FIRST CONFIRMED RECORD OF THE NEAR-THREATENED BOMBAY DUCK (Harpadon nehereus) IN CILACAP WATERS, INDONESIA

REKAMAN TERKONFIRMASI PERTAMA IKAN KADAL (Harpadon nehereus) YANG HAMPIR TERANCAM PUNAH DI PERAIRAN CILACAP, INDONESIA

Authors

  • Sugeng Hartono Study Program of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Jl. Dr. Soeparno, Purwokerto Utara, Banyumas 53122, Indonesia https://orcid.org/0000-0002-2317-7648
  • Novia Nurul Afiyah Study Program of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Jl. Dr. Soeparno, Purwokerto Utara, Banyumas 53122, Indonesia https://orcid.org/0009-0001-3638-8639
  • Mustathi' Zulfa Study Program of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Jl. Dr. Soeparno, Purwokerto Utara, Banyumas 53122, Indonesia
  • Muhammad Browijoyo Santanumurti Department of Aquaculture, Faculty of Fisheries and Marine, Airlangga University, Jl. Mulyorejo, Surabaya 60115, Indonesia https://orcid.org/0000-0003-0846-9447
  • Muyassar Hamid Abualreesh 1) Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Al Oloum St., Jeddah 22254, Saudi Arabia; 2) Center of Excellence for Environmental Studies (CEES), King Abdulaziz University, Idara St., Jeddah 22254, Saudi Arabia https://orcid.org/0000-0003-3170-3609
  • Gondo Puspito Department of Fisheries Resource Utilization, Faculty of Fisheries and Marine Sciences, IPB University, Jl. Agatis, IPB Dramaga Campus, Bogor 16680, Indonesia https://orcid.org/0000-0002-1573-7334
  • Muhammad Natsir Kholis Department of Fisheries Resources Utilization, Faculty of Fisheries and Marine Sciences, Riau University, Jl. Muchtar Lutfi, Pekanbaru 28293, Indonesia https://orcid.org/0000-0001-9172-4490

DOI:

https://doi.org/10.24319/jtpk.17.278-290

Keywords:

Bombay duck, DNA barcoding, fisheries management, species identification

Abstract

Accurate species identification is an essential foundation for effective fisheries management and conservation in Indonesia, particularly for near‑threatened species. This study aims to identify Bombay duck (Harpadon nehereus) from Cilacap Waters through morphological and molecular analyses, document its first record in Cilacap Waters, and provide a scientific basis for population studies, fisheries management, and conservation. Morphological identification was performed using physical characteristics such as shape, colour, and general features for morphometric and meristic analyses, guided by identification keys. Molecular confirmation was carried out through DNA barcoding of the mitochondrial COI gene. Primer Fish F1 and Fish R1 were used, along with the Sanger dideoxy sequencing method. The subfamily was confirmed by the presence of inner rays of the pelvic fin that are subequal or slightly longer than the outer rays. The genus was identified by the lateral‑line scales being enlarged and extending as a median lobe of the caudal fin. The primary rays of the caudal fin were without scales, and the body was compressed. The species was identified as H. nehereus because the pectoral fins reach beyond the origin of the dorsal fin. The obtained sequence (accession PV688437.1) showed approximately 96.928–99.495% identity with conspecific references in global databases and formed the same clade with other H. nehereus sequences in phylogenetic analysis, confirming its genetic identity. As the first confirmed record of H. nehereus in Cilacap, these findings provide essential baseline data for stock assessment, fisheries management, and conservation efforts in Indonesian waters.

Downloads

Download data is not yet available.

References

Andres KJ, Lodge DM, Sethi SA, Andrés J. 2023. Detecting and Analysing Intraspecific Genetic Variation with eDNA: From Population Genetics to Species Abundance. Molecular Ecology. 32(15): 4118–4132. DOI: https://doi.org/10.1111/mec.17031.

Andriyono S, Alam MJ, Kim HW. 2020. The Jawa and Bali Island Marine Fish Molecular Identification to Improve 12S rRNA-tRNA Valin-16S rRNA Partial Region Sequences on the GenBank Database. Thalassas. 36: 343–356. DOI: https://doi.org/10.1007/s41208-020-00196-x.

