Fisheries and Aquatic Sciences

The Korean Society of Fisheries and Aquatic Science (한국수산과학회)
권호 표지
DOI QR코드

DOI QR Code

DNA barcoding for fish species identification and diversity assessment in the Mae Tam reservoir, Thailand

  • Received : 2023.03.10
  • Accepted : 2023.06.27
  • Published : 2023.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

The purposes of this research were to identify fish species using DNA barcodes or partial sequences of cytochrome b (Cytb) and to assess the diversity of fish in the Mae Tam reservoir, Phayao province, Thailand. Fish samples were collected 3 times, during the winter, summer, and rainy seasons, from 2 sampling sites using gillnets with 3 mesh sizes (30, 50, and 70 mm). A total of 34 representative samples were classified into 12 species, 7 families and 6 orders by morphological- and DNA barcoding-based identifications. However, one cichlid species, Cichlasoma trimaculatum, could only be identified using DNA barcoding. Family Cyprinidae had the greatest diversity, 50.00%. The diversity, richness and evenness indices ranged from 0.43-0.65, 0.64-1.46, and 0.27-0.40, respectively, indicating that fish diversity at both sampling sites was relatively low. A comparison of the catch per unit effort (CPUE) with 3 different mesh sizes found that the 50 mm mesh size was the best (474.80 ± 171.56 g/100 m2/night), followed by the 70 mm (417.41 ± 176.24 g/100 m2/night) and 30 mm mesh sizes (327.88 ± 115.60 g/100 m2/night). These results indicate that DNA barcoding is a powerful tool for species identification. Our data can be used for planning the sustainable management of fisheries resources in the Mae Tam reservoir.

Keywords

Acknowledgement

This research was supported by the University of Phayao (Grant No. R020058209013) and the Unit of Excellence 2023 on Biodiversity and Natural Resources Management, University of Phayao (Grant No. FF66-UoE003).

