Advertisement

DNA Barcoding of Ichthyoplankton and Juvenile Fishes of a Tropical River in Malaysia

  • B. Akbar John
  • Hassan I. Sheikh
  • K. C. A. Jalal
  • B. Y. Kamaruzzaman
  • H. Sanower
  • M. Nur Hanisah
  • M. H. Rahman
  • M. Rozihan
Chapter

Abstract

Taxonomic identification of early larval stages of fishes using conventional morphological keys is extremely laborious due to the overlapping characters shared between genetically closer species. Especially, species-level differentiation during their ontological development is challenging due to paucity of information on their diagnostic features. In the present study, we aimed to use universal DNA barcoding technology to identify ichthyoplankton and juvenile fishes of a tropical river (Kuantan River in Pahang) in Malaysia. This sampling station was chosen in order to check the distribution of juvenile and fish ichthyoplankton samples after the recent massive flood encountered in East Peninsular Malaysia during 2014. We adopted mitochondrial cytochrome oxidase C subunit 1 gene sequencing to identify fish samples. A total of 28 species from 15 families and 5 orders were identified successfully to the species level from the total of 58 DNA barcodes. Unlike the previous report, the most dominant fishes in this study belong to the Cyprinidae family followed by Toxotidae, Ambassidae, and Eleotridae. We admit that the modified bubu light trap method adopted for larval collection in this study has its limitation to attract larvae which had negative phototactic behavior (i.e., Ariidae fishes). Phylogenetic and BLAST analysis showed accuracy of species identification with high bootstrap and percentage similarity value, respectively. Results in this study confirmed the efficiency of universal DNA barcode technology in species-level delimitation of morphologically cryptic species identification. The data presented in this study is valuable for analyzing post-flood effect on fish distribution in tropical river and implementing plans for future fishery resource management in Kuantan River, Pahang, Malaysia.

Keywords

DNA barcoding COX1 gene Fish larvae Ichthyoplankton Kuantan River 

Notes

Acknowledgment

The research work was sponsored under special flood Fundamental Research Grant Scheme (FRGS), Ministry of Science and Technology, Malaysia.

