Molecular markers and their applications in fisheries and aquaculture

Tanya Chauhan, Kumar Rajiv

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DOI: 10.4236/abb.2010.14037                

Abstract

Genetic variation in a species enhances the capability of organism to adapt to changing environment and is necessary for survival of the species. Genetic variation arises between individuals leading to differentiation at the level of population, species and higher order taxonomic groups. The genetic diversity data has varied application in research on evolution, conservation and management of natural resources and genetic improvement programmes, etc. Development of Molecular genetic markers has powerful ability to detect genetic studies of individuals, populations or species. These molecular markers combined with new statistical developments have revolutionized the analytical power, necessary to explore the genetic diversity. Molecular markers and their statistical analysis revolutionized the analytical power, necessary to explore the genetic diversity. Various molecular markers, protein or DNA (mt-DNA or nuclear DNA such as microsatellites, SNP or RAPD) are now being used in fisheries and aquaculture. These markers provide various scientific observations which have importance in aquaculture practice recently such as: 1) Species Identification 2) Genetic variation and population structure study in natural populations 3) Comparison between wild and hatchery populations 4) Assessment of demographic bottleneck in natural population 5) Propagation assisted rehabilitation programmes. In this review article, we have concentrated on the basics of molecular genetics, overview of commonly used markers and their application along with their limitations (major classes of markers) in fisheries and aquaculture studies.

Keywords

Genetic Diversity; Molecular Markers; Microsatellite; Aquaculture

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Fisher, R.A. (1930) The Genetical Theory of Natural Selection. Oxford University Press, UK.
[2]	Avise, J.C. (1994) Molecular Markers, Natural History and Evolution. Chapman and Hall, New York, London.
[3]	Linda, K.P. and Paul, M. (1995) Developments in molecular genetic techniques in fisheries. In: G.R. Carvalho and T.J. Pitcher, Eds., Molecular Genetics in Fisheries, Chapman and hall, London, 1-28.
[4]	Hillis, D.M., Mable, B.K. and Moritz, C. (1996) Applications of molecular systematics: The state of the field and a look to the future. In: Hillis, D.M., Moritz, C. and Mable, B.K. Eds., Molecular systematics, Sinauer Associates, Massachusetts, 515-543.
[5]	Ferguson, A., Taggart, J.B., Prodohl, P.A., McMeel, O., Thompson, C., Stone, C., McGinnity, P. and Hynes, R.A. (1995) The application of molecular markers to the study and conservation of fish populations with special reference to Salmo. Journal of Fish Biology, 47(A), 103-126.
[6]	Neff, B.D. and Gross, M.R. (2001) Microsatellite evolution in vertebrates: Inference from AC dinucleotide repeats. Evolution, 55(9), 1717-1733.
[7]	Jehle, R. and Arntzen, J.W. (2002) Microsatellite markers in amphibian conservation genetics. Herpetological Jour nal, 12, 1-9.
[8]	Wasko, A.P., Martins, C., Oliveira, C. and Foresti, F. (2003) Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales. Hereditas, 138(3), 161-165.
[9]	Morin, P.A., Luikart, G., Wayne, R.K. and the SNP working group, SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19(4), 208-216.
[10]	Liu, Z.J. and Cordes, J.F. (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238, 1-37.
[11]	O’Brien, S.J. (1991) Molecular genome mapping: lessons and prospects. Current Opinion in Genetic Development, 1(1), 105-111.
[12]	Brown, B. and Epifanio, J. (2003) Nuclear DNA. In: Hallermann, E.M. Ed., Population Genetics: Principles and Applications for Fisheries Scientists, American Fisheries Society, Bethesda, 458-472.
[13]	Suneetha, B.K. (2000) Interspecific and inter specific genetic variation in selected mesopelagic fishes with emphasis on microgeographic variation and species characterization. Dr. Scient. Dissertation, Department of Fisheries and Marine Biology, University of Bergen, Bergen, Norway.
[14]	Menezes, M.R., Naik, S. and Martins, M. (1993) Genetic characterization in four sciaenid species from the Arabian Sea. Journal of Fish Biology, 43(1), 61-67.
[15]	Markert, C.L. and Moller, F. (1959) Multiple forms of enzymes: Tissue, ontogenetic and species-specific patterns. Proceedings of the Naionall Academy of Science (USA), 45(5), 753-763.
