DNA barcoding and morphometric of Rastrelliger spp. in North Maluku Sea, Indonesia
Abstract
High exploration activity is feared to have an impact to mackerel populations. A sustainable management approach should be taken to provide information about the status of mackerel populations. Study of mackerel population status can be carried out through genetic information. The DNA of the fish samples were collected at traditional fish markets (Morotai, Bacan and Ternate). Laboratory works such as extraction, amplification, electrophoresis and DNA sequencing were analysis at the Indonesian Biodiversity Laboratory (Bionesia). The molecular characteristics of Rastrelliger kanagurta were 374 base pairs (bp). The composition of nucleotides showed the similarity of frequencies between species. Phylogenetic relationship of R. kanagurta in North Maluku Sea suggested that there was any differentiation. The genetic diversity of R. kanagurta was high with a total number of haplotypes and diverse nucleotide diversity. The minimum spawning networks (MSN) found 5 haplotype networks from a total of 12 samples. Morphological measurements of standard length, head height, body width, pectoral fin length and tail were found to have variable values. The length of the weight of the fish is obtained of b = 3, indicating that the growth pattern was isometric or weight gain was equivalent to the growth of the fish length.
Keywords: Biodiversity, conservation, ecology, morphology, species
Full Text:
PDFReferences
Abdullah, A., Sativa H. A., Nurhayati, T., Nurilmala, M. 2019. Pemanfaatan DNA barcoding untuk ketertelusuran label berbagai produk olahan ikan berbasis surimi komersial. Jurnal Pengolahan Hasil Perikanan Indonesia, 22 (3), 508-519
Achmad, M..J.,Djamhur, M., Fabanyo,M.A., Akbar, N. 2019. Aplikasi DNA barcoding ikan julung-julung (Hemirhampus sp.) di Perairan Laut Maluku Utara. Journal of ichthyology of Indonesia, 19(3), 463-473
Akbar, N., Zamani N. P; Madduppa, H. H. 2014. Keragaman genetik ikan tuna sirip kuning (Thunnus albacares) dari dua populasi di Laut Maluku, Indonesia. Depik, 3(1), 65-73.
Aris, M; Akbar, N; Labenua, R. 2017. Variasi genetik dan filogenetik ikan tuna sirip kuning (Thunnus albacares) sebagai basis pengelolaan perikanan berkelanjutan di Maluku Utara. Int J Pharma Bio Sci ,8 (4), 419-426
Akbar, N., Aris, M., Irfan M., Tahir, I., Baksir, A., Surahman., Madduppa, H.H., Kotta, R. 2018. Filogenetik ikan tuna (Thunnus spp.) di Perairan Maluku Utara, Indonesia. Jurnal Iktiologi Indonesia, 18(1): 1-11
Akbar, N; Labenua, R. 2018. Genetic diversity of skipjack (Katsuwonus pelamis) in North Maluku Sea. Depik, 7 (2), 164 – 176
Akbar, N; Irfan, M; Aris, M. 2018. Population Genetics and Phylogeography of Bigeye Tuna in Moluccas Seas, Indonesia. Indonesian Journal of Marine Sciences, 23(4), 145-155
Akib, N. A. M; Tam, M. B; Phumee, P; Abidin, M. Z; Tamadoni, S; Mather, P. B; Nor, S. A. M. 2015. High connectivity in Rastrelliger kanagurta: influence of historical signatures and migratory behaviour inferred from mtDNA Cytochrome b. PLoS ONE, 10 (3), e0119749.
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.
Avise, J. C., Bowen, B. W., Lamp, T. 1989. DNA fingerprint from hypervariable mitochondrial genotypes. Moleculer Biologi Evolution, 6, 258-269.
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.
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 Reserch, 79, 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 Reserch, 90, 305-312.
Darlina, M. N; Masazurah, A, R; Jayakansar, P; Samsari, A. F. J; Siti, A. M. N. (2011). Morphometric and molecular analysis of mackerel (Rastrelliger spp) from the west coast of Peninsular Malaysia. Genetics and Molecular Research, 10 (3), 2078-2092
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, 2727-2740.
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; Lischer, H. 2009. Arlequin ver 3.5 user manual ; an integrated software package for population genetics data analysis. Swiss Institute of Bioinformatics Graham CA, Hill AJM. 2001. DNA Sequencing Protocols Second Edition. Humana Press. Totowa, New Jersey.
FAO. 1974. FAO species identification sheets for fisheries purpose food and agriculture organisation of united nation. Rome.
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.
Ferguson, A; Taggart; Prodohl, T. B; McMeel, O; Thompson, C; Stone, C; McGinnity, P; Hynes, R. A. 1995. The application of moleculer markers to study and conservation of fish population, with special reference to Salmo. J. of Fish Biology, 47, 103-126.
