The genomic basis of yeast adaptation to limiting glucose
- Adaptive evolution by natural selection is largely responsible for the variety of forms and functions observable in the natural world. Identifying the genetic changes underlying adaptive evolution of organisms to their environment is of fundamental importance in understanding the history of life, as well as predicting how organisms will evolve to novel environments in the future. Experimental evolution of microbes in the laboratory provides a precisely controlled environment for investigations into the genetic basis of adaptation, while also allowing for large population sizes and experimental replication, benefits that are often not available in natural populations. Recent technologies have enabled the identification of the genetic changes responsible for adaptive evolution genome-wide, giving us a genomic view of adaptation during evolution experiments. Here, I have added to our understanding of the genomic basis of adaptation by investigating how Saccharomyces cerevisiae adapts to limiting glucose environments during experimental evolution. Throughout this work, I utilize next- generation, whole-genome sequencing to identify the mutations responsible for adaptation. In Chapter 1, I investigate how genetic interactions define the fitness landscape, and find that very strong negative epistasis between two beneficial mutations creates a fitness valley, so each mutation effectively determines the evolutionary trajectory of adaptation. In Chapter 2, I take a step back and look more broadly at adaptation while asking the question: is there a general functional theme for the genomic basis of adaptation to limiting glucose? To facilitate answering this question in an unbiased manner, I develop a whole-population, whole-genome sequencing technique, and find that the theme of adaptation in the constant and predictable environment of the glucose-limited chemostat is for the yeast to lose function of signaling networks responsible for sensing environmental stimulus, effectively decoupling environmental sensing from response. In Chapter 3, in a collaborative project, we seek to understand the extent that genotypic convergence underlies phenotypic convergence by evolving genetically distinct yeast under different conditions. We find a single gene is recurrently mutated across most genetic backgrounds, suggesting that genotypic convergence plays a large role in adaptive evolution.
|Type of resource
|electronic; electronic resource; remote
|1 online resource.
|Kvitek, Daniel Jeffrey
|Stanford University, Department of Genetics
|Petrov, Dmitri Alex, 1969-
|Petrov, Dmitri Alex, 1969-
|Statement of responsibility
|Daniel Jeffrey Kvitek.
|Submitted to the Department of Genetics.
|Thesis (Ph.D.)--Stanford University, 2012.
- © 2012 by Daniel Jeffrey Kvitek
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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