硨磲貝生長於淺水域珊瑚礁區，是具有高度經濟價值的物種，也是早期用來製作干貝的主要原料，現今族群量大幅減少，被CITES列為世界稀有海洋生物。本研究探討不同樣本保存方式對基因序列鑑定硨磲貝物種能力的影響，並檢測市售干貝是否仍有保育類的硨磲貝。從墾丁、綠島、蘭嶼、小琉球及澎湖的珊瑚礁區，採集硨磲蛤科和江珧蛤科物種，並購買市售的干貝產品，利用四段DNA序列（COI, 16S, 18S, 28S）及外型特徵鑑定物種，並檢測-70 ℃冷凍保存、70 %酒精保存、烘乾、冷凍乾燥四種樣本保存方式對DNA的影響。由DNA序列結果可知，COI 及16S序列的物種鑑別力高；18S與28S屬於較保守的序列片段，這兩段序列在同科的物種間變異性低，因此這兩段序列較適合做高階層物種鑑定，序列結果並顯示長硨磲貝Tridacna maxima中有一隱藏種為諾亞硨磲貝Tridacna noae；四種保存方式的硨磲貝樣本萃取都可以得到10Kb以上的DNA，單一個體四段序列四種處理間差異大多在0 - 0.020內，而樣本的種內個體間差異為0 - 0.070，四種保存方式中，並沒有特別不適用的保存方式。檢測市售干貝的製作原料，發現所有的干貝都是由扇貝製成，其中大部分是帆立貝Patinopecten yessoensis少部分為海灣扇貝Argopecten irradians，顯示硨磲貝與江珧蛤已非製作干貝的原料。

Giant clams (Tridacnidae) are economic species which have been the main materials for ganbei. Due to a huge decline in population size, it was reported as an endangered species in CITES list. In this study, the effects of different preservative methods on the expression of DNA sequences in giant clams were examined and whether ganbai is made from giant clams were also determined. I collected samples from Kenting, Green Island, Orchid Island, Shaio-Liu-Chu and Penghu Islands. And, ganbei were bought from markets. Species identification was based on four DNA sequences (COI, 16S, 18S, 28S) and morphological characters. The distinction power of four preservative methods (-70 ℃ frozen, 70 % ethanol, dried and freeze dried) on clam samples was evaluated. DNA sequences of CO1 and 16S are the best fragments to distinguish samples at species level. Additionally, a cryptic species of Tridacna noae was found from Tridacna maxima. The 18S and 28S sequences have low variation among giant clam species which are more suitable for higher level of phylogeny. The DNA fragments with different preservative methods were mostly in good condition having extracted DNA size up to 10 Kb. The sequencing divergences of the four preservation were 0 - 0.020 within an individual and 0 - 0.070 among individuals. In conclusion, the four preservative methods are similar in sequence expression. Ganbei made from giant clams was not found in the market. Instead, commercial ganbei are made from scallops, mostly Patinopecten yessoensis and some Argopecten irradians.

謝辭…………………………………………………………………………………..………i
中文摘要…………………………………………………….………………………………ii
英文摘要……………………………………………………………………………………iii
目錄…………………………………………………………………………………………iv
表目錄……………………………………………………………………...………...……...v
圖目錄……………………………………………………………………………….……...vi
附錄目錄………………………………………………………………….………………..vii
前言……………………………………………………………………....…….…………….1
材料與方法………………………………………………………………….……………….7
結果…………………………………………………………………………….……..…….11
討論……………………………………………………………………………....…………16
參考文獻……………………………………………………………………….…...………22
表...…………………………………………………………………………………...……..28
圖...……………………………………………………………………………………...…..34
附錄………………………………………………………………………………………....60

http://www.cites.org/ Convention on International Trade in Endangered Species of Wild Fauna and Flora.
http://www.wow.org.tw/ 東亞野生物貿易研究委員會。
澎湖海域硨磲渠貝人工繁養殖及發展生態旅遊之運用
http://www.fao.org/fishery/culturedspecies/Patinopecten_yessoensis/en Fisheries and Aquaculture Department.
