Plant pathogens specialise to the infection of distinct hosts. Host specialisation involves changes in sequence composition and gene regulation that allow the pathogen to overcome host defences.

Genome data provides a rich resource to identify rapidly evolving genes or regulatory sequences with a role in host infection. These may be identified as regions exhibiting signatures of positive (arms race) or balancing (trench-warfare) selection.

Evolutionary analyses that include both polymorphism and divergence data can be used to disentangle the type of selection acting along the genome.

Plant pathogens can have complex life cycles and theoretical developments are necessary to improve our power to detect selection and understand pathogen evolution.

Identifying traits involved in plant–pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant–pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant–pathogen ecology and adaptive evolution.

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