Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand
Main Article Content
Abstract
Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The AMOVA analysis, pairwise FST, and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.
Article Details
This work is licensed under a Creative Commons Attribution 4.0 International License.
References
Antoro S, Na-Nakorn U and Koedprang W. (2006). Study of genetic diversity of orangespotted grouper, Epinephelus coioides, from Thailand and Indonesia using microsatellite markers. Marine Biotechnology 8: 17–26. https://doi.org/10.1007/s10126-005-5026-0
Avise J C. (2000). Phylogeography. London: Harvard University Press. https://doi.org/10.1006/rwgn.2001.1470
Bartáková V, Reichard M, Janko K, Pola?ik M, Blažek R, Reichwald K, Cellerino A and Bryja J. (2013). Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique. BMC Evolutionary Biology 13: 196. https://doi.org/10.1186/1471-2148-13-196
Bussarawit S and Simonsen V. (2006). Genetic variation in populations of white scar (Crassostrea belcheri) and black scar oysters (C. iredalei) along the coast of Thailand by means of isozymes. Phuket Marine Biological Center Research Bulletin 67: 11–21.
Cassone B J and Boulding E G. (2006). Genetic structure and phylogeography of the lined shore crab, Pachygrapsus crassipes, along the northeastern and western Pacific coasts. Marine Biology 149: 213–226. https://doi.org/10.1007/s00227-005-0197-9
Chambers M D, van Blaricom G R, Hauser L, Utter F and Friedman C S. (2006). Genetic structure of black abalone (Haliotis cracherodii) populations in the California islands and central California: Impacts of larval dispersal and decimation from withering syndrome. Journal of Experimental Marine Biology and Ecology 331: 173–185. https://doi.org/10.1016/j.jembe.2005.10.016
Darriba D, Taboada G L, Doallo R and Posada D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9: 772. https://doi.org/10.1038/nmeth.2109
Di Battista J D, Berumen M L, Gaither M R, Rocha L A, Eble J A, Choat J H, Craig M T, Skillings D J and Bowen B W. (2013). After continents divide: Comparative phylogeography of reef fishes from the Red Sea and Indian Ocean. Journal of Biogeography 40: 1170–1181. https://doi.org/10.1111/jbi.12068
Drummond A J, Suchard M A, Xie D and Rambaut A. (2012). Bayesian phylogenetics with BEAUTi and the BEAST 1.7. Molecular Biology and Evolution 29: 1969–1973. https://doi.org/10.1093/molbev/mss075
Edwards S, Claude J, van Vuuren B J and Matthee C A. (2011). Evolutionary history of the Karoo bush rat, Myotomys unisulcatus (Rodentia: Muridae): Disconcordance between morphology and genetics. Biological Journal of the Linnean Society 102(3): 510–526. https://doi.org/10.1111/j.1095-8312.2010.01583.x
Excoffier L and 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. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Fishery Statistics Analysis and Research Group. (2017). Fisheries statistics of Thailand 2010, No. 5/2017. Department of Fisheries. Ministry of Agriculture and Cooperatives, Thailand. (in Thai)
Fu F X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915–925. https://doi.org/10.1093/genetics/147.2.915
Grant W S and Bowen B W. (1998). Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89: 415–426. https://doi.org/10.1093/jhered/89.5.415
Harpending H C. (1994). Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology 66: 591–600.
Hastuti K S, Yonvitner Y and Boer M. (2017). Indicator parameters population for the management of threadfin bream (Nemipterus spp.) in the inshore Java Sea, Indonesia. International Research Journal of Applied Sciences 33(3): 35–51.
Held C, Koenemann S and Schubart C D. (2011). Phylogeography and population genetics in crustacea. New York: CRC press.
Hung K, Russell B C and Chen W. (2017). Molecular systematics of threadfin breams and relatives (Teleostei, Nemipteridae). Zoologica Scripta 46(5): 536–551. https://doi.org/10.1111/zsc.12237
Iamsuwansuk A and Denduangboripant J. (2011). Phylogenetic study of shovel-nosed lobster Thenus indicus in Thailand. Proceeding of the 37th Congress on Science and Technology of Thailand. Bangkok, Thailand, 10–12 October 2011.
Klangnurak W, Phinchongsakuldit J and James T. (2012). Population structure and genetic connectivity of Lutjanus russelli (Lutjanidae) in Thailand. Proceeding of the 12th International Coral Reef Symposium. Cairns, Australia, 9–13 July 2012.
