Integrative Taxonomy of Riverine Cyprinids (Genera Henicorhynchus and Labiobarbus) in the Mekong Delta: Morphological and DNA Barcoding Approaches
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Abstract
Riverine cyprinids, known as "ca linh" in Viet Nam play a vital role in the economic and ecological systems of the Mekong Delta, particularly during the flooding season. These fish include four species from two genera: Labiobarbus (L. leptocheilus and L. siamensis) and Henicorhynchus (H. entmema and H. siamensis). Identifying species within each genus is challenging for non-ichthyologists due to their similar external appearance, particularly at early developmental stages. This study aimed to combine morphological and DNA-based approaches to comprehensively analyze morphological variations and DNA barcoding of riverine cyprinids in the Mekong Delta, Viet Nam. Fish samples were collected along the Mekong River during the flooding seasons. Initially, morphological classification was performed, including the measurement of meristic and morphometric parameters. The results revealed additional morphometric differences between congeneric species. Subsequently, the cytochrome c oxidase subunit I (COI) gene of each species was sequenced. The Kimura 2-parameter (K2P) genetic distances between the two species within each genus, Labiobarbus and Henicorhynchus, were 0.0878±0.0135 and 0.1005±0.123, respectively. Meanwhile, intraspecific genetic distances ranged from 0 to 0.0046. The findings emphasize the importance of integrating traditional morphological taxonomy with molecular methods to overcome challenges in fish species identification.
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References
Bhattacharya, M., A.R. Sharma, B.C. Patra, G. Sharma, E.M. Seo, J.S. Nam, C. Chakraborty and S.S. Lee. 2016. DNA barcoding to fishes: Current status and future directions. Mitochondrial DNA 27(4): 2744–2752. DOI: 10.3109/19401736.2015.1046175.
Bingpeng, X., H. Heshan, Z. Zhilan, C. Chunguang, Y. Yanguo and J. Jianjun. 2018. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS ONE 13(6): e0198109. DOI: 10.1371/journal.pone.0198109.
Chen, W., C. Li, J. Yang, S. Zhu, J. Li, Y. Li and X. Li. 2021. Temporal species–level composition of larvae resources in the lower Pearl River drainage and implications for species’ reproductive cycles. Gene 776: 145351. DOI: 10.1016/j.gene.2020.145351.
Chhorn, M. and T.Y. Duong. 2022. Identification of Phalacronotus bleekeri (Günther, 1864) (Siluridae) from the Mekong Delta, Vietnam, and use of morphological analysis to separate populations. Asian Fisheries Science 35: 139–148. DOI: 10.33997/j.afs.2022.35.2.005.
Ciccotto, P.J. and L.M. Page. 2020. Revision of the genus Henicorhynchus, with a revised diagnosis of Gymnostomus (Cyprinidae: Labeoninae). Copeia 108(3): 485–502. DOI: 10.1643/CI–19–304.
Collins, R.A., K.F. Armstrong, R. Meier, Y. Yi, S.D.J. Brown, R.H. Cruickshank, S. Keeling and C. Johnston. 2012. Barcoding and border biosecurity: Identifying cyprinid fishes in the aquarium trade. PLoS ONE 7(1): e28381. DOI: 10.1371/journal.pone.0028381.
Duong, T.Y., L.V.D. Tran, N.T.T. Nguyen, J.A.F. Jamaluddin and M.N.S. Azizah. 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. DOI: 10.4081/tz.2020.72.
Elliott, N.G., K. Haskard and J.A. Koslow. 1995. Morphometric analysis of orange roughy (Hoplostethus atlanticus) off the continental slope of southern Australia. Journal of Fish Biology 46(2): 202–220. DOI: 10.1111/j.1095–8649.1995.tb05962.x.
Fadli, N., A. Damora, Z.A. Muchlisin, M. Ramadhaniaty, N.M. Razi, S.R. Rahayu, E.D. Macusi, A. Habib and M.N. Siti–Azizah. 2023. Morphometric and genetic variations of three grouper species (genus Epinephelus) from the northern region of Aceh province, Indonesia. Zoologischer Anzeiger 307: 89–95. DOI: 10.1016/j.jcz.2023.10.002.
Fricke, R., W.N. Eschmeyer and J.D. Fong. 2025. Eschmeyer’s catalog of fishes: Species by family/subfamily. https://researcharchive.calacademy.org. Cited 11 Jan 2025.
