This dissertation concerns the coevolution of pathogens and their hosts. For my thesis, I have worked with Escherichia coli and phage using experimental evolution, molecular biology, and theory that describes general host-pathogen interactions. This work centers on three themes of broad interest to evolutionary biology and microbiology: coevolutionary origins of novelty and diversity, the role of tradeoffs in constraining evolvability, and the ecological impacts of host resistance.In Chapter 1, I worked with a set of experimentally coevolved E. coli/ communities to investigate the bacterial genes that gained mutations and whether fitness tradeoffs had constrained the evolution of those mutations. To do this, I isolated bacteria from the coevolution experiment and sequenced the genomes of the isolates. I found resistance mutations that modified the expression or sequence of proteins used by during infection: LamB and OmpF at the outer membrane, and ManY and ManZ at the inner membrane. To test for fitness tradeoffs, I estimated the isolates’ fitness in the presence and absence of . Phage selection strongly favored resistance mutations, despite those mutations incurring pleiotropic costs related to resource acquisition and homeostasis.For my second chapter, I was particularly interested in the E. coli manY and manZ mutations that allowed phage to adsorb to the outside of the cell but limited the phage’s ability to eject its genome into the cytoplasm. I thought that these mutations might effectively “trap” phage in non-productive infections, thereby accelerating the rate of phage loss from the extracellular environment. However, I found no evidence for such traps; instead, had evolved independence of manY and manZ. These results indicate that for each of the known resistance-conferring mutations evolved by E. coli, the coevolving populations discovered evolutionary routes to circumvent the resistance. For Chapter 3, I shifted briefly from laboratory experiments to mathematical theory to further investigate the trap idea. Although it turned out that the manY and manZ mutations don’t act as traps, I was more generally interested in host defenses on the inside of the cell, such as CRISPR-Cas defense and restriction enzymes, which exist for many bacterial species. Comparable to other studies on parasite traps in animal hosts, I used theory to predict that in the presence of trap alleles, bacteriophage densities would be lower than they otherwise would be, even if more permissive hosts were available to them.In my final chapter, I returned to the coevolution experiment with E. coli and . Although it was known that laboratory populations of phage evolved to use OmpF, and that this function required multiple mutations in the phage J gene, it was unknown how those mutations accumulated. I studied how both phage J gene mutations and bacterial malT (a positive regulator of lamB) mutations influenced the phage’s adaptive landscape. I found that bacterial evolution strongly affected selection patterns on different phage genotypes: in many cases the evolution of host resistance more strongly favored increased phage adsorption rate. Because of that, the evolutionary intermediates between the ancestral and OmpF-infecting phage were positively selected, revealing that host coevolution can increase the rate at which phage evolve to use novel host structures.
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