The cornerstone of the phylodynamic approach is revealing link between epidemiological scale dynamics, such as patterns of disease incidence, and phylogenetic scale dynamics as manifest in the structure of phylogenetic trees. Marrying these two scales can provide profound insights into infectious disease epidemiology. To understand the potential impact of emerging diseases on human and animal populations we aim to provide a quantitative understanding of the processes that determine the phylodynamic patterns of a wide range of viral infections. We are particularly interested in those viruses that pose a threat to health of the Australian population (such as dengue) or Australian animal species. For example, how does the remarkable range of habitats and animal species in Australia shape patterns of disease transmission? We also aim to integrate evolutionary and epidemiological dynamics at the intra- and inter-host scales.