Hebert, P.D.N., A. Cywinska, S.L. Ball and J.R. deWaard. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270(1512): 313–321. DOI: 10.1098/rspb.2002.2218.
Hebert, P.D.N. and T.R. Gregory. 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54: 852–859. DOI: 10.1080/10635150500354886.
Hubert, N., R. Hanner, E. Holm, et al. 2008. Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 3: e2490. DOI: 10.1371/journal.pone.0002490.
Ivanova, N.V., T.S. Zemlak, R.H. Hanner and P.D.N. Hebert. 2007. Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7(4): 544–548. DOI: 10.1111/j.1471–8286.2007.01748.x.
Kappel, K. and U. Schröder. 2020. Difficulties in DNA barcoding–based authentication of snapper products due to ambiguous nucleotide sequences in public databases. Food Control 118: 107348. DOI: 10.1016/j.foodcont.2020.107348.
Kottelat, M. 2001. Fishes of Laos. WHT Publications Ltd., Colombo 5, Sri Lanka. 198 pp.
Kottelat, M. 2003. Nomenclatural status of Crossocheilus burmanicus, C. horai and C. multirastellatus (Osteichthyes: Cyprinidae). Raffles Bulletin of Zoology, 51(2): 399–401.
Kottelat, M. 2013. The fishes of the inland waters of Southeast Asia: A catalogue and core bibliography of the fishes known to occur in freshwaters, mangroves and estuaries. Raffles Bulletin of Zoology, Supplement 27: 1–663.
Kumar, S., G. Stecher, M. Li, C. Knyaz and K. Tamura. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution 35(6): 1547–1549. DOI: 10.1093/molbev/msy096.
Lakra, W.S., M.S. Verma, M. Goswami, K.K. Lal, V. Mohindra, P. Punia, A. Gopalakrishnan, K.V. Singh, R.D. Ward and P. Hebert. 2011. DNA barcoding Indian marine fishes. Molecular Ecology Resources 11: 60–71. DOI: 10.1111/j.1755–0998.2010.02894.x.
Mekong River Commission (MRC). 2024. Mekong Basin. Mekong River Commission for Sustainable Development. https://www.mrcmekong.org/. Cited 30 May 2024.
Nagao Natural Environment Foundation. 2021. Fishes of the Indochinese Mekong. Nagao Natural Environment Foundation, Tokyo, Japan. 546 pp.
Page, L.M., B.C. Ray, S. Tongnunui, D.A. Boyd and Z.S. Randall. 2020. Garra surinbinnani, a new species of labeonine from the Mae Khlong basin of Thailand (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters 29(4): 321–335. DOI: 10.23788/IEF–1117.
Panprommin, D., N. Iamchuen, K. Soontornprasit and S. Tuncharoen. 2020. The utility of DNA barcoding for the species identification of larval fish in the lower Ing River, Thailand. Turkish Journal of Fisheries and Aquatic Sciences 20(9): 671–679. DOI: 10.4194/1303–2712–v20_9_02.
Panprommin, D., K. Soontornprasit, S. Tuncharoen and N. Iamchuen. 2021. Efficacy of DNA barcoding for the identification of larval fish species in the upper and middle Ing River, Thailand. Gene Reports 23: 101057. DOI: 10.1016/j.genrep.2021.101057.
Pasco–Viel, E., L. Yang, M. Veran, V. Balter, R.L. Mayden, V. Laudet and L. Viriot. 2014. Stability versus diversity of the dentition during evolutionary radiation in cyprinine fish. Proceedings of the Royal Society B: Biological Sciences 281: 20132688. DOI: 10.1098/rspb.2013.2688.
Rahayu, S.R., Z.A. Muchlisin, N. Fadli, et al. 2023. Morphometric and genetic variations of four dominant species of snappers (Lutjanidae) harvested from the Northern Coast of Aceh waters, Indonesia. Zoologischer Anzeiger 303: 26–32. DOI: 10.1016/j.jcz.2023.01.008.
Rainboth, W.J. 1996. Fishes of the Cambodian Mekong. FAO Species Identification Field Guide for Fishery Purposes. Food and Agriculture Organization of the United Nations, Rome, Italy. 310 pp.
Rainboth, W.J., C. Vidthayanon and M.D. Yen. 2012. Fishes of the Greater Mekong Ecosystem with Species List and Photographic Atlas. Miscellaneous publications, Museum of Zoology, University of Michigan, Michigan State, USA. 173 pp.
