DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Liu, Shang Yin Vanson ^a,b   Chan, Chia Ling Carynn ^a   Lin, Oceana ^c   Hu, Chieh Shen ^c   Chen, Chaolun Allen ^a,d,e  

^a BIODIVERSITY RESEARCH CENTER   (Taiwan)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Society of Wilderness   (Taiwan)

^d ACADEMIA SINICA   (Taiwan)

^e NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALS; DNA BARCODING, TAXONOMIC; MEAT; PHYLOGENY; SHARKS; TAIWAN;

EID: 84894221554     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079373     Document Type: Article

References (61)

1. Dulvy NK, Baum JK, Clarke S, Compagno LJV, Cortés E, et al. (2008) You can swim but you can't hide: the global status and conservation of oceanic pelagic sharks and rays. Aquat Conserv 18: 459-482.
2. Ferretti F, Myers RA, Serena F, Lotze HK (2008) Loss of large predatory sharks from the Mediterranean Sea. Conserv Biol 22: 952-964.
3. Worm B, Davis B, Kettemer L, AW-P Christine, Chapman D, et al. (2013) Global catches, exploitation rates, and rebuilding options for sharks. Mar Policy 40: 194-204.
4. Libralato S, Christensen V, Pauly D (2005) A method for identifying keystone species in food web models. Ecol Model 195: 153-171.
5. Stevens JD (1999) Variable resistance to fishing pressure in two sharks: The significance of different ecological and life history parameters. In: editor Musick JA Life in the Slow Lane: Ecology and Conservation of Long-Lived Marine Animals American Fisheries Society, Bethesda, MD, 11-15.
6. Lack M, Sant G (2011). The Future of Sharks: A Review of Action and Inaction. TRAFFIC International and the Pew Environment Group.
7. Lucifora LO, Garci'a VB, Worm B (2011) Global Diversity Hotspots and Conservation Priorities for Sharks. PLoS ONE 6: e19356.
8. Taiwan Fisheries Agency (2006) Taiwan's National Plan of Action for the Conservation and Management of Sharks. Fisheries Agency, Taipei, Taiwan. www.fa.gov.tw/eng/guide/npoasharke.php, accessed 28 January 2007.
9. Camhi MD (2008) Conservation Status of Pelagic Elasmobranchs. In: Camhi, EK Pikitch, EA Babcock editors Sharks of the open ocean: Biology, Fisheries and Conservation. 397-417.
10. Tillett BJ, Field IC, Johnson G, Buckworth R, Meekan MG, et al. (2012) Accuracy of species identification by fisheries observers in a north Australian shark fishery. Fish Res 127-128: 109-115.
11. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci 360: 1847-1857. (Pubitemid 44365045)
12. Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, et al. (2008) Identifying Canadian Freshwater Fishes through DNA Barcodes. PLoS ONE 3: e2490.
13. Steinke D, Zemlak TS, Hebert PDN (2009) Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS ONE 4: e6300.
14. Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74: 329-356.
15. Ward RD, Holmes BH, White WT, Last PR (2008) DNA barcoding Australasian chondrichthyans: results and possible uses in conservation. Mar Freshwater Res 59: 57-71. (Pubitemid 351170398)
16. Holmes BH, Steinke D, Ward RD (2009) Identification of shark and ray fins using DNA barcoding. Fish Res 95: 280-288.
17. Wong EH-K, Shivji MS, Hanner RH (2009) Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resour 9 (s1): 243-256.
18. Moftah M, Abdel Aziz SH, Elramah S, Favereaux A (2011) Classification of Sharks in the Egyptian Mediterranean Waters Using Morphological and DNA Barcoding Approaches. PLoS ONE 6: e27001.
19. Ward RD (2009) Shark fin identification through DNA barcoding. Endangered species update 26: 3-9.
20. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3: 294-297.
21. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680. (Pubitemid 24354800)
22. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739.
23. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands oftaxa and mixed models. Bioinformatics 22: 2688-2690.
24. Kimura M (1980) A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
25. Clarke SC, Magnussen JE, Abercrombie DL, McAllister MK, Shivji MS (2006) Identification of shark species composition and proportion in the Hong Kong shark fin market based on molecular genetics and trade records. Conserv Biol 20: 201-211.
26. Zhang J, Hanner R (2012) Molecular approach to the identification of fish in the South China Sea. PLoS ONE 7(2): e30621.
27. Liu SYV, Ho HHC, Dai CF (2013) A New species of Pomacentrus (Actinopterygii: Pomacentridae) from Micronesia, with comments on its phylogenetic relationships. Zool Stud 52(6).
28. Martin A, PhD Dissertation, University of Hawaii, Honolulu, HI, 1992.
29. Iglésias SP, Lecointre G, Sellos DY (2005) Extensive paraphylies within sharks of the order Carcharhiniformes inferred from nuclear and mitochondrial genes. Mol Phylogenet Evol 34: 569-583. (Pubitemid 40427968)
30. Human BA, Owen EP, Compagno LJV, Harley EH (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. Mol Phylogenet Evol 39: 384-391.
31. Lopez JA, Ryburn JA, Fedrigo O, Naylor GJ (2006) Phylogeny of sharks of the family Triakidae (Carcharhiniformes) and its implications for the evolution of carcharhiniform placental viviparity. Mol Phylogenet Evol 40: 50-60. (Pubitemid 43903653)
32. Vélez-Zuazo X, Agnarsson I (2011) Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes) Mol Phylogenet Evol 58: 207-217.
33. Compagno LJV, Dando M, Fowler S (2005) Sharks of the World. Princeton University Press, Princeton and Oxford.
34. Last PR, Stevens JD (2009) Sharks and Rays of Australia. CSIRO Australia, Collingwood, Vic.
35. Dosay-Akbulut M (2008) The phylogenetic relationship within the genus Carcharhinus. C. R. Biologies 331: 500-509.
36. Rodrigues-Filho L, Rocha T, Rêgo P, Schneider H, Sampaio I, et al. (2009) Identification and phylogenetic inferences on stocks of sharks affected by the fishing industry off the Northern coast of Brazil. Genet and Mol Biol 32: 405-413.
37. Duncan KM, Martin AP, Bowen BW, De Couet HG (2006) Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini). Mol Ecol 15: 2239-2251. (Pubitemid 43876463)
38. Quattro JM, Stoner DS, Driggers WB, Anderson CA, Priede KA, et al. (2006) Genetic evidence of cryptic speciation within hammerhead sharks (Genus Sphyrna). Mar Biol 148: 1143-1155. (Pubitemid 43289564)
39. Corrigan S, Huveneers C, Schwartz TS, Harcourt RG, Beheregaray LB (2008) Genetic and reproductive evidence for two species of ornate wobbegong shark on the Australian East Coast. J Fish Biol 73: 1662-1675.
40. Trejo T (2005) Global phylogeography of thresher sharks (Alopias spp.) inferred from mitochondrial DNA control region sequences". M.Sc. thesis. Moss Landing Marine Laboratories, California State University.
41. Naylor GJP, Caira JN, Jensen K, Rosana KAM, White WT, et al. (2012) A DNA sequence-based approach to the identification of shark and ray species and its implications for global Elasmobranch diversity and parasitology. Bull Am Mus Nat Hist 367: 1-262.
42. Compagno LJV (2001) Sharks of the World. Bullhead, mackeral and carpet sharks (Heterodontiformes, Lamniformes and Orectolobiformes). FAO Species Catalogue 2, 78.
