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研究生:柯蕾
研究生(外文):Claire Samantha T. Juanico
論文名稱:運用分子標記鑑別野生草蝦之遺傳品系與保育單元
論文名稱(外文):Application of molecular markers in identification of genetic stocks and conservation units of wild black tiger shrimp (Penaeus monodon)
指導教授:于宏燦于宏燦引用關係
指導教授(外文):Alex Hon-Tsen Yu
口試委員:黃曉薇邱臺生王慧瑜
口試委員(外文):Shiao-Wei HuangTai-Sheng ChiuHui-Yu Wang
口試日期:2014-06-30
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:生命科學系
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2014
畢業學年度:102
語文別:英文
論文頁數:91
中文關鍵詞:草蝦D-loop區微隨體族群遺傳學赫胥黎線演化顯著單位管理單位
外文關鍵詞:Penaeus monodond-loopmicrosatellitespopulation geneticsevolutionary significant unitsmanagement units
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D-loop區(粒線DNA)和微隨體可應用於個體鑑識、測試海洋生物地理假說,以及確認需保育族群等各方面。草蝦(Penaeus monodon)是應用此類分析之理想對象,因其分佈廣泛、橫跨於「赫胥黎線」(生物地理線)兩側;此外為確保養殖種蝦之來源與品質,亦需持續對野生族群進行監測。
本研究利用D-loop區序列以及6個微隨體基因座,對菲律賓的Leyte、Surigao 、印尼的Pangandaran等三個野生草蝦族群,各30隻個體進行族群遺傳分析。使用6個微隨體基因座進行個體鑑識分析,其鑑別率在印尼的Pangandaran族群和菲律賓的Surigao族群可達100%;在菲律賓的Leyte族群則為92.31%。在鑑別演化單位方面,由親緣關係分析可知,並無任何單一族群可視為「演化顯著單位」;惟結合菲律賓的二個族群可視為一個「管理單位」。而影響此三族群分佈的主要因素,除「赫胥黎線」外,更新世時的海平面變化以及現今的海洋環流亦有影響。


D-loop (mitochondrial/mtDNA) and microsatellites (nuclear) could assign individuals to populations for aquaculture, test marine biogeographical hypotheses on the distribution of organisms and identify populations to be prioritized for conservation. The black tiger shrimp, Penaeus monodon, is ideal for d-loop and microsatellite analyses because it is widely distributed throughout a biogeographic line called Huxley’s Line and monitoring of wild populations is necessary to maintain the quality of the shrimp seed sources.
This study amplified d-loop sequences and tested six microsatellites on wild populations of black tiger shrimp from Leyte; Surigao del Norte and Pangandaran, West Java. Thirty individuals were collected from each population. The proportions of properly assigned samples using microsatellites were 100% in Pangandaran and Surigao and 92.31% in Leyte. No population was considered as an evolutionary significant unit because there was no reciprocal monophyly based on the resulting phylogenetic tree. Only Leyte combined with Surigao can be considered as management unit because it passed a test on significant divergence of allele frequencies at nuclear loci. Pleistocene sea levels and present-day ocean circulation rather than the Huxley’s line alone affect the distribution of the three populations


Table of contents
Chinese abstract………………………………………………………………………………I
Abstract……………………………………………………………………………………....II
Table of contents…………………………………………………………………………….III
List of tables…………………………………………………………………………………VI
List of figures……………………………………………………………………………….VII
List of appendices…………………………………………………………………………VIII
Introduction…………………………………………………………………………………..1
A. Black tiger shrimp……………………………………………………………………2
B. Molecular Population Genetics………………………………………………………2
C. Applications of Molecular Population Genetics……………………………………..5
C.1 Genetic Stock Identification……………………………………………………..5
C.2 Identification of conservation units…………………………………………….7
D. Molecular Markers…………………………………………………………………..10
D.1 Mitochondrial control region………………………………………………….10
D.2 Microsatellites………………………………………………………………...12
E. Molecular population genetic studies of shrimps……………………………………12
F. Marine biogeography………………………………………………………………...14
G. Biogeographic boundary lines……………………………………………………….18
G.1 Huxley’s Line…………………………………………………………………18
H. Rationale…………………………………………………………………………….19
Materials and Methods……………………………………………………………………..20
A. Sample collection and DNA extraction……………………………………………..20
B. Microsatellite analysis/Genotyping…………………………………………………20
C. Mitochondrial control region amplification………………………………………….21
C.1 PCR……………………………………………………………………………..22
C.2 Cloning…………………………………………………………………………21
C.2.1 DNA Gel extraction……………………………………………………..22
C.2.2 Ligation………………………………………………………………….22
C.2.3 Transformation…………………………………………………………..23
C.2.4 Colony check……………………………………………………………23
D. Sequencing…………………………………………………………………………..23
E. Preparation of sequences and file conversion………………………………………..23
F. Genetic Diversity……………………………………………………………………..24
G. Genetic Structure…………………………………………………………………….24
H. Population assignment……………………………………………………………….25
I. Phylogenetic analyses………………………………………………………………...26
J. Analyses for identification of Conservation units…………………………………….26
K. Demographic History………………………………………………………………..27
Results……………………………………………………………………………………….28
A. Microsatellite analyses……………………………………………………………...28
A.1 Genetic variability……………………………………………………………...28
A.2 Population differentiation……………………………………………………...28
A.3 Clusters of genotypes…………………………………………………………..29
B. Mitochondrial d-loop sequence analyses…………………………………………….29
B.1Sequence variation and genetic diversity………………………………………..29
B.2 Demographic history……………………………………………………………30
C. Over-all genetic differentiation microsatellites genotypes
and mitochondrial d-loop sequences………………………………………………31
Discussion................................................................................................................................32
A. Genetic diversity and connectivity………………………………………………...32
B. Genetic structure……………………………………………………………………..36
C. Population assignment……………………………………………………………….38
D. Analyses for identification of conservation units……………………………………39
Conclusion...............................................................................................................................41
References…………………………………………………………………………………...42


Allen, G.R. 2008. “Conservation Hotspots of Biodiversity and Endemism for Indo-Pacific Coral Reef Fishes.” Aquatic Conservation: Marine and Freshwater Ecosystems 18 (5): 541–56. doi:doi: 10.1002/aqc.880.