[16]	Starck, M.G. (1998) Isozymes in Molecular tools for screening biodiversity. In: Angela, K., Peter, G.I. and. David, S.I. Eds., Chapmann and Hall, London, 75-80.
[17]	Murphy, R.W., Sites, J.J.W. Buth, D.G. and Haufler, C.H. (1996) Proteins I: Isozyme electrophoresis. In: Hillis, D.M., Moritz, C. and Mable, B.K. Eds., Molecular Systematics, Sinauer Associates, Sunderland, 51-132.
[18]	Brown, W.M. (1985) The mitochondrial genome of animals. In: MacIntyre, R.J. Ed., Molecular Evolutionary Genetics, Plenum, New York, 95-130.
[19]	Wilson, A.C., Cann, R.L., Carr, S.M., George, M., Gyllensten, U.B., Helm-Bychowski, K.M., Higuchi, R.G., Palumbi, S.R. and Prager, E.M. (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biological Journal of Linnean Society, 26(4), 375-400.
[20]	Birky, C.W., Fuerst, P. and Maruyama, T. (1989) Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effect of heteroplasmic cells, and comparison to nuclear genes. Genetics, 121(3), 613-627.
[21]	Meyer, A. (1993) Evolution of mitochondrial DNA in fishes. In: Mochachka, P.W. and Mommsen, T.P. Eds., Biochemistry and molecular biology of fishes. Elsevier Press Amsterdam, New York, 1-38.
[22]	Brown, J.R., Bechenbach, A.T. and Smith, M.J. (1993) Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus). Molecular Biology Evolution, 10(2), 326-341.
[23]	Chow, S., Okamoto, H., Uozumi, Y., Takeuchi, Y. and Takeyama, H. (1997) Genetic stock structure of the swordfish (Xiphias gladius) inferred by PCR-RFLP analysis of the mitochondrial DNA control region. Marine Biology, 127(3), 359-367.
[24]	Gold, J.R. Sun, F. and Richardson, L.R. (1997) Population structure of red snapper from the Gulf of Mexico as inferred from analysis of mitochondrial DNA. Transaction of American Fisheries Society, 126(3), 386-396.
[25]	Chow, S. and Kishino, H. (1995) Phylogenetic relationships between tuna species of the genus Thunnus (Scombriidae: Teleosrei): Inconsistent implications from morphology, nuclear and mitochondrial genomes. Journal of Molecular Evolution, 41, 741-748.
[26]	Avise, J.C., Helfman, G.S., Saunders, N.C. and Hales, L.S. (1986) Mitochondrial DNA differentiation in North Atlantic eels: Population genetic consequences of an unusual life history pattern. Proceeding of the National Academy Science (USA), 83(12), 4350-4354.
[27]	Graves, J.E., McDowell, J.R. and Jones, M.L. (1992) A genetic analysis of weakfish Cynoscion regalis stock structure along the mid-Atlantic coast. Fisheries Bulletin, 90, 469-475.
[28]	Gold, J.R., Richardson, L.R., Furman, C. and King, T.L. (1993) Mitochondrial DNA differentiation and population structure in red drum (Sciaenops ocellatus) from the Gulf of Mexico and Atlantic Ocean. Marine Biology, 116(2), 175-185.
[29]	Chow, S., Clarke, M.E. and Walsh, P.J. (1993) PCR-RFLP analysis of thirteen western Atlantic snappers (subfamily Lutjaninae): A simple method for species and stock identification. Fisheries Bulletin (US), 91, 619-627.
[30]	Heist, E.J. and Gold, J.R. (1999) Microsatellite DNA variation in sandbar sharks (Carcharhinus plumbeus) from the Gulf of Mexico and mid-Atlantic bight. Copeia, 1, 182-186.
[31]	Baker, A.J. and Marshall, H.D. (1997) Molecular evolution of the mitochondrial genome. In: Mindell, D.P. Ed., Avian Molecular Evolution and Systematics, Academic Press, San Diego, 51-82.
[32]	Greenberg, R., Cordero, P.J., Droege, S. and Fleischer, R.C. (1998) Morphological adaptation with no mitochondrial DNA differentiation in the coastal plain swamp sparrow. Journal of American Ornithologists' Union, 115(3), 706-712.
[33]	Mila, B., Girman, D.J., Kimura, M. and Smith, T.B. (2000) Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird. Proceedings of the Royal Society London Series B, 267(1447), 1033-1040.
