Population genetic structure of blue swimming crab (Portunus pelagicus) in the Gulf of Thailand
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Supmee V, Sawusdee A, Sangthong P, Suppapan J. 2020. Population genetic structure of Blue Swimming Crab (Portunus pelagicus) in the Gulf of Thailand. Biodiversitas 21: 4260-4268. The Blue Swimming Crab (Portunus pelagicus) is an important commercial fishery product in the Gulf of Thailand. To provide a strategy for management, information on genetic features is needed. In our study, the population genetic structure and demographic history of the P. pelagicus living in the Gulf of Thailand were analyzed based on the variation of the nucleotide sequence of the mitochondrial DNA in the control region (mtDNA CR). Ninety-seven samples were collected from 5 sampling sites: Rayong, Chonburi, Chumphon, Surat Thani, and Nakhon Si Thammarat provinces in the Gulf of Thailand. Forty-nine haplotypes were identified and 39 private haplotypes were found. An AMOVA showed no genetic structure among populations. The pairwise FST also indicated no statistically significant difference between all possible regional combinations. The topology of a minimum spanning network revealed a star-like topology that was not separated by geographic structure. The historical demographic analysis revealed a stable population size for a long period and followed by a very recent expansion. An absence of a population structure of the P. pelagicus was possibly caused by a high level of gene flow. The results of this study differ from previous studies that used genetic markers in nuclear DNA. Thus, to clear the genetic structure information of P. pelagicus in the Gulf of Thailand, we suggested that more sensitive markers to detect genetic structure should be used in further analysis.
##plugins.themes.bootstrap3.article.details##
References
Amaral MRX, Albrecht M, McKinley AS, de Carvalho AMF, de Sousa JSC, Diniz FM. 2015. Mitochondrial DNA variation reveals a sharp genetic break within the distribution of the blue land crab Cardisoma guanhumi in the Western Central Atlantic. Molecules 20: 15158-15174.
Chai CJ, Esa YB, Ismail MFS, Kamarudin MS. 2017. Population structure of the blue swimmer crab Portunus pelagicus in coastal areas of Malaysia inferred from microsatellites. Zool Stud 56: 26, doi:10.6620/ZS.2017.56-26
Choudhuri S. 2014 Bioinformatics for Beginners. Elsevier Inc. All rights reserved. DOI https://doi.org/10.1016/C2012-0- 07153-0
Chu TJ, Wang D, Huang HL, Lin FJ, Tzeng TD. 2012. Population structure and historical demography of the whiskered velvet shrimp (Metapenaeopsis barbata) of China and Taiwan inferred from the mitochondrial control region. Zool Stud 51: 99-107.
Croos MDST, Pálsson S. 2010. Mitochondrial DNA variation and population genetic structure of white shrimp
Fenneropenaeus indicus along the coastal belt of Sri Lanka. Aquat Living Resour 23: 315-323.
Culver SJ, Leorri E, Mallinson DJ, Corbett, D R, Shazili NAM. 2015. Recent coastal evolution and sea-level rise, Setiu Wetland, Peninsular Malaysia. Palaeogeogr. Palaeoclimatol. Palaeoecol 417: 416-421.
Diringer B, Pretell K, Avellan R, Chanta C, Cedeño V, Gentile G. 2019. Genetic structure, phylogeography, and demography of Anadara tuberculosa (Bivalvia) from East Pacific as revealed by mtDNA: Implications to conservation. Ecol Evo. 9: 4392-4402.
Donrung P, Tunkijjanukij S, Jarayabh P, Poompuang S. 2011. Spatial genetic structure of the Surf Clam Paphia undulata in Thailand waters. Zool Stud 50(2): 211-219.
Drumm DT, Kreiser B. 2012. Population genetic structure and phylogeography of Mesokalliapseudes macsweenyi (Crustacea: Tanaidacea) in the northwestern Atlantic and Gulf of Mexico. J Exp Mar Biol Ecol 412: 58-65.
Drummond A J, Suchard M A, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUTi and the BEAST 1.7. Mol Biol Evol 29: 1969-1973.
Efrizal E. 2016. Effects of temperature on survival rate and larval development of blue swimming crab, Portunus pelagicus (Linnaeus, 1758) under laboratory conditions. Asian J Appl Sci 4(1): 120-134.
Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analysis under Linux and Windows. Mol Ecol Resour 10: 564-567.
