紅斑赤蝦 (Metapenaeopsis barbata)，俗稱火燒蝦或鬚赤蝦，分布在東海、台灣海峽及南海等地，是拖網漁業中具高經濟價值之漁獲物。為恐紅斑赤蝦因過度捕撈而枯竭，瞭解紅斑赤蝦族群結構與動態並制定適當的漁業管理措施，以確保其永續利用乃當務之急。因此本研究蒐集來自東海、南海及台灣海峽6個不同漁場 (日本、台中、茄萣、長江口、福建及南海) 總共214隻紅斑赤蝦的樣本，根據粒線體的COI序列和本研究找出的8組細胞核微衛星(microsatellite) 基因座，來分析紅斑赤蝦的族群遺傳結構。從COI的結果顯示族群呈現擴張現象，推測紅斑赤蝦因最後一次冰河時期影響，造成瓶頸效應並且產生分群，之後因海平面上升而造成其擴張。從微衛星資料顯示近期紅斑赤蝦族群間基因交流順暢，成為一隨機交配群 (panmictic group)，推測是在幼苗時期因洋流的傳送而造成族群遺傳變異的均質化。族群分化方面，COI資料顯示長江口族群與其他族群呈現分化狀態 (FST > 0.05)，推測是因此族群生活環境跟其他族群不同所致；微衛星資料則顯示族群間無顯著的差異。然而COI的核苷酸歧異度 (π) 與微衛星的對偶基因豐富度 (AR) 都顯示出具有較低的遺傳歧異度，因此為達永續利用之目的，仍需對紅斑赤蝦進行長時間的調查。

The red-spot prawn (Metapenaeopsis barbata), a commercially important shrimp, is a demersal species widely distributed in the East China Sea, the Taiwan Strait and the South China Sea. For protecting the overexploited, threatened natural resources of M. barbata, suitable strategies to maintain sustainable populations are urgently required. However, little is known about the genetic diversity and population structure. In this study, population genetic structure of M. barbata was investigated based on mitochondrial COI and microsatellite fingerprinting. A total of 214 samples were collected from six fishing grounds of the East China Sea, the South China Sea and the Taiwan Strait (Japan, Taichung, Cheding, Yangtze River, Fujian and Hong Kong). Analyses of the COI data revealed that M. barbata experienced demographic bottlenecks during the past glaciation and a subsequent population expansion. Microsatellite data revealed that M. barbata represent a single panmictic population mediated with frequent gene flow among subpopulations, largely due to larval dispersal with ocean currents. In contrast, higher genetic differentiation based on the COI variation was detected between populations of the Yangtze River and others, suggesting the existence of certain habitat heterogeneities. Analyses of COI and microsatellite data all revealed a low genetic variation. The information obtained in this study offers insights into future fishery management measures.

Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press,Cambridge, MA.
Avise JC, Arnold J, Ball RM, et al. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual review of ecology and systematics 18, 489-522.
Babbucci M, Buccoli S, Cau A, et al. (2010) Population structure, demographic history, and selective processes: Contrasting evidences from mitochondrial and nuclear markers in the European spiny lobster Palinurus elephas (Fabricius, 1787). Molecular Phylogenetics and Evolution 56, 1040-1050.
Baker AJ (2000) Molecular Methods In Ecology.Wiley-Blackwell, Malden,MA.
Ball AO, Chapman RW (2003) Population genetic analysis of white shrimp, Litopenaeus setiferus, using microsatellite genetic markers. Molecular Ecology 12, 2319-2330.
Barcia AR, Lopez GE, Hernandez D, Garcia ME (2005) Temporal variation of the population structure and genetic diversity of Farfantepenaeus notialis assessed by allozyme loci. Molecular Ecology 14, 2933-2942.
Bohlen J, lechtova V, Doadrio I, Rab P (2007) Low mitochondrial divergence indicates a rapid expansion across Europe in the weather loach, Misgurnus fossilis (L.). Journal of Fish Biology 71, 186-194.
Brown A (1978) Isozymes, plant population genetic structure and genetic conservation. TAG Theoretical and Applied Genetics 52, 145-157.
Budowle B, Chakraborty R, Giusti AM, Eisenberg AJ, Allen RC (1991) Analysis of the VNTR locus D1S80 by the PCR followed by high-resolution PAGE. American Journal of Human Genetics 48, 137.
Carvalho G (1993) Evolutionary aspects of fish distribution: genetic variability and adaptation. Journal of Fish Biology 43, 53-73.
Chareontawee K, Poompuang S, Na-Nakorn U, Kamonrat W (2007) Genetic diversity of hatchery stocks of giant freshwater prawn (Macrobrachium rosenbergii) in Thailand. Aquaculture 271, 121-129.
Chiang TY, Lin HD, Chan TY, Hung CY, Lin FJ (2008) Isolation and characterization of microsatellite loci in the commercially important mudshrimp Austinogebia edulis (Upogebiidae) using PCR-based isolation of microsatellite arrays (PIMA). Conservation Genetics 9, 1653-1655.
