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theses

In an attempt to combat emerging and re-emerging viral pathogens and to understand the deep evolutionary origins of viruses, a vast amount of research effort is being devoted to the study of virus evolution. Of the many viral entities on this planet, fast-evolving viruses are most problematic and most intriguing. Using experimental evolution and comparative computational methods, this dissertation addresses questions in virus evolution of fast-evolving viruses at various timescales. A model RNA virus, the Pseudomonas bacteriophage phi6, was used for experimental evolution studies on genetic diversity. Starting from an overnight growth on an agar plate, three phi6 genotypes were assessed for their mutational frequency on a novel host. It was observed that extant host range mutations are epistatically constraining subsequent host range mutational neighborhoods during sequential host shift events. Next, genotypic generalist and ecological generalist were compared to specialist during long term experimental evolution to see if their evolutionary advantages can be attributed to higher genetic diversity. Ecological history was the major determinant of population genetic diversity in this study, in which selection on novel hosts purged generalist populations' genetic diversity and the specialist ecology was better at maintained higher levels of genetic diversity. Moving on to a larger timescale and to the fast-evolving single-stranded DNA viruses, 926 replication-associated protein (Rep) sequences of circular Rep-encoding ssDNA (CRESS DNA) viruses were collected from GenBank RefSeq database and used to estimate a Rep specific amino acid substitution matrix to model the evolutionary patterns of this homologous protein. Amidst the many recent taxonomic revisions in the CRESS DNA viruses, we contributed a novel matrix and a complete Rep tree as the accurate backbone for future classifications. Finally, the longest timespan covered in this dissertation was reached in the final chapter, on paleovirology of CRESS DNA viruses. Endogenous Rep sequences were found in 163 unique species, 24 different eukaryotic phyla across the tree of life using a relaxed tblastn search in the non-redundant eukaryotic nucleotide database. Apart from expansion on previous findings, genomovirus Reps were shown to exclusively group with endogenous sequences from fungal pathogens, where the only characterized genomovirus was isolated, suggesting potential hosts for uncharacterized members of the family. This dissertation uses many techniques to study dynamics in virus evolution and advances our ability to study both RNA and CRESS DNA viruses.

ETD_9408

Ph.D.

Includes bibliographical references

by Lele Zhao

doi:10.7282/t3-y2v8-9704

ETD doctoral

The author owns the copyright to this work.