Genetic Population Structure of Yellowfin Tuna (Thunnus albacares) as Based Data of Fish Conservation in North Mallucas Sea

Nebuchadnezzar Akbar, Muhammad Aris


Tuna is a migratory species with high economic value. Utilization of tuna is increasing and growing every year. Fishing intensity of tuna in the Maluku Sea is high and can disrupt the population. The existence of the population will be threatened if not managed properly. The latest genetic information approach is necessary to prevent the population decline. The purpose of this research was to know the genetic structure of yellowfin tuna in North Maluku waters, Indonesi. Sampling was conducted in May-July 2016 in Morotai Island, Obi and Sanana, while secondary data was gathered in Ternate Island, Bacan and Ambon. A total of 72 samples were collected and analyzed. The result of the study found that the base length (bp) of the control region of mtDNA was found to be 512 bp (base pairs). the genetic distance in the nearest population is at Sanana and Obi (0.025). The results of genetic distance analysis between population found genetic similarity between Morotai-Sanana (0,021), Obi-Sanana (0,025), Obi-Morotai (0,026) and Ambon-Sanana (0,026), while the furthest genetic distance was found in Ternate-Bacan (0,040) and Ternate-Obi (0,042). The pairwise comparison test (Fst) shows a few genetic differentiation between yellowfin tuna populations. The value (Fst) of the yellowfin tuna population shows a strong gene flow between populations. The haplotype distribution shows a relationship between haplotypes in both yellowfin tuna, thus failing to show clade between different geographic locations. Unsustainable use can harm the population through genetic quality. Several approaches should be taken to support the life cycle of yellowfin tuna. The overall result shows that there has not been any change of genetic structure of yellowfin tuna in North Maluku Sea. Keywords : Haplotype, genetic distance, North Maluku, yellowfin tuna, pairwise comparison test

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Aguila R.D. Perez S.K.L, Catacutan B.J.N, Lopez G.V, Barut N.C, Santos M.D. 2015. Distinct Yellowfin Tuna (Thunnus albacares) Stocks Detected in Western and Central Pacific Ocean (WCPO) Using DNA Microsatellites. Journal Plos One, 10(9); 1-14 p.

Akbar N, Zamani NP, Madduppa HH. 2014a. Genetic diversity, population structure and phylogenetic yellowfin tuna (Thunnus albacares) in North Mallucas Sea and Ambon, Indonesia. Thesis. Bogor Agricutural University .Bogor.

Akbar N, Zamani NP, Madduppa HH. 2014b. Genetic diversity of yellowfin tuna (Thunnus albacares) from two populations in the Moluccas Sea, Indonesia. Depik, 3(1): 65-73.

Akbar N, Zamani NP, Madduppa HH. 2015. Genetic population stucture yellowfin tuna (Thunnus albacares) from two populations in Mallucas Sea. Nasional seminar proceeding. The inovatif result University. 337-348 page.

Allen G.R, Erdmann M.V, Dudgeon C.L. 2013. Hemiscyllium halmahera, a new species of Bamboo Shark (Hemiscylliidae) from Indonesia. aqua, International Journal of Ichthyology, 19 (3); 123-136 p.

Appleyard, S.M., P.M. Grewe, B.H. Innes., R.D. Ward. 2001. Population structure of yellowfin tuna (Thunnus albacores) in the western Pasific Ocean, inferred from microsatellite loci. Marine Biology, 139: 383-393.

Bailey M, Flores J, Pokajam S, Sumaila UR. 2012. Towards better management of Coral Triangle tuna. Ocean & Coastal Management Journal, 63 ; 30-42.

Barber P.H, Erdmann M.V. Palumbi S.R. 2006. Comparative Phylogeography of Three Codistributed Stomatopods: Origins and Timing of Regional Lineage Diversification in The Coral Triangle. Journal Evolution, 60(9) 1825-1839 pp.

Bremer JRA, Stequert B, Robertson NW, Ely B. 1998. Genetic evidence for inter-oceanic subdivision of bigeye tuna (Thunnus obesus) populations. Marine Biology,132: 547-557.

