KERAGAMAN GENETIK KIMA KECIL (Tridacna maxima) DI PULAU KUR, PULAU BIAK, DAN MANADO SERTA IMPLIKASINYA UNTUK KONSERVASI
Abstract
Kima merupakan jenis kerang yang secara ekologis penting pada ekosistem terumbu karang. Biota laut ini mengalami tekanan antropogenik hampir di sebagian besar wilayah Indonesia. Meskipun status spesies kima ini dilindungi berdasarkan Peraturan Pemerintah (PP) No. 7 tahun 1999, namun aktivitas pengambilan ilegal kima di alam masih terjadi. Hal ini tidak hanya menyebabkan penurunan jumlah jenis dan kelimpahan individu, tetapi dapat mengurangi keragaman genetik jenis kima tersebut. Oleh karena itu perlu dilakukan penelitian keragaman genetik Tridacna maxima berdasarkan marka genetik COI dari Pulau Kur, Pulau Biak dan Manado. Penelitian menggunakan 15 sampel dari Pulau Kur (Penelitian ini), kemudian dibandingkan dengan data genbank (11 sampel dari Biak dan 8 sampel dari Manado). Analisis sekuens DNA mitokondria (mtDNa) T. maxima menghasilkan 432 pasang basa. Terdapat 23 haplotipe dengan jumlah situs bervariasi sebanyak 59 situs. Hasil penelitian menunjukkan bahwa keragaman genetik populasi T. maxima termasuk sangat tinggi, yaitu 0,95. Jarak genetik antar populasi, berkisar antara 0,009 (Kur-Manado) sampai 0,051 (Biak-Manado). Hasil analisis pohon filogenetik menunjukkan dua kluster utama, yaitu kluster Kur, Biak, dan Manado, dan kluster Biak. Hasil analis Fst berpasangan menunjukkan perbedaan struktur genetik yang signifikan pada populasi T. maxima di Kur dengan Biak (Fst = 0,558; p = 0,000) dan Manado dengan Biak (Fst = 0,427; p = 0,012), sedangkan populasi Kur dan Manado tidak menunjukkan perbedaan genetik yang signifikan (Fst = 0,087; p = 0,064). Upaya Konservasi pada populasi T. maxima di Pulau Kur dapat dilakukan melalui penerapan konservasi sumber daya alam dalam bentuk kearifan lokal berupa sasi yang diperkuat dengan pembentukan kawasan konservasi laut daerah (KKLD) di lokasi penelitian. sedangkan untuk populasi Manado dan biak adalah penetapan wilayah konservasi. Selain itu, upaya pengawasan dan penegakan hukum terhadap aktifitas perburuan liar perlu ditingkatkan agar upaya konservasi tersebut dapat berhasil sehingga populasi kima tetap lestari.
Giant clams are ecologically important bivalves in coral reefs. These marine organisms have been under anthropogenic pressures in almost all part of Indonesia. Even though this species is protected under Government Regulation (PP) No. 7, 1999, but the illegal harvesting is still happened. This not only caused the declining the number of individual and species, but also could lead to a decrease the genetic diversity of this species. Therefore, it is necessary to conduct research on the genetic diversity of Tridacna maxima based on COI genetic markers from Kur Island, Biak Island and Manado. The study used 15 samples T. maxima from Kur Islan (This study) then compared with genbank data (11 samples from Biak and 8 samples from Manado). Sequence analysis of mitochondrial (mt) DNA T. maxima resulted 432 base pairs, which contained 23 haplotypes with total numbers of 59 polymorphic sites. The results show that genetic diversity of the T. maxima population was very high (0.95). The genetic distance between populations in this study ranged from the lowest (0,009) for Kur vs Manado to the highest (0,043) for Biak vs Manado. The filogenetic tree showed that there were two main clades, i.e. 1) T. maxima calde of Kur, Biak, and Manado and 2) T. maxima clade of Biak. The pairwise method analysis (FST) showed a significant genetic structure in the population of T. maxima in Kur with Biak (Fst = 0.558; p = 0.000) and Manado with Biak (Fst = 0.427; p = 0.012), whereas there was relatively no significant differentiation within population in Kur and Manado (Fst = 0.087; p = 0.064). The conservation effort for T. maxima population in Kur island is prioritized by implementing the local wisdom called Sasi with strengthened by the formation of regional marine conservation area on research sites.
