Disentangling the Effects of Mutation and Selection on the Evolution of Gene Expression.

Abstract

Mutation is the ultimate source of phenotypic variation. However, little is known about the effects of new mutations in the absence of natural selection and whether these effects can influence the course of evolution. This is particularly true for changes in gene expression and regulation. In this thesis I measure the effects of new cis- and trans-regulatory mutations on the expression of the Saccharomyces cerevisiae TDH3 gene. Using these measurements, I show that cis- and trans-regulatory mutations have fundamentally different effects on gene expression. In particular, I find that cis-regulatory mutations are on average larger than trans-regulatory mutations and skewed towards decreases in TDH3 expression, while trans-regulatory mutations are often, but not always, more common than cis-regulatory mutations and skewed towards increases in TDH3 expression. To determine how natural selection has acted on these differences, I generate genome sequences and genetically tractable versions of over 60 diverse S. cerevisiae strains previously isolated from a range of environments. I use these strains to determine the effects of cis- and trans-regulatory polymorphism on TDH3 expression. Comparing these effects to the effects of new mutations, I find that natural selection has acted on both cis- and trans-regulatory variants. Interestingly, the effects of selection varies between cis- and trans-regulatory changes due to differences in the effects of new mutations. Using the same approach, I also identify differences in the action of natural selection on cis- and trans-regulatory changes for the variability in expression amongst genetically identical individuals, i.e. gene expression noise. Finally, I determine the evolution of regulatory changes over long evolutionary timescales in Saccharomyces. I find widespread evidence for compensatory changes in regulation, particularly for trans-regulatory changes that act in opposite directions. Consistent with this finding, I identify hundreds of trans-acting QTL affecting TDH3 expression amongst four strains of S. cerevisiae. Together these results suggest that trans-regulatory changes are a common, but individually small, source of regulatory variation. In total, this thesis shows that understanding the effects of new mutations and comparing these effects to observed differences in natural populations can be a powerful approach for elucidating the underlying molecular mechanisms governing evolution.