過去西太平洋親緣地理研究主要偏向於大尺度範圍探討遺傳結構與地理分布，然而從未有研究指出對於小尺度範圍的是否會有明顯的遺傳結構與地理分布的關係。因此，在本篇研究中，將利用粒線體DNA細胞色素b序列，以臺灣島為一小尺度探討周圍海域花身鯻之族群結構及其親緣地理。研究上採用11個族群，西邊從臺北到高雄，東邊為宜蘭、花蓮港、花蓮豐濱溪、台東，離島澎湖以及大陸廣東省饒平市，共97個個體。由類聚分析法(Neighbor-joining)重建親緣關係樹以及Nested clade analysis分析，可分為兩個大譜系(Lineage A,B)，但無法以地理或河域區分，型態上測量兩譜系中花身鯻側線鱗數目，發現兩譜系的側線鱗數目並無差異。所有樣本、譜系A以及譜系B的單型基因歧異度(H)為0.94、0.90和0.94以及核苷酸歧異度(π)為0.00567、0.00229和0.00465。在族群遺傳結構中，分子變異分析(AMOVA)結果顯示主要變異來自個體間的差異。族群間分化指數0到0.20306之間。關於族群歷史動態方面，在Tajima’s D值，譜系A、譜系B為負值，只有譜系A達到顯著水準；在Fu’s FS test中，譜系A、譜系B為負值，只有譜系B未達到顯著水準，不過可知道譜系A都曾經歷過族群擴張現象，另外譜系B則是屬於較弱的族群擴張，這現象也可以在適合度檢定(Goodness-of-fit test)和族群變異分佈檢測(mismatch distribution)中得知。綜合上述結果我們可以知道臺灣周圍海域花身鯻均曾發生過族群擴張現象。此現象可能與過去更新世時代，冰河時期海平面波動導致族群產生分隔效應，但在冰河退卻後，各族群間產生基因交流有關，可能是造成現在臺灣周圍海域花身鯻族群遺傳與族群變動的原因，這結果也能從貝氏天際線點圖得知族群擴張時間約在一萬到兩萬五千前之間，並與更新世時期最後一次冰河時期時間(約一萬到七萬年前)相符合。

In the past studies, phylogeography and population genetics of marine fishes were focused on large-scale research. However, to date, none of previous studies on marine fishes were conducted with a small sampling rage to show lack of genetic structure in a limited area. Taiwan, a small island, would be an ideal locality to test whether population genetic structure can be observed in small geological range. In this study, we examined cytochrome b sequences to estimate population genetics of Terapon. jarbua around Taiwan. Ninety seven individuals were sampled from 10 localities throughout Taiwan and one locality in Guangdong. NJ tree and NCA show T. jarbua are divided into two groups, but correlation of sampling localities to genetic structure is absent and gene flow among localities is common. High level of haplotype diversity (H=0.935) are detected, indicating a high level of genetic diversity and low level of nucleotide diversity (π=0.00567). Conventional population FST (0~0.2031) comparisons revealed lack of significant genetic structure indicated that T. jarbua likely experienced a demographic expansion and that is also supported by mismatch distribution and goodness-of-fit test. Based on the data from this study, we suggest T. jarbua around Taiwan experienced expansion. According to Bayesian skyline plot T. jarbua experienced population expansion since 10,000 to 25,000 BP, which matched the last glacier between 10,000 to 70,000 BP in the Pleistocene. Sea-level changes might exert efforts on population isolation. After the glacial, frequent gene flows among populations would be the reason for shaping population genetic and population demographic of T. jarbua around Taiwanese waters.

論文審定書------- i
謝辭----------------- ii
中文摘要-----------iii
英文摘要-----------iv
目錄-----------------vi
表目錄--------------vii
圖目錄--------------viii
附錄-----------------ix
壹、前言------------1
貳、材料與方法--8
參、結果-----------16
肆、討論-----------21
伍、結論-----------27
參考資料-----------28
附表-----------------36
附圖-----------------44
附錄-----------------50

沈世傑. 1987. 臺灣近海魚類圖鑑。臺灣省立博物館,台北,臺灣.