Klinbunga S, Yuvanatemiya V, Wongphayak S, Khetpu K, Menasveta P and 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. https://doi.org/10.4238/vol9-3gmr886
Lacson J M. (1992). Minimal genetic variation among samples of six species of coral reef fishes collected at La Parguera, Puerto Rico, and Discovery Bay, Jamaica. Marine Biology 112: 327–331. https://doi.org/10.1007/BF00702479
Librado P and Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Ma C Y, Cheng Q Q, Zhang Q Y, Zhuang P V and 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. https://doi.org/10.1016/j.jembe.2010.01.015
Mahidol C, Na-Nakorn U, Sukmanomon S, Taniguchi N and Nguyen T T T. (2007). Mitochondrial DNA diversity of the asian moon scallop, Amusium pleuronectes (Pectinidae), in Thailand. Marine Biotechnology 9: 352–359. https://doi.org/10.1007/s10126-006-6137-y
McManus J W. (1985). Marine speciation, tectonics and sea level changes in Southeast Asia. Proceedings of the 5th International Coral Reef Congress. Tahiti, 4: 133–138.
McMillan W O and Palumbi S R. (1995). Concordant evolutionary patterns among Indo West Pacific butterfly fishes. Proceedings of the Royal Society of London. Series B. Biological Sciences 260: 229–236. https://doi.org/10.1098/rspb.1995.0085
Nakthon N. (1992). Marine territory of Thailand and neighboring countries. Unpublished Master’s thesis, Hydrograph Department, Royal Thai navy, Thailand (in Thai).
Nalinanon S, Benjakul S, Kishimura H and Kazufumi O. (2011). Type I collagen from the skin of ornate threadfin bream (Nemipterus hexodon): Characteristics and effect of pepsin hydrolysis. Food Chemistry 125: 500–507. https://doi.org/10.1016/j.foodchem.2010.09.040
Neethling M, Matthee C A, Bowie R C K and von der Heyden S. (2008). Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae). BMC Evolutionary Biology 8: 325. https://doi.org/10.1186/1471-2148-8-325
Nei M. (1987). Molecular evolutionary genetics. New York: Columbia University Press. https://doi.org/10.7312/nei-92038
Nei M and Tajima F. (1981). DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145–163.
Ovenden J R, Brasher D J and White R W. (1992). Mitochondrial DNA analyses of the red rock lobster Jasus edwardsii supports an apparent absence of population subdivision throughout Australasia. Marine Biology 112: 319–326. https://doi.org/10.1007/BF00702478
Panithanarak T, Karuwancharoen R, Na-Nakorn U and Nguyen T T T. (2010). Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters: Implications for conservation. Zoological Studies 49: 564–576.
Prakoon W, Tunkijjanukij S, Nguyen T T T and Na-Nakorn U. (2010). Spatial and temporal genetic variation of green mussel, Perna viridis in the Gulf of Thailand and implication for aquaculture. Marine Biotechnology 12: 506–515. https://doi.org/10.1007/s10126-009-9234-x
Ragionieri L, Fratini S, Vannini M and Schubart C D. (2009). Phylogenetic and morphometric differentiation reveal geographic radiation and pseudo-cryptic speciation in a mangrove crab from the Indo-West Pacific. Molecular Phylogenetics and Evolution 52: 825–834. https://doi.org/10.1016/j.ympev.2009.04.008
Rambaut A, Suchard M A, Xie D and Drummond A J. (2014). Tracer v1.6. http://beast.bio.ed.ac.uk/Tracer (accessed on 12 October 2019).
Ramirez-Soriano A, Ramos-Onsins S E, Rozas J, Calafell F and Navarro A. (2008). Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics 179: 555–567. https://doi.org/10.1534/genetics.107.083006
Rogers A R. (1995). Genetic evidence for a Pleistocene population explosion. Evolution 49: 608–615. https://doi.org/10.1111/j.1558-5646.1995.tb02297.x
Rogers A R and Harpending H. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552–569. https://doi.org/10.1111/j.1558-5646.1995.tb02297.x
Russell B C. (1990). FAO species catalogue. Vol. 12. Nemipterid fishes of the world. (Threadfin breams, whiptail breams, monocle breams, dwarf monocle breams, and coral breams). Family Nemipteridae. An annotated and illustrated catalogue of nemipterid species known to date. FAO Fishes Synopsis 125(12): pp. 149.
Russell B, Lawrence A and Smith-Vaniz W F. (2016). Nemipterus hexodon. The IUCN red list of threatened species 2016: e.T69539271A69539701. https://doi.org/10.2305/IUCN.UK.2016-3.RLTS.T69539271A69539701.en (accessed on 16 October 2019).
Russo C A M, Sole-cava A M and 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. https://doi.org/10.1007/BF00349566
Schneider S and Excoffier L. (1999). Estimation of past demographic parameters from the distribution of pairwise differences when mutation rates vary among sites: Application to human mitochondrial DNA. Genetics 152: 1079–1089.