[34]	Zink, R.M., Barrowclough, G.F., Atwood, J.L. and Blackwell-Rago, R.C. (2000) Genetics, taxonomy, and conservation of the threatened California gnatcatcher. Conservation Biology, 14(5), 1394-1405.
[35]	Menotti-Raymond, M. and O’Brien, S.J. (1993) Dating the genetic bottleneck of the African cheetah. Proceedings of the National Academy of Science (USA.), 90(8), 3172-3176.
[36]	Avise, J.C., Walker, D. and Johns, G.C. (1998) Speciation durations and Pleistocene effects on vertebrate phylogeography. Proceedings of the Royal Society of London Series B, 265(1407), 1707-1712.
[37]	Serb, J.M., Phillips, C.A. and Iverson, J.B. (2001) Molecular phylogeny and biogeography of Kinosternon flavenscens based on complete mitochondrial control region sequences. Molecular Phylogenetics and Evolution, 18(1), 149-162.
[38]	Riberon, A., Sotiriou, E., Miaud, C., Andreone, F. and Taberlet, P. (2002) Lack of genetic diversity in Salamandra lanzai revealed by cytochrome b gene sequences. Copeia, 2002, 229-232.
[39]	Shanker, K., Ramadevi, J., Choudhaury, B.C., Singh, L. and Aggarawal, R.K. (2004) Phylogeny of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory. Moelcular Ecology, 13(7), 1899-1909.
[40]	Mamuris, Z., Sfougaris, A.I., Stamatis, C. and Suchentrunk, F. (2002) Assessment of genetic structure of Greek Brown Hare (Lepus europeaus) populations based on variation in Random Amplified Polymorphic DNA (RAPD). Biochemical Genetics, 40(9-10), 323- 338.
[41]	Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18(22), 6531-6535.
[42]	Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research, 18(24), 7213-7218.
[43]	Haymer, D.S. (1994) Random amplified polymorphic DNAs and microsatellites: what are they, and can they tell us anything we don’t already know? Annals of Entomological Society of American, 87, 717-722.
[44]	Wirgin, I.I. and Waldman, J.R. (1994) What DNA can do for you? Fisheries, 19, 16-27.
[45]	Hecker, K.H., Taylor, P.D. and Gjerde, D.T. (1999) Mutation detection by denaturing DNA chromatography using fluorescently labeled polymerase chain reaction products. Analytical Biochemistry, 272(2), 156-164.
[46]	Tautz, D. (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research, 17(16), 6463-6471.
[47]	Litt, M. and Luty, J.A. (1989) A hypervariable microsatellite revealed by in-vitro amplification of dinucleotide repeat within the cardiac muscle actin gene. American of Journal of Human Genetics, 44(3), 397-401.
[48]	Wright, J.M. (1993) DNA fingerprinting in fishes. In: W. Hochachka, P. and Mommsen, T. Eds., Biochemistry and Molecular Biology of Fishes, Elsevier, Amsterdam, 58-91.
[49]	Liu, Z.J., Li, P., Kocabas, A., Ju, Z., Karsi, A., Cao, D. and Patterson, A. (2001) Microsatellite-containing genes from the channel catfish brain: evidence of trinucleotide repeat expansion in the coding region of nucleotide excision repair gene RAD23B. Biochemical Biophysical Research Communication, 289(2), 317-324.
[50]	Taylor, A.C., Sherwin, W.B. and Wayne, R.K. (1994) Genetic variation of microsatellite loci in a bottlenecked species: The northern hairy-nosed wombat Lasiorhinus krefftii. Molecular Ecology, 3(4), 277-290.
[51]	Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., Kerlavage, A.R., McCombie, W.R. and Venter, J.C. (1991) Complementary DNA sequencing: Expressed sequence tags and human genome project. Science, 252(5013), 1651-1656.
[52]	Wang, K., Gan, L., Jeffry, E., Gayle, M., Gown, A.M., Skelly, M., Nelson, P.S., Ng, W.V., Schummer, M., Hood, L. and Mulligan, J. (1999) Monotoring gene expression profile changes in ovarian carcinomas using cDNA microarray. Gene, 229(1-2), 101-108.
[53]	Boguski, M.S.and Schuler, G.D. (1995) Establishing a human transcript map. Nature Genetics, 10(4), 369-371.
[54]	Cox, D.R., Burmeister, M., Price, E., Kim, S. and Myers, R.M. (1990) Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution map of mammalian chromosomes. Science, 250(4978), 245-250.