沈世傑主編. 1993, 台灣魚類誌。國立臺灣大學動物學系,台北,臺灣.
何源興, 劉燈城. 1991. 花身雞魚(Terapon jarbua)之繁殖試驗. 台灣省水產試驗所試驗報告(50):255-265.
林丞坤、吳小根. 1999. 長江徑流量特性及其重要意義的研究. 自然雜誌 21(4):200-205.
周銘泰、高瑞卿. 2013. 臺灣淡水及河口魚圖鑑. 晨星出版社. 台中, 臺灣.
許桂菁、蔡昆展、邵廣昭、王建平和林宏都. 2005. 大眼華編親緣地理與族群遺傳結構之研究. Bio Formosa 40(2):58-67.
陳義雄、方力行. 1999. 臺灣淡水及河口魚類誌. 國立海洋生物博物館籌備處.屏東,臺灣.
游蒼林, 游健安. 1987. 放養密度對花身雞魚成長之影響. 台灣省水產試驗所試驗報告43:1-6.
黃鎮國、張偉強、鍾新基、陳俊鴻、陳偉光. 1999. 台灣板塊構造與環境演變。海洋出版社. 北京, 中國.
劉振鄉. 1978. 花身雞魚生態調查及試驗. 台灣省水產試驗所試驗報. 30:321-326.
Abirami, J., M. Bharathi, and S. Kumaresan. 2012. Studies on toxicity effects of Endosulfan on Terapon jarbua and some aspects of histopathology and biochemical compositions. Journal of Pharmacy Research 5(2):754-759.
Avise, J. C., and coauthors. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics:489-522.
Bing-xian, G. 1994. Patterns and structures of the currents in Bohai, Huanghai and East China Seas. Pages 17-26 in Oceanology of China Seas. Springer.
Bowen, B., A. Bass, L. Rocha, W. Grant, and D. R. Robertson. 2001. Phylogeography of the trumpetfishes (Aulostomus): ring species complex on a global scale. Evolution 55(5):1029-1039.
Brown, W. M., M. George, and A. C. Wilson. 1979. Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences 76(4):1967-1971.
Chang, C. W., Y. Wang, and W. N. Tzeng. 2010. Morphological study on vertebral deformity of the thornfish Terapon jarbua in the thermal effluent outlet of a nuclear power plant in Taiwan. Journal of The Fisheries Society of Taiwan 37(1):1-11.
Cheang, C. C., and coauthors. 2012. Phylogeography of the cold‐water barnacle Chthamalus challengeri in the north‐western Pacific: effect of past population expansion and contemporary gene flow. Journal of Biogeography 39(10):1819-1835.
Chen, C. A., and coauthors. 2004. Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China Sea revealed by mitochondrial control region sequences. Marine Biotechnology 6(4):312-326.
Chen, C. C., F. K. Shiah, K. P. Chiang, G. C. Gong, and W. M. Kemp. 2009. Effects of the Changjiang (Yangtze) River discharge on planktonic community respiration in the East China Sea. Journal of Geophysical Research: Oceans (1978–2012) 114(C03005).
Chen, S. F., B. Q. Huang, and Y. Y. Chien. 1998. Histochemical characteristics of sonic muscle fibers in tigerperch, Terapon jarbua. Zoological Studies 37:56-62.
Chen, S. P., T. Liu, Z. F. Li, and T. X. Gao. 2008. Genetic population structuring and demographic history of red spotted grouper (Epinephelus akaara) in South and East China Sea. African Journal of Biotechnology 7(20). 3354-3562.
Chen, X. L., and coauthors. 2007. Mitochondrial DNA phylogeography of Glyptothorax fokiensis and Glyptothorax hainanensis in Asia. Journal of Fish Biology 70(sa):75-93.
