臺灣博碩士論文加值系統

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

王智文。2005。臺灣及大陸東南地區中華花鰍(Cobitis sinensis)種群形態系統分類、分子地理親緣與生殖生態之研究。國立中山大學海洋生物研究所碩士論文。
林忠暉。2010。臺灣東部尖頭細身飛魚耳石年齡與成長研究及其在漁業管理上之意涵。國立中山大學海洋事務研究所碩士論文。
江欣潔。2001。以生物指標研究全球海域大目鮪族群之分佈。國立臺灣大學海洋研究所碩士論文。
吳卓臻。2007。以粒線體DNA標記建立西北太平洋長鰭鮪之族群結構。國立臺灣大學分子與細胞生物學研究所碩士論文。
邵廣昭。臺灣魚類資料庫 網路電子版version 2008/11。 http://fishdb.sinica.edu.tw, (2011-5-30)。
張水鍇。2008。飛魚面面觀。漁業推廣，261：32-36。
張水鍇。2009。飛魚資源之地理分佈及管理之研究。行政院農委會漁業署計畫報告。
張水鍇。2010。利用密度及生殖腺指數探討黑潮海域黑鰭飛魚洄游路徑與可能產卵場。行政院國家科學委員會補助專題研究計畫。
臺灣大學生物多樣化研究中心。2006。漁業文化。臺灣的自然資源與生態資料庫. III, 農林漁牧－第十二章/ 李培芬等撰文.臺北市：農委會林務局。
陳文義、江偉全、許紅虹、許儷玉及蘇偉成。1999。臺灣東部海域鬼頭刀漁獲量變動趨勢與成長參數之研究。水產研究，7(1&2): 1-8。
陳美惠、袁孝維、林曜松。2004。臺大實驗林研究報告，18(2): 65-75。
Aars, J., R. A. Ims, H. P. Liu, M. Mulvey and M. H. Smith. 1998. Bank voles in linear habitats show restricted gene flow as revealed by mitochondrial DNA (mtDNA). Molecular Ecology 7: 1383-1389.
Adkins, R. M. and R. L. Honeycutt. 1994. Evolution of the primate cytochrome c oxidase subunit Ⅱ gene. J. Molecular Ecology 38: 215-231.
Avise, J. C., J. Arnold, R. M. Ball, E. Berminhan, T. Lamb, J. E. Neigel, C. A. Reeb and N.C. Saunder. 1987. Interspecific phylogeography: The mitochondrial DNA bridgebetween population and genetic and systematics. Annual Review of Ecology, Evolution, and Systematics 18: 489-522.
Avise, J. C. 1994. Molecular Markers, Natural History and Evolution. Champman & Hall. New York.
Avise, J.C. 2000. Phylogeography. In: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
Barrett, R.D.H., and Hebert, P.D.N. 2005. Identifying spiders through DNA barcodes.
Canadian Journal of Zoology/Revue Canadien de Zoologie 83: 481–491.
Bendall, K. E., V. A. Macaulay, J. R. Baker and B. C. Skyes. 1996. Heteroplasmic point mutations in the human mtDNA control region. American Journal of Human Genetics 59: 1276-1287.
Brown, W. M., M. George, Jr. and A. C. Wilson. 1979. Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America 76: 1967-1971.
Brown, G. C. 1992. Control of respiration and ATP synthesis in mammalian mitochondria and cells. Biochemical Journal 284: 1-13.
Calloway, C. D., R. L. Reynolds, G. L. Herrin, Jr. and W. W. Anderson. 2000. The frequency of heteroplasmy in the HVⅡ region of mtDNA differs across tissue types and increases with age. American Journal of Human Genetics 66: 1384-1397.
Cantatore, P., M. Roberti, G. Pesole, A. Ludovico, F. Milella, M. N. Gadaleta and C. Saccone. 1994. Evolutionary analysis of cytochrom b sequences in some perciformes: evidence for a slower rate of evolution than in mammals. Journal of Molecular Evolution 39: 589-597.