Fishery Statistics Analysis and Research Group. 2017. Fisheries Statistics of Thailand, No. 5/2017. Department of Fisheries. Ministry of Agriculture and Cooperatives, Thailand. [Thai]
Fourdrilis S, de Frias Martins AM, Backeljau T. 2018. Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda. Sci Rep 8:17964. https://doi.org/10.1038/s41598-018-36428-7
Fu FX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
Garrigan D, Lewontin R, Wakeley J. 2010. Measuring the sensitivity of single-locus ‘‘Neutrality Tests’’ using a direct perturbation approach. Mol Biol Evol 27(1):73-89.
Guo E, Li X, Liu Y, Cheng Y, Wu CX. 2011. Genetic variation and population structure of swimming crab (Portunus trituberculatus) inferred from mitochondrial control region. Mol Biol Rep doi 10.1007/s11033-011-0882-3.
Hamid A, Lumban Batu DTF, Riani E, Wardiatno Y. 2016. Reproductive biology of blue swimming crab (Portunus pelagicus Linnaeus, 1758) in Lasongko Bay, Southeast Sulawesi-Indonesia. Aquac Aquar Conserv Legis 9(5): 1053-1066.
Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66: 591-600.
Kembaren DD, Zairion Z, Kamal MM, Wardiatno Y. 2018. Abundance and spatial distribution of blue swimming crab (Portunus pelagicus) larvae during east monsoon in the East Lampung waters, Indonesia. Biodiversitas 19(4): 1326-1333.
Klinbunga S, Khetpu K, Khamnamtong B, Menasveta P. 2007. Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis. Biochem Genet 45: 725-736.
Klinbunga S, Yuvanatemiya V, Wongphayak S, Khetpu K, Menasveta P, Khamnamtong B. 2010. Genetic population differentiation of the blue swimming crab Portunus pelagicus (Portunidae) in Thai waters revealed by RAPD analysis. Genet Mol Res 9(3): 1615-1624.
Kong XY, Li YL, Kong WSJ. 2010. Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences. Genet Mol Biol 33(2):
379-389.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A,
Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23(21): 2947-2948.
McMillen-Jackson A, Bert TM. 2003. Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Mol Eco 12: 2895-2905.
Nei M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Nei M, Tajima F. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145-163.
Omori R, Wu J. 2017. Tajima’s D and site specific nucleotide frequency in a population during an infectious disease outbreak. Siam J Appl Math 77(6): 2156-2171.
Ragionieri L, Fratini S, Vannini M, Schubart CD. 2009. Phylogenetic and morphometric differentiation reveal geographic radiation and pseudo-cryptic speciation in a mangrove crab from the Indo-West Pacific. Mol Phylogenet Evol 52: 825-834.
Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014. Tracer v1.6. http://beast.bio.ed.ac.uk/Tracer. (accessed on 23 June 2020).
Ren G, Miao G, Ma C, Lu J, Yang X, Ma H. 2018. Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene. Mitochondrial DNA A DNA Mapp Seq Anal 29:(2) 192-198.
Rhodes BP, Kirby ME, Jankaew K, Choowong M. 2011. Evidence for a mid-Holocene tsunami deposit along the Andaman coast of Thailand preserved in a mangrove environment. Mar Geol 282: 255-267.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol Evol 34: 3299-3302.
Saramul S. 2017. Seasonal monsoon variations in surface currents in the Gulf of Thailand revealed by high frequency radar. Eng J 21(4): DOI:10.4186/ej.2017.21.4.25
Shan B, Hui M, Zhang X, Liu S, Cai S, Song N, Tu Z, Wang Y, Wang S, Gao T. 2018. Genetic effects of released swimming crab (Portunus trituberculatus) on wild populations inferred from mitochondrial control region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 29(6): 856-861.
Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
Silva IC, Mesquita N, Paula J. 2010. Lack of population structure in the fiddler crab Uca annulipes along an East African latitudinal gradient: genetic and morphometric evidence. Mar Biol 157: 1113-1126.
Srinulgray T. and Piyapattanakorn S. 2009 Genetic diversity of short mackerel Rastrelliger brachysoma populations in the Gulf of Thailand and Andaman Sea revealed by ISSR marker. In: Kasetsart University, (eds.). Proceedings of 47th Kasetsart University Annual Conference: Science, Bangkok (Thailand). Kasetsart University. Bangkok, 17-20 March 2009. [Thailand]
Supmee V, Ngernsiri L, Sriboonlert A, Wonnapinij P, Sangthong P. 2012. Population genetic analysis of violet vinegar crab (Episesarma versicolor) along the Andaman Sea coast of Thailand. Zool Stud 51(7): 1040-1050.
Suppapan J, Pechsiri J, O-Thong S, Vanichanon A, Sangthong P, Supmee V. 2017. Population genetic analysis of Oceanic paddle crab (Varuna litterata) in Thailand. Sains Malays 46(12): 2251-2261.