[55]	Korwin-Kossakowska, A., Reed, K.M., Pelak, C., Krause, E., Morrison, L. and Alexander, L.J. (2002) Radiation hybrid mapping of 118 new porcine microsatellites. Animal Genetics, 33(3), 224-227.
[56]	McCoard, S.A., Fahrenkrug, S.C., Alexander, L.J., Freking, B.A., Rohrer, G.A., Wise, T.H. and Ford, J.J. (2002) An integrated comparative map of the porcine X chromosome. Animal Genetics, 33(3), 178-185.
[57]	Liu, Z.J., Karsi, A. and Dunham, R.A. (1999) Development of polymorphic EST markers suitable for geneticlinkage mapping of catfish. Marine Biotechnology, 1(5), 437-447.
[58]	Dobson, A.P., Rodriguez, J.P., Roberts, W.M. and Wilcove, D.S. (1997) Geographic distribution of endangered species in the United States. Science, 275(5299), 550- 555.
[59]	Daugherty, C.H., Cree, A., Hay, J.M. and Thompson, M.B. (1990) Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature, 347(6289), 177- 179.
[60]	Faith, D.P. (1994) Genetic diversity and taxonomic priorities for conservation. Biological Conservation, 68(1), 69-74.
[61]	Crozier, R.H. (1997) Preserving the information content of species: genetic diversity, phylogeny, and conservation worth. Annual Review of Ecology and Systematics, 28(1), 243-268.
[62]	Haig, S.M. (1998) Molecular contributions to conservation. Ecology, 79(2), 413-425.
[63]	Soltis, P.S. and Gitzendanner, M.A. (1999) Molecular systematics and the conservation of rare species. Conservation Biology, 13(3), 471-483.
[64]	Moritz, C. (2002) Strategies to protect diversity and the evolutionary processes that sustain it. Systematic Biology, 51(2), pp. 238-254.
[65]	McKinney, M.L. (1999) High rates of extinction and threat in poorly studied taxa. Conservation Biology, 13(6), 1273-1281.
[66]	Novotny, V., Basset, Y., Miller, S.E., Weiblen, G.D., Bremer, B., Cizek, L. and Drozd, P. (2002) Low host specificity of herbivorous insects in a tropical forest. Nature, 416, 841-844.
[67]	Hebert, P.D.N., Ratnasingham, S. and deWaard, J.R. (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Royal Society London, 270 (Suppl 1), S96-S99.
[68]	Stoeckle, M. (2003) Taxonomy, DNA, and the bar code of life. BioScience, 53(9), 2-3.
[69]	Stoeckle, M., Janzen, D., Hallwachs, W., Hanken, J. and Baker, J. (2003) Taxonomy, DNA, and the barcode of life,” Draft conference report. Rubinoff DNA Barcodes and Conservation Barcode Conference, The Rockefeller University, New York, http://phe.rockefeller.edu/BarcodeConference/docs/B2summary.doc.
[70]	Hebert, P.D.N., Stoeckle, M.Y., Zemlak, T.S. and Francis, C.M., (2004) Identification of birds through DNA barcodes. PLoS Biology, 2(10), 312-316.
[71]	Rocha-Olivares, A., Moser, H.G. and Stannard, J. (2000) Molecular identification and description of pelagic young of the rockfishes Sebastes constellatus and Sebastes ensifer. Fisheries Bulletin, 98, 353-363.
[72]	Backer, J., Bentzen, P. and Moran, P. (2002) Molecular markers distinguish coastal cutthroat trout from coastal rainbow trout/steelhead and their hybrids. Transaction of American Fisheries Society, 131(3), 404-417.
[73]	Asensio, L., Gonzalez, I., Fernandez, A., Rodriguez, M.A., Lobo, E., Hernandez, P.E., Garcia, T. and Martin, R. (2002) Application of random amplified polymorphic DNA (RAPD) analysis for identification of grouper (Epinephelus guaza), wreckfish (Polyprion americanus), and nile perch (Lates niloticus) fillets. Journal of Food Product, 65(2), 432-435.
[74]	Rasmussen, C., Ostberg, C.O., Clifton, D.R., Holloway, J.L. and Rodriguez, R.J. (2003) Identification of a genetic marker that discriminates ocean-type and stream-type Chinook salmon in the Columbia River Basin. Transaction American Fisheries Society, 132(1), 131-142.