Allendorf, F., N. Ryman, and F. Utter. 1987. “Genetics and Fishery Management: Past, Present and Future.” In Population Genetics and Fishery Management, 1–18. Seattle: University of Washington Press.
Anderson, J.D., and W.J. Karel,. 2009. “A Genetic Assessment of Current Management for Spotted Seatrout in Texas.” Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 1 (1): 121–32. doi:10.1577/C09-001.1.
Ashley, M.V., M.F. Wilson, O.R.W. Pergams, D.J. O’Dowd, S.M. Gende, and J.S. Brown. 2003. “Evolutionarily Enlightened Management.” Biological Conservation 111 (2): 115–23. doi: 10.1016/S0006-3207(02)00279-3.
Atkins, H., J. Preston, and Q.C.B. Cronk. 2001. “A Molecular Test of Huxley’s Line: Cyrtandra (Gesneriaceae) in Borneo and the Philippines.” Biological Journal of the Linnean Society 72 (1): 143–59. doi:10.1111/j.1095-8312.2001.tb01306.x.
Aubert, H., and D. Lightner. 2000. “Identification of Genetic Populations of the Pacific Blue Shrimp Penaeus stylistoris of the Gulf of California, Mexico.” Marine Biology 137: 875–85.
Avise, J.C. 2000. Phylogeography: The History and Formation of Species. Cambridge, MA: Harvard University Press.
Aziz, D., S.S. Siraj, S.K. Daud, J.M. Panandam, and M.F. Othman. 2011. “Genetic Diversity of Wild and Cultured Populations of Penaeus monodon Using Microsatellite Markers.” Journal of Fisheries and Aquatic Science 6 (6): 614–23.
Bailey-Brook, J.H., and S.M. Mass. 1992. “Penaeid Taxonomy, Biology and Zoogeography.” In Marine Shrimp Culture: Principles and Practices, 9–23. Amsterdam: Elsevier Science Publishers.
Baldwin, J.D., and A. L. Bass. 1998. “Molecular Phylogeny and Biogeography of the Marine Shrimp Penaeus.” Molecular Phylogenetics and Evolution 10 (3): 399–407.
Barber, P.H., S.R. Palumbi, M.V. Erdmann, and M.K. Moosa. 2000. “A Marine Wallace’s Line.” Nature 406: 692–93.
Benzie, J.A.H., E. Ballment, A.T. Forbes, N.T. Demetriades, and K. Sugama. 2002. “Mitochondrial DNA Variation in Indo-Paci&;#64257;c Populations of the Giant Tiger Prawn, Penaeus monodon.” Molecular Ecology 11 (2): 2553–69.
Billington, N. 2003. “Mitochondrial DNA.” In Population Genetics: Principles and Applications for Fisheries Scientists, 59–100. Bethesda, Maryland.: American Fisheries Society.
Bird, C.E., S.A. Karl, P.E. Smouse, and R.J. Toonen. 2011. “Detecting and Measuring Genetic Differentiation.” In Phylogeography and Population Genetics in Crustacea, 31–55. Crustacean Issues 19. Florida: Taylor&;Francis Group.
Bird, M.I., D. Taylor, and C. Hunt. 2005. “Paleoenvironments of Insular Southeast Asia during the Last Glacial Period: A Savanna Corridor in Sundaland?” Quaternary Science Reviews 24 (20-21): 2228–42. doi:10.1016/j.quascirev.2005.04.004.
Bjornstad, G., and K.H. Roed. 2002. “Evaluation of Factors Affecting Individual Assignment Precision Using Microsatellite Data from Horse Breeds and Simulated Breed Crosses.” Animal Genetics 33 (4): 264–70.
Blott, S.C., J.L. Williams, and C.S. Haley. 1999. “Discriminating among Cattle Breeds Using Genetic Markers.” Heredity 82: 613–19.
Bouckaert, R., J. Heled, D. Kuhnert, T.G. Vaughan, C.-H. Wu, D. Xie, M.A. Suchard, A. Rambaut, and A.J. Drummond. 2014. “BEAST2: A Software Platform for Bayesian Evolutionary Analysis.” PLOS Computational Biology 10 (4): e1003537.