Apriliyanti MS, Sutanti S, Utomo DSC. 2018. Identifikasi Plankton di Kawasan Budidaya Rumput Laut Kabupaten Bantaeng, Sulawesi Selatan Dengan Metode DNA Barcoding. Jurnal Teknologi Perikanan dan Kelautan. 9(1): 65–72. DOI: https://doi.org/10.24319/jtpk.9.65-72.

Azizah Y, Marliana I, Agustina S, Natsir M. 2023. Kondisi Stok Perikanan di WPPNRI 573. Bogor (ID): Fisheries Resources Center of Indonesia, Rekam Nusantara Foundation.

Bacich DJ, Sobek KM, Cummings JL, Atwood AA, O'Keefe DS. 2011. False Negative Results from Using Common PCR Reagents. BMC Research Notes. 4: 457. DOI: https://doi.org/10.1186/1756-0500-4-457.

Brett JR. 1979. 10 - Environmental Factors and Growth. Fish Physiology. 8: 599–675. DOI: https://doi.org/10.1016/S1546-5098(08)60033-3.

Carpenter KE, Niem VH. 1999. The Living Marine Resources of the Western Central Pacific (Vol. 3), Batoid Fishes, Chimaeras, and Bony Fishes, Part 1 (Elopidae to Linophrynidae). Rome (IT): FAO.

Choi SW, Yu HJ, Kim JK. 2024. Comparative Ontogeny and Phylogenetic Relationships of Eight Lizardfish Species (Synodontidae) from the Northwest Pacific, with a Focus on Trachinocephalus Monophyly. Journal of Fish Biology. 104(1): 284–303. DOI: https://doi.org/10.1111/jfb.15595.

Cilacap Ocean Fishing Port. 2024. Fisheries Statistics 2023. https://ppid.kkp.go.id/upt/pelabuhan-perikanan-samudera-cilacap/informasi-publik/berkala/. [February 12, 2026].

Dong H, Yuan H, Yang X, Shan W, Zhou Q, Tao F, Zhao C, Bai J, Li X, Ma Y, et al. 2023. Phylogenetic Analysis of Some Species of the Anopheles hyrcanus Group (Diptera: Culicidae) in China Based on Complete Mitochondrial Genomes. Genes. 14(7): 1453. DOI: https://doi.org/10.3390/genes14071453.

Froese R, Pauly D (Eds.). 2025. FishBase, World Wide Web Electronic Publication (Version 04/2025). www.fishbase.org. [February 12, 2026].

Garcia-Vazquez E, Machado-Schiaffino G, Campo D, Juanes F. 2012. Species Misidentification in Mixed Hake Fisheries May Lead to Overexploitation and Population Bottlenecks. Fisheries Research. 114: 52–55. DOI: https://doi.org/10.1016/j.fishres.2011.05.012.

Gregory TR (Ed.). 2011. The Evolution of the Genome. Amsterdam (NL): Elsevier.

Hariyadi, Hutabarat J, Sugianto DN, Hartoko A, Maro JF, Nugraha E. 2021. Analysis of Specific Shallow-water Current for Endemic Fish Conservation at Natuna Islands, Indonesia. AACL Bioflux. 14(4): 1908–1917.

Hasin T. 2016. Length-Weight Relationship and Condition Factor of Bombay Duck Harpadon nehereus from Landings of Fishery Ghat, Chittagong. Research in Agriculture Livestock and Fisheries. 3(2): 355–360. DOI: https://doi.org/10.3329/ralf.v3i2.29367.

Hebert PDN, Cywinska A, Ball SL, de Waard JR. 2003a. Biological Identifications through DNA Barcodes. Proceedings of the Royal Society of London B: Biological Sciences. 270(1512): 313–321. DOI: https://doi.org/10.1098/rspb.2002.2218.

Hebert PDN, Ratnasingham S, de Waard JR. 2003b. Barcoding Animal Life: Cytochrome C Oxidase Subunit 1 Divergences Among Closely Related Species. Proceedings of the Royal Society of London B: Biological Sciences. 270 (Suppl_1): S96–S99. DOI: https://doi.org/10.1098/rsbl.2003.0025.

