臺灣博碩士論文加值系統

摘要
本論文係利用分子族群遺傳學(Molecular Population Genetics)方法，研析印度洋產劍旗魚尾柄肌肉細胞中粒線體DNA(mtDNA)鹼基序列特徵，俾據以釐清該魚種資源之系群結構，以供該魚種資源評估及管理之參考依據。DNA定序所需之劍旗魚肌肉樣本，係委託印度洋作業之台灣鮪延繩釣漁船船長於1999年1月至2001年5月期間，在北緯2度至南緯22度及東經43度至122度海域範圍，由西向東分別採得：Ming、Red、New、F、Cen及East等6個區域樣本，共61尾劍旗魚肌肉樣本。
結果顯示：(1)印度洋劍旗魚mtDNA中之D-loop全長為837鹼基對(bp)，61尾樣本中，共發現115個變異點，且多出現於5’端1∼300bp片段；(2)Kimura’s 2-parameter model法求得個別魚體間遺傳距離值之分布範圍為0.000∼0.033；(3)區域樣本間固定指數FST (Fixation index)值之比較結果顯示Ming與其他區域樣本間之數值偏高(0.203~0.103)；(4)將FST值視為距離矩陣以UPGMA及Neighbor-Joining兩方法建構區域樣本之樹型圖均顯示：Ming與其他區域樣本間有明顯分離的現象；(5)以分子變異數分析法(AMOVA)檢定區域樣本間之親疏結果亦顯示：Ming區域與其他五個區域之間有顯著差異。
綜合以上結果皆顯示印度洋產劍旗魚，應可分為兩個不同系群。亦即：位於馬達加斯加島北部Ming區域的劍旗魚資源系群，應不同於來自中部及東部印度洋之劍旗魚資源系群。

目錄
目錄 ………………………………………………………………… i
摘要 ………………………………………………………………… ii
第一章前言 …………………………………………………………1
第二章材料與方法 …………………………………………………4
2-1 肌肉樣本之採集
2-2 粒線體DNA片段之定序
2-2-1粒線體DNA之抽取
2-2-2粒線體DNA(mitochondrial DNA；mtDNA)特定片段之製備
2-2-3 T-A cloning
2-2-4 DNA的定序：
2-3 鹼基序列間之親疏判釋
2-3-1 D-loop基因範圍之界定
2-3-2 歧異度分析
2-3-3 區域樣本間FST值與Nm值比較分析
2-3-4 AMOVA檢定與分析
第三章研究結果 ……………………………………………………13
3-1 粒線體DNA鹼基序列之組成特徵
3-2 鹼基序列之岐異度指標
3-3區域樣本間Fst值與Nm值分析結果
3-4 分子序列變方分析(AMOVA)檢定結果
第四章討論 …………………………………………………………16
參考文獻 …………………………………………………………… 21附表 ………………………………………………………………… 27
附圖 ………………………………………………………………… 39
附錄 ………………………………………………………………… 50

參考文獻：
Alvarado Bremer J. R., Baker A. J. and Mejuto J. (1995) Mitochondrial DNA control region sequences indicate extensive mixing of swordfish (Xiphias gladius) populations in the Atlantic Ocean. Can J Fish aquat Sciences 52: 1720-1732
Bartoo, N. W. and Coan, A. L. Jr (1989). An assessment of the Pacific swordfish resource. In: Stroud, R. H. (ed.) Proc. 2nd Int. Billfish Symp., Kaila-Kona, Hawaii, 1-5 August 1988, Part 1. p. 137-151. National Coalition for Marine Conservation, Inc., Savannah, GA.
