Genetic conservation of two grouper species (Epinephelus) through DNA barcoding in Palu Bay, Indonesia
DOI:
https://doi.org/10.51179/jipsbp.v7i1.2986Kata Kunci:
Conservation, DNA Barcoding, Epinephelinae, GrouperAbstrak
Grouper resources in various Indonesian waters face several issues, primarily due to decreased total catch and overexploitation of stocks. The risk of overfishing can impact genetic diversity. Therefore, understanding the population structure of grouper is crucial as an initial step in identifying potential genetic declines. Information on population structure is obtained through molecular approaches using the Cytochrome Oxidase subunit I as a DNA marker. The research aims to reconstruct the phylogenetics of grouper and analyze their genetic structure in Palu Bay, Central Sulawesi, for genetic conservation purposes. The collected samples consisted of two species from the genus Epinephelus. Fin samples were taken approximately 10 gr and processed for DNA extraction. The extraction method followed the DNeasy Tissue Kits protocol. The extraction results were then analyzed by Polymerase Chain Reaction followed by DNA sequencing using the Sanger dideoxy method. Phylogenetic reconstruction used MEGA X software, while haplotype diversity (Hd), nucleotide diversity (Pi), and fixation index (Fst) analysis used ARLEQUIN 3.1 software. Phylogenetic reconstruction found two different grouper species clades, Epinephelus coioides and E. bontoides. Genetic diversity in E. coioides was found to be moderate, while it was low in E. bontoides. Genetic conservation approaches through hybridization can be applied to both grouper species in Palu Bay as an effort to recover declining genetic resources.
Unduhan
Biografi Penulis
Muh. Saleh Nurdin
Aquatic Resources, Faculty of Animal Husbandry and Fisheries, Tadulako University, Jl. Soekarno Hatta Km. 9, Tondo, Mantikulore, Palu, Sulawesi Tengah, Indonesia
Nur Hasanah
Aquatic Resources, Faculty of Animal Husbandry and Fisheries, Tadulako University, Jl. Soekarno Hatta Km. 9, Tondo, Mantikulore, Palu, Sulawesi Tengah, Indonesia
Novalina Serdiati
Aquatic Resources, Faculty of Animal Husbandry and Fisheries, Tadulako University, Jl. Soekarno Hatta Km. 9, Tondo, Mantikulore, Palu, Sulawesi Tengah, Indonesia
Aswad Eka Putra
Marine Science, Faculty of Animal Husbandry and Fisheries, Tadulako University, Jl. Soekarno Hatta Km. 9, Tondo, Mantikulore, Palu, Sulawesi Tengah, Indonesia
Kasim Mansyur
Aquculture, Faculty of Animal Husbandry and Fisheries, Tadulako University, Jl. Soekarno Hatta Km. 9, Tondo, Mantikulore, Palu, Sulawesi Tengah, Indonesia
Achmad Rizal
Marine Science, Faculty of Animal Husbandry and Fisheries, Tadulako University, Jl. Soekarno Hatta Km. 9, Tondo, Mantikulore, Palu, Sulawesi Tengah, Indonesia
Referensi
Abbas, E. M., Abdelsalam, K. M., Mohammed-Geba, K., Ahmed, H. O., & Kato, M. (2016). Genetic and morphological identification of some crabs from the Gulf of Suez, Northern Red Sea, Egypt. Egyptian Journal of Aquatic Research, 42(3), 319–329. doi: 10.1016/j.ejar.2016.08.003
Achmad, D. S., Gani, S., Ardiansyah, W., Mokoginta, M. M., Nurdin, M. S., Jompa, J., Indrianti, M. A., & Achmad, N. (2022). Population dynamics of reef fish in the Kwandang Bay, Sulawesi Sea, Indonesia. Biodiversitas, 23(10), 5217–5226. doi: 10.13057/biodiv/d231030
Achmad, D. S., Nurdin, M. S., Azmi, F., Indrianti, M. A., Hulukati, E., Jompa, J., Haser, T. F., & Achmad, N. (2023). Species Composition and Growth Pattern of a Multi-Species Grouper in Kwandang Bay, Sulawesi Sea, Indonesia. Jurnal Ilmiah Perikanan Dan Kelautan, 15(1), 31–43. doi: 10.20473/jipk.v15i1.36673
