Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences
RESEARCH ARTICLE

DNA barcoding Australasian chondrichthyans: results and potential uses in conservation

Robert D. Ward A B , Bronwyn H. Holmes A , William T. White A and Peter R. Last A
+ Author Affliations
- Author Affliations

A Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania 7001, Australia.

B Corresponding author. Email: Bob.Ward@csiro.au

Marine and Freshwater Research 59(1) 57-71 https://doi.org/10.1071/MF07148
Submitted: 16 August 2007  Accepted: 17 December 2007   Published: 25 January 2008

Abstract

DNA barcoding – sequencing a region of the mitochondrial cytochrome c oxidase 1 gene (cox1) – promises a rapid and accurate means of species identification, and of any life history stage. For sharks and rays, it may offer a ready means of identifying legal or illegal shark catches, including shark fins taken for the profitable shark fin market. Here it is shown that an analysis of sequence variability in a 655 bp region of cox1 from 945 specimens of 210 chondrichthyan species from 36 families permits the discrimination of 99.0% of these species. Only the two stingarees Urolophus sufflavus and U. cruciatus could not be separated, although these could be readily distinguished from eight other congeners. The average Kimura 2 parameter distance separating individuals within species was 0.37%, and the average distance separating species within genera was 7.48%. Two specimens that clustered with congeners rather than with their identified species-cluster were noted: these could represent instances of hybridisation (although this has not be documented for chondrichthyans), misidentification or mislabelling. It is concluded that cox1 barcoding can be used to identify shark and ray species with a very high degree of accuracy. The sequence variability characteristics of individuals of five species (Aetomylaeus nichofii, Dasyatis kuhlii, Dasyatis leylandi, Himantura gerrardi and Orectolobus maculatus) were consistent with cryptic speciation, and it is suggested that these five taxa be subjected to detailed taxonomic examination to confirm or refute this suggestion. The present barcoding study holds out great hope for the ready identification of sharks, shark products and shark fins, and also highlights some taxonomic issues that need to be investigated further.

Additional keywords: chimaerid, COI, cox1, cytochrome c oxidase, identification, mitochondrial DNA, ray, shark.


Acknowledgements

We thank members of the Biodiversity Institute of Ontario for their considerable assistance in sequencing and in BOLD databasing, especially Paul Hebert, Sujeevan Ratnasingham, Dirk Steinke and Tyler Zemlak. We thank Alastair Graham and Gordon Yearsley of CSIRO Marine and Atmospheric Research (CMAR) for their indispensable assistance with specimen identification and database preparation, and various people for help in collecting specimens, especially Richard Pillans, John Salini and John Stevens of CMAR, Jenny Ovenden, Jenny Giles and Raewyn Street of the Queensland Department of Primary Industries and Fisheries (QDPIF), Fahmi of the Indonesian Institute of Sciences (LIPI) and Dharmadi of the Research Centre for Capture Fisheries (RCCF) in Jakarta, Indonesia. We would also like to thank Janine Caira, Kirsten Jensen and Gavin Naylor for their assistance during National Science Foundation (NSF) funded surveys of the chondrichthyan fishes of Malaysian Borneo, from which some comparitive tissue samples were obtained. We thank Sharon Appleyard and John Pogonoski of CMAR, and three anonymous referees, for helpful comments on an earlier version of the paper.


References

Abercrombie D. (2004). Efficient PCR-based identification of shark products in global trade: applications for the management and conservation of commercially important mackerel sharks (family Lamnidae), thresher sharks (family Alopiidae) and hammerhead sharks (family Sphyrnidae). M.S. thesis. Nova Southeastern University Oceanographic Center, Dania Beach, Florida.

