Population structure of the giant tiger shrimp Penaeus monodon in Bangladesh based on variation in microsatellites and immune-related genes

References

• Ahmed N, Troell M. 2010. Fishing for prawn larvae in Bangladesh: an important coastal livelihood causing negative effects on the environment. Ambio 39:20–29. doi:10.1007/s13280-009-0002-y
   PubMed Web of Science ®Google Scholar
• Alam MMM, Westfall KM, Pálsson S. 2016. Mitogenomic variation of Bangladesh Penaeus monodon (Decapoda, Penaeidae) and reassessment of its phylogeography in the Indo-West Pacific region. Hydrobiologia 763(1):249–65. doi:10.1007/s10750-015-2381-3
   Web of Science ®Google Scholar
• Azad AK, Jensen KR, Lin CK. 2009. Coastal aquaculture development in Bangladesh: unsustainable and sustainable experiences. Environmental Management 44:800–09. doi:10.1007/s00267-009-9356-y
   PubMed Web of Science ®Google Scholar
• Aziz D, Siraj SS, Daud SK, Panandam JM, Othman MF. 2011. Genetic diversity of wild and cultured populations of Penaeus monodon using microsatellite markers. Journal of Fisheries and Aquatic Science 6(6):614–23. doi:10.3923/jfas.2011.614.623
   Google Scholar
• Baranski M, Gopikrishna G, Robinson NA, Katneni VK, Shekhar MS, Shanmugakarthik J, et al. 2014. The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs. PLoS One 9(1):e85413. 13 pages. doi:10.1371/journal.pone.0085413
   PubMed Web of Science ®Google Scholar
• Benzie JAH. 2000. Population genetic structure in penaeid prawns. Aquaculture Research 31:95–119. doi:10.1046/j.1365-2109.2000.00412.x
   Web of Science ®Google Scholar
• Benzie JAH, Ballment E, Forbes AT, Demetriades NT, Sugama K, Haryanti Moria S. 2002. Mitochondrial DNA variation in Indo-Pacific populations of the giant tiger prawn, Penaeus monodon. Molecular Ecology 11:2553–69. doi:10.1046/j.1365-294X.2002.01638.x
   PubMed Web of Science ®Google Scholar
• Carvalho GR, Hauser L. 1994. Molecular genetics and the stock concept in fisheries. Reviews in Fish Biology and Fisheries 4:326–50. doi:10.1007/BF00042908
   Web of Science ®Google Scholar
• Chapuis MP, Estoup A. 2007. Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24:621–31. doi:10.1093/molbev/msl191
   PubMed Web of Science ®Google Scholar
• Christiansen FB. 1988. The Wahlund effect with overlapping generations. The American Naturalist 131:149–56. doi:10.1086/284782
   Web of Science ®Google Scholar
• Debnath P, Karim M, Belton B. 2014. Comparative study of the reproductive performance and White Spot Syndrome Virus (WSSV) status of black tiger shrimp (Penaeus monodon) collected from the Bay of Bengal. Aquaculture 424-425:71–77. doi:10.1016/j.aquaculture.2013.12.036
   Web of Science ®Google Scholar
• Debnath P, Khan SH, Karim M, Belton B, Mohan CV, Phillips M. 2015. Review of the history, status and prospects of the black tiger shrimp (Penaeus monodon) hatchery sector in Bangladesh. Reviews in Aquaculture 2015. 13 pages. doi:10.1111/raq.12094
   Google Scholar
• Department of Fisheries Bangladesh. 2002. Balancing Resource Conservation with Livelihood Protection for Shrimp Fry Collectors: An Integrated Approach to Managing Coastal Resources. Dhaka, Bangladesh: Department of Fisheries, Ministry of Fisheries and Livestock. 15 pages.