Akbar, N., & Labenua, R. (2020). Genetic Structure Populations Skipjack, Katsuwonus pelamis (Linneaus, 1758) in North Maluku Sea, Indonesia. Jurnal Ilmu Dan Teknologi Kelautan Tropis, 12(2), 409–421. doi: 10.29244/jitkt.v12i2.24274
Alcantara, S. G., & Yambot, A. V. (2016). DNA barcoding of commercially important Grouper species (Perciformes, Serranidae) in the Philippines. Mitochondrial DNA Part A, 27(6), 3837–3845. doi: 10.3109/19401736.2014.958672
Almodóvar, A., Nicola, G. G., Ayllón, D., Leal, S., Marchán, D. F., & Elvira, B. (2023). A Benchmark for Atlantic Salmon Conservation: Genetic Diversity and Structure in a Southern European Glacial Refuge before the Climate Changed. Fishes, 8(6), 321. doi: 10.3390/fishes8060321
Amorim, P., Choat, J. H., Fenessy, S., Law, C., Ma, K., Myers, R., Nair, R. J., Rhodes, K., Sadovy, Y., Samoilys, M., Suharti, S., & To, A. (2018). Epinephelus coioides, Orange-spotted Grouper. The IUCN Red List of Threatened Species 2018: E.T44674A2999451. doi: 10.2305/IUCN.UK.2018- 2.RLTS.T44674A2999451.en
Amorim, P., Sousa, P., Jardim, E., Azevedo, M., & Menezes, G. M. (2020). Length-frequency data approaches to evaluate snapper and grouper fisheries in the Java Sea, Indonesia. Fisheries Research, 229(March), 105576. doi: 10.1016/j.fishres.2020.105576
Andriyono, S., Damora, A., & Hidayani, A. A. (2020). Genetic diversity and phylogenetic reconstruction of grouper (Serranidae) from Sunda Land, Indonesia. Egyptian Journal of Aquatic Biology and Fisheries, 24(3), 403–415. doi: 10.21608/EJABF.2020.92320
Antoro, S., Na-Nakorn, U., & Koedprang, W. (2006). Study of Genetic Diversity of Orange-Spotted Grouper, Epinephelus coioides, from Thailand and Indonesia Using Microsatellite Markers. Marine Biotechnology, 8, 17–26. doi: 10.1007/s10126-005-5026-0
Aziz, N. M. A., Esa, Y., & Arshad, A. (2016). DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene. Journal of Environmental Biology, 37(Special Issue), 725–733.
Basith, A., Abinawanto, A., Kusrini, E., & Yasman, Y. (2021). Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas Journal of Biological Diversity, 22(10), 4282–4290. doi: 10.13057/biodiv/d221020
Basith, A., Abinawanto, Kusrini, E., & Yasman. (2022). DNA Barcode Characterization of Chocolate Hind Grouper (Cephalopholis boenak) in Several Indonesia Waters with the New Sequences Record from Madura Island. HAYATI Journal of Biosciences, 29(6), 733–741. doi: 10.4308/hjb.29.6.733-741
Bawole, R., Mudjirahayu, Rembet, U. N. W. J., Amir, A., Runtuboi, F., & Sala, R. (2018). Exploitation rate of Plectropomus leopardus (Pisces: Serranidae) taken from Rumberpon Island water, Cenderawasih Bay National Park, Indonesia. AACL Bioflux, 11(1), 19–28.
Bemis, K. E., Girard, M. G., Santos, M. D., Carpenter, K. E., Deeds, J. R., Pitassy, D. E., Flores, N. A. L., Hunter, E. S., Driskell, A. C., Macdonald, K. S., Weigt, L. A., & Williams, J. T. (2023). Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens. Scientific Data, 10, 411. doi: 10.1038/s41597-023-02306-9
Benjamin, A., May, B., O’Brien, J., & Finger, A. J. (2016). Conservation Genetics of an Urban Desert Fish, the Arroyo Chub. Transactions of the American Fisheries Society, 145(2), 277–286. doi: 10.1080/00028487.2015.1121925
Bostrom, M. A., Collette, B. B., Luckhurst, B. E., Reece, K. S., & Graves, J. E. (2002). Hybridization between two serranids, the coney (Cephalopholis fulva) and the creole-fish (Paranthias furcifer), at Bermuda. Fishery Bulletin, 100(4), 651–661.