Bremer JRA, Vinas J, Mejuto J, Ely B, Pla C. 2005. Comparative phylogeography of Atlantic bluefin tuna and swordfish: the combined effects of vicariance, secondary contact, introgression, and population expansion on the regional phylogenies of two highly migratory pelagic fishes. Molecular Phylogenetics and Evolution 36: 169-187.

Carpenter KE, Barber PH, Crandall ED, Ablan-Lagman MCA, Ambariyanto, Mahardika GN.2011. Comparative phylogeography of the Coral Triangle and implications for marine management. Jounal Marine Biology.14p.

Carvalho GR, Creer S, Allen M, Costa FO., others. 2010. Genomics in the discovery and monitoring of marine biodiversity. In: Cock JM, Tessmar-Raible K, Boyen C, Viard, F (eds) An introduction to marine genomics. Springer, Dordrecht, p 1−32

Chiang HC, Hsu CC, Lin HD, Ma GC, Chiang TY, Yang HY. 2006. Population structure of bigeye tuna (Thunnus obesus) in the South China Sea, Philippine Sea and western Pacific Ocean inferred from mitochondrial DNA. Fisheries Reserch, 79: 219-225.

Chiang HC, Hsu CC, Wu GCC, Chang SK, Yang HY. 2008. Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA. Fisheries Reserch, 90: 305-312.

Chow S, Kishino H. 1995. Phylogenetic Relationships Between Tuna Species of the Genus Thunnus (Scombridae: Teleostei): Inconsistent Implications from Morphology, Nuclear and Mitochondrial Genomes. Journal Moleculer Evolution, 41:741-748.

Chow S, Okamoto H, Miyabe N, Hiramatsu, K, Barut N, 2000. Genetic divergence between Atlantic and Indo-Pacific stocks of bigeye tuna (Thunnus obesus) and admixture around South Africa. Moleculer Ecology, 9: 221-227

Collette BB, Carpenter KE, Polidoro BA, Juan-Jordá MJ. 2011a. High value and long life-double jeopardy for tunas and billfishes. Science 333: 291-292

Collette BB, Carpenter KE, Polidoro BA, Jorda MJJ, Boustany A, Die DJ, Elfes C, Fox W, Graves J, Harrison LR, McManus R, Vera CVM, Nelson RVR, Schratwieser J, Sun CL, Amorim A, Peres MB, Canales C, Cardenas G, Chang SK, Chiang WC, NdO Leite, Harwell JrH, Lessa R, Fredou FL, Oxenford HA, Serra R, Shao KT, Sumaila R, Wang SP, Watson R, Yanez E. 2011b. High Value and Long Life Double Jeopardy for Tunas and Billfi shes. Science, 333 ; 291-292.

Dammannagoda ST. 2007. Genetik stock structure and inferred migratory pattern of skipjack tuna (Katsuwonus pelamis) and yellowfin tuna (Thunnus albacares) in Sri Lankan waters. Dissertation. School of Natural Resource Science. Queensland University of Technology Gardens Point Campus Brisbane, Australia.

Durand J.D., Collet A., Chow., Guinand B., Borsa P. 2005. Nuclear and mitochondrial DNA markers indicate unidirectional gene flow of Indo-Pacific to Atlantic bigeye tuna (Thunnus obesus) populations, and their admixture off southern Africa. Marine Biology, 147: 313-322.

Ely B, Vinas J, Alvarado Bremer JR, Black D, Lucas L, Covello K, Labrie AV, Thelen E. 2005. Consequences of the historical demography on the global population structure of two highly migratory cosmopolitan marine fishes: the yellowfin tuna (Thunnus albacares) and the skipjack tuna (Katsuwonus pelamis). BMC Evol. Biol. 5, 19.

Exoffier L, Smouse P.E, Quattro J.M. 1992. Analysis of moleculer variance inferred from metric distance among DNA haplotypes; application to human mitochondrial DNA restriction data. Genetics. (131) : 479-491.