[75]	Compton, D. and Utter, F.M. (1985) Natural hybridization between steelhead trout (Salmo gairdneri) and coastal cutthroat trout (Salmo clarki clarki) in two Puget sound streams. Canadian Journal of Fisheries and Aquatic Science, 42, 110-119.
[76]	Olivar, M.P., Moser, H.G. and Beckley, L.E. (1999) Lantern fish larvae from the Agulhas current (SW Indian Ocean). Science of Marine, 63, 101-120.
[77]	McAndrew, B.J. and Majumdar, K.C. (1983) Tilapia stock identification using electrophoretic markers. Aquaculture, 30(1-4), 249-261.
[78]	Bartly, D.M. and Gall, G.A.E. (1991) Genetic identification of native cutthroat trout (Onchorynchus clarki) and introgressive hybridization with introduced rainbow trout (O. mykiss) in streams associated with the Alvord basin, Oregon and Nevada. Copeia, 3, 854-859.
[79]	Lee, S.C., Tosi, S.C.M., Cheng, H.L. and Chang, J.T. (1997) Identification of Anguilla Japonica and A. marmorata elvers by allozyme electrophoresis. Journal of Fish Biology, 51(1), 208-210.
[80]	Rossi, A.R., Capula, M., Crosetti, D., Sola, L. and Campton, D.E. (1998) Allozyme variation in global populations of striped mullet, Mugil cephalus (Pisces: Mugilidae). Marine Biololgy, 131(2), 203-212.
[81]	Carmichael, G.J., Hanson, J.N., Schmidt, M.E. and Morizot, D.C. (1993) Introgression among apache, cutthroat and rainbow trout in Ariozona. Transaction of American Fisheries Society, 122, 121-130
[82]	Wooten, M.C. and Lydeard, C. (1990) Allozyme variation in a natural contact zone between Gambusia affinis and Gambusia holbrooki. Biochemical Systematics and Ecology, 18(2-3), 169-173.
[83]	Wang-Hurng, Y., Lee, S.C. and Yu, M.J. (1997) Genetic evidence to clarify the systematic status of the genra Zacco and Candidia (Cypriniformes: Cprinidae). Zoological Studies, 36(3), 170-177.
[84]	Perdices, A., McChordom, A. and Doadrio, I. (1996) Allozyme variation and relationships of the endangered cyprinodontid genus Valencia and its implications for conservation. Journal of Fish Biology, 49(6), 1112-1127.
[85]	Mamuris, Z., Apostolidis, A.P. and Triantaphyllidis, C. (1998) Genetic protein variation in red mullet (Mullus barbatus) and striped red mullet (M. surmuletus) populations from the Mediterranean sea. Marine Biology, 130(3), 353-360.
[86]	Roldán, M.I. and Pla, C. (2001) Species identification of two sympatric hakes by allozyme markers. Science of Marine, 65, 81-84.
[87]	Callejas, C. and Ochando, M.D. (1998) Identification of Spanish barbel species using the RAPD technique. Journal of Fish Biology, 53(1), 208-215.
[88]	Callejas, C. and Ochando, M.D. (2002) Phylogenetic relationships among Spanish Barbus species (Pisces, Cyprinidae) shown by RAPD markers. Heredity, 89(1), 36- 43.
[89]	Barman, H.K., Barat, A., Yadav, B.M., Banerjee, S., Meher, P.K., Reddy, P.V.G.K. and Jana, R.K. (2003) Genetic variation between four species of Indian major carps as revealed by random amplified polymorphic DNA assay. Aquaculture, 217(1-4), 115-123.
[90]	Takagi, M. and Taniguchi, N. (1995) Random amplified polymorphic DNA (RAPD) for identification of three species of Anguilla, A. japonica, A. australis and A. bicor. Fisheries Science, 61, 884-885.
[91]	Chow, S. and Inoue, S. (1993) Intra-and interspecific restriction fragment length polymorphism in mitochondrial genes of Thunnus tuna species. Bulletin of National Research Institute of Far Seas Fisheries, 30, 229-248.
[92]	Finnerty, J.R. and Block, B.A. (1992) Direct sequencing of mitochondrial DNA detects highly divergent haplotypes in blue marlin (Makaira nigricans). Molecular Marine Biology and Biotechnology, 1(3), 206-214.
[93]	Hare, J.A., Crown, R.K., Zehr, J.P., Juanes, F. and Day, K.H. (1998) A correction to: biological and oceanographic insights from larval labrid (Pisces: Labridae) identification using mtDNA sequences. Marine Biology, 130(4), 589-592.
