* Corresponding Author
The Molecular Study on the Identity, Genetic Composition, and Phylogenetic Relationships of Carcharhinus (Blainville, 1816) Sharks in the Western Waters of Aceh
https://doi.org/10.22146/jfs.111404 Samsul Bahri(1*), Arina Ruzanna(2), Burhanis Burhanis(3)
(1) Department of Marine Sciences, Faculty of Fisheries and Marine Sciences, Teuku Umar University, West Aceh Regency, Aceh, Indonesia
(2) Department of Marine Sciences, Faculty of Agriculture, Malikussaleh University, North Aceh, Aceh, Indonesia
(3) Department of Marine Sciences, Faculty of Fisheries and Marine Sciences, Teuku Umar University, West Aceh Regency, Aceh, Indonesia
(*) Corresponding Author
Abstract
The shark genus Carcharhinus faces high exploitation pressure in the Western Waters of Aceh, while comprehensive genetic data to support conservation remains limited. This study aimed to identify species, analyze nucleotide composition, and reconstruct the phylogenetic relationships of Carcharhinus sharks using the Cytochrome c oxidase subunit I (COI) gene as a molecular marker. A total of 14 tissue samples were collected from three fish landing sites: Aceh Jaya, West Aceh, and Southwest Aceh. Standard procedures included DNA extraction, PCR amplification, sequencing, and bioinformatic analysis using BLAST for identification and MEGA for phylogenetic analysis via the Neighbor-Joining method. Molecular identification successfully confirmed the presence of six species: Carcharhinus falciformis (n=7), C. sorrah (n=3), C. brevipinna (n=1), C. amboinensis (n=1), C. amblyrhynchos (n=1), and C. limbatus (n=1), with identity matches ranging from 99.23-100%. Nucleotide composition analysis revealed a consistent bias towards Adenine and Thymine bases (AT-rich), a common characteristic of the elasmobranch mitochondrial genome. The reconstructed phylogenetic tree demonstrated that each species formed a solid monophyletic group with high bootstrap support. The analysis also confirmed C. brevipinna and C. amboinensis as sister taxa. No clear geographic population structure was found for widespread species, indicating high population connectivity within these waters. This molecular baseline data is crucial for supporting evidence-based fisheries management and conservation strategies for threatened shark species in Indonesia.
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Aisyah, S., R. Hidawati, O. Supratman & A.F. Syarif. 2020. DNA barcoding and conservation status of sharks (Hemiscylliidae and Charcharhinidae) landed at the Sungailiat Bangka PPN. JFMR (Journal of Fisheries and Marine Research). 4 (3): 316-323. https://doi.org/10.21776/ub.jfmr.2020.004.03.1
Altschul, S.F., W. Gish, W. Miller, E.W. Myers & D.J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology. 215 (3): 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
Ambon, A.N., M.A. Rizal & R.A. Harahap. 2020. Sex ratio and size composition of hammerhead sharks (Sphyrna lewini) caught in Aceh waters, Indonesia. Scientific Journal of Fisheries and Marine. 12 (2): 165-171. https://doi.org/10.20473/jipk.v12i2.21396
Astuti, R., Y. Wardiatno & S. Haryani. 2017. Molecular identification of shark species using DNA barcoding approach in Central Java, Indonesia. Journal of Biodiversity. 18 (4): 1435-1441. https://doi.org/10.13057/biodiv/d180436
Bahri, S., H. Hafinuddin & N. Hikmah. 2023. Molecular analysis and status of shark populations landed at West Aceh Fishing Port. Enggano Journal. 8 (1): 37-44. https://doi.org/10.31186/j.enggano.8.1.37-44
Bonfil, R. 2008. The biology and ecology of the silky shark, Carcharhinus falciformis. Sharks of the Open Ocean: Biology, Fisheries and Conservation. 10: 114-127. https://doi.org/10.1002/9781444302516.ch10
Chin, A., C.A. Simpfendorfer & T.L. Werry. 2020. The ecological role of sharks in coral reef ecosystems: A review. Coral Reefs. 39 (3): 567-580. https://doi.org/10.1007/s00338-020-01931-1
Chythanya, R., I. Karunasagar & I. Karunasagar. 2002. Inhibition of shrimp pathogenic vibrios by a marine Pseudomonas I-2 strain. Aquaculture. 208 (1-2): 1-10. https://doi.org/10.1016/S0044-8486(01)00714-1
Clarke, B.M., T.G. Baker, E.C. Macaya & B.S. Stewart. 2020. Optimizing tissue preservation for environmental DNA analysis. Environmental DNA. 2 (3):424–434.