Bravo-Calderon, A., Saenz-Arroyo, A., Fulton, S., Espinoza-Tenorio, A., & Sosa-Cordero, E. (2021). Goliath grouper Epinephelus itajara oral history, use, and conservation status in the Mexican Caribbean and Campeche Bank. Endangered Species Research, 45, 283–300. doi: 10.3354/esr01135
Carlson, S. M., Cunningham, C. J., & Westley, P. A. H. (2014). Evolutionary rescue in a changing world. Trends in Ecology & Evolution, 29(9), 521–530. doi: 10.1016/j.tree.2014.06.005
Chan, W. Y., Hoffmann, A. A., & van Oppen, M. J. H. (2019). Hybridization as a conservation management tool. Conservation Letters, 12(5), e12652. doi: 10.1111/conl.12652
Chang, C., Shao, K., Lin, H., Chiu, Y., Lee, M., Liu, S., & Lin, P. (2017). DNA Barcodes of the native ray‐finned fishes in Taiwan. Molecular Ecology Resources, 17(4), 796–805. doi: 10.1111/1755-0998.12601
Chong-Montenegro, C., & Kindsvater, H. K. (2022). Demographic Consequences of Small-Scale Fisheries for Two Sex-Changing Groupers of the Tropical Eastern Pacific. Frontiers in Ecology and Evolution, 10(March), 850006. doi: 10.3389/fevo.2022.850006
Condini, M. V., García-Charton, J. A., & Garcia, A. M. (2018). A review of the biology, ecology, behavior and conservation status of the dusky grouper, Epinephelus marginatus (Lowe 1834). Reviews in Fish Biology and Fisheries, 28, 301–330. doi: 10.1007/s11160-017-9502-1
Dimarchopoulou, D., Mous, P. J., Firmana, E., Wibisono, E., Coro, G., & Humphries, A. T. (2021). Exploring the status of the Indonesian deep demersal fishery using length-based stock assessments. Fisheries Research, 243(April), 106089. doi: 10.1016/j.fishres.2021.106089
Dwifajri, S., Tapilatu, R. F., Pranata, B., & Kusuma, A. B. (2022). Molecular phylogeny of grouper of Epinephelus genus in Jayapura, Papua, Indonesia inferred from Cytochrome Oxidase I (COI) gene. Biodiversitas, 23(3), 1449–1456. doi: 10.13057/biodiv/d230332
Efendi, D. S., Adrianto, L., Yonvitner, Wardiatno, Y., & Agustina, S. (2020). The economic performance of grouper (Serranidae) and snapper (lutjanidae) fisheries in Saleh Bay, Indonesia. AACL Bioflux, 13(5), 2431–2444.
Excoffier, L., Laval, G., & Schneider, S. (2005). Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1, 117693430500100. doi: 10.1177/117693430500100003
Fadli, N., Damora, A., Muchlisin, Z. A., Dewiyanti, I., Ramadhaniaty, M., Razi, N. M., Jamaluddin, J. A. F., Macusi, E. D., & Siti-Azizah, M. N. (2023). Phylogeographic Insights of Five Co-Habiting Grouper Species in The Indo-Malaya Archipelago. HAYATI Journal of Biosciences, 30(4), 743–756. doi: 10.4308/hjb.30.4.743-756
Fadli, N., Muchlisin, Z. A., & Siti-Azizah, M. N. (2021). DNA barcoding of commercially important groupers (Epinephelidae) in Aceh, Indonesia. Fisheries Research, 234, 105796. doi: 10.1016/j.fishres.2020.105796
Fatma, F., Mallawa, A., Najamuddin, N., Zainuddin, M., & Ayyub, F. R. (2021). A Study of Brown-Marbled Grouper (Epinephelus fuscoguttatus) Population Dynamics in Takabonerate National Park Waters, South Sulawesi, Indonesia. Biodiversitas Journal of Biological Diversity, 22(10), 4298–4307. doi: 10.13057/biodiv/d221022
Ferse, S. C. A., Glaser, M., Neil, M., & Schwerdtner Máñez, K. (2014). To cope or to sustain? Eroding long-term sustainability in an Indonesian coral reef fishery. Regional Environmental Change, 14(6), 2053–2065. doi: 10.1007/s10113-012-0342-1
Fitzpatrick, S. W., Gerberich, J. C., Angeloni, L. M., Bailey, L. L., Broder, E. D., Torres‐Dowdall, J., Handelsman, C. A., López‐Sepulcre, A., Reznick, D. N., Ghalambor, C. K., & Chris Funk, W. (2016). Gene flow from an adaptively divergent source causes rescue through genetic and demographic factors in two wild populations of Trinidadian guppies. Evolutionary Applications, 9(7), 879–891. doi: 10.1111/eva.12356
Frisch, A. J., Cameron, D. S., Pratchett, M. S., Williamson, D. H., Williams, A. J., Reynolds, A. D., Hoey, A. S., Rizzari, J. R., Evans, L., Kerrigan, B., Muldoon, G., Welch, D. J., & Hobbs, J.-P. A. (2016). Key aspects of the biology, fisheries and management of Coral grouper. Reviews in Fish Biology and Fisheries, 26, 303–325. doi: 10.1007/s11160-016-9427-0
