Date of Award

Spring 2022

Project Type


Program or Major

Molecular and Evolutionary Systems Biology

Degree Name

Doctor of Philosophy

First Advisor

Cheryl P Andam

Second Advisor

David Plachetzki

Third Advisor

W Kelley Thomas


Genetic recombination is a major driving evolutionary force across the Tree of Life, but it plays a special role in bacteria. In the absence of sexual reproduction, bacteria rely on horizontal transmission to recombine their genetic material. Horizontally transferred genes can spread rapidly across a population, greatly expanding the niches available to bacteria. We are only beginning to understand the degree to which recombination varies between and even within bacterial taxa. In the first part of this dissertation (Chapter 1 and Chapter 2), I investigate how patterns of recombination influence bacterial diversity. In Chapter 1, I studied the pan-genome of Cronobacter sakazakii, an emerging neonatal pathogen. I identified a suite of frequently recombined genes that may contribute to the success of C. sakazakii as a pathogen, with many of these genes playing roles in virulence, antibiotic resistance, and niche-specific adaptation. In Chapter 2, I compare the pan-genomes of Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis, three opportunistic pathogens. Although all three species exhibit recombination, I identified differences among them in the quantity of recombined genes, the clinical relevance of these genes, and the mobile genetic elements used in their spread. The second part of this dissertation (Chapter 3) covers how recombination affects cooperation within bacterial populations. While cooperation is widespread among bacteria, it can quickly degrade in the absence of a way to enforce it. I propose the recombination can function as an enforcement mechanism for cooperation, that increased cooperation can also lead to conditions favorable to recombination, and that recombination itself is an altruistic activity. Overall, this dissertation covers the many ways genetic recombination can affect the evolutionary dynamics of bacterial populations, from promoting genome diversity and adaptation in pathogens to enforcing uniformity in cooperative local populations.