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ORIGINAL ARTICLES

Assessing the genetic diversity of the mangrove oyster Crassostrea rhizophorae (Bivalvia, Ostreidae) by microsatellite markers in southeastern Brazil

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Pages 944-954 | Accepted 17 Apr 2015, Published online: 07 Aug 2015

References

  • Anderson JD, Karel WJ, Mace CE, Bartram BL, Matthew PH. 2014. Spatial genetic features of eastern oysters (Crassostrea virginica) in the Gulf of Mexico: Northward movement of a secondary contact zone. Ecology and Evolution 4:167–85.
  • Beerli P, Felsenstein J. 1999. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763–73.
  • Beerli P, Felsenstein J. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences 98:4563–68.
  • Bernardes MEC, Miranda LB de. 2001. Circulação estacionária e estratificação de sal em canais estuarinos: Simulação com modelos analíticos. Revista Brasileira de Oceanografia 49:115–32.
  • Billotte N, Lagoda PJL, Risterucci A-M, Baurens F-C. 1999. Microsatellite-enriched libraries: Applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–88.
  • Brookfield JFY. 1996. A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology 5:453–55.
  • Brumfield RT, Beerli P, Nickerson DA, Edwards SV. 2003. The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology & Evolution 18:249–56.
  • Cornuet JM, Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–14.
  • DeWoody JA, Avise JC. 2000. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. Journal of Fish Biology 56:461–73.
  • Di Rienzo AA, Peterson JC, Carza AM, Valdes M, Slatkin M, Freimer NB. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences 91:3166–70.
  • Erse EB, Bernardes MA. 2008. Levantamento de estoques da ostra Crassostrea sp. em bancos naturais no litoral paranaense. Biotemas 21:57–63.
  • Faurby S, King TL, Obst M, Hallerman EM, Pertoldi C, Funch P. 2010. Population dynamics of American horseshoe crabs – Historic climatic events and recent anthropogenic pressures. Molecular Ecology 19:3088–100.
  • Galindo-Sánchez CE, Gaffney PM, Pérez-Rostro CI, Rosa-Vélez J la, Ceela J, Cruz P. 2008. Assessment of genetic diversity of the eastern oyster Crassostrea virginica in Veracruz, Mexico, using microsatellite markers. Journal of Fish Biology 27:721–27.
  • Galvão MSN, Pereira OM, Hilsdorf AWS. 2013. Molecular identification and distribution of mangrove oysters (Crassostrea) in an estuarine ecosystem in Southeast Brazil: Implications for aquaculture and fisheries management. Aquaculture Research 44:1589–601.
  • Gerlach G, Jueterbock A, Kraemer P, Deppermann J, Harmand P. 2010. Calculations of population differentiation based on Gst and D: Forget GST but not all of statistics! Molecular Ecology19:3845–52.
  • Goudet J. 2002. FSTAT: A Program to Estimate and Test Gene Diversities and Fixation Indices. Version 2.9.3.2. Lausanne: University of Lausanne, Department of Ecology & Evolution. Computer program.
  • Guo S, Thompson E. 1992. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48:361–72.
  • Haque CM, Deb AK, Medeiros D. 2009. Integrating conservation with livelihood improvement for sustainable development: The experiment of an oyster producers’ cooperative in Southeast Brazil. Society and Natural Resources 22:554–70.
  • Hauser L, Seeb JE. 2008. Advances in molecular technology and their impact on fisheries genetics. Fish and Fisheries 9:473–86.
  • Hedgecock D, Li G, Hubert S, Bucklin K, Ribes V. 2004. Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster, Crassostrea gigas. Journal of Shellfish Research 23:379–85.
  • Hedrick PW. 2005. A standardized genetic differentiation measure. Evolution 59:1633–38.
  • Hoover CA, Gaffney PM. 2005. Geographic variation in nuclear genes of the eastern oyster, Crassostrea virginica. Journal of Shellfish Research 24:103–12.
  • Huvet A, Boudry P, Ohresser M, Delsert C, Bonhomme F. 2000a. Variable microsatellites in the Pacific oyster Crassostrea gigas and other cupped oyster species. Animal Genetics 31:68–79.
