A polyetic modelling framework for plant disease emergence

Plant disease emergences have dramatically increased recently as a result of global changes, especially with respect to trade, host genetic uniformity, and climate change. A better understanding of the conditions and processes determining epidemic outbreaks caused by the emergence of a new pathogen, or pathogen strain, is needed to develop strategies and inform decisions to manage emerging diseases. A polyetic process-based model is developed to analyse conditions of disease emergence. This model simulates polycyclic epidemics during successive growing seasons, the yield losses they cause, and the pathogen survival between growing seasons. This framework considers an immigrant strain coming into a system where a resident strain is already established. Outcomes are formulated in terms of probability of emergence, time to emergence, and yield loss, resulting from deterministic and stochastic simulations. An analytical solution to determine a threshold for emergence is also derived. Analyses focus on the effects of two fitness parameters on emergence: the relative rate of reproduction (speed of epidemics), and the relative rate of mortality (decay of population between seasons). Analyses revealed that stochasticity is a critical feature of disease emergence. The simulations suggests that: (1) emergence may require a series of independent immigration events before a successful invasion takes place; (2) an explosion in the population size of the new pathogen (or strain) may be preceded by many successive growing seasons of cryptic presence following an immigration event, and; (3) survival between growing seasons is as important as reproduction during the growing season in determining disease emergence