Dedman, S., G. Cliff & P. D'Arcy. 2024. Ecological roles and importance of sharks in the Anthropocene Ocean. Fish and Fisheries. 25 (4): 519-536. https://doi.org/10.1111/faf.12879
Dharmadi, D., A. Wujdi & S. Surbakti. 2021. Current status of shark and ray fisheries in Indonesia: A review. IOP Conference Series: Earth and Environmental Environment. 941 (1). 012028. https://doi.org/10.1088/1755-1315/941/1/012028
Dharmadi, D., F. Fahmi & F. Satria. 2016. Fisheries management and conservation of sharks in Indonesia. Indonesian Journal of Ichthyology. 16 (1): 1-13. https://doi.org/10.32439/jii.v16i1.1
Dulvy, N. K., C.A. Simpfendorfer & P.M. Kyne. 2021. The conservation status of the world's sharks, rays, and chimaeras. Science. 372 (6537): eabc0474. https://doi.org/10.1126/science.abc0474
Fahmi, F & A. Sumiarsa. 2017. Catch composition and some biological aspects of sharks in Western Sumatra Waters of Indonesia. Journal of Oceanography. 13 (2): 99-108. https://doi.org/10.15578/js.v13i2.6074
Felsenstein, J. 985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39 (4): 83-791. https://doi.org/10.2307/2408640
Ferizal, M., P. Nurani & N.N. Fitriana. 2025. Preliminary study of shark identification and conservation status in Tukak Waters, South Bangka. Journal of Equatorial Seas. 8 (1): 47–55. https://doi.org/10.26418/jlk.v8i1.88263
Ferretti, F., B. Worm & M.R. Heithaus. 2015. Ecological and conservation insights from shark populations. Ecology Letters. 18 (9): 922-934. https://doi.org/10.1111/ele.12450
Galván-Tirado, C., F. Galván-Magaña & R.I. Ochoa-Báez. 2015. Reproductive biology of the silky shark Carcharhinus falciformis in the Southern Mexican Pacific. Journal of the Marine Biological Association of the United Kingdom. 95 (3): 561-567. https://doi.org/10.1017/S0025315414001970
Hanner, R.H., M. Shivji & A. Fields. 2016. DNA barcoding of threatened sharks in the global shark fin trade. Conservation Genetics Resources. 8 (2): 297-302. https://doi.org/10.1007/s12686-015-0453-2
Harahap, R.A., S. Syahrir & I. Irwan. 2024. The effect of chlorophyll-a and sea surface temperature on shark catches in West Aceh waters, Indonesia. Scientific Journal of Fisheries and Marine. 16 (1): 1-8. https://doi.org/10.20473/jipk.v16i1.40871
Hebert, P.D.N., A. Cywinska, S.L. Ball & J.R. deWaard. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences. 270 (1525): 313–321. https://doi.org/10.1098/rspb.2002.2218
Heupel, M.R., J.K. Carlson & C.A. Simpfendorfer. 2007. Shark nursery areas: Concepts, definition, characterization and assumptions. Marine Ecology Progress Series. 337: 287-297. https://doi.org/10.3354/meps
Iqbal, M., M. Arifin & F.T. Imanto. 2020. The presence of bull shark Carcharhinus leucas (Elasmobranchii: Carcharhinidae) in the fresh waters of Sumatra, Indonesia. Biodiversity Journal of Biological Diversity 21 (10): 4509-4515. https://doi.org/10.13057/biodiv/d211026
Jabado, R.W., P.M. Kyne & N.K. Dulvy. 2022. Threats, conservation, and research needs for the carcharhinid sharks. Reviews in Fish Biology and Fisheries. 32 (1): 227-254. https://doi.org/10.1007/s11160-022-09727-x
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution. 16 (2): 111-120. https://doi.org/10.1007/BF01731581
Kottillil, S., C. Rao & B.W. Bowen. 2023. Phylogeography of sharks and rays: A global review based on life history traits and biogeographic partitions. Journal of Fish Biology. 103 (1): 23-45. https://doi.org/10.1111/jfb.15405
Kousteni, V., S. Mazzoleni, K. Vasileiadou & M. Rovatsos. 2021. Complete mitochondrial DNA genome of nine species of sharks and rays and their phylogenetic placement among modern elasmobranchs. Genetics. 12 (3): 324. https://doi.org/10.3390/genes12030324
Kumar, S., G. Stecher, M. Li, C. Knyaz & K. Tamura. 2018. MEGA X: Molecular evolutionary genetics analysis across platforms. Molecular Biology and Evolution. 35 (6): 1547–1549. https://doi.org/10.1093/molbev/msy096
MacFaddin, J.F. 1980. Biochemical Test for Identification of Medical Bacteria. Second Edition. Williams & Wikins. Baitimore/ London. 370-389 pp.
