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Phylogeographic Study of Freshwater Fish Channa striata (Bloch) and Channa punctata (Bloch) Construed Using DNA Barcodes Between Three Rivers in Southern Tamil Nadu Region, India


Channa striata and Channa punctata are freshwater fishes with good nutritional and economic importance. The genus Channa had been reported as a species complex till date and hence, the phylogeographic study based on DNA barcodes for two Channa sp. was initiated to substantiate the genetic diversity with respect to their geographic location. In this study, fish samples of C. striata and C. punctata collected from selected sites in three major rivers (Cauvery, Vaigai and Thamirabarani) flowing through Southern Tamil Nadu region, India. Morphometric and meristic characteristics were recorded. PCR amplification of Cytochrome Oxidase I gene from fishes in each location was sequenced and submitted to Barcode of Life Data System. Three Barcode Index Numbers (BIN’s) were obtained, C. punctata from all sites shared a common BIN AAE8814, C. striata from Cauvery had a different BIN ACB7973 whereas C. striata from Thamirabarani and Vaigai shared an identical BIN AAB2498. The phylogeographic analysis based on Mantel’s test for C. striata yielded a positive correlation between the genetic divergence and geographical distance but for C. punctata it showed negative correlation.

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  1. Adamson, Eleanor A.S., David A. Hurwood, and Peter B. Mather. 2012. Insights into historical drainage evolution based on the phylogeography of the chevron snakehead fish (Channa striata) in the Mekong Basin. Freshwater Biology 57: 2211–2229.

  2. April, J., R.L. Mayden, R.H. Hanner, and L. Bernatchez. 2011. Genetic calibration of species diversity among North Americas freshwater fishes. Proceedings of the National Academy of Sciences 108: 10602–10607.

  3. Avise, J.C., J. Arnold, R.M. Ball, E. Bermingham, T. Lamb, J.E. Neigel, C.A. Reeb, and N.C. Saunders. 1987. Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics. 18: 489–522.

  4. Bernardi, Giacomo, and Nicole L. Crane. 1999. Molecular phylogeny of the humbug damselfishes inferred from mtDNA sequences. Journal of Fish Biology 54: 1210–1217.

  5. Bhat, A.A., M.A. Haniffa, M.J. Milton, B.A. Paray, P.R. Divya, and A. Gopalakrishnan. 2014. Genetic variation of striped snakehead (Channa striatus Bloch, 1793) populations using random amplified polymorphic DNA (RAPD) markers. International Journal of Biodiversity and Conservation 6(5): 363–372.

  6. Bhattacharjee, Maloyjo J., Boni A. Laskar, Bishal Dhar, and Sankar K. Ghosh. 2012. Identification and re-evaluation of freshwater catfishes through DNA Barcoding. PLoS ONE 7: e49950.

  7. Bhuiyan, A.L. 1964. Fishes of Dacca (No. 13). Asiatic Society of Pakistan, 148 pp.

  8. Blagoev, Gergin A., Jeremy R. Dewaard, Sujeevan Ratnasingham, Stephanie L. Dewaard, Lu Liuqiong, James Robertson, Angela C. Telfer, and Paul D.N. Hebert. 2015. Untangling taxonomy: a DNA barcode reference library for Canadian spiders. Molecular Ecology Resources 16: 325–341.

  9. Courtenay, Walter R., and James D. Williams. 2004. Snakeheads (Pisces, Channidae): A biological synopsis and risk assessment. Circular.

  10. Hebert, Paul D.N., Sujeevan Ratnasingham, and Jeremy R. De Waard. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences 270(1): S96–S99.

  11. Kashyap, A., M. Awasthi, and M. Serajuddin. 2016. Geographic morphometric variations of freshwater murrel, Channa punctatus from northern and eastern parts of India. Proceedings of the National Academy of Sciences, India, Section B 86: 367–373.

  12. Lakra, W.S., M. Goswami, A. Gopalakrishnan, D.P. Singh, A. Singh, and N.S. Nagpure. 2010. Genetic relatedness among fish species of Genus Channa using mitochondrial DNA genes. Biochemical Systematics and Ecology 38: 1212–1219.

  13. Li, Xia, Prachya Musikasinthorn, and Yoshinori Kumazawa. 2006. Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences. Ichthyological Research 53: 148–159.

  14. Lombarte, Antoni, Ana Gordoa, Alan K. Whitfield, Nicola C. James, and Víctor M. Tuset. 2012. Ecomorphological analysis as a complementary tool to detect changes in fish communities following major perturbations in two South African estuarine systems. Environmental Biology of Fishes 94: 601–614.

  15. Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27: 209–220.

  16. Mayr, Ernest. 1942. Systematics and the origin of species: From the viewpoint of a zoologist. Nature.

  17. Meier, Rudolf, Guanyang Zhang, and Farhan Ali. 2008. The use of mean instead of smallest interspecific distances exaggerates the size of the “Barcoding Gap” and leads to misidentification. Systematic Biology 57: 809–813.

  18. Muirhead, Jim R., Derek K. Gray, David W. Kelly, Sandra M. Ellis, Daniel D. Heath, and Hugh J. Macisaac. 2008. Identifying the source of species invasions: sampling intensity vs. genetic diversity. Molecular Ecology 17: 1020–1035.

  19. Nagarajan, M., M.A. Haniffa, A. Gopalakrishnan, V.S. Basheer, and A. Muneer. 2006. Genetic variability of Channa punctatus populations using randomly amplified polymorphic DNA. Aquaculture Research 37: 1151–1155.

  20. Negi, R.K., Bheem Dutt Joshi, J.A. Johnson, Rahul De, and Surendra P. Goyal. 2017. Phylogeography of freshwater fish Puntius sophore in India. Mitochondrial DNA Part A 1: 1–13.