Abercrombie, D. L. , Clarke, S. C. , and Shivji, M. S. (2005). Global-scale genetic identification of hammerhead sharks: application to assessment of the international fin trade and law enforcement. Conservation Genetics 6, 775–788.
CrossRef |

Baum, J. K. , and Myers, R. A. (2004). Shifting baselines and the decline of pelagic sharks in the Gulf of Mexico. Ecology Letters 7, 135–145.
CrossRef |

Baum, J. K. , Kehler, D. , and Myers, R. A. (2005). Robust estimates of decline for pelagic shark populations in the northwest Atlantic and Gulf of Mexico. Fisheries 30(10), 27–29.


Burgess, G. H. , Beerkircher, L. R. , Cailliet, G. M. , Carlson, J. K. , Cortés, E. , Goldman, K. J. , Grubbs, R. D. , Musick, J. A. , Musyl, M. K. , and Simpfendorfer, C. A. (2005). Is the collapse of shark populations in the Northwest Atlantic Ocean and Gulf of Mexico real? Fisheries 30(10), 19–26.
CrossRef |

Casey, J. M. , and Myers, R. A. (1998). Near extinction of a large, widely distributed fish. Science 281, 690–692.
CrossRef | PubMed |

Castro J. I., Woodley C. M., and Brudeck R. L. (1999). A preliminary evaluation of the status of shark species. Fisheries Technical Paper 380 (Food and Agriculture Organisation, Rome.)

Chapman, D. D. , Abercrombie, D. L. , Douady, C. J. , Pikitch, E. K. , Stanhope, M. J. , and Shivji, M. S. (2003). A streamlined, bi-organelle, multiplex PCR approach to species identification: application to global conservation and trade monitoring of the great white shark, Carcharodon carcharias. Conservation Genetics 4, 415–425.
CrossRef |

Compagno L. J. V., Dando M., and Fowler S. (2005). ‘A Field Guide to Sharks of the World.’ (Harper Collins Publishing Ltd: London.)

Daley R. K., Stevens J. D., Last P. R., and Yearsley G. K. (2002). ‘Field Guide to Australian Sharks and Rays.’ (CSIRO Publishing: Melbourne, Australia.)

Dasmahapatra, K. K. , and Mallet, J. (2006). DNA barcodes: recent successes and future prospects. The Journal of Heredity 97, 254–255.
CrossRef |

Dudley, S. F. J. , and Simpfendorfer, C. A. (2006). Population status of 14 shark species caught in the protective gillnets off KwaZulu-Natal beaches, South Africa, 1978–2003. Marine and Freshwater Research 57, 225–240.
CrossRef |

Folmer, O. , Black, M. , Hoeh, W. , Lutz, R. , and Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294–299.
PubMed |

Gardner J. P. A. (1997). Hybridization in the sea. In ‘Advances in Marine Biology’. (Eds J.H.S. Blaxter and A.J. Southward.) Vol 31, pp. 2–78. (Academic Press: New York.)

Graham, K. J. , Andrew, N. L. , and Hodgson, K. E. (2001). Changes in relative abundance of sharks and rays on Australian South East Fishery trawl grounds after twenty years of fishing. Marine and Freshwater Research 52, 549–561.
CrossRef |

Greig, T. W. , Moore, M. K. , Woodley, C. M. , and Quattro, J. M. (2005). Mitochondrial gene sequences useful for species identification of western North Atlantic Ocean sharks. Fishery Bulletin 103, 516–523.


Hajibabaei, M. , de Waard, J. R. , Ivanova, N. V. , Ratnasingham, S. , Dooh, R. T. , Kirk, S. L. , Mackie, P. M. , and Hebert, P. D. N. (2005). Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360, 1959–1967.
CrossRef | PubMed |

Hajibabaei, M. , Smith, M. A. , Janzen, D. H. , Rodriguez, J. J. , Whitfield, J. B. , and Hebert, P. D. N. (2006). A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes 6, 959–964.
CrossRef |

Hauser L. (2007). The molecular ecology of dogfish sharks (Squalus acanthias). In ‘Proceedings of the First International Symposium on Management and Biology of Dogfish Sharks, Seattle June 2006’. (American Fisheries Society Proceedings, in press.)