  • Huvet A, Lapègue S, Magoulas A, Boudry P. 2000b. Mitochondrial and nuclear DNA phylogeography of Crassostrea angulata, the Portuguese oyster endangered in Europe. Conservation Genetics 1:251–62.
  • Ignacio BL, Absher TM, Lazoski C, Solé-Cava AM. 2000. Genetic evidence of the presence of two species of Crassostrea (Bivalvia: Ostreidae) on the coast of Brazil. Marine Biology 136:987–91.
  • Jost L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17:4015–26.
  • Kalinowski ST. 2006. HW-QuickCheck: A computer program for checking genotypes for agreement with Hardy-Weinberg expectations. Molecular Ecology Notes 6:974–79.
  • King TLR, Ward R, Zimmerman EG. 1994. Population structure of eastern oysters (Crassostrea virginica) inhabiting the Laguna Madre, Texas, and adjacent bay systems. Canadian Journal of Fisheries and Aquatic Sciences 51:215–22.
  • Lapègue S, Boutet I, Leitão A, Heurtebise S, Garcia P, Thiriot-Quiévreux C, et al. 2002. Trans-Atlantic distribution of a mangrove oyster species revealed by 16S mtDNA and karyological analyses. The Biological Bulletin 202:232–42.
  • Launey S, Ledu C, Boudry P, Bonhomme F, Naciri-Graven Y. 2002. Geographic structure in the European flat oyster (Oyster edulis L.) as revealed by microsatellite polymorphism. Journal of Heredity 93:331–38.
  • Lazoski C, Gusmão J, Boudry P, Solé-Cava AM. 2011. Phylogeny and phylogeography of Atlantic oyster species: Evolutionary history, limited genetic connectivity and isolation by distance. Marine Ecology Progress Series 426:197–212.
  • Li Q, Yu H, Yu R. 2006. Genetic variability assessed by microsatellites in cultured populations of the Pacific oyster (Crassostrea gigas) in China. Aquaculture 259:95–102.
  • Luikart G, Cornuet JM. 1997. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology 12:228–37.
  • Meirmans PG. 2006. Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60:2399–402.
  • Meistertzheim A-L, Arnaud-Haond S, Boudry P, Tébaut MT. 2013. Genetic structure of wild European populations of the invasive Pacific oyster Crassostrea gigas due to aquaculture practices. Marine Biology160:453–63.
  • Melo AGC de, Varela ES, Beasley CR, Schneider H, Sampaio I, Gaffney PM, et al. 2010. Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea). Genetics and Molecular Biology 33:564–72.
  • Miller PA, Elliott NG, Koutoulis A, Kube PD, Vaillancourt RE. 2012. Genetic diversity of cultured, naturalized, and native Pacific oysters, Crassostrea gigas, determined from multiplexed microsatellite markers. Journal of Shellfish Research 31:611–17.
  • Miranda LB, Castro-Filho BM. 1996. On the salt transport in the Cananeia Sea during a spring tide experiment. Revista Brasileira de Oceanografia 44:123–33.
  • Miyao SY,Nishihara L, Sarti CC. 1986. Características físicas e químicas do sistema estuarino-lagunar de Cananéia-Iguape. Boletim do Instituto Oceanográfico 34:23–36.
  • Morin PA, Aitken NC, Rubio-Cisneros N, Dizon AE, Mesnick S. 2007. Characterization of 18 SNP markers for sperm whale (Physeter macrocephalus). Molecular Ecology Notes 7:626–30.
  • Nascimento IA. 1991. Crassostrea rhizophorae (Guilding) and C. brasiliana (Lamarck) in South and Central America. Chapter 10. In: Menzel W, editor. Estuarine and Marine Bivalve Mollusk Culture. Boca Raton, FL: CRC Press, p126–33.
  • Nei M. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press.512 pages.
  • Pereira OM, Machado IC, Henriques MB, Galvão MSN, Bastos AA. 2000. Avaliação do estoque da ostra Crassostrea brasiliana (Lamarck, 1819) no manguezal da região estuarino-lagunar de Cananéia (25ºS; 48ºW). Boletim do Instituto de Pesca 26:49–62.
  • Pereira OM, Machado IC, Henriques MB, Galvão MSN, Yamanaka N. 2001. Avaliação do estoque da ostra Crassostrea brasiliana em rios e gamboas da região estuarino-lagunar de Cananéia (São Paulo, Brasil). Boletim do Instituto de Pesca 27:85–95.