Momigliano, P., R. Harcourt, W.D. Robbins & A. Stow. 2015. Connectivity in grey reef sharks (Carcharhinus amblyrhynchos) determined using empirical and simulated genetic data. Scientific Reports. 5 (1): 13229. https://doi.org/10.1038/srep13229
Naylor, G.J., J.N. Caira, K. Jensen, K.A. Rosana, N. Straube & C. Lakner. 2012. Elasmobranch phylogeny: A mitochondrial estimate based on 595 species. Biology of sharks and their relatives. 2: 31-56. Biology of Sharks and Their Relatives
Pramudji, A., D. Dharmadi & A. Widodo. 2021. Growth and mortality of grey reef shark Carcharhinus amblyrhynchoides in Makassar Strait, Indonesia. Indonesian Journal of Ichthyology. 21 (3): 227-238. https://doi.org/10.32439/jii.v21i3.1091
Prehadi, P., A. Sembiring, E.M. Kurniasih, D. Arafat, B. Subhan & H.H. Madduppa. 2015. DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port. Biodiversity: Journal of Biological Diversity. 16 (1): 55-61. https://doi.org/10.13057/biodiv/d160109
Saghai-Maroof, M.A., K.M. Soliman, R.A. Jorgensen & R.W. Allard. 1984. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences. 81 (24): 8014–8018. https://doi.org/10.1073/pnas.81.24.8014
Sahaba, A.M., S. Sadiyah, D. Nurcahyanti & N.N. Fitriana. 2022. DNA Barcoding for the authentication of fresh shark products from West Nusa Tenggara waters. Journal of Indonesian Fishery Product Processing. 25 (2): 426-435. https://doi.org/10.17844/jphpi.v25i2.38318
Saputra, R., A. Alfi & N. Nurdin. 2023. Molecular identification of sharks and rays species from Aceh waters, Indonesia. Depik Journal of Aquatic, Coastal and Fisheries Sciences. 12 (1): 1-10. https://doi.org/10.13170/depik.12.1.29136
Saputra, R., V.T. Manurung, K. Khairunnisa & F. Lubis. 2024. The first report of DNA barcoding of commercially important fish in Nias Islands, Indonesia. Biodiversity: Journal of Biological Diversity. 25 (2): 795-802. https://doi.org/10.13057/biodiv/d250210
Sembiring, A., N.P.D. Pertiwi, A. Mahardini, R. Wulandari, E.M. Kurniasih, A.W. Kuncoro & G.N. Mahardika. 2015. DNA barcoding reveals targeted fisheries for endangered sharks in Indonesia. Fisheries Research. 164: 130-134. https://doi.org/10.1016/j.fishres.2014.11.003
Shah, A.F. 2021. The role of the government in shark protection in Indonesia. Journal of Law and Humanities. 3 (2): 145-156. https://doi.org/10.14710/jihh.v3i2.11210
Shiffman, D.S & C. Philipp. 2016. Contemporary shark fisheries and their implications for conservation. Reviews in Fish Biology and Fisheries. 26 (3): 449-470. https://doi.org/10.1007/s11160-016-9430-y
Shivji, M.S., S. Clarke & M. Rechi. 2002. Genetic identification of shark body parts for conservation and fisheries management. Conservation Biology. 16 (5): 1083-1097. https://doi.org/10.1046/j.1523-1739.2002.01188.x
Simeon, B.M., I. Fajri, S. Ula, E. Muttaqin, M. Ichsan, D.A. Dharmadi & A. Sarong. 2020. Technical report on monitoring shark and ray catches in Aceh Province. Wildlife Conservation Society.
