臺灣博碩士論文加值系統

鯊形總目(Selachomorpha)隸屬於軟骨魚綱(Chondrichthyes)的板鰓亞綱(Elasmobranchii)，下含八個目。已往對其親緣關係及分類上的瞭解皆是基於形態上的證據且尚未得到定論。此外，目前首目及目間之分類系統仍有爭議，因此本研究使用DNA序列為工具重建鯊形總目之分子親緣關係。
本研究採集期間自2004年9月至2005年8月，以南方澳、成功漁港為主要採集地點。利用聚合酶連鎖反應(PCR)方法，以粒線體DNA之12S rRNA序列探討台灣周邊海域產鯊形總目間之親緣關係，並討論其生殖上與演化之關聯。以黑線銀鲛為外群，分析10目24科44種共計117尾樣本，所得結果如下: (1)鼠鮫目、鬚鮫目及白眼鮫目均為一單系群；鼠鮫目與異齒鮫目為同一群；鋸鮫目為最早衍化群；白眼鮫目為最晚衍生群。(2)在白眼鮫目中丫髻鮫科為一單系群及丫髻鮫科為最晚衍生群；在鼠鮫目中鯖鮫科與狐鮫科均為一單系群，食人鮫屬的姊妹群為鼠鮫屬＋鯖鮫屬，深海狐鮫的姊妹群為狐鮫＋淺海狐鮫，砂鮫屬為最早衍化群，鯖鮫屬為最晚衍生群。

Taxonomically, Selachomorpha is included in subclass Elasmobranchii under class Chondrichthyes, being divided 8 order. The phylogenetic relationships within Selachomorpha are still in vague. Furthermore, the systematics of First order and order remains controversial, we reconstruct their molecular phylogeny by using mitochondrial DNA sequences.
Most of the specimens were collected in Nan-Fang-Ao and Cheng-kung Port from September 2004 to August 2005 in this study. Using PCR methods to obtain mtDNA 12S rRNA sequencing inferred phylogenetic relationships of Selachomorpha with their reproductive evolution in the surrounding waters of Taiwan. Forty-four species, 24 families, 10 order and 117 specimen were analyiszed in this study. The results show (1) Lamniformes, Orectolobiformes, Carcharhiniformes can be respectively a monophyletic group; Lamniformes and Heterodontiformes can be the same group; Pristiophoriformes can be the most earlist devired group; Carcharhiniformes can be the latest devired group. (2) Sphyrnidae can be respectively a monophyletic group and can be the latest devired group in Carcharhiniformes; Alopiidae and Lamnidae can be respectively a monophyletic group, Carcharodon is considered as the sister group of Isurus and Lamna, Alopias superciliosus is considered as the sister group of Alopias superciliosus and Alopias vulpinus, Eugomphodus can be the most earlist devired group, Isurus can be the latest devired group in Lamniformes.

中文摘要…………………………………………...……………….. .….....I
英文摘要…………………………………………………...…………..…III
誌謝…………………………………………………...……………….…..V
目錄…………………………………………………..………………….VII
表目錄………………………………………………...…………………..IX
圖目錄……………………………………………...……………………...X
前言………………………………………………...………………….…...1
(一) 軟骨魚類的概述………………….……………..….…......1
(二) 粒線體DNA特性………………….….……………..........4
(三) 軟骨魚類的生殖模式………………..……………………..…...6
(四) 軟骨魚類的分子親緣關係研究回顧……..………………..…….7
(五) 研究目的……………………………..……………..………..……9
材料與方法………………………………...…………………….……….11
(一) 標本採集……………….………………………………….11
(二) 粒線體DNA之定序……….………..…...…………….…….…...11
1. 粒線體DNA之萃取……………………..………………..…...11
2. 引子(Primer)之設計…………………..…………………..…..13
3. 粒線體DNA片段之大量增幅…………..…………………….14
4. 資料分析……………………………...…………………….…15
結果………………………………………………...…………….……….17
(一) DNA序列的分析…………………………...…………….……....17
1. 鹼基的組成…………………………...…………………….....17
2. 遺傳距離……………………………...………………….……18
(二) 鯊形總目的親緣關係…………………..…………………..…....20
(三) 演化時間的推估…………………………..……………………..21
討論………………………………………………...….……………….....23
(一) 分子演化上的訊息……………………………..………………..23
(二) 鯊形總目各目間的親緣關係…………………..…………..……24
(三) 鯊形總目各目內各科間的親緣關係…………..…………..…....26
(四) 親緣關係與其生殖演化及棲息環境間的關聯性……........…....27
參考文獻………………………………………………………………….29
表……………………………………………………………...…….…….37
圖…………………………………………………………...…..…………68

