Tradeoffs, Mobile Genetic Elements and Horizontal Gene Transfers in Microbial Evolution

Many novel evolutionary phenomena have been discovered via utilizing laboratory populations. In this thesis, I have investigated a series of interrelated evolutionary processes through a combination of experimental and computational work to address questions in adaptation and genome evolution based on both laboratory and natural populations. From the aspect of phenotypic changes, tradeoffs between selected and non-selected environments are often assumed to exist during adaptation. In this thesis, an asymmetric, bimodal tradeoff has been found during adaptation of experimental populations. Related to the frequent observations of tradeoffs between C1 and multi-carbon metabolism in natural populations of methylotrophs, this result suggests recurrent encounter of C1 compounds is required for the long-term maintenance of methylotrophy.;Form the aspect of genotypic changes, my work has concentrated on a particularly interesting type of elements that mediate distinct genomic changes - mobile genetic elements (MGEs). MGEs are widespread across microbial genomes but the reasons for them to persist in genomes are unclear. In this thesis, two distinct results were retrieved from studies on laboratory and natural populations, respectively. Strong evidence from experimental populations indicates that MGEs promote adaptation by generating beneficial mutations, whereas a study of 1012 microbial genomes supports the hypothesis of MGEs as genomic parasites proliferating by periodic extinction-reinfection cycles. Based on the difference in time frame between the studies of laboratory and natural populations, it was hypothesized that MGEs may provide benefits to hosts early in adaptation but pose a deleterious effect when stabilized in the long term (analogous to what is proposed for mutator alleles). By connecting experimental and computational techniques, metagenomics may provide a means to study the ecological and temporal dynamics of MGEs in natural populations, a critical aspect for understanding the role of MGEs in microbial evolution.