Inferring Epidemiological Dynamics from Phylogenetic Trees

Synopsis

Viruses evolve as they spread, accumulating genetic differences throughout their genomes as they are transmitted from host to host.  The field of phylodynamics aims to infer the dynamics of an infectious disease from the evolutionary history of viruses (graphically represented as a phylogenetic tree).  Here I provide an introduction to the field of phylodynamics, presenting a general phylodynamic model incorporating a wide range of existing approaches based on birth-death stochastic processes.  I then use this general model to identify and characterize the limitations to this approach that arise from the un-identifiability of dynamical parameters.  I conclude by proposing a way forward, a shift from phylodynamics to ``phylomechanics’’ which combines traditional and genomic epidemiological models with the goal of inferring the mechanism of disease spread from evolutionary patterns.