Strains within pathogen populations compete for hosts through the cross-protection conferred by cross-immunity, in a frequency-dependent manner akin to stabilizing niche differences in ecological systems. Strain theory and phylodynamics have been increasingly used to explore the joint evolutionary and competitive dynamics, and the resulting patterns of genetic and antigenic diversity, within pathogen populations. The macroscopic empirical patterns that emerge in pathogen genealogies and in the structure of antigenic diversity for coexisting strains contain information on the underlying processes that permit coexistence of diverse assemblages. Theory relying on individual-based, stochastic models for the population dynamics of evolving pathogens allows us to address this relationship between pattern and process, as a basis for inference.
Results/Conclusions
This talk introduces the symposium with an ecological perspective on phylodynamics and strain theory that explicitly draws parallels to concepts and questions in community ecology. Using a general transmission model motivated by influenza where pathogens are represented as repertoires of antigenic traits, I illustrate how the rates of evolution and competition determine different dynamical regimes of replacement vs. coexistence. I focus then on pathogens that evolve via recombination/reassortment, two powerful mechanisms that potentially oppose the formation of strain structure. I will use empirical results from studies of rotavirus and Plasmodium falciparum that demonstrate (antigenic) strain structures with limited overlap, in patterns essentially synonymous with niches in host immune space. The potential implications of these patterns for epidemiology will be discussed, together with limitations on inferring underlying processes that motivate following presentations.