Bowen, B.W. 1999. “Preserving Genes, Species, or Ecosystems? Healing the Fractured Foundations of Conservation Policy.” Molecular Ecology 8: S5–S10.
Briggs, J.C. 2007. “Marine Longitudinal Biodiversity: Causes and Conservation.” Diversity and Distributions 13 (5): 544–55. doi:DOI: 10.1111/j.1472-4642.2007.00362.x.
Brooker, A.L., J.A.H. Benzie, and D. Blair. 2000. “Population Structure of the Giant Tiger Prawn Penaeus monodon in Australian Waters Determined Using Microsatellite Markers.” Marine Biology 136: 149–57.
Brown, B., and J. Epifanio. 2003. “Nuclear DNA.” In Population Genetics: Principles and Applications for Fisheries Scientists, 101-26. Bethesda, Maryland.: American Fisheries Society.
Brown, J.R., A.T. Beckenbach, and M.J. Smith. 1993. “Intraspecific DNA Sequence Variation of the Mitochondrial Control Region of White Sturgeon (Acipenser transmontanus).” Molecular Biology and Evolution 10 (2): 326–41.
Brown, W.M., M.J. George, and A.C. Wilson. 1979. “Rapid Evolution of Animal Mitochondrial DNA.” Proceedings of National Academy of Science U.S.A. 76 (4): 1967–71.
Brown, W.M., E.M. Prager, A. Wang, and A.C. Wilson. 1982. “Mitochondrial DNA Sequences of Primates: Tempo and Mode of Evolution.” Journal of Molecular Evolution 18 (4): 225–39.
Bruford, M.W., D.J. Cheesman, T. Coote, H.A.A. Green, S.A. Haines, C. O’Ryan, and T.R. Williams. 1996. “Microsatellites and Their Application to Conservation Genetics.” In Molecular Genetic Approaches in Conservation, 278–97. New York: Oxford University Press.
Carpenter, K.E., P.H. Barber, E.D. Crandall, M.A.A. Ablan-Lagman, Ambariyanto, G.N. Mahardika, B.M. Manjaji-Matsumoto, et al. 2011. “Comparative Phylogeography of the Coral Triangle and Implications for Marine Management.” Journal of Marine Biology 2011. doi:10.1155/2011/396982.
Carpenter, K.E., and V.G. Springer. 2005. “The Center of the Center of Marine Shorefish Distribution: The Philippine Islands.” Environment Biology of Fishes 72: 467–80.
Carr, S.M., S.W. Ballinger, J.N. Derr, L.H. Blankenship, and J.W. Bickman. 1986. “Mitochondrial DNA Analysis of Hybridization between Sympatric White-Tailed Deer and Mule Deer in West Texas.” Proceedings of National Academy of Science U.S.A. 83 (24): 9576–80.
Castric, V., F. Bonney, V. Castric, F. Bonney, and L. Bernatchez. 2001. “Landscape Structure and Hierarchical Genetic Diversity in the Brook Charr, Salvelinus fontinalis.” Evolution 55 (5): 1016–28. doi:10.1111/j.0014-3820.2001.tb00618.x.
Cavalli-Sforza, L.L., and A.W.F. Edwards. 1967. “Phylogenetic Analysis Models and Estimation Procedures.” American Journal of Human Genetics 19: 233–57.
Chapuis, M.P., and A. Estoup. 2007. “Microsatellite Null Alleles and Estimation of Population Differentiation.” Molecular Biology and Evolution 24 (3): 621–31.
Ciofi, C., M.C. Milinkovitch, J.P. Gibbs, A. Caccone, and J.R. Powell. 2002. “Microsatellite Analysis of Genetic Divergence among Populations of Giant Galapagos Tortoises.” Molecular Ecology 11 (11): 2265–83.
Cox, C.B., and P.D. Moore. 2000. Biogeography: An Ecological and Evolutionary Approach. Great Britain: Alden Press.
Crandall, K.A., O.R.P. Bininda-Emonds, G.M. Mace, and R.K. Wayne. 2000. “Considering Evolutionary Processes in Conservation Biology.” Trends in Ecology and Evolution 15 (7): 290–95.
Crawford, N.G. 2010. “SMOGD: Software for the Measurement of Genetic Diversity.” Molecular Ecology Resources 10 (3): 556–57.
DeBoer, T.S., M.R.A. Naguit, M.V. Erdmann, M.C.A. Ablan-Lagman, Ambariyanto, K.E. Carpenter, A.H.A. Toha, and P.H. Barber. 2014. “Concordance between Phylogeographic and Biogeographic Boundaries in the Coral Triangle: Conservation Implications Based on Comparative Analyses of Multiple Giant Clam Species.” Bulletin of Marine Science 90 (1): 277–300.
DeBruyn, M., J.A. Wilson, and P.B. Mather. 2004. “Huxley’s Line Demarcates Extensive Gentic Divergence between Eastern and Western Forms of the Giant Freshwater Prawn, Macrobrachium rosenbergii.” Molecular Phylogenetics 30 (1): 251–57.
Dickerson, R.E. 1928. “Distribution of Life in the Philippines.” Monograph: Bureau of Science Manila 21: 1–322.