Halim, A., Wiryawan, B., Loneragan, N. R., Hordyk, A., Sondita, M. F. A., White, A. T., Koeshendrajana, S., Ruchimat, T., Pomeroy, R. S., & Yuni, C. (2019). Developing a functional definition of small-scale fisheries in support of marine capture fisheries management in Indonesia. Marine Policy, 100(April), 238–248. doi: 10.1016/j.marpol.2018.11.044
Hassanien, H. A., & Al-Rashada, Y. (2021). Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf. Saudi Journal of Biological Sciences, 28(3), 1779–1786. doi: 10.1016/j.sjbs.2020.12.020
Hauser, L., Adcock, G. J., Smith, P. J., Bernal Ramírez, J. H., & Carvalho, G. R. (2002). Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedings of the National Academy of Sciences, 99(18), 11742–11747. doi: 10.1073/pnas.172242899
Hebert, P. D. N., Cywinska, A., Ball, S. L., & DeWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270(1512), 313–321. doi: 10.1098/rspb.2002.2218
Hidayani, A. A., Tasakka, A. C. M. A. R., Umar, W., Alam, M. J., Neogi, A. K., & Andriyono, S. (2022). Low Genetic Diversity Study on Leopard Coral Grouper Plectropomus leopardus (Perciformes: Serranidae) from Sulawesi, Indonesia. Jurnal Ilmiah Perikanan Dan Kelautan, 14(2), 349–359. doi: 10.20473/jipk.v14i2.32815
Huang, W., Liu, Q., Xie, J., Wang, W., Xiao, J., Li, S., Zhang, H., Zhang, Y., Liu, S., & Lin, H. (2016). Characterization of triploid hybrid groupers from interspecies hybridization (Epinephelus coioides ♀ × Epinephelus lanceolatus ♂). Aquaculture Research, 47(7), 2195–2204. doi: 10.1111/are.12672
Iswarya Deepti, V., Kandula, S., & Khedkar, G. D. (2017). DNA barcoding of five species of groupers (Pisces: Serranidae) off Visakhapatnam, central eastern coast of India. Mitochondrial DNA Part A, 29(5), 659–663. doi: 10.1080/24701394.2017.1339188
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. doi: 10.13057/biodiv/d160221
Kamal, M. M., Hakim, A. A., Butet, N. A., Fitrianingsih, Y., & Astuti, R. (2019). Autenthication of the grouper species using MT-COI gene from Peukan Bada waters, Aceh. Jurnal Biologi Tropis, 19(2), 116–123. doi: 10.29303/jbt.v19i2.1245
Kiriyakit, A., Gallardo, W. G., & Bart, A. N. (2011). Successful hybridization of groupers (Epinephelus coioides x Epinephelus lanceolatus) using cryopreserved sperm. Aquaculture, 320(1–2), 106–112. doi: 10.1016/j.aquaculture.2011.05.012
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), 1547–1549. doi: 10.1093/molbev/msy096
Lu, J., Chen, Y., Wang, Z., Zhao, F., Zhong, Y., Zeng, C., & Cao, L. (2023). Larval Dispersal Modeling Reveals Low Connectivity among National Marine Protected Areas in the Yellow and East China Seas. Biology, 12(3), 396. doi: 10.3390/biology12030396
Ma, K. Y., Craig, M. T., Choat, J. H., & van Herwerden, L. (2016). The historical biogeography of groupers: Clade diversification patterns and processes. Molecular Phylogenetics and Evolution, 100, 21–30. doi: 10.1016/j.ympev.2016.02.012
Madduppa, H., Ayuningtyas, R. U., Subhan, B., Arafat, D., & Prehadi. (2016). Exploited but Unevaluated: DNA Barcoding Reveals Skates and Stingrays (Chordata, Chondrichthyes) Species Landed in the Indonesian Fish Market. ILMU KELAUTAN: Indonesian Journal of Marine Sciences, 21(2), 77–84. doi: 10.14710/ik.ijms.21.2.77-84
Madduppa, H., Martaulina, R., Zairion, Z., Renjani, R. M., Kawaroe, M., Anggraini, N. P., Subhan, B., Verawati, I., & Sani, L. M. I. (2021). Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA Implication to sustainable fishery. PLoS ONE, 16(2), e0240951. doi: 10.1371/journal.pone.0240951
Murata, O., Itakura, S., Yamamoto, S., Hattori, N., Kurata, M., Ohta, H., & Masuma, S. (2017). Interspecific hybridization of longtooth grouper Epinephelus bruneus × giant grouper E. lanceolatus and growth of hybrid larvae and juveniles. Aquaculture Science, 65(1), 93–95. doi: 10.11233/aquaculturesci.65.93
Nei, M. (1987). Molecular Evolutionary Genetics. In Columbia University Press. Columbia University Press. doi: 10.7312/nei-92038
Patanda, M., Wisudo, S. H., Monintja, D. R., & Wiryawan, B. (2017). Sustainability for reef fish resource based on productivity and susceptibility in Wangi-Wangi Island, Southeast Sulawesi, Indonesia. AACL Bioflux, 10(4), 861–874.