Brown, G. G., Gadaleta, G., Pepe, G., Saccone, C. and Sbisa, E. (1986). Structural Conservation and Variation in the D-loop containing Region of Vertebrate Mitochondrial DNA. J. Mol. Biol. 192: 503-511
Brown, J. R., Beckenbach, A. T. and Smith, M. J. (1993). Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus). Mol. Biol. Evol. 10(2): 326-341
Carey, F. G. and Robison, B. J. (1981) Daily patterns in the activities of swordfish, Xiphias gladius, observed by acoustic telemetry. Fish Bull US 79: 277-292
Chow, S., Okamoto, H., Uozumi, Y., Takeuchi, Y. and Takeyama, H. (1997).Genetic stock structure of the swordfish (Xiphias gladius) inferred by PCR-RFLP analysis of the mitochondrial DNA control region. Mar. Bio. 127: 359-367
Doda, J. N., Wright, C. T. and Clayton, D. A. (1981). Elongation of Displacement Loop Strands in Human and Mouse Mitochondrial DNA is Arrested Near Specific Template Sequences. Proc. Natl. Acad. Sci. U.S.A. 78: 6116-6120
Doiron, S., Blier, P. U. and Bernatchez, L. Submitted (1999) A comparative analysis of complete sequence of mitochondrial genome between brook char (Salvelinus fontinalis) and arctic char. (Salvelinus. alpinus) Biology, Universite Laval, Cite Universitaire, Ste-Foy, Quecbec G1K 7P4, Canada.
Excoffier, L., Smouse, P. E. and Quattro, J. M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491
Fajen, A. and Breden F. (1992) Mitochondrial DNA sequence variation among natural populations of the Trinidad guppy, Poecilia reticulata. Evolution 46: 1457-1465
Grall C., de Sylva D. P. and Houde E. D. (1983) Distribution, relative abundance and seasonality of swordfish larvae. Trans. Am. Fish. Soc. 112: 235-246
Grijalva—Chon, J. M., de la Rosa-Velez, J. and Sosa-Nishizaki, O. (1996) Allozyme variability in two samples of swordfish,Xiphias gladius L., in the North Pacific Ocean. Fishery Bulletin 94: 589-594
Grijalva — Chon J. M., Numachi, K., Sosa-Nishizaki, O. and de la Rosa-Velez, J. (1994) Mitochondrial DNA analysis of north Pacific swordfish (Xiphias gladius) population structure. Mar. Ecol. Prog. Ser. 115: 15-19
Gulland, J. A. (1983) Fish stock assessment: a manual of basic methods. FAO/Wiley series on food and agriculture. Volume 1. 223pp.
Hillis, D. M. and Moritz, C. (1990) Molecular systematics. Sinauer Associates. Sunderland.
Hudson, R. R., Slatkin, M. and Maddison, W. P. (1992) Estimation of levels of gene flow from DNA sequence data. Genetics. 132: 583-589.
Innis, M. A., Gelfand, D. H., Sninsky, J. J. and White, T. J. (1989) PCR protocols: a guide to methods and applications., Academic Press Inc. pp.21-53
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. Mol. Evol. 16: 111-120
Kocher, T. D., Thomas, W. K., Meyer, A., Edwards, S. V., Paabo, S., Villablanca, F. X. and Wilson, A. C. (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primes. Proc. Natl. Acad. Sci. U.S.A. 86: 6196-6200
Kotoulas, G., Magoulas, A., Tsimenides, N. and Zouros, E. (1995) Marked mitocondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius. Mole. Ecol. 4: 473-481.
Kumar, S., Tamura, K., Ingrid B. J. and Nei, M. (2001) MEGA2: Molecular Evolutionary Genetics Analysis software, Bioinformatics (submitted).
Larkin, P. A. (1972) The stock concept and management of Pacific salmon, p.11-15.In Pacific salmon, H. R. MacMillan Lectures in Fisheries. Univ. of British Columbia, Vancouver, B. C.
Nakamura (1985) Billfishes of the world. An annotated and illustrated catalogue of marlins, sailfishes, spearfishes and swordfishes known to date. FAO (Food and Agriculture Organisation of the United Nations) Fisheries Synopsis, 125.
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press. New York.
Nei, M. and Tajima, F. (1981). DNA polymorphism detectable by restriction endonucleases. Genetics. 97: 145-163.
