Garrett KA, Thomas-Sharma S, Forbes GA, Hernandez Nopsa JF, Plex Sulá AI. 2023. Climate change and plant pathogen invasions. Chapter 3. In: Ziska L. Invasive species and global climate change, 2nd edition. CAB International: 22-49.
Alcalá-Briseño RI, Plex Sulá AI, Etherton BA, Andersen Onofre KF, Poudel R, Xing Y, Garrett KA. 2025. Adapting crop disease management to global change. Chapter in Vegetable Disease
Management. Invited, currently in review.
3 Manuscripts in Review
Plex Sulá AI, Batuman O, Cellier G, Dufault NS, Etherton BA, Hodges A, Lowe-Power TM, Paret M, Penca C, Schroeder K, Takeuchi Y, Stilian E, Suder P, Tonnang H, Wang Y, Garrett KA. An integrated risk assessment framework for proactive global surveillance of invasive pathogens and pests. In review, Science Advances. A copy is available at
Mouafo-Tchinda RA, Plex Sulá AI, Etherton BA, Okonya JS, Valentine Nakato GV, Xing Y, Robledo Buritica J, Adhikari A, Blomme G, Kantungeko D, Nduwayezu A, Kreuze J, Kroschel J, Legg J, Garrett KA. Pathogen and pest communities in agroecosystems across climate gradients: Anticipating future challenges in the highland tropics. Preprint available at DOI: 10.1101/2025.01.08.631994
Mouafo-Tchinda RA, Etherton BA, Plex Sulá AI, Andrade-Piedra J, Ogero K, Omondi BA, McEwan M, Tene Tayo PM, Harahagazme D, Cherinet M, Gebeyehu S, Sperling L. Garrett KA. 2024. Pathogen and pest risks to vegetatively propagated crops in humanitarian contexts: Geographic priorities for Cameroon and Ethiopia. Preprint available at DOI: 10.1101/2024.02.12.580019
8 research projects in progress
Plex Sulá AI, Sarwar MA, Ali S, Qureshi N, Saleem K, Singh PK, Garrett KA, Afzal Z. A nationwide assessment of major wheat diseases and pests in Pakistan. Target journal: Phytopathology. Preprint available at DOI: 10.31220/agriRxiv.2025.00366
📖 Abstract
Wheat production in Pakistan faces persistent threats from diseases and pests. However, limited geographic information exists on local risks, economic impacts, and management practices. We conducted an expert knowledge elicitation to provide the first integrated assessment of wheat health in Pakistan. Experts mapped yield losses for major diseases and pests at the district level. We analyzed networks of seed and grain exchange and stakeholder interactions. Analysis of wheat cropland connectivity identified locations that are likely to play important epidemiological roles. Cumulative yield losses estimated by experts ranged from 4% to 16%, with hotspots in central Punjab and northern Sindh. Stripe rust, leaf rust, and aphids remain top threats, with climate change and pathogen subpopulation structure identified as major determinants of yield losses. Experts indicated that national wheat networks have informal channels for seed and grain exchange, highlighting key pathways for potential spread of seedborne pathogens. Expert-characterized networks of stakeholders suggest that farmer associations and seed dealers are strategic points for both information sharing and seed health monitoring. Cropland connectivity analysis identified a highly connected wheat landscape along the Indus River, overlapping with national disease hotspots and facilitating pathogen proliferation. Pakistan has a moderate vulnerability to wheat blast introduction, yet climate change and informal seed movement could increase this potential. These findings provide farmers, researchers, and policymakers with actionable control points to enhance wheat health systems in Pakistan. This study established a rapid information baseline to support geographically targeted surveillance, coordinated seed system interventions, and epidemic preparedness planning.