Surakiatchai P, Choowong M, Charusiri P, Charoentitirat T, Chawchai S, Pailoplee S, Chabangborn A, Phantuwongraj S, Chutakositkanon V, Kongsen S, Nimnate P, Bissen R. 2018. Paleogeographic reconstruction and history of the sea level change at Sam Roi Yot national park, Gulf of Thailand. Trop Nat Hist 18(2): 112-134.
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics
123: 585-595.
Wanna W, Rolland JL, Bonhomme F, Phongdara A. 2004. Population genetic structure of Penaeus merguiensis in Thailand based on nuclear DNA variation. J Exp Mar Biol 311: 63-78.
Chai CJ, Esa YB, Ismail MFS, Kamarudin MS. 2017. Population structure of the blue swimmer crab Portunus pelagicus in coastal areas of Malaysia inferred from microsatellites. Zool Stud 56: 26, doi:10.6620/ZS.2017.56-26
Choudhuri S. 2014 Bioinformatics for Beginners. Elsevier Inc. All rights reserved. DOI https://doi.org/10.1016/C2012-0- 07153-0
Chu TJ, Wang D, Huang HL, Lin FJ, Tzeng TD. 2012. Population structure and historical demography of the whiskered velvet shrimp (Metapenaeopsis barbata) of China and Taiwan inferred from the mitochondrial control region. Zool Stud 51: 99-107.
Croos MDST, Pálsson S. 2010. Mitochondrial DNA variation and population genetic structure of white shrimp
Fenneropenaeus indicus along the coastal belt of Sri Lanka. Aquat Living Resour 23: 315-323.
Culver SJ, Leorri E, Mallinson DJ, Corbett, D R, Shazili NAM. 2015. Recent coastal evolution and sea-level rise, Setiu Wetland, Peninsular Malaysia. Palaeogeogr. Palaeoclimatol. Palaeoecol 417: 416-421.
Diringer B, Pretell K, Avellan R, Chanta C, Cedeño V, Gentile G. 2019. Genetic structure, phylogeography, and demography of Anadara tuberculosa (Bivalvia) from East Pacific as revealed by mtDNA: Implications to conservation. Ecol Evo. 9: 4392-4402.
Donrung P, Tunkijjanukij S, Jarayabh P, Poompuang S. 2011. Spatial genetic structure of the Surf Clam Paphia undulata in Thailand waters. Zool Stud 50(2): 211-219.
Drumm DT, Kreiser B. 2012. Population genetic structure and phylogeography of Mesokalliapseudes macsweenyi (Crustacea: Tanaidacea) in the northwestern Atlantic and Gulf of Mexico. J Exp Mar Biol Ecol 412: 58-65.
Drummond A J, Suchard M A, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUTi and the BEAST 1.7. Mol Biol Evol 29: 1969-1973.
Efrizal E. 2016. Effects of temperature on survival rate and larval development of blue swimming crab, Portunus pelagicus (Linnaeus, 1758) under laboratory conditions. Asian J Appl Sci 4(1): 120-134.
Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analysis under Linux and Windows. Mol Ecol Resour 10: 564-567.
Fishery Statistics Analysis and Research Group. 2017. Fisheries Statistics of Thailand, No. 5/2017. Department of Fisheries. Ministry of Agriculture and Cooperatives, Thailand. [Thai]
Fourdrilis S, de Frias Martins AM, Backeljau T. 2018. Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda. Sci Rep 8:17964. https://doi.org/10.1038/s41598-018-36428-7
Fu FX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
Garrigan D, Lewontin R, Wakeley J. 2010. Measuring the sensitivity of single-locus ‘‘Neutrality Tests’’ using a direct perturbation approach. Mol Biol Evol 27(1):73-89.
Guo E, Li X, Liu Y, Cheng Y, Wu CX. 2011. Genetic variation and population structure of swimming crab (Portunus trituberculatus) inferred from mitochondrial control region. Mol Biol Rep doi 10.1007/s11033-011-0882-3.
Hamid A, Lumban Batu DTF, Riani E, Wardiatno Y. 2016. Reproductive biology of blue swimming crab (Portunus pelagicus Linnaeus, 1758) in Lasongko Bay, Southeast Sulawesi-Indonesia. Aquac Aquar Conserv Legis 9(5): 1053-1066.
Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66: 591-600.
Kembaren DD, Zairion Z, Kamal MM, Wardiatno Y. 2018. Abundance and spatial distribution of blue swimming crab (Portunus pelagicus) larvae during east monsoon in the East Lampung waters, Indonesia. Biodiversitas 19(4): 1326-1333.