Keywords
Full Text:
PDFReferences
Allentoft, M. E., & O’Brien, J. (2010). Global Amphibian Declines, Loss of Genetic Diversity and Fitness: A Review. Divers. 2: 47-71. doi: 10.3390/d2010047.
Ambariyanto, A. (2007). Pengelolaan kima di Indonesia: Menuju budidaya berbasis konservasi. Dalam: Ambariyanto, A. (ed.). Penelitian, Konservasi Dan Ekonomi (pp. 1-11). Semarang: Prosiding Seminar Nasional Moluska.
Bahri, S. (2017). Struktur populasi dan keragaman genetik penyu lekang (Lepidochelys olivacea) dan kaitannya dengan sirkulasi arus di Indonesia. Thesis. Institut Pertanian Bogor.
Beckvar, N. (1981). Cultivation, spawning and growth of the giant clams Tridacna gigas, Tridacna derasa and Tridacna squamosa in Palau, Caroline Islands. Aquaculture. 24: 21-30.
Ben Othmen, A., Abhary, M., Deli, T., Ouanes, Z., Alhuwaiti, N., Dimassi, N., & Mansour, M. (2020). Lack of mitochondrial genetic structure in the endangered giant clam populations of Tridacna maxima (Bivalvia: Cardiidae: Tridacninae) across the Saudi Arabian coast. Acta Oceanol Sin. 39 (2): 28–37. doi: 10.1007/s13131-020-1547-7....
Benzie, J. A. H., & Williams, S. T. (1992a). Genetic structure of giant clam (Tridacna maxima) populations from reefs in the Western Coral Sea. Coral Reefs. 11(3): 135–141, doi: 10.1007/BF00255467.
Benzie, J. A. H., & Williams S T. 1992b. No genetic differentiation of giant clam (Tridacna gigas) populations in the Great Barrier Reef, Australia. Marine Biology. 113(3): 373–377, doi: 10.1007/BF00349161.
Bonde, R. K., Mc Guire, P. M., & Hunter, M. E. (2012). A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations. JMATE. 5 (1) : 8-19.
Cabaitan, P.C., Gomez, E.D., & Alino, P.M. (2008). Effects of coral transplantation and giant clam restocking on the structure of fish communities on degraded patch reefs. Journal of Experimental Marine Biology and Ecology, 357 (1): 85–98. doi:10.1016/j.jembe.2008.01.001.
Chiu, Y., Bor, H., Tan, M., Lin, H., & Jean, C. (2013). Phylogeography and Genetic Differentiation among Populations of the Moon Turban Snail Lunella granulata Gmelin. 1791 (Gastropoda: Turbinidae). Int J Mol Sci. 14: 9062-9079. doi: 10.3390/ijms14059062.
Crispo, E., & Chapman, L. J. (2008). Population genetic structure across dissolved oxygen regimes in an African cichlid fish. Mol Ecol. 17: 2134–2148. doi: 10.1111/j.1365-294X.2008.03729.x.
Deboer, T. S., Subia, M. D., Ambariyanto, Erdmann, M. V., Kovitvongsa, K., & Barber, P. H. (2008). Phylogeography and limited genetic connectivity in the endangered boring giant clam across The Coral Triangle. Conservation Biology. 22 (5): 1255-1266. doi: 10.1111/j.1523-1739.2008.00983.x.
Deboer, T. S., Naguit, M. R. A., Erdmann, M. V., Ablan-Lagman, M. C. A., Carpenter, K. E., Toha, A. H. A., & Barber, P. H. (2014). Concordant phylogenetic patterns inferred from mitochondrial and microsatellite DNA in the giant clam Tridacna crocea. Bulletin of Marine Science. 90: 301–329. doi: 10.5343/bms.2013.1002.
