Nebuchadnezzar Akbar, Muhammad Aris, Muhammad Irfan, Irmalita Tahir, Abdurrachman Baksir


Ikan tuna (Thunnus Spp) adalah ikan pelagis yang memilili kemampuan migrasi dan nilai komersial. Kondisi oseanografie Maluku Utara dan Ambon mendukung kelimpahan stok populasi sumberdaya. Pengetahuan filogenetik dapat membantu menunjukan hubungan evolusioner dari suatu organisme yang disimpulkan dari data morfologi dan molekuler. Tujuan penelitian untuk mengetahui filogenetik ikan tuna di perairan Maluku Utara dan Ambon. Penelitian ini menggunakan metode PCR-Sequencing. Analisis molekuler menggunakan Polymerase Chain Reaction (PCR) dengan primer CRK-CRE, elektroforesis. Rekonstruksi pohon filogenetik menggunakan metode Neighbor joining dan model evolusi Kimura 2-parameter dilakukan dengan aplikasi MEGA5. Hasil penelitian filogenetik menemukan terdapat empat empat clade spesies ikan tuna yang saling berbeda (tuna mata besar ; tuna sirip kuing ; tuna alalunga ; cakalang ). Jarak genetik tuna mata besar (T.obesus)  dengan tuna sirip kuning (T.albacares)  adalah 0.09, tuna mata besar (T.obesus)  dengan tuna alalunga (T.albacore) adalah 0.19, tuna sirip kuning (T.albacares)  dengan tuna alalunga (T.albacore),  sebesar 0.21,  tuna mata besar (T.obesus)  dengan tuna alalunga (T.albacore)  cakalang (K.pelamis) adalah 0.34, cakalang (K.pelamis) dengan tuna alalunga (T.albacore) adalah  0.39 dan tuna sirip kuning (T.albacares)  dengan Cakalang (K.pelamis) adalah 0.34. Semua hasil menunjukan perbedaan genetik yang signifikan, genetik spesies tuna berasal dari satu kelompok dan filogeografi memiliki batas distribusi yang nyata antar satu dengan yang lain.

Kata Kunci :     Thunnus, Polymerase Chain Reaction (PCR), Pohon Filogenetik, primer CRK-CRE, , Neighbor joining, Kimura 2-parameter, jarak genetik, MEGA5, filogeografi. 


Tuna (Thunnus Spp) is a pelagic fish that has migration capabilities and commercial value. The condition of North Maluku and Ambon oceanographies supports the abundance of resource population stocks. Phylogenetic knowledge can help show the evolutionary relationship of an organism inferred from morphological and molecular data. The aim of the study was to determine phylogenetic of tuna in the waters of North Maluku and Ambon. This study used the PCR-Sequencing method. Molecular analysis uses a polymerase chain reaction (PCR) with CRK-CRE primer, electrophoresis. Reconstruction of the phylogenetic tree using the Neighbor joining method and the Kimura 2-parameter evolution model was carried out with the MEGA5 application. The results of phylogenetic research found that there were four four different clades of tuna species (bigeye tuna; kuing fin tuna; alalunga tuna; cakalang). The genetic distance of big eye tuna (T.obesus) with yellow fin tuna (T.albacares) is 0.09, bigeye tuna (T.obesus) with tuna alalunga (T.albacore) is 0.19, yellow fin tuna (T.albacares) with tuna alalunga (T.albacore), for 0.21, big eye tuna (T.obesus) with alalunga tuna (T.albacore) cakalang (K.pelamis) is 0.34, cakalang (K.pelamis) with alalunga tuna (T.albacore) is 0.39 and yellow fin tuna (T.albacares) with Cakalang (K. pelamis) are 0.34. All results show significant genetic differences, genetic tuna species come from one group and filogeography has a real distribution boundary between one another.

Keywords: Thunnus, Polymerase Chain Reaction (PCR), Phylogenetic Tree, CRK-CRE primer, Neighbor joining, Kimura 2-parameter, genetic distance, MEGA5, filogeography.


Baldauf, S. L. (2003). Phylogeny for the faint of heart: a tutorial. TRENDS in Genetics, 19(6), 345-351.

Bailey, M., Flores, J., Pokajam, S., & Sumaila, U. R. (2012). Towards better management of Coral Triangle tuna. Ocean & coastal management, 63, 30-42.

Borsa, P. (2003). Genetic structure of round scad mackerel Decapterus macrosoma (Carangidae) in the Indo-Malay archipelago. Marine Biology, 142(3), 575-581.

Bremer AJR, Naser I, Ely B. (1997). Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region. Journal of Fish Biology, 50(3), 540-554.

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.

Campbell NA, Reece BJ, Urry LA, Cain ML, Wasserman SA, Minorsky PV, Jackson RB. 2012. Biologi edisi kedelapan jilid 2. Penerbit Erlangga. Jakarta.

Chiang, H. C., Hsu, C. C., Lin, H. D., Ma, G. C., Chiang, T. Y., & Yang, H. Y. (2006). Population structure of bigeye tuna (Thunnus obesus) in the South China Sea, Philippine Sea and western Pacific Ocean inferred from mitochondrial DNA. Fisheries Research, 79(1-2), 219-225.

Chiang, H. C., Hsu, C. C., Wu, G. C. C., Chang, S. K., & Yang, H. Y. (2008). Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA. Fisheries Research, 90(1-3), 305-312.

Chen IC, Lee PF, Tzeng WN. (2005). Distribution of albacore (Thunnus alalunga) in the Indian Ocean and its relation to environmental factors. Fisheries Oceanography, 14(1), 71-80.