Excoffier L, and H. Lischer. 2009. Arlequin ver 3.5 user manual ; An integrated software package for population genetics data analysis. Swiss Institute of Bioinformatics. 174 p.

Fakhri F, Narayani I, Mahardika I.G.N.K. 2015. Keragaman Genetik Ikan Cakalang (Katsuwonus Pelamis) dari Kabupaten Jembrana dan Karangasem, Bali. Jurnal Biologi 19(1); 11-14.

FAO.2010. The State of World Fisheries and Aquaculture. 218 page. Rome, Italy.

FAO.2012. The State of World Fisheries and Aquaculture. 230 page. Rome, Italy.

Freeland J.R. 2005. Molecular ecology. British library cataloguing in publication data. Minion-regular by Thomson press (India) limited. New Delhi, India. 388 p.

Grant WS. 1985. Biochemical genetic stock culture of the Southern African Anchovy. Engraulis capensis Gilchrist. Journal Of Biology, 27: 23-29.

Grewe P, Hampton J. 1998. An assessment of bigeye (Thunnus obesus) population structure in the Pasific Ocean, based on mitochondrial DNA and DNA microsatellite analysis. Marine Research. Commonwealth Scientific and Industrial Research Organitation, Australia.

Grewe P.M, Feutry P, Hill P.L, Gunasekera R.M, Schaefer K.M, Itano D.G, Fuller D.W, Foster S.D, Davies C.R.2015. Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource. Scientific Reports 5:16916. 1-9 pp

Guan S, Liu H, Zheng Y, Yu D, Nie A, Liu M. 2014. Inference of phylogenetics and evolution of Epinephelus septemfasciatus and 48 other species of Epinephelus Genus using mitochondrial CO1 fragment sequences. Pakistan J Zool 46: 67-74.

International Seafood Sustainability Foundation. 2015. ISSF Tuna Stock Status Update 2015 ; Status of the World Fisheries for Tuna. Technical Report 2015. United Stated of America

Jackson AM, Ambariyanto, Erdmann MV, Toha AHA,Stevens LA, Barber PH.2014. Phylogeography of commercial tuna and mackerel in the Indonesian Archipelago. Bulletin Marine Science. 90(1):471–492

Jefri E, Zamani NP,Subhan B, Madduppa HH. 2015. Molecular phylogeny inferred from mitochondrial DNA of the grouper Epinephelus spp. in Indonesia collected from local fish market. Biodiversitas 16 (2): 254-263

Kawimbang E, Paransa IJ, Kayadoe ME.2012. An estimation of garfish stock and its fishing season in Tagulandang waters, Siau Tagulandang Biaro Regency. Jurnal Ilmu dan Teknologi Perikanan Tangkap 1(1): 10-17

Ministry of Marine Affair and Fisheries Republic of Indonesia. 2015. Ministry of Marine Affair and Fisheries in figures 2015. Information and statistic data center, Jakarta

Kunal SP, Kumar G. 2013. Cytochrome oxidase I (COI) sequence conservation and variation patterns in the yellowfin and longtail tunas. International Journal Bioinformation Research, 9(3): 301-309

Kunal, SP, Kumar G, Menezes MR. 2014. Genetic variation in yellowfin tuna (thunnus albacares) (Bonnaterre, 1788) along Indian Coast using PCR-RFLP analysis of mitochondrial Dna D-Loop Region. International Journal of Scientific Research, 3(1): 25-30.

Moria BS, Permana GN, Hutapea JH. 2009. Characteristic three locus microsatelite on eggs and larva yellowfin tuna (Thunnus albacares). Jurnal Perikanan, 11 (2): 144-149.

Kusuma, Bengen D.G, Madduppa H, Subhan B, Arafat D, Negara. B.F.S.P. 2016. Close genetic connectivity of soft coral Sarcophyton trocheliophorum in Indonesia and its implication for marine protected area. Aceh Journal of Animal Science 1(2): 50-57

Koesmawati T.A,Buchari B, Amran M.B, Kardono, L.B.S. 2015. Determination of Total Arsenic in Indonesian Tuna Fish Sample. Journal of Applied Pharmaceutical Science Vol. 3 (07); 116-121

Lailossa G.W. 2015. Preliminary Study, Risk Analysis and HACCP in Cold Chain System, Frozen Yellow Fin Tuna in Moluccas.Journal of Agricultural Studies, 3 (2) ; 248-257.

