Identifikasi Molekuler dan Posisi Filogenetik Ikan Sili (Mastacembelidae: Macrognathus) dari Sungai Brantas, Jawa Timur, berdasarkan DNA mitokondria Gen COI

Wahyu Endra Kusuma; Ifa Sufaichusan; Bela Fatma Hani Ayu Lestari; Yuni Widyawati

doi:10.46252/jsai-fpik-unipa.2023.Vol.7.No.2.308

Authors

Wahyu Endra Kusuma Program Studi Budidaya Perairan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Brawijaya, Jalan Veteran, Ketawangede, Lowokwaru, Kota Malang, 65145, Indonesia
Ifa Sufaichusan Program Studi Budidaya Perairan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Brawijaya, Jalan Veteran, Ketawangede, Lowokwaru, Kota Malang, 65145, Indonesia
Bela Fatma Hani Ayu Lestari Program Studi Budidaya Perairan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Brawijaya, Jalan Veteran, Ketawangede, Lowokwaru, Kota Malang, 65145, Indonesia
Yuni Widyawati Program Studi Budidaya Perairan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Brawijaya, Jalan Veteran, Ketawangede, Lowokwaru, Kota Malang, 65145, Indonesia

DOI:

https://doi.org/10.46252/jsai-fpik-unipa.2023.Vol.7.No.2.308

Keywords:

Bayesian Inference, conservation, domestication, morphological analysis, molecular divergence

Abstract

The spiny eels (family Mastacembelidae) is a fish that naturally and widely distributed on Java Island, especially in the Brantas River of East Java. This fish has high economic value, as a source of protein for local people and has recently popular as an ornamental fish among hobbyists. To fulfill market needs, fishermen must catch the fish from nature, leading to a severe population decline. Basic scientific information regarding species identification and determining the phylogenetic position fish species including the spiny eels is very important in order to support aquaculture, domestication and maintain its sustainability in nature. Specimens of the spiny eels were collected from Brantas River basin, East Java, at two localities in Malang and Kediri. Mitochondrial DNA from the cytochrome c oxidase subunit I was then sequenced on several randomly selected specimens. Results of morphological and genetic analysis using BLASTn showed that the specimens under study could be confirmed as Macrognathus aculeatus. Phylogenetic analysis using the Bayesian Inference method showed that M. aculeatus in this study has the closest relative to M. arai from Bangladesh. The phylogenetic reconstruction showed that individuals of M. aculeatus from Malang and Kediri were clustered together with individuals from Mojokerto with very shallow molecular divergence, indicating that they possibly originated from the same population. The results of this study can be used as basic information to design effective management of domestication, aquaculture, and conservation in the future.

Downloads

Download data is not yet available.

References

Andani, A., Herawati, T., Zahidah, Hamdani, H. (2017). Identifikasi dan inventarisasi ikan yang dapat beradaptasi di Waduk Jatigede pada tahap inundasi awal. Jurnal Perikanan dan Kelautan, 8(2): 28-35).

Asahida, T., Kobayashi, T., Saitoh, K., Nakayama, I., 1996. Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffer containing high concentration of urea. Fisheries Science, 62, 727-730.

Austen, G., Bindemann, M., Griffiths, R. Roberts, D. L. (2016). Species identification by experts and non-experts: comparing images from field guides. Scintific Reports, 6, 33634. DOI: https://doi.org/10.1038/srep33634.

Britz, R. (1996). Ontogeny of the ethmoidal region and hyopalatine arch in Macrognathus pancalus (Percomorpha, Mastacembeloidei), with critical remarks on Mastacembeloid inter- and intrarelationships. American Museum Navitates, 3181:1-18.

Cheng, J., Kao, H., & Dong, S. (2020). Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing. BMC Plant Biology, 20, 391. DOI: https://doi.org/10.1186/s12870-020-02594-y.

Cleary, L., & DeVantier, L. (2011). Indonesia: Threats to the country’s biodiversity. Encyclopedia of Environmental Health, 187-197. DOI: https://doi.org/10.1016/B978-0-444-52272-6.00504-3.

Dahruddin, H., Hutama, A., Busson, F., Sauri, S., Hanner, R., Keith, P., Hadiaty, R., Hubert, N. (2017). Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Molecular Ecology Resources, 17(2): 288-299. DOI: https://doi.org/10.1111/1755-0998.12528.