Chinnasamy K, Pitchamuthu M, Doss PS, Marimuthu G, Rajan KE (2011) Genetic diversity and population structure of leaf-nosed bat Hipposideros speoris (Chiroptera: Hipposideridae) in Indian subcontinent. African Journal of Biotechnology 10, 1320-1328.
Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144, 2001.
Dixon TJ, Coman GJ, Arnold SJ, et al. (2008) Shifts in genetic diversity during domestication of Black Tiger shrimp, Penaeus monodon, monitored using two multiplexed microsatellite systems. Aquaculture 283, 1-6.
Donaldson SL, Chopin T, Saunders GW (2000) An assessment of the AFLP method for investigating population structure in the red alga Chondrus crispus Stackhouse (Gigartinales, Florideophyceae). Journal of Applied Phycology 12, 25-35.
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7, 214.
Drummond A, Rambaut A, Shapiro B, Pybus O (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution 22, 1185.
Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology 11, 2571-2581.
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 2611-2620.
Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics 1, 47-50.
Excoffier L, Smouse PE (1994) Using allele fequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136, 343-359.
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294.
Freeland JR (2005) Molecular Ecology. John Wiley & Sons, Chichester, UK.
Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915.
George M, Muthu M (1968) On the occurrence of Metapenaeopsis barbata (De Haan)(Decapoda: Penaeidae) in Indian waters with taxonomic notes on the genus. Journal of the Marine Biological Association of India 10, 286-291.
Grant W, Bowen B (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.
Hamrick J (1982) Plant population genetics and evolution. American Journal of Botany 69, 1685-1693.
Han ZQ, Gao TX, Yanagimoto T, Sakurai Y (2008) Genetic population ructure of Nibea albiflora in Yellow Sea and East China Sea. Fisheries Science 74, 544-552.
Harrison S (2004) Evolution, biogeography, and the utility of mitochondrial 16S and COI genes in phylogenetic analysis of the crab genus Austinixa (Decapoda: Pinnotheridae). Molecular Phylogenetics and Evolution 30, 743-754.
Hedrick PW (1984) Population Biology: The Evolution and Ecology of Populations. Jones and Bartlett publishers, Boston, USA.
Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405, 907-913.
Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58, 247-276.
Hillis DM, Moritz C, Mable BK, Olmstead RG (1996) Molecular Systematics. Sinauer Associates, Sunderland, MA.
Hsu KC, Wang JP, Chen XL, Chiang TY (2004) Isolation and characterization of microsatellite loci in Acrossocheilus paradoxus (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA). Conservation Genetics 5, 113-115.
Hudson RR, Slatkin M, Maddison W (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583.
Jan S, Wang J, Chern CS, Chao SY (2002) Seasonal variation of the circulation in the Taiwan Strait. Journal of Marine Systems 35, 249-268.
Kim WJ, Kim KK, Han HS, et al. (2010) Population structure of the olive flounder (Paralichthys olivaceus) in Korea inferred from microsatellite marker analysis. Journal of Fish Biology 76, 1958-1971.
Knowlton N, Weigt LA (1998) New dates and new rates for divergence across the Isthmus of Panama. Proceedings of the Royal Society of London. Series B: Biological Sciences 265, 2257.
Lambeck K, Esat TM, Potter EK (2002) Links between climate and sea levels for the past three million years. Nature 419, 199-206.
Lee HJ, Chao SY (2003) A climatological description of circulation in and around the East China Sea. Deep Sea Research Part II: Topical Studies in Oceanography 50, 1065-1084.
Li YL, Kong XY, Yu ZN, et al. (2010) Genetic diversity and historical demography of Chinese shrimp Feneropenaeus chinensis in Yellow Sea and Bohai Sea based on mitochondrial DNA analysis. African Journal of Biotechnology 8, 1193-1202.
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451.
Liu JX, Gao T-X, Wu S-F, Zhang Y-P (2006a) Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Molecular Ecology 16, 275-288.
Liu JX, Gao TX, Zhuang ZM, et al. (2006b) 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, 712-723.
Lunt D, Hutchinson, WF Carvalho G (1999) An efficient method for PCR-based isolation of microsatellite arrays (PIMA). Molecular Ecology 8, 891-894.
Lynch M, Milligan B (1994) Analysis of population genetic structure with RAPD markers. Molecular Ecology 3, 91-99.
Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York, USA.
Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29, 1-10.
Neigel J, Avise J (1986) Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. Evolutionary Processes and Theory, 515-534.
O'reilly P, Wright J (1995) The evolving technology of DNA fingerprinting and its application to fisheries and aquaculture. Journal of Fish Biology 47, 29-55.
Palero F, Abello P, Macpherson E, Gristina M, Pascual M (2008) Phylogeography of the European spiny lobster (Palinurus elephas): Influence of current oceanographical features and historical processes. Molecular Phylogenetics and Evolution 48, 708-717.
Pepin P, Carr S (1993) Morphological, meristic, and genetic analysis of stock structure in juvenile Atlantic cod (Gadus morhua) from the Newfoundland Shelf. Canadian Journal of Fisheries and Aquatic Sciences 50, 1924-1933.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945.