Chiang, W.C., W.C. Su, C.L. Sun and S.Z. Yeh. 2004. Age and growth of sailfish (Istiophorus platypterus) in waters off eastern Taiwan. Fishery Bulletin 102: 251-263.
Davenport, J. 1994. How and why do flying fish fly? Reviews in Fish Biology and Fisheries 4: 184-214.
Faber, J. E. and Stepien CA. 1998. Tandemly repeated sequences in the mitochondrial DNA control region and phylogeography of the Pike-Perches Stizostedion. Molecular Phylogenetics and Evolution 10: 310-22.
Fish, F. E. 1990. Wing design and scaling of flying fish with regard to flight performance. Journal of Zoology 221: 391-403.
Grant, W. A. S. and B. W. Bowen. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89: 415-426.
Hebert, D. N, Sujeevan Ratnasingham and Jeremy R. deWaard. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B-Biological Sciences 270: 96-99.
Hebert, P. D. N., Ratnasingham S, DeWaard JR. 2003. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B: Biological Sciences 270: S596–S599.
Hebert, P. D. N., Stoeckle, M. Y., Zemlak T. S., Francis, C. M. 2004. Idenfication of
bird through DNA Barcodes. PLoS Biology 10: 1657-1663
Hochachka, P. W. and Mommsen, T. P. 2005. Biochemistry and Molecular Biology of Fishes. Amsterdam.
Hudson, R. R., M. Slatkin and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
Hunte, W., H.A. Oxenford and R. Mahon. 1995. Distribution and relative abundance of flyingfish (Exocoetidae) in the eastern Caribbean. II. Spawning substrata, eggs and larvae. Marine Ecology Progress Sereies 117: 25-37.
Ichimaru T. 2005. The life cycle of three species of flying fish in the north western waters of Kyusyu and the recruitment of young flying fish to the fishing ground. Bulletin of Nagasaki Prefectural Institute of Fisheries 33: 7-110.
Johns, G.C. and J. C. Avise. 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution 15: 1481-1490.
Khohiattiwong, S., R. Mahon and W. Hunte. 2000. Seasonal abundance and reproduction of the fourwing flyingfish, Hirundichthys affinis, off Barbados. Environment Biology of Fishes 59: 43-60.
Lee, W-J., J. Conroy, W. H. Howell, and T. D. Kocher. 1995. Structure and
evolution of teleost mitochondrial control regions. Evolution 41: 54-66.
Lewallen Eric A. 2011. Molecular systematics of flyingfishes (Teleostei:Exocoetidae): evolution in the epipelagic zone. Biological Journal of the Linnean Society 102: 161–174.
Liang, W.-D., T. Y. Tang, Y. J. Yang, M. T. Ko, and W.-S. Chuang, 2003: Upper-ocean currents around Taiwan. Deep-Sea Research 50: 1085-1105.
Macey, J. R., A. Larson, N. B. Ananjeva, Z. Fang and T. J. Papenfuss. 1997. Two novelgene orders and the role of light-strand replication in rearrangement of thevertebrate mitochondrial genome. Molecular Biology and Evolution 14: 91-104.
Martins, C., A. P. Wasko, C. Oliveira and F. Foresti. 2003. Mitochondrial DNA variation in wild populations of Leporinus elongatus from the Paraná River basin. Genetics and Molecular Biology 26: 33-38.
Meyer A. 1993. Evolution of mitochondrial DNA in fish. In: Biochemistry and Molecular Biology of Fish, Vol. 2, Pages 1-38 in P. W. Hochachka and P. Mommsen, editors. Elsevier Press, New York, NY.
Nosek J, Tomaska L, Fukuhara H, Suyama Y and Kovac L. 1998. Linear mitochondrial genomes – 30 years down the line. Trends in Genetics 14: 184–188.
