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Strain diversity and spatial distribution are linked to epidemic dynamics in host populations

Citation

Eck, Jenalle et al. (2021), Strain diversity and spatial distribution are linked to epidemic dynamics in host populations, Dryad, Dataset, https://doi.org/10.5061/dryad.rjdfn2z94

Abstract

The inherently variable nature of epidemics renders predictions of when and where infection is expected to occur challenging. Differences in pathogen strain composition, diversity, fitness, and spatial distribution are generally ignored in epidemiological modeling and are rarely studied in natural populations, yet they may be important drivers of epidemic trajectories. To examine how these factors are linked to epidemics in natural host populations, we collected epidemiological and genetic data from fifteen populations of the powdery mildew fungus, Podosphaera plantaginis, on Plantago lanceolata in the Åland Islands, Finland. In each population, we tracked spatiotemporal disease progression throughout one epidemic season and coupled our survey of infection with intensive field sampling of the pathogen. We found that strain composition varied greatly among populations in the landscape. Within populations, strain composition was driven by the sequence of strain activity: early-active strains reached higher abundances, leading to consistent strain compositions over time. Co-occurring strains also varied in their contribution to the growth of the local epidemic, and these fitness inequalities were linked to epidemic dynamics: a higher proportion of hosts became infected in populations containing strains that were more similar in fitness. Epidemic trajectories in the populations were also linked to strain diversity and to spatial dynamics: higher infection rates occurred in populations containing higher strain diversity, while spatially-clustered epidemics experienced lower infection rates. Together, our results suggest that spatial and/or temporal variation in strain composition, diversity, and fitness of pathogen populations are important factors generating variation in epidemiological trajectories among infected host populations.

Methods

We collected epidemiological and genetic data from fifteen populations of the powdery mildew fungus, Podosphaera plantaginis, on Plantago lanceolata in the Åland Islands, Finland. In each population, we tracked spatiotemporal disease progression throughout one epidemic season and coupled our survey of infection with intensive field sampling of the pathogen. Pathogen samples were assigned multi-locus genotypes ("strains") using a SNP panel.

Usage Notes

Please see the README file associated with this dataset for descriptions of the variables and values.

Funding

Academy of Finland, Award: 296686

European Research Council, Award: Starting Grant PATHEVOL 281517

European Research Council, Award: Consolidator Grant RESISTANCE 724508