| With the increasing number of zoonotic infections that are rising today, examining the underlying reasons why only some pathogens are able to spread successfully in new host populations warrants further investigation. RNA viruses constitute the majority of these zoonotic infections largely due to their high mutational rates and population sizes. Why some RNA viruses are able to sustain transmission in new host populations is uncertain, but the adaptation of the virus to the host is likely to play a major role. The examination of genome-wide patterns of RNA viruses reveals the genetic diversity that may be needed for emergence. Comparing and contrasting the genomes of zoonotic or newly emerged viruses to monophyletic members within a viral family allows us to build a model of evolution, and to make predictions as to what genetic components are important for the adaptation of the virus to the new host population. The combination of phylogenetics and bioinformatics has the potential to reveal important evolutionary patterns in the emergence of RNA viruses.;This thesis examines the usefulness of phylogenetic and bioinformatic techniques in examining the molecular evolution of recently emerged RNA viruses. Different models of evolution were used to explore relatedness among viral sequences, rates of evolution, divergence times, as well as the role of recombination in the generation of genetic diversity within a viral family. Bioinformatic techniques were used to measure trends in base composition (G+C, G+U, G+A) and synonymous GC changes at the third codon position across genomes. Results from using these techniques are detailed, and discussions of important evolutionary trends are presented. Areas for future work are then outlined. |
