Publication Cover
Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 27, 2016 - Issue 1
214
Views
4
CrossRef citations to date
0
Altmetric
Full Length Research Paper

Population genetics of the black scar oyster, Crassostrea iredalei: repercussion of anthropogenic interference

, , , , &
Pages 647-658 | Received 18 Nov 2013, Accepted 05 Apr 2014, Published online: 02 May 2014

References

  • Arnaud-Haond S, Vonau V, Rouxel C, Bonhomme F, Prou J, Goyard E, Boudry P. (2008). Genetic structure at different spatial scales in the pearl oyster (Pinctada margaritifera cumingii) in French Polynesian lagoons: Beware of sampling strategy and genetic patchiness. Marine Biol 155:147–57
  • Arnaud S, Monteforte M, Galtier N, Bonhomme F, Blanc F. (2000). Population structure and genetic variability of pearl oyster Pinctada mazatlanica along Pacific coasts from Mexico to Panama. Conserv Genet 1:299–308
  • Avise JC. (1994). Molecular markers, natural history and evolution. New York: Chapman & Hall. 511pp
  • Avise JC, Neigel JE, Arnold J. (1984). Demographic influences on mitochondrial DNA lineage survivorship in animal populations. J Mol Evol 20:99–105
  • Bahr LM, Lanier WP. (1981). The ecology of intertidal oyster reefs of the South Atlantic coast: A community profile. US Fish and Wildlife Service, Official of Biological Services, Washington, DC FWS/OBS-81/15. 105pp
  • Berthou P, Poutiers J-M, Goulletquer P, Dao J-C. (2009). Shelled molluscs in fisheries and aquaculture, from encyclopedia of life support systems (EOLSS), Developed under the Auspices of the UNESCO. Oxford, UK: Eolss Publisher
  • Bohonak AJ. (1999). Dispersal, gene flow, and population structure. Q Rev Biol 74:21–45
  • Boudry P, Heurtebise S, Collet B, Cornette F, Gérard A. (1998). Differentiation between populations of the Portuguese oyster, Crassostrea angulata (Lamark) and the Pacific oyster, Crassostrea gigas (Thunberg), revealed by mtDNA RFLP analysis. J Exp Marine Biol Ecol 226:279–91
  • Boudry P, Heurtebise S, Lapègue S. (2003). Mitochondrial and nuclear DNA sequence variation of presumed Crassostrea gigas and Crassostrea angulata specimens: A new oyster species in Hong Kong? Aquaculture 228:15–25
  • Burbrink FT, Fontanella F, Alexander Pyron R, Guiher TJ, Jimenez C. (2008). Phylogeography across a continent: The evolutionary and demographic history of the North American racer (Serpentes: Colubridae: Coluber constrictor). Mol Phylogenet Evol 47:274–88
  • Bussarawit S, Simonsen V. (2006). Genetic variation in populations of white scar (Crassostrea belcheri) and black scar oysters (C. iredalei) along the coast of Thailand by means of isozymes. Phuket Marine Biological Center. Res Bull 67:11–21
  • Chen CA, Ablan MCA, Mcmanus JW, Bell JD, Tuan VS, Cabanban AS, Shao K-T. (2004). Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China Sea revealed by mitochondrial control region sequences. Marine Biotechnol 6:312–26
  • Ciftci Y, Okumus İ. (2002). Fish population genetics and applications of molecular markers to fisheries and aquaculture: I-basic principles of fish population genetics. Turkish J Fish Aquat Sci 2:145–55
  • Cross T, Dillance E, Galvin P. (2000). Which molecular markers should be chosen for different specific applications in fisheries and aquaculture? National University of Ireland. Available from: http://www.ucc.ie/ucc/research/adc/molmark/index.html (Accessed 23 April 2014)
  • Darriba D, Taboada GL, Doallo R, Posada D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nat Methods 9:772
  • Devakie M, Ali A. (2000). Effects of storage temperature and duration on the setting and post-set spat survival of the tropical oyster, Crassostrea iredalei (Faustino). Aquaculture 190:369–76
  • Devakie M, Ali A. (2002). Effective use of plastic sheet as substrate in enhancing tropical oyster Crassostrea iredalei (Faustino) larvae settlement in the hatchery. Aquaculture 212:277–87
  • Devakie N, Robert H, Charles L. (1993). Small scale oyster culture on the west coast of Peninsular Malaysia. BOBP/REP/63. GCP/RAS/118/MUL. BOBP, Madras, India
  • Du X, Chen Z, Deng Y, Wang Q. (2009). Comparative analysis of genetic diversity and population structure of Sipunculus nudus as revealed by mitochondrial COI sequences. Biochem Genet 47:884–91
  • Durand J, Blel H, Shen K, Koutrakis E, Guinand B. (2013). Population genetic structure of Mugil cephalus in the Mediterranean and Black Seas: A single mitochondrial clade and many nuclear barriers. Marine Ecol Prog Ser 474:243–61