   Google Scholar
• Department of Fisheries Bangladesh. 2013. National Fish Week 2013 Compendium. Dhaka, Bangladesh: Department of Fisheries, Ministry of Fisheries and Livestock. 144 pages. (in Bengali)
   Google Scholar
• Department of Fisheries Bangladesh. 2014. National Fish Week 2014 Compendium. Dhaka, Bangladesh: Department of Fisheries, Ministry of Fisheries and Livestock. 144 pages. (in Bengali)
   Google Scholar
• Escobedo-Bonilla CM, Alday-Sanz V, Wille M, Sorgeloos P, Pensaert MB, Nauwynck HJ. 2008. A review on the morphology, molecular characterization, morphogenesis and pathogenesis of white spot syndrome virus. Journal of Fish Diseases 31:1–18. doi:10.1111/j.1365-2761.2007.00877.x
   PubMed Web of Science ®Google Scholar
• Foll M. 2012. BayeScan v 2.1 user manual. Ecology 20:1450–62.
   Google Scholar
• García DL, Dallas JF, Chatain B, Canonne M, Versini JJ, Bonhomme F. 1995. Development and use of microsatellite markers in seabass, Dicentrarchus labrax (Linnaeus 1758) (Perciformes: Serranidae). Molecular Marine Biology and Biotechnology 4:62–68.
   PubMedGoogle Scholar
• Ghosh A, Schmidt S, Fickert T, Nüsser M. 2015. The Indian sundarban mangrove forests: history, utilization, conservation strategies and local perception. Diversity 7:149–69. doi:10.3390/d7020149
   Google Scholar
• Gjedrem T, Robinson N, Rye M. 2012. The importance of selective breeding in aquaculture to meet future demands for animal protein: a review. Aquaculture 350-353:117–29. doi:10.1016/j.aquaculture.2012.04.008
   Web of Science ®Google Scholar
• Goudet J. 2005. HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes 5(1):184–86. doi:10.1111/j.1471-8286.2004.00828.x
   Web of Science ®Google Scholar
• Hayes BJ, Gitterle T, Gopikrishna G, Gopal C, Krishna G, Jahageerdar S, et al. 2010. Limited evidence for genetic variation for resistance to the white spot syndrome virus in Indian populations of Penaeus monodon. Aquaculture Research 41:e872–e877. doi:10.1111/j.1365-2109.2010.02611.x
   Google Scholar
• Hoq ME. 2007. An analysis of fisheries exploitation and management practices in Sundarbans mangrove ecosystem, Bangladesh. Ocean & Coastal Management 50:411–27. doi:10.1016/j.ocecoaman.2006.11.001
   Web of Science ®Google Scholar
• Hoq ME, Islam MN, Kamal M, Wahab MA. 2001. Abundance and seasonal distribution of Penaeus monodon postlarvae in the Sundarbans mangrove, Bangladesh. Hydrobiologia 457:97–104. doi:10.1023/A:1012266623308
   Web of Science ®Google Scholar
• Jeswin J, Anju A, Thomas PC, Paulton MP, Vijayan KK. 2013. Survivability of Penaeus monodon during white spot syndrome virus infection and its correlation with immune related genes. Aquaculture 380-383:84–90. doi:10.1016/j.aquaculture.2012.12.004
   Web of Science ®Google Scholar
• Jombart T, Collins C, Kamvar ZN, Lustrik R, Solymos P, Ahmed I, et al. 2015. Exploratory Analysis of Genetic and Genomic Data. http://adegenet.r-forge.r-project.org/
   Google Scholar
• Jost L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17:4015–26. doi:10.1111/j.1365-294X.2008.03887.x
   PubMed Web of Science ®Google Scholar
• Kamal AHM, Khan MAA. 2009. Coastal and estuarine resources of Bangladesh: management and conservation issues. Maejo International Journal of Science and Technology 3(2):313–42.