Cheng, H. L., S. Huang, and S. C. Lee. 2005. Phylogeography of the endemic goby, Rhinogobius maculafasciatus (Pisces: Gobiidae), in Taiwan. Zoological Studies 44(3):329.
Chiang, H.-C., C.-C. Hsu, G. C.-C. Wu, S.-K. Chang, and H.-Y. Yang. 2008. Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA. Fisheries Research 90(1):305-312.
Clary, D. O., and D. R. Wolstenholme. 1985. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. Journal of Molecular Evolution 22(3):252-271.
Clement, M., D. Posada, and K. A. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9(10):1657-1659.
Davis, A., P. Unmack, B. J. Pusey, J. Johnson, and R. Pearson. 2012. Marine–freshwater transitions are associated with the evolution of dietary diversification in terapontid grunters (Teleostei: Terapontidae). Journal of evolutionary biology 25(6):1163-1179.
Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC evolutionary biology 7(1):214.
Durand, J.-D., C. S. Tsigenopoulos, E. Ünlü, and P. Berrebi. 2002. Phylogeny and Biogeography of the Family Cyprinidae in the Middle East Inferred from Cytochrome b DNA—Evolutionary Significance of This Region. Molecular Phylogenetics and Evolution 22(1):91-100.
Excoffier, L., and H. E. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10(3):564-567.
Excoffier, L., and S. Schneider. 1999. Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions. Proceedings of the National Academy of Sciences 96(19):10597-10602.
Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131(2):479-491.
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
Fu, Y. X., and W. H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133(3):693-709.
Gifford, M. E., R. Powell, A. Larson, and R. L. Gutberlet Jr. 2004. Population structure and history of a phenotypically variable teiid lizard (Ameiva chrysolaema) from Hispaniola: the influence of a geologically complex island. Molecular Phylogenetics and Evolution 32(3):735-748.
Golani, D., and B. Appelbaum-Golani. 2010. First record of the Indo-Pacific fish the Jarbua terapon (Terapon jarbua)(Osteichthyes: Terapontidae) in the Mediterranean with remarks on the wide geographical distribution of this species. Scientia Marina 74(4):717-720.
Grant, W., and B. 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(5):415-426.
Han, Z. Q., T. X. Gao, T. Yanagimoto, and Y. Sakurai. 2008a. Genetic population structure of Nibea albiflora in Yellow Sea and East China Sea. Fisheries Science 74(3):544-552.
Han, Z. Q., Y. Z. Li, G. B. Chen, and T. X. Gao. 2008b. Population genetic structure of coral reef species Plectorhinchus flavomaculatus in South China Sea. African Journal of Biotechnology 7(11).
Harpending, H. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology:591-600.
Hewitt, G. 2000. The genetic legacy of the Quaternary ice ages. Nature 405(6789):907-913.
Hewitt, G. M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58(3):247-276.
Hillis, D. M., C. Moritz, B. K. Mable, and R. G. Olmstead. 1996. Molecular systematics, volume 23. Sinauer Associates Sunderland, MA.
Hua, X., and coauthors. 2009. Phylogeographical analysis of an estuarine fish, Salanx ariakensis (Osmeridae: Salanginae) in the north‐western Pacific. Journal of Fish Biology 75(2):354-367.
Hudson, R. R., M. Slatkin, and W. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132(2):583-589.
Ichikawa, H., and R. C. Beardsley. 2002. The current system in the Yellow and East China Seas. Journal of Oceanography 58(1):77-92.
Jackson, D., F. Lewis, G. Taylor, A. Boylston, and P. Quirke. 1990. Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction. Journal of Clinical Pathology 43(6):499-504.
Jan, S., J. Wang, C.-S. Chern, and S.-Y. Chao. 2002. Seasonal variation of the circulation in the Taiwan Strait. Journal of Marine Systems 35(3):249-268.
Ju, Y. M., and coauthors. 2013. Population structure and demographic history of Sicyopterus japonicus (Perciformes; Gobiidae) in Taiwan inferred from mitochondrial control region sequences. Genetics and Molecular Research: GMR 12(3):4046-4059.