Excoffier, L., & Lischer, H. E. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetic analysis under Linux and Windows. Mol. Ecol. Resour. 10: 564–567. doi: 10.1111/j.1755-0998.2010.02847.x.
Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of moleculer variance inferred from metric distance among DNA haplotipes; application to human mitochondrial DNA restriction data. Genetics (131): 479-491.
Fauvelot, C., Bernardi, G., & Planes, S. (2003). Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change. Evolution. 57: 1571"1583. doi: 10.1554/02-173.
Findra, M.N., Setyobudiandi, I., Butet, N.A., & Solihin, D.D. (2017). Genetic profile assessment of giant clam genus Tridacna as a basis for resource management at Wakatobi National Park Waters. ILMU KELAUTAN: Indonesian Journal of Marine Sciences, 22(2): 67-74. doi:10.14710/ik.ijms.22.2.67-74.
Fitt, W. K. (1991). Mariculture of giant clams. In: Menzel, W. (ed) Estuarine and marine bivalve mollusk culture. Florida (US): CRC Press.
Fu, Y. X. (1997). Statistical test of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147: 915"925.
Gordon, A. L., & Fine, R. A. (1996). Pathway of water between the Pasific and Indian Oceans in the Indonesia seas. Nature. 379: 146-149. doi:10.1038/379146a0.
Hamilton, M. B. (2009). Population Genetics. NJ: John Wiley & Sons, Ltd Publication.
Hasni, Sadarun B, Ira. (2017). The diversity and density of giant clam in Wawosunggu Island waters, South Konawe. Sapa Laut. 2(4): 113-118.
Harahap SA, Yanuar Y, Ilham Y. (2018). Diversity and abundance of giant clams in Anambas Islands, Indonesia. E3S Web of Conferences 47: 1-9. doi:10.1051/e3sconf/20184703005.
Hedgecock, D. (1986). Is gene flow from pelagic larval dispersal important in the adaptation and evolution of marine invertebrates?. Bulletin of Marine Science. 39 (2): 550"564.
Hedgecock, D., Barber, P.H., & Edmands, S. (2007). Genetic approaches to measuring connectivity. Oceanography. 20 (3): 70-79. doi: 10.5670/oceanog.2007.30.
Hernawan, U. E. (2008). Symbiosis between the giant clams (Bivalvia: Cardiidae) and zooxanthellae (Dinophyceae). Biodiversitas. 9(1): 53-58. doi: 10.13057/biodiv/d090113
Hernawan, U. E. (2010). Study on giant clams (Cardiidae) population in Kei Kecil waters, Southeast Maluku. Widyariset. 13 (3): 101-108. doi: 10.14203/widyariset.13.3.2010.101–108.
Huffard, C.L., Erdmann, M.V., & Gunawan, T. (2012). Defining geographic priorities for marine biodiversity conservation in Indonesia. Jakarta: Conservation Internasional.
Hughes, A. R., Inouye, B. D., Johnson, M. T. J., Underwood, N., & Vellend, M. (2008). Ecological consequences of genetic diversity. Ecology Letters. 11: 609-623. doi: 10.1111/j.1461-0248.2008.01179.x.
Hui, M., Kraemer, W. E., Seidel, C., Nuryanto, A., Joshi, A., & Kozhius, M. (2016). Comparative genetic population structure of three endangered giant clams (Cardiidae: Tridacna species) throughout the Indo-West Pacific: Implications for divergence, connectivity and conservation. Journal of Molluscan studies 2 (3): 403-414. doi: 10.1093/mollus/eyw001.
Jameson SC (1976) Early life history of the giant clams Tridacna crocea Lamarck, Tridacna maxima (Röding), and Hippopus hippopus (Linnaeus). Pac Sci. 30:219–233.