Hubert N, Kadarusman, Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre JC, et al. 2015. DNA Barcoding Indonesian Freshwater Fishes: Challenges and Prospects. DNA Barcodes. 3(1): 144–169. DOI: https://doi.org/10.1515/dna-2015-0018.

Hutubessy BG, Mosse JW. 2015. Ecosystem Approach to Fisheries Management in Indonesia: Review on Indicators and Reference Values. Procedia Environmental Sciences. 23: 148–156. DOI: https://doi.org/10.1016/j.proenv.2015.01.023.

Kalhoro MA, Qun L, Memon KH, Chang MS, Jatt AN. 2013. Estimation of Maximum Sustainable Yield of Nomei, Harpadon nehereus Fishery in Pakistan Using the CEDA and ASPIC Packages. Pakistan Journal of Zoology. 45(6): 1757–1764.

Kholis MN, Puspito G, Mawardi W, Imron M, Wiryawan B. 2024. Analysis of the Composition of Tidal Trap (Gombang) Catches Based on Time of Catching Operations in the Bengkalis Strait, Riau Province, Indonesia. AACL Bioflux. 17(5): 2310–2323.

Kinne O. 1960. Growth, Food Intake, and Food Conversion in an Euryplastic Fish Exposed to Different Temperatures and Salinities. Ecological and Evolutionary Physiology. 33(4): 288–317. DOI: https://doi.org/10.1086/physzool.33.4.30152673.

Koya KM, Sreenath KR, Muktha M, Dash G, Sen S, Zacharia PU, Kumari S, Makwana NK, Dhokia HK, Polera JP, et al. 2017. Stock Assessment of Bombayduck Harpadon nehereus (Hamilton, 1822) from Gujarat Coast Using Non-equilibrium Production Model. Indian Journal of Fisheries. 64(Special Issue): 179–181. DOI: https://doi.org/10.21077/ijf.2017.64.special-issue.76260-25.

Kumar VV, Reddy DA, Choudhury SR, Balakrishna CH, Satyanaryana Y, Nagesh TS, Das SK. 2014. Morphometry and Meristic Counts of Bombay Duck, Harpadon nehereus (Hamilton, 1822) Along Sunderban Region of West Bengal, India. Proceedings of the International Academy of Ecology and Environmental Sciences. 4(3): 95–105.

Kumar S, Stecher G, Suleski M, Sanderford M, Sharma S, Tamura K. 2024. MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing. Molecular Biology and Evolution. 41(12): msae263. DOI: https://doi.org/10.1093/molbev/msae263.

Landi M, Dimech M, Arculeo M, Biondo G, Martins R, Carneiro M, Carvalho GR, Brutto SL, Costa FO. 2014. DNA Barcoding for Species Assignment: The Case of Mediterranean Marine Fishes. PLoS ONE. 9(9): e106135. DOI: https://doi.org/10.1371/journal.pone.0106135.

Lawrence AJ, Hemingway KL (Eds.). 2008. Effects of Pollution on Fish: Molecular Effects and Population Responses. Chichester (GB): John Wiley & Sons.

Liang C, Pauly D. 2017. Growth and Mortality of Exploited Fishes in China's Coastal Seas and their Uses for Yield-per-recruit Analyses. Journal of Applied Ichthyology. 33(4): 746–756. DOI: https://doi.org/10.1111/jai.13379.

Macusi ED, Katikiro RE, Deepananda KHMA, Jimenez LA, Conte AR, Fadli N. 2011. Human Induced Degradation of Coastal Resources in Asia Pacific and Implications on Management and Food Security. Journal of Nature Studies. 9(10): 13–28.

Meliyana DF, Mashar A, Zairion Z. 2024. Determinasi Struktur Stok Ikan Kembung Lelaki Menggunakan Metode PCR-RFLP di WPP-NRI 711, 572, dan 573. Jurnal Teknologi Perikanan dan Kelautan. 15(2): 161–172. DOI: https://doi.org/10.24319/jtpk.15.161-172.

Melo BF, Ochoa LE, Vari RP, Oliveira C. 2016. Cryptic Species in the Neotropical Fish Genus Curimatopsis (Teleostei, Characiformes). Zoologica Scripta. 45(6): 650–658. DOI: https://doi.org/10.1111/zsc.12178.

