My dissertation spans two dichotomies: evolution in the laboratory versus evolution in nature, and asexual versus sexual evolutionary dynamics. In Chapter 1 I describe asexual evolutionary dynamics in one population of Lenski’s long-term evolution experiment with Escherichia coli. I describe cohorts of mutations that sweep to fixation together as characteristic of clonal interference dynamics. I also describe an ecological interaction that evolved and then went extinct after thousands of generations, and discuss how such interactions affect cohorts of mutations. In Chapter 2 I report that conserved core genes tend to be targets of selection in the long-term experiment. In Chapter 3, I investigate the surprising observation that synonymous genetic diversity is not uniform across the genomes of natural E. coli isolates. This observation is surprising because in clonal organisms with a constant point mutation rate, synonymous diversity should be constant across the genome. I use patterns of synonymous mutations in the long-term experiment to argue that genome-wide variation in the mutation rate does not adequately explain patterns of synonymous genetic diversity. In Chapter 4, I propose that recombination and gene flow could account for genome-wide variation in synonymous genetic diversity. In Chapter 5, I analyze E. coli genomes isolated from an evolution experiment with recombination in which E. coli K-12 with known growth defects could donate genetic material to recipient populations founded by long-term experiment clones. The degree of recombination varied dramatically across sequenced clones. The strongest predictor of successful transfer was proximity to the oriT origin of transfer in the K-12 donors. Donor alleles close to oriT replaced their recipient counterparts at a high rate, and in many of those cases, known beneficial mutations in the recipients were replaced by donor alleles.
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