Skip to main content

Advertisement

SpringerLink
Log in

DNA barcoding to characterize biodiversity of freshwater fishes of Egypt

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity (π) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W (2018) DNA barcoding for identification of fish species in the Taiwan Strait. PLoS ONE 13(6):e0198109

    PubMed  PubMed Central  Google Scholar 

  2. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc B Biol Sci 360(1462):1847–1857

    CAS  Google Scholar 

  3. Rasmussen RS, Morrissey MT, Hebert PDN (2009) DNA barcoding of commercially important salmon and trout species (Oncorhynchus and Salmo) from North America. J Agric Food Chem 57(18):8379–8385

    CAS  PubMed  Google Scholar 

  4. Ardura A, Planes S, Garcia-Vazquez E (2013) Applications of DNA barcoding to fish landings: authentication and diversity assessment. ZooKeys 365:49

    Google Scholar 

  5. Vartak VR, Narasimmalu R, Annam PK, Singh DP, Lakra WS (2015) DNA barcoding detected improper labelling and supersession of crab food served by restaurants in India. J Sci Food Agric 95(2):359–366

    CAS  PubMed  Google Scholar 

  6. Triantafyllidis A, Bobori D, Koliamitra C, Gbandi E, Mpanti M, Petriki O, Karaiskou N (2011) DNA barcoding analysis of fish species diversity in four north Greek lakes. Mitochondrial DNA 22(sup1):37–42

    CAS  PubMed  Google Scholar 

  7. Zhang J-B, Hanner R (2011) DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochem Syst Ecol 39(1):31–42

    Google Scholar 

  8. Keskİn E, Atar HH (2013) DNA barcoding commercially important fish species of Turkey. Mol Ecol Resour 13(5):788–797

    PubMed  Google Scholar 

  9. Steinke D, Zemlak TS, Hebert PDN (2009) Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS ONE 4(7):e6300

    PubMed  PubMed Central  Google Scholar 

  10. Landi M, Dimech M, Arculeo M, Biondo G, Martins R, Carneiro M, Carvalho GR, Brutto SL, Costa FO (2014) DNA barcoding for species assignment: the case of Mediterranean marine fishes. PLoS ONE 9(9):e106135

    PubMed  PubMed Central  Google Scholar 

  11. Ali FS, Ismail M, Mamoon A (2019) Comparative molecular identification of genus dicentrarchus using mitochondrial genes and internal transcribed spacer region. Egypt J Aquat Biol Fish 23(3):371–384. https://doi.org/10.21608/ejabf.2019.47385

    Article  Google Scholar 

  12. Handy SM, Deeds JR, Ivanova NV, Hebert PDN, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF (2011) A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. J AOAC Int 94(1):201–210

    CAS  PubMed  Google Scholar 

  13. Costa FO, Antunes PM (2012) The contribution of the Barcode of Life initiative to the discovery and monitoring of biodiversity. In: Mendonca A, Cunha A, Chakrabarti R (eds) Natural resources, sustainability and humanity. Springer, Berlin, pp 37–68

    Google Scholar 

  14. Iyiola OA, Nneji LM, Mustapha MK, Nzeh CG, Oladipo SO, Nneji IC, Okeyoyin AO, Nwani CD, Ugwumba OA, Ugwumba AAA (2018) DNA barcoding of economically important freshwater fish species from north-central Nigeria uncovers cryptic diversity. Ecol Evol 8(14):6932–6951

    PubMed  PubMed Central  Google Scholar 

  15. Hebert PDN, Ratnasingham S, De Waard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond Ser B Biol Sci 270(suppl_1):S96–S99

    CAS  Google Scholar 

  16. Staffen CF, Staffen MD, Becker ML, Löfgren SE, Muniz YCN, de Freitas RHA, Marrero AR (2017) DNA barcoding reveals the mislabeling of fish in a popular tourist destination in Brazil. PeerJ 5:e4006

    PubMed  PubMed Central  Google Scholar 

  17. FAO (2018) The state of world fisheries and aquaculture 2018-meeting the sustainable development goals. FAO, Rome

    Google Scholar 

  18. Hughes JB, Daily GC, Ehrlich PR (1997) Population diversity: its extent and extinction. Science 278(5338):689–692

    CAS  PubMed  Google Scholar 

  19. El Sayed SM, Hegab MH, Mola HRA, Ahmed NM, Goher ME (2020) An integrated water quality assessment of Damietta and Rosetta branches (Nile River, Egypt) using chemical and biological indices. Environ Monit Assess 192(4):1–16

