Epidemiology is the science of how disease develops in populations, in the context here in plant populations. It is a subdiscipline within plant pathology, and is concerned with the study of temporal and spatial changes that occur during epidemics caused by populations of pathogens in populations of plants. Epidemiology has developed and matured since the mid-20th century, and it has influenced and been influenced by developments in plant pathology more generally. There was an early phenomenological emphasis on temporal disease progress curves, the dynamic pattern of how an epidemic develops, and how these could be used to compare epidemics, both qualitatively and quantitatively. Techniques for the quantification of disease progression had been worked out and were extended further over the next three decades. Much of the work during this period was directed at epidemics of fungal foliar pathogens; procedures were subsequently explored for a range of other aspects, including plant virus epidemics, the linking of spatial and temporal aspects in an overall assessment of epidemic progress, disease management practices, soil-borne diseases, biological control, crop loss, disease resistance, and disease in mixed-species populations. Throughout, broader aspects of global food production and access to food have been a main concern of epidemiology—aspects with profound ecological underpinnings to which plant disease epidemiology has made an important contribution. Additionally, epidemiology is concerned with disease affecting nonfood crops, forage, forestry, grasslands, and the associated native plant communities where an ecological perspective is essential. A deliberate attempt is made in this bibliography to be inclusive about a broad range of research areas that typify the multidisciplinary nature of epidemiology. We review the current state of plant disease epidemiology, concentrating in particular on original research published since the early 21st century that is illustrative of new developments in the discipline.
Historical Developments: Epidemiology as a Subdiscipline within Plant Pathology
The year 1963 was seminal for plant pathology. Initial discussions at the First International Symposium in Soil-Borne Plant Pathogens, held in Berkeley, California, that year, led directly to a proposal at the 10th International Botanical Congress in Edinburgh in 1964 that there should be an International Congress of Plant Pathology. The First International Congress of Plant Pathology duly took place in London in the summer of 1968. The next International Congress of Plant Pathology (the 11th) will be held in Boston in 2018, fifty years after the first. The year 1963 also saw the publication of Plant Diseases: Epidemics and Control (Van der Plank 1963, following the author’s chapter in Horsfall and Dimond 1960), the first book devoted to the discipline. It was also the year of an International Plant Disease Epidemiology Workshop held in Pau, France, as a specialized Working Group of the Third International Biometeorological Congress. A second workshop under the auspices of a NATO Advanced Study Institute was held in Wageningen, The Netherlands in 1971. There was then some time before the next workshop, held at Pennsylvania State University in 1979 (Pennypacker and Madden 1980), followed by regularly held international workshops (under the auspices of the International Society of Plant Pathologists since 1984). Presentations at the last three workshops have been published, either as keynote papers (Savary and Cooke 2006) or as conference proceedings (Gadoury, et al. 2009; Ma 2013). The last workshop, the 11th, was held in Beijing in 2013, fifty years after the first. The workshops have made important contributions to the dialogue among plant disease epidemiologists, led to international collaborations, and contributed significantly to the development of epidemiology within plant pathology. Thus, the emergence of plant disease epidemiology as a discipline within plant pathology was associated initially with international congresses with broader terms of reference and scope, botany and biometeorology, and with recognition of the key role of plant pathology in agriculture, horticulture, and forestry. The association of plant disease epidemiology with ecology is a more recent development that is receiving increasing emphasis. The development of plant disease epidemiology throughout this period is covered in the comprehensive text Madden, et al. 2007. A short contribution on plant disease epidemiology is included in the online Encyclopaedia of Life Sciences (Jeger 2009) published by Wiley. Two more recent texts have been published on related areas: the application of information theory (Hughes 2012), and the population biology of plant pathogens (Milgroom 2015).
Gadoury, D. M., R. C. Seem, M. M. Moyer, and W. E. Fry, eds. 2009. Proceedings of the 10th International Epidemiology Workshop. Geneva, NY: New York State Agricultural Experiment Station.
These proceedings contain seventy-three extended summaries covering the presentations made at the workshop. Topic covered include perspectives on the future of epidemiology, population biology, weather and epidemics, quantitative epidemiology, spatiotemporal analysis, new technologies, disease management and monitoring, models, sampling, and dealing with an anticipated data overload.
Horsfall, J. G., and A. E. Dimond, eds. 1960. Plant pathology: An advanced treatise. Vol. 3, The diseased population. New York: Academic Press.
