Sains Malaysiana 52(2)(2023): 369-380

http://doi.org/10.17576/jsm-2023-5202-05

Population Genetic Structure of the Blue Swimming Crab (Portunus pelagicus) along the Andaman Sea Coast of Thailand

(Struktur Genetik Populasi Ketam Renang Biru (Portunus pelagicus) di sepanjang Pantai Laut Andaman, Thailand)

JUTHAMAS SUPPAPAN¹, APIRAK SONGRAK², WORAWITOO MEESOOK³ & VERAKIAT SUPMEE ^3,*

¹Master of Education in Science Program, Faculty of Education, Nakhon Si Thammarat Rajabhat University, Nakhon Si Thammarat, Thailand

²Department of Fishery Technology, Faculty of Science and Fisheries Technology, Rajamangala University of Technology Srivijaya, Trang Campus, Trang, Thailand

³Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat Campus, Nakhon Si Thammarat, Thailand

  Received: 31 August 2022/Accepted: 11 November 2022

Abstract

The blue swimming crab (Portunus pelagicus) is a valuable commercial species. In Thailand, the consumption of the blue swimming crab is increasing. To construct an effective sustainable management plan, genetic information is required. Knowledge of natural stock genetic information can help policymakers design fishing and conservation management policies to maintain genetic diversity. In our study, we examined the genetic structure of the blue swimming crab population on the Andaman Sea coast of Thailand. Partial sequences of the mitochondrial DNA control region (mtDNA CR) with a size of 369-371 base pairs were studied in 150 individuals collected from five sampling sites along Thailand's Andaman Sea coast. Seventy-one haplotypes were characterized by 127 polymorphic sites, indicating high haplotype diversity but low nucleotide diversity across five localities. The multiple tests of population genetic analysis showed a lack of genetic structure. The absence of genetic structure was possibly caused by a high level of gene flow due to the larval blue swimming crab's high dispersal ability. Demographic history findings indicate that the blue swimming crab population has expanded. The findings of our study can be used to guide the management of the blue swimming crab in this region of the Andaman Sea to conserve genetic diversity.

Keywords: Andaman Sea; genetic diversity; marine crab; mitochondrial DNA

Abstrak

Ketam renang biru (Portunus pelagicus) adalah spesies komersial yang berharga. Di Thailand, pengambilan ketam renang biru semakin meningkat. Untuk membina pelan pengurusan mampan yang berkesan, maklumat genetik diperlukan. Pengetahuan tentang maklumat genetik stok semula jadi boleh membantu penggubal dasar membentuk dasar pengurusan perikanan dan pemuliharaan untuk mengekalkan kepelbagaian genetik. Dalam penyelidikan ini, kami mengkaji struktur genetik populasi ketam renang biru di pantai Laut Andaman, Thailand. Jujukan separa kawasan kawalan DNA mitokondria (mtDNA CR) dengan saiz 369-371 pasangan asas telah dikaji dalam 150 individu yang dikumpulkan dari lima tapak persampelan di sepanjang pantai Laut Andaman, Thailand. Tujuh puluh satu haplotip dicirikan oleh 127 tapak polimorfik, menunjukkan kepelbagaian haplotaip yang tinggi tetapi kepelbagaian nukleotida rendah merentas lima lokaliti. Pelbagai ujian analisis genetik populasi mendedahkan kekurangan struktur genetik. Ketiadaan struktur genetik mungkin disebabkan oleh tahap aliran gen yang tinggi disebabkan oleh keupayaan penyebaran tinggi ketam renang biru larva. Penemuan sejarah demografi menunjukkan bahawa populasi ketam renang biru telah berkembang. Penemuan kajian kami boleh digunakan sebagai bimbingan pengurusan ketam renang biru di wilayah Laut Andaman ini untuk memulihara kepelbagaian genetik.

Kata kunci: DNA mitokondria; kepelbagaian genetik; ketam marin; Laut Andaman

REFERENCES

Amaral, M.R.X., Albrecht, M., McKinley, A.S., de Carvalho, A.M.F. & de Sousa, J.S.C. & Diniz, F.M. 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.

Avise, J.C. 2000. Phylogeography. London: Harvard University Press.

Ayala, F.J. 1982. Population and Evolutionary Genetics: A Primer. California: The Benjamin Cummings Pub. Co. Inc.

Bert, T.M., Crawford, C.R., Tringali, M.D., Seyoum, S., Galvin, J.L., Higham, M. & Lund, C. 2007. Genetic management of hatchery-based stock enhancement. In Ecological and Genetic Implications of Aquaculture Activities. Methods and Technologies in Fish Biology and Fisheries, volume 6, edited by Bert, T.M. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6148-6_8

Boore, J.L. 1999. Survey and summary animal mitochondria genome. Nucleic Acids Research 27(8): 1767-1780.

Brown, B.E. 2007. Coral reefs of the Andaman Sea-An integrated perspective. Oceanography and Marine Biology: An Annual Review 45: 173-194.