馬國欽 2006. 台灣鱲屬魚類(鲤目：鲤科)之系統分類、族群遺傳結構及生物親緣地理研究。國立台灣大學動物學研究研究所博士學位論文，114頁。
唐瀅清 2005. 以形態學及分子生物學的證據探討長硨磲貝（Tridacna maxima)之系統分類地位。國立臺灣海洋大學環境生物與漁業科學學系碩士學位論文，78頁。
郭筱清 2007. 台灣產擬鱸科系統分類研究。國立中山大學海洋生物研究所碩士學位論文，126頁。
朱育民 2001. 台灣產瓢鰭鰕虎屬之形態分類與mtDNA分子演化及日本瓢鰭鰕虎生殖生態之研究。國立中山大學海洋資源研究所碩士學位論文，61頁。
邵廣昭、彭鏡毅、吳文哲 2008. 台灣物種多樣性 II.物種名錄，行政院農業委員會林務局出版，796頁。
奧谷喬司 2000. 日本近海產貝類圖鑑，東海大學出版會。
王智文 2005. 台灣及大陸東南地區中華花鰍（Cobitis sinensis）種群型態系統分類、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學位論文，86頁。
王如才，1988. 中國水生貝類原色圖鑒，浙江科學技術出版社，。
吳全橙 1989. 漫談干貝。潮訊 3: 6-7.
久保弘文、岩井憲司. 2007. 同種として扱われていたシラナミ類２種について（シラナミの漁業資源生物学的研究）. J-Global. 2006: 205-210.
久保弘文、岩井憲司、井上顕. 2008. シラナミ類の保護水面等における資源実態について（シラナミの漁業資源生物学的研究）. 沖縄水海研セ事報 69: 103-107.
久保弘文、井上顕. 2008. シラナミ生殖腺の成熟について（シラナミの漁業資源生物学的研究）. 沖縄水海研セ事報 69: 108-112.
Arévalo, E., Y. Zhu, J. M. Carpenter and J. E. Strassmann. 2004. The Phylogeny of the Social Wasp Subfamily Polistinae: Evidence from Microsatellite Flanking Sequences, Mitochondrial COI Sequence, and Morphological Characters. BMC Evolutionary Biology. 4: 16p.
ANNEX D: Fish and Invertebrates Prepared for the CITES Animals Committee, CITES Secretariat. 2004. p.185-206.
Andre’fouet, S., A. Gilbert, L. Yan, G. Remoissenet, C. Payri and Y. Chancerelle. 2005. The Remarkable Population Size of the Endangered Clam Tridacna maxima Assessed in Fangatau Atoll (Eastern Tuamotu, French Polynesia) Using in situ and Remote Sensing Data. ICES Journal of Marine Science, 62: 1037-1048.
Blankenship, L. E. and A. A. Yayanos. 2005. Universal Primers and PCR of Gut Contents to Study Marine Invertebrate Diets. Molecular Ecology 14: 891–899.
Braley, R.D.. 1989. A Giant Clam Stock Survey and Preliminary Investigation of Pearl Oyster Resource in the Tokelau Islands. Zoology Department, James Cook University Townsville, Qld. 4811, Australia.
Canapa, A., M. Barucca, A. Marinelli and Ettore Olmo. 2000. Molecular Data from the 16S rRNA Gene for the Phylogeny of Pectinidae (Mollusca: Bivalvia). Journal of Molecular Evolution. 50: 93-97.
Canapa, A., M. Barucca, A. Marinelli and Ettore Olmo. 2001. A Molecular Phylogeny of Heterodonta (Bivalvia) Based on Small Ribosomal Subunit RNA Sequences. Molecular Phylogenetics and Evolution. 21: 156-161.