朱元鼎、孟慶聞 (2001) 中國動物誌：圓口綱，軟骨魚綱。科學出 版社，北京，552頁。
沈世傑、李信撤、邵廣昭、陳哲聰、陳春暉、莫顯喬 (1993) 台灣 魚類誌。國立台灣大學動物學系，台北，960頁。
王建勳 (2001) 以粒線體之12S核糖體RNA探討海鰱首目魚類的親緣關係。海洋生物研究所碩士論文，國立中山大學，87頁。
李柏鋒 (2003) 台灣海域角鯊目(棘鮫目)之系統分類及分子類緣關係之研究。海洋研究所碩士論文，國立臺灣大學，139頁。
陳進生 (2000) 以粒線體之12S核糖體DNA探討鯆魮目魚類的親緣關係。漁業科學研究所碩士論文，國立台灣海洋大學，74頁。
Adachi, J. and M. Hasegawa (1995) Phylogeny of whales: Dependence of the inference on species sampling. Molecular Biology Evolution, 12: 177–179.
Allard, M. W., M. M. Miyamoto, K. A. Bjorndal, A. B. Bolten and B. W. Bowen (1994) Support for Natal Homing in Green Turtles from Mitochondrial-DNA Sequences. Copeia: 34-41.



Ashley, M. V. and B. D. Dow (1994) The use of microsatellite analysis in population biology: Background, methods and potential applications, pp. 185-201. In B. Schierwater, B. Streit and R. DeSalle (Eds.), Molecular Ecology and Evolution: Approaches and Applications. Birkhauser Verlag, Basel, Switzerland.
Brown, W. M. (1980) Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. Proceedings of the National Academy of Sciences of the United States of America, 77: 3605-3609.
Brown, W. M., M. G. Jr and A. C. Wilson (1979) Rapid evolution of amimal mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America, 76: 1967-1971.
Brown, W. G., G. Gadaleta, G. Pete, C. Ssccone and E. Sbisa (1986) Structureal conservation and variation in the D-loop containing region of vetebrate mitochondrial DNA. Journal of Molecular Biology, 192: 503-511.
Brown, J. R., C. J. Douady, M. J. Italia, W. E. Marshall and M. J. Stanhope (2001) Universal trees based on large combined protein sequence data sets. Nature Genetics, 28: 281–285.
Bernardi, G and D. A. Powers (1992) Molecular phylogeny of the prickly shark, Echinorhinus cookei, based on a nuclear (18S rRNA) and a mitochondrial (cytochrome b) gene. Molecular Phylogenetics and Evolution, 1 (2): 161-167.