[94]	Suneetha, B.K. and Dahle, G. (2000) Analysis of mitochondrial DNA sequences from Benthosema glaciale and two other myctophids (Pisces: Myctophiformes): Intra- and interspecific genetic variation. In: Interspecific and inter specific genetic variation in selected mesopelagic fishes with emphasis on microgeographic variation and species characterization, Dr. Scient. Dissertation, Departement of Fisheries and Marin Biology, University of Bergen, Bergen, Norway.
[95]	Murgia, R., Tola, G., Archer, S.N., Vallerga, S. and Hirano, J. (2002) Genetic identification of grey mullet species (Mugilidae) by analysis of mitochondrial DNA sequence: application to identify the origin of processed ovary products (bottarga). Marine Biotechnology, 4(2), 119-126.
[96]	Miya, M. and Nishida, M. (1998) Molecular phylogeny and evolution of the deep-sea fish genus Sternoptyx. Molecular Phylogenetics and Evolution, 10(1), 11-22.
[97]	Miya, M.and Nishida, M. (1996) Molecular phylogenetic perspective on the evolution of the deep-sea fish genus Cyclothone (Stomiiformes: Gonostomatidae). Ichthyolgical Research, 43(4), 375-398.
[98]	Reed, K.M., Dorschner, M.O., Todd, T.N. and Phillips, R.B. (1998) Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): Taxonomic implications for the Great Lake species flock. Molecular Ecology, 7(9), 1091-1096.
[99]	Prioli, S.M.A.P., Prioli, A.J. and Julio, H.F.J. (2002) Identification of Astyanax altiparanae (Teleostei, Characidae) in the Iguacu River, Brazil, based on mitochondrial DNA and RAPD markers. Genetics and Molecular Biology, 25(4), 421-430.
[100]	Doukakis, P., Birstein, V.J., Ruban, G.I. and Desalle, R. (1999) Molecular genetic analysis among subspecies of two Eurasian sturgeon species, Acipenser baerii and A. stellatus. Molecular Ecology, 8(12 Suppl 1), 117-127.
[101]	Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
[102]	Ryman, N., (2002) Population genetic structure. NOAA Technical Memoranda, Northwest Fisheries Science Centre Publication Page, http://www.nwfsc.noaa.gov/ publications/techmemos/index.cfm
[103]	Piry, S., Alapetite, A., Cornuet, J.M., Paetkau, D., Baudoiin, L. and Estoup, A. (2004) Geneclass2: A software for genetic assignment and first generation migrant detection. Journal of Heredity, 95(6), 536-539.
[104]	Luikart, G. and Cornuet, J.M. (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology, 12(1), 228-237.
[105]	Luikart, G. and Cornuet, J.M. (1999) Estimating the effective number of breeders from heterozygote excess in progeny. Genetics, 151(3), 1211-1216.
[106]	Weir, B.S. and Cockerham, C.C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38(6), 1358-1370.
[107]	Nei, M. (1983) Genetic Polymorphism and the role of mutation in evolution. In: Nei, M. and Kohen, R.K. Eds., Evolution of Gene and Proteins, Sinaver Associates, Sunderlans, 165-190.
[108]	Raymond, M. and Rouseet, F. (1995) An exact test for population differentiation. Evolution, 49, 1280-1283.
[109]	Fonseca, D.M., Dennis, A., Pointe, L. and Fleischer, C. (2000) Bottlenecks and multiple introductions: Population genetics of the vector of avian malaria in Hawaii. Molecular Ecology, 9(11), 1803-1814.
[110]	Zhang, Y.P., Wang, X.X., Ryder, O.A., Li, M.P., Zhang, Y. Yong, H.M. and Wang, P.Y. (2002) Genetic diversity and conservation of endangered animal species. Pure Applied Chemestry, 74(4), 575-584.
[111]	Efremov, V.V., (2002) Allozyme Variation in Pink Salmon Oncorhynchus gorbuscha from Sakhalin Island. Journal of Ichthyology, 42, 339-347.
[112]	Salini, J.P., Milton, D.A., Rahaman, M.J. and Hussein, M.G. (2004) Allozyme and morphological variation throughout the geographic range of the tropical shad, hilsa Tenualosa ilisha. Fisheries Research, 66(1), 53-69.
