Sains Malaysiana 46(12)(2017): 2251–2261

http://dx.doi.org/10.17576/jsm-2017-4612-01

 

Population Genetic Analysis of Oceanic Paddle Crab (Varuna litterata) in Thailand

(Analisis Populasi Genetik Ketam Meranduk Laut (Varuna litterata) di Thailand)

JUTHAMAS SUPPAPAN¹, JAMJUN PECHSIRI¹, SOMPONG O-THONG¹, ARUNRAT VANICHANON¹, PRADIT SANGTHONG² & VERAKIAT SUPMEE^3*

 

¹Biotechnology Program, Faculty of Science, Thaksin University, Phattalung Campus

Phattalung 93100, Thailand

 

²Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

 

³Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat Campus, Nakhon Si Thammarat, 80110 Thailand

 

Received: 7 August 2016/Accepted: 22 May 2017

 

ABSTRACT

Population genetic structure of Varuna litterata living along the coast of Thailand were examined in this study. The samples were collected from 3 coastal regions: The Andaman sea (Satun, Trang, Phang Nga), the lower Gulf of Thailand (Pattani, Songkhla, Nakhon Si Thammarat) and the upper Gulf of Thailand (Petchburi, Samut Songkram, Rayong, Trat). Intraspecific variation was determined based on partial sequences of the cytochrome oxidase subunits I gene. A total of 182 samples were collected but only 32 haplotypes were obtained from these samples. An excess of rare haplotypes indicated that the female effective population size of V. litterata living along the coast of Thailand is large. Estimated values of haplotype diversity and nucleotide diversity were 0.790 and 0.003, respectively. The AMOVA (analysis of molecular variance) and phylogenetic analysis results showed that based on genetic variation, the population of this organism was found to have 2 genetically different populations: The Andaman sea population and the Gulf of Thailand population. Genetic exchange of V. litterata among populations inhabiting along the coast of Thailand could be described by the stepping stone model. The results of neutrality tests, both Tajima's D and Fu's Fs statistics, yielded negative values (-1.992 and -26.877, respectively) and statistically significant deviation from the neutrality, indicating that the V. litterata living along the Thailand coast had experienced population expansion. Mismatch distribution analysis indicated that a possible expansion occurred 211,428 years ago during the Pleistocene glaciations period.

 

Keywords: COI gene; genetic diversity; grapsid crab; mitochondrial DNA

 

ABSTRAK

 

Struktur populasi genetik Varuna litterata yang hidup di sepanjang pesisir pantai di Thailand telah dikaji. Sampel dikumpul daripada tiga rantau pesisir pantai: Laut Andaman (Satun, Trang, Phang Nga), bahagian bawah Teluk Thailand (Pattani, Songkhla, Nakhon Si Thammarat) dan di bahagian atas Teluk Thailand (Petchburi, Samut Songkram, Rayong, Trat). Variasi intraspesies ditentukan berdasarkan urutan separa subunit sitokrom oksidase gen I. Sejumlah 182 sampel telah diambil tetapi hanya 32 haplotip telah diperoleh daripada sampel tersebut. Lebihan haplotip langka menunjukkan saiz populasi betina V. litterata yang berkesan hidup di sepanjang Pantai di Thailand adalah besar. Anggaran nilai kepelbagaian haplotip dan kepelbagaian nukleotida masing-masing adalah 0.790 dan 0.003. Keputusan AMOVA (analisis molekul varians) dan analisis filogeni menunjukkan bahawa berdasarkan variasi genetik, populasi organisma ini didapati mempunyai dua populasi genetik berbeza: Populasi Laut Andaman dan Teluk Thailand. Pertukaran genetik V. litterataantara populasi yang mendiami di sepanjang Pantai Thailand dapat diterangkan dengan model batu loncatan. Ujian keputusan berkecuali, kedua-dua statistik D Tajima dan Fs Fu masing-masing menghasilkan nilai negatif (-1.992 dan -26.877) dan signifikan secara statistik sisihan daripada yang berkecuali, menunjukkan bahawa V. litteratayang hidup di sepanjang Pantai Thailand telah mengalami pengembangan populasi. Analisis pengagihan tak sepadan menunjukkan potensi pengembangan berlaku di 211,428 tahun yang lalu semasa tempoh Pleistocene glaciations.