Lee WJ, Conroy J, Howell WH, Kocher TD. 1995. Structure and evolution of teleost mitochondrial control regions. Moleculer Evolution, 41: 54-66.

Lin T, Liu L. 2008. Low Levels of Genetic Differentiation among Populations of the Coral-Inhabiting Snail Coralliophila violacea (Gastropoda: Coralliophilidae) in Regions of the Kuroshio and South China Sea. Zoo Stud 47: 17-24.

Martinez P, Zardoya R. 2005. Genetic struktur of bigeye tuna (Thunnus obesus) in the Atlantic Ocean. Collective Volume of Scientific Papers, 57(1): 195-205.

Martinez P, Gonzales GE, Castilho R, Zardoya R. 2006. Genetic diversity and historical demography of Atlantic bigeye tuna (Thunnus obesus). Molecular Phylogenetics and Evolution, 39:404-416

McQuinn IH. 1997. Metapopulations and the Atlantic herring. Fish Biology Fish. 7(3):297-329.

Melmambessy E.H.P.2010. Pendugaan Stok Ikan Tongkol di Selat Makassar Sulawesi Selatan. Jurnal Ilmiah agribisnis dan Perikanan, 3(1); 53-61.

Montes I, Iriondo M, Manzano C, Arrizabalaga H, Jiménez E, Pardo M.A, Goñi N, Davies C.A, Estonba1 A. 2012. Worldwide genetic structure of albacore Thunnus alalunga revealed by microsatellite DNA markers. Journal Marine Ecology Progress Series, 471: 183–191.

Moria BS, Permana GN, Hutapea JH. 2009. Karakterstik tiga lokus mikrosatelit pada telur dan larva ikan tuna sirip kuning (Thunnus albacares). Jurnal Perikanan, 11 (2): 144-149.

Nesbo CL, Rueness EK, Iversen SA, Skagen DW, Jakobsen KS. 2000. Phylogeography and population history of Atlantic mackerel (Scomber scombrus L.): a genealogical approach reveals genetic structuring among the eastern Atlantic stocks. Proc Roy Soc B-Biol Sci. 267(1440):281–292.

Nei M. 1972. Genetic distance between population. American Nature, 106: 283-292.

Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89: 583-590

Nikolic N, Bourjea J. 2012. Analysis of the genetic structure and life history of albacore tuna in terms of diversity, abundance and migratory range at the spatial and time scales. Report IOTC (Indian Ocean Tuna Commission) 24 November 2012.

Nishida T, Chow S, Grewe P. 1998. Review and Research Plan on the Stock Structure of Yellowfin Tuna (Thunnus albacares) and Bigeye Tuna (Thunnus obesus) in The Indian Ocean. IOTC Proceedings ; 230-236 pp

Nugraha, B. 2009. Studi tentang genetika populasi ikan tuna mata besar (Thunnus obesus) hasil tangkapan tuna longline yang didaratkan di Benoa. Tesis. Pascasarjana Institut Pertanian Bogor, Bogor

Permana GN, Hutapea JH, Haryanti, Sembiring SBM. 2007. Variasi genetik ikan tuna sirip kuning (Thunnus albaceras) dengan analisis elektroforesis allozyme dan mtDNA. Jurnal Riset Akuakultur, 2 (1):41-50.

Perwati L.K. 2009. Analisis derajat ploidi dan pengaruhnya terhadap variasi ukuran stomata dan spora pada Adiantum raddianum. Bioma, 11(2): 39-44.

Prehadi, Sembiring A, Kurniasih AM, Rahmad, Arafat D, Subhan B, Madduppa H. 2014. DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port. Biodiversitas 16: 55-61.