    Google Scholar 

  20. Abdel-Satar AM, Ali MH, Goher ME (2017) Indices of water quality and metal pollution of Nile River, Egypt. Egypt J Aquat Res 43(1):21–29

    Google Scholar 

  21. Hamza W (2014) The Nile fishes and fisheries. In: Grillo O (ed) Biodiversity-the dynamic balance of the planet. Rijeka, Intech, pp 349–370

    Google Scholar 

  22. Mahmoud HH, Mazrouh MM (2008) Biology and fisheries management of Tilapia species in Rosetta branch of the Nile River, Egypt. Egypt J Aquat Res 30:272–285

    Google Scholar 

  23. Reid GM (2013) Introduction to freshwater fishes and their conservation. Int Zoo Yearb 47(1):1–5

    Google Scholar 

  24. Nwani CD, Becker S, Braid HE, Ude EF, Okogwu OI, Hanner R (2011) DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species. Mitochondrial DNA 22(sup1):43–51

    CAS  PubMed  Google Scholar 

  25. Swartz ER, Mwale M, Hanner R (2008) A role for barcoding in the study of African fish diversity and conservation. S Afr J Sci 104(7–8):293–298

    Google Scholar 

  26. 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):342–352

    CAS  PubMed  Google Scholar 

  27. Lakra WS, Singh M, Goswami M, Gopalakrishnan A, Lal KK, Mohindra V, Sarkar UK, Punia PP, Singh KV, Bhatt JP (2016) DNA barcoding Indian freshwater fishes. Mitochondrial DNA Part A 27(6):4510–4517

    CAS  Google Scholar 

  28. Fouda MM (2014) Egypt fifth national report to the convention on biological diversity. https://www.cbd.int/doc/world/eg/eg-nr-05-en.pdf

  29. Abdel-Meguid AM (2017) Ecosystem and biodiversity in the Nile Basin case study: Lake Nasser. In: Negm AM (ed) The Nile River. Springer, Basel, pp 305–353

    Google Scholar 

  30. Khalifa US, Agaypi MZ, Adam HA (2000) The population dynamics of Oreochromis niloticus and Sarotherodon galilaeus. In: Craig JF (ed) Sustainable fish production in Lake Nasser ecological basis and management policy. ICLARM, Philippines, pp 161–184

    Google Scholar 

  31. Shalloof KA, El-Far A (2010) Population structure and catch per unit effort (CPUE) in the main stream, Rosetta and Damietta branches of the River Nile, Egypt. Egypt J Aquat Res 36(3):435–443

    Google Scholar 

  32. Boulenger GA (1909) Catalogue of the fresh-water fishes of Africa in the British Museum (Natural History), vol I. FRS, London

    Google Scholar 

  33. Boulenger GA (1911) Catalogue of the fresh-water fishes of Africa in the British Museum (Natural History), vol II. FRS, London

    Google Scholar 

  34. Boulenger GA (1915) Catalogue of the fresh-water fishes of Africa in the British Museum (Natural History), vol III. FRS, London

    Google Scholar 

  35. Boulenger GA (1916) Catalogue of the fresh-water fishes of Africa in the British Museum (Natural History), vol IV. FRS, London

    Google Scholar 

  36. Froese R, Pauly D (2019) FishBase. World wide web electronic publication. Accessed 12 May 2019

  37. Ali FS, Mamoon A (2019) Population genetic studies of genus Dicentrarchus reveal loss of genetic diversity in Egyptian waters. Reg Stud Mar Sci 31:100783

    Google Scholar 

  38. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium, London. Information Retrieval Ltd., pp 95–98

  39. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425

    CAS  PubMed  Google Scholar 

  40. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120

    CAS  PubMed  Google Scholar 

  41. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE 8(7):e66213. https://doi.org/10.1371/journal.pone.0066213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Pulliandre N, Lambert A, Brouillet S, Achaz G (2011) ABGD, automated barcode gap discovery for primary species delineation. Mol Ecol 21:1864–1877

    Google Scholar 

  44. Nei M, Miller JC (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 125(4):873–879

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 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