   Web of Science ®Google Scholar
• Kruskal JB. 1964. Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29:1–27. doi:10.1007/BF02289565
   Web of Science ®Google Scholar
• Kumar N, Lakra WS, Majumdar KC, Goswami M, Ravinder K. 2007. Genetic diversity in the Indian population of Penaeus monodon (Fabricius, 1798) as revealed by mtDNA sequence analysis. Aquaculture Research 38:862–69. doi:10.1111/j.1365-2109.2007.01740.x
   Web of Science ®Google Scholar
• Li Y, Wongprasert K, Shekhar M, Ryan J, Dierens L, Meadows J, et al. 2007. Development of two microsatellite multiplex systems for black tiger shrimp Penaeus monodon and its application in genetic diversity study for two populations. Aquaculture 266:279–88. doi:10.1016/j.aquaculture.2007.01.038
   Web of Science ®Google Scholar
• Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. 2003. The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics 4(12):981–94. doi:10.1038/nrg1226
   PubMed Web of Science ®Google Scholar
• Mandal A, Rao D, Karuppaiah D, Gopalakrishnan A, Pozhoth J, Chellamma Y, et al. 2012. Population genetic structure of Penaeus monodon, in relation to monsoon current patterns in Southwest, East and Andaman coastal waters of India. Gene 491:149–57. doi:10.1016/j.gene.2011.10.002
   PubMed Web of Science ®Google Scholar
• Maniatis T, Fritsch EF, Sambrook J. 1982. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 545 pages.
   Google Scholar
• Mantel NA. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27:209–20.
   PubMed Web of Science ®Google Scholar
• Maralit BA, Ventolero MFH, Maningas MBB, Amar EC, Santos MD. 2014. Subtracted transcriptome profile of tiger shrimp (Penaeus monodon) that survived WSSV challenge. Dataset Papers in Science 2014:807806. 11 pages. doi:10.1155/2014/807806
   Google Scholar
• Meirmans PG, Hedrick PW. 2011. Assessing population structure: FST and related measures. Molecular Ecology Resources 11:5–18. doi:10.1111/j.1755-0998.2010.02927.x
   PubMed Web of Science ®Google Scholar
• Moss SM, Moss DR, Arce SM, Lightner DV, Lotz JM. 2012. The role of selective breeding and biosecurity in the prevention of disease in penaeid shrimp aquaculture. Journal of Invertebrate Pathology 110:247–50. doi:10.1016/j.jip.2012.01.013
   PubMed Web of Science ®Google Scholar
• Motoh H. 1985. Biology and ecology of Penaeus monodon. In: Taki Y, Primavera JH, Llobrera JA, editors. Proceedings of the First International Conference on the Culture of Penaeid Prawns/Shrimps. Iloilo City, Philippines, p 27–36.
   Google Scholar
• Pan Y, Chou H, You E, Yu H. 2004. Isolation and characterization of 23 polymorphic microsatellite markers for diversity and stock analysis in tiger shrimp (Penaeus monodon). Molecular Ecology Notes 4:345–47. doi:10.1111/j.1471-8286.2004.00692.x
   Web of Science ®Google Scholar
• Paradis E. 2012. Analysis of Phylogenetics and Evolution with R. New York: Springer. 386 pages.
   Google Scholar
• Quader O. 2010. Coastal and marine biodiversity of Bangladesh (Bay of Bengal). In: Proceedings of International Conference on Environmental Aspects of Bangladesh (ICEAB10), Fukuoka, Japan, p 83–86.
   Google Scholar
• R Core Team. 2015. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org/.
   Google Scholar
• Rice WR. 1989. Analyzing tables of statistical tests. Evolution 43:223–25. doi:10.2307/2409177
   PubMed Web of Science ®Google Scholar
• Robinson NA, Gopikrishna G, Baranski M, Katneni VK, Shekhar MS, Shanmugakarthik J, et al. 2014. QTL for white spot syndrome virus resistance and the sex-determining locus in the Indian black tiger shrimp (Penaeus monodon). BMC Genomics 15(1):731. 21 pages. doi:10.1186/1471-2164-15-731
   PubMed Web of Science ®Google Scholar
• Rousset F. 2008. GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103–06. doi:10.1111/j.1471-8286.2007.01931.x
   PubMed Web of Science ®Google Scholar
• Smith BJ. 2007. BOA: an R package for MCMC output convergence assessment and posterior inference. Journal of Statistical Software 21(11):1–37. doi: 10.18637/jss.v021.i11
   Web of Science ®Google Scholar
• Song X, Zhang H, Zhao J, Wang L, Qiu L, Mu C, et al. 2010. An immune responsive multidomain galectin from bay scallop Argopectens irradians. Fish & Shellfish Immunology 28(2):326–32. doi:10.1016/j.fsi.2009.11.016
   PubMed Web of Science ®Google Scholar
• Stentiford GD, Neil DM, Peeler EJ, Shields JD, Small HJ, Flegel TW, et al. 2012. Disease will limit future food supply from the global crustacean fishery and aquaculture sectors. Journal of Invertebrate Pathology 110:141–57. doi:10.1016/j.jip.2012.03.013
   PubMed Web of Science ®Google Scholar
• Tassanakajon A, Tiptawonnukul A, Supungul P, Rimphanitchayakit V, Cook D, Jarayabhand P, et al. 1998. Isolation and characterization of microsatellite markers in the black tiger prawn Penaeus monodon. Molecular Marine Biology and Biotechnology 7:55–61.