Utama, N.P., A. Sembiring & A. Purbayanto. 2018. Genetic diversity of grey reef shark (Carcharhinus amblyrhynchos) in Seribu Islands, Indonesia using mitochondrial DNA COI gene. Journal of Marine Science. 23 (3): 105-112. https://doi.org/10.14710/jik.v23i3.10998
Utami, N.A.N., A. Sembiring & Z. Rabbani. 2021. Population parameters of kejen shark (Carcharhinus falciformis) in the Southern Waters of West Nusa Tenggara. Journal of Fisheries Research. 13 (2): 99-108. https://doi.org/10.15578/bawal.v13i2.5939
Varela, P.R., A.A. Luque & M.I. Roldán. 2016. Present and future potential habitat distribution of Carcharhinus falciformis and Canthidermis maculata by-catch species in the tropical tuna purse-seine fishery under climate change. Frontiers in Marine Science. 3: 34. https://doi.org/10.3389/fmars.2016.00034
Varela, P.R., F.J. Abascal & M.I. Roldán. 2022. Evaluation of shifts in the potential future distributions of carcharhinid sharks under different climate change scenarios. Frontiers in Marine Science. 8: 745501. https://doi.org/10.3389/fmars.2021.745501
Vélez-Zuazo, X & I. Agnarsson. 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular phylogenetics and evolution. 58 (2): 207-217. https://doi.org/10.1016/j.ympev.2010.11.018
Ward, R.D., T.S. Zemlak, B.H. Innes, P.R. Last & P.D. Hebert. 1847. DNA barcoding Australia's fish species. Philos. TR Soc. B. 2005. 360: 1847-1857. https://doi.org/10.1098/rstb.2005.1716
Wardiatno, Y., F. Fahmi, H. Yulianto & E.M. Kurniasih. 2023. DNA barcoding of six commercially important groupers (Epinephelidae) from Langsa, Aceh, Indonesia. HAYATI Journal of Biosciences. 30 (4): 540-549. https://doi.org/10.4308/hjb.30.4.540-549
Wiryawan, B., D. Simbolon, T. Ruchimat, R. Saputra & M. Riyanto. 2024. Conservation status and diversity of shark species landed at Tanjung Luar Fishing Port, West Nusa Tenggara Province, Indonesia. Aquaculture, Aquarium, Conservation & Legislation. 17 (6): 3086-3100. https://bioflux.com.ro/docs/2024.3086-3100.pdf
Wong, E.H.K & R.H. Hanner. 2012. DNA barcoding of commercially important fish in and around Singapore. Journal of Fish Biology. 80 (1): 38-48. https://doi.org/10.1111/j.1095-8649.2011.03149.x
Wulandari, E., R. Kurnia & M.A. Handayani. 2021. Economic value of shark fisheries in Cilacap, Indonesia. Indonesian Aquaculture Journal. 20 (2): 121-129
Yusri, Y., M. Mahfud & Z. Zulfahmi. 2022. Long-term relationship with weight and shark diversity index landed at PPI Rigaih, Aceh Jaya Regency. Journal of Aceh Aquatic Science. 3 (1): 47-56. https://doi.org/10.53696/jaas.v3i1.47-56
How to Cite this Article:
Bahri, S., A. Ruzanna & B. Burhanis. 2025. The molecular study on the identity, genetic composition, and phylogenetic relationships of Carcharhinus (Blainville, 1816) sharks in the Western Waters of Aceh. Jurnal Perikanan Universitas Gadjah Mada. 27 (2): xx-xx. https://doi.org/10.22146/jfs.111404
DOI: https://doi.org/10.22146/jfs.111404
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