This volume is dedicated to disease in populations, with chapters by many of the pioneers who laid the foundations for modern epidemiology.
Hughes, G. 2012. Application of information theory to epidemiology. St. Paul, MN: American Phytopathological Society.
This book describes new tools in diagnostic decision making by bringing together applications of information theory, developed largely in the clinical (medical and veterinary) arenas, and illustrates their relevance for plant disease epidemiology and plant pathology more generally.
Jeger, M. J. 2009. Epidemiology of plant disease. In Encyclopaedia of life sciences. Chichester, UK: John Wiley.
This mini-review introduced the basic concepts of plant disease epidemiology and the practical applications of the discipline. A tool-kit for analysis of epidemics is described, and where additions to this tool-kit are required as the discipline matures and extends its range of applications. Available online by subscription.
Ma, Z., ed. 2013. Proceedings of the 11th International Epidemiological Workshop, 22–25 August 2013. Beijing: China Agricultural Univ.
These proceedings contain sixty-three extended summaries covering topics such as multiple pathosystems, disease decision support systems, statistical methods, network analysis and game theory, and the link between theoretical and molecular-based approaches in epidemiology.
Madden, L. V., G. Hughes, and F. van den Bosch. 2007. The study of plant disease epidemics. St. Paul, MN: American Phytopathological Society.
This book introduces the essential features of plant disease epidemiology. Great emphasis is placed on how to utilize and interpret epidemiological data obtained from field studies. Models, both statistical and mathematical, are considered essential tools in describing and understanding epidemics, and the book provides an organized exposition for the plant pathology reader.
Milgroom, M. G. 2015. Population biology of plant pathogens: Genetics, ecology and evolution. St. Paul, MN: American Phytopathological Society.
This comprehensive book on population biology, the first such book for twenty-five years, explains how population genetics are applied in plant pathology. It provides a conceptual framework covering genetics, ecology, and evolution of plant pathogens across all taxa, and illustrates applications in epidemiology.
Pennypacker, S. P., and L. V. Madden, eds. 1980. Special issue: Epidemiology. Protection Ecology 2:157–158.
This special issue contains seventeen full papers presented at the Epidemiology Workshop held at The Pennsylvania State University in 1979. The journal has since ceased publication, being subsumed by the Agriculture, Ecosystems and Environment journal.
Savary, S., and B. M. Cooke, eds. 2006. Plant disease epidemiology: Facing challenges of the 21st century. Dordrecht, The Netherlands: Springer.
This book, reprinted from a special issue of the European Journal of Plant Pathology (Vol. 115.1), contains nine chapters based on keynote presentations made at the 9th International Epidemiology Workshop held in Landernau, France, in 2005.
Van der Plank, J. E. 1963. Plant diseases: Epidemics and control. New York: Academic Press.
J. E. Van der Plank collated a systematic approach to analyzing epidemic data by defining calculation tools that could be used to characterize temporal disease progress and to evaluate disease control options. The techniques developed continue to be used, although a disconnect remains with similar tools developed in human and animal epidemiology; when applied to host plant resistance, the conceptual framework proposed remains controversial.
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- Accounting for Ecological Capital
- Allocation of Reproductive Resources in Plants
- Animals, Functional Morphology of
- Animals, Reproductive Allocation in
- Animals, Thermoregulation in
- Antarctic Environments and Ecology
- Applied Ecology
- Aquatic Conservation
- Aquatic Nutrient Cycling
- Archaea, Ecology of
- Assembly Models
- Bacterial Diversity in Freshwater
- Benthic Ecology
- Biodiversity and Ecosystem Functioning
- Biodiversity Patterns in Agricultural Systms
- Biological Chaos and Complex Dynamics
- Biome, Alpine
- Biome, Boreal
- Biome, Desert
- Biome, Grassland
- Biome, Savanna
- Biome, Tundra
- Biomes, African
- Biomes, East Asian
- Biomes, Mountain
- Biomes, North American
- Biomes, South Asian
- Bryophyte Ecology
- Butterfly Ecology
- Carson, Rachel
- Chemical Ecology
- Classification Analysis
- Coastal Dune Habitats
- Communities and Ecosystems, Indirect Effects in
- Communities, Top-Down and Bottom-Up Regulation of
- Community Concept, The
- Community Ecology
- Community Genetics
- Community Phenology
- Competition and Coexistence in Animal Communities
- Competition in Plant Communities
- Complexity Theory
- Conservation Biology
- Conservation Genetics
- Coral Reefs
- Darwin, Charles
- Dead Wood in Forest Ecosystems
- De-Glaciation, Ecology of
- Disease Ecology
- Drought as a Disturbance in Forests
- Early Explorers, The
- Earth’s Climate, The
- Eco-Evolutionary Dynamics
- Ecological Dynamics in Fragmented Landscapes
- Ecological Informatics
- Ecological Relevance of Speciation
- Ecology, Microbial (Community)
- Ecology of Emerging Zoonotic Viruses
- Ecosystem Engineers
- Ecosystem Multifunctionality
- Ecosystem Services
- Ecosystem Services, Conservation of
- Elton, Charles
- Endophytes, Fungal
- Energy Flow
- Environments, Extreme
- Ethics, Ecological
- Facilitation and the Organization of Communities
- Fern and Lycophyte Ecology
- Fire Ecology
- Food Webs
- Foraging Behavior, Implications of
- Foraging, Optimal
- Forests, Temperate Coniferous
- Forests, Temperate Deciduous
- Freshwater Invertebrate Ecology
- Genetic Considerations in Plant Ecological Restoration
- Genomics, Ecological
- Geographic Range
- Gleason, Henry
- Greig-Smith, Peter
- Gymnosperm Ecology
- Habitat Selection
- Harper, John L.