Indaryanto, F. R; Imai, H; Wardiatno, Y. 2015. Genetic variation of short body Mackerel, Rastrelliger brachysoma of Jawa Island, Indonesia Based on mtDNA Control Region Sequences. AACL Bioflux, 8 (5), 648-655
Jayasankar, P; Thomas P. C; Paulton, M. P; Mathew, J. 2004. Morphometric and genetic analyzes of indian Mackerel (Rastrelliger kanagurta) from Peninsular India. Asian Fisheries Science, 17, 201-215
Jefri, E; Zamani N. P; Subhan, B; Madduppa, H. H. 2015. Molecular phylogeny inferred from mitochondrial DNA of the Grouper epinephelus spp. In Indonesia collected from local fish market. Biodiversitas, 16 (2), 254-263.
Kartika, G. R. A; Sartimbul, A; Widodo. 2017. Genetic variance of Sardinela Lemuru in the Bali Strait Waters. Jurnal Kelautan, 10 (1), 21-28
Kielpinski, M; Kempter, J; Panicz, R; Keszka, S. 2014. Genetic identifiability of selected populations of indian Mackerel, Rastrelliger kanagurta (Actinopterygii: Perciformes: Scombridae)-Celfish Project-Part 1. Acta Ichthyologica Et Piscatoria, 44 (2), 145–152
Kusuma, A; Bengen, D. G; Madduppa, H. H; Subhan, B; Arafat, D; Negara, B.F.S.P. 2016b. 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
Lante, S; Tenriulo, A; Parenrengi, A; Rachmansyah; Malina, A. C. 2011. Keragaman genetik populasi ikan Beronang (Siganus Guttatus) di Selat Makassar dan Teluk Bone menggunakan metode random amplified polymorphic DNA (RAPD). J. Ris. Akuakultur, 6 (2), 211-224
Liu, Z. J; Li, P; Argue, B. J; Dunham, R. A. (1999). Random amplified polymorphic DNA markers: usefulness for gene mapping and analysis of genetic variation of catfish. Aquaculture, 174, 59-68.
Madduppa, H. H; Putri, A. S. P; Wicaksono, R. Z; Subhan, B; Akbar, N; Ismail, F; Arafat, D; Prabuning, D; Sani, L. M. I; Srimariana, E. S; Baksir A; Bengen, D. G. 2020. Morphometric and DNA Barcoding of endemic Halmaheran walking shark (Hemiscyllium halmahera, Allen, 2013) in North Maluku, Indonesia. Biodiversitas, 21 (7), 3331-3343
Munpholsri, N; Poompuang, S; Senanan, W; Kamonrat, W. 2013. Microsatellite markers suggested moderate genetic variation in indian Mackerel (Rastrelliger kanagurta) populations from the Andaman Sea, Thailand. Kasetsart Journal-Natural Science, 47, 853 - 863
Muchlisin, Z. A; Masazurah, A. R; Abu, T, A; Siti, A. M. N; Samsudin, B; Jamsari A. F. J. 2009. Genetic identification of four Malaysian mackerel species off coast of Peninsular Malaysia based on molecular marker. In: 8th Malaysia Genetic Congress: Role of Genetics in Wealth Creation and Quality of Life , 4–6 August 2009, Awana Genting, Pahang, Malaysia, pp. 74–77.
Nei, M. (1972). Genetic distance between population. American Nature, 106, 283-292.
Nei, M. (1987). Moleculer evolutionary genetics. New York. Columbia University. Press. New York.
Nuryanto, A; Kochzius, M. (2009). Highly restricted gene flow and deep evolutionary lineages in the giant clam Tridacna maxima. Coral Reefs, 28, 607-619.
Nugroho, E; Subagja, J; Asih, S; Kurniasih, T. (2006). Evaluasi keragaman genetik ikan Kancra dengan Marker mtDNA D-loop dan Random Amplified Polymorphism DNA (RAPD). Jurnal Riset Akuakultur 1(2), 211-217.
Nugraha, B. (2009). Studi Tentang Genetika Populasi Ikan Tuna Mata Besar (Thunnus Obesus) Hasil Tangkapan Tuna Longline yang Didaratkan di Benoa. Thesis. Pascasarjana Institut Pertanian Bogor. Bogor.
Permana, G. N; Hutapea, J. H; Haryanti; Sembiring, S. B. M. 2007. Variasi genetik ikan tuna sirip kuning (Thunnus albaceras) dengan analisis elektroforesis allozyme dan mtDNA. Jurnal Riset Akuakultur, 2 (1), 41-50.
