Table 3. Novel hypotheses to be tested concerning the impact of substrates other than host plants on the evolutionary potential of plant pathogens.

Evolutionary Forcea	Novel Hypothesis Arising from Expanded Paradigms about the Evolution of Plant Pathogenicity Concerning:
Mutation	Modifications of the genome.
	Relative to its association with cultivated plant hosts, association of the pathogen with a given nonagricultural substrate leads to:
	• a significantly greater overall mutation rate.
	• a greater rate of transposition of insertion sequences or of transposable elements.
	• more frequent mutations or transpositions that target genes involved in pathogenicity.
	• a higher probability of acquisition of alien nucleic acids.
	• genetic exchange with more phylogenetically diverse microbes.
Genetic drift	Effective population size.
	The effective sub-population size of a pathogen associated with a given nonagricultural (or nonplant) substrate is significantly different from that for sub-populations from cultivated host plants. This could lead to genetic and/or phenotypic differentiation of sub-populations based on substrate of origin.
Gene flow	Dissemination.
	The habitats occupied by the plant pathogen influence the mode(s) of dissemination, thereby influencing the distance of dissemination and the spatial and temporal scales of gene flow.
Mode of reproduction (recombination)	Genetic recombination.
	The frequency of recombination (via sexual cycle or other means) varies among strains of plant pathogens as a function of the habitat or substrate.
Selection	Selective pressures and impact on fitness.
	Strains of pathogens adapted to a broad range of habitats have the greatest parasitic fitness.

^aThe evolutionary forces listed here are those that have been considered for plant pathogens in agricultural contexts [56]. These hypotheses concern pathogens with a marked saprophytic phase or for which nonagricultural or nonplant substrates can be a notable reservoir for survival. Reservoirs can include irrigation water, natural waterways and bodies of water, biological vectors (animals, fungi, etc.), abiotic vectors (aerosols, clouds, precipitation), wild plants and weeds, soil, and physical structures in agricultural systems (greenhouse materials, tubing, plastics).