Chow S, Nohara T, Tanabe T, Itoh S, Tsuji Y. Nishikawa S. Uyeyanagi K, Uchikawa. (2003). Genetic and morphological identification of larval and small juvenile tunas (Pisces: Scombridae) caught by a mid-water trawl in the western Pacific. Bull of Fisheries Research Agency, 8: 1-14.

Davies, C. A., Gosling, E. M., Was, A., Brophy, D., & Tysklind, N. (2011). Microsatellite analysis of albacore tuna (Thunnus alalunga): population genetic structure in the North-East Atlantic Ocean and Mediterranean Sea. Marine biology, 158(12), 2727-2740.

De Jong, R. (1998). Halmahera and Seram: different histories, but similar butterfly faunas. Biogeography and geological evolution of SE Asia, 315-325.

Durand, J. D., Collet, A., Chow, S., 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(2), 313-322.

Elliott, N. G., & Ward, R. D. (1995). Genetic relationships of eight species of Pacific tunas (Teleostei: Scombridae) inferred from allozyme analysis. Marine and Freshwater Research, 46(7), 1021-1032.

FAO. (1963). Synopsis on the biology of bigeye tuna parathunnus mebachi kishinouye 1923 (Indian Ocean). Fisheries division, biology branch food and agriculture organization of the united nations. Rome, 1963

Finnerty JR, Block AB. 1995. Evolution of cytochrome b in the Scombroidei (Teleostei: molecular insights into billfish (Istiophoridae and Xiphiidae relationships). Fishery Bulletin, 93, 78-96.

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

Gaylord, B., & Gaines, S. D. (2000). Temperature or transport? Range limits in marine species mediated solely by flow. The American Naturalist, 155(6), 769-789.

Gordon, A. L., & Fine, R. A. (1996). Pathways of water between the Pacific and Indian oceans in the Indonesian seas. Nature, 379(6561), 146.

Gordon AL. (2005). the Indonesian seas oceanography of and their throughflow. Oceanography, 18, 14-27.

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. CSRIO.

Graham CA, Hill AJM. (2001). DNA Sequencing Protocols Second Edition. Humana Press Totowa, New Jersey.

Hall R. (1998). The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. in Hall, R. & J. D. Holloway (eds.). 1998. Biogeography and Geological Evolution of SE Asia. Backhuys Publisher, Leiden.

Kementerian Kelautan dan Perikanan. (2011). Kelautan dan perikanan dalam angka 2011. Jakarta.

Kunal, S. P., & Kumar, G. (2013). Cytochrome oxidase I (COI) sequence conservation and variation patterns in the yellowfin and longtail tunas. International journal of bioinformatics research and applications, 9(3), 301-309.

Laevastu T, Hayes ML. (1981). Fisheries oceanography and ecology. New York: Fishering News Book Ltd.

Lee, W. J., Conroy, J., Howell, W. H., & Kocher, T. D. (1995). Structure and evolution of teleost mitochondrial control regions. Journal of Molecular Evolution, 41(1), 54-66.

Martínez, P., & Zardoya, R. (2005). Genetic structure of bigeye tuna (Thunnus obesus) in the Atlantic Ocean. Collect. Vol. Sci. Pap, ICCAT, 57(1), 195-205.

Martínez, P., González, E. G., Castilho, R., & Zardoya, R. (2006). Genetic diversity and historical demography of Atlantic bigeye tuna (Thunnus obesus). Molecular phylogenetics and evolution, 39(2), 404-416.

Matsumoto WM, Skiliman RA, Dizon AE. (1984). Synopsis of biological data on skipjack tuna, katsuwonus pelamis. NOAA Technical Report NMFS Circular 451. FAO Fisheries Synopsis (FAO). no. 136.

Molcard R, Feux M, Syamsudin F. (2001). The Indonesian throughflow within Ombai strait. J. Deep Sea. Res. 48,1237-1253.

Nei M. (1972). Genetic distance between population. american nature. 106,283-292.

Nei M. (1987). moleculer evolutionary genetics. new york. columbia university. Press.

Permana GN, Hutapea JH, Haryanti, Sembiring SBM. (2007). Variasi genetic ikan tuna sirip kuning (Thunnus albaceras) dengan analisis elektroforesis allozyme dan mt-

DNA. Jurnal Riset Akuakultur, 2(1), 41-50.

Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X., & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18), 2496-2497.

Sanger F, Nicklen S, Coulson AR. (1977). DNA sequencing with chain-terminating inhibitors. proc. natn. acad. sci. usa 74, 5463±5467.

Saunders, N. C., Kessler, L. G., & Avise, J. C. (1986). Genetic variation and geographic differentiation in mitochondrial DNA of the horseshoe crab, Limulus polyphemus. Genetics, 112(3), 613-627.

Suman A, Irianto HE, 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. Indian Ocean Tuna Commission, 8, 1-14.

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution, 28(10), 2731-2739.

Tseng, M. C., Jean, C. T., Smith, P. J., & Hung, Y. H. (2012). Interspecific and intraspecific genetic diversity of Thunnus species. In analysis of genetic variation in animals. InTech.

Ubadillah R, Sutrisno H. (2009). Pengantar Biosistematik: Teori dan Praktek. Museum Zoologicum Bogoriense, Pusat Penelitian Biologi Lembaga Ilmu Pengetahuan Indonesia Bogor. LIPI Press. Jakarta.

Viñas, J., & Tudela, S. (2009). A validated methodology for genetic identification of tuna species (genus Thunnus). PLOS one, 4(10), e7606.

Walsh, P. S., Metzger, D. A., & Higuchi, R. (1991). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques, 10(4), 506-513.

DOI: https://doi.org/10.21107/jk.v11i2.3459


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