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RESEARCH ARTICLE
Contents Vol 59(3)

Molecular barcoding of north-east Atlantic deep-water sharks: species identification and application to fisheries management and conservation

Teresa Moura A C E , Mónica C. Silva B , Ivone Figueiredo A , Ana Neves C , Pablo Durán Muñoz D , Maria Manuela Coelho B and Leonel S. Gordo C
+ Author Affiliations
- Author Affiliations

A Unidade de Recursos Marinhos e Sustentabilidade, Instituto de Investigação das Pescas e do Mar (IPIMAR-INRB), Av. Brasília, 1449-006 Lisboa, Portugal.

B Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Bloco C2-3°Piso, Campo Grande, 1749-016 Lisboa, Portugal.

C Departamento de Biologia Animal and Instituto de Oceanografia, Faculdade de Ciências, Universidade de Lisboa, Bloco C8, Campo Grande, 1749-016 Lisboa, Portugal.

D Instituto Español de Oceanografía, Programa de Pesquerías Lejanas, Centro Oceanográfico de Vigo, Apartado 1552, Spain.

E Corresponding author. Email: tmoura@ipimar.pt

Marine and Freshwater Research 59(3) 214-223 https://doi.org/10.1071/MF07192
Submitted: 19 October 2007  Accepted: 26 January 2008   Published: 30 April 2008

Abstract

Two genera of elasmobranchii, Centrophorus and Centroscymnus, include species that represent the highest landings of deep-water sharks caught by fishing fleets operating in the north-east Atlantic. There are morphology-based identification problems among and within genera, and landings of processed shark products further prevent an objective assessment of these species. The present study is the first attempt to test the suitability of using a DNA barcode approach to discriminate accurately among the four most important commercial deep-water shark species: Centrophorus squamosus, Centrophorus granulosus, Centroscymnus coelolepis and, recently discovered in Portuguese ports, Centroscymnus owstoni. Sequence analyses of the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene revealed low levels of haplotypic and genetic diversities. Higher levels of inter-specific relative to intra-specific divergences allowed discrimination among species, which form reciprocally monophyletic clades. Inclusion of published COI sequences from other species within the same genera revealed haplotype sharing among species, which calls into question the current taxonomy and accuracy of fisheries data available. Amplification of the COI gene coupled with MboI restriction digests was found to be a fast and inexpensive strategy to resolve within genera identification problems. Molecular barcoding constitutes a critical tool for the assessment and implementation of urgent management policies for this group of species.

Additional keywords: Centrophorus, Centroscymnus, coxI, cytochrome c oxidase subunit I, restriction digest fragment analysis.


Acknowledgements

We would like to thank the members of the M. Coelho laboratory, B. Pereira (IPIMAR) and P. Machado (IPIMAR) for their expertise and help at various stages of this work. We also thank the crew of the ‘AQUIVARI’ (Sesimbra) for the support and providing tissue samples. J. C. Silva, M. A. Aboim, A. R. Amaral provided helpful comments on the manuscript. We are also grateful to Dr Robert Ward, the editor and an anonymous referee for their useful comments and suggestions. T. Moura and M. C. Silva were each funded by grants from the Fundação para a Ciência e a Tecnologia, respectively SFRH/BD/29052/2006 and SFRH/BPD/22276/2005. The present study was partially supported by the Project TUBAPROF (MARE 22–05–01-FEDER-00028, co-financed by the EU) and PNAB EU/DCR. A special thanks to the Project ECOVUL/ARPA 2005/10 of the C. O. de Vigo from the Instituto Español de Oceanografía, which allowed the collection of the Hatton Bank samples.


References

Amaral, A. R. , Sequeira, M. , and Coelho, M. M. (2007). A first approach to the usefulness of cytochrome c oxidase I barcodes in the identification of closely related delphinid cetacean species. Marine and Freshwater Research 58, 505–510.
| Crossref | GoogleScholarGoogle Scholar | Avise J. C. (2000). ‘Phylogeography: the History and Formation of Species.’ (Harvard University Press: Cambridge, MA.)

Bikandi, J. , San Millán, R. , Rementeria, A. , and Garaizar, J. (2004). In silico analysis of complete bacterial genomes: PCR, AFLP-PCR, and endonuclease restriction. Bioinformatics 20, 798–799.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Castro J. I., Woodley C. M., and Brudek R. L. (1999). ‘A preliminary evaluation of the status of shark species.’ Food and Agriculture Organization of the United Nations, FAO Fisheries Technical Paper No. 380, Rome.

