Molecular and Phenotypic Evolution of Niche Breadth in Escherichia Virus T4
Pham, Jenny Yen
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CitationPham, Jenny Yen. 2019. Molecular and Phenotypic Evolution of Niche Breadth in Escherichia Virus T4. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences.
AbstractAs Earth’s most numerous biological entity, and by nature of their infection specificity, bacterial viruses are promising agents of modern therapeutics and substantial drivers of ecological processes. Bacterial viruses rely on bacterial hosts for propagation; as such, the range of susceptible hosts constitutes the niche breadth of a virus. Despite the significance of virus-host interactions, the manifestations and mechanisms of niche breadth evolution are relatively unexplored elements in bacterial viruses. Experimental evolution of T4, an ideal representative of bacterial viruses, in distinct hosts and environmental conditions provides an opportunity to examine bacterial viruses during the process of niche breadth evolution. There are two ends in the niche breadth continuum: specialists, which have maximized fitness on one resource, and generalists, which display similar fitness over a broad range of resources. In the context of this framework, I performed laboratory experimental evolution on T4 for 50 generations in conditions that were expected to promote the evolution of specialists or generalists. Following this, I measured populations for changes in viral productivity in multiple environmental contexts. All populations exhibited changes in viral productivity; some cases confirmed whereas others defied theoretical expectations, which demonstrates the complexity of niche breadth evolution and the difficulty of using viral traits as approximations of more holistic properties, such as fitness or performance. I performed next-generation sequencing of evolved populations, which revealed signatures that indicate niche breadth evolution was influenced by selection in structural genes and mutational biases. I examined individual virions sampled from T4 specialist populations for trade-offs and found that patterns of variation contradicted expectations; specifically, I observed a trend of diminishing costs, where individuals that exhibited improved productivity in the selective environment also tended to fare better in alternate environments. I sequenced T4 specialist populations over several time-points, which permitted a study of the dynamics of molecular evolution. This revealed parallelism and divergence during viral adaptation and a lack of signatures that typically characterize asexual populations, such as clonal interference. I sequenced individual virions to obtain haplotypes for the assessment of genetic exchange, which indicated that recombination had indeed occurred during viral adaptation.
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