Fast-evolving RNA viruses are a leading cause of morbidity and mortality among human
and animal populations, contributing significantly to both global health and economic
burden. The advent and revolution of high-throughput sequencing has empowered
phylogenetic analyses with increasing amounts of temporally and spatially sampled
viral data. Moreover, the parallel advancement in molecular evolution and phylogenetic
methods has provided investigators with a unique opportunity to gain detailed
insight into the evolutionary and epidemiological dynamics of emerging viral pathogens.
Using state-of-the-art statistical approaches, this thesis addresses some of the important
but controversial questions in viral emergence. Chapter 2 introduces a new
framework to quantify and investigate reassortment events in influenza A viruses. By
developing a computationally efficient algorithm to calculate the largest common subtree
for a pair of tree sets, which are estimated from diffe rent parts of the genome for
the same taxa set, the level of phylogenetic incongruency due to reassortment can be
appropriately ascertained. Chapters 3, 4 and 5 investigate the evolutionary origins of
three diff erent viruses: the novel emergence and cross-species transmission of SARSCoV,
the genesis and dissemination of the unique HCV circulating recombinant form,
and the ancient divergence of all influenza viruses, respectively. Moreover, Chapter 4
presents an improved statistical framework, which provides more precise evolutionary
estimates, by utilizing the hierarchical bayes approach to investigate recombination
events in emerging RNA viruses. The last empirical study, presented in Chapter 6, applies
the recently developed Bayesian phylogeography models to a large viral sequence
dataset sampled from southern Viet Nam to examine the fine-scale spatiotemporal dynamics
of endemic dengue in Southeast Asia.
The work presented here reflects both the advancements made in sequencing technology
and statistical phylogenetics, along with some of the challenges that remain in
studying the emergence of fast-evolving RNA viruses. This thesis proposes new and
improved solutions to these evolutionary problems, such as incorporating non-vertical
evolution (i.e. homologous recombination and reassortment) into the phylodynamic
framework, with the aim of facilitating future investigations of emerging viral diseases