Saleky D, Setyobudiandi I, Toha H.A, Takdir M, Madduppa H.H.2016. Length-weight relationship and population genetic of two marine gastropods species (Turbinidae: Turbo sparverius and Turbo bruneus) in the Bird Seascape Papua, Indonesia. Biodiversitas,17 (1) ; 208-217

Sanger F, Nicklen S. & Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. National Academical Science, United Stated of America, 74 (12): 5463-5467.

Santos MD, Lopez GV, Barut NC. 2010. A pilot study on the genetic variation of eastern little tuna (Euthynnus affinis) in Southeast Asia. Philippine Journal of Science, 139 (1): 43-50.

Scoles DR, Graves JE. 1993. Genetic analysis of the population structure of yellowfin tuna, Thunnus albacares, from the Pacific Ocean. Fisheries Bulletin, 91:690-698.

Sembiring A, Pertiwi NPD, Mahardini A, Wulandari R, Kurniasih EM, Kuncoro AW, Cahyani NKD, Anggoro AW, Ulfa M, Madduppa H, Carpenter KE, Barber PH, Mahardika GN. 2015. DNA barcoding reveals targeted fisheries for endangered sharks in Indonesia. Fish Res 164: 130-134.

Seafish. 2015. Seafish ethics profile-Indonesia. Seafish Industry Authority, Origin Way, Europarc, Grimsby, DN37 9TZ . 6 pp.

Slamat, Thohari AM, Soelistyowati DT. 2011. Keanekaragaman genetik ikan betok (Anabas testudinius) pada tiga ekosistem perairan rawa di Kalimantan Selatan. Agroscientia, 18 (3): 129-135.

Sibagariang O.P, Fauziyah, Agustriani F. 2011. Analisis Potensi Lestari Sumberdaya Perikanan Tuna Longline di Kabupaten Cilacap, Jawa Tengah. Maspari Journal 03;24-29.

Sibert J, Hampton J, Kleiber P, Maunder M. 2009. Biomass, size and trophic status of top predators in the Pacific Ocean. Science, 314: 1773-1775.

Suman A, Irianto H.E, Amri K, Nugraha B. 2013. Population structure and reproduction of bigeye tuna (Thunnus Obesus) in Indian Ocean at Western part of Sumatera and Southern part of Java and Nusa Tenggara, dalam Prosiding Indian Ocean Tuna Commission, 8 Oktober, 2013.

Sriati. 2011. Kajian Bio-Ekonomi Sumberdaya Ikan Kakap Merah yang Didaratkan di Pantai Selatan Tasikmalaya, Jawa Barat. Jurnal Akuatika 2 (2);79-90.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likehood, evolutionary distance, and maximum parsimony method. Moleculer Biology Evolution, 28(10): 2731-2739.

Walsh PS, Metzger DA, Higuchi R. 1991. Chelex-100 as a medium for Simple extraction of DNA for PCR based typing from forensic material. Biotechniques, 10: 506-513

Ward RD, Woodwark M, Skibinski DOF. 1994. A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes. Journal Fish Biology, 44 (2) :213-232.

Wijana IMS, Mahardika IGN. 2010. Struktur genetika dan filogeni yellowfin tuna (Thunnus albacores) berdasarkan sekuen DNA mitokondria control region sitokrom oksidase I pada diversitas zone biogeografi. Jurnal Bumi Lestari. 10 (2): 270-274.

White C, Kimberly SA, Watson JSA, David ZC, Danielle TJ, Robert. 2010. Ocean currents help explain population genetic structure. Proceedings of the Royal Society, 277: 1685-1694.

Wyrtki K. 1961. Physical oceanography of the Southeast Asian waters. Naga report.Volumer 2. Scripps Institution of Oceanography. The University of California. La Jolla, California. 195 halaman.

Wu GCC, Chiang HC, Chou YW, Wong WR, Chen CC, Yang HY. 2010. Phylogeography of yellowfin tuna (Thunnus albacares) in the Western Pacific and the Western Indian Oceans inferred from mitochondrial DNA. Fisheries Research, 105: 248-253


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