Chai, C.J., Esa, Y.B., Ismail, M.F.S. & Kamarudin, M.S. 2017. Population structure of the blue swimmer crab Portunus pelagicus in coastal areas of Malaysia inferred from microsatellites. Zoological Studies 56: 26.

Chatterjee, A., Shankar, D., McCreary, J.P., Vinayachandran, P.N. & Mukherjee, A. 2021. Dynamics of Andaman Sea circulation and its role in connecting the equatorial Indian Ocean to the Bay of Bengal. Journal of Geophysical Research: Oceans 122: 3200-3218.

Crandall, E.D., Taffel, J.R. & Barber, P.H. 2010. High gene flow due to pelagic larval dispersal among South Pacific archipelagos in two amphidromous gastropods (Neritomorpha: Neritidae). Heredity 104: 563-572.

Dang, B.T., Rahman, M.A., Tran, S.Q. & Glenner, H. 2019. Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline. PLoS ONE 14(11): e0224473.

Excoffier, L. & Lischer, H.E.L. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analysis under Linux and Windows. Molecular Ecology Resources 10: 564-567.

Fishery Statistics Analysis and Research Group. 2012. Fisheries Statistics of Thailand 2010, No. 12/2012. Department of Fisheries. Ministry of Agriculture and Cooperatives, Thailand.

Fishery Statistics Analysis and Research Group. 2022. Fisheries Statistics of Thailand 2020, No. 4/2022. Department of Fisheries. Ministry of Agriculture and Cooperatives, Thailand.

Fu, F.X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.

Harpending, R.C. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology 66: 591-600.

Hui, M., Shi, G., Sha, Z., Liu, Y. & Cu, Z. 2019. Genetic population structure in the swimming crab, Portunus trituberculatus and its implications for fishery management. Journal of the Marine Biological Association of the United Kingdom 99(4): 891-899.

Josileen, J. & Menon, N.G. 2005. Growth of the blue swimmer crab, Portunus pelagicus(Linnaeus, 1758) (Decapoda, Brachyura) in captivity. Crustaceana 78(1): 1-18.          

Kembaren, D.D., Zairion, Z., Kamal, M.M. & 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.

Khamnamtong, B., Prasertlux, S., Janpoom, S. & Klinbunga, S. 2021. Genetic differentiation of the blue swimming crab Portunus pelagicus along the coastal Thai waters revealed by SSCP analysis of cytochrome c oxidase subunit I. Genetics of Aquatic Organisms 5(2): 55-65.

Kiran, S.R. 2017. General circulation and principal wave modes in Andaman Sea from observations. Indian Journal of Science and Technology 10(24): 1-11. DOI: 10.17485/ijst/2017/v10i24/115764

Kittiwattanawong, K. 1997. Genetic structure of giant clam, Tridacna maxima in the Andaman Sea, Thailand. Phuket Marine Biological Center Special Publication 17(1): 109-114.

Klinbunga, S., Khetpu, K., Khamnamtong, B. & Menasveta, P. 2007. Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis. Biochemical Genetics 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. Genetics and Molecular Research 9(3): 1615-1624.

Kumar, S., Stecher, G. & Tamura, K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7): 1870-1874.

Lu, Y.M., Shih, C.H., Chen, P.C., Kao, W.C., Lee, Y.C., Han, Y.S. & Tzeng, T.D. 2022. Genetic variations and expansion of the blue swimmer crab (Portunus pelagicus) in Southeast Asia. Journal of Marine Science and Engineering 10: 1071.

Ma, C.Y., Cheng, Q.Q., Zhang, Q.Y., Zhuang, P.V. & Zhao, Y.L. 2010. Genetic variation of Coiliaectenes (Clupeiformes: Engraulidae) revealed by the complete cytochrome b sequences of mitochondrial DNA. Journal of Experimental Marine Biology and Ecology 385: 14-19.

Madduppa, H., Martaulina, R., Zairion, Z., Renjani, R.M., Kawaroe, M., Anggraini, N.P., Subhan, B., Verawati, I. & Sani, L.M.I. 2021. Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery. PLoS ONE 16(2): e0240951.

Marini, M., Pedrosa-Gerasmio, I.R., Santos, M.D., Shibuno, T., Daryani, A., Romana-Eguia, M.R.R. & Wibowo, A. 2021. Genetic diversity, population structure and demographic history of the tropical eel Anguilla bicolor pacifica in Southeast Asia using mitochondrial DNA control region sequences. Global Ecology and Conservation 26(3): e01493.

Ninwichian, P. & Klinbunga, S. 2020. Population genetics of sandfish (Holothuria scabra) in the Andaman Sea, Thailand inferred from 12S rDNA and microsatellite polymorphism. Regional Studies in Marine Science 35: 101189.

Nitiratsuwan, T., Tanyaros, S. & Panwanitdumrong, K. 2013. Distribution of berried female blue swimmer crabs (Portunus pelagicus Linneaus, 1758) in the coastal waters of Trang province, southern Thailand. Maejo International Journal of Science and Technology 7(Special Issue): 52-59.

Nei, M. & Li, W.H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America 76(10): 5269-5273. 