Duda, T.F.J., and S.R. Palumbi. 1999. “Population Structure of the Black Tiger Prawn, Penaeus monodon, among Western Indian Ocean and Western Paci&;#64257;c Populations.” Marine Biology 134: 705–10.
Endler, J.A. 1977. Geographic Variation, Clines, and Speciation. Princeton, N.J.: Princeton University Press.
Erwin, T.L. 1991. “An Evolutionary Basis for Conservation Strategies.” Science 253 (5021): 750–52.
Esselstyn, J.A., C.H. Oliveros, R.G. Moyle, A. Townsend Peterson, J.A. McGuire, and R.M. Brown. 2010. “Integrating Phylogenetic and Taxonomic Evidence Illuminates Complex Biogeographic Patterns along Huxley”s Modification of Wallace’s Line.” Journal of Biogeography 37 (11): 2054–66.
Ewens, W.J. 2004. Mathematical Population Genetics I: Theoretical Introduction. 2nd ed. New York: Springer.
Excoffier, L., G. Laval, and S. Schneider. 2005. “Arlequin Ver. 3.0: An Integrated Software Package for Population Genetics Data Analysis.” Evolutionary Bioinformatics Online 1: 47–50.
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: 479–91.
Fan, B., Y.Z. Chen, C. Moran, S.H. Zhao, B. Liu, M. Yu, M.J. Zhu, T.A. Xiong, and K. Li. 2005. “Individual-Breed Assignment Analysis in Swine Populations by Using Microsatellite Markers.” Australian Journal of Animal Science 18 (11): 1529–34.
Fang, G., R. Dwi Susanto, S. Wirasantosa, F. Qiao, A. Supangat, B. Fan, Z. Wei, B. Sulistiyo, and S. Li. 2010. “Volume, Heat and Freshwater Transports from the South China Sea to Indonesian Seas in the Boreal Winter of 2007-2008.” Journal of Geophysical Research: Oceans (1978-2012) 115 (C12). doi:10.1029/2010JC006225.
Fang, G., Y. Wang, Z. Wei, Y. Fang, F. Qiao, and X. Hua. 2009. “Interocean Circulation and Heat and Freshwater Budgets of the South China Sea Based on a Numerical Model.” Dynamics of Atmospheres and Ocean 47 (1-3): 55–72.
Ferris, S.D., R.D. Sage, C.-M. Huang, J.T. Nielsen, U.W. Rittel, and A. Wilson. 1983. “Flow of Mitochondrial DNA across a Species Boundary.” Proceedings of National Academy of Science U.S.A. 80 (8): 2290–94.
“Final Report: The Philippine Biodiversity Conservation Priorities, A Second Iteration of the National Biodiversity and Action Plan.” 2002. Department of Environment and Natural Resources – Protected Areas and Wildlife Bureau (DENR-PAWB), Conservation International Philippines, Biodiversity Conservation Program – University of the Philippines Center for Integrative and Development Studies, and Foundation for the Philippine Environment.
Fisch, K.M., J.M. Henderson, R.S. Burton, and B. May. 2011. “Population Genetics and Conservation Implications for the Endangered Delta Smelt in the San Francisco Bay-Delta.” Conservation Genetics 2011 (12): 1421–34.
Ford, M.J. 2011. “Status Review Update for Pacific Salmon and Steelhead Listed under the Endangered Species Act: Pacific Northwest”. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-113.
Fraser, D.J., and L. Bernatchez. 2001. “Adaptive Evolutionary Conservation: Towards a Unified Concept for Defining Conservation Units.” Molecular Ecology 10 (12): 2741–52.
Fu, Y.-X. 1997. “Statistical Tests of Neutrality against Population Growth, Hitchhiking and Background Selection.” Genetics 147 (2): 915–25.
Funk, D.J., and K.E. Omland. 2003. “Species-Level Paraphyly and Polyphyly: Frequency, Causes and Consequences with Insights from Animal Mitochondria DNA.” Annual Review of Ecology and Evolution and Systematics 34: 397–423.
Garcia-Machado, E., A. Robainas, G. Espinosa, M. Oliva, J. Paez, N. Verdecia, and M. Monnerot. 2001. “Allozyme and Mitochondrial DNA Variation in Cuban Populations of the Shrimp Farfantepenaeus notialis (Crustacea: Decapoda).” Marine Biology 138: 701–7.
Gillespie, J.H. 1995. “On Ohta’s Hypothesis: Most Amino Acid Substitutions Are Deleterious.” Journal of Molecular Evolution 40: 64–69.
Gordon, A.L., and R.A. Fine. 1998. “Pathways of Water between the Pacific and Indian Oceans in the Indonesian Sea.” Nature 379: 146–48.
Greenberg, B.D., J.E. Newbold, and A. Sugino. 1983. “Intraspecific Nucleotide Sequence Variability Surrounding the Origin of Replication in Human Mitochondrial DNA.” Gene 21 (1-2): 33–49.
Hallerman, E.M. 2003. Population Genetics: Principles and Applications for Fisheries Scientists. Bethesda, Maryland.: American Fisheries Society.
Hamilton, M.B. 2009. Population Genetics. Chichester, UK; Hoboken, NJ: Wiley-Blackwell.