Quan J, Zhuang Z, Deng J, Dai J, Zhang Y (2004) Phylogenetic Relationships of 12 Penaeoidea Shrimp Species Deduced from Mitochondrial DNA Sequences. Biochemical Genetics 42, 331-345.
Rogers A (1995) Multiregional Demography: Principles, Methods and Extensions. Wiley New York, New York, USA.
Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9, 552.
Ronquillo JD, Saisho T (1997) Larval development of Metapenaeopsis barbata (de Haan, 1844)(Crustacea: Decapoda: Penaeidae). Marine and freshwater research 48, 401-414.
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132, 365-386.
Sakaji H, Tokai T, Sato R (1992) Growth and maturation of whiskered velvet shrimp Metapenaeopsis barbata (De Haan) in Aki-nada area, the Seto inland sea [Japan]. Bulletin of the Japanese Society of Scientific Fisheries 58, 1021-1027.
Sala-Bozano M, Ketmaier V, Mariani S (2009) Contrasting signals from multiple markers illuminate population connectivity in a marine fish. Molecular Ecology 18, 4811-4826.
Schubart CD, Diesel R, Hedges SB (1998) Rapid evolution to terrestrial life in Jamaican crabs. Nature 393, 363-365.
Suen TC, Hung MC (1990) Multiple cis-and trans-acting elements involved in regulation of the neu gene. Molecular and Cellular Biology 10, 6306.
Tajima F (1989) Statistical-Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics 123, 585-595.
Tamura K, Peterson D, Peterson N, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution (accepted).
Tong J, Chan TY, Chu K (2000) A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penaeidae) based on mitochondrial DNA sequences of selected species from the Indo-West Pacific. Journal of Crustacean Biology 20, 541-549.
Tripp-Valdez MA, García de León FJ, Ortega-García S, et al. (2010) Population genetic structure of dolphinfish (Coryphaena hippurus) in the Gulf of California, using microsatellite loci. Fisheries Research 105, 172-177.
Tzeng TD, Chiu CS, Yeh SY (2001) Morphometric variation in red-spot prawn (Metapenaeopsis barbata) in different geographic waters off Taiwan.
Fisheries Research 53, 211-217.
Tzeng TD, Chiu CS, Yeh SY (2005) Growth and mortality of the red-spot prawn (Metapenaeopsis barbata) in the northeastern coast off Taiwan. Journal of The Fisheries Society Of Taiwan 32, 229-238.
Tzeng TD, Yeh SY (1995) Growth parameters of red-spot shrimp, Metapenaeopsis barbata, from the adjacent waters off Taichung Harbor. Journal of The Fisheries Society of Taiwan 22, 53-68.
Tzeng TD, Yeh SY, Hui CF (2004) Population genetic structure of the kuruma prawn (Penaeus japonicus) in East Asia inferred from mitochondrial DNA sequences. ICES Journal of Marine Science: Journal du Conseil 61, 913.
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535-538.
Voloch CM, Freire PR, Russo CAM (2005) Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers. Genetics and Molecular Research 4, 668-674.
Wright S (1984) Evolution and The Genetics of Populations, Volume 4: Variability Within and Among Natural Populations. University of Chicago Press, Chicago, USA.
Xu J, Chan TY, Tsang LM, Chu KH (2009) Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia: Pleistocene isolation, population expansion and secondary contact. Molecular Phylogenetics and Evolution 52, 45-56.
You EM, Chiu TS, Liu KF, et al. (2008) Microsatellite and mitochondrial haplotype diversity reveals population differentiation in the tiger shrimp (Penaeus monodon) in the Indo-Pacific region. Animal Genetics 39, 267-277.
Zitari-Chatti R, Chatti N, Fulgione D, et al. (2009) Mitochondrial DNA variation in the caramote prawn Penaeus (Melicertus) kerathurus across a transition zone in the Mediterranean Sea. Genetica 136, 439-447.
宋海棠、俞存根、薛利建、 姚光展 。2006。東海經濟蝦蟹類。海洋出版社。
中國。47-48頁。
吳全橙。1984。台灣海峽蝦類資源調查與紅斑赤蝦生物學之研究。臺灣省水產
試驗所試驗報告第37期。67-82頁。
吳全橙。1985。臺灣蝦漁業及其漁場調查研究。臺灣省水產試驗所試驗報告第
39期。169-197頁。
李長縈。1986。台灣西南海域紅斑赤蝦之漁業生物學研究。國立台灣海洋大學
漁業研究所碩士論文。70頁。
邵廣昭、陳天任、賴景陽、何平合、柳芝蓮 、陳章波。1996。台灣常見魚介貝類圖說 (上) — 海藻與無脊椎動物。行政院農委會漁業署出版。台北。51頁。
游祥平、陳天任。1986。原色台灣對蝦圖鑑。南天書局。台北。158頁。
劉瑞玉、鍾振如。1986。南海對蝦類。農業出版社。中國。217-220頁。
漁業年報。2009。漁業資訊服務網。行政院農委會漁業署。台北。