Phylogenetic Approaches to Studying the Evolution, Ecology, and Epidemiology of Pathogens and Host-Associated Bacteria

Pathogen genomes preserve a record of their evolutionary past, allowing us to reconstruct their history and understand the processes that shape their emergence, adaptation, and spread. I will present several phylogenetic approaches that incorporate new, biologically realistic models to study pathogen evolution. Over deep evolutionary timescales, these analyses reveal previously unappreciated transitions from protist-associated bacteria to modern-day human pathogens, highlighting aquatic environments as a reservoir for emerging pathogens. At shallow timescales, I present new models to identify how substitution rates of viral genes vary, providing new insights into virus evolution. Extending these approaches to host-associated microbiomes, I introduce a method that accounts for evolutionary relationships among hosts and show how ignoring these relationships can bias biological interpretations. The above work is conducted in collaboration with Haiwei Luo, Andrew Meade, Mario dos Reis, among others.