Hampton, J.O., P.B.S. Spencer, D.L. Alpers, L.E. Twigg, A.P. Woolnough, J. Doust, T. Higgs, and J. Pluske. 2004. “Molecular Techniques, Wildlife Management and the Importance of Genetic Population Structure and Dispersal: A Case Study with Feral Pigs.” Journal of Applied Ecology 41 (4): 735–43.
Han, W., A.M. Moore, J. Levin, B. Zhang, H.G. Arango, E. Di Lorenzo, A.L. Gordon, and J. Lin. 2009. “Seasonal Surface Ocean Circulation and Dynamics in the Philippine Archipelago Region 2004 – 2008.” Dynamics of Atmospheres and Ocean 47 (1-3): 114–37.
Hansen, M.M., E. Kenchington, and E.E. Nielsen. 2001. “Assigning Individual Fish to Populations Using Microsatellite DNA Markers.” Fish and Fisheries 2 (2): 93–112.
Harpending, H. 1994. “Signature of Ancient Population Growth in a Low Resolution Mitochondrial DNA Mismatch Distribution.” Human Biology 66 (4): 591–600.
Hartl, D.L., and A.G. Clark. 2007. Principles of Population Genetics. 4th ed. Sunderland, Mass.: Sinauer Associates.
Hastings, A. 1993. “Complex Interactions between Dispersal and Dynamics: Lessons from Coupled Logistic Equations.” Ecology 74 (5): 1362–72.
Hauser, L., and J.E. Seeb. 2008. “Advances in Molecular Technology and Their Impact on Fisheries Genetics.” Fish and Fisheries 9 (4): 473–86.
Hautala, S.L., J. Sprintall, J.T. Potemra, J.C. Chong, W. Pandoc, N. Bray, and A. Gani Ilahude. 2001. “Velocity Structure and Transport of the Indonesian Throughflow in the Major Straits Restricting Flow into the Indian Ocean.” Journal of Geophysical Research: Oceans (1978-2012) 106 (C9): 19527–46.
Heaney, L.R. 2004. “Conservation Biogeography in Oceanic Archipelagoes.” In Frontiers of Biogeography: New Directions in the Geography of Nature, 436. Sunderland, Mass.: Sinauer Associates.
Hedgecock, D., and A.I. Pudovkin. 2011. “Sweepstakes Reproductive Success in Highly Fecund Marine Fish and Shellfish: A Review and Commentary.” Bulletin of Marine Science 87 (4): 971–1002.
Hellberg, M.E., R.S. Burton, J.E. Neigel, and S.R. Palumbi. 2002. “Genetic Assessment of Connectivity among Marine Populations.” Bulletin of Marine Science 70 (1): SUPPL.:273–290.
Horai, S., and K. Hayasaka. 1990. “Intraspecific Nucleotide Sequence Differences in the Major Noncoding Region of Human Mitochondrial DNA.” American Journal of Human Genetics 46 (4): 828–42.
Jablonski, D., J.J. Sepkoski, D.J. Bottjer, and P.M. Sheehan. 1983. “Onshore-Offshore Patterns in the Evolution of Phanerozoic Communities.” Science 222 (4628): 1123–25.
Jost, L. 2008. “GST and Its Relatives Do Not Measure Differentiation.” Molecular Ecology 17 (18): 4015–26.
Kalinowski, S.T., and M.L. Taper. 2006. “Maximum Likelihood Estimation of the Frequency of Null Alleles at Microsatellite Loci.” Conservation Genetics 7 (6): 991–95.
Kenway, M., and M.R. Hall. 1999. “The Supply of Black Tiger Prawn Broodstock for Aquaculture.” AustAsia Aquaculture, no. June/July 1999: 38–48.
Kizirian, D., and M.A. Donelly. 2004. “The Criterion of Reciprocal Monophyly and Classification of Nested Diversity at the Species Level.” Molecular Phylogenetics and Evolution 32: 1072–76.
Kongkeo, H. 2005. “Cultured Aquatic Species Information Programme. Penaeus monodon. Cultured Aquatic Species Information Programme.” Food and Agriculture Organization. http://www.fao.org/fishery/culturedspecies/Penaeus_monodon/en#tcNA00EA.
Lahood, E.S., P. Moran, J. Olsen, W.S. Grant, and L.K. Park. Mol Ecol Notes. “Microsatellite Allele Ladders in Two Species of Pacific Salmon: Preparation and Field-Test Results.” Molecular Ecology Notes 2 (2): 187–90.
Leese, F., and C. Held. 2011. “Analyzing Intraspecific Genetic Variation: A Practical Guide Using Mitochondrial DNA and Microsatellites.” In Phylogeography and Population Genetics in Crustacea, 3–30. Crustacean Issues 19. Florida: CRC Press.
Lehman, N. 1991. “Introgression of Coyote Mitochondrial DNA into Sympatric North American Gray Wolf Populations.” Evolution 45 (1): 104–19.
Li, W.-H., and D. Graur. 1991. Fundamentals of Molecular Evolution. 2nd ed. Sunderland, Mass.: Sinauer Associates.