Prahadina, V. D; Boer, M; Fahrudin, A. 2015. Resources of Indian Mackerel (Rastrelliger kanagurta Cuvier 1817) in Sunda Strait water that landed on PPP Labuan, Banten. Marine Fisheries, 6 (2 ), 169-175
Prehadi; Sembiring, A; Kurniasih, A. M, Rahmad; Arafat, D; Subhan, B; Madduppa, H. 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.
Rozas, J; Sanchez-DeI Barrio, J. C; Messeguer; Rozas, X. R. (2003). DnaSP, DNA Polymorphism Analyses By the Coalescent and Other Methods. Bioinformatics, 19, 2496-2497.
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, A. R. (1977). DNA sequencing with chain-terminating inhibitors. National Academical Science, United Stated of America, 74 (12), 5463-5467.
Santos, M. D; Lopez, G. V; Barut, N. C. (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.
Sembiring, A; Pertiwi, N. P. D; Mahardini, A; Wulandari, R; Kurniasih, E. M; Kuncoro, A. W; Cahyani, N. K. D; Anggoro, A. W; Ulfa, M; Madduppa, H. H; Carpenter, K. E; Barber, P. H; Mahardika, G. N. 2015. DNA barcoding reveals targeted fisheries for endangered sharks in Indonesia. Fish Res, 164, 130-134.
Shizuka, D; Lyon, B.E. 2008. Improving the reliability of molecular sexing using a W-specific marker. Molecular Ecology Resources (8), 1249-1253.
Sonodihardjo, A. S; Yahya, M. A. 2015. Structure population of Indian Mackerel, Rastrelliger kanagurta Catch in Pancana Waters, Barru District. Jurnal Galung Tropika, 4 (1), 42-49
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. Indian Ocean Tuna Commission, 8 oktober 2013, 1-14 pages.
Susanto, A. H; Suryaningsih, S. 2006. Variasi biokimia genetik ikan betutu (Oxyeleotris marmorata. BLKR) di waduk penjalin Brebes. Jurnal Biota, 11 (3), 136-141.
Suruwaky AM, Gunaisah E. 2013. Identifikasi Tingkat Eksploitasi Sumber Daya Ikan Kembung Lelaki (Rastrelliger kanagurta) Ditinjau dari Hubungan Panjang Berat. Jurnal Akuatika, 4 (2), 131-140
Suwarso. 2002. Variasi geografik dalam struktur genetik populasi ikan kakap merah, Lutjanus malabaricus, (Lutjanidae) dan interaksi lingkungan di Laut Jawa. Thesis. Bogor : Program Pascasarjana, Institut Pertanian Bogor.
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.
Tangke, U. 2014. Pemantaun parameter dinamika populasi ikan Kembung (Rastrelliger sp) di Perairan Pesisir Pulau Ternate Provinsi Maluku Utara. Jurnal Ilmiah agribisnis dan Perikanan, 7 (2), 8-14
Telleng, A. T. R. 2010. Indian Mackerel (Rastrelliger sp.) fisheries on Buyat bay. Maritek, 10 (1), 51-59
Toha, A. H. A; Binur, R; Suhaemi; Lutfi; Hakim; Luchman; Widodo, N; Sumitro, S. B. 2014. Genetic aspects of the commercially used sea Urchin Tripneustes gratilla. A review. Journal of Biological Researches, 20, 12-17
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, 506-513.
Williams, J. G. K; Kubelik, A. R; Livak, K. J; Rafalski, J. A; Tingey, S.V. (1990). DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531-6535.
Zamroni, A; Suwarso; Mukhlis, N. A. 2008. Biologi reproduksi dan genetik populasi ikan Kembung (Rastrelliger brachysoma, Famili Scombridae) di pantai Utara Jawa. Jurnal Penelitian Perikanan Indonesia, 14 (2), 215-226.
Zamroni, A; Suwarso; Kuswoyo, A. 2017. Genetic variation of Indian Mackerel, Rastrelliger kanagurta (Cuvier, 1817) in the waters of Eastern Indonesia. Bawal, 9 (2),123-131
Zardoya, R; Castilho, R; Grande, C; Favre-Krey, L; Caetano, S; Marcato, S; Krey, G; Patarnello, T. 2004. Differential population structuring of two closely related fish species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus), in the Mediterranean Sea. Moleculer Ecology 13,1785-1798
DOI: https://doi.org/10.13170/ajas.7.3.26530
Article Metrics
Abstract view : 0 timesPDF - 0 times
Refbacks
- There are currently no refbacks.
DETAIL VISITORS STATISTIC COUNTER CLICK HERE
This work is licensed under a Creative Commons Attribution - 4.0 International Public License (CC - BY 4.0).