The genomics of adaptation to mutational degradation in hypermutator Pseudomonas aeruginosa

Genetic diversity is generated and maintained even in the simplest of environments. Because interactions between pairs of mutations are incredibly common, genetic diversity may interact with incoming beneficial mutations and alter the evolutionary paths that are available to different genotypes. In this thesis I have explored how divergent genotypes respond to evolutionary forces like drift and selection with a particular focus on the initial fitness of these genotypes. In order to generate genetically divergent starting populations, in Chapter 1 I performed a mutation accumulation (MA) experiment using a hypermutator strain of Pseudomonas aeruginosa. This allowed me to characterize the rate and effect of spontaneous mutations in this system, and I found that fitness is strongly influenced by rare mutations of large effect. In Chapter 2 I evolved several replicates of each of these genetically divergent lines under laboratory conditions and sequenced their genomes to determine the genetic mechanisms underpinning adaptation to mutational degradation. Interestingly, acquiring general laboratory adaptation mutations was more important than specifically compensating for the mutations that occurred during MA. Furthermore, fitness of anMA line prior to recovery played a large role in determining the ruggedness of the adaptive landscape experienced by evolving populations. Given the importance of initial fitness in evolution that I observed in Chapter 2, in Chapter 3 I directly tested whether the initial fitness of a strain could influence the fitness effect of incoming mutations in the context of antibiotic resistance evolution. Adaptation to a novel environment could decrease the cost of antibiotic resistance, but there was no systematic relationship between initial fitness and cost. Taken together, my work has contributed to our understanding of how the fitness of a genotype and the nature of incoming mutations (i.e. beneficial or deleterious) interact to influence the outcome of evolution.