Liao, P.-C., D.-C. Kuo, C.-C. Lin, K.-C. Ho, T.-P. Lin, and S.-Y. Hwang. “Historical Spatial Range Expansion and a Very Recent Bottleneck of Cinnamomum kanehirae Hay. (Lauraceae) in Taiwan Inferred from Nuclear Genes.” BMC Evolutionary Biology 10 (124). doi:10.1186/1471-2148-10-124.
Librado, P., and J. Rozas. 2009. “DnaSP v5: A Software for Comprehensive Analysis of DNA Polymorphism Data.” Bioinformatics 25 (11): 1451–52.
Lischer, H.E.L., and L. Excoffier. 2012. “PGDSpider: An Automated Data Conversion Tool for Connecting Population Genetics and Genomics Programs.” Bioinformatics 28 (2): 298–99.
Lohman, D.J., M. DeBruyn, T. Page, K. von Rintelen, R. Hall, P.K.L. Ng, H.-T. Shih, G.R. Carvalho, and T. von Rintelen. 2011. “Biogeography of Indo-Australian Archipelago.” Annual Review of Ecology and Evolution and Systematics 42: 205–26.
Lourie, S.A., and A.C.J. Vincent. 2004. “A Marine Fish Follows Wallace’s Line: The Phylogeography of the Three-Spot Seahorse (Hippocampus trimaculatus, Syngnathidae, Teleostei) in Southeast Asia.” Journal of Biogeography 31 (12): 1975–85.
Lowe, W.H., and F. Allendorf. 2010. “What Can Genetics Tell Us about Population Connectivity?” Molecular Ecology 19 (15): 3038–51.
Mace, G.M., and A. Purvis. 2008. “Evolutionary Biology and Practical Conservation: Bridging a Widening Gap.” Molecular Ecology 17 (1): 9–19.
Magno, M., and C. Villanoy. 2006. “Quantifying the Complexity of Philippine Coastlines for Estimating Entrainment Potential.” In , 1471–76. Okinawa.
Magsino, R.M., and M.A. Juinio-Menez. 2008. “The Influence of Contrasting Life History Traits and Oceanic Processes on Genetic Structuring of Rabbitfish Populations Siganus argenteus and Siganus fuscescens along the Eastern Philippine Coasts.” Marine Biology 154: 519–32.
Mayr, E., and W.J. Bock. 2002. “Classifications and Other Ordering Systems.” Journal of Zoological Systematics and Evolutionary Research 40 (4): 169–94.
McManus, J.W. 1985. “Marine Speciation, Tectonics and Sea Level Changes in Southeast Asia.” In Proceedings of the Fifth International Coral Reef Congress. Vol. 4. Tahiti.
McMillen-Jackson, A.L., and T.M. Bert. 2004. “Genetic Diversity in the MtDNA Control Region and Population Structure in the Pink Shrimp Farfantepenaeus duorarum.” Journal of Crustacean Biology 24 (1): 101–9.
Meyer, C.P., J.B. Geller, and G. Paulay. 2005. “Fine Scale Endemism on Coral Reefs: Archipelagic Differentiation in Turbinid Gastropods.” Evolution 59 (1): 113–25.
Michalakis, Y., and L. Excoffier. 1996. “A Generic Estimation of Population Subdivision Using Distances between Alleles with Reference for Microsatellite Loci.” Genetics 142 (3): 1061–64.
Miller, A.D., V.L. Versace, T.G. Matthews, S. Montgomery, and K.C. Bowie. 2013. “Ocean Currents Influence the Genetic Structure of an Intertidal Mollusk in Southern Australia - Implications for Predicting the Movement of Passive Dispersers across a Marine Biogeographic Barrier.” Ecology and Evolution 3 (5): 1248–61.
Miller, K.A., D.G. Chapple, D.R. Towns, P.A. Ritchie, and N.J. Nelson. 2009. “Assessing Genetic Diversity for Conservation Management: A Case Study of a Threatened Reptile.” Animal Conservation 12 (2): 163–71.
Morin, P.A., and A.E. Dizon. 2009. “Genetics for Management.” In Encyclopedia of Marine Mammals. Amsterdam: Elsevier Science Publishers.
Morin, P.A., K.K. Martien, F.I. Archer, F. Cipriano, D. Steel, J. Jackson, and B.L. Taylor. 2010. “Applied Conservation Genetics and the Needs for Quality Control and Reporting of Genetic Data Used in Fisheries and Wild Management.” Journal of Heredity 101 (1): 1–10.
Moritz, C. 1994. “Defining ‘evolutionary Significant Units’ for Conservation.” Trends in Ecology and Evolution 9: 373–75.
———. 1995. “Uses of Molecular Phylogenies for Conservation.” Philosophical Transactions of the Royal Society. Series B. Biological Science 349: 113–18.
Motoh, H. 1981. Studies on the Fisheries Biology of the Giant Tiger Prawn, Penaeus monodon in the Philippines. Tigbauan, Iloilo, Philippines: Aquaculture Department, Southeast Asian Fisheries Development Center.
Nei, M. 1972. “Genetic Distance between Populations.” American Naturalist 106: 283–92.
———. 1978. “Estimation of Average Heterozygosity and Genetic Distance from a Small Number of Individuals.” Genetics 89: 583–90.