Dinh, T. D., Ngatia, J. N., Cui, L. Y., Ma, Y., Dhamer, T. D., Xu, Y. C. (2019). Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines. Forensic Science International: Genetics, 40, 85–95.

Direktorat Jenderal Konservasi Sumber Daya Alam dan Ekosistem. (2019). The sixth national report to the convention on biological diversity. Kementerian Lingkungan Hidup dan Kehutanan.

Duong, T. Y., Tran, L. V. D., Nguyen, N. T. T., Jamaluddin, J. A. F., Azizah, M. N. S. (2020). Unravelling taxonomic ambiguity of the Mastacembelidae in the Mekong delta (Viet nam) through DNA barcoding and morphological approaches. Tropical Zoology, 33 (2): 63–76.

Fadli, N., Mohd Nor S. A., Othman, A. S., Sofyan, H., Muchlisin, Z. A. (2020). DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia. PeerJ. 5(8): e9641. doi: https://doi.org/10.7717/peerj.9641.

Fricke, R., Eschmeyer, W. N., & Van der Laan, R. (eds) 2023. Eschmeyer’s catalog of fishes: genera, species, references. (http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp). Electronic version accessed 29 January 2023.

Froese, R., & Pauly, D., (Eds.). (2022). FishBase. World Wide Web electronic publication. Available from http://fishbase.org/. Accessed on December 23, 2022.

Gustiano, R., Kurniawan, K., Haryono, H. (2021). Optimizing the utilization of genetic resources of Indonesian native freshwater fish. Asian Journal of Conservation Biology, 10(2): 189-196. DOI: https://doi.org/10.53562/ajcb.67022

Hadiaty, R. K. (2011). Diversitas dan hilangnya jenis-jenis ikan di Sungai Ciliwung dan Sungai Cisadane. Berita Biologi, 10(4): 491-504.

Hartl, D. L., & Clark, G. C. (1997) Principles of Population Genetics. Sinauer Associates, Sunderland.

Hebert, P. D., Cywinska A., Ball S. L., DeWaard J. R. (2003a). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270: 313-321. DOI: https://doi.org/10.1098/rspb.2002.2218.

Hebert, P. D., Ratnasingham S., DeWaard J. R. (2003b). Barcoding animal life: cytochrome c oxidase subunit 1 divergence among closely related species. Proceedings of the Royal Society B: Biological Sciences (Suppl), 270: S96-S99. DOI: https://doi.org/10.1098/rsbl.2003.0025.

Kottelat, M., & Widjanarti, E. (2005). The fishes of the Danau Sentarum National Park and the Kapuas Lakes area, Kalimantan Barat, Indonesia. Raffles Bulletin of Zoology, Supplement, 13: 139-173.

Kottelat, M., Whitten, A. J., Kartikasari, S. N., Wirjoatmodjo, S. (1993). Freshwater fishes of western Indonesia and Sulawesi. Periplus Editions, Hong Kong. 221p.

Leray, M., Knowlton, N., Ho, S. L., Machida, R. J. (2019). GenBank is a reliable resource for 21st century biodiversity research. Proceedings of the National Academy of Sciences USA, 116(45): 22651-22656. DOI: https://doi.org/10.1073/pnas.1911714116.

Locatelli, N. S., McIntyre, P. B., Therkildsen, N. O., Baetscher D. S. (2020). GenBank's reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA. Proceedings of the National Academy of Sciences USA. 117(51):32211-32212. DOI: htpps://doi.org/10.1073/pnas.2007421117.

Lusiana, N., & Rahadi, B. (2018). Prediksi distribusi pencemaran air sungai brantas hulu kota batu pada musim hujan dan kemarau menggunakan metode spasial inverse distance weighted. Ecotrophic, 12(2): 211-224.

Maddison, W. P., & Maddison, D. R. (2017). Mesquite: a modular system for evolutionary analysis. Version 3.11 http://mesquiteproject.org

Meijaard, E., Sheil, D., Nasi, R., Augeri, D., et al. (2006). Hutan pasca pemanenan: Melindungi satwa liar dalam kegiatanhutan produksi di Kalimantan. Bogor: CIFOR, 384p.

