Rapid identification of shark species on mislabelled seafood products in Mexican markets
Alexis Alejandro Jiménez-Pérez
A
B
C
D
Abstract
Sharks have been captured globally for decades. Shark exploitation lacks appropriate regulation, hindering an assessment of captured and traded individuals. This necessitates the development of a method to quickly and easily identify shark species.
We aim to standardise and validate a rapid, effective method of shark species identification from Mexican markets.
Loop-Mediated Isothermal Amplification (LAMP) assays were developed for the identification of five commercially important shark species in the north-west region of Mexico: Carcharhinus falciformis, Prionace glauca, Isurus oxyrinchus, Sphyrna zygaena and Sphyrna lewini. A total of 350 samples was collected from markets and samples were labelled as ‘cazón’ (small shark), ‘marlín’ (marlin) and ‘tiburón’ (shark).
Through LAMP assay standardisation, individuals of five species were able to be identified: 17 individuals of S. zygaena, 17 of S. lewini, 24 of C. falciformis, 26 of P. glauca and 85 of I. oxyrinchus. To validate species identification by LAMP, sequences of COI and ITS2 were obtained and analysed by BLASTn. A 100% match identity for LAMP assays and associated sequences was obtained. Additionally, the DNA limit of detection was determined down to 0.1 ng/μL of shark DNA.
These results highlight an urgent need to effectively identify commercially traded species, some of which may be endangered and to establish species-level labelling in national policies.
Application of correct species labels to national seafood products could encourage consumers to make responsible food choices.
Keywords: applied biotechnology, conservation biology, conservation genetics, forensic genetics, LAMP, management improvement, marine resources, mislabelled seafood products, sustainable trade.
References
Alacs EA, Georges A, FitzSimmons NN, Robertson J (2010) DNA detective: a review of molecular approaches to wildlife forensics. Forensic Science, Medicine, and Pathology 6(3), 180-194.
| Crossref | Google Scholar | PubMed |
Aljanabi SM, Martinez I (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Research 25(22), 4692-4693.
| Crossref | Google Scholar |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215(3), 403-410.
| Crossref | Google Scholar | PubMed |
Becker S, Hanner R, Steinke D (2011) Five years of FISH-BOL: brief status report. Mitochondrial DNA 22(S1), 3-9.
| Crossref | Google Scholar |
But GW, Wu H-Y, Shao K-T, Shaw P-C (2020) Rapid detection of CITES-listed shark fin species by loop-mediated isothermal amplification assay with potential for field use. Scientific Reports 10(2), 4455.
| Crossref | Google Scholar |
Cardeñosa D, Fields A, Abercrombie D, Feldheim K, Shea SKH, Chapman DD (2017) A multiplex PCR mini-barcode assay to identify processed shark products in the global trade. PLoS ONE 12(10), e0185368.
| Google Scholar |
Castillo-Géniz JL, Márquez-Farias JF, Rodriguez de la Cruz MC, Cortés E, Cid del Prado A (1998) The Mexican artesanal shark fishery in the Gulf of Mexico: towards a regulated fishery. Marine and Freshwater Research 49(7), 611-620.
| Crossref | Google Scholar |
Chapman DD, Abercrombie DL, Douady CJ, Pikitch EK, Stanhope MJ, Shivji MS (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 | Google Scholar |
Cisneros-Montemayor AM, Cisneros-Mata MA, Harper S, Pauly D (2013) Extent and implications of IUU catch in Mexico’s marine fisheries. Marine Policy 39, 283-288.
| Crossref | Google Scholar |
Cruz MM, Szynwelski BE, Ochotorena de Freitas TR (2021) Biodiversity on sale: the shark meat market threatens elasmobranchs in Brazil. Aquatic Conservation: Marine and Freshwater Ecosystems 31(12), 3437-3450.
| Crossref | Google Scholar |
Dawnay N, Ogden R, McEwing R, Carvalho GR, Thorpe RS (2007) Validation of the barcoding gene COI for use in forensic genetic species identification. Forensic Science International 173(2), 1-6.
| Crossref | Google Scholar | PubMed |
Dulvy NK, Pacoureau N, Rigby CL, Pollom RA, Jabado RW, Ebert DA, Finucci B, Pollock CM, Cheok J, Derrick DH, Herman KB, Sherman CS, VanderWright WJ, Lawson JM, Walls RHL, Carlson JK, Charvet P, Bineesh KK, Fernando D, Ralph GM, Matsushiba JH, Hilton-Taylor C, Fordham SV, Simpfendorfer CA (2021) Overfishing drives over one-third of all sharks and rays toward a global extinction crisis. Current Biology 31(21), 4773-4787.e8.
| Crossref | Google Scholar | PubMed |
Endo T, Hotta Y, Haraguchi K, Sakata M (2003) Mercury contamination in the red meat of whales and dolphins marketed for human consumption in Japan. Environmental Science & Technology 37(12), 2681-2685.
| Crossref | Google Scholar | PubMed |
Gram L, Melchiorsen J (1996) Interaction between fish spoilage bacteria Pseudomonas sp. and Shewanella putrefaciens in fish extracts and on fish tissue. Journal of Applied Bacteriology 80(6), 589-595.
| Crossref | Google Scholar | PubMed |
Heylar SJ, Lloyd HaD, de Bruyn M, Leake J, Bennet N, Carvalho GR (2014) Fish product mislabelling: faillings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing. PLoS ONE 9(6), e98691.
| Google Scholar |
Holts DB, Julian A, Sosa-Nishizaki O, Bartoo NW (1998) Pelagic shark fisheries along the west coast of the United States and Baja California, Mexico. Fisheries Research 39(2), 115-125.
| Crossref | Google Scholar |
Jalal KCA, Akbar JB, Nurul L, Faizul HN, Isma Y, Irwandi J, Mahbuba B (2017) Comparative study on spoilage and pathogenic bacteria in selected commercial marine and freshwater fishes. International Food Research Journal 24, 298-304.
| Google Scholar |
Kim Y-K, Lee C-H, Lee Y-D, Han S-H (2019) Development of species-specific PCR for the identification of three grouper fish species (Epinephelus septemfasciatus, E. bruneus and E. akaara). Indian Journal of Animal Research 53(4), 482-484.
| Crossref | Google Scholar |
Kircher M, Kelso J (2010) High-throughput DNA sequencing – concepts and limitations. BioEssays 32(6), 524-536.
| Crossref | Google Scholar | PubMed |
Koehler L, Lowther J (2022) Policy making for sharks and the role and contribution of non-governmental organisations in the fulfilment of international legal obligations. Marine Policy 144, 105228.
| Crossref | Google Scholar |
Kroetz K, Luque GM, Gephart JA, Jardine SL, Lee P, Moore KC, Cole C, Steinkruger A, Donlan