Tremendous diversity, both in terms of core genomes and effector repertoires, can be maintained in populations of the plant pathogen, Pseudomonas syringae. The labs of Joy Bergelson and Mercedes Pascual have come together to combine coevolutionary theory with empirical studies of plant – bacterial interactions to understand the eco-evolutionary forces maintaining this genetic variation. The team aims to develop theory to understand the contribution of microbes’ non-core genomic elements, particularly virulence factors that are secreted by pathogen isolates, to shaping the pattern of genomic diversity among pathogens strains. These non-core genetic elements are good candidates for driving eco-evolutionary dynamics because they sit at the frontline of the interaction between host and pathogen and are specific in terms of which plant genotypes elicit a response. Our theory reveals that shared positive effects of virulence effects (common goods) but specific negative effects associated with host recognition of virulence factors (specific bads) enhance the probability that mixtures of virulence effectors will coexist. Our empirical results demonstrate that the interactions between Arabidopsis thaliana and the virulence factors of P. syringae do, in fact, conform to this pattern. Analysis of the repertoires of virulence factors from P. syringae from both a metapopulation of Arabidopsis thaliana and from a global collection across crop species revealed two additional patterns. First, we find a strong pattern of modularity, consistent with selection in our model. Second, we find a strong phylogenetic signal, which was surprising given the observation of lateral gene transfer (LGT) among P. syringae strains. To better understand the maintenance of this phylogenetic signal, we have extended our model of negative frequency dependent selection to include LGT and mutational processes. While we are currently working to refine our estimate of recombination rate, we find that the modular structure we observe is relatively robust to LGT. These results are interesting in suggesting that NFDS, mediated through interactions between the host and its accessory genome, can maintain complex patterns of coexistence in this host-pathogen system.