 

Kata kunci: DNA mitokondrium; gen COI; kepelbagaian genetik; ketam grapsid

REFERENCES

Antoro, S., Na-Nakorn, U. & Koedprang, W. 2006. Study of genetic diversity of orange-spotted grouper, Epinephelus coioides, from Thailand and Indonesia using microsatellite markers. Mar. Biotechnol. 8: 17-26.

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

Carpenter, K.E. & Niem, V.H. 1998. FAO Species Identification Guide for Fishery Purposes: The Living Marine Resources of the Western Central Pacific Volume 2: Cephalopods, Crustaceans, Holothurians and Shark. Food and Agriculture Organization of the United Nations.

Chu, T.J., Wang, D., Huang, H.L., Lin, F.J. & Tzeng, T.D. 2012. Population structure and historical demography of the whiskered velvet shrimp (Metapenaeopsis barbata) off China and Taiwan inferred from the mitochondrial control region. Zool. Stud. 51: 99-107.

Croos, M.D.S.T. & Pálsson, S. 2010. Mitochondrial DNA variation and population genetic structure of white shrimp Fenneropenaeus indicusalong the coastal belt of Sri Lanka. Aquat. Living Resour. 23: 315-323.

Donrung, P., Tunkijjanukij, S., Jarayabh, P. & Poompuang, S. 2011. Spatial genetic structure of the surf clam Paphia undulatain Thailand waters. Zool. Stud. 50(2): 211-219.

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. Mol. Eco. Resour. 10: 564-567.

Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.

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

Garcia-Merchan, V.H., Robainas-Barcia, A., Abello, P., Macpherson, E., Palero, F. & Garcia-Rodriguez, M. 2012. Phylogeographic patterns of decapod crustaceans at the Atlantic-Mediterranean transition. Mol. Phylogenet. Evol. 62: 664-672.

Gillikin, D.P & Schubart, C.D. 2004. Ecology and systematics of mangrove crabs of the Genus Perisesarma (Crustacea: Brachyura: Sesarmidae) from East Africa. Zool. J. Linnean Soc. 141: 435-445.

Gradstein, F.M., Ogg, J.G. & Smith, A.G. 2004. A Geologic Time Scale. New York: Cambridge University Press.

Harpending, H.C. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66: 591-600.

He, L., Zhang, A., Weese, D., Zhu, C., Jiang, C. & Qiao, Z. 2010. Late Pleistocene population expansion of Scylla paramamosainalong the coast of China: A population dynamic response to the last interglacial sea level high stand. J. Exp. Mar. Biol. Ecol. 385: 20-28.

Huang, X. & Madan, A. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877.

Kimura, M. & Weiss, G.H. 1964. The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49: 561-576.

Kong, X.Y., Li, Y.L. & Kong, W.S.J. 2010. Genetic variation and evolutionary demography of Fenneropenaeus chinensispopulations, as revealed by the analysis of mitochondrial control region sequences. Genet. Mol. Biol. 33(2): 379-389.

Lewontin, R.C. 1974. The Genetic Basis of Evolutionary Change. New York: Columbia University Press.

Librado, P. & Rozas, J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.

Mahidol, C., Na-Nakorn, U., Sukmanomon, S., Taniguchi, N. & Nguyen, T.T.T. 2007. Mitochondrial DNA diversity of the Asian moon scallop, Amusium pleuronectes(Pectinidae), in Thailand. Mar. Biotechnol. 9: 352-359.

McMillan, W.O. & Palumbi, S.R. 1995. Concordant evolutionary patterns among Indo West Pacific butterfly fishes. Proc. R. Soc. Lond. B. 260: 229-236.

Naiyanetr, P. 2007. Checklist of Crustacean Fauna in Thailand (Decapoda, Stomatopoda, Anostraca, Myodocopa and Iopoda). Office of natural resources and environmental policy and planning. Bangkok. Thailand.

Nakthon, N. 1992. Marine territory of Thailand and neighbouring countries. MSc. Thesis. Hydrograph Department. Royal Thai navy. Thailand. (in Thai).

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.

Palumbi, S.R. 2003. Population genetics, demographic connectivity, and the design of marine protected reserves. Ecol. Appl. 13: 146-158.

Panithanarak, T., Karuwancharoen, R., Na-Nakorn, U. & Nguyen, T.T.T. 2010. Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters: Implications for conservation. Zool. Stud. 49: 564- 576.