Crandall, K. A., D. J. Harris and J. W. Fetzner Jr.. 2000. The Monophyletic Origin of Freshwater Crayfish Estimated from Nuclear and Mitochondrial DNA Sequences. Proceedings. Biological sciences / The Royal Society. 267: 1679-1686.
Ellis, S.. 1998. Spawning and Early Larval Rearing of Giant Clams (Bivalvia: Tridacnidae). Center for Tropical and Subtropical Aquaculture Publication Number No. 130.
Fay, C. W., R. J. Neves and Garland B. Pardue. 1983. Species Profiles: Life Histories and Environmental Requirement of Coastal Fishes and Invertebrates (Mid-Atlantic). Fish and Wildlife Service. pp.17.
Felsenstein, J.. 1985. Confidence Limit on Phylogenies: an Approach Using the Bootstrap. Evolution. 39: 783-791.
Folmer, O., M. Black, W. Hoeh, R. Lutz and R. Vrijenhoek. 1994. DNA Primer for Amplification of Mitochondrial Cytochrome c Oxidase Subunit I from Diverse Metazoan Invertebrate. Molecular Marine Biology and Biotechnology. 3: 294-299.
Gilbert, A., S. Andre’fouet, L. Yan and G. Remoissenet. 2006. The Giant Clam Tridacna maxima Communities of Three French Polynesia Islands: Comparison of Their Population Sizes and Structures at Early Stages of Their Exploitation. ICES Journal of Marine Science, 63: 1573-1589.
Hajibabaei, M., D. H. Janzen, J. M. Burns, W. Hallwachs and P. D. N. Hebert. 2006. DNA Barcodes Distinguish Species of Tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America. 103: 968-971.
Hajibabaei, M., J. R. deWaard, N. V. Ivanova, S. Ratnasingham, R. T. Dooh, S. L. Kirk, P. M. Mackie and P. D. N. Hebert. 2005. Critical Factors for Assembling a High Volume of DNA Barcodes. Philosophical Transaction of the Royal Society. 360: 1959-1697.
Hajibabaei, M., M. A. Smith, D. H. Janzen, J. J. Rodriguez, J. B. Whitfield and P. D. N. Hebert. 2006. A Minimalist Barcode can Identify a Specimen Whose DNA is Degraded. Molecular Ecology Note. 6: 959-964.
Hebert , P. D. N., A. Cywinska, S. L. Ball and J. R. deWaard. 2003. Biological Identifications through DNA Barcodes. The Royal Society. 270: 313–321.
Hebert, P. D. N., S. Ratnasingham and J. R. deWaard. 2003. Barcoding Animal Life: Cytochrome c Oxidase Subunit I Divergences Among Closely Related Species. Proceedings. Biological sciences / The Royal Society. 270: 96-99.
Hsieh, H. J., Y. L. Hsien, W. S. Tsai, C. A. Chen, W. C. Su, M. S. Jeng. 2008. Tropical Fishes Killed by The Cold. Coral Reefs. pp. 1.
Jamison, B. G. M., S. Tillier, A. Tilliier, J.-L. Justine, E. Ling, S. James, K. McDonald, A. F. Hugall. 2002. Phylogeny of the Megascolecidae and Crassiclitellata (Annelida, Oligochaeta): Combined Versus Partitioned Analysis Using Nuclear (28S) and Mitochondrial (12S, 16S) rDNA. Zoosystema. 24: 707-734.
Järnegren, J., C. Schander, J. A. Sneli, V. Rønningen, C. M. Young. 2007. Four Genes, Morphology and Ecology: Distinguishing a New Species of Acesta (Mollusca; Bivalvia) from the Gulf of Mexico. Marine Biology. 152: 43-55.
