Community ecologists and disease ecologists have been asking very similar questions at different levels of organization on the dominant processes underlying the coexistence of diverse assemblages, whether composed of species in a rainforest or strains in an infectious agent. In particular, the search for signatures that would identify non-neutral processes of coexistence has led to an increased interest in macroscopic patterns at the interface of ecology and evolution, in areas such as ‘strain theory’ and ‘phylodynamics’ for pathogens and ‘community phylogenetics’ for free-living species and microbes. These processes include in particular niche partitioning from competitive interactions, and niche formation by evolution of traits underlying competition. Signatures of patterns that can be used to identify them, vs. pure neutrality resulting from the demographic forces of stochastic extinction and colonization, have remained for the most part elusive. Besides their long conceptual history in ecology, questions on the dominant forces that structure and maintain diversity (also as a function of spatial scale) are fundamental to the dynamical consequences of this structure for responses to perturbations, such as species losses in ecosystems and intervention measures in epidemiology. Theory on the structure, maintenance and dynamical consequences of diversity has developed for the most part independently in disease ecology and community ecology. This symposium explores the conceptual and methodological connections across these systems, to ask what can be learned from the other side of the aisle. Our central goal is to identify novel signatures of niche diversification and coexistence in phylogenetic structure and present-day distributions of traits among organisms. In answering this question, we see the opportunity for cross-fertilization of the major paradigms in these two fields.