Population Structure of Phytophthora ×alni on a Local Scale and Its Temporal Development

Within Phytophthora alni, an invasive pathogen of alders (Alnus spp.), three species have been identified. The most frequent and pathogenic species is P. ×alni. It has a variable intraspecific structure, with the dominance of the Pxa-1 genotype and the presence of dozens of rare genotypes (in most cases derived from Pxa-1). Its local populations are highly variable, and their population structure and development remain unknown. We compared two sets of strains isolated from identical sites during the epidemic (2005–2010) and post-epidemic (2020–2024) phases of the disease in the Vltava River basin (Czech Republic) and studied them using microsatellite marker analysis and fitness tests (sporangia production, growth, and virulence). We acquired 151 P. ×alni isolates of 23 multilocus genotypes. We found that during the post-epidemic phase, genetic diversity decreased, and the dominance and incidence of the Pxa-1 genotype increased. Only the dominant genotype (Pxa-1) was repeatedly isolated from the same sites, whereas the rare genotypes were replaced. During the post-epidemic phase, both the incidence of rare genotypes and the degree of their derivation from Pxa-1 decreased. The rare genotypes had lower fitness than Pxa-1 (the more changes there were, the worse the fitness was). These results allow us to hypothesize the evolution of local populations of P. ×alni in Europe, as the most pathogenic genotype, Pxa-1, will also prevail during the late phases of the disease and the risk of further damage to the surviving host populations will persist.