Jorgensen, A., T. K. Kristensen and H. Madsen. 2007. A Molecular Phylogeny of Apple Snails (Gastropoda, Caenogastropoda, Ampullariidae) with an Emphasis on African Species. Zoologica Scripta, 37: 245-252
Kimura, M.. 1980. A Simple Method for Estimating Evolutionary Rate of Base Substitutions through Comparative Studies of Nucleotide Sequence. Journal of Molecular Evolution. 16: 111-120.
Knop D.. 1996. Giant Clams: A Comprehensive Guide to the Identification and Care of Tridacnid Clams. Kraft Druck GmbH. pp. 255.
Kumar S., K. Tamura and M. Nei. 2004. Integrated Software for Molecular Evolutionary Genetic Analysis and Sequences Alignment. Briefings in Bioinformatics. 5: 150-163.
McLean R. A.. 1947. A Revision of the Pelecypod Family Tridacnidae. The Academy of Nature Sciences of Philadelphia. Notulae Naturae. Number 195.
Meusnier, I., G. A. C. Singer, J. F. Landry, D. A. Hickey, P. D. N. Hebert and M. Hajibabaei. 2008. A Universal DNA Mini-barcode for Biodiversity Analysis. BMC Genomics 9: 214.
Richter, C., H. Roa-Quiaoit, C. Jantzen, M. Al-Zibdah and M. Kochzius. 2008. Collapse of a New Living Species of Giant Clam in the Red Sea. Current Biology. 18: 1349-1354.
Roa-Quiaoit, H. A. F.. 2005. The Ecology and Culture of Giant Clams (Tridacnidae) in the Jordanian Sector of the Gulf of Aqaba, Red Sea. The Thesis of University of Bremen. pp. 100.
Second International Barcode of Live Conference: Conference Abstracts. 2007. pp. 160.
Tisdell, C. and Cheng-Ho Chen. 1992. Notes on the Use Giant Clam Meat for Food in Taiwan. Research Report and Paper in Economics of Giant Clam Mariculture. No. 36. pp. 24.
Van Oppen, M. J. H., B. J. McDonald, B. Willis and D. J. Miller. 2001. The Evolutionary History of the Coral Genus Acropora (Scleractinia, Cnidaria) Based on a Mitochondrial and a Nuclear Marker: Reticulation, Incomplete Lineage Sorting, or Morphological Convergence? Molecular Biology and Evolution. 18:1315–1329.
Wang, Y., H. Zhao and J. Hao. 2005. Phylogenetic Analyses Among the Main Lineages of Gastropoda (Mollusca) Based on Partial 28S rRNA Gene Sequences. Journal of Genetics and Molecular Biology. 16: 117-127.
Ward, R. D., T. S. Zemlak, B. H. Innes, P. R. Last and P. D. N. Hebert. 2005. DNA Barcoding Australia’s Fish Species. Philosophical Transaction of the Royal Society. 360: 1847-1857.
Williams, D., T. P. Gillis and W. G. Dupree. 1995. Ethanol Fixation of Sputum Sediments for DNA-Based Detection of Mycobacterium tuberculosis. Journal of Clinical Mircrobiology. 33: 1558-1561.
Williams, S.T. D.G. Reid and D.T.J. Littlewood. 2003. A Molecular Phylogeny of the Littorininae (Gastropoda: Littorinidae): Unequal Evolutionary Rates, Morphological Parallelism, and Biogeography of the Southern Ocean. Molecular Phylogenetics and Evolution. 28: 60-86.
Winnepenninckx, B. M. H., D, G. Reid, T, Backeljau. 1998. Performance of 18S rRNA in Littorinid Phylogeny (Gastropoda: Caenogastropoda). Journal of Molecular Evolution. 47: 586-596.
Zimmermann, J., M. Hajibabaei, D. C. Blackburn, J. Hanken, E. Cantin, J. Posfai1 and T. C. Evans Jr.. 2008. DNA Damage in Preserved Specimens and Tissue Samples: a Molecular Assessment. Frontiers in Zoology. 5:18 pp. 13.