Date of Award
Doctor of Philosophy
Ecology and Evolutionary Biology
Michael A. Gilchrist
Sergey Gavrilets, Louis Gross, James Fordyce, Russell Zaretzki
The genetic code is redundant, with most amino acids coded by multiple codons. In many organisms, codon usage is biased towards particular codons. A variety of adaptive and non-adaptive explanations have been proposed to explain these patterns of codon usage bias. Using mechanistic models of protein translation and population genetics, I explore the relative importance of various evolutionary forces in shaping these patterns. This work challenges one of the fundamental assumptions made in over 30 years of research: codons with higher tRNA abundances leads to lower error rates. I show that observed patterns of codon usage are inconsistent with selection for translation accuracy. I also show that almost all the variation in patterns of codon usage in S. cerevisiae can be explained by a model taking into account the effects of mutational biases and selection for efficient ribosome usage. In addition, by sampling suboptimal mRNA secondary structures at various temperatures, I show that melting of ribosomal binding sites in a special class of mRNAs known as RNA thermometers is a more general phenomenon.
Shah, Premal R., "On the evolution of codon usage bias. " PhD diss., University of Tennessee, 2011.