Moran Z, Orth DJ, Schmitt JD, Hallerman EM, Aguilar R. 2016. Effectiveness of DNA Barcoding for Identifying Piscine Prey Items in Stomach Contents of Piscivorous Catfishes. Environmental Biology of Fishes. 99(1): 161–167. DOI: https://doi.org/10.1007/s10641-015-0448-7.

Mostarda E, Japp D, Heinecken C, Stiassny M, Clerkin P, Ebert DA, Tracey D. 2016. Marine Species Biological Data Collection Manual. Rome (IT): FAO.

Nakabo T (Ed.). 2002. Fishes of Japan with Pictorial Keys to the Species (English Edition I). Tokyo (JP): Tokai University Press.

Newman L, Duffus AL, Lee C. 2016. Using the Free Program MEGA to Build Phylogenetic Trees from Molecular Data. The American Biology Teacher. 78(7): 608–612. DOI: https://doi.org/10.1525/abt.2016.78.7.608.

Nugroho D, Faizah R, Prasetyo AP, Badrudin M. 2015a. Bio-exploitation Status of Bombay Duck (Harpadon nehereus Hamilton, 1822) on Trawl Fishery in Tarakan Waters. Indonesian Fisheries Research Journal. 21(1): 53–59. DOI: https://doi.org/10.15578/ifrj.21.1.2015.53-59.

Nugroho ED, Rahayu DA, Amin M, Lestari U. 2015b. Morphometric Characters of Marine Local Fish (Harpadon sp.) from Tarakan, Northern Borneo. Berkala Penelitian Hayati. 21(1): 41–45. DOI: https://doi.org/10.23869/bphjbr.21.1.20158.

Nugroho ED, Nawir D, Amin M, Lestari U. 2017. DNA Barcoding of Nomei Fish (Synodontidae: Harpadon sp.) in Tarakan Island, Indonesia. AACL Bioflux. 10(6): 1466–1474.

Prasetyo AP, Nugroho D, Wudianto, Irianto HE. 2014. The Implementation of Tarakan East Kalimantan Demonstration Site of the SCSSFMP, Documentation for GEF/UNOPS Project Sulu-Celebes Sea Sustainable Fisheries Management Project. Jakarta (ID): Research Center for Fisheries Management and Conservation.

Russell BC. 1999. Synodontidae: Lizardfishes (Also Bombay Ducks, Sauries). In: Carpenter KE, Niem VH (Editors.). The Living Marine Resources of the Western Central Pacific (Vol. 3), Batoid Fishes, Chimaeras, and Bony Fishes, Part 1 (Elopidae to Linophrynidae). Rome (IT): FAO.

Russell B, Govender A, Borsa P. 2019. Harpadon nehereus, Bombay Duck Lizardfish. The IUCN Red List of Threatened Species 2019: e.T75143569A75144431. DOI: https://doi.org/10.2305/IUCN.UK.2019-2.RLTS.T75143569A75144431.en.

Santanumurti MB, Suciyono, Syaifurrisal A, Adiputra YT, El-Regal MAA. 2024a. Morphological and Molecular Comparison of Areolate Grouper (Epinephelus areolatus) from Saudi Arabia and Indonesia. Jurnal Ilmu dan Teknologi Kelautan Tropis. 16(2): 193–209. DOI: https://doi.org/10.29244/jitkt.v16i2.57410.

Santanumurti MB, Suciyono, El-Regal MAA. 2024b. Morphological and Molecular Identification of Saurida spp. (Teleostei: Synodontidae) from Saudi Arabia and Indonesia. Makara Journal of Science. 28(4): 276–286. DOI: https://doi.org/10.7454/mss.v28i4.2432.

Sarker MN, Humayun M, Rahman MA, Uddin MS. 2017. Population Dynamics of Bombay Duck Harpadon nehereus (Hamilton, 1822) of the Bay of Bengal along Bangladesh Coast. Bangladesh Journal of Zoology. 45(2): 101–110. DOI: https://doi.org/10.3329/bjz.v45i2.35705.

Setiawan R, Suharti R, Rachmad B, Zulkifli D, Irawan H. 2020. Studi Karakter Morfometrik dan Meristik Ikan Nomei (Harpadon nehereus) di Kalimantan Utara. Jurnal Kelautan dan Perikanan Terapan. 3(1): 9–16. DOI: https://doi.org/10.15578/jkpt.v3i1.8267.

