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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.


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