References

  1. Burgener M. Molecular species differentiation of fish and mammals [Ph.D. dissertation]. Bern: University of Bern; 1997.
  2. Chamason O, Janekitkarn S. Distribution of fishes in Pasak Jolasid reservoir, Lop Buri province. In: Proceedings of 43rd Kasetsart University Annual Conference: Fisheries, Natural Resources and Environmental Economics; 2005; Bangkok, Thailand.
  3. Ciftci Y, Eroglu O, Firidin S. Mitochondrial cytochrome b sequence variation in three sturgeon species (A. stellatus Pallas, 1771, A. gueldenstaedtii Brandt, 1833, H. huso Linnaeus, 1758) from the Black Sea coasts of Turkey. Turk J Fish Aquat Sci. 2013;13:291-303.
  4. Daniel N, Praveenraj J, Suresh E, Karal Marx K, Felix S. Report on the occurrence of invasive alien fish, Cichlasoma trimaculatum (Gunther, 1867) at freshwater lake of Chennai. J Entomol Zool Stud. 2020;8:2418-20.
  5. Doadrio I, Dominguez O. Phylogenetic relationships within the fish family Goodeidae based on cytochrome b sequence data. Mol Phylogenet Evol. 2004;31:416-30. https://doi.org/10.1016/j.ympev.2003.08.022
  6. Guo Q, Liu X, Ao X, Qin J, Wu X, Ouyang S. Fish diversity in the middle and lower reaches of the Ganjiang river of China: threats and conservation. PLOS ONE. 2018;13:e0205116.
  7. Henderson PA, Crampton WGR. A comparison of fish diversity and abundance between nutrient-rich and nutrient-poor lakes in the Upper Amazon. J Trop Ecol. 1997;13:175-98. https://doi.org/10.1017/S0266467400010403
  8. Kartavtsev YP, Park TJ, Vinnikov KA, Ivankov VN, Sharina SN, Lee JS. Cytochrome b (Cyt-b) gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae), with phylogenetic and taxonomic insights. Mar Biol. 2007;152:757-73. https://doi.org/10.1007/s00227-007-0726-9
  9. Keawkhiew P, Keawtip S, Seetakoses P, Montien-art B. Biodiversity of fish in Maesaw creek at the Intiative Highland Agricultural Development Station Project, Ban Santisuk, Khunkual subdistrict, Phong district, Phayao province. J Fish Tech Res. 2013;7:70-81.
  10. Kolding J. The fish resources of Lake Turkana and their environment [Ph.D. dissertation]. Bergen: University of Bergen; 1989.
  11. Krebs CJ. Ecological methodology. New York, NY: Harper & Row; 1989.
  12. Kurzel K, Kaiser S, Lorz AN, Rossel S, Paulus E, Peters J, et al. Correct species identification and its implications for conservation using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a proxy. Front Mar Sci. 2022;8:795196.
  13. Li X, Shen X, Chen X, Xiang D, Murphy RW, Shen Y. Detection of potential problematic Cytb gene sequences of fishes in GenBank. Front Genet. 2018;9:30.
  14. Lin WF, Shiau CY, Hwang DF. Identification of four Thunnus tuna species using mitochondrial cytochrome b gene sequence and PCR-RFLP analysis. J Food Drug Anal. 2005;13:382-7. https://doi.org/10.38212/2224-6614.2566
  15. MaeKa Subdistrict Municipality. Mae Tam reservoir [Internet]. 2023 [cited 2023 Sep 11]. https://online.fliphtml5.com/ghuwe/rzme/#p=2
  16. Malvandi H, Moghanizade R, Abdoli A. The use of biological indices and diversity indices to evaluate water quality of rivers in Mashhad, Iran. Biologia. 2021;76:959-71.
  17. Margalef R. Perspectives in ecological theory. Chicago, IL: University of Chicago Press; 1968.
  18. Nasution SH, Akhdiana I, Muchlis AM, Cinnawara HT. Size distribution and length-weight relationship of invasive species flowerhorn (Cichlasoma trimaculatum (Gunther, 1867) in Lake Mahalona, South Sulawesi. IOP Conf Ser Earth Environ Sci. 2022;1062:012002.
  19. Nelson JS, Grande TC, Wilson MVH. Fishes of the world. 5th ed. Hoboken, NJ: John Wiley & Sons; 2016.
  20. Nguyen HV, Nguyen MT, Vo ND, Phan NTT, Hoang QT. Genetic diversity of spotted scat (Scatophagus argus) in Vietnam based on COI genes. Fish Aquat Sci. 2022;25:637-47. https://doi.org/10.47853/FAS.2022.e58
  21. Noquilla GM. On the occurrence and successful establishment of Cichlasoma trimaculatum (gunther, 1867), an invasive species of cichlid, in Lake Buluan, Philippines. Uttar Pradesh J Zool. 2021;42:1095-9.
  22. Panprommin D, Manosri R. DNA barcoding as an approach for species traceability and labeling accuracy of fish fillet products in Thailand. Food Control. 2022;136:108895.
  23. Parson W, Pegoraro K, Niederstatter H, Foger M, Steinlechner M. Species identification by means of the cytochrome b gene. Int J Legal Med. 2000;114:23-8. https://doi.org/10.1007/s004140000134