- Heavy Metal Tolerance
- Himalaya, Ecology of the
- Host-Parasitoid Interactions
- Human Ecology
- Human Ecology of the Andes
- Hutchinson, G. Evelyn
- Indigenous Ecologies
- Industrial Ecology
- Insect Ecology, Terrestrial
- Introductory Sources
- Invasive Species
- Island Biogeography Theory
- Island Biology
- Kin Selection
- Landscape Dynamics
- Landscape Ecology
- Laws, Ecological
- Legume-Rhizobium Symbiosis, The
- Leopold, Aldo
- Lichen Ecology
- Life History
- Literature, Ecology and
- MacArthur, Robert H.
- Mangrove Zone Ecology
- Marine Fisheries Management
- Mathematical Ecology
- Mating Systems
- Maximum Sustainable Yield
- Metabolic Scaling Theory
- Metacommunity Dynamics
- Metapopulations and Spatial Population Processes
- Microclimate Ecology
- Mutualisms and Symbioses
- Mycorrhizal Ecology
- Natural History Tradition, The
- Networks, Ecological
- Niche Versus Neutral Models of Community Organization
- Nutrient Foraging in Plants
- Odum, Eugene and Howard
- Old Fields
- Ordination Analysis
- Organic Agriculture, Ecology of
- Parental Care, Evolution of
- Patch Dynamics
- Phenotypic Selection
- Philosophy, Ecological
- Phylogenetics and Comparative Methods
- Physiological Ecology of Nutrient Acquisition in Animals
- Physiological Ecology of Photosynthesis
- Physiological Ecology of Water Balance in Terrestrial Anim...
- Plant Disease Epidemiology
- Plant Ecological Responses to Extreme Climatic Events
- Plant-Insect Interactions
- Polar Regions
- Pollination Ecology
- Population Dynamics, Density-Dependence and Single-Species
- Population Dynamics, Methods in
- Population Ecology, Animal
- Population Ecology, Plant
- Population Fluctuations and Cycles
- Population Genetics
- Population Viability Analysis
- Populations and Communities, Dynamics of Age- and Stage-St...
- Predation and Community Organization
- Predator-Prey Interactions
- Reductionism Versus Holism
- Religion and Ecology
- Remote Sensing
- Restoration Ecology
- Ricketts, Edward Flanders Robb
- Seed Ecology
- Serpentine Soils
- Shelford, Victor
- Simulation Modeling
- Soil Biogeochemistry
- Soil Ecology
- Spatial Pattern Analysis
- Spatial Patterns of Species Biodiversity in Terrestrial En...
- Species Extinctions
- Species Responses to Climate Change
- Species-Area Relationships
- Stability and Ecosystem Resilience, A Below-Ground Perspec...
- Stoichiometry, Ecological
- Stream Ecology
- Systems Ecology
- Tansley, Sir Arthur
- Terrestrial Nitrogen Cycle
- Terrestrial Resource Limitation
- Thermal Ecology of Animals
- Tragedy of the Commons
- Trophic Levels
- Vegetation Classification
- Vegetation Mapping
- Weed Ecology
- Whittaker, Robert H.
- Wildlife Ecology