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RESEARCH ARTICLE
Contents Vol 59(1)

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 Affiliations
- Author Affiliations

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 | GoogleScholarGoogle Scholar | 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 | GoogleScholarGoogle Scholar | 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 | GoogleScholarGoogle Scholar | 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 | GoogleScholarGoogle Scholar | 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 | GoogleScholarGoogle Scholar | 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 | GoogleScholarGoogle Scholar | 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 | GoogleScholarGoogle Scholar | 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 | GoogleScholarGoogle Scholar | PubMed |