  24. Pielou EC. Species-diversity and pattern-diversity in the study of ecological succession. J Theor Biol. 1966;10:370-83. https://doi.org/10.1016/0022-5193(66)90133-0
  25. Rayan S, Chartchumni B, Kaewdonree S, Rayan W. Fish species composition and catch per unit effort in Nong Han wetland, Sakon Nakhon province, Thailand. Songklanakarin J Sci Technol. 2020;42:795-801.
  26. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-25.
  27. Sambrook J, Russell DW. Molecular cloning: a laboratory manual. 3rd ed. Long Island, NY: Cold Spring Harbor Laboratory Press; 2001.
  28. Sezaki K, Kuboshima Y, Mitani I, Fukui A, Watabe S. Identification of chub and spotted mackerels with mitochondrial cytochrome b gene and its application to respective pelagic eggs fixed with formalin. Nihon Suisan Gakkaishi. 2001;67:17-22. https://doi.org/10.2331/suisan.67.17
  29. Shannon CE, Weaver W. The mathematical theory of communication. Urbana, IL: The University of Illinois Press; 1949.
  30. Shen YY, Chen X, Murphy RW. Assessing DNA barcoding as a tool for species identification and data quality control. PLOS ONE. 2013;8:e57125.
  31. Silarudee S, Kongchum P. Masculinization of flowerhorn by immersion in androgens. Silpakorn U Science & Tech J. 2008;2:26-32.
  32. Soontornprasit K, Panprommin D, Khungboon L. Fish communities structure and catch efficiency from gillnets in the Kwan Phayao, Phayao province. Khon Kaen Agr J. 2019a;47:655-66.
  33. Soontornprasit K, Sangsrichan T. Efficiency and selectivity of gillnets in Mae Tam reservoir, Phayao province. In: Proceedings of Phayao Research Conference; 2014; Phayao, Thailand.
  34. Soontornprasit K, Wongkunpilat K, Thammawanta H, Sudrakam S, Sansupa I. Fish communities structure and catch efficiency from gillnets in the Nong Leng Sai Wetland, Phayao province. Khon Kaen Agr J. 2019b;47:1183-94.
  35. Sotelo CG, Calo-Mata P, Chapela MJ, Perez-Martin RI, Rehbein H, Hold GL, et al. Identification of flatfish (Pleuronectiforme) species using DNA-based techniques. J Agric Food Chem. 2001;49:4562-9. https://doi.org/10.1021/jf010452a
  36. Sricharoendham B, Boonthongchuay J, Poomikong P. Spatio-temporal variations in fish community of the Chao Phraya river between 2008 and 2014. Thai Fish Gazette (Thailand). 2015;68:201-23.
  37. Stoneking M, Soodyall H. Human evolution and the mitochondrial genome. Curr Opin Genet Dev. 1996;6:731-6. https://doi.org/10.1016/S0959-437X(96)80028-1
  38. Swingle HS. Relationships and dynamics of balanced and unbalanced fish populations. Alabama: Agricultural Experiment Station of the Alabama Polytechnic Institute Auburn; 1950. Report No.: 274.
  39. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38:3022-7. https://doi.org/10.1093/molbev/msab120
  40. Tobe SS, Kitchener AC, Linacre AMT. Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome B and cytochrome oxidase subunit I mitochondrial genes. PLOS ONE. 2010;5:e14156.
  41. Tuncharoen S, Panprommin D, Soonthornprasit K, Pitakpol S. Spawning season of fishes in Kwan Phayao, Phayao province. Khon Kaen Agr J. 2018;46:147-54.
  42. Tuncharoen S, Uppapong S, Soontornprasit K. Diversity of fishes in Nong Leng Sai Wetland, Phayao province. Khon Kaen Agr J. 2020;48:283-92.
  43. Ulfah M, Fajri SN, Nasir M, Hamsah K, Purnawan S. Diversity, evenness and dominance index reef fish in Krueng Raya Water, Aceh Besar. IOP Conf Ser Earth Environ Sci. 2019;348:012074.
  44. United Nations. Convention on biological diversity [Internet]. 1992 [cited 2023 Feb 9]. https://www.cbd.int/doc/legal/cbden.pdf
  45. Vidthayanon C. Checklist of freshwater fishes in Thailand. Bangkok: Office of Natural Resources and Environmental Policy and Planning; 2017.
  46. Vidthayanon C, Karnasuta J, Nabhitabhata J. Diversity of freshwater fishes in Thailand. Bangkok: Office of Environmental Policy and Planning; 1997.
  47. Ward RD, Hanner R, Hebert PDN. The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol. 2009;74:329-56. https://doi.org/10.1111/j.1095-8649.2008.02080.x
  48. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci. 2005;360:1847-57. https://doi.org/10.1098/rstb.2005.1716
  49. Wilhm JL, Dorris TC. Biological parameters for water quality criteria. BioScience. 1968;18:477-81. https://doi.org/10.2307/1294272
  50. Yang Z, Huang S, Kong W, Yu H, Li F, Khatoon Z, et al. Effect of different fish feeds on water quality and growth of crucian carp (Carassius carassius) in the presence and absence of prometryn. Ecotoxicol Environ Saf. 2021;227:112914.