Population genetics of bacterial adaptation: Experiments with Escherichia coli and a simulation model.

摘要

This dissertation presents empirical examples of the population genetics of adaptation in microbial populations. Three of the four chapters of this dissertation deal directly with the long-term evolution experiment with E. coli. The long-term experiment is twelve initially identical populations that are allowed to evolve in identical environments. This classic study in evolution sketches the entire process of evolution, including the origin, fate and later consequences of variation that arises. As important as its elegance is the longevity of the long-term experiment, both in the number of generations and the time devoted to its study. It is this accumulated understanding that has allowed novel discoveries to come to light, including those in this dissertation.;Chapter 1 uses four previously identified candidate beneficial mutations in one population to search for parallel genetic evolution in the remaining populations. Parallel evolution is seen at the level of locus, and less frequently at the level of nucleotide. Furthermore, different loci differ in the degree of parallelism they display. Four independent tests, based on population genetics theory, show that this parallel molecular evolution was driven by natural selection.;Chapter 2 uses a computer simulation model of large asexual populations to investigate the population dynamics of adaptation. This model was used to quantify the number of beneficial mutation that arise in asexual populations, the frequencies they reach, and the phylogenetic structure among them. Three patterns emerged. First, multiple independent beneficial mutations arise and compete with each other. Second, when multiple lineages arise and coexist, each may pick up several mutations before one eventually prevails. Third, as these coexisting lineages each pick up beneficial mutations, mean fitness tends to increase in a step-like manner even without allelic fixation events. Finally, a hypothesis for indirect selection for evolvability is proposed and shown to work with simulations.;Chapter 3 returns to the long-term E. coli experiment and focus on a single evolving population to show the patterns from Chapter 2. Six beneficial mutations were tracked as they spread through this one population over 5000 generations. Multiple independent beneficial mutations arose and competed with each other, several lineages that eventually became extinct nonetheless accumulated several beneficial mutations, and mean fitness increases in a step-like manner even without allelic fixation events.;Chapter 4 uses the same population to test the hypothesis of indirect selection for evolvability that was developed in Chapter 2, which requires the clonal interference dynamics that were shown to be present in Chapter 3. This hypothesis further requires that the independent subpopulations differ in their ability to adapt. Representative clones from an early time point, whose descendants went on to compete and further adapt before one eventually displaced all others, were sampled from the population and used to found new populations. These new populations founded with clones of the eventual winners adapted more quickly and reach higher fitness than the populations of the eventual losers. Thus, the eventually successful genotype was the more evolvable one.