References

  1. Baumgartner G, Nakatani K, Gomes LC, Bialetzki A, Sanches PV (2004) Identification of spawning sites and natural nurseries of fishes in the upper Paraná River, Brazil. Environ Biol Fish 71(2):115–125CrossRefGoogle Scholar
  2. Brown SD, Collins RA, Boyer S, Lefort MC, Malumbres-Olarte J, Vink CJ, Cruickshank RH (2012) Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Mol Ecol Resour 12(3):562–565CrossRefPubMedGoogle Scholar
  3. Bucklin A, Steinke D, Blanco-Bercial L (2011) DNA barcoding of marine metazoa. Annu Rev Mar Sci 3:471–508CrossRefGoogle Scholar
  4. Choat HJ, Doherty PP, Kerrigan BB, Leis JJ (1993) A comparison of towed nets, purse seine and light-aggregation devices for sampling of larvae and pelagic stages of coral reef fishes. Fish Bull 91:195–209Google Scholar
  5. Cooper WJ, Smith LL, Westneat MW (2009) Exploring the radiation of a diverse reef fish family: phylogenetics of the damselfishes (Pomacentridae), with new classifications based on molecular analyses of all genera. Mol Phylogenet Evol 52(1):1–16CrossRefGoogle Scholar
  6. Cowan RS, Chase MW, Kress WJ, Savolainen V (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55(3):611–616CrossRefGoogle Scholar
  7. David O, Larédo C, Leblois R, Schaeffer B, Vergne N (2012) Coalescent-based DNA barcoding: multilocus analysis and robustness. J Comput Biol 19(3):271–278CrossRefPubMedGoogle Scholar
  8. Decru E, Moelants T, De Gelas K, Vreven E, Verheyen E, Snoeks J (2016) Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north-eastern part of the Congo basin. Mol Ecol Resour 16(1):342–352CrossRefPubMedGoogle Scholar
  9. DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc B Biol Sci 360(1462):1905–1916CrossRefGoogle Scholar
  10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  11. Frantine-Silva W, Sofia S, Orsi M, Almeida F (2015) DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring. Mol Ecol Resour 15(5):1226–1237CrossRefPubMedGoogle Scholar
  12. Gleason LU, Burton RS (2012) High-throughput molecular identification of fish eggs using multiplex suspension bead arrays. Mol Ecol Resour 12(1):57–66CrossRefPubMedGoogle Scholar
  13. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci U S A 103(4):968–971CrossRefPubMedPubMedCentralGoogle Scholar
  14. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Paper presented at the Nucleic acids symposium seriesGoogle Scholar
  15. Hausmann A, Miller SE, Holloway JD, deWaard JR, Pollock D, Prosser SW, Hebert PD (2016) Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae) 1. Genome 59(9):671–684CrossRefPubMedGoogle Scholar
  16. Hubert N, Paradis E, Bruggemann H, Planes S (2011) Community assembly and diversification in Indo-Pacific coral reef fishes. Ecol Evol 1(3):229–277CrossRefPubMedPubMedCentralGoogle Scholar
  17. Hubert N, Espiau B, Meyer C, Planes S (2015) Identifying the ichthyoplankton of a coral reef using DNA barcodes. Mol Ecol Resour 15(1):57–67CrossRefPubMedGoogle Scholar
  18. Jalal K, Azfar MA, John BA, Kamaruzzaman Y, Shahbudin S (2012) Diversity and community composition of fishes in tropical estuary Pahang Malaysia. Pak J Zool 44(1):181–187Google Scholar
  19. John BA, Sheikh HI, Jalal K, Zaleha K, Kamaruzzaman B (2016) Revised phylogeny of extant Xiphosurans (Horseshoe Crabs) DNA barcoding in marine perspectives. Springer, Switzerland, pp 113–130CrossRefGoogle Scholar
  20. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120CrossRefGoogle Scholar
  21. Ko H-L, Wang Y-T, Chiu T-S, Lee M-A, Leu M-Y, Chang K-Z, Shao K-T (2013) Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS One 8(1):e53451CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kochzius M, Seidel C, Antoniou A, Botla SK, Campo D, Cariani A, Hjörleifsdottir S (2010) Identifying fishes through DNA barcodes and microarrays. PLoS One 5(9):e12620CrossRefPubMedPubMedCentralGoogle Scholar
  23. Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948CrossRefPubMedPubMedCentralGoogle Scholar
  24. Lewis LA, Richardson DE, Zakharov EV, Hanner R (2016) Integrating DNA barcoding of fish eggs into ichthyoplankton monitoring programs. Fish Bull 114(2):153–166CrossRefGoogle Scholar
  25. Loh W, Bond P, Ashton K, Roberts D, Tibbetts I (2014) DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples. J Fish Biol 85(2):307–328CrossRefPubMedGoogle Scholar
  26. Marques SC, Azeiteiro UM, Marques JC, Neto JM, Pardal MÂ (2006) Zooplankton and ichthyoplankton communities in a temperate estuary: spatial and temporal patterns. J Plankton Res 28(3):297–312CrossRefGoogle Scholar