Jena, S. N., Srivastava, A., Singh, U. M., Roy, S., Banerjee, N., Rai, K. M., … Sawant, S.V. (2011). Analysis of genetic diversity, population structure and linkage disequilibrium in elite cotton (Gossypium L.) germplasm in India. Crop & Past Sci. 62: 859–875. doi: 10.1071/CP11161.
Keller, L. F., & Waller, D. M. (2002). Inbreeding effects in wild populations. TREE. 17:230-241. doi: 10.1016/S0169-5347(02)02489-8.
Kochzius, M., & Nuryanto, A. (2008). Strong genetic population structure in the boring giant clam, Tridacna crocea, across the Indo-Malay Archipelago: implications related to evolutionary processes and connectivity. Moleculer Ecology, 17 (17): 3775–3787. doi:10.1111/j.1365-294X.2008.03803.x.
Kombong, C.B. S., & Arisuryanti, T. (2018). Komposisi nukleotida sekuen gen mitokondria 16s dan coi ikan gabus (Channa striata Bloch,1793) dari Danau Sentani, Jayapura, Papua. Jurnal Perikanan Universitas Gadjah Mada, 20 (2): 57-62. doi: 10.22146/jfs.35551.
Launey, S., & Hedgecock, D. (2001). High genetic load in the Pacific oyster Crassostrea gigas. Genetics. 159: 255–265.
Lucas, J.S. (1988). Giant clams: description, distribution, and life-history. In: Copland, J. W., & Lucas, J. S. (eds.), Giant clams in Asia and the Pasific. Canberra (AU): ACIAR Monograph 9.
Madduppa, H. H., Timm, J., & Kochzius, M. (2018). Reduced genetic diversity in the clown anemonefifish Amphiprion ocellaris in exploited reefs of Spermonde Archipelago, Indonesia. Front. Mar. Sci. 5 (80): 1-8. doi: 10.3389/fmars.2018.00080.
Mies, M., & Sumida, P. Y. G. (2012). Giant clam aquaculture: a review on induced spawning and larval rearing. Int’l Journal of Marine Science. 2 (9): 62-69. doi: 10.5376/ijms.2012.02.0009.
Macaranas, J. M., Ablan, C. A., Pante, M. J. R., Benzie, J. A. H., Williams, S. T. (1992). Genetic structure of giant clam (Tridacna derasa) populations from reefs in the Indo-Pacific. Marine Biology.113(2): 231–238. doi:10.1007/BF00347276.
Mohamed, N.A., Yu, Q., Chanfi, M. I., Li, Y., Wang, S., Bao, Z., & Huang, X. (2016). Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers. Springer Plus. 5 (1852): 1-7. doi: 10.1186/s40064-016-3513-6.
Naguit, M. R. A., Tisera, W. L., & Calumpong, H. P. (2012). Ecology and genetic structure of giant clams around Savu Sea, East Nusa Tenggara Province, Indonesia. Asian Journal of Biodiversity. 3: 174–194. doi: 10.7828/ajob.v3i1.89.
Nei, M. (1972). Genetic distance between population. Am Nat. 106 (949): 283-292.
Nei, M. (1987). Moleculer evolutionary genetics. New York: Columbia University Press.
Nei, M., & Jin, L. (1989). Variances of the average numbers of nucleotides substitutions within and between populations. Mol Biol Evol. 6: 290-300.
Neo, M. L., Eckman, W., Vicentuan, K., Teo, S. L. M., & Todd, P. A. (2015). The ecological significance of giant clams in coral reef ecosystems. Biological Conservation, 181 (2015):111–23. doi: 10.1016/j.biocon.2014.11.004.
Neo, M.L., Liu, L. L., Huang, D., & Soong, K. (2018). Thriving population with low genetic diversity in giant clam species Tridacna maxima and Tridacna noae, at Dongsha Atoll, South China Sea. Regional Studies in Marine Science. 24: 278-287. doi: 10.1016/j.rsma.2018.09.001.
