遺傳上的變異如何影響物種演化一直是分子演化想要解答的議題，先前的研究大都著重在少數基因如何造成表型乃至於個體適應性的演化。例如：OdsH的基因研究指出，其因為正向選汰而造成的快速演化,形成擬黃果蠅種群之生殖隔離。本研究探討OdsH是否曾多次地受到正向選汰壓力而造成快速演化，並參與其他物種的種化的過程。過去十年中分子演化和族群遺傳學因為定序技術的發展而顯著進展，許多物種基因體的定序均已完成，分析比較多種果蠅的分子演化，本研究發現OdsH快速演化而造成種化的機制，僅出現在擬黃果蠅種群中。接下來分析基因體中各個基因的親緣關係以驗證擬黃果蠅種群中的不完全譜系分類，再次支持了大部份的基因都是屬於中性或是類中性選汰的說法。最後，藉由黃果蠅鹼基組成的分析，本研究發現黃果蠅的偏好密碼子在近期出現改變，傾向於使用AT組成較多的密碼子。近年來，由於全基因組的遺傳變異分析逐步建立，對於影響基因體結構的各種因素已逐步建立，藉由這些序列資料上的分析，本研究提出之具體貢獻為１）建立OdsH在Drsophila genus的分子演化史；２）全面檢視在遺傳隔離尚未建立的種群中，不完全譜系分枝在基因體中的分布；３）提出黃果蠅偏好密碼子改變的證據。

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.

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