Hebert, P. D. N. , Cywinska, A. , Ball, S. L. , and de Waard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B, Biological Sciences 270, 313–322.
CrossRef |

Hebert, P. D. N. , Penton, E. H. , Burns, J. M. , Janzen, D. H. , and Hallwachs, W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America 101, 14812–14817.
CrossRef | PubMed |

Hebert, P. D. N. , Stoeckle, M. Y. , Zemlak, T. S. , and Francis, C. M. (2004b). Identification of birds through DNA barcodes. PLoS Biology 2, e312.
CrossRef | PubMed |

Heist, E. J. , and Gold, J. R. (1999). Genetic identification of sharks in the U.S. Atlantic large coastal shark fishery. Fishery Bulletin 97, 53–61.


Hogg, I. D. , and Hebert, P. D. N. (2004). Biological identification of springtails (Collembola: Hexapoda) from the Canadian Arctic, using mitochondrial DNA barcodes. Canadian Journal of Zoology 82, 749–754.
CrossRef |

Human, B. A. , Owen, E. P. , Compagno, L. J. V. , and Harley, E. H. (2006). Testing morphologically based phylogenetic theories within the cartilaginous fishes with molecular data, with special reference to the catshark family (Chondrichthyes; Scyliorhinidae) and the interrelationships within them. Molecular Phylogenetics and Evolution 39, 384–391.
CrossRef | PubMed |

Iglésias, S. P. , Lecointre, G. , and Sellos, D. Y. (2005). Extensive paraphylies within sharks of the order Carcharhiniformes inferred from nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 34, 569–583.
CrossRef | PubMed |

Jensen, A. C. (1966). Life history of the spiny dogfish. Fishery Bulletin 65, 527–554.


Kimura, M. (1980). A simple method of estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111–120.
CrossRef | PubMed |

Kumar, S. , Tamura, K. , and Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5, 150–163.
CrossRef | PubMed |

Last P. R., and Stevens J. D. (1994). ‘Sharks and Rays of Australia.’ CSIRO Publishing: Melbourne, Australia.

Last P. R., White W. T., and Pogonoski J. J. (2007). ‘Descriptions of New Dogfishes of the Genus Squalus (Squaloidea: Squalidae).’ CSIRO Marine and Atmospheric Research Paper 014, Hobart, Australia.

Lipscomb, D. , Platnick, N. , and Wheeler, Q. (2003). The intellectual content of taxonomy: a comment on DNA taxonomy. Trends in Ecology & Evolution 18, 65–66.
CrossRef |

Moritz, C. , and Cicero, C. (2004). DNA barcoding: promise and pitfalls. PLoS Biology 2(10), e354.
CrossRef | PubMed |

Moura, T. , Silva, M. C. , Figueiredo, I. , Neves, A. , Coelho, M. M. , Muñoz, D. , and Gordo, L. (2008). Molecular barcoding of NE Atlantic deep-water sharks: species identifications and application to fisheries management and conservation. Marine and Freshwater Research ,(submitted).


Musick, J. A. , Burgess, G. H. , Camhi, M. , Cailliet, G. , and Fordham, S. (2000). Management of sharks and their relatives (Elasmobranchii). Fisheries 25(3), 9–13.
CrossRef |

Nielsen J. T. (2004). Molecular genetic approaches to species identification and delineation in elasmobranchs. M.S. thesis. (Nova Southeastern University Oceanographic Center, Dania Beach, Florida.)