Cappetta, H. (1987) Chondrichthyes II. Mesozoic and Cenozoic Elasmobranchii. In: L. H. P. Schultze, M. O. Kuhn (Eds.), Handbook of Paleoichthyology, vol. 3B. Gustav Fisher Verlag, Stuttgart and New York, pp. 1-139.
Case, G. R. (1981) Late Eocene selachians from south-central Georgia. Paleontographica, A176: 52-79.
Compagno, L. J. V. (1973) Interrelationships of living elasmobranchs. Zoological Journal of the Linnean Society, 53: 15–61.
Compagno, L. J. V. (1977) Phyletic relationships of living sharks and rays. American Zoologist, 17: 303-322.
Compagno, L. J. V. (1984) FAO species catalogue. VOL. 4. Sharks of the world. An annotated and illustrated catalogue of shark species known to date. FAO Fisheries Synopsis, 125 (1): 470- 472.
Compagno, L. J. V. (1988) Sharks of the Order Carcharhiniformes. Princeton University Press, Princeton, New Jersey, pp. 572.
Compagno, L. J. V. (1990) Alternative life history styles of cartilaginous fishes in time and space. Environmental Biology of Fishes, 28: 33-75.
Compagno, L. J. V. (1999) Checklist of living elasmobranchs. In: W. C. Hamlett (Eds.) Sharks, skates and rays: the biology of elasmobranch fishes. The Johns Hopkins Univeristy Press, Baltimore & London. I-X, 1-515.
Cortés, E. (2000) Life History Patterns and Correlations in Sharks. Reviews of Fishery Sciences, 8: 299-344.
Douady, C. J., M. Dosay, M. S. Shivji and M. J. Stanhope (2003) Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Molecular Phylogenetics and Evolution, 26: 215–221.
Dlayton, D. A. (1982) Replication of animal mitochondrial DNA. Cell, 28: 693-705.
De Carvalho, M. R. (1996) Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly. In: M. L. J Stassny, L. R. Parenti, G. D. Johnson (Eds.) Interrelationships of Fishes. Academic Press, San Diego, pp. 35–62.
Espinosa-Arrunbarrena, L. (1987) Neogene species of the genus Isurus (Elasmobranchii, Lamnidae) in Southern California, U. S. A. and Baja California Sur, Mexico. M. S. thesis. California State University, Long Beach.
Greig, T. W., M. Katherine Moore, C. M. Woodley (2005) Mitochondrial gene sequence useful for species identification of western North Atlantic Ocean sharks. Scientific Editor Fisheries Bulletin, 103: 516-523.
Hoenig, J. M. and S. H. Gruber (1990) Life history patterns in the elamobranchs: implications for fisheries management, pp. 1-16. In: Elasmobranchs as living resources: Advances in the Biology, Ecology, Systematics, and the Status of the Fisheries. (H. L. Pratt, S. H. Gruber, and T. Taniuchi (Eds.) NOAA Tech. Rep. NMFS 90, U. S. Dept. of Comm., Washington, D. C.

Human, B. A., E. P. Owen, L. J. V. Compagno, E. H. Harley (2005) Testing morphologically based phylogenetic theories within the cartilaginous fishes with molecular data, with special reference to the catshark family (Chondrichthyes; Scyliorhinidae) and the interrelationships within them. Molecular Phylogenetics and Evolution, 36: 1-8.
Iglésias, S. P., G. Lecointre, D. Y. Sellos (2005) Extensive paraphylies within sharks of the order Carcharhiniforms inffered from nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution, 34: 560-583.
Kitamura, T., A. Takemura, S. Watabe, T. Taniuchi, and M. Shimizu (1996) Mitochondrial DNA Analysis for the Cytochrome b Gene and D-loop Region from the Bull Shark Carcharhinas leucas. Fisheries Science, 62 (1): 21-27.
Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Paabo, F. X. Villablanca and A. C. Wilson (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America, 86: 6196-6200.
Kumar, S., K. Tamura and M. Nei (1993) MEGA: Molecular evolutionary genetics analysis version 1.02. Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, USA.
Lavery, S. (1992) Electrophoretic analysis of phylogenetic relationships among Australian carcharhinid sharks. Australian Journal of Marine and Freshwater Research, 43: 97–108.
Maisey, J. G. (1984) Higher elasmobranch phylogeny and biostratigraphy. Zoological Journal of the Linnean Society, 82: 33–54.
Martin, A. P. and G. J. P. Naylor (1997) Independent origins of filter feeding in megamouth and basking sharks (Order Lamniformes) inferred from phylogenetic analysis of cytochrome b gene sequences. In: K. Yano, J. F. Morrissey, Y. Yabumoto, K. Nakaya (Eds.) Biology of the Megamouth Shark. Tokai University Press, Japan, pp. 39–50.
Martin, A. P., G. J. P. Naylor and S. R. Palumbi (1992) Rate of mitochondrial DNA evolution is slow in sharks compared to mammals. Nature 357: 153-155.
May, B (2003) Allozymes. In E. M. Hallerman (Ed.), Population Genetics: Principles and Applications for Fisheries Scientists. American
Fisheries Society, Bethesda, MD.
Moritz, C., T. E. Dowling and W. M. Brown (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systwmatic. Annual Review of Ecology and Systematics, 18: 269-292.
Morrissey, J. F., K. A. Dunn and F. Mule (1997) The Phylogenetic Position of Megachasma pelagios Inferred from mtDNA Sequence Data. Biology of the Megamouth Shark. Tokai University Press, Japan, pp. 33–37.


