Genetic Background Effects on Adaptation and Gene Function Evolution

Thesis (Ph.D.)--University of Washington, 2017-06The ability to predict phenotype from genotype is the ultimate goal of genomic research. Achieving this goal requires understanding, on a systems level, how natural variation between genetic backgrounds can influence overall allelic effects. Understanding the relationship between sequence variation and phenotypic variation for complex traits will provide insights that are important for not only predicting adaptive evolution outcomes, but also for predicting disease risks in human populations and help improve personalized therapeutic treatments and selective breeding in agriculturally important plants and animals. In this thesis, I have investigated the impact of genetic background on adaptation and gene function evolution across diverged species of yeast spanning the Saccharomyces clade. In chapter one I give an overview of molecular mechanisms of adaptation and gene function characterization in the context of genome dependencies. I discuss general concepts of comparative genomic studies and adaptation and provide background information on gene function characterization. Chapter two of this thesis describes my work addressing the dependence of cellular fitness and adaptation on genetic backgrounds of different yeast species. The comprehensive work in this chapter tests several hypotheses to explain differential amplification events between paralogs and illustrates how changes in regulatory sequence amid divergent genetic contexts can influence adaptive routes taken to achieve increased cellular fitness in sulfate-limited growth conditions. To expand comparisons of divergence to all orthologs between S. cerevisiae and S. uvarum, I describe a random mutagenesis method applied to S. uvarum to interrogate gene dispensability in chapter three of this thesis. Using this method, I created a pool of ~50,000 mutants in a diploid strain of S. uvarum and made comparisons against a haploid pool of ~40,000 mutants to: 1) prioritize candidate essential genes, 2) identify genes that differ in dispensability between species, and 3) investigate cis vs. trans effects to explain differential essentiality using cross-species complementation assays. Ongoing work described in chapter four explores centromere sequences to compare required functional elements between S. cerevisiae and S. uvarum as a means to explore centromeric evolution between these two species. I conclude with chapter five where I summarize the results of my thesis work, discuss ideas for future projects, and address the implications of these results in a broader context of functional comparative genomic research. Collectively, the work presented in this thesis furthers our understanding of genetic context and its impact on phenotypic outcomes associated with molecular evolution