Renaud, F.G. and C. Kuenzer. 2012. The Mekong Delta System: Interdisciplinary Analyses of a River Delta. Springer Environmental Science and Engineering, Dordrecht, Netherlands. 464 pp.
Roberts, T.R. 1993. Systematic revision of the Southeast Asian cyprinid fish genus Labiobarbus (Teleostei: Cyprinidae). Raffles Bulletin of Zoology 41: 315–329.
Sade, A. and H. Biun. 2012. The ichthyofauna of Maliau Basin buzzer zone at Maliau Basin Conservation Area, Sabah, Malaysia. Journal of Tropical Biology and Conservation 9(1): 105–113.
Saporito–Irwin, S.M., T. Geist and D.H. Gutmann. 1997. Ammonium acetate protocol for the preparation of plasmid DNA suitable for mammalian cell transfections. BioTechniques 23(3): 424–427. DOI: 10.2144/97233bm16.
Schneider, C.A., W.S. Rasband and K.W. Eliceiri. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9(7): 671–675. DOI: 10.1038/nmeth.2089.
Shen, Y., L. Guan, D. Wang and X. Gan. 2016. DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecology and Evolution 6(9): 2702–2713. DOI: 10.1002/ece3.2060.
Sor, R., P.B. Ngor, S. Lek, K. Chann, R. Khoeun, S. Chandra, Z.S. Hogan and S.E. Null. 2023. Fish biodiversity declines with dam development in the Lower Mekong Basin. Scientific Reports 13: 8571. DOI: 10.1038/s41598–023–35665–9.
Tamura, K. and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10: 512–526.
Tran, D.D., K. Shibukawa, T.P. Nguyen, P.H. Ha, X.L. Tran, V.H. Mai and K. Utsugi. 2013. Fishes of the Mekong Delta, Viet Nam. Can Tho University Publishing House, Can Tho, Viet Nam. 174 pp.
Tsoupas, A., S. Papavasileiou, S. Minoudi, K. Gkagkavouzis, O. Petriki, D. Bobori, A. Sapounidis, E. Koutrakis, I. Leonardos, N. Karaiskou and A. Triantafyllidis. 2022. DNA barcoding identification of Greek freshwater fishes. PLoS ONE 17: e0263118. DOI: 10.1371/journal.pone.0263118.
Van der Walt, K.A., T. Mäkinen, E.R. Swartz and O.L.F. Weyl. 2017. DNA barcoding of South Africa’s ornamental freshwater fish–are the names reliable? African Journal of Aquatic Science 42(2): 155–160. DOI: 10.2989/16085914.2017.1343178.
Van Ginneken, M., E. Decru, E. Verheyen and J. Snoeks. 2017. Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa. European Journal of Taxonomy 310: 1–32. DOI: 10.5852/ejt.2017.310.
Vu, D.H.Q., T.B. Dang, T.O. Truong and T.P.L. Thai. 2014. DNA barcoding of freshwater fishes in the Mekong Delta. Can Tho University Journal of Science Special Issue 1: 123–131.
Ward, R.D., R. Hanner and P.D.N. Hebert. 2009. The campaign to DNA barcode all fishes, FISH–BOL. Journal of Fish Biology 74: 329–356. DOI: 10.1111/j.1095–8649.2008.02080.x.
Ward, R.D., T.S. Zemlak, B.H. Innes, P.R. Last and P.D.N. Hebert. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 360(1462): 1847–1857. DOI: 10.1098/rstb.2005.1716.
Yang, L., M. Arunachalam, T. Sado, et al. 2012. Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). Molecular Phylogenetics and Evolution 65(2): 362–379. DOI: 10.1016/j.ympev.2012.06.007.
Zhang, J.B. and R. Hanner. 2011. DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochemical Systematics and Ecology 39(1): 31–42. DOI: 10.1016/j.bse.2010.12.017.
Zheng, L.P., J.X. Yang, X.Y. Chen and W.Y. Wang. 2010. Phylogenetic relationships of the Chinese Labeoninae (Teleostei, Cypriniformes) derived from two nuclear and three mitochondrial genes. Zoologica Scripta 39(6): 559–571. DOI: 10.1111/j.1463–6409.2010.00441.x.
Zheng, L.P., J.X. Yang and X.Y. Chen. 2012. Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography. Current Zoology 58(6): 837–850. DOI: 10.1093/czoolo/58.6.837.