Sharp G D. (1996). Oceanography of the Indonesian Archipelago and adjacent areas. In: Pauly D and Martosubroto P (eds.), Baseline studies of biodiversity: The fish resources of Western Indonesia. Philippines: International Center for Living Aquatic Resources Management (ICLARM), 7–14.
Silva I C, Mesquita N and 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. https://doi.org/10.1007/s00227-010-1393-9
Slatkin M and Hudson R R. (1991). Pairwise comparisons ofmitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555–562. https://doi.org/10.1093/genetics/129.2.555
Stobutzki I C, Silvestre G T, Tali A A, Krongprom A, Supongpan M, Khemakorn P, Armada N and Garces L R. (2006). Decline of demersal fisheries resources in three developing Asian countries. Fisheries Research 78: 130–142. https://doi.org/10.1016/j.fishres.2006.02.004
Sukumaran S, Sebastian W and Gopalakrishnan A. (2016). Population genetic structure of Indian oil sardine, Sardinella longiceps along Indian coast. Gene 576: 372–378. https://doi.org/10.1016/j.gene.2015.10.043
Sun P, Shi Z H, Yin F and Peng S M. (2011). Genetic variation analysis of Mugil cephalus in China sea based on mitochondrial COI gene sequences. Biochemical Genetics 50(3–4): 180–191. https://doi.org/10.1007/s10528-011-9460-6
Supmee V, Ngernsiri L, Sriboonlert A, Wonnapinij P and Sangthong P. (2012). Population genetic analysis of violet vinegar crab (Episesarma versicolor) along the Andaman sea coast of Thailand. Zoological Studies 51(7): 1040–1050.
Suppapan J, Pechsiri J, O-Thong S, Vanichanon A, Sangthong P and Supmee V. (2017). Population genetic analysis of Oceanic paddle crab (Varuna litterata) in Thailand. Sains Malaysiana 46(12): 2251–2261. https://doi.org/10.17576/jsm-2017-4612-01
Supungul P, Sootanan P, Klinbunga S, Kamonrat W, Jarayabh P and Tassanakajon A. (2000). Microsatellite polymorphism and the population structure of the black tiger shrimp (Penaeus monodon) in Thailand. Marine Biotechnology 2: 339–347. https://doi.org/10.1007/s101260000012
Tajima F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595. https://doi.org/10.1093/genetics/123.3.585
Tang S, Tassanakajorn A, Klinbunga S, Jarayaphand P and Menasveta P. (2005). Population structure of tropical abalone (Haliotis asinina) in coastal waters of Thailand determined using microsatellite markers. Marine Biotechnology 6: 604–611. https://doi.org/10.1007/s10126-004-2300-5
Thompson J D, Higgins D G and Gibson T J. (1994). CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680. https://doi.org/10.1093/nar/22.22.4673
Uthicke S and 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. https://doi.org/10.1046/j.1365-294X.2003.01954.x
Voris H K. (2000). Maps of Pleistocene sea levels in Southeast Asia: Shorelines, river systems and time durations. Journal of Biogeography 27: 1153–1167. https://doi.org/10.1046/j.1365-2699.2000.00489.x
Wang W, Ma C, Chen W, Zhang H, Kang W, Ni Y and Ma L. (2017). Population genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI gene sequences. Biochemical Systematics and Ecology 71: 114–120. https://doi.org/10.1016/j.bse.2017.01.002
Wanna W, Rolland J, Bonhomme F and Phongdara A. (2004). Population genetic structure of Penaeus merguiensis in Thailand based on nuclear DNA variation. Journal of Experimental Marine Biology and Ecology 311: 63–78. https://doi.org/10.1016/j.jembe.2004.04.018
Watterson A. (1984). Allele frequencies after a bottleneck. Theoretical Population Biology 26: 387–407. https://doi.org/10.1016/0040-5809(84)90042-X
Xu H, Zhang Y, Xu D, Lou B, Guo Y, Sun X and Guo B. (2014). Genetic population structure of Miiuy croaker (Miichthys miiuy) in the Yellow and East China Seas base on mitochondrial COI sequences. Biochemical Systematics and Ecology 54: 240–246. https://doi.org/10.1016/j.bse.2014.01.013
Yang Z. (2006). Computational molecular evolution. New York: Oxford University Press. https://doi.org/10.1093/acprof:oso/9780198567028.001.0001
Zhang Y, Yang F, Wang Z, You Q, Lou B, Xu D, Chen R, Zhan W and Liu F. (2017). Mitochondrial DNA variation and population genetic structure in the Small yellow croaker at the coast of Yellow Sea and East China Sea. Biochemical Systematics and Ecology 71: 236–243. https://doi.org/10.1016/j.bse.2017.03.003