Nitani, H. 1972. “Beginning of the Kuroshio.” In Kuroshio: Its Physical Aspects, 129–63. Tokyo: University of Tokyo Press.
Ohta, T. 1992. “The Nearly Neutral Theory of Molecular Evolution.” Annual Review of Ecology and Evolution and Systematics 23: 263–86.
Olsen, M.T., L.W. Andersen, R. Dietz, J. Teilmann, T. Harkonen, and H.R. Siegismund. 2012. “Integrating Genetic Data and Population Viability Analyses for the Identification of Harbor Seal (Phoca vitulina) Populations and Management Units.” Molecular Ecology 23 (4): 815–31.
Palsboll, P.J., M. Berube, and F. Allendorf. 2006. “Identification of Management Units Using Population Genetic Data.” Trends in Ecology and Evolution 22 (20): 11–16.
Palumbi, S.R. 1994. “Genetic Divergence, Reproductive Isolation and Marine Speciation.” Annual Review of Ecology and Evolution and Systematics 25: 547–72.
———.1996. “What Can Molecular Genetics Contribute to Marine Geography? An Urchin’s Tale.” Journal of Experimental Marine Biology and Ecology 203 (1): 75–92.
Pan, Y.-W., H.-H. Chou, E.-M. You, and H.-T. Yu. 2004. “Isolation and Characterization of 23 Polymorphic Microsatellite Markers for Diversity and Stock Analysis in Tiger Shrimp (Penaeus monodon).” Molecular Ecology Notes 4 (3): 345–47.
Piry, S., A. Alapetite, J.-M. Cornuet, D. Paetkau, L. Baudouin, and A. Estoup. 2004. “GENECLASS2: A Software for Genetic Assignment and First-Generation Migrant Detection.” Journal of Heredity 95 (6): 536–39.
Pritchard, J.K., M. Stephens, and P. Donelly. 2000. “Inference of Population Structure Using Multilocus Genotype Data.” Genetics 155: 945–59.
Rannala, B., and J.L. Mountain. 1997. “Detecting Immigration by Using Multilocus Genotype Data.” Proceedings of National Academy of Science U.S.A. 94: 9197–9201.
Ravago-Gotanco, R.G., and M.A. Juinio-Menez. 2010. “Phylogeography of the Mottled Spinefoot Siganus fuscescens: Pleistocene Divergence and Limited Genetic Connectivity across the Philippine Archipelago.” Molecular Ecology 19: 4520–34.
Ravago-Gotanco, R.G., R.M. Magsino, and M.A. Juinio-Menez. 2007. “Influence of the North Equatorial Current on the Population Genetic Structure of Tridacna crocea (Mollusca: Tridacnidae) along the Eastern Philippine Seaboard.” Marine Ecology Progress Series 336: 161–68.
Raymond, M., and F. Rousset. 1995. “GENEPOP (version 1.2): Population Genetics Software for Exact Tests and Ecumenicism.” Journal of Heredity 86: 248–49.
Rogers, A.R. 1995. “Genetic Evidence for a Pleistocene Population Explosion.” Evolution 49 (4): 608–15.
Rogers, A.R., and H. Harpending. 1992. “Population Growth Makes Waves in the Distribution of Pairwise Genetic Differences.” Molecular Biology and Evolution 9: 552–69.
Rouget, M., R.M. Cowling, A.T. Lombard, and I.H.K. Graham. “Designing Large-Scale Conservation Corridors for Pattern and Process.” Conservation Biology 20: 549–61.
Ryder, O.A. 1986. “Species Conservation and Systematics: The Dilemma of the Subspecies.” Trends in Ecology and Evolution 1: 9–10.
Schneider, S., and L. Excoffier. 1999. “Estimation of Past Demographic Parameters from the Distribution of Pairwise Differences When the Mutation Rates Vary among Sites: Application to Human Mitochondrial DNA.” Genetics 152: 1079–89.
Shaklee, J.B., and P.K. Currens. 2003. “Genetic Stock Identification and Risk Assessment.” In Population Genetics: Prinsciples and Applications for Fisheries Scientists, 291–328. Bethesda, Maryland.: American Fisheries Society.
Shih, C.-H., H.-L. Haung, T.-J. Chu, Y.-C. Lee, C.-M. Wang, and Tzeng, T.-D. 2011. “Genetic Diversity and Historical Demography of Kuruma Shrimp (Penaeus japonicus) Species Complex off China Based on Mitochondrial DNA Analysis.” African Journal of Biotechnology 10 (7): 1065–72.
Simpson, G.G. 1977. “Too Many Lines: The Limits of the Oriental and Australian Zoogeographic Regions.” Proceedings of the American Philosophical Society 121 (2): 107–20.
Slatkin, M. 1995. “A Measure of Population Differentiation Based on Microsatellite Allele Frequencies.” Genetics 139: 457–62.
Sorensen, L., J.R. McDowell, T. Knott, and J.E. Graves. 2013. “Assignment Test Method Using Hypervariable Markers for Blue Marlin (Makaira nigricans) Stock Identification.” Conservation Genetic Resources 5: 293–97.