Jukes, T., and C. Cantor. 1969. Evolution of protein molecules, Munro HN, Mammalian protein metabolism. Pages 21-132 in. Academic Press, New York.
Kalyabina, S., and coauthors. 2001. Phylogeography and systematics of Lacerta agilis based on mitochondrial cytochrome b gene sequences: first results. Russian Journal of Herpetology 8(2):149-158.
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16(2):111-120.
Kimura, M. 1983. Rare variant alleles in the light of the neutral theory. Molecular Biology and Evolution 1(1):84-93.
King, J. L., T. H. Jukes, and B. Clarke. 1969. Non-darwinian evolution. Bobbs-Merrill.
Kokita, T., and K. Nohara. 2011a. Phylogeography and historical demography of the anadromous fish Leucopsarion petersii in relation to geological history and oceanography around the Japanese Archipelago. Molecular Ecology 20(1):143-164.
Kokita, T., and K. Nohara. 2011b. Phylogeography and historical demography of the anadromous fish Leucopsarion petersii in relation to geological history and oceanography around the Japanese Archipelago. Molecular Biology 20(1):143-164.
Librado, P., and J. Rozas. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451-1452.
Lin, H., and coauthors. 2008. Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation. Journal of Fish Biology 72(8):2011-2025.
Lin, K., and S. C. Lee. 1991. Feeding Habits of the Thornfish, Terapon Jarbua (Forskal) from the Estuary of Tanshui River and Its Adjacent Waters. Journal of The Fisheries Society of Taiwan 18(4):257-264.
Lin, Y. 1995. Study on the relationship between high water temperature and malformed thornfish (Terapon jarbua). MS Thesis, Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan.
Liu, J. X., T. X. Gao, S. F. Wu, and Y. P. Zhang. 2007a. Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Molecular Ecology 16(2):275-288.
Liu, J. X., and coauthors. 2007b. Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis). Molecular Phylogenetics and Evolution 40(3):712-723.
Liu, S. Y. V., T. Kokita, and C. F. Dai. 2008. Population genetic structure of the neon damselfish (Pomacentrus coelestis) in the northwestern Pacific Ocean. Marine Biology 154(4):745-753.
Manoharan, J., A. Gopalakrishnan, D. Varadharajan, B. Thilagavathi, and S. Priyadharsini. 2012. Stomach content analysis of Terapon jarbua(Forsskal) from Parangipettai coast, South East Coast of India. Advances in Applied Science Research 3:2605-2621.
Martinez-solano, I., J. Teixeira, D. Buckley, and M. GARCÍA‐PARÍS. 2006. Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic. Molecular ecology 15(11):3375-3388.
McManus, J. 1985. Marine speciation, tectonics and sea-level changes in southeast Asia. Pages 133-138 in Proceedings of the Fifth International Coral Reef Congress, Tahiti.
Miu, T. C., S. C. Lee, and W. N. Tzeng. 1990. Reproductive biology of Terapon jarbua from the estuary of Tamshui River. Journal of The Fisheries Society of Taiwan 17(1):9-20.
Moravec, F., A. Gopalakrishnan, M. Rajkumar, A. Saravanakumar, and S. Kaliyamoorthy. 2011. A new gonad-infecting species of Philometra Costa, 1845 (Nematoda: Philometridae) from the marine fish Terapon jarbua (Forsskål)(Terapontidae) off the eastern coast of India. Systematic Parasitology 80(1):23-33.
Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press.
Nei, M., and F. Tajima. 1983. Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105(1):207-217.
Neigel, J. E., and J. C. Avise. 1993. Application of a random walk model to geographic distributions of animal mitochondrial DNA variation. Genetics 135(4):1209-1220.
Nelson, J. S. 2006. Fishes of the World. John Wiley & Sons.New York.
Okimoto, R., J. Macfarlane, D. Clary, and D. Wolstenholme. 1992. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130(3):471-498.