    CAS  PubMed  Google Scholar 

  46. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York

    Google Scholar 

  47. Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9(5):945–967

    CAS  Google Scholar 

  48. Sparks JS, Smith WL (2004) Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae). Cladistics 20(6):501–517

    PubMed  Google Scholar 

  49. Nile Basin Initiative (2012) State of the River Nile Basin Report. Entebbe, Uganda

    Google Scholar 

  50. Pradhan V, Kamble Y, Ladniya V, Mogul M (2015) An overview of species identification by DNA barcoding. Int J Curr Microbiol Appl Sci 4(4):127–140

    CAS  Google Scholar 

  51. van der Walt KA, Mäkinen T, Swartz ER, Weyl OLF (2017) DNA barcoding of South Africa’s ornamental freshwater fish—are the names reliable? Afr J Aquat Sci 42(2):155–160

    Google Scholar 

  52. Wang L, Wu Z, Liu M, Liu W, Zhao W, Liu H, You F (2018) DNA barcoding of marine fish species from Rongcheng Bay, China. PeerJ 6:e5013

    PubMed  PubMed Central  Google Scholar 

  53. Lakra WS, Verma MS, Goswami M, Lal KK, Mohindra V, Punia P, Gopalakrishnan A, Singh KV, Ward RD, Hebert P (2011) DNA barcoding Indian marine fishes. Mol Ecol Resour 11(1):60–71

    CAS  PubMed  Google Scholar 

  54. Deichmann JL, Mulcahy DG, Vanthomme H, Tobi E, Wynn AH, Zimkus BM, McDiarmid RW (2017) How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation. PLoS ONE 12(11):e0187283

    PubMed  PubMed Central  Google Scholar 

  55. Hinchliff CE, Smith SA (2014) Some limitations of public sequence data for phylogenetic inference (in plants). PloS ONE 9(7):e1001127

    Google Scholar 

  56. Lin XL, Stur E, Ekrem T (2018) Exploring species boundaries with multiple genetic loci using empirical data from non-biting midges. Zoolog Scr 47(3):325–341

    Google Scholar 

  57. Nneji LM, Adeola AC, Okeyoyin AO, Oladipo OC, Saidu Y, Usongo JY, Ugwumba AAA (2019) Assessing the effectiveness of molecular data for species identification and diversity studies of Nigerian herpetofauna. Mitochondrial DNA Part B 4(1):589–593

    Google Scholar 

  58. Salzburger W (2009) The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes. Mol Ecol 18(2):169–185

    PubMed  Google Scholar 

  59. Nelson JS, Grande TC, Wilson MVH (2016) Fishes of the World. Wiley, New Jersey

    Google Scholar 

  60. Barasa JE, Abila R, Grobler JP, Agaba M, Chemoiwa EJ, Kaunda-Arara B (2016) High genetic diversity and population differentiation in Clarias gariepinus of Yala Swamp: evidence from mitochondrial DNA sequences. J Fish Biol 89(6):2557–2570

    CAS  PubMed  Google Scholar 

  61. 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

    PubMed  PubMed Central  Google Scholar 

  62. GAFRD (2019) 2017 fish statistics yearbook, vol 27. General Authority for Fish Resources Development, Ministry of Agriculture, Egypt

    Google Scholar 

Download references

Acknowledgements

This study was funded by the National Institute of Oceanography and Fisheries (NIOF), Egypt. We deeply thank Dr. Mohammed Saad for his assistance during the samples collection and Dr. Ahmed Mamoon for his help in sequencing procedures.

Author information

Authors and Affiliations

  1. Genetics Laboratory, Aquaculture Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt

    Fawzia S. Ali

  2. Genetics Department, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt

    Mohamed Ismail

  3. Fisheries Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt

    Walid Aly

Authors
  1. Fawzia S. Ali
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mohamed Ismail
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Walid Aly
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fawzia S. Ali.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Ethical approval

We did not require ethical approval as samples were collected from the commercial fisheries then transferred frozen to the laboratory.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 3766 kb)

Supplementary material 2 (DOCX 4407 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ali, F.S., Ismail, M. & Aly, W. DNA barcoding to characterize biodiversity of freshwater fishes of Egypt. Mol Biol Rep 47, 5865–5877 (2020). https://doi.org/10.1007/s11033-020-05657-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-020-05657-3

Keywords

Search

Navigation