Genetic and morphological analyses of Ngongok fish (Hampala macrolepidota) from Ngebel Lake, Ponorogo District, Indonesia
Article Sidebar
Abstract Views: 174
File Views: 79
Main Article Content
Abstract
Abstract. Amalia E, Paricahya AF, Dailami M, Faqih AR, Kusuma WE. 2026. Genetic and morphological analyses of Ngongok fish (Hampala macrolepidota) from Ngebel Lake, Ponorogo District, Indonesia. Biodiversitas 27 (4): d270410. https://doi.org/10.13057/biodiv/d270410. Hampala macrolepidota is a freshwater fish widely distributed in Southeast Asia and plays an important ecological and economic role. However, increasing anthropogenic pressures raise concerns about population structure and genetic integrity. This study aimed to confirm species identity and assess genetic diversity and population differentiation using an integrated morphological and molecular approach. Specimens were collected from Ngebel Lake (Ponorogo, East Java) and compared with populations from East Java, South Sumatra, and Thailand. The morphological identification and inventory profile of H. macrolepidota, combined with genetic studies based on Cytochrome b (Cytb) of mitochondrial DNA (mtDNA) at the population level in Ngebel Lake, have not been explored before. Ngongok fish in Ngebel Lake has been confirmed as H. macrolepidota based on morphological and genetic studies. H. macrolepidota sequences from Ngebel Lake represent the Insular Asia region separated from the Mainland Asia region population based on haplotype network, phylogenetics, and genetic p-distance measurements. The H. macrolepidota population in Ngebel Lake has historically experienced rapid growth, as indicated by high genetic diversity (hd = 1.0000, π = 0.0086) and a favorable demographic history (D = 0.6479, Fs = -0.4208). The genetic closeness of H. macrolepidota and Cyprinus carpio presents potential for hybridization in the future. Despite morphological similarity across regions, genetic divergence highlights the importance of molecular data in resolving population-level differences. These findings suggest that H. macrolepidota populations are shaped by geographic and biogeographic barriers, with potential implications for conservation and management. The observed genetic patterns also suggest a potential hybridization risk under increasing environmental pressure, although further investigation using nuclear markers is required.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Afriansyah A, Muslim M, Irawan R. 2023. Sexual dimorphism, length-weight relationship, and condition factor of Hampala ampalong (Bleeker, 1852) from Kalong Floodplain, Ogan Komering Ilir Regency. Intl J Sci Res Arch 10 (1): 666-674. https://doi.org/10.30574/ijsra.2023.10.1.0800.
Alam MA, Parvez I, Ara Y, Khan MN, Nehrin S, Mahajebin T, Hassan MM. 2021. Phylogenetic relations of the cyprinid fishes (Cyprinidae) in Bangladesh inferred from morphological traits and Cytochrome b gene sequences. AACL Bioflux 14 (3): 1631-1644.
Angkasawan NO, Sulistyo I, Rukayah S, Lestari W. 2022. Aspek reproduksi spesies asli ikan Palung (Hampala macrolepidota CV 1823) di Waduk PB. Soedirman Banjarnegara, Jawa Tengah. Jurnal Maiyah 1 (1): 36-48. https://doi.org/10.20884/1.maiyah.2022.1.1.6633. [Indonesian]
Asiah N, Junianto J, Yustiati A, Sukendi S, Fahmi MR, Muchlisin ZA, Kadapi M, Windarti W. 2020. Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using Cytochrome C Oxidase Subunit 1. F1000Research 8: 177. https://doi.org/10.12688/f1000research.17319.3.
Baisvar VS, Kumar R, Singh M, Kushwaha B. 2019. Cytochrome-C Oxidase I gene-based genetic divergence and molecular phylogeny among the species of the fish genus Channa. Proc Natl Acad Sci India Sect B Biol Sci 89: 1455-1463. https://doi.org/10.1007/s40011-018-01070-w.
Baladia Y, Ben-Haddad M, Laadel N, Hermas J, Agnaou M, Oualid JA. 2025. Factors associated with fish mass mortality events in North African freshwater ecosystems, Morocco as a case study. Environ Sci Pollut Res 32: 8010-8024. https://doi.org/10.1007/s11356-025-36176-y.
Bañón R, Baldó F, Serrano A, Barros‐García D, de Carlos A. 2022. Gaidropsarus gallaeciae (Gadiformes: Gaidropsaridae), a new Northeast Atlantic rockling fish, with commentary on the taxonomy of the genus. Biology 11 (6): 860. https://doi.org/10.3390/biology11060860.
Bedassa SB. 2019. Identification of possible causes of fish death in Lake Kabo. Intl J Fish Aquac 11 (2): 29-36. https://doi.org/10.5897/ijfa2018.0721.
Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. 2018. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One 13 (6): e0198109. https://doi.org/10.1371/journal.pone.0198109.
Budi DS, Davinci L, Ardiyan AP, Herjayanto M. 2025. Natural occurrence of hybrid koi and mahseer in artificial ponds: Evidence of the dangers of releasing non-native fish into the wild. J Aquac Sci 10 (1): 32-39. https://doi.org/10.20473/joas.v10i1.68203.
Chan J, Li W, Hu X, Liu Y, Xu Q. 2016. Genetic diversity and population structure analysis of Qinghai-Tibetan Plateau schizothoracine fish (Gymnocypris dobula) based on mtDNA D-loop sequences. Biochem Syst Ecol 69: 152-160. https://doi.org/10.1016/j.bse.2016.09.004.
Das JC, Chakraborty S. 2025. Gaining insight into the codon structuring of mitochondrial ND1 gene of freshwater fish under Cichlidae family. Ecol Environ Conserv 31: S218-S227. https://doi.org/10.53550/eec.2025.v31i04s.032.
Doi A, Taki Y. 1994. A new cyprinid fish, Hampala salweenensis, from the Mae Pai River System, Salween Basin, Thailand. Jpn J Ichthyol 40 (4): 405-412. https://doi.org/10.11369/jji1950.40.405.
Fan P, Song G, Qiao H, Zhang D, Ji Y, Qu Y, Fjeldså J, Lei F. 2024. Revaluation of the genetic diversity-area relationship by integrating nucleotide and haplotype diversity. Curr Zool 71 (5): 645-651. https://doi.org/10.1093/cz/zoae078.
Ferreira DG, Souza-Shibatta L, Shibatta OA, Sofia SH, Carlsson J, Dias JHP, Makrakis S, Makrakis MC. 2017. Genetic structure and diversity of migratory freshwater fish in a fragmented Neotropical River system. Rev Fish Biol Fish 27: 209-231. https://doi.org/10.1007/s11160-016-9441-2.
Garcia E, Wright D, Gatins R, Roberts MB, Pinheiro HT, Salas E, Chen J-Y, Winnikoff JR, Bernardi G. 2021. Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks. PLoS One 16 (6): e0251878. https://doi.org/10.1371/journal.pone.0251878.
Gozlan RE, Britton JR, Cowx I, Copp GH. 2010. Current knowledge on non-native freshwater fish introductions. J Fish Biol 76 (4): 751-786. https://doi.org/10.1111/j.1095-8649.2010.02566.x.
Grant WAS, Bowen BW. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J Hered 89 (5): 415-426. https://doi.org/10.1093/jhered/89.5.415.
Haraningtias H, Utami S, Primiani CN. 2018. Anatomi dan biometri sistem pencernaan ikan air tawar famili Cyprinidae di Telaga Ngebel Ponorogo. In: Prosiding Seminar Nasional 3. Universitas PGRI Madiun, Madiun, Jawa Timur, 15 September 2018. [Indonesian]
Hui TH, Grinang J. 2025. Two new species of Hampala from Borneo (Teleostei: Cyprinidae). Raffles Bull Zool 73: 243-260. https://doi.org/10.26107/rbz-2025-0018.
Inger RF, Kong CP. 1962. The Freshwater Fishes of North Borneo. Chicago Natural History Museum, Chicago, Illinois, USA.
Iskandar A, Muslim M, Hendriana A, Wiyoto W. 2020. Jenis-jenis ikan Indonesia yang kritis dan terancam punah. Jurnal Sains Terapan 10 (1): 53-59. https://doi.org/10.29244/jstsv.10.1.53-59. [Indonesian]
Kenthao A, Wangsomnuk PP, Jearranaiprepame P. 2018. Genetic variations and population structure in three populations of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) inferred from mitochondrial Cytochrome b sequences. Mitochondrial DNA A DNA Mapp Seq Anal 29 (1): 82-90. https://doi.org/10.1080/24701394.2016.1242581.
Kim K-R, Sung M-S, Hwang Y, Lee MS, Jeong JH, Kim H, Yu J-N. 2023. Analysis of genetic diversity across newly occupied habitats within the Goryeong population of Pungitius kaibarae using the mitochondrial Cytb gene. Korean J Ichthyol 35 (4): 217-223. https://doi.org/10.35399/isk.35.4.1. [Korean]
Kristensen TN, Ketola T, Kronholm I. 2020. Adaptation to environmental stress at different timescales. Ann N Y Acad Sci 1476 (1): 5-22. https://doi.org/10.1111/nyas.13974.
Kuang T, Shuai F, Li X, Chen W, Lek S. 2021. Genetic diversity and population structure of Hemibagrus guttatus (Bagridae, Siluriformes) in the larger Subtropical Pearl River based on COI and Cyt b genes analysis. Ann Limnol Intl J Lim 57: 7. https://doi.org/10.1051/limn/2021005.
Kumar M. 2023. The importance of genetic diversity in conservation biology. J Biodivers Endanger Species 11 (3): 477. https://doi.org/10.37421/2332-2543.2023.11.477.
Lamadi A, Paricahya AF, Iranawati F, Widodo MS, Wiadnya DGR. 2023. Genetic and morphological analysis of complex Giuris group species from Limboto Lake, Gorontalo Province, Indonesia. Biodiversitas 24 (10): 5223-5233. https://doi.org/10.13057/biodiv/d241002.
Luthfi OM. 2017. Bathymetry of Lake Ngebel, an old crater on the Wilis volcanic complex, East Java, Indonesia. Intl J Earth Sci Eng 10 (6): 1143-1146. https://doi.org/10.21276/ijee.2017.10.0606.
Makmur S, Arfiati D, Bintoro G, Ekawati AW. 2014. Morphological, meristic characteristics, and mtDNA analysis of Hampala fish (Hampala macrolepidota Kuhl & Van Hasselt 1823) from Ranau Lake, Indonesia. J Biodiv Environ Sci 5 (2): 447-455.
Makmur S, Muthmainnah D, Subagdja S. 2018. Pengelolaan ikan hampal (Hampala macrolepidota Kuhl & Van Hasselt 1823) di Danau Ranau, Sumatera Selatan dan Lampung. Jurnal Kebijakan Perikanan Indonesia 9 (2): 61-70. https://doi.org/10.15578/jkpi.9.2.2017.61-70. [Indonesian]
Martinez AS, Willoughby JR, Christie MR. 2018. Genetic diversity in fishes is influenced by habitat type and life-history variation. Ecol Evol 8 (23): 12022-12031. https://doi.org/10.1002/ece3.4661.
Melisa E, Siregar AS, Rukayah S. 2021. Komposisi dan luas relung makanan ikan Palung (Hampala macrolepidota C.V.1823) di Waduk PB. Soedirman Banjarnegara, Jawa Tengah. Florea 8 (2): 69-81. https://doi.org/10.25273/florea.v8i2.11049. [Indonesian]
Meng W, Yang T, Hai S, Ma Y, Cai L, Ma X, Gao T, Guo Y. 2015. Extensive genetic divergence among Diptychus maculatus populations in Northwest China. Chin J Oceanol Limnol 33: 577-584. https://doi.org/10.1007/s00343-015-4137-3.
Mills MD, Rader RB, Belk MC. 2004. Complex interactions between native and invasive fish: The simultaneous effects of multiple negative interactions. Oecologia 141: 713-721. https://doi.org/10.1007/s00442-004-1695-z.
Moghaddam YF, Aliabadian M, Daud SK, Seifali M. 2013. Molecular phylogeny of the Puntius (Hamilton, 1822) based on nuclear gene RAG2. Prog Biol Sci 2 (2): 66-75.
Nabilsyafiq MH, Gan HM, Abd Mazlan AG, Mat Jaafar TNA, Danish-Daniel M, Sung YY, Tan MP. 2019. ND5 gene marker reveals recent population expansion of wild pearse’s mudskipper (Periophthalmus novemradiatus Hamilton) inhabits Setiu Wetlands in East Peninsular Malaysia. Malays Appl Biol 48 (1): 87-93.
Nishida K, Koizumi N, Minagawa A, Mori A, Watabe K, Takemura T. 2025. Phylogeographic pattern of Rhynchocypris lagowskii (Actinopterygii: Cypriniformes) with evidence of large-scale introduction in Japan, revealed by mitochondrial DNA D-loop analysis. Biogeography 27: 33-41. https://doi.org/10.11358/biogeo.27.33.
Njiru J, Morara G, Waithaka E, Mugo J. 2015. Fish kills in Lake Naivasha, Kenya: What was the probable cause? Intl J Fish Aquat Stud 3 (1): 179-184.
Nugroho IF, Pramudita D, Ekayani M. 2022. Dampak ekonomi dan pengembangan wisata Telaga Ngebel, Kecamatan Ngebel, Kabupaten Ponorogo. Indones J Agric Resour Environ Econ 1 (1): 11-24. https://doi.org/10.29244/ijaree.v1i1.41547. [Indonesian]
Ouassal K, Doadrio I, Yahyaoui A, Jaziri H. 2024. Cytochrome b mitochondrial gene revealed a strong genetic differentiation between two populations of the endemic freshwater fish Moroccan loach Cobitis maroccana Pellegrin, 1929. Turk J Fish Aquat Sci 24 (11): TRJFAS24858. https://doi.org/10.4194/TRJFAS24858.
Pan Z, Zhao H, Zhu C, Chen H, Zhao P, Cheng Y. 2021. Genetic diversity analysis of crucian carp (Carassius auratus) based on Cyt b and D-loop-containing region around Hongze Lake. Environ Biol Fish 104: 1401-1420. https://doi.org/10.1007/s10641-021-01175-8.
Panitvong N, Hui TH. 2025. A new species of Hampala (Teleostei: Cyprinidae) from the Lower Tenasserim Basin of Thailand. Raffles Bull Zool 73: 67-72. https://doi.org/10.26107/rbz-2025-0006.
Pante E, Puillandre N, Viricel A, Arnaud-Haond S, Aurelle D, Castelin M, Chenuil A, Destombe C, Forcioli D, Valero M, Viard F, Samadi S. 2014. Species are hypotheses: Avoid connectivity assessments based on pillars of sand. Mol Ecol 24 (3): 525-544. https://doi.org/10.1111/mec.13048.
Paricahya AF, Kholil KNA, Saputri RRL, Herjayanto M, Wiadnya DGR, Faqih AR, Marhendra APW. 2024. Molecular analysis using Cytochrome Oxidase Subunit I (COI) to confirm new recorded Oryzias hubbsi in the Central East Java Ecoregion. Jurnal Penelitian Pendidikan IPA 10 (7): 3541-3547. https://doi.org/10.29303/jppipa.v10i7.6802.
Permana R, Delami AN. 2022. Kajian analisis kearifan lokal sebagai landasan konservasi ikan Barau (Hampala macrolepidota). Organisms: J Biosci 2 (1): 25-33. https://doi.org/10.24042/organisms.v2i1.11756. [Indonesian]
Prasetyowati AA, Harahab N, Soemarno S. 2014. Tourist perceptions on supporting infrastructure facilities and climate-based visiting time of Ngebel Lake, Ponorogo. J Indones Tour Dev Stud 2 (2): 47. https://doi.org/10.21776/ub.jitode.2014.002.02.02.
Primiani CN, Prayitno TA, Dinka E. 2020. Developing of fish anatomy learning module based on local wisdom in Ngebel Lake, Ponorogo, East Java. Jurnal Pendidikan Biologi Indonesia 6 (2): 283-292. https://doi.org/10.22219/jpbi.v6i2.11813.
Raja UKS, Ebenezer V, Kumar A, Sanjeevi P, Murugesan M. 2019. Mass mortality of fish and water quality assessment in the tropical Adyar Estuary, South India. Environ Monit Assess 191: 512. https://doi.org/10.1007/s10661-019-7636-4.
Reddythota D, Timotewos MT. 2022. Evaluation of pollution status and detection of the reason for the death of fish in Chamo Lake, Ethiopia. J Environ Public Health 2022 (1): 5859132. https://doi.org/10.1155/2022/5859132.
Restuningsih FD, Elvyra R, Haryono H. 2023. Karakteristik morfometrik Hampala macrolepidota Kuhl & Van Hasselt, 1823 di Indonesia. J Bios Logos 13 (2): 92-100. https://doi.org/10.35799/jbl.v13i2.48688. [Indonesian]
Risdawati R. 2011. Cirolana sp. salah satu endoparasit di Danau Singkarak Sumatera Barat. Jurnal Pelangi 3 (2): 103-108. https://doi.org/10.22202/jp.2011.v3i2.24. [Indonesian]
Ryan JRJ, Esa YB. 2006. Phylogenetic analysis of Hampala fishes (subfamily Cyprininae) in Malaysia inferred from partial mitochondrial Cytochrome b DNA sequences. Zool Sci 23 (10): 893-901. https://doi.org/10.2108/zsj.23.893.
Saddhono K, Pertiwi KR, Anggrahini D. 2019. Larung sesaji tradition: Symbolic meaning and ritual value with water concept in Lake Ngebel, Ponorogo, East Java. In: Proceedings of the 1st International Conference on Life, Innovation, Change and Knowledge (ICLICK 2018). https://doi.org/10.2991/iclick-18.2019.80.
Skovrind M, Castruita JAS, Haile J, Treadaway EC, Gopalakrishnan S, Westbury MV, Heide-Jørgensen MP, Szpak P, Lorenzen ED. 2019. Hybridization between two high Arctic cetaceans confirmed by genomic analysis. Sci Rep 9: 7729. https://doi.org/10.1038/s41598-019-44038-0.
Soetignya WP, Suryoboroto B, Kamal MM, Boediono A. 2016. Population and potential spawning sites of Bornean endemic Hampala bimaculata in Betung Kerihun National Park, West Kalimantan Province, Indonesia. Intl J Sci Basic Appl Res 29 (3): 278-287.
Sudasinghe H, Ranasinghe T, Herath J, Wijesooriya K, Pethiyagoda R, Rüber L, Meegaskumbura M. 2021. Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka. BMC Ecol Evol 21: 203. https://doi.org/10.1186/s12862-021-01923-5.
Sumarsono H, Arti WH, Soesilo YH. 2020. The development strategy of the tourism sector in Ponorogo, Indonesia. In: Proceedings of the 4th Padang International Conference on Education, Economics, Business and Accounting (PICEEBA-2 2019). https://doi.org/10.2991/aebmr.k.200305.169.
Suryaningsih S, Simanjuntak SBI, Sukmaningrum S. 2018. Genetic variation of the Hampala fish (Hampala macrolepidota) population in PB. Soedirman Reservoir and Serayu River. Biosaintifika 10 (1): 145-152. https://doi.org/10.15294/biosaintifika.v10i1.12092.
Taki Y, Kawamoto A. 1977. Differentiation of the cyprinids, Hampala macrolepidota and H. dispar. Jpn J Ichthyol 24 (1): 61-65. https://doi.org/10.11369/jji1950.24.61.
Tang KL, Agnew MK, Hirt MV, Sado T, Schneider LM, Freyhof J, Sulaiman Z, Swartz E, Vidthayanon C, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL. 2010. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol 57 (1): 189-214. https://doi.org/10.1016/j.ympev.2010.05.021.
Wang X, Li J, He S. 2007. Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol 42 (1): 157-170. https://doi.org/10.1016/j.ympev.2006.06.014.
Wang Y-J, Lu J-H, Liu Z, Zhang J-P. 2021. Genetic diversity of Gymnocypris chilianensis (Cypriniformes, Cyprinidae) unveiled by the mitochondrial DNA D-loop region. Mitochondrial DNA B Resour 6 (4): 1292-1297. https://doi.org/10.1080/23802359.2021.1906172.
Wiradana PA, Yudha IKW, Mukti AT. 2022. Mass tilapia (Oreochromis mossambicus) mortality in floating net cages at Batur Lake, Bangli Regency, Bali Province: A case report. IOP Conf Ser: Earth Environ Sci 1036: 012068. https://doi.org/10.1088/1755-1315/1036/1/012068.
Yudiantoro DF, Ratnaningsih R, Pratiknyo P, Mahreni M, Sayudi DS, Paramitahaty I, Ismunandar W, Sampurno DG, Muhammad R, Abdurrachman M. 2020. Development of Ngebel Volcano as geoheritage and tourism education of volcano, electric energy, and geothermal, Ponorogo, East Java. In: Proceeding LPPM UPN "Veteran" Yogyakarta Conference Series 2020-Engineering and Science Series 1 (1): 18-32. https://doi.org/10.31098/ess.v1i1.90.
Zeng L, Wen J, Fan S, Chen Z, Xu Y, Sun Y, Chen D, Zhao J. 2018. Species identification of fish maw (Porcupinefish) products sold on the market using DNA sequencing of 16S rRNA and COI genes. Food Control 86: 159-162. https://doi.org/10.1016/j.foodcont.2017.11.031.
Zhao Y, Zheng X, Zhu X, Kuang Y, Sun X. 2020. Genetic variation of common carp Cyprinus carpio L. in China based on mitochondrial COII gene. Aquac Rep 18: 100462. https://doi.org/10.1016/j.aqrep.2020.100462.