  • Eck R, Dayhoff M. (1966). Atlas of protein sequence and structure National Biomedical Research Foundation. Maryland: Springs Silver
  • Ewens WJ. (1972). The sampling theory of selectively neutral alleles. Theor Population Biol 3:87–112
  • Excoffier L, Laval G, Schneider S. (2005). Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50
  • 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. Mol Marine Biol Biotechnol 3:294–9
  • Fu Y-X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–25
  • Gjedrem T. (1992). Breeding plans for rainbow trout. Aquaculture 100:73–83
  • Grant W, Bowen B. (1998). Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J Heredity 89:415–26
  • Gum B, Gross R, Geist J. (2009). Conservation genetics and management implications for European grayling, Thymallus thymallus: Synthesis of phylogeography and population genetics. Fish Manag Ecol 16:37–51
  • Hedgecock D, Chow V, Waples RS. (1992). Effective population numbers of shellfish broodstocks estimated from temporal variance in allelic frequencies. Aquaculture 108:215–32
  • Hedgecock D, Sly F. (1990). Genetic drift and effective population sizes of hatchery-propagated stocks of the Pacific oyster, Crassostrea gigas. Aquaculture 88:21–38
  • Hoskin M. (1997). Effects of contrasting modes of larval development on the genetic structures of populations of three species of prosobranch gastropods. Marine Biol 127:647–56
  • Hudson R, Boos DD, Kaplan N. (1992). A statistical test for detecting geographic subdivision. Mol Biol Evol 9:138–51
  • Hurwood DA, Adamson EA, Mather PB. (2006). Identifying stock structure of two Henicorhynchus species in the Mekong River using mitochondrial DNA. Proceedings of 7th technical symposium on Mekong fisheries; 2006. p 253–63
  • Hurwood DA, Hughes J, Bunn S, Cleary C. (2003). Population structure in the freshwater shrimp (Paratya australiensis) inferred from allozymes and mitochondrial DNA. Heredity 90:64–70
  • Huvet A, Boudry P, Ohresser M, Delsert C, Bonhomme F. (2000). Variable microsatellites in the Pacific oyster Crassostrea gigas and other cupped oyster species. Anim Genet 31:71–2
  • Kochzius M, Nuryanto A. (2008). Strong genetic population structure in the boring giant clam, Tridacna crocea, across the Indo-Malay Archipelago: Implications related to evolutionary processes and connectivity. Mol Ecol 17:3775–87
  • Lam K, Morton B. (2003). Mitochondrial DNA and morphological identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China. Aquaculture 228:1–13
  • Larget B, Simon DL. (1999). Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750–9
  • Lavery S, Moritz C, Fielder D. (1996). Genetic patterns suggest exponential population growth in a declining species. Mol Biol Evol 13:1106–13
  • Littlewood D. (1994). Molecular phylogenetics of cupped oysters based on partial 28S rRNA gene sequences. Mol Phylogenet Evol 3:221–9
  • Luttikhuizen P, Drent J, Baker A. (2003). Disjunct distribution of highly diverged mitochondrial lineage clade and population subdivision in a marine bivalve with pelagic larval dispersal. Mol Ecol 12:2215–29
  • Lynch M, Crease TJ. (1990). The analysis of population survey data on DNA sequence variation. Mol Biol Evol 7:377–94
  • Medley TL. (2010). Wild oysters, Crassostrea virginica, in the Hudson River Estuary: Growth, health and population structure. [3426793 Ph.D.]. New York: City University of New York
  • Meistertzheim A-L, Arnaud-Haond S, Boudry P, Thébault M-T. (2013). Genetic structure of wild European populations of the invasive Pacific oyster Crassostrea gigas due to aquaculture practices. Marine Biol 160:453–63
  • Najiah M, Nadirah M, Lee K, Lee S, Wendy W, Ruhil H, Nurul F. (2008). Bacteria flora and heavy metals in cultivated oysters Crassostrea iredalei of Setiu Wetland, East Coast Peninsular Malaysia. Vet Res Commun 32:377–81
  • Nei M. (1973). Analysis of gene diversity in subdivided populations. Proc Nat Acad Sci 70:3321–3
  • Nei M. (1987). Molecular evolutionary genetics. New York: Columbia University Press
  • Ng FO. (1979). Experimental culture of aflat oyster (Ostrea folium L.) in Malaysian waters. Malaysian Agri J 52:103–13
  • Page RD. (2001). TreeView. Glasgow, UK: Glasgow University
  • Perdices A, Sayanda D, Coelho M. (2005). Mitochondrial diversity of Opsariichthys bidens (Teleostei, Cyprinidae) in three Chinese drainages. Mol Phylogenet Evol 37:920–7
  • Posada D. (2004). Collapse 1.2. Provo, Utah: Brigham Young University