  27. Meier R, Shiyang K, Vaidya G, Ng PK (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 55(5):715–728CrossRefGoogle Scholar
  28. Mukai Y, Tuzan AD, Lim LS, Wahid N, Raehanah S, Senoo S (2008) Development of sensory organs in larvae of African catfish Clarias gariepinus. J Fish Biol 73(7):1648–1661CrossRefGoogle Scholar
  29. Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R (2008a) Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst Biol 57(5):750–757CrossRefPubMedGoogle Scholar
  30. Munch K, Boomsma W, Willerslev E, Nielsen R (2008b) Fast phylogenetic DNA barcoding. Philos Trans R Soc Lond B Biol Sci 363(1512):3997–4002CrossRefPubMedPubMedCentralGoogle Scholar
  31. Nakatani K (2001) Ovos e larvas de peixes de água doce: desenvolvimento e manual de identificação: Eletrobrás. Uem 2001:ilGoogle Scholar
  32. Nakatani K, Baumgartner G, Latini JD (1998) Morphological description of larvae of the mapara Hypophthalmus edentatus (Spix)(Osteichthyes, Hypophthalmidae) in the Itaipu reservoir (Parana River, Brazil). Revista Brasileira de Zoologia 15(3):687–696CrossRefGoogle Scholar
  33. Overdyk LM, Holm E, Crawford SS, Hanner RH (2016) Increased taxonomic resolution of Laurentian Great Lakes ichthyoplankton through DNA barcoding: a case study comparison against visual identification of larval fishes from Stokes Bay, Lake Huron. J Great Lakes Res 42(4):812–818CrossRefGoogle Scholar
  34. Pegg GG, Sinclair B, Briskey L, Aspden WJ (2006) MtDNA barcode identification of fish larvae in the southern Great Barrier Reef–Australia. Sci Mar 70(S2):7–12CrossRefGoogle Scholar
  35. Pereira LH, Hanner R, Foresti F, Oliveira C (2013) Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genet 14(1):20CrossRefPubMedPubMedCentralGoogle Scholar
  36. Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Vogler AP (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55(4):595–609CrossRefGoogle Scholar
  37. Puillandre N, Lambert A, Brouillet S, Achaz G (2012) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol 21(8):1864–1877CrossRefGoogle Scholar
  38. Ratnasingham S, Hebert PD (2007) BOLD: the barcode of life data system. Mol Ecol Notes 7(3):355–364. http://www.barcodinglife.orgCrossRefPubMedPubMedCentralGoogle Scholar
  39. Ratnasingham S, Hebert PD (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One 8(7):e66213CrossRefPubMedPubMedCentralGoogle Scholar
  40. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425PubMedPubMedCentralGoogle Scholar
  41. Satoh S, Tanoue H, Ruitton S, Mohri M, Komatsu T (2017) Morphological and behavioral ontogeny in larval and early juvenile discus fish Symphysodon aequifasciatus. Ichthyol Res 64(1):37–44CrossRefGoogle Scholar
  42. Spasojevic T, Kropf C, Nentwig W, Lasut L (2016) Combining morphology, DNA sequences, and morphometrics: revising closely related species in the orb-weaving spider genus Araniella (Araneae, Araneidae). Zootaxa 4111(4):448–470CrossRefPubMedGoogle Scholar
  43. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  44. Taylor H, Harris W (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 12(3):377–388CrossRefPubMedGoogle Scholar
  45. Valdez-Moreno M, Vásquez-Yeomans L, Elías-Gutiérrez M, Ivanova NV, Hebert PD (2010) Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula, Mexico: potential in fisheries management. Mar Freshw Res 61(6):655–671CrossRefGoogle Scholar
  46. Vences M, Thomas M, Bonett RM, Vieites DR (2005) Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philos Trans R Soc Lond B Biol Sci 360(1462):1859–1868CrossRefPubMedPubMedCentralGoogle Scholar
  47. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci 360(1462):1847–1857CrossRefPubMedPubMedCentralGoogle Scholar
  48. Ward RD, Hanner R, Hebert PD (2009) The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74(2):329–356CrossRefPubMedGoogle Scholar
  49. Westneat MW, Alfaro ME (2005) Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Mol Phylogenet Evol 36(2):370–390CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • B. Akbar John
    • 1
  • Hassan I. Sheikh
    • 2
  • K. C. A. Jalal
    • 1
  • B. Y. Kamaruzzaman
    • 2
  • H. Sanower
    • 2
  • M. Nur Hanisah
    • 2
  • M. H. Rahman
    • 2
  • M. Rozihan
    • 3
  1. 1.INOCEM Research Station (IRS), Kulliyyah of ScienceInternational Islamic University Malaysia (IIUM)KuantanMalaysia
  2. 2.Department of Biotechnology, Kulliyyah of ScienceInternational Islamic University Malaysia (IIUM)KuantanMalaysia
  3. 3.Department of AquacultureUniversity Putra Malaysia (UPM)SelangorMalaysia

Personalised recommendations