Plex Sulá AI, Keshav K, Adhikari A, Choudhary M, Mouafo-Tchinda RA, Robledo Buritica J, Shah
S, Garrett KA. geohabnet: An R package for mapping habitat connectivity for biosecurity and conservation. Target journal: Methods in Ecology and Evolution. geohabnet is available in CRAN, GitHub, and its own webpage. Preprint available at DOI: 10.1101/2024.02.12.580019
📖 Abstract
Mapping habitat quality, in terms of factors like host availability and environmental suitability, is a common approach to determining which locations are important for the spread of a species. Mapping habitat connectivity takes geographic analyses a step further, evaluating the potential roles of locations in epidemics, invasions, or species conservation. Locations with high habitat quality may play a minor role in species spread if they are geographically isolated. Yet, a location with lower habitat quality may play a major role in a species’ spread if it acts as a bridge between regions that would otherwise be physically fragmented. Here we introduce the geohabnet R package, which evaluates the likely importance of locations for the spread of species through habitat landscapes. Unlike most software analyzing landscape connectivity, geohabnet incorporates key factors such as dispersal probability and habitat availability in a network framework. These factors are often needed to better understand habitat connectivity for host-dependent species like pathogens, arthropod pests, or pollinators. geohabnet uses publicly available or user-provided datasets, six network centrality metrics, and a user-selected geographic scale (global, national, or regional). We provide examples for the use of geohabnet for surveillance prioritization of emerging plant pathogens in Africa and the Americas. These examples illustrate how users can apply geohabnet for their species of interest and generate maps of the estimated importance of geographic locations during a species’ spread. geohabnet provides a quick, open-source, and reproducible baseline approach to quantify a species’ habitat connectivity across a wide range of geographic scales and evaluates potential scenarios for the expansion of a species through habitat landscapes. Ultimately, geohabnet could support biosecurity programs, invasion science, and conservation biology in prioritizing management efforts for transboundary pathogens and pests or endangered species.
Plex Sulá AI, Robledo Buritica J, Choudhary M, Garrett KA. Future scenarios for pest and disease management of major crops in California. Report pending approval by the California Department of Food and Agriculture (CDFA). Contact reference: Brianna McGuire (bmcguire@ucdavis.edu) A copy is available at
📖 Abstract
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Plex Sulá AI, Alcalá Briseño RI, Xing Y, Etherton BA, Andersen Onofre K, Andrade-Piedra JL,
Avelino J, Carvajal-Yepes M, Cuellar W, Dita Rodriguez MA, Gazis R, Hodson D, Jarvis A, Kenyon
L, Kreuze JF, Legg J, Mosquera Cifuentes GM, Sonder K, Mahabaleswara SL, Vallad G, Garrett KA. Proactive global biosecurity priorities for pest invasions on crop landscapes and trade networks. Target journal: Nature Communications. A copy is available at
📖 Abstract
An unresolved issue faced by the plant health community is where to prioritize proactive biosecurity responses globally. Here, we address this problem by identifying candidate priority locations for the potential spread of emerging pathogens and pests through global crop-species networks crucial to pursuing sustainability. Candidate global priorities posing high epidemic risks include locations usually having or connecting to croplands with large host populations, and countries with high imports or acting as trade intermediaries. Our simulations indicate that epidemics may expand more rapidly in countries with larger cropland networks. Trade networks exhibit different priority locations compared to those in cropland networks, underscoring the need for a multi-purpose strategy to mitigate these crop epidemic challenges worldwide. These network-based priorities are starting points for strengthening surveillance efforts in global and national preparedness strategies, especially when integrating additional geographic factors, such as climate suitability, genetic host vulnerability, and socioeconomic affordability.
Mouafo-Tchinda RA, Plex Sulá AI, Etherton B, Choudhury R, Gazis R, Crane J, Garrett KA. A global risk assessment and surveillance strategy for laurel wilt. Target journal: Nature Ecology and Evolution. A copy is available at
📖 Abstract
Globally, threats to forest ecosystem health from emerging infectious diseases are increasing. Quantitative assessments to guide spatially explicit disease surveillance in forests need to integrate multiple geographic risk factors, yet data and effective methods are often lacking for emerging plant diseases. There are many analyses of the future risk of plant disease under climate change, but here we incorporate the geographic distribution of host availability. We provide an approach to assessing the potential spread of plant pathogens through heterogeneous host landscapes and global trade networks, for both current and future climate scenarios, based on regional and continental epidemiology. As a pilot study, we applied this epidemiological approach to quantify the potential spread of laurel wilt, which affects many tree species in the Lauraceae, including devastating yield reductions in avocado. The global network of the movement of wood packing materials likely poses high risks for introducing the laurel wilt pathogen in new regions, unless effective international biosecurity practices are in place. In this global network, countries with laurel wilt (China, India, Japan, Myanmar, Taiwan, and the USA) are highly connected to 36 avocado-producing countries where the disease has not been reported. The spatial distribution of host species in the Lauraceae is also important to understanding potential spread of laurel wilt locally. Based on the reported distribution of 2271 Lauraceae species potentially susceptible to laurel wilt, host availability is particularly high for disease establishment in central and southern Mexico, northern Costa Rica, and the Colombian Andes. However, the main hotspot for disease spread is the Lauraceae-rich forests in Amazonia if the pathogen reaches them, based on the relative likelihood of pathogen dispersal between host locations. For current environmental conditions, two widely used machine learning models (Maxent and Random Forest) identify Bangladesh, central Bolivia, central Nepal, Japan, southern Brazil, southern Paraguay, and Uruguay as having very similar climate conditions to locations where laurel wilt is reported present. However, our projections indicate that the geographical regions with potentially suitable environments for laurel wilt establishment may expand toward the poles by 2100 under future climate scenarios. Together these findings identify locations that are candidate priorities for targeting proactive surveillance efforts and provide an essential component for building an early warning system for laurel wilt. More broadly, we propose this epidemiological approach, incorporating climate, host availability, and trade, as a key component to evaluate the potential spread of plant pathogens in other agroecosystems and to design geographically explicit surveillance strategies for plant diseases and pests.
