Abstract
There are three chapters in this dissertation and I focus on the comparison and modification of methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. In chapter 1, I describe the background and terminology of evolutionary change in nucleotide sequences. I also introduce the derivations of two methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993). In chapter 2, I compared three frequently used methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993), and Goldman and Yang (1994) as in the PAML package. These methods were evaluated and compared for their accuracies and are denoted by LWL85, LPB93, and GY94, respectively. After comparing their performance, I proposed a correction to improve the accuracies of LWL85 and LPB93 and a modification method, denoted by M-LWL85. In chapter 3, I describe the comparative analysis of the receptor-like kinase family in Arabidopsis thaliana and Rice. This is an application of estimating Ka and Ks in the comparison between different species.