[113]	Lal, K.K., Kumar, D., Srivastava, S.K., Mukherjee, A., Mohindra, V., Prakash, S., Sinha, M. and Ponniah, A.G. (2004) Genetic variation in Hilsa shad (Tenualosa ilisha) population in River Ganges. Indian Journal of Fisheries, 51, 33-42.
[114]	Meggs, L.B., Austin, C.M. and Coutin, P.C. (2003) Low allozyme variation in snapper, Pagrus auratus, in Victoria, Australia. Fisheries Management and Ecology, 10(3), 155-162.
[115]	Dong, Z., Zhu, J., Yuan, X. and Wang, J. (2002) RAPD analysis of the genome DNA of Jian carp. Journal of Zhanjiang Ocean University, 22, 3-6.
[116]	Chang, Y., Sun, Y. and Liang, A. (2003) Study on cold tolerant traits for common carp Cyprinus carpio. Journal of Shanghi Fisheries University, 12, 102-105.
[117]	Feng, J., Zhang, X., Zhou, X., Chen, J. and Wang, L. (2003) RAPD markers and genetic diversity of Carassius auratus in the Qihe River. Transaction of Oceanology and Limnology, 4, 90-94.
[118]	Zheng, L. and Liu, C. (2002) Studies on random amplified polymorphic DNA (RAPD) of Epinephelus merra Bloch. Journal of Zhanjiang Ocean University, 22, 14- 18.
[119]	Exadactylos, A., Geffen, A.J., Panagiotaki, P. and Thorpe, J.P. (2003) Population structure of Dover sole Solea solea: RAPD and allozyme data indicate divergence in European stocks. Marine Ecollogy Progress Series, 246, 253-264.
[120]	Mamuris, Z., Stamatis, C. and Triantaphyllidis, C. (1999) Intraspecific genetic variation of striped red mullet (Mullus surmuletus L.) in the Mediterranean Sea assessed by allozyme and random amplified polymorphic DNA (RAPD) analysis. Heredity, 83(pt1), 30-38.
[121]	Almeida, F.S., Fungaro, M.H.P. and Sodré, L.M.K. RAPD and isoenzyme analysis of genetic variability in three allied species of catfishes (Siluriformes: Pimelodidae) from the Tibagi river, Brazil. Journal of Zoology, 253, 113-120.
[122]	Nelson, R.J., Wood, C.C., Cooper, G., Smith, C. and Koop, B. (2003) Population structure of sockeye salmon of the central coast of British Columbia: Implications for recovery planning. North American Journal of Fisheries Management, 23, 703-720.
[123]	Beacham, T.D., Supernault, K.J., Wetklo, M., Deagle, B., Labaree, K., Irvine, J.R., Candy, J.R., Miller, K.M., Nelson, R.J. and Withler, R.E. (2003) The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha). Fisheries Bulletin, 101, 229-242.
[124]	Brunner, P.C., Douglas, M.R. and Bernatchez, L. (1998) Microsatellite and mitochondrial DNA assessment of population structure and stocking effects in Arctic charr Salvelinus alpinus (Teleostei: Salmonidae) from central Alpine lakes. Molecular Ecology, 7, 209-223.
[125]	Adams, B.K. and Hutchings, J.A. (2003) Microgeographic population structure of brook charr: A comparison of microsatellite and mark-recapture. Journal of Fish Biology, 62(3), 517-533.
[126]	Senanan, W. and Kapuscinski, A.R. (2000) Genetic relationships among populations of northern pike (Esox lucius). Canadian Journal Fisheries Aquatic Science, 57, 391-404.
[127]	Salgueiro, P., Carvalho, G., Collares-Pereira, M.J. and Coelho, M.M. (2003) Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation. Biological Conservation, 109(1), 47-56.
[128]	Palm, S., Dannewitz, J., Jaervi, T., Petersson, E., Prestegaard, T. and Ryman, N. (2003) Lack of molecular genetic divergence between sea-ranched and wild sea trout (Salmo trutta). Molecular Ecology, 12(8), 2057- 2071.
[129]	Elliott, N.G. and Reilly, A. (2003) Likelihood of bottleneck event in the history of the Australian population of Atlantic salmon (Salmo salar L.). Aquaculture, 215(1-4), 31-44.
[130]	Alarcon, J.A., Magoulas, A., Georgakopoulos, T., Zouros, E. and Alvarez, M.C. (2004) Genetic comparison of wild and cultivated European populations of the Gilthead Sea bream (Sparus aurata). Aquaculture, 230(1-4), 65-80.
