommodation providers and rooms contained in statistical area level 2 categories. 37 4.2 Geographic distribution of tourist rooms across Australia. 38 4.3 Top) Distance from major Australian international airports; Bottom) Dis- tance weight score. 40 4.4 The geographic distribution of human population across Australia. 42 4.5 Top) Distance from Cairns International Airport; Bottom) Distance weight score. ....................................... 44 4.6 Log10 proportion of fertiliser tonnage deposited per grid cell. 47 4.7 Geographic distribution of secondary ALUMC classifications. 55 5.1 A female oriental fruit fly, Bactrocera dorsalis, laying eggs by inserting her ovipositor in the skin of a papaya. 57 5.2 CLIMEX, GARP and Maxent model estimates of the global distribution of suitable climate for oriental fruit fly (Bactrocera dorsalis) or its synonym Bactrocera invadens................................ 60 5.3 Global climatic suitability for oriental fruit fly estimated from range bag- ging. ........................................ 63 5.4 Australian projected climatic suitability for oriental fruit fly derived from range bagging. 64 5.5 Average Normalised Differential Vegetation Index (NDVI) observed be- tween October 2018 and March 2019. 67 5.6 Distribution of suitable biotic environment for oriental fruit fly. 68 5.7 Estimated environmental suitability for oriental fruit fly. 70 5.8 National establishment likelihood map for oriental fruit fly. 71 5.9 Oriental fruit fly establishment likelihood map for greater Cairns. 72 5.10 Oriental fruit fly establishment likelihood map for greater Brisbane. 73 5.11 Oriental fruit fly establishment likelihood map for greater Sydney. 74 5.12 Oriental fruit fly establishment likelihood map for greater Melbourne. 75 5.13 Oriental fruit fly establishment likelihood map for greater Hobart. 76 5.14 Oriental fruit fly establishment likelihood map for greater Adelaide. 77 5.15 Oriental fruit fly establishment likelihood map for greater Perth. 78 5.16 Oriental fruit fly establishment likelihood map for greater Darwin. 79 Camac et al. 2020 Centre of Excellence for Biosecurity Risk Analysis 6.1 An adult khapra beetle (Trogoderma granarium). 80 6.2 Log10 vessel pathway distance decay weights for khapra beetle. 82 6.3 Distribution of suitable biotic environment for khapra beetle. 85 6.4 National establishment likelihood map for khapra beetle. 87 6.5 Khapra beetle establishment likelihood map for greater Cairns. 88 6.6 Khapra beetle establishment likelihood map for greater Brisbane. 89 6.7 Khapra beetle establishment likelihood map for greater Sydney. 90 6.8 Khapra beetle establishment likelihood map for greater Melbourne. 91 6.9 Khapra beetle establishment likelihood map for greater Hobart. 92 6.10 Khapra beetle establishment likelihood map for greater Adelaide. 93 6.11 Khapra beetle establishment likelihood map for greater Perth. 94 6.12 Khapra beetle establishment likelihood map for greater Darwin. 95 7.1 Adult brown marmorated stink bug (Halyomorpha halys).......... 96 7.2 Published brown marmorated stink bug (Halyomorpha halys) CLIMEX (Kriticos et al., 2017) and Maxent (Zhu et al., 2012) distribution models. 100 7.3 Brown marmorated stink bug (Halyomorpha halys) Random forest, Max- ent and Support Vector Machine distribution models published in Fraser et al. (2017)..................................... 101 7.4 Global climatic suitability of brown marmorated stink bug derived from range bagging. 104 7.5 Australian climatic suitability for brown marmorated stink bug derived from range bagging. 105 7.6 Distribution of suitable biotic environment for brown marmorated stink bug. ........................................ 108 7.7 Estimated environmental suitability for brown marmorated stink bug. 110 7.8 National establishment likelihood map for brown marmorated stink bug. 111 7.9 Brown marmorated stink bug establishment likelihood map for greater Cairns. ...................................... 112 7.10 Brown marmorated stink bug likelihood of establishment map for greater Brisbane. ..................................... 113 7.11 Brown marmorated stink bug establishment likelihood map for greater Sydney....................................... 114 7.12 Brown marmorated stink bug establishment likelihood map for greater Melbourne. .................................... 115 7.13 Brown marmorated stink bug establishment likelihood map for greater Hobart. ...................................... 116 7.14 Brown marmorated stink bug establishment likelihood map for greater Adelaide. ..................................... 117 7.15 Brown marmorated stink bug establishment likelihood map for greater Perth. ....................................... 118 7.16 Brown marmorated stink bug establishment likelihood map for greater Darwin. ...................................... 119 8.1 Female Asian gypsy moth (Lymantria dispar asiatica). 120 8.2 Log10 vessel pathway distance decay weights for gypsy moth. 122 8.3 Published gypsy moth CLIMEX (Paini et al., 2018) and GARP ensemble (Peterson et al., 2007) distribution models. 125 8.4 Global climatic suitability for gypsy moth derived from range bagging. 126 vi Camac et al.