43. Chen GCT, Liu KM, Joung SJ, Phipps MJ (1996) "TRAFFIC report on shark fisheries and trade in Taiwan", in "TRAFFIC report on shark fisheries and trade in the East Asian region", of the "The world trade in sharks: a compendium of TRAFFIC's regional studies volume I", TRAFFIC.
44. Liu K-M, Tsai W-P (2011) Catch and life history parameters of pelagic sharks in the Northwest Pacific. ISC Shark Working Group Meeting, April 19-21, Keelung, Taiwan. ISC/11SHARKWG-1/6, 12 pp.
45. Tsai W-P, Liu K-M, Joung S-J (2010) Demographic analysis of the pelagic thresher shark, Alopias pelagicus, in the north-western Pacific using a stochastic stage-based model. Mar Freshwater Res 61: 1056-1066.
46. Reardon M, Márquez F, Trejo T, Clarke SC (2009) Alopias pelagicus. In: IUCN 2012. IUCN Red List of Threatened Species.
47. Compagno LJV (1984) Sharks of the World. An Annotated and Illustrated Catalogue of Shark Species Known to Date. FAO Species Catalogue. Vol. 4, Part 2.
48. FAO Fisheries Synopsis, 125. FAO, Rome, Italy.
49. Cailliet GM, Cavanagh RD, Kulka DW, Stevens JD, Soldo A, et al. (2009) Isurus oxyrinchus. In: IUCN 2012. IUCN Red List of Threatened Species.
50. Holts DB, Julian A, Sosa-Nishizaki O, Bartoo NW (1998) Pelagic shark fisheries along the west coast of the United Status and Baja California, Mexico Fish Res 39: 115-125. (Pubitemid 29020216)
51. Baum JK, Kehler D, Myers RA (2005) Robust estimates of decline for pelagic shark populations in the Northwest Atlantic and Gulf of Mexico. Fisheries 30: 27-30. (Pubitemid 41616896)
52. White WT, Last PR, JD Stevens, Yearsley GK, Fahmi, etal. (2006) Economically important sharks and rays of Indonesia. Canberra, Australia, Australian Centre for International Agricultural Research.
53. Joung SJ, Hsu HH (2005) Reproduction and Embryonic Development of the Shortfin Mako, Isurus oxyrinchus Rafinesque, 1810, in the Northwestern Pacific. Zool Stud 44: 337-346.
54. Campana SE, Marks L, Joyce W, Kohler N (2004) Influence of recreational and commercial fishing on the blue shark (Prionace glauca) population in Atlantic Canadian waters. CSAS Res. Doc. 2004/069. 68 p.
55. Fowler GM, Campana SE (2009) Commercial by-catch rates of blue shark (Prionace glauca) from longline fisheries in the Canadian Atlantic. Collect. Vol. Sci. Pap. ICCAT 64: 1650-1667.
56. Liu K-M, Joung SJ, Tsai W-P (2009) Preliminary estimates of blue and mako sharks by-catch and CPUE of the Taiwanese longline fishery in the Atlantic Ocean. Collect Vol Sci Pap ICCAT 64: 1703-1716.
57. Simpfendorfer CA, Heuter RE, Bergman U, Connett SMH (2002) Results of a fishery independent survey for pelagic sharks in the western North Atlantic, 1977-1994. Fisher Res 55: 175-192. (Pubitemid 34119577)
58. Ward P, Myers RA (2005) Shifts in open-ocean fish communities coinciding with the commencement of commercial fishing. Ecology 86: 835-847. (Pubitemid 40483369)
59. Nakano H, Clarke S (2005) Standardized CPUE for blue sharks caught by the Japanese longline fishery in the Atlantic Ocean, 1971-2003. ICCAT Collective Volume of Scientific Papers 58: 1127-1134.
60. Babcock EA, Nakano H (2008) Data collection, research, and assessment efforts for pelagic sharks by the International Commission for the Conservation of Atlantic Tunas. In: Camhi MD, Pikitch EK, Babcock EA editors Sharks of the Open Ocean: Biology, Fisheries and Conservation.Blackwell Publishing, Oxford, UK.
61. Hueter RE, Simpfendorfer CA (2008) Case study: Trends in blue shark abundance in the western North Atlantic as determined by a fishery-independent survey. In: Camhi MD, Pikitch EK, Babcock EA editors Sharks of the Open Ocean: Biology, Fisheries and Conservation.Blackwell Publishing, Oxford, UK.