The loss of phenotypes, a phenomenon capable of leading to ecological specialization, has been observed to occur readily during evolution and is an important contributor to the phenotypic variation observed in nature. While the loss of phenotypes is often observed, the population genetic processes responsible for phenotypic loss are not well understood. This lack of understanding is due to the complexity of evolutionary process and the intricacy of how information from the genotype develops into the phenotype. The work presented in this dissertation is a first attempt to disentangle the complexity of the population genetics of trait loss in experimental populations of Bacillus subtilis, a bacterium of the low G+C Gram positive group. The experiments described in this dissertation showed that the deletion of two complex phenotypes occurred throughout evolutionary time. While there is evidence suggesting that this phenotypic loss may be due to trade-offs between traits that were lost and those important for fitness, i.e . selection, the contribution of neutral mutation accumulation cannot be ruled out. Genomic studies identified candidate expression changes potentially able to explain the observed phenotypic loss, paving the way for future work linking the observed phenotypic changes with their underlying genetic and developmental cause(s). The results from this dissertation work speak to the complexity of trait loss and the difficulty of explicitly determining whether selective or neutral processes are responsible for trait loss in nature.
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