  21. Nelson, Joseph S. 2006. Fishes of the world. Bulletin of Marine Science. Vol. 3rd Edition.

  22. Rahman, A.K.A. 2005. Freshwater fishes of Bangladesh, 2nd ed, 394. Dhaka: Zoological Society of Bangladesh, University of Dhaka.

  23. Rahim, M.H.A., A. Rozila, and A.M. Mat Jais. 2009. The Physical-Chemical and Morphological Study of Haruan Channa striatus in Peninsular Malaysia. Research Journal of Biological Sciences 4: 994–1009.

  24. Rainboth, Walter. 1994. Inland fishes of India and adjacent countries. Reviews in Fish Biology and Fisheries 4: 135–136.

  25. Recasens, L., A. Lombarte, and P. Sanchez. 2006. Teleostean fish assemblages in an artificial reef and a natural rocky area in Catalonia (Northwestern Mediterranean): An ecomorphological approach. Bulletin of Marine Science 78: 71–82.

  26. Ruzzante, D.E., C.T. Taggart, D. Cook, and S. Goddard. 1996. Genetic differentiation between inshore and offshore Atlantic Cod (Gadus morhua) Off Newfoundland: Microsatellite DNA variation and antifreeze level. Canadian Journal of Fisheries and Aquatic Sciences 53: 634–645.

  27. Serajuddin, M. 2004. Intraspecific diversity of riverine populations of spiny eel, Mastacembelus armatus. Applied. Fisheries and Aquaculture 4: 25–29.

  28. Shafi, M., and M.M.A. Quddus. 2001. Bangladesher Matsho Shampad (Fisheries of Bangladesh), 301–302. Bangladesh: Kabir publication. Dhaka. (in Bengali).

  29. Siti-Balkhis, Abu Bakar, Amirul Firdaus Jamaluddin Jamsari, Tan Shau Hwai, Zulfigar Yasin, and Mohd Nor Siti-Azizah. 2011. Evidence of geographical structuring in the Malaysian Snakehead, Channa striata based on partial segment of the CO1 gene. Genetics and Molecular Biology 34: 520–523.

  30. Song, Li Min, Kaviarasu Munian, Zulkafli Abd Rashid, and Subha Bhassu. 2013. Characterisation of Asian snakehead Murrel Channa striata (Channidae) in Malaysia: An insight into molecular data and morphological approach. The Scientific World Journal.

  31. Sujeevan, Ratnasingham, and Paul D.N. Hebert. 2013. A DNA-Based registry for all animal species: The Barcode Index Number (BIN) System. PLoS ONE.

  32. Talwar, P. K., and A. G. Jhingran. 1991. Inland fishes of India and adjacent countries, Vol I & II. New Delhi: Oxford & IBH Publishing Co., Pvt. Ltd.

  33. Tan, Min Pau, Amirul Firdaus Jamaluddin Jamsari, and Mohd Nor Siti Azizah. 2012. Phylogeographic Pattern of the Striped Snakehead, Channa striata in Sundaland: Ancient river connectivity, geographical and anthropogenic signatures. PLoS ONE.

  34. Villeger, Sébastien, Julia Ramos Miranda, Domingo Flores Hernandez, and David Mouillot. 2012. Low functional β-Diversity despite high taxonomic β-diversity among tropical estuarine fish communities. PLoS ONE.

  35. Vishwanath, W., and K. Geetakumari. 2009. Diagnosis and interrelationships of fishes of the genus Channa scopoli (Teleostei: Channidae) of northeastern India. Journal of Threatened Taxa 1: 97–105.

  36. Wang, Kaixi, Baosen Wang, Jiongtang Li, Kunci Chen, Xu Peng, and Xiaowen Sun. 2013. The complete mitochondrial genome of Channa maculata (Perciformes: Channidae). Mitochondrial DNA 24: 362–364.

  37. Ward, R.D., R. Hanner, and P.D.N. Hebert. 2009. The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology.

  38. 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 B: Biological Sciences 360: 1847–1857.

  39. Weigt, Lee A., Carole C. Baldwin, Amy Driskell, David G. Smith, Andrea Ormos, and Eric A. Reyier. 2012. Using DNA barcoding to assess Caribbean reef fish biodiversity: Expanding taxonomic and geographic coverage. PLoS ONE.

  40. Zhu, Shu-Ren, Ke-Yi Ma, Zhi-Jun Xing, Nan Xie, Yu-Xi Wang, Qun Wang, and Jia-Le Li. 2012. The complete mitochondrial genome of Channa argus, Channa maculata and hybrid snakehead fish [Channa maculata (♀) × Channa argus (♂)]. Mitochondrial DNA 1: 1–2.

  41. Zhu, Shu Ren, Fu Jian Jun, Qun Wang, and Jia Le Li. 2013. Identification of Channa species using the partial cytochrome c oxidase subunit I (COI) gene as a DNA barcoding marker. Biochemical Systematics and Ecology 51: 117–122.

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The financial support of DST SERB YSP File No: SB/YS/LS-62/2013 and the Instrumentation Facility of CEGS, NRCBS—MKU, CAS is highly acknowledged.

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Correspondence to Ramesh Uthandakalaipandian.

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Kuppu, R., Manoharan, S. & Uthandakalaipandian, R. Phylogeographic Study of Freshwater Fish Channa striata (Bloch) and Channa punctata (Bloch) Construed Using DNA Barcodes Between Three Rivers in Southern Tamil Nadu Region, India. Proc Zool Soc 73, 59–67 (2020).

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  • Murrel
  • Morphometric and meristic characters
  • DNA Barcodes
  • BOLD
  • Phylogeography