Onuki, A., and H. Somiya. 2007. Innervation of sonic muscles in teleosts: occipital vs. spinal nerves. Brain, behavior and evolution 69(2):132-141.
Peng, S., and coauthors. 2009. Genetic diversity of silver pomfret (Pampus argenteus) populations from the China Sea based on mitochondrial DNA control region sequences. Biochemical Systematics and Ecology 37(5):626-632.
Peng, Z., S. He, and Y. Zhang. 2004. Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences. Molecular Phylogenetics and Evolution 31(3):979-987.
Perdices, A., C. Cunha, and M. Coelho. 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(1):192-203.
Ramos-Onsins, S. E., and J. Rozas. 2002. Statistical properties of new neutrality tests against population growth. Molecular Eiology and Evolution 19(12):2092-2100.
Ravago-gotanco, and M. Juinio-menez. 2010. Phylogeography of the mottled spinefoot Siganus fuscescens: Pleistocene divergence and limited genetic connectivity across the Philippine archipelago. Molecular Ecology 19(20):4520-4534.
Rogers, A. R. 1995. Genetic evidence for a Pleistocene population explosion. Evolution:608-615.
Rogers, A. R., and H. Harpending. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9(3):552-569.
Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4):406-425.
Schneider, S., D. Roessli, and L. Excoffier. 2000. Arlequin ver. 2.000. A software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
Slatkin, M., and R. R. Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129(2):555-562.
Szabó, Z., B. Snelgrove, M. T. Craig, L. A. Rocha, and B. W. Bowen. 2014. Phylogeography of the manybar goatfish, Parupeneus multifasciatus, reveals isolation of the Hawaiian Archipelago and a cryptic species in the Marquesas Islands. Bulletin of Marine Science 90(1):493-512.
Tamura, K., and coauthors. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28(10):2731-2739.
Tsang, L. M., B. K. Chan, K. Y. Ma, and K. H. Chu. 2008. Genetic differentiation, hybridization and adaptive divergence in two subspecies of the acorn barnacle Tetraclita japonica in the northwestern Pacific. Molecular Ecology 17(18):4151-4163.
Wang, B. D., X. L. Wang, and R. Zhan. 2003. Nutrient conditions in the Yellow Sea and the East China Sea. Estuarine, Coastal and Shelf Science 58(1):127-136.
Wang, D. Y., and B. Q. Huang. 1999. TBT (Tributyltin) Toxicity to the Visual and Olfactory Functions of Tigerperch (Terapon jarbua Forsskal). Zoological Studies 38(2):189-195.
Wang, J. P., K. C. Hsu, and T. Y. Chiang. 2000. Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan. Molecular Ecology 9(10):1483-1494.
Wang, P. 1999. Response of Western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features. Marine Geology 156(1):5-39.
Wang, P. C., and coauthors. 2009. Nocardia seriolae infection in the three striped tigerfish, Terapon jarbua (Forsskål). Journal of fish diseases 32(4):301-310.
Wang, T. Y., T. Y. Liao, and C. S. Tzeng. 2007. Phylogeography of the Taiwanese endemic hillstream loaches, Hemimyzon formosanus and H. taitungensis (Cypriniformes: Balitoridae). Zoological studies 46(5):547.
Whitfield, A., and S. Blaber. 1978. Scale‐eating habits of the marine teleost Terapon jarbua (Forskål). Journal of Fish Biology 12(1):61-70.
Wright, S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395-420.
Xiao, Y., and coauthors. 2009a. Genetic diversity in the mtDNA control region and population structure in the small yellow croaker Larimichthys polyactis. Environmental Biology of Fishes 85(4):303-314.
Xiao, Y. S., and coauthors. 2009b. Genetic diversity in the mtDNA control region and population structure in the small yellow croaker Larimichthys polyactis. Environmental Biology of Fishes 85(4):303-314.
Xu, X., and M. Oda. 1999. Surface-water evolution of the eastern East China Sea during the last 36,000 years. Marine Geology 156(1):285-304.