  • Pereira OM, Henriques MB, Machado IC. 2003. Estimativa da curva de crescimento da ostra Crassostrea brasiliana em bosques de mangue e proposta para sua extração ordenada no estuário de Cananéia, SP, Brasil. Boletim do Instituto de Pesca 29:19–28.
  • Pie MR, Ribeiro RO, Boeger WA, Ostrensky A, Falleiros RM, Angelo L. 2006. A simple PCR-RFLP method for the discrimination of native and introduced oyster species (Crassostrea brasiliana, C. rhizophorae and C. gigas; Bivalvia: Ostreidae) cultured in Southern Brazil. Aquaculture Research 37:1598–600.
  • Piry S,Luikart G, Cornuet JM. 1999. BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity 90:502–03.
  • Pritchard DW. 1967. What is an estuary: Physical view-point. In: Lauff GH, editor. Estuaries. Washington DC: American Association for the Advancement of Science, p 3–5.
  • Raymond M, Rousset F. 1995. GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicism. Journal of Heredity 86:248–49.
  • Reeb CA, Avise JC. 1990. A genetic discontinuity in a continuously distributed species: Mitochondrial DNA in the American oyster, Crassostrea virginica. Genetics 124:397–406.
  • Rios EC. 1994. Seashells of Brazil, 2nd edition. Rio Grande: Fundação Universidade do Rio Grande.481 pages.
  • Rithidech K,Dunn JJ. 2003. Combining multiplex and touchdown PCR for microsatellite analysis. Methods in Molecular Biology 266:295–99.
  • Romiguier J,Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, et al. 2014. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515:261–63.
  • Schlötterer C. 2000. Evolutionary dynamics of microsatellite DNA. Chromosoma 109:365–71.
  • Shaklee JB, Bentzen P. 1998. Genetic identification of stocks of marine fish and shellfish. Bulletin of Marine Science 62:589–621.
  • Shaklee JB, Beacham TD, Seeb L, White BA. 1999. Managing fisheries using genetic data: Case studies from four species of Pacific salmon. Fisheries Research 43:45–78.
  • Sterner T. 2007. Unobserved diversity, depletion and irreversibility. The importance of subpopulations for management of cod stocks. Ecological Economics 61:566–74.
  • Storey JD. 2002. A direct approach to false discovery rates. Journal of the Royal Statistical Society B 64:479–98.
  • Storey JD, Tibshirani R. 2003. Statistical significance for genome-wide experiments. Proceedings of the National Academy of Sciences 100:9440–45.
  • Thorpe JP, Solé-Cava AM, Watt PC. 2000. Exploited marine invertebrates: Genetics and fisheries. Hydrobiology 428:165–84.
  • UNESCO 1999. IUCN Evaluation of Nominations of Natural and Mixed Properties to the World Heritage List. Bureau of the World Heritage Committee, Twenty-third Extraordinary Session, 26–27 November 1999, Marrakesh, Morocco. Paris: UNESCO, p 11–15.
  • 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 4:135.
  • Varney RL, Galindo-Sánchez CE, Cruz P, Gaffney PM. 2009. Population genetics of the eastern oyster Crassostrea virginica (Gmelin, 1791) in the Gulf of Mexico. Journal of Shellfish Research 28:855–64.
  • Wakamatsu T. 1973. A Ostra de Cananéia e seu Cultivo. São Paulo: Superintendência do Desenvolvimento do Litoral Paulista (SUDELPA), Instituto Oceanográfico da Universidade de São Paulo. 141 pages.
  • Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358–70.
  • Xiao J, Cordes JF, Wang H, Guo X, Reece KS. 2010. Population genetics of Crassostrea ariakensis in Asia inferred from microsatellite markers. Marine Biology 157:1767–81.
  • Xiao J,Cordes JF, Moss JA, Reece KS. 2011. Genetic diversity in US hatchery stocks of Crassostrea ariakensis (Fujita, 1913) and comparison with natural populations in Asia. Journal of Shellfish Research 30:751–60.
  • Yu H, Li Q. 2007. Genetic variation of wild and hatchery populations of the Pacific oyster Crassostrea gigas assessed by microsatellite markers. Journal of Genetics and Genomics 34:1114–22.
  • Yu H, Li Q, Yu R. 2008. Genetic differentiation between Zhe oyster Crassostrea plicatula and Pacific oyster Crassostrea gigas populations in China assessed by microsatellite analysis. Fisheries Science 74:88–97.

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