Steinke D, Hanner R. 2011. The FISH-BOL Collaborators' Protocol. Mitochondrial DNA. 22(S1): 10–14. DOI: https://doi.org/10.3109/19401736.2010.536538.

Tillett BJ, Field IC, Bradshaw CJ, Johnson G, Buckworth RC, Meekan MG, Ovenden JR. 2012. Accuracy of Species Identification by Fisheries Observers in a North Australian Shark Fishery. Fisheries Research. 127–128: 109–115. DOI: https://doi.org/10.1016/j.fishres.2012.04.007.

Vences M, Stützer D, Raminosoa NR, Ziegler T. 2022. Towards a DNA Barcode Library for Madagascar's Threatened Ichthyofauna. PLoS ONE. 17(8): e0271400. DOI: https://doi.org/10.1371/journal.pone.0271400.

von Bertalanffy L. 1957. Quantitative Laws in Metabolism and Growth. The Quarterly Review of Biology. 32(3): 217–231.

Ward RD, Hanner R, Hebert PDN. 2009. The Campaign to DNA Barcode All Fishes, FISH-BOL. Journal of Fish Biology. 74(2): 329–356. DOI: https://doi.org/10.1111/j.1095-8649.2008.02080.x.

Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA Barcoding Australia's Fish Species. Philosophical Transactions of the Royal Society B: Biological Sciences. 360(1462): 1847–1857. DOI: https://doi.org/10.1098/rstb.2005.1716.

Winans GA. 1985. Using Morphometric and Meristic Characters for Identifying Stocks of Fish. In: Kumpf HE, Vaught RN, Grimes CB, Johnson AG, Nakamura EL (Editors.). Proceedings of the Stock Identification Workshop, November 5–7, 1985, Panama City Beach, Florida. 25–62.

Wittmeier P, Hummel S. 2022. Agarose Gel Electrophoresis to Assess PCR Product Yield: Comparison with Spectrophotometry, Fluorometry and qPCR. BioTechniques. 72(4): 155–158. DOI: https://doi.org/10.2144/btn-2021-0094.

Yang T, Huang X, Jiang Y. 2022. Reveal the Population Genetic Characteristics of Bombay Duck (Harpadon nehereus) in Coastal Waters of China with Genotyping-by-Sequencing Technique. Journal of Ocean University of China. 21: 1373–1380. DOI: https://doi.org/10.1007/s11802-022-5019-x.

Zafar S, Shahzadi S, Farhat Jabeen F, Zafar T, Zafar A, Sajjad A. 2025. Unveiling Intraspecific Variations in Notopterus notopterus and Chitala chitala through Landmark-based Morphometry and Mitochondrial DNA Barcoding. International Journal of Biological Reports. 3(1): 83–108. DOI: https://doi.org/10.22034/INJBIR.3.1.83.

Zemlak TS, Ward RD, Connell AD, Holmes BH, Hebert PDN. 2009. DNA Barcoding Reveals Overlooked Marine Fishes. Molecular Ecology Resources. 9(s1): 237–242. DOI: https://doi.org/10.1111/j.1755-0998.2009.02649.x.

Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A Greedy Algorithm for Aligning DNA Sequences. Journal of Computational Biology. 7(1–2): 203–214. DOI: https://doi.org/10.1089/10665270050081478.

Downloads

Published

2026-06-16

Issue

Section

JTPK MAY 2026

How to Cite

Hartono, S., Afiyah, N. N. ., Zulfa, M. ., Santanumurti, M. B. ., Abualreesh, M. H. ., Puspito, G., & Kholis, M. N. . (2026). FIRST CONFIRMED RECORD OF THE NEAR-THREATENED BOMBAY DUCK (Harpadon nehereus) IN CILACAP WATERS, INDONESIA: REKAMAN TERKONFIRMASI PERTAMA IKAN KADAL (Harpadon nehereus) YANG HAMPIR TERANCAM PUNAH DI PERAIRAN CILACAP, INDONESIA. Jurnal Teknologi Perikanan Dan Kelautan, 17(2), 278-290. https://doi.org/10.24319/jtpk.17.278-290