Klinbunga S, Khetpu K, Khamnamtong B, Menasveta P. 2007. Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis. Biochem Genet 45: 725-736.
Klinbunga S, Yuvanatemiya V, Wongphayak S, Khetpu K, Menasveta P, Khamnamtong B. 2010. Genetic population differentiation of the blue swimming crab Portunus pelagicus (Portunidae) in Thai waters revealed by RAPD analysis. Genet Mol Res 9(3): 1615-1624.
Kong XY, Li YL, Kong WSJ. 2010. Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences. Genet Mol Biol 33(2):
379-389.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A,
Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23(21): 2947-2948.
McMillen-Jackson A, Bert TM. 2003. Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Mol Eco 12: 2895-2905.
Nei M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Nei M, Tajima F. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145-163.
Omori R, Wu J. 2017. Tajima’s D and site specific nucleotide frequency in a population during an infectious disease outbreak. Siam J Appl Math 77(6): 2156-2171.
Ragionieri L, Fratini S, Vannini M, Schubart CD. 2009. Phylogenetic and morphometric differentiation reveal geographic radiation and pseudo-cryptic speciation in a mangrove crab from the Indo-West Pacific. Mol Phylogenet Evol 52: 825-834.
Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014. Tracer v1.6. http://beast.bio.ed.ac.uk/Tracer. (accessed on 23 June 2020).
Ren G, Miao G, Ma C, Lu J, Yang X, Ma H. 2018. Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene. Mitochondrial DNA A DNA Mapp Seq Anal 29:(2) 192-198.
Rhodes BP, Kirby ME, Jankaew K, Choowong M. 2011. Evidence for a mid-Holocene tsunami deposit along the Andaman coast of Thailand preserved in a mangrove environment. Mar Geol 282: 255-267.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol Evol 34: 3299-3302.
Saramul S. 2017. Seasonal monsoon variations in surface currents in the Gulf of Thailand revealed by high frequency radar. Eng J 21(4): DOI:10.4186/ej.2017.21.4.25
Shan B, Hui M, Zhang X, Liu S, Cai S, Song N, Tu Z, Wang Y, Wang S, Gao T. 2018. Genetic effects of released swimming crab (Portunus trituberculatus) on wild populations inferred from mitochondrial control region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 29(6): 856-861.
Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
Silva IC, Mesquita N, Paula J. 2010. Lack of population structure in the fiddler crab Uca annulipes along an East African latitudinal gradient: genetic and morphometric evidence. Mar Biol 157: 1113-1126.
Srinulgray T. and Piyapattanakorn S. 2009 Genetic diversity of short mackerel Rastrelliger brachysoma populations in the Gulf of Thailand and Andaman Sea revealed by ISSR marker. In: Kasetsart University, (eds.). Proceedings of 47th Kasetsart University Annual Conference: Science, Bangkok (Thailand). Kasetsart University. Bangkok, 17-20 March 2009. [Thailand]
Supmee V, Ngernsiri L, Sriboonlert A, Wonnapinij P, Sangthong P. 2012. Population genetic analysis of violet vinegar crab (Episesarma versicolor) along the Andaman Sea coast of Thailand. Zool Stud 51(7): 1040-1050.
Suppapan J, Pechsiri J, O-Thong S, Vanichanon A, Sangthong P, Supmee V. 2017. Population genetic analysis of Oceanic paddle crab (Varuna litterata) in Thailand. Sains Malays 46(12): 2251-2261.
Surakiatchai P, Choowong M, Charusiri P, Charoentitirat T, Chawchai S, Pailoplee S, Chabangborn A, Phantuwongraj S, Chutakositkanon V, Kongsen S, Nimnate P, Bissen R. 2018. Paleogeographic reconstruction and history of the sea level change at Sam Roi Yot national park, Gulf of Thailand. Trop Nat Hist 18(2): 112-134.
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics
123: 585-595.
Wanna W, Rolland JL, Bonhomme F, Phongdara A. 2004. Population genetic structure of Penaeus merguiensis in Thailand based on nuclear DNA variation. J Exp Mar Biol 311: 63-78.
Most read articles by the same author(s)
- JUTHAMAS SUPPAPAN, PRADIT SANGTHONG, , APIRAK SONGRAK, VERAKIAT SUPMEE, Population genetic structure of hard clam (Meretrix lyrata) along the Southern coast of Thailand , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 5 (2021)
- VERAKIAT SUPMEE, PRADIT SANGTHONG, APIRAK SONGRAK, JUTHAMAS SUPPAPAN, Population genetic structure of Asiatic Hard Clam (Meretrix meretrix) in Thailand based on Cytochrome Oxidase subunit I gene sequence , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 6 (2020)