Neimann, A. C. and Gill, D. A. (1961) Circulation of the Red Sea in early summer. Deep-Sea Research. 8: 223-235
Nishikawa, Y., and Ueyanagi, S. (1974) The distribution of the Larvae of swordfish, Xiphias gladius, in the Indian and Pacific Ocean. U. S. Dep. Commer., NOAA, Tech. Rep., NMFS; SSRF-675: 261-264
Reeb, C. A., Arcangeli, L. and Block, B. A. (2000) Structure and migration corridors in Pacific populations of the Sworsfish (Xiphias gladius) as inferred through analyses of mitochondrial DNA. Mar. Biol. 136: 1123-1131
Roe, B. A., Ma, D. P., Wilson, R. K. and Wong, J. F. H. (1985) The complete sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260: 9759-9774
Rosel, P. E. and Block, B. A. (1996) Mitochondrial control region variability and global population structure in the swordfish, Xiphias gladius. Mar. Biol. 125: 11-22
Rozas, J. and Rozas R. (1999) DnaSP version 3 : an integrated program for molrcular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175
Saccone, C., Pesole, G. and Sbisa, E. (1991) The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. molec. Evolut 33: 83-91
Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
Sambrook, J., Fritsch, E. J. and Maniatis, T. (1989). Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2nd ed.
Sanger, F., Nicklen, S. and Coulson, A. R. (1977). Dna sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74: 5463-5467
Saunders, N. C., Kessler, L. G. and Avise, J. C. (1986) Genetic variation and geographic differentiation in mitochondrial DNA of the horseshoe crab, Limulus polyphemus. Genetics 112: 613-627
Skillman, R. A. (1989b). Stock identification and billfish management. In: Stroud, R. H. (ed) Proc. 2nd Int. Billfish Symp., Kaila-Kona, Hawaii, 1-5 August 1988, Part 1. National Coalition for Marine Conservation, Inc., Savannah, GA
Shedlock, A. M., Parker, J. D., Crispin, D. A., Pietsh, T. W. and Burmer, G. C. (1992) Evolution of the salmonid mitochondrial control region. Molecular Phylogenetics and Evolution 1(3): 179-192
Smith, P. J., Jamieson, A. and Birley, A. J. (1990) Electrophoretic studies and the stock concept in marine teleosts. J. Cons. Int. Explor. Mer., 47: 231-245.
Stanley, H. F., Casey, S., Carnahan, J. M., Goodman, S., Harwood, J. and Wayne, K. (1996) Worldwide patterns of mitochondrial DNA differentiation in the harbor seal (Phoca vitulina). Mol. Biol. Evol.13: 368-382.
Taylor, R. G, and Murphy, M. D. (1992) Reproductive biology of the swordfish Xiphias gladius in the strait of Florida and adjacent waters. Fishery Bulletin of the USA, 90: 809-816
Walberg, M. W. and Clayton, D. A. (1981) Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA, Nucleic. Acids. Res. 9: 5411-5421
Waldman, J. R., Grossfield, J. and Wirgin, I. (1988) Review of stock discrimination techniques for striped bass. North Am. J. Fish. Man., 8: 410-425
Williams, J. F. (1987) Optimization strategies for the polymerase chain reaction. Bio. Tech. 7(7): 762-767
Wright, S. (1951) The genetical structure of populations. Ann. Eugenics, 15: 323-354
桑自剛。(1992) 利用粒線體去氧核醣核酸序列分析日本鰻之族群結構。國立海洋大學漁業科學研究所碩士論文。51頁。
曾宗德。(1998) 東海及台灣峽產班節蝦資源系群結構與評估。國立台灣大學海洋所博士論文。134頁。
簡春潭。(1995) 台灣周邊海域鯛亞科鱸形目：鯛科魚類種間親緣關係及種內族群遺傳研究。國立台灣海洋大學漁業科學研究所博士論文。199頁。