Pank, M. , Stanhope, M. , Natanson, L. , Kohler, N. , and Shivji, M. (2001). Rapid and simultaneous identification of body parts from the morphologically similar sharks Carcharhinus obscurus and Carcharhinus plumbeus (Carcharhinidae) using multiplex PCR. Marine Biotechnology 3, 213–240.
CrossRef |

Quattro, J. M. , Stoner, D. S. , Driggers, W. B. , Anderson, C. A. , Priede, K. A. , Hoppmann, E. C. , Campbell, N. H. , Duncan, K. M. , and Grady, J. M. (2006). Genetic evidence of cryptic speciation within hammerhead sharks (genus Sphyrna). Marine Biology 148, 1143–1155.
CrossRef |

Ratnasingham, S. , and Hebert, P. D. N. (2007). BOLD: the Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes 7, 355–364.
CrossRef |

Robbins, W. D. , Hisano, M. , Connolly, S. R. , and Choat, J. H. (2006). Ongoing collapse of coral-reef shark populations. Current Biology 16, 2314–2319.
CrossRef | PubMed |

Rocco, L. , Liguori, I. , Costagliola, D. , Morescalchi, M. M. , Tinti, F. , and Stingo, V. (2007). Molecular and karyological aspects of Batoidea (Chondrichthyes, Elasmobranchi) phylogeny. Gene 389, 80–86.
CrossRef | PubMed |

Shivji, M. , Clarke, S. , Pank, M. , Natanson, L. , Kohler, N. , and Stanhope, M. (2002). Genetic identification of pelagic shark body parts for conservation and trade monitoring. Conservation Biology 16, 1036–1047.
CrossRef |

Spies, I. B. , Gaichas, S. , Stevenson, D. E. , Orr, J. W. , and Canino, M. F. (2006). DNA-based identification of Alaska skates (Amblyraja, Bathyraja and Raja: Rajidae) using cytochrome c oxidase subunit I (coI) variation. Journal of Fish Biology 69(Suppl. B), 283–292.
PubMed |

Stevens, J. D. , Bonfil, R. , Dulvy, N. K. , and Walker, P. A. (2000). The effects of fishing on sharks, rays, and chimaeras (chondrichthyans), and the implications for marine ecosystems. ICES Journal of Marine Science 57, 476–494.
CrossRef |

Vogler, A. P. , and Monaghan, M. T. (2007). Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research 45, 1–10.
CrossRef |

Walsh, P. S. , Metzger, D. A. , and Higuchi, R. (1991). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10, 506–513.
PubMed |

Waples, R. S. (1998). Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity 89, 438–450.
CrossRef |

Ward, R. D. , and Holmes, B. H. (2007). An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (coxI) in fishes. Molecular Ecology Notes 7, 899–907.
CrossRef |

Ward, R. D. , Woodwark, M. , and Skibinski, D. O. F. (1994). A comparison of genetic diversity levels in marine, freshwater and anadromous fish. Journal of Fish Biology 44, 213–232.
CrossRef |

Ward, R. D. , Zemlak, T. S. , Innes, B. H. , Last, P. R. , and Hebert, P. D. N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360, 1847–1857.
CrossRef | PubMed |

Ward R. D., Holmes B. H., Zemlak T. S., and Smith P. J. (2007). DNA barcoding discriminates spurdogs of the genus Squalus. In ‘Descriptions of New Dogfishes of the Genus Squalus (Squaloidea: Squalidae.)’ (Eds P. R. Last, W. T. White and J. J. Pogonoski.) pp. 117–130. CSIRO Marine and Atmospheric Research Paper 014, Hobart, Australia.

White W. T., Last P. R., Stevens J. D., and Yearsley G. K. Fahmi, and Dharmadi. (2006). ‘Economically Important Sharks and Rays of Indonesia.’ (ACIAR Monograph Series, No 124, ACIAR Publishing, Canberra.)

Winchell, C. J. , Martin, A. P. , and Mallatt, J. (2004). Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes. Molecular Phylogenetics and Evolution 31, 214–224.
CrossRef | PubMed |



Rent Article (via Deepdyve) Supplementary MaterialSupplementary Material (839 KB) Export Citation Cited By (139)