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. Estuar. Coast. Shelf Sci. 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.

Rhodes, B.P., Kirby, M. E., 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.

Riginos, C. & Nachman, M.W. 2001. Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus. Mol. Ecol. 10:1439-1453.

Rogers, A. R. & Harpending, H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569.

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. Mar. Biol. 119: 267-276.

Ryan, P.A. & Choy, S.C. 1990. Observations on the mass upstream migration of Varuna litterata(Fabricius) Megalopae (Decapoda, Brachyura, Grapsidae) in Fiji. Crustaceana 5 8 (3): 237-249.

Saitou, N. & Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.

Schmidt, P.S. & Rand, D.M. 1999. Intertidal microhabitat and selection at MPI: interlocuscontrasts in the northern acorn barnacle, Semibalanus balanoides. Evol. Int. J. Org. Evol. 53:135-146.

Silva, I.C., Mesquita, N. & Paula, J. 2010. Lack of population structure in the fiddler crab Uca annulipesalong an East African latitudinal gradient: genetic and morphometric evidence. Mar. Biol. 157:1113-1126.

Snidvong, A. & Sojisuporn, P. 1999. Numerical simulations of the current in the Gulf of Thailand under different monsoon regimes. In Proceedings of the first technical seminar on marine fishery resources survey in the South China Sea. Samutprakan. Thailand. pp. 54-72.

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

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. In Proceeding of the 38th Congress on Science and Technology of Thailand (STT38). Chiang Mai, Thailand. pp.1-4 (I_I0003).

Supungul, P., Sootanan, P., Klinbunga, S., Kamonrat, W., Jarayabh, P. & Tassanakajon, A. 2000. Microsatellite polymorphism and the population structure of the black tiger shrimp (Penaeus monodon) in Thailand. Mar. Biotechnol. 2: 339-347.

Tan, S.G., Adibah, A.B. & Ng, W.L. 2015. The Malay Peninsula as a barrier to gene flow in an Asian horseshoe crab species, Carcinoscorpius rotundicaudaLatreille. Biochem. Syst. Ecol. 60: 204-210.

Tanabe, S., Saito, Y., Sato, Y., Suzuki, Y., Sinsakul, S., Tiyapairach, S. & Chaimanee, N. 2003. Stratigraphy and Holocene evolution of the mud dominated Chao Phraya delta, Thailand. Quat. Sci. Rev. 22 : 789-807.

Tang, B., Zhou, K., Song, D., Yang, G. & Dai, A. 2003. Molecular systematic of the Asian mitten crabs, genus Eriocheir (Crustacea: Brachyura). Mol. Phylogenet. Evol. 29:309-316.

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

Tamura, K., Dudley, J., Nei, M & Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Bio.and Evol. 24:1596-1599.

Tassanakajon, A., Pongsomboon, S., Jarayabhand, P., Klinbunga, S. & Boonsaeng, V. 1998. Genetic structure in wild populations of black tiger shrimp (Penaeus monodon) using randomly amplified polymorphic DNA analysis. J. Mar. Biotechnol. 6 : 249-254.

Thia-Eng, C., Ingrid, R.L., Gorre, S., Ross, A., Bernad, S.R., Gervacio, B. & Ebarvia, M.C. 2000.The Malacca straits. Mar. Pollut. Bull. 41(1-6) : 160-178.

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 Res. 22: 4673-4680.

Tiensongrasamee, B. 2009. Vinegar crabs. The Thailand Research Fund. Bangkok. Thailand. (in Thai)

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. Mol. Ecol. 12: 2635-2648.

Vanschoenwinkel, B., Pinceel, T., Vanhove, M.P.M., Denis, C., Jocque, M., Timms, B.V. & Brendonck, L. 2012. Toward a Global Phylogeny of the ‘‘Living Fossil’’ Crustacean Order of the Notostraca. PLoSONE 7(4): e34998. doi:10.1371/ journal.pone.0034998.

Voris, H.K. 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J. Biogeogr. 27 : 1153-1167.

Watterson, A. 1984. Allele frequencies after a bottleneck. Theor. Populat. Biol. 26: 387-407.

Xu, Q., Liu, R. & Liu, Y. 2009. Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences. J. Exp. Mar. Bio. Ecol. 371: 121-129.

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

 

 

*Corresponding author; email: audy422r@yahoo.com