Parin, N.V. 1996. On the species composition of flying fishes (Exocoetidae) in the West-Central part of tropical Pacific. Journal of Ichthyology 36: 357-364.
Parin, N.V. and T.N. Belyanina. 1998. Age and geographic variability and distribution of the flyingfish Cheilopogon furcatus (Exocoetidae, Beloniformes), with a description of two new subspecies. Journal of Ichthyology 38: 557–573.
Parin, N.V. 1999. The living marine resources of the WCP. Rome.
Parin, N.V. and I.B. Shakhovskoy. 2000. A review of the flying fish genus Exocoetus (Exocoetidae) with descriptions of two new species form the southern Pacific Ocean. Journal of Ichthyology 40: 31–63
Perdices A, Cunha C and Coelho MM. 2004. Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (= Yangtze) drainage inferred from cytochrome b sequences. Molecular Phylogenetics and Evolution 31:192–203.
Rand, D. M. 1994. Thermal habit, metabolic rate and the evolution of mitochondrial
DNA. Trends in Ecology and Evolution 9: 121-131.
Sano, N., A. Kurabayashi, T. Fujii, H. Yonekawa and M. Sumida. 2004. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the bell- ring frog, Buergeria buergeri (family Rhacophoridae) . Genes & Genetic Systems 79: 151-163.
Slade, R. W., C. Moritz and A. Heideman. 1994. Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny. Molecular Phylogenetics and Evolution 11: 341-356.
Tajima, F. 1996. The amount of DNA polymorphism maintained in a finite population when the nutral mutation rate varies among sites. Genetics 143: 1457-1465.
Tang, T. Y., Y. Hsueh, Y. J. Yang, and J. C. Ma, 1999. Continental slope flow northeast of Taiwan. Journal of Physical Oceanography 29: 1353-1362.
Tang, T. Y., J. H. Tai, and Y. J. Yang, 2000: The flow pattern north of Taiwan and the migration of the Kuroshio. Continental Shelf Research 20: 349-371.
Vigilant, L., R. Pennington, H. Harpending, T. D. Kocher and A. C. Wilson. 1989.
Mitochondrial DNA sequences in single hairs from a southern Africanpopulation. Proceedings of the National Academy of Sciences of the United
States of America 86: 9350-9354.
Wang, J. P. , Hsu, K. C. and Chiang T. Y. 2000. Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan. Molecular Ecology 9:1483–1494.
Wang J. P. , Lin HD, Huang S, Pan CH, Chen XL and Chiang TY. 2004. Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes. Molecular Phylogenetics and Evolution 31: 1143–1156.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding
Australia’s fish species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360: 1847–1857.
Ward, R. D. and Holmes, B. H. 2007. An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes. Molecular Ecology Notes 7: 899–907.
Watson, W. 1996. Exocoetidae: flyingfishes. Pages 643-657 in H.G. Moser, editors. The early stages of fishes in the California Current Region. California Cooperative Oceanic Fisheries Investigations (CalCOFI) Atlas No. 33. Allen Press, Inc., Lawrence, Kansas.
Wenink, P. W., A. J. Baker and M. G. J. Taianus. 1993. Hypervariable-control-region sequences reveal global population structuring in a long-distance migrant shorebirds, the Dunlin (Calidris alpina). Proceedings of National Acdemic Sciences 90: 94-98.
Wolstenholme, D. R. 1992. Animal mitochondrial DNA: structure and evolution. International Review of Cytology 141: 173-216.
Wright, S., 1978. Evolution and Genetics of Populations, vol. 4. Variability Within and Among Natural Populations. University of Chicago Press, Chicago, IL.
Wu, C.C., J.C. Lin and W.C. Su. 2006. Diet and feeding habits of dolphin fish (Coryphaena Hippurus) in the waters off eastern Taiwan. Journal of Taiwan Fisheries Research 14: 13-27.
Zardoya, R., and A. Meyer. 1996. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Molecular Phylogenetics and Evolution 13: 933-942.