  • Posada D, Crandall KA. (2001). Intraspecific gene genealogies: Trees grafting into networks. Trends Ecol Evol 16:37–45
  • Rahim MHA, Ismail P, Alias R, Muhammad N, Mat Jais AM. (2012). PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia. Gene 494:1–10
  • Ramos-Onsins SE, Rozas J. (2002). Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19:2092–100
  • Ray N, Currat M, Excoffier L. (2003). Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol 20:76–86
  • Richard GM. (2006). Genetic structure of Crassostrea virginica (American oyster) reefs along the Alabama Gulf Coast. [1433231 M.Sc.]. University of South Alabama, Alabama. Available from: http://search.proquest.com/docview/304962253accountid=14645 ProQuest Dissertations & Theses (PQDT) database
  • Rodrigues R, Schneider H, Santos S, Vallinoto M, Sain-Paul U, Sampaio I. (2008). Low levels of genetic diversity depicted from mitochondrial DNA sequences in a heavily exploited marine fish (Cynoscion acoupa, Sciaenidae) from the Northern coast of Brazil. Genet Mol Biol 31:487–91
  • Rogers AR, Fraley AE, Bamshad MJ, Watkins WS, Jorde LB. (1996). Mitochondrial mismatch analysis is insensitive to the mutational process. Mol Biol Evol 13:895–902
  • Rogers AR, Harpending H. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–69
  • Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, et al. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–42
  • Rozas J, Sánchez-Delbarrio JC, Messeguer X, Rozas R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–7
  • Sacco F. (1897). I molluschi dei terreni Terziarii del Piemonte e della liguria, pt XXII, Scaphopoda. pis
  • Saitou N, Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–25
  • Shanks AL, Grantham BA, Carr MH. (2003). Propagule dispersal distance and the size and spacing of marine reserves. Ecol Appl 13:159–69
  • Shefer S, Abelson A, Mokady O, Geffen E. (2004). Red to Mediterranean Sea bioinvasion: Natural drift through the Suez Canal, or anthropogenic transport? Mol Ecol 13:2333–43
  • Siddiqui G, Ahmed M. (2002). Oyster species of the sub tropical coast of Pakistan (northern Arabian Sea). Ind J Marine Sci 31:108–18
  • Siegel D, Kinlan B, Gaylord B, Gaines S. (2003). Lagrangian descriptions of marine larval dispersion. Marine Ecol Prog Ser 260:83–96
  • Suzana M. (2011). Population genetics and molecular taxonomy of two important cultured oyster species in Malaysia, Crassostrea iredalei (Faustino, 1932) and Crassostrea belcheri (Sowerby, 1871) [MSc]. Malaysia: Universiti Sains Malaysia
  • Suzana M, Lutfi AM, Hadi AA, Devakie MN, Azizah MNS. (2011). Genetic variation in Malaysian oysters: Taxonomic ambiguities and evidence of biological invasion. Biol Invasions 13:1893–900
  • Tajima F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–95
  • Tamura K. (1992). Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+ C-content biases. Mol Biol Evol 9:678–87
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9
  • Treml E, Halpin P, Urban D, Pratson L. (2008). Modeling population connectivity by ocean currents, a graph-theoretic approach for marine conservation. Landscape Ecol 23:19–36
  • Uthicke S, Benzie J. (2003). Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific. Mol Ecol 12:2635–48
  • 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. J Shellfish Res 28:855–64
  • Vermeij GJ. (1987). The dispersal barrier in the tropical Pacific: Implications for molluscan speciation and extinction. Evolution 41:1046–58
  • Visootiviseth P, Day A, Siwadune T. (1998). Electrophoretic and morphometric analyses in species differentiation of small oysters, Saccostrea spp. Thailand. J Sci Soc Thailand 24:24–36
  • Xia X. (2013). DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 30:1720–8
  • Xiao J. (2009). Assessing genetic variation within and among native populations and hatchery stocks of Crassostrea ariakensis using microsatellite markers [Ph.D. 3353206]. The College of William and Mary
  • Xiao J, Cordes JF, Wang H, Guo X, Reece KS. (2010). Population genetics of Crassostrea ariakensis in Asia inferred from microsatellite markers. Marine Biol 157:1767–81
  • Yu D. (2006). Molecular phylogenetics and population genetics of pearl oysters in Pinctada Roding, 1798 [3241030 Ph.D]. Hong Kong: The Chinese University of Hong Kong
  • Zulfigar Y, Aileen T. (2000). A review of oyster culture in Malaysia. Mollusk research in Asia. Bangkok: Thailand Research Fund

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.