[131]	Kanda, N. (1998) Genetics and conservation of Bull trout: Comparison of population genetic structure among different genetic markers and hybridization with brook trout. Dissertation Abstracts International Part B: Science and Engineering, University of Montana, Missoula.
[132]	Kanda, N. and Allendorf, F.W. (2001) Genetic population structure of Bull trout from the Flathead River basin as shown by microsatellite and mitochondrial DNA marker. Transaction of American Fisheries Society, 130, 92-106.
[133]	Cagigas, M.E., Vazquez, E., Blanco, G. and Sanchez, J.A. (1999) Genetic effects of introduced hatchery stocks on indigenous brown trout (Salmo trutta L.) populations in Spain. Ecological of Freshwater Fish, 8(3), 141-150.
[134]	Chenoweth, S.F., Hughes, J.M., Keenan, C.P. and Shane, L. (1998) Concordance between dispersal and mitochon- drial gene flow: Isolation by distance in a tropical teleost, Lates calcarifer (Australian barramundi). Heredity, 80, 1897-1907.
[135]	Gysels, E.S., Hellemans, B., Pampoulie, C. and Volckaert, F.A. (2004) Phylogeography of the common goby, Pomatoschistus microps, with particular emphasis on the colonization of the Mediterranean and the North Sea. Molecular Ecololgy, 13(2), 403-417.
[136]	Marzano, F.N., Corradi, N., Papa, R., Tagliavini, J. and Gandolfi, G. (2003) Molecular evidence for introgression and loss of genetic variability in Salmo (trutta) macrostigma as a result of massive restocking of Apennine populations (Northern and Central Italy). Environmental Biology of Fishes, 68(4), 349-356.
[137]	Jerry, D.R. (1997) Population genetic structure of the catadromous Australian bass from through out its range. Journal of Fish Biology, 51(5), 909-920.
[138]	Perkins, D.L. and Krueger, C.C. (1993) Heritage brook trout in northeastern USA: Genetic variability within and among populations. Transaction of American Fisheries Society, 122, 1515-1532.
[139]	Norris, A.T., Bradley, D.G. and Cunningham, E.P. (1999) Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations. Aquaculture, 180(3-4), 247-264.
[140]	Palma, J., Alarcon, J.A., Alvarez, C., Zouros, E., Magoulas, A. and Andrade, J.P. (2001) Developmental stability and genetic heterozygosity in wild and cultured stocks of gilthead sea bream. Journal of Marine Biological Association of United Kingdom, 81(2), 283-288.
[141]	Wright, S. (1931) Evolution in Mendelian populations. Genetics, 16(2), 97-159.
[142]	Nei, M., Maruyama, T. and Chakraborty, R. (1975) The bottleneck effect and genetic variability in populations. Evolution, 29(1), 1-10.
[143]	Tessier, N. and Bernatchez, L. (1999) Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatric populations of landlocked Atlantic salmon (Salmo salar L.). Molecular Ecology, 8, 169-179.
[144]	Nielsen, E.E., Hansen, M.M. and Loeschcke, V. (1999) Genetic variation in time and space: Microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution, 53, 261-268.
[145]	Lundy, J.C., Rico, C. and Hewitt, M.G. (2000) Temporal and spatial genetic variation in spawning grounds of European hake (Merluccius merluccius) in the Bay of Biscay. Molecular Ecology, 9(12), 2067-2079.
[146]	Heath, D.D., Bryden, C.A., Shrimpton, J.M., Iwama, G.K., Kelly, J. and Heath, J.W. (2002) Relationships between heterozygosity, allelic distance (d2), and reproductive traits in Chinook salmon, Oncorhynchus tshawytscha. Canadian Journal of Fisheries and Aquatic Science, 59, 77-84.
[147]	Larson, S., Jameson, R., Etnier, M., Flemings, M. and Bentzen, P. (2002) Loss of genetic diversity in sea otters (Enhydra lutris) associated with the fur trade of the 18th and 19th centuries. Molecular Ecology, 11(10), 1899- 1903.
[148]	Beaudou, D., Baril, D., Roche, ?.B. and Le. Baron, M. (1995) Recolonization in a devastated Corsican river: Respective contribution of wild and domestic brown trout. Bulletin Francais de la Peche et de la Pisciculture, 337, 259-266.