Integration of community ecology with disease biology is viewed as a promising avenue for uncovering determinants of pathogen diversity, and for predicting disease risks. Plant-infecting viruses represent a vastly underestimated component of biodiversity with potentially important ecological and evolutionary roles. We performed hierarchal spatial analysis of wild plant populations to characterise the diversity and coexistence structure of within-host virus communities, and their predictors. Our results show that these virus communities are characterised by single infections of few, dominating virus taxa as well as diverse, non-random coinfections. Using a novel graphical modelling framework we demonstrate that after accounting for environmental heterogeneity at the level of both individual host plants and populations, most virus co-occurrence patterns can be attributed to virus-virus associations. Moreover, we show that conditioning variables changed virus association networks especially through their indirect effects. This highlights a previously underestimated mechanism of how human-driven environmental change can influence disease risks.

The trade-off between within-host infection load and transmission to new hosts is predicted to constrain pathogen evolution, and to maintain polymorphism in pathogen populations. The life-history stages and their correlations that underpin infection development may change under coinfection with other parasites as they compete for the same limited host resources. Cross-kingdom interactions are common among pathogens in both natural and cultivated systems yet their impact on disease ecology and evolution are rarely studied. Host plant Plantago lanceolata is naturally infected by both Phompopsis subordinaria, a seed killing fungus, as well as Plantago lanceolata latent virus (PlLV) in the Åland Islands, SW Finland. We performed an inoculation assay to test whether coinfection with PlLV affects performance of two P. subordinaria strains, and the correlation between within-host infection load and transmission potential. The strains differed in the measured life-history traits and their correlations. Moreover, we found that under virus coinfection, within-host infection load of P. subordinaria was lower but transmission potential was higher compared to strains under single infection. The negative correlation between within-host infection load and transmission potential detected under single infection became positive under coinfection with PlLV. In wild populations, within-host infection load was positively associated with within-population disease prevalence. Jointly, our results suggest that the trade-off between within-host infection load and transmission may be strain specific, and that the pathogen life-history that underpin epidemics may change depending on the diversity of infection, generating variation in disease dynamics.

Phenotypic plasticity can mask population genetic differentiation, reducing the predictability of trait-environment relationships. In short-lived plants, reproductive traits may be more genetically determined due to their direct impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with global field observations for the short-lived Plantago lanceolata, we 1) disentangled the genetic and plastic responses of functional traits to a set of environmental drivers and 2) assessed the utility of trait-environment relationshisps inferred from observational data for predicting genetic differentiation. Reproductive traits showed distinct genetic differentiation that was highly predictable from observational data, but only when correcting traits for differences in their (labile) biomass component. Vegetative traits showed higher plasticity and contrasting genetic and plastic responses, leading to unpredictable trait patterns. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related with fitness.

High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. Molecular processes associated with this variation in nature are still poorly known, although theory predicts resistance to evolve at specific loci driven by selection associated with the response to pathogen. Nucleotide-binding leucine-rich repeat (NLR) genes play an important role in pathogen recognition, downstream defense responses and defense signaling. Identifying the natural variation in NLRs has the potential to increase our understanding of how NLR diversity is generated and maintained, and how to manage disease resistance. Here, we sequenced the transcriptomes of five different Plantago lanceolata genotypes when inoculated by the same strain of obligate fungal pathogen Podosphaera plantaginis. A de novo transcriptome assembly of RNA-sequencing data yielded 24,332 gene models with N50 value of 1,329 base pairs and gene space completeness of 66.5%, suggesting a high-quality assembly. The gene expression data showed highly varying responses where each plant genotype demonstrated a unique expression profile in response to the pathogen, regardless of the resistance phenotype. Analysis on the conserved NB-ARC domain demonstrated a diverse NLR repertoire in P. lanceolata consistent with the high phenotypic resistance diversity in this species. We find evidence of selection generating diversity at some of the NLR loci. Jointly, our results demonstrate that phenotypic resistance diversity results from a crosstalk between different defense mechanisms. In conclusion, characterizing the architecture of resistance in natural host populations may shed unprecedented light on the potential of evolution to generate variation.

High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. To date, the molecular processes associated with this variation in nature are poorly known, although theory predicts resistance to evolve at specific loci in response to pathogen -imposed selection. Nucleotide-binding leucine-rich repeat (NLR) genes play an important role in pathogen recognition, downstream defense responses and defense signaling. Exploring the depth of NLR natural variation has the potential to increase our understanding of how NLR diversity is generated and maintained, and how to manage disease resistance. Here, we sequenced the transcriptomes of five different Plantago lanceolata genotypes in response to inoculation by the same strain of obligate fungal pathogen Podosphaera plantaginis. A de novo transcriptome assembly of RNA-sequencing data yielded 24332 gene models with N50 value of 1329 base pairs and gene space completeness of 66.5%, suggesting a high-quality assembly. The gene expression data showed highly varying responses, with each plant genotype having a unique gene expression profile in response to the pathogen, regardless of the resulting resistance phenotype. We discovered a diverse NLR repertoire in P. lanceolata which is consistent with high phenotypic resistance diversity and high genetic diversity of the species. We find evidence of selection generating diversity at some of the NLR loci. Jointly, our results demonstrate that phenotypic resistance diversity results from a crosstalk between different defense mechanisms. In conclusion, characterizing the architecture of resistance in natural host populations may shed unprecedented light on the potential of evolution to generate variation.