   Google Scholar
• Van Oosterhout C, Weetman D, Hutchinson WF. 2006. Estimation and adjustment of microsatellite null alleles in nonequilibrium populations. Molecular Ecology Notes 6:255–56. doi:10.1111/j.1471-8286.2005.01082.x
   Web of Science ®Google Scholar
• Vaseeharan B, Rajakamaran P, Jayaseelan D, Vincent AY. 2013. Molecular markers and their application in genetic diversity of penaeid shrimp. Aquaculture International 21:219–41. doi:10.1007/s10499-012-9582-9
   Web of Science ®Google Scholar
• Venables WN, Ripley BD. 2002. Random and mixed effects. In: Venables WN, Ripley BD, editors. Modern Applied Statistics with S. New York: Springer, p 271–300.
   Google Scholar
• Walker PJ, Mohan CV. 2009. Viral disease emergence in shrimp aquaculture: origins, impact and the effectiveness of health management strategies. Reviews in Aquaculture 1:125–54. doi:10.1111/j.1753-5131.2009.01007.x
   PubMed Web of Science ®Google Scholar
• Wan Q, Wu H, Fujihara T, Fang S. 2004. Which genetic marker for which conservation genetics issue? Electrophoresis 25:2165–76. doi:10.1002/elps.200305922
   PubMed Web of Science ®Google Scholar
• Wang X, Xu J, Zhao X, Vasta GR, Wang J. 2014. A shrimp C-type lectin inhibits proliferation of the hemolymph microbiota by maintaining the expression of antimicrobial peptides. Journal of Biological Chemistry 289(17):11779–90. doi:10.1074/jbc.M114.552307
   PubMed Web of Science ®Google Scholar
• Waqairatu SS, Dierens L, Cowley JA, Dixon TJ, Johnson KN, Barnes AC, Li Y. 2012. Genetic analysis of black tiger shrimp (Penaeus monodon) across its natural distribution range reveals more recent colonization of Fiji and other South Pacific Islands. Ecology and Evolution 2(8):2057–71. doi:10.1002/ece3.316
   PubMed Web of Science ®Google Scholar
• Willette DA, Allendorf FW, Barber PH, Barshis DJ, Carpenter KE, Crandall ED, et al. 2014. So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute. Bulletin of Marine Science 90(1):79–122. doi:10.5343/bms.2013.1008
   Web of Science ®Google Scholar
• Winter D, Green P, Kamvar Z, Gosselin T. 2015. Package ‘MMOD’: modern measures of population differentiation. https://github.com/dwinter/mmod. Computer program.
   Google Scholar
• You EM, Chiu TS, Liu KF, Tassanakajon A, Klinbunga S, Triwitayakorn K, et al. 2008. Microsatellite and mitochondrial haplotype diversity reveals population differentiation in the tiger shrimp (Penaeus monodon) in the Indo-Pacific region. Animal Genetics 39:267–77. doi:10.1111/j.1365-2052.2008.01724.x
   PubMed Web of Science ®Google Scholar
• Zeng D, Chen X, Xie D, Zhao Y, Yang C, Li Y, et al. 2013. Transcriptome analysis of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Taura Syndrome Virus (TSV) experimental infection. PLoS One 8(2):e57515. 8 pages. doi:10.1371/journal.pone.0057515
   PubMed Web of Science ®Google Scholar