Abstract
The goal of molecular evolution is to understand the forces that have an impact on the levels of genetic variation. Previous studies have been dedicated to identify significant genetic variations that attribute to phenotypic change and eventually alter fitness of individuals. For example, the studies on OdsH have shown clear evidence of positive selection and pointed out that OdsH plays a major role in the formation of reproductive isolation. However, it has been questioned whether OdsH undergoes recurrent selection and contributes to the species formation in other Drosophila species clades. In the past decade, the field of molecular evolution and population genetics has made tremendous progress mainly due to recent development of sequencing technology. As several Drosophila genome projects are completed, it is feasible the pattern of molecular evolution in a wide range of Drosophila species, and find that rapid divergence driven by positive selection of OdsH is only present within Drosophila simulans species complex. Besides, the patterns of incomplete lineage sorting among newly diverged species were dissected employing phylogenetic analysis on genome-wide data, and supported the view that most of genetic variations were selected neutral or nearly neutral. Finally, I focus on base composition evolution, which is attributed to weak selection, in D. melanogaster population. and suggested a recent preferred codon shift towards AT-rich codons. By means of studying genome-wide genetic variation, the knowledge of how forces shape the genome structure could be established. Major contributions of this thesis are 1) to reconstruct of history of molecular evolution of OdsH is the genus of Drosophila; 2) to survey the genomic pattern of incomplete lineage sorting among the species which genetic barrier has not been established; 3) to show the evidence of AT-ending codons could currently be favored by natural selection in the D. melanogaster lineage.