Population genetic structure of Asiatic Hard Clam (Meretrix meretrix) in Thailand based on Cytochrome Oxidase subunit I gene sequence
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Abstract. Supmee V, Sangthong P, Songrak A, Suppapan J. 2020. Population genetic structure of Asiatic Hard Clam (Meretrix meretrix) in Thailand based on Cytochrome Oxidase subunit I gene sequence. Biodiversitas 21: 2702-2709. The Asiatic hard clam (Meretrix meretrix) is an important commercial clam in Thailand. Last decade, this species had a dramatic decrease. Thus, to conserve this species, genetic information is essential. In our study, 135 samples of M. meretrix were collected from 7 sampling sites along the Thailand coast. The genetic structure was examined based on the variation of the nucleotide sequence in cytochrome oxidase subunit I gene. Twenty haplotypes were identified. Numerous rare haplotypes were revealed indicating the existence of a large female effective population size. In the northern Gulf of Thailand population, the genetic diversity was low. The neutrality test and minimum spanning network showed experienced expansion events of M. meretrix in Thailand. The genetic structure showed that the M. meretrix population was separated into the Gulf of Thailand and the Andaman population. This finding was possibly caused by a disruption of gene flow from the Thai-Malay Peninsula and larval behavior. Our finding suggested that the construction management program to maintain the genetic diversity of this species could be separated into 2 conservation units.
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References
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Wang W, Ma C, Chen W, Zhang H, Kang W, Ni Y. 2017b. Population Genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI
gene sequences. Biochem Syst Ecol 71: 114-120.
Xue DX, Wang HY, Zhang T, Liu JX. 2014. Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers. PLoS ONE 9(4): e95436.
doi:10.1371/journal.pone.0095436.
Zheng J, Nie H, Yang F, Yan X. 2019. Genetic variation and population structure of different geographical populations of Meretrix petechialis based on mitochondrial gene COI. J Genet 98: 68.
https://doi.org/10.1007/s12041-019-1111-4
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.
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.
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.
Fernández-Pérez J, Froufe E, Nantón A, Gaspar MB, Méndez J. 2017. Genetic diversity and population genetic analysis of Donax vittatus (Mollusca: Bivalvia) and phylogeny of the genus with
mitochondrial and nuclear markers. Est Coast Shelf Sci 197: 126-135.
Fishery Statistics Analysis and Research Group. 2017. Fisheries Statistics of Thailand, No. 5/2017. Department of Fisheries. Ministry of Agriculture and Cooperatives, Thailand. (in 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.
Gilleard JS, Redman E. 2016. Chapter Two - Genetic diversity and population structure of Haemonchus contortus. Adv Parasitol 93:31-68.
Gu XF, Dong YH, Yao HH, Zhou XL, Qi XY, Lin ZH. 2015. Microsatellite marker analysis reveals the distinction between the north and south groups of hard clam (Meretrix meretrix) in China. Genet Mol
Res 14(1): 1210-1219.
Hamli H, Idris MH, Hena MKA, Rajee AH. 2019. Fisheries assessment, gametogenesis and culture practice of local bivalve: A review. Pertanika J Trop Agric Sci 42(1): 103-124.
Johannesson K, Ring AK, Johannesson KB, Renborg E, Jonsson PR, Havenhand JN. 2018. Oceanographic barriers to gene fow promote genetic subdivision of the tunicate Ciona intestinalis in a North
Sea archipelago. Mar Biol 165:126 https://doi.org/10.1007/s00227-018-3388-x
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7): 1870-1874.
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.
Li HJ, Zhang JJ, Yuan XT, Zhang AG, Liu GZ, Shao KS, Wang L. 2016. Genetic diversity and differentiation of seven geographical populations of hard clam (Meretrix meretrix) assessed by COI and
microsatellite markers. Acta Ecologica Sin 36: 499-507.
Ma C, Cheng Q, Zhang Q, Zhuang P, Zhao Y. 2010. Genetic variation of Coilia ectenes (Clupeiformes: Engraulidae) revealed by the complete cytochrome b sequences of mitochondrial DNA. J Exp Mar
Bio Ecol 385:14-19.
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.
Neo ML, Todd PA. 2012. Population density and genetic structure of the giant clams Tridacna crocea and T. squamosa on Singapore’s reefs. Aquat Biol 14: 265-275.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.
Panithanarak T, Karuwancharoen R, Na-Nakorn U, Nguyen TTT. 2010. Population genetics of the Spotted seahorse (Hippocampus kuda) in Thai waters: Implications for conservation. Zool Stud 49(4):
564-576.
Phinchongsakuldit J, Chaipakdee P, Collins JF, Jaroensutasinee M, Brookfield JFY. 2013. Population genetics of cobia (Rachycentron canadum) in the Gulf of Thailand and Andaman Sea: fisheries
management implications. Aquacult Int 21:197-217.
Prakoon W, Tunkijjanukij S, Nguyen TTT, Na-Nakorn U. 2010. Spatial and temporal genetic variation of green mussel, Perna viridis in the Gulf of Thailand and implication for aquaculture. Mar
Biotechnol 12: 506-515.
Ramirez-Soriano A, Ramos-Onsins SE, 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.
Rosly HAM, Mohd-Nor SA, Yahya K, Naim DM. 2013. Mitochondrial DNA diversity of mud crab Scylla olivacea (Portunidae) in Peninsular Malaysia: a preliminary assessment. Mol Biol Rep 40(11):
6407-6418.
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.
Sienes RKA, Juranes RSJ, Metillo EB. 2018. Lunar periodicity in reproduction of two venerid clams Meretrix meretrix and Katelysia hiantina in Panguil Bay, Northern Mindanao, Philippines. Int J Biosci
13(6): 70-81.
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
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.
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
Trang VT, Quynh LT, Thiet CCC, Duc NH, Ha TTT. 2018. Genetic relationship of asiatic hard clam populations collected in northern coastal provinces in Vietnam based on mtDNA sequence analysis.
J Aquac Mar Biol 7(1): 00184. DOI: 10.15406/jamb.2018.07.00184
Wang C, Chen AH, Cao YW, Yang P, Zhang Y, Yao GX, Cai YX. 2016. Genetic relationship analysis of six Meretrix meretrix populations from different sea areas. Mar Fish 3: 262-272.
Wang IJ, Glor RE, Losos JB. 2013. Quantifying the roles of ecology and geography in spatial genetic divergence. Ecol Lett 16:175-182.
Wang X, Kong L, Chen J, Matsukuma A, Li K. 2017a. Phylogeography of bivalve Meretrix petechialis in the Northwestern Pacific indicated by mitochondrial and nuclear DNA data. PLoS ONE 12(8):
e0183221.
Wang W, Ma C, Chen W, Zhang H, Kang W, Ni Y. 2017b. Population Genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI
gene sequences. Biochem Syst Ecol 71: 114-120.
Xue DX, Wang HY, Zhang T, Liu JX. 2014. Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers. PLoS ONE 9(4): e95436.
doi:10.1371/journal.pone.0095436.
Zheng J, Nie H, Yang F, Yan X. 2019. Genetic variation and population structure of different geographical populations of Meretrix petechialis based on mitochondrial gene COI. J Genet 98: 68.
https://doi.org/10.1007/s12041-019-1111-4
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