飛魚是台灣東部重要經濟魚種如旗魚、鬼頭刀的食餌對象之一，位處食物鏈中之低階消費者，維持黑潮海洋生態系的穩定。本研究之尖頭細身飛魚為台灣東北部飛魚卵漁業主要漁獲對象之親魚，也是台灣東部海域飛魚優勢種之一，但在2006∼2007年飛魚及飛魚卵漁獲量的顯著下降和其對生態與漁業之影響，引起了漁業界和學界的重視，為了能有效管理此種飛魚資源，必須先瞭解其親緣關係和族群結構。
本研究以粒線體脫氧核糖核酸中的細胞色素氧化酶I (cytochrome oxidase I, COI) 片段來探討西北太平洋尖頭細身飛魚之親緣關係，從2008年7月到2010年11月間，分別從基隆、宜蘭、花蓮、綠島四個地區採集共55尾飛魚樣本。另於2009年9月，取得日本種子島、屋久島尖頭細身飛魚共計8尾，經定序結果，自台灣樣本共定序出33個單倍基因型，COI序列長度為657bp，平均遺傳距離為0.6%。以相鄰連接法與最大似然法建構之親緣關係樹，推測可將台灣東部尖頭細身飛魚分成兩群，分別為來自基隆、宜蘭之「基隆沿岸群」以及主要來自綠島之「黑潮群」。經分子變方分析，得出兩群間之差距為61.75%；日本樣本定序出8個單倍基因型，COI序列長度為657bp，平均遺傳距離為0.53%，在樹形圖中被歸為黑潮群，分子變方分析的結果顯示與基隆沿岸群差距為60%。在這個推測下，會分成兩群的原因可能與黑潮在台灣東北部海域流向的不同有關；而日本樣本與黑潮群來自同一群，推估兩者皆位於黑潮主流，故親緣關係相近。然而使用不同的統計參數結論差異很大，有可能會產生只有單一群之結果，因此仍待進一步研究確認。

As one of the major preys of many important economic fish species such as swordfish and dolphinfish in waters off estern Taiwan, flyingfish belongs to low-end consumers in the food chain with the function of maintaining the stability of the Kuroshio marine ecosystem. Hirundichthys oxycephalus is the primary component of flyingfish-egg fishery captures in the northeastern waters of Taiwan, and is also one of the dominant species of flyingfish in eastern waters of Taiwan. However, the significant drop of the flyingfish and flyingfish-egg catch from 2006 to 2007 and the effects on ecosystem and fishery caused major concern from the fishery sector and academic field. In order to manage this marine resource effectively, the phylogenetic relationships and population structure needed to be characterized first.
In this study, the phylogenetic relationships of Hirundichthys oxycephalus of Northwestern Pacific was characterized based on the mitochondrial COI fragment. Totally 55 samples were collected between July, 2008 and November, 2010 in waters of Keelung, Ilan, Hualian, and Green Island. In addition, 12 more samples were obtained in Sebtember, 2009 from Tanegashima Island, and Yakushima Island of Japan. The DNA sequencing results of samples from Taiwan showed a total number of 29 haplotypes. The length of partial COI sequence was found to be 657 bp while the mean genetic distance was found to be 0.6%. In phylogenetic analyses, two major groups were identified in the phylogenetic trees by neighbor-joining and maximum-likelihood methods. The majority of "Keelung inshore group" came from Keelung and Ilan waters. The main population of "Kuroshio group" came from Green Island. The variation between two groups was found to be 61.75% by amova. The DNA sequencing results of samples from Japan showed a total number of 8 haplotypes. The length of partial COI sequences was found to be 657 bp with a mean genetic distance of 0.53%. In the phylogenetic tree, the samples from Japan were found to belong to "Kuroshio group". The variation between the two major groups was found to be 60% by amova. It was inferred that the differentiation of flyingfish into the two major groups in Taiwan was due to the flow pattern difference of Kuroshio in northeast waters of Taiwan. It was also inferred that phylogenetic similarity of the samples from Japan and the Kuroshio group was due to the distribution of both groups locating on the same path of the main current of Kuroshio. However, applying different distribution assumption may result in different conclusion such as one single stock hypothesis. Further studies will be needed to confirm the stock structure of the species.

謝辭………………………………………………………………………………I
中文摘要……………………………………………………………………………II
英文摘要………………………………………………………………………….…III
目錄…………………………………………………………………………………V
表目錄………………………………………………………………………………VI
圖目錄……………………………………………………………………...………VII
前言……………………………………………………………………………………1
材料與方法……………………………………………………………………………6
結果…………………………………………………………………………………10
討論…………………………………………………………………………………14
參考文獻……………………………………………………………………………19
表……………………………………………………………………………………27
圖……………………………………………………………………………………41

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