Molecular Evolution and Population Genetics of Infectious Diseases

The rapid emergence and spread of infections and the rapid evolution of established pathogens affect our ability to monitor and control disease. Continually, we are reminded of the challenges of controlling disease, not only of pathogens affecting human health, but also those indirectly affecting human activities such as food production. Phylogenetic coalescent methods are conventionally used to infer evolutionary relationships and processes from patterns of homologous characters including genomic data. Viral and bacterial pathogens are especially fit for such inferences, as opposed to in phylogenetic systematics, due to their short generation times, large population sizes, and high substitution rates. These traits enable us to observe changes at the genomic level that are causally linked or correlated to ecological and evolutionary processes. Traditionally, phylogenetic methods, typically used by systematists, have been co-opted and applied to human-related pathogens of health importance; however, little has been done regarding pathogens that affect food production and/or public safety. This work aimed to review the breadth of phylogenetic applications to microorganisms, particularly viruses; and to apply these methods to questions about molecular evolution and population genetics of non-model microorganisms that impair food production.;The first section reviews phylogenetic approaches applied to the study of the model organism Human Immunodeficiency Virus (HIV). I review applications to viral origin, global dispersal, and population genetics of within- and among-host infections.;The second section deals with relative performance of multi locus sequence typing (MLST) in molecular epidemiology, and whether different molecular survey approaches, namely MLST, single nucleotide polymorphisms, and/or genomes yield comparable inferences regarding origin and dispersal of select agents.;Lastly, the third section shows two case studies: a disease outbreak investigation of Infectious Salmon Anemia Virus (ISAV) in Chile with negative consequences to salmon farming, and a Lactococcus phage investigation to understand transmission between affected cheese factories in Australia. In aggregate, this body of work demonstrates the challenges and benefits of using phylogenetic methods to study the evolution of infectious diseases.