Murphy, R. W., J. M. J. Sites, D. G. Buth and C. H. Haufler (1996) Proteins: Isozyme Electrophoresis, pp. 51-120. In D. M. Hillis, C. Moritz and B. K. Mable (Eds.), Molecular Systematics. Sinauer Associates Inc., Sunderland, MA.
Musick, J. A., M. M. Harbin and L. J. V. Compagno (2004) Historical Zoogeography of the Selachii. pp. 33-77. In J. C. Carrier, J. A. Musick and M. R. Heithaus (Eds.), Biology of Sharks and Their Relatives. CRC Press, Boca Raton, Florida.
Naylor, G. J. P., A. P. Martin, E. G. Mattison and W. M. Brown (1997) Interrelationships of lamniform Sharks: testing phylogenetic hypotheses with sequence data. In: T. D. Kocher and C. A. Stepien (Eds.) Molecular Systematics of Fishes. Academic Press, London, pp. 199-218.
Nelson, J. S. (1994) Fishes of the world. 3rd ed. John Wiley & Sons, Inc. New Work, pp. 600.
Purdy, R. W. (1993) Paleoecology of fossil great white sharks: symposium on the biology of the white shark, Carcharodon carcharias. Bodega Marine Laboratory, University of California, Davis. (Abstract, p. 27)
Ruvolo, M. (1997) Molecular phylogeny of the hominoids: Inferences from multiple independent DNA sequence data sets. Molecular Biology Evolution, 14: 248–265.
Siverson, M (1992) Biology, dental morphology and taxonomy of Lamniform sharks from the Campanian of the Kristianstad Basin, Sweden. Paleontology, 35: 519-554.
Taniuchi, T. (1978) Reproductive strategy of the sharks. Maryland Science Monthly, 10: 45-51.
Wu, C. I. (1991) Inferences of species phylogeny in relation to segregation of ancestral polymorphisms. Genetics, 127: 429–435.
Wang H. Y., M. P. Tsai, M. C. Tu and S. C. Lee (2000) Universal Primers for Amplification of the Complete Mitochondrial 12S rRNA Gene in Vertebrates. Zoological Studies, 39(1): 61-66.
Winchell, C. J., A. P. Martin, J. Mallatt (2004) Phylogeny of elasmobranches based on LSU and SSU ribosomal RNA genes. Molecular Phylogenetics and Evolution, 31: 214–224.
Wolstenholme, D. R and K. W. Jeon (1992) Mitochondrial Genomes. International Review of Cytology, vol. 141. Academic Press, San Diego.
Wourms, J. P. (1977) Reproduction and development in chondrichthyan fishes. American Zoologist, 17: 379-410.
Wourms, J. P., B. D. Grove and J. Lombardi (1988) The maternal-embryonic relationship in viviparous fishes. In: W. S. Hoar and D. J. Randall (Eds.) Fish physiology, Vol. 11, Academic Press, San Diego, pp. 1-134.
Xia, X. (2000) DAMBE: Data analysis in Molecular Biology and Evolution. Department of Ecology and Biodiversity, University of Hong Kong.