Nei, M. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press.

Ragionieri, L., Cannicci, S., Schubart, C.D. & Fratini, S. 2010. Gene flow and demographic history of the mangrove crab Neosarmatium meinerti: A case study from the western Indian Ocean. Estuarine, Coastal and Shelf Science 86: 179-188.

Ramirez-Soriano, A., Ramos-Onsins, S.E., Rozas, J., Calafell, F. & Navarro, A. 2008.  Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics 179: 555-567.

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 Part A: DNA Mapping, Sequencing, and Analysis 29(2): 192-198.

Roldan, M.I., Perrotta, M., Cortey, R.G. & Pla, C. 2000. Molecular and morphologic approaches to discrimination of variability patterns in chub mackerel, Scomber japonicus. Journal of Experimental Marine Biology and Ecology 253: 63-74.

Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E. & Sánchez-Gracia, A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Molecular Biology and Evolution 34: 3299-3302.

Russo, C.A.M., Sole-Cava, A.M. & Thorpe, J.P. 1994. Population structure and genetic variation in two tropical sea anemones (Cnidaria, Actinidae) with different reproductive strategies. Marine Biology 119: 267-276.

Silva, I.C., 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. Marine Biology 157: 1113-1126.

Slatkin, M. & Hudson, R.R. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.

Subramani, T., Gunasagaran, K. & Natesan, M. 2021. Genetic diversity and population structure of Artemia franciscana from southeast coast of India. Journal of Sea Research 178: 102127.

Sukimin, I.R., Esa, Y.B. & Amin, S.M.N. 2017. High genetic similarities between Portunus pelagicus from Teluk Kemang, Port Dickson and Batu Pahat, Johor as inferred from mitochondrial cytochrome c oxidase I (COI) sequences. Malaysian Applied Biology 46(2): 145-148.

Sun, P., Yu, J., Tang, B. & Liu, Z. 2021. Gene variation and population structure of Pampus chinensis in the China coast revealed by mitochondrial control region sequences. Mitochondrial DNA Part B: Resources 6(8): 2240-2245.

Supmee, V., Songrak, A., Suppapan, J. & Sangthong, P. 2021. Population genetic structure of the wedge clam (Donax scortum) along the Andaman Sea coast of Thailand. Journal of Fisheries and Environment 45(1): 85-97.

Supmee, V., Sawasdee, A., Sangthong, P. & Suppapan, J. 2020a. Population genetic structure of blue swimming crab (Portunus pelagicus) in the Gulf of Thailand. Biodiversitas 21(9): 4260-4268.

Supmee, V., Sangthong, P., Songrak, A. & Suppapan, J. 2020b. Population genetic structure of Asiatic hard clam (Meretrix meretrix) in Thailand based on cytochrome oxidase subunit I gene sequence. Bodiversitas 21(6): 2702-2709.

Supmee, V., Suppapan, J., Pechsiri, J. & Sangthong, P. 2017. Population genetic structure of greenback mullet (Liza subviridis) along the Andaman Sea coast of Thailand. Journal of Fisheries Technology Research 11(2): 98-112.

Supmee, V., Ngernsiri, L., Sriboonlert, A., Wonnapinij, P. & Sangthong, P. 2012a. Population genetic analysis of violet vinegar crab (Episesarma versicolor) along the Andaman Sea coast of Thailand. Zoological Studies 51(7): 1040-1050.

Supmee, V., Ngernsiri, L., Swatdipong, A., Wonnapinij, P., Sangthong, D. & Sangthong, P.  2012b. A single population of Thai vinegar crab (Episesarma mederi) living in the Gulf of Thailand. Proceeding of the 38th Congress on Science and Technology of Thailand (STT38), 17-19 October 2012, Chiang Mai, Thailand.

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 Malaysiana 46(12): 2251-2261.

Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.

Thompson, J.D., Higgins, D.G. & Gibson, T.J. 1994. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.

Tudela, S., Garcya-Marynn, J.L. & Pla, C. 1999. Genetic structure of the European anchovy, Engraulis encrasicolus, in the north-west Mediterranean. Journal of Experimental Marine Biology and Ecology 234: 95-109.

Uthicke, S. & Benzie, J.A.H. 2003. Gene flow and population history in high dispersal marine invertebrates: Mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from Indo-Pacific. Molecular Ecology 12: 2635-2648.

Waples, R.S. & Gaggiotti, O. 2012. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15: 1419-1439.

Waples, R.S., Hindar, K. & Hard, J.J. 2012. Genetic Risks Associated with Marine Aquaculture.  NOAA technical memorandum NMFS-NWFSC119. U.S. Department of commerce.

Watterson, G.A. 1984. Allele frequencies after a bottleneck. Theoretical Population Biology 26: 387-407.

William, L.F. & Allendorf, F.W. 2007. Conservation and the Genetics of Populations. United Kingdom: Blackwell Publishing.

Yang, Z. 2006. Computational Molecular Evolution. New York: Oxford University Press.

^*Corresponding author; email: verakiat.s@rmutsv.ac.th