Spalding, M.D., H.E. Fox, G.R. Allen, N. Davidson, Z.A. Ferdana, M. Finlayson, B.S. Halpern, M.A. Jorge, A. Lomabana, and S.A. Lourie. 2007. “Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas.” BioScience 57 (7): 573–83.
Sugama, K., Haryanti, J.A.H. Benzie, and E. Ballment. “Genetic Variation and Population Structure of the Giant Tiger Prawn, Penaeus monodon, in Indonesia.” Aquaculture 205: 37–48.
Supungul, P., P. Sootanan, S. Klinbunga, W. Kamonrat, P. Jarayabhand, and A. Tassanakajon. 2000. “Microsatellite Polymorphism and the Population Structure of the Black Tiger Shrimp (Penaeus monodon) in Thailand.” Marine Biotechnology 2: 339–47.
Taberlet, P. 1996. “The Use of Mitochondrial Dna Control Region Sequencing in Conservation Genetics.” In Molecular Genetic Approaches in Conservation, 12–142. New York: Oxford University Press.
Tamura, K., G. Stecher, D. Peterson, A. Filipski, and S. Kumar. 2013. “MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0.” Molecular Biology and Evolution 30: 2725–29.
Tassanakajon, A., S. Pongsomboon, P. Jarayabhand, S. Klinbunga, and V. Boonsaeng. 1998. “Genetic Structure in Wild Populations of the Black Tiger Shrimp (Penaeus monodon) Using Randomly Amplified Polymorphic DNA Analysis.” Journal of Marine Biotechnology 6: 249–54.
Tegelstrom, H. 1987. “Transfer of Mitochondrial DNA from the Northern Red-Backed Vole (Chlethrionomys rutilus) to the Bank Vole (C. glareolus).” Journal of Molecular Evolution 24: 218–27.
Toews, D.P., and A. Brelsford. 2012. “The Biogeography of Mitochondrial and Nuclear Discordance in Animals.” Molecular Ecology 21: 3907–30.
Turner, H., P. Hovenkamp, and P.C. van Welzen. 2001. “Biogeography of Southeast Asia and the West Pacific.” Journal of Biogeography 28: 217–30.
Valles-Jimenez, R., P.M. Gaffney, and R. Perez-Enriquez. 2006. “RFLP Analysis of the mtDNA Control Region in White Shrimp (Litopenaeus vannamei) Populations from the Eastern Pacific.” Marine Biology 148: 867–73.
Van Oosterzee, P. 1997. Where Worlds Collide: The Wallace Line. New York: Cornell University Press.
Vaseeharan, B., P. Rajakamaran, D. Jayaseelan, and A.Y. Vincent. 2012. “Molecular Markers and Their Application in Genetic Diversity of Penaeid Shrimp.” Aquaculture International 21 (2): 219–41.
Vernesi, C., B. Crestanello, E. Pecchili, D. Tartari, D. Carmelli, H. Hauffe, and G. Bertorelle. 2003. “The Genetic Impact of Demographic Decline and Reintroduction in the Wild Boar (Sus scrofa): A Microsatellite Analysis.” Molecular Ecology 12: 585–95.
Waples, R.S. 1991. “Pacific Salmon, Oncorhynchus Spp. &; the Definition of ‘species’ under the Endangered Species Act.” Marine Fisheries Reviews 53: 11–22.
Wolfus, G.M., D.K. Garcia, and A.A. Alcivar-Warren. 1997. “Application of the Microsatellite Technique for Analyzing Genetic Diversity in Shrimp Breeding Programs.” Aquaculture 152: 35–47.
Wyrtki, K. 1961. Scientific Results of Marine Investigations of the South China Sea and the Gulf of Thailand, 1959-1961, Volume 2, Physical Oceanography of Southeast Asian Waters, NAGA. 2. San Diego, La Jolla.: Scripps Inst.of Oceanogr., Univ. of Calif.
Xu, Z., J.H. Primavera, L. Dela Pena, P. Pettit, J. Belak, and A.A. Alcivar-Warren. 2001. “Genetic Diversity of Wild and Cultured Black Tiger Shrimp Penaeus monodon in the Philippines Using Microsatellites.” Aquaculture 199: 13–40.
Yednock, B.K., and J.E. Neigel. 2011. “Rethinking the Mechanisms That Shape Marine Decapod Population Structure.” In Phylogeography and Population Genetics in Crustacea, 57–73. Crustacean Issues 19. Florida: CRC Press.
You, E.-M., K.F. Chiu, F. Liu, A. Tassanakajon, S. Klinbunga, and K. Triwatayakorn. 2008. “Microsatellite and Mitochondrial Haplotype Diversity Reveals Population Differentiation in the Tiger Shrimp (Penaeus monodon) in the Indo-Paci&;#64257;c Region.” Animal Genetics 39: 267–77.
Yue, G.H., J.H. Xia, P. Liu, and F. Sun. 2012. “Tracing Asian Seabass Individuals to Single Fish Farms Using Microsatellites.” PLOS One 7 (12): e52721. doi:10.1371/journal.pone.0052721.
Zeisset, I., and T.J.C. Beebee. 2001. “Determination of Biogeographical Range: An Application of Molecular Phylogeography to the European Pool Frog Rana lessonae.” Royal Society of London. Series B. Biological Sciences 268: 933–38.


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