Plex Sulá AI, Adhikari A, Arinaitwe W, Choudhary M, Choudhury RA, Delaquis E, Etherton BA,
Yubak Dhoj GC, Hamelin F, Jones C, McVay JD, Mouafo-Tchinda RA, Navarrete I, Robledo
Buritica J, Tankam I, With KA, Garrett KA. Nine principles for surveillance of pathogens and pests in regional landscapes: A primer on network perspectives. Target journal: Methods in Ecology and Evolution. A copy is available at
📖 Abstract
Given the increasing number of biological invasions globally, geographic surveillance is more crucial than ever to safeguard natural and agricultural systems. We provide nine guiding principles, most based on network science, for effective surveillance planning of invasive species. (1) The goal of surveillance determines the requirements of a surveillance plan. (2) The value of information gained from surveillance should justify the cost of the information. (3) A landscape of habitat can be represented as an invasion network, in which a target species spread. (4) Network analysis can identify candidate priority locations for surveillance across an invasion network. (5) Identifying nodes in each network cluster can streamline surveillance. (6) Identifying species introduction points reshapes geographic surveillance priorities. (7) A multistage process can improve surveillance plans based on new detections over time. (8) Iterative assessments of the performance of surveillance can improve current and future strategies. (9) Creative engagement can strengthen stakeholder networks for surveillance through collective action. These principles can help to boost the intuition of scientists responsible for rapid decision-making for surveillance and can be applied in computational scenario analyses to evaluate potential surveillance strategies.
Plex Sulá AI, Garrett KA. Pathogenica: A global data compilation of epidemiological traits of 1000+ pathogens. Target journal: Scientific Data. A piece of Pathogenica is available at the Garrett Lab.
📖 Abstract
Global pathogen bioinformatics is foundational for developing effective pandemic preparedness policies. Here, we present Pathogenica – a new global dataset that compiles five biogeographical aspects and ten epidemiological traits of 1,518 plant pathogens. Biogeographical information spans country-level distribution, within-country extent, georeferenced occurrences, climate regions occupied, and year of occurrence. Epidemiological traits include host species, cardinal temperatures, dispersal mechanisms, vector strategy, and key environmental factors. No comparable dataset was available for economically important plant pathogens. Pathogenica mobilizes disaggregated, digitally accessible sources accumulated over 190 years into a machine-readable reference database. Pathogenica will serve as a public good for global stakeholder communities addressing plant health challenges, from foundational research to biosecurity applications.
Plex Sulá AI, Adikari A, Wang Y, Goss E, Garrett KA. The global population genetic structure of Potato spindle tuber viroid in major agroecosystems. Target journal: Phytopathology. A copy is available at
📖 Abstract
Potato spindle tuber viroid (PSTVd) has been reported in 50 countries, with multiple introductions of the pathogen to new regions over the past two decades. PSTVd causes disease in potato and tomato and naturally infects more than 50 host species, yet we lack an assessment of whether there are major genetic groups in the global population of PSTVd. Using PSTVd genome resources in the NCBI database, this study evaluated the global population structure of PSTVd. We hypothesized that the observed structure of PSTVd populations will reflect either host or geographic sources. Our phylogenetic network analysis using the NeighborNet algorithm identified four major clusters of PSTVd populations. Group 1 included all sequences collected from potato and a few from tomato. Group 2 included PSTVd sequences from Cestrum spp. The other two groups had isolates from Atriplex, Capsicum, Nicandra (Group 3), Brugmansia, Petunia, and Streptosolen (Group 4). PSTVd samples from Solanum spp. were scattered in the phylogenetic network. A Discriminant Analysis of Principal Components (DAPC) identified three main genomic clusters of PSTVd representing distinct geographic regions. The three genomic clusters included isolates from Oceania and Africa (Cluster 1); Russia and Asia (Cluster 2); and Europe (Cluster 3). Isolates from the Americas were shared among the clusters. Understanding the global population structure of PSTVd is important for the design of genomic surveillance strategies for solanaceous food crop industries and ornamental markets.