Nuryanto, A., Duryadi, D., Soedharma, D., & Bloom, D. (2007). Molecular phylogeny of giant clams based on mitochondrial DNA cytochrome c oxidase I gene. HAYATI Journal of Biosciences. 14 (4): 162-166. doi:10.4308/hjb.14.4.162.
Prehadi, P., Sembiring, A., Kurniasih, E.M., Rahmad, R., Arafat, D., Subhan, B., & Madduppa, H.H. (2015). DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port. Biodiversitas. 16(1):55–61. doi: 10.13057/biodiv/d160107.
Rizkifar, M. A., Ihsan, Y. N., Hamdani, H., & Sunarto. (2019). Kepadatan dan preferensi habitat kima (Tridacnidae) di perairan Pulau Semak Daun Provinsi DKI Jakarta. Jurnal Perikanan dan Kelautan. 10 (1): 74-83.
Rozas, J. J., Sanchez-DelBarrio, C., Messequer, X., & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19: 2496-2497.
Selkoe, K. A., Henzler, C. M., & Gaines, S. D. (2008). Seascape genetics and the spatial ecology of marine populations. Fish and Fisheries. 9: 363"377. doi: 10.1111/j.1467-2979.2008.00300.x.
Soo, P., & Todd, P. A. (2014). The behaviour of giant clams (Bivalvia: Cardiidae: Tridacninae). Mar Biol. 161: 2699–2717. doi: 10.1007/s00227-014-2545-0.
Spalding, M.D., Fox, H.E., Allen, G.R., Davidson, N., Ferdana, Z.A., Finlayson, M.,… Robertson, J. (2007). Marine ecoregion of the world: a bioregionalization of coastal and shelf areas. Bioscience. 57 (7): 573-583. doi:10.1641/B570707.
Tajima, F. (1989). Statistical method for testing neutral mutation hypothesis by DNA polymorphism. Genetics. 123: 585"595.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30(12):2725-2729. doi: 10.1093/molbev/mst197.
Toha, A.H.A., Widodo, N., Hakim L., & Sumitro, S.B. (2015). Sekilas tentang mutasi. Kons. Biod. Raja Ampat. 7: 9-13.
Toro, M.A., Meuwissen, T.H.E., Ferna´ndez, J., Shaat, I., & ki-Tanila A.M. (2011). Assessing the genetic diversity in small farm animal populations. Animal, page 1 of 15 & The Animal Consortium 2011. doi:10.1017/ S1751731111000498.
Triandiza, T., & Kusnadi, A. (2013). Induced spawning and larval rearing technique of scaly clams (Tridacna squamosa lamarck) in the laboratory. OLDI. 39 (1): 1-11.
Triandiza, T., Zamani, N. P., Madduppa, H., & Hernawan, UE. (2019). Distribution and abundance of the giant clams (Cardiidae: Bivalvia) on Kei Islands, Maluku, Indonesia. Biodiversitas 20: 884-892. doi: 10.13057/biodiv/d200337.
Wakum, A., Takdir, M., & Talakua, S. (2017). Jenis – jenis kima dan kelimpahannya di perairan Amdui Distrik Batanta Selatan Kabupaten Raja Ampat. Jurnal Sumberdaya Akuatik Indopasifik. 1:43-51.
Zein, M. S. A. (2007). Keragaman daerah kontrol DNA Mitokondria Rusa Timor (Cervus timorensis timorensis) di PulauTimor, Alor dan Pantar. Biota. 12(3): 138-144. doi:10.24002/biota.v12i3.2799.
Yu, S., Liu, S., Jiang, K., Zhang, J., Jiang, Z., Wu, Y.,…Trevathan-Tackett, S. M. (2018). Population genetic structure of the threatened tropical seagrass Enhalus acoroides in Hainan Island, China. Aquatic Botany. 150:64–70. doi:10.1016/j.aquabot.2018.07.005.
DOI: http://dx.doi.org/10.15578/jppi.26.3.2020.167-179
Jurnal Penelitian Perikanan Indonesia is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
