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Since its origins, thousands of years ago, agriculture has been challenged by the presence of evolving plant pathogens. Temporal rotations of host and non-host crops have helped farmers to control epidemics among other utilities, but further efforts for strategy assessment are needed. Here, we present a methodology for developing crop rotation strategies optimal for control of pathogens informed by numerical simulations of eco-evolutionary dynamics in one field. This approach can integrate agronomic criteria used in crop rotations—soil quality and cash yield—and the analysis of pathogen evolution in systems where hosts are artificially selected. Our analysis shows which rotation patterns perform better in maximising crop yield when an unspecified infection occurs, with yield being dependent on both soil quality and the strength of the epidemic. Importantly, the use of non-host crops, which both improve soil quality and control the epidemic results in similar rational rotation strategies for diverse agronomic and infection conditions. We test the repeatability of the best rotation patterns over multiple decades, an essential end-user goal. Our results provide sustainable strategies for optimal resource investment for increased food production and lead to further insights into the minimisation of pesticide use in a society demanding ever more efficient agriculture.

Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations