Mitochondrial phylogeny and genetic diversity of Hampala barb (Hampala macrolepidota) from the Brantas River, Indonesia
Article Sidebar
Abstract Views: 480
File Views: 302
Main Article Content
Abstract
Abstract. Amalia E, Sufaichusan I, Dailami M, Faqih AR, Widodo MS, Wiadnya DGR, Kusuma WE. 2025. Mitochondrial phylogeny and genetic diversity of Hampala barb (Hampala macrolepidota) from the Brantas River, Indonesia. Biodiversitas 26: 5694-5702. Hampala barb (Hampala macrolepidota), a native freshwater fish species in the Brantas River, East Java, is currently under severe threat due to intense fishing and environmental perturbations. The urgency of this situation necessitates the immediate implementation of effective genetic management and conservation programs, which rely on basic scientific information such as genetic characterization. This study aimed to assess the phylogenetic relationships, genetic diversity, population structure, and demographic history of H. macrolepidota using a 1,095 bp sequence of the mitochondrial DNA cytochrome b from 23 individuals collected across four sampling locations. Phylogenetic analysis showed that H. macrolepidota from the Brantas River clustered together and formed a single group with very shallow genetic divergence. Population structure analyses (both ?st and AMOVA) showed high gene flow and an absence of significant genetic clustering, suggesting the sampled area constitutes a single, interconnected population unit. The combination of high haplotype diversity (hd: 0.714-1.000) but low nucleotide diversity (?: 0.00156-0.00728), along with the negative Tajima’s D and Fu’s Fs values, suggested that the species has likely experienced a bottleneck effect followed by a rapid expansion in the past. This decline of genetic diversity points to a reduced long-term adaptive potential, causing the species to be highly vulnerable to future environmental changes, despite its current abundance. The results highlight the urgent need for effective genetic management and conservation programs for the species to focus on maintaining genetic connectivity and minimizing anthropogenic pressures to preserve the genetic integrity and long-term viability of the population. Future studies incorporating nuclear or genome-wide markers would provide finer resolution of population structure and complement the mitochondrial data presented here.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Alves MJ, Coelho H, Collares-Pereira MJ, Coelho MM. 2001. Mitochondrial DNA variation in the highly endangered cyprinid fish Anaecypris hispanica: Importance for conservation. Heredity 87 (Pt 4): 463-473. DOI: 10.1046/j.1365-2540.2001.00929.x.
Andersson A, Karlsson S, Ryman N, Laikre L. 2022. Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator. Mol Ecol 31 (24): 6422-6439. DOI: 10.1111/mec.16710.
Astuti SS, Hariati AM, Kusuma WE, Wiadnya DGR. 2020. Genetic differences and population structure of spotted barb (Cyprinidae) collected from three rivers in Java Island. J Phys: Conf Ser 1665: 012002. DOI: 10.1088/1742-6596/1665/1/012002.
Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16 (1): 37-48. DOI: 10.1093/oxfordjournals.molbev.a026036.
Baselga A, Gómez?Rodríguez C, Vogler AP. 2015. Multi?hierarchical macroecology at species and genetic levels to discern neutral and non?neutral processes. Glob Ecol Biogeogr 24 (8): 873-882. DOI: 10.1111/geb.12322.
Blanton RE, Brumley JF, Thomas MR, Simmons JW, Brandt SL, Floyd MA. 2025. Impacts of habitat loss by reservoir inundation on occurrence, abundance, and genetic diversity of an imperiled, river-adapted, benthic-specialist fish, Etheostoma lemniscatum (Tuxedo Darter). Conserv Genet 26: 1-18. DOI: 10.1007/s10592-024-01628-4.
Bowen W, Bass AL, Rocha LA, Grant WS, Robertson DR. 2001. Phylogeography of the trumpetfishes (Aulostomus): Ring species complex on a global scale. Evolution 55 (5): 1029-1039. DOI: 10.1554/0014-3820(2001)055[1029:pottar]2.0.co;2.
Cano?Barbacil C, Radinger J, Grenouillet G, García?Berthou E. 2022. Phylogenetic signal and evolutionary relationships among traits of inland fishes along elevational and longitudinal gradients. Freshw Biol 67 (5): 912-925. DOI: 10.1111/fwb.13890.
Cavalcante LL, Occhi TVT, Olden JD, Padial AA. 2025. Non-native species drive the global loss of freshwater fish beta-diversity. NeoBiota 97: 257-277. DOI: 10.3897/neobiota.97.126607.
Cottet M, Visser TAM. 2017. Fish catch and fishing practices in the Nam Theun 2 Reservoir and watershed (Lao PDR). Lakes Reserv Sci Policy Manag Sustain Use 22 (4): 334-348. DOI: 10.1111/lre.12196.
Dornburg A, Near TJ. 2021. The emerging phylogenetic perspective on the evolution of Actinopterygian fishes. Ann Rev Ecol Evol Syst 52: 427-452. DOI: 10.1146/annurev-ecolsys-122120-122554.
Dudgeon D, Arthington AH, Gessner MO, Kawabata ZI, Knowler DJ, Lévêque C, Naiman AH, Richard PD, Soto ML, Stiassny, Sullivan, CA. 2006. Freshwater biodiversity: Importance, threats, status and conservation challenges. Biol Rev 81 (2): 163-182. DOI: 10.1017/S1464793105006950.
Edler D, Klein J, Antonelli A, Silvestro D. 2021. RaxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML. Methods Ecol Evol 12 (2): 373-377. DOI: 10.1111/2041-210X.13512.
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. DOI: 10.1007/s11160-016-9441-2.
Eschmeyer WN, Fricke R, van der Laan R. 2025. Catalog of Fishes: Genera, Species, References. California Academy of Sciences, San Francisco, California. www.researcharchive.calacademy.org/research/ ichthyology/catalog/fishcatmain.asp.
Froese R, Pauly D. 2025. FishBase. World Wide Web electronic publication. (https://www.fishbase.se/search.php). Electronic version accessed 25 May 2025).
Fu Y-X. 1996. New statistical tests of neutrality for DNA samples from a population. Genetics 143: 557-570. DOI: 10.1093/genetics/143.1.557.
Goodall-Copestake WP, Tarling GA, Murphy EJ. 2012. On the comparison of population-level estimates of haplotype and nucleotide diversity: A case study using the gene cox1 in animals. Heredity 109 (1): 50-56. DOI: 10.1038/hdy.2012.12.
Gonzalez EB, Espeland SH, Jentoft S, Hansen MM, Robalo JI, Stenseth NC, Jorde PE. 2019. Interbreeding between local and translocated populations of a cleaner fish in an experimental mesocosm predicts risk of disrupted local adaptation. Ecol Evol 9 (11): 6665-6677. DOI: 10.1002/ece3.5246.
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. DOI: 10.1093/jhered/89.5.415.
Hall SJG. 2022. Genetic differentiation among livestock breeds-values for Fst. Animals 12 (9): 1115. DOI: 10.3390/ani12091115.
Hartini ASA, Dewi RS. 2021. Identifikasi kandungan mikroplastik pada ikan dan air hilir Sungai Brantas. Environ Pollut J 1 (2): 67-75. DOI: 10.58954/epj.v1i2.9. [Indonesian]
He Z-Z, Shao W-W, Honnay O et al. 2025. Temporal dynamics of genetic diversity in protected and unprotected wild rice (Oryza rufipogon) populations: Implications for conservation. Mol Ecol 34 (9): e17750. DOI: 10.1111/mec.17750.
Hidayat M, Maulizar S, Batubara AS, Kautsari N, Latuconsina H, Nur FM, Zulfahmi I. 2023. Ichthyofauna of Merbau River, Leuser Ecosystem Area, Indonesia: Species composition, diversity, biometric condition, potency, and conservation status. Eur Zool J 90 (2): 747-761. DOI: 10.1080/24750263.2023.2272634.
IUCN. 2025. The IUCN Red List of Threatened Species. Version 2025-1. https://www.iucnredlist.org. Accessed on 23 May 2025.
Kenthao A, Jearranaiprepame P. 2020. Ecomorphological diversification of some barbs and carps (Cyprininae, Cyprinidae) in the lower Mekong Basin of Thailand. Zoology 143: 125830. DOI: 10.1016/j.zool.2020.125830.
Kim E-M, Park YJ, Lee HM, Noh ES, Kang J-H, Nam B-H, Kim Y-O, Choi T-J. 2022. Analysis of genetic differentiation and population structure of the Korean-peninsula-endemic genus, Semisulcospira, using mitochondrial markers. Fish Aquat Sci 25 (12): 601-618. DOI: 10.47853/FAS.2022.e55.
Kim K, Omori R, Ito K. 2017. Inferring epidemiological dynamics of infectious diseases using Tajima's D statistic on nucleotide sequences of pathogens. Epidemics 21: 21-29. DOI: 10.1016/j.epidem.2017.04.004.
Kitada S, Nakajima K, Hamasaki K. 2017. Population panmixia and demographic expansion of a highly piscivorous marine fish Scomberomorus niphonius. J Fish Biol 91 (5): 1435-1448. DOI: 10.1111/jfb.13466.
Kusuma WE, Ratmuangkhwang S, Kumazawa Y. 2016. Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): Cryptic species and west-to-east divergences. Mol Phylogenet Evol 105: 212-223. DOI: 10.1016/j.ympev.2016.08.014.
Kusuma WE, Widyawati Y, Dailami M, Kholil KNA, Paricahya AF, Sufaichusan I, Wiadnya DGR. 2024. Posisi filogenetik ikan kotes (Channa gachua (Hamilton, 1822)) dan ikan kutuk (Channa striata (Bloch, 1793)) dari Jawa Timur berdasarkan urutan DNA mitokondria cytochrome c oxidase subunit 1. Berita Biologi 23: 269-283. DOI: 10.55981/beritabiologi.2024.4937. [Indonesian]
LaCava MEF, Gagne RB, Gustafson KD, Oyler?McCance S, Monteith KL, Sawyer H, Kauffman MJ, Thiele DJ, Ernest HB. 2021. Functional connectivity in a continuously distributed, migratory species as revealed by landscape genomics. Ecography 44 (7): 987-999. DOI: 10.1111/ecog.05600.
Li H, Slone J, Fei L, Huang T. 2019. Mitochondrial DNA variants and common diseases: A mathematical model for the diversity of age-related mtDNA mutations. Cells 8: 608. DOI: 10.3390/cells8060608.
Listyarini DW, Sulmartiwi L, Hasan V, Andriyono S. 2022. Karakteristik morfologi dua spesies Mahseer (Cyprinidae; Torinae) asal Jawa Timur. Jurnal Kelautan Perikanan Terapan 5 (2): 171-178. DOI: 10.15578/jkpt.v5i2.11781. [Indonesian]
Loog L. 2021. Sometimes hidden but always there: The assumptions underlying genetic inference of demographic histories. Philos Trans R Soc Lond B Biol Sci 376: 20190719. DOI: 10.1098/rstb.2019.0719.
Maddison DR, Maddison WP. 2018. Mesquite: A modular system for evolutionary analysis. Mesquite 3.5.1.
Makmur S, Muthmainnah D, Subagdja. 2020. Fishery activities and environmental condition of Maninjau Lake, West Sumatra. IOP Conf Ser: Earth Environ Sci 564: 012025. DOI: 10.1088/1755-1315/564/1/012025.
Manel S, Guerin P-E, Mouillot D, Blanchet S, Velez L, Albouy C, Pellisier L. 2020. Global determinants of freshwater and marine fish genetic diversity. Nat Commun 11 (1): 692. DOI: 10.1038/s41467-020-14409-7.
Mar'ie ZA, Allam M. 2019. Molecular phylogenetic linkage for nile and marine puffer fishes using Mitochondrial DNA sequences of cytochrome b and 16S rRNA. Egypt J Aquat Biol Fish 23 (5): 67-80. DOI: 10.21608/ejabf.2019.63606.
Martin AR, Karczewski KJ, Kerminen S et al. 2018. Haplotype sharing provides insights into fine-scale population history and disease in Finland. Am J Hum Genet 102 (5): 760-775. DOI: 10.1016/j.ajhg.2018.03.003.
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. DOI: 10.1002/ece3.4661.
Mesquita N, Carvalho G, Shaw P, Crespo E, Coelho MM. 2001. River basin-related genetic structuring in an endangered fish species, Chondrostoma lusitanicum, based on mtDNA sequencing and RFLP analysis. Heredity 86: 253-264. DOI: 10.1046/j.1365-2540.2001.00776.x.
Milla S, Pasquet A, El Mohajer L, Fontaine P. 2021. How domestication alters fish phenotypes. Rev Aquac 13 (1): 388-405. DOI: 10.1111/raq.12480.
Okonechnikov K, Golosova O, Fursov M, Ugene Team. 2012. Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics 28 (8): 1166-1167. DOI: 1093/bioinformatics/bts091.
Paradis E. 2018. Analysis of haplotype networks: The randomized minimum spanning tree method. Methods Ecol Evol 9 (5): 1308-1317. DOI: 10.1111/2041-210X.12969.
Pavlova A, Beheregaray LB, Coleman R, Gilligan D, Harrisson KA, Ingram BA, Kearns J, Lamb AM, Lintermans M, Lyon J, Nguyen TTT, Sasaki M, Tonkin Z, Yen JDL, Sunnucks P. 2017. Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow. Evol Appl 10 (6): 531-550. DOI: 10.1111/eva.12484.
Paz-Vinas I, Loot G, Stevens VM, Blanchet S. 2015. Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems. Mol Ecol 24: 4586-4604. DOI: 10.1111/mec.13345.
Pereira E, Mateus CS, Alves MJ, Almeida R, Pereira J, Quintella BR, Almeida PR. 2023. Connectivity patterns and gene flow among Chelon ramada populations. Estuar Coast Shelf Sci 281 (12): 108209. DOI: 10.1016/j.ecss.2022.108209.
Pérez-Rodríguez R, Esquivel-Bobadilla S, Orozco-Ruíz AM, Olivas-Hernández JL, García-De León FJ. 2021. Genetic structure and historical and contemporary gene flow of Astyanax mexicanus in the Gulf of Mexico slope: A microsatellite-based analysis. PeerJ 9: e10784. DOI: 10.7717/peerj.10784.
Perini VR, Paschoalini AL, Bazzoli N, Rizzo E, Carvalho DC. 2021. Metapopulation dynamics of the migratory fish Prochilodus lineatus (Characiformes: Prochilodontidae) in a lotic remnant of the Grande River, Southeastern Brazil. Neotrop Ichthyol 19 (4): e200046. DOI: 10.1590/1982-0224-2020-0046.
Phillips JD, Gillis DJ, Hanner RH. 2019. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol Evol 9 (5): 2996-3010. DOI: 10.1002/ece3.4757.
Posada D. 2008. jModelTest: Phylogenetic model averaging. Mol Biol Evol 25 (7): 1253-1256. DOI: 10.1093/molbev/msn083.
Priatna DE, Purnomo T, Kuswanti N. 2016. Kadar logam berat timbal (Pb) pada air dan ikan bader (Barbonymus gonionotus) di Sungai Brantas wilayah Mojokerto. Lentera Bio 5 (1): 48-53. [Indonesian]
Rainboth WJ. 1996. Fishes of the Cambodian Mekong. FAO Species Identification Field Guide For Fishery Purposes. FAO, Rome.
Ren Q, Yang L, Chang C-H, Mayden RL. 2020. Molecular phylogeny and divergence of major clades in the Puntius complex (Teleostei: Cypriniformes). Zool Scr 49 (6): 697-709. DOI: 10.1111/zsc.12442.
Robert TR. 1989. The Freshwater Fishes of Western Borneo. Memoirs of The California Academy of Sciences, San Fransisco.
Rougemont Q, Moore J-S, Leroy T, Normandeau E, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. 2020. Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon. PLoS Genet 16 (8): e1008348. DOI: 10.1371/journal.pgen.1008348.
Rossi G, Plazzi F, Zuffi G, Marchi A, De Bonis S, Valli M, Marinšek P, Falconi R. 2021. Mitochondrial phylogeny and taxonomic revision of Italian and Slovenian fluvio-lacustrine barbels, Barbus sp. (Cypriniformes, Cyprinidae). BMC Zool 6: 8. DOI: 10.1186/s40850-021-00073-x.
Roy S, Behera BK, Ramya VL, Rout AK, Kumar V, Parida PK, Jana AK, Das P, Meena DK, Bhakta D, Alam A, Das BK, Jena J. 2024. Genetic characterization of minor carp (Labeo gonius) from Indian rivers revealed through mitochondrial ATPase 6/8 and D-loop region analysis: Implications for conservation and management. Front Mar Sci 11: 1345649. DOI: 10.3389/fmars.2024.1345649.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34 (12): 3299-3302. DOI: 10.1093/molbev/msx248.
Ryan JRJ, Esa YB. 2006. Phylogenetic analysis of hampala fishes (subfamily Cyprininae) in Malaysia inferred from partial mitochondrial cytochrome B DNA sequences. Zoolog Sci 23 (10): 893-901. DOI: 10.2108/zsj.23.893.
Schwartz MK, Luikart G, Waples RS. 2007. Genetic monitoring as a promising tool for conservation and management. Trends Ecol Evol 22 (1): 25-33. DOI: 10.1016/j.tree.2006.08.009.
Selle ML, Steinsland I, Lindgren F, Brajkovic V, Cubric-Curik V, Gorjanc G. 2021. Hierarchical modelling of haplotype effects on a phylogeny. Front Genet 11: 531218. DOI: 10.3389/fgene.2020.531218.
Souza-Shibatta L, Kotelok-Diniz T, Ferreira DG, Shibatta OA, Sofia SH, de Assumpção L, Pini SFR, Makrakis S, Makrakis MC. 2018. Genetic diversity of the endangered neotropical cichlid fish (Gymnogeophagus setequedas) in Brazil. Front Genet 9: 13. DOI: 10.3389/fgene.2018.00013.
Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30 (9): 1312-1313. DOI: 10.1093/bioinformatics/btu033.
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (3): 585-595. DOI: 10.1093/genetics/123.3.585.
Tang KL, Agnew MK, Hirt MV et al. 2010. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol 57 (1): 189-214. DOI: 10.1016/j.ympev.2010.05.021.
Vidthayanon C. 2002. Peat Swamp Fishes of Thailand. Office of Environmental Policy and Planning, Bangkok.
Wang J, Wu J, Yang J, Chen J, Yang J, Li C, Lin H-D, Zhao J. 2023. Phylogeography and demographic history of the cyprinid fish Barbodes semifasciolatus: Implications for the history of landform changes in south mainland China, Hainan and Taiwan. Front Ecol Evol 11: 1193619. DOI: 10.3389/fevo.2023.1193619.
Washburn BA, Cashner MF, Blanton RE. 2020. Small fish, large river: Surprisingly minimal genetic structure in a dispersal-limited, habitat specialist fish. Ecol Evol 10 (4): 2253-2268. DOI: 10.1002/ece3.6064.
Waskitho NT, Wibowo FAC. 2024. Brantas watershed sustainability analysis: Water quality aspects. Bio Web Conf 143: 01013. DOI: 10.1051/bioconf/202414301013.
Wright S. 1978. The relation of livestock breeding to theories of evolution. J Anim Sci 46: 1192-1200. DOI: 10.2527/jas1978.4651192x.
Zhai D-D, Li W-J, Liu H-Z, Cao W-X, Gao X. 2019b. Genetic diversity and temporal changes of an endemic cyprinid fish species, Ancherythroculter nigrocauda, from the upper reaches of Yangtze River. Zool Res 40 (5): 427-438. DOI: 10.24272/j.issn.2095-8137.2019.027.
Zhai D-D, Zhang Z, Zhang F, Liu H-Z, Cao W-X, Gao X. 2019a. Genetic diversity and population structure of a cyprinid fish (Ancherythroculter nigrocauda) in a highly fragmented river. J Appl Ichthyol 35: 701-708. DOI: 10.1111/jai.13897.
Zhang Q, Sun C, Zhu Y, Xu N, Liu H. 2020. Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management. Glob Ecol Conserv 21: e00876. DOI: 10.1016/j.gecco.2019.e00876.
Zhang Q, Tyler-Smith C, Long Q. 2015. An extended Tajima’s D neutrality test incorporating SNP calling and imputation uncertainties. Stat Interface 8 (4): 447-456. DOI: 10.4310/SII.2015.v8.n4.a4.
Zhang W, Jiang S, Salumy KR, Xuan Z, Xiong Y, Jin S, Gong Y, Wu Y, Qiao H, Fu H. 2022. Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences. Aquac Rep 23: 101086. DOI: 10.1016/j.aqrep.2022.101086.