Clarke, M. , Borges, L. , and Officer, R. (2005). Comparisons of trawl and longline catches of deep-water elasmobranchs west and north of Ireland. Journal of Northwest Atlantic Fishery Science 35, 429–442.
| Crossref | GoogleScholarGoogle Scholar | Compagno L. J. V., and Niem V. H. (1998). Squalidae. In ‘FAO Species Identification Guide for Fishery Purposes: The Living Marine Resources of the Western Central Pacific. Volume 2: Cephalopods, crustaceans, holothurians and sharks’. (Eds K. E. Carpenter and V. H. Niem.) pp. 1213–1232. (FAO: Rome.)

Compagno L., Dando M., and Fowler S. (2005). ‘Sharks of the World: Collins Field Guide.’ (Harper Collins Publishers: London.)

Duncan, K. M. , Martin, A. P. , Bowen, B. W. , and Couet, H. G. (2006). Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini). Molecular Ecology 15, 2239–2251.
| Crossref | GoogleScholarGoogle Scholar | PubMed | FAO (1997). ‘Review of the state of world fishery resources: marine fisheries.’ Food and Agriculture Organization of the United Nations, FAO Fisheries Circular No. 920, Rome. Available at http://www.fao.org/docrep/003/W4248E/w4248e00.htm [Accessed 7 February 2008].

Feldheim, K. A. , Gruber, S. H. , and Ashley, M. V. (2001). Population genetic structure of the lemon shark (Negaprion brevirostris) in the western Atlantic: DNA microsatellite variation. Molecular Ecology 10, 295–303.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Fowler S. L. (2003). Centrophorus niaukang. In ‘IUCN 2007. 2007 IUCN Red List of Threatened Species’. Available at http://www.iucnredlist.org [Accessed 7 February 2008].

Fu, Y. X. , and Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics 133, 693–709.
| PubMed | Heist E. J. (2004). Genetics of sharks, skates and rays. In ‘Biology of Sharks and Their Relatives’. (Eds J. C. Carrier, J. A. Musick and M. R. Heithaus.) pp. 471–486. (CRC Press LLC: Boca Raton, FL.)

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.
ICES (2005). ‘Report of the Working Group on Elasmobranch Fishes (WGEF), 14–21 June 2005, ICES CM 2006/ACFM: 03, Lisbon, Portugal.’

ICES (2006). ‘Report of the Working Group on Elasmobranch Fishes (WGEF), 14–21 June 2006, ICES CM 2006/ACFM: 31, Lisbon, Portugal.’

IUCN (2007). ‘2007 IUCN Red List of Threatened Species.’ Available at www.iucnredlist.org [Accessed on 31 August 2007].

Keeney, D. B. , Heupel, M. R. , Hueter, R. E. , and Heist, E. J. (2005). Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea. Molecular Ecology 14, 1911–1923.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Moura T., Figueiredo I., Neves A., Farias I., Serra-Pereira B., and Gordo L. S. First occurrence of the deep-water shark Centroscymnus owstoni on the Portuguese continental slope. Cybium, In Press.

Musick J. A., Harbin M. N., and Compagno L. J. V. (2004). Historical zoogeography of the Selachii. In ‘Biology of Sharks and Their Relatives’. (Eds J. C. Carrier, J. A. Musick and M. R. Heithaus.) pp. 33–78. (CRC Press LLC: Boca Raton, FL.)

Nylander J. A. A. (2004). ‘MrModeltest.’ Program distributed by the author. Evolutionary Biology Center, Uppsala University, Sweden. Available from http://people.scs.fsu.edu/~nylander/mrmodeltest2/mrmodeltest2.html [Accessed 7 February 2008].

Posada, D. , and Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817–818.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Sambrook J., Fristsh E. F., and Maniatis T. (1989). ‘Molecular Cloning: A Laboratory Manual.’ (Cold Spring Harbour Laboratory Press: New York.)

Smith, P. J. (1986). Low genetic variation in sharks. Copeia 1986, 202–207.
| Crossref | GoogleScholarGoogle Scholar | Swofford D. L. (2003). ‘Phylogenetic Analysis Using Parsimony and Other Methods.’ (Sinauer Associates: Sunderland, MA.)

Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.
| PubMed | Vannuccini S. (1999). ‘Shark utilization, marketing and trade.’ Food and Agriculture Organization of the United Nations, FAO Fisheries Technical Paper No. 389, Rome. Available at http://www.fao.org/docrep/005/x3690e/x3690e00.htm [Accessed 7 February 2008].

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

Ward, R. D. , Holmes, B. H. , White, W. T. , and Last, P. R. (2008). DNA barcoding Australasian chondrichthyans: results and potential uses in conservation. Marine and Freshwater Research 59, 57–71.
| Crossref | GoogleScholarGoogle Scholar |