Petit-Marty, N., Liu, M., Tan, I. Z., Chung, A., Terrasa, B., Guijarro, B., Ordines, F., Ramírez-Amaro, S., Massutí, E., & Schunter, C. (2022). Declining Population Sizes and Loss of Genetic Diversity in Commercial Fishes: A Simple Method for a First Diagnostic. Frontiers in Marine Science, 9, 872537. doi: 10.3389/fmars.2022.872537
Razi, N. M., Muchlisin, Z. A., Maulida, S., Ramadhaniaty, M., Nur, F. M., Damora, A., Buang Manalu, S. L., & Fadli, N. (2021). Grouper DNA barcoding studies in Indonesia: A short review. Depik Jurnal Ilmu-Ilmu Perairan, Pesisir Dan Perikanan, 10(2), 186–193. doi: 10.13170/depik.10.2.21255
Russell, B. (2018). Epinephelus bontoides. The IUCN Red List of Threatened Species 2018: E.T132813A100461359. doi: 10.2305/IUCN.UK.2018-2.RLTS.T132813A100461359.en
Saleky, D., & Dailami, M. (2021). Genetic Conservation of White Snapper Fish (Lates calcarifer, Bloch, 1790) through DNA Barcoding Approach and Phylogenetic Analysis in Kumbe River Merauke Papua. Jurnal Kelautan Tropis, 24(2), 141–150. doi: 10.14710/jkt.v24i2.10760
Sarhan, M., Azab, A. M., Khalaf-Allah, H. M. M., & Afifi, M. A. M. (2019). DNA barcoding supports sexual dimorphism in two Labrid species; Cheilinus lunulatus and Halichoeres hortulanus (Family Labridae) in Red Sea, Egypt. Egyptian Journal of Aquatic Research, 45(4), 395–401. doi: 10.1016/j.ejar.2019.10.002
Suryani, S. A. M. P., & Arya, I. W. (2019). Genetic diversity of three sunu groupers species (Plectropomus spp). Journal of Physics: Conference Series, 1402, 033063. doi: 10.1088/1742-6596/1402/3/033063
Tapilatu, R. F., Tururaja, T. S., Sipriyadi, & Kusuma, A. B. (2021). Molecular phylogeny reconstruction of grouper (Serranidae: Epinephelinae) at northern part of bird’s head seascape-Papua inferred from COI gene. Fisheries and Aquatic Sciences, 24(5), 181–190. doi: 10.47853/FAS.2021.e18
Vega‐Trejo, R., Head, M. L., & Jennions, M. D. (2015). Evidence for inbreeding depression in a species with limited opportunity for maternal effects. Ecology and Evolution, 5(7), 1398–1404. doi: 10.1002/ece3.1445
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1847–1857. doi: 10.1098/rstb.2005.1716
Yang, K., Lin, H., Liu, R., & Ding, S. (2022). Genetic Structure and Demographic History of Yellow Grouper (Epinephelus awoara) from the Coast of Southeastern Mainland China, Inferred by Mitochondrial, Nuclear and Microsatellite DNA Markers. Diversity, 14, 439. doi: 10.3390/d14060439
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