Meiklejohn, K. A., Damaso, N., Robertson, J. M. (2019) Assessment of BOLD and GenBank – Their accuracy and reliability for the identification of biological materials. PLoS ONE, 14(6): e0217084. DOI: https://doi.org/10.1371/journal.pone.0217084.

Mukti, A. T., Arief, M., Satyantini, W. H., Mubarak, A. S. (2009). Kajian penyebaran populasi dan reproduksi serta upaya domestikasi budidaya ikan sili (Macrognathus aculeatus) sebagai komoditas unggulan daerah kabupaten Lamongan. Laporan Hibah Penelitian Strategis Nasional, Universitas Airlangga, Surabaya.

Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. B., Kent, J. (2000). Biodiversity hotspots for conservation priorities. Nature. 403:853–858. DOI: https://doi.org/10.1038/35002501.

Nelson, J.S., Grande, T. C., Wilson, M. V. H. (2016). Fishes of the world. Fifth edition. John Wiley & Sons, Inc., New York. 725 p.

Pandey, P. K., Singh, Y. S., Tripathy, P. S., Kumar, R., Abujam, S. K., Parhi, J. (2020). DNA barcoding and phylogenetics of freshwater fish fauna of Ranganadi River, Arunachal Pradesh. Gene. 2020 Sep 5;754:144860. doi: https://doi.org/10.1016/j.gene.2020.144860.

Rahma, Y. A. (2021). Kajian morfologi ikan sili pada nasi boranan makanan khas daerah Lamongan Provinsi Jawa Timur. Jurnal Matematika dan Sains, 1(1): 23-30. DOI: https://doi.org/10.55273/jms.v1i1.78.

Roberts, T. R. (1985). Systematic review of the Mastacembelidae or siny eels of Burma and Thailand, with description of two news species of Macrognathus. Japanese Journal of Ichthtyology, 33(2): 95-109.

Ronquist, F., Huelsenbeck, J.P., 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574.

Ryder, O. A. (1986). Species conservation and systematics: the dilemma of subspecies. Trends in Ecology & Evolution, 1(1): 9-10.

Sundqvist, L., Keenan, K., Zackrisson, M., Prodöhl, P., Kleinhas, D. (2016). Directional genetic differentiation and relative migration. Ecology and Evolution, 6(11): 3461-3475. DOI: https://doi.org/10.1002/ece3.2096.

Strecker, A. L., Olden, J. D., Whittler, J. B., Paukert, C. P. (2011). Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity. Ecological Application, 21(8): 3002-3013.

Syafei, L. S., Sudinno, D. (2018). Ikan asing invasif, tantangan keberlanjutan biodiversitas perairan. Jurnal Penyuluhan Perikanan dan Kelautan, 12(3): 145-161. DOI: https://doi.org/10.33378/jppik.v12i3.106.

Teletchea, F. (2009). Molecular identification methods in fish species: reassessment and possible applications. Reviews in Fish Biology and Fisheries, 19:265-293. DOI: https://doi.org/10.1007/s11160-009-9107-4.

Tran, D.D., Shibukawa, K., Nguyen, T. P., Ha, P. H., Tran, X. L., Mai, V. H., Utsugi, K. (2013). Fishes of the Mekong Delta, Viet Nam. Viet Nam: Can Tho University Publishing House.174 pp.

von Rintelen, K., Arida, E., Häuser, C. (2017). A review of biodiversity-related issues and challanges in megadiverse Indonesia and other Southeast Asian countries. Research Ideas and Outcomes, 3: 220860. DOI: https://doi.org/10.3897/rio.3.e20860

Wibowo, A., Atminarso, D., Baumgartner, L., Vasemagi, A. (2019). High prevalance of non-native fish species in a remote region of the Memberamo River, Indonesia. Pacific Conservation Biology, 26(3): 293-300. DOI: https://doi.org/10.1071/PC19004.

Wiley, E. O. (2010). Why Trees Are Important. Evolution: Education and Outreach, 3: 499–505. https://doi.org/10.1007/s12052-010-0279-0.

Wright, S. (1978). Evolution and the genetics of population, variability within and among natural populations. The University of Chicago Press, Chicago.

Yetti, E., Soedharma, D., Haryadi, S. (2011). Evaluasi kualitas air sungai-sungai di kawasan das brantas hulu malang dalam kaitannya dengan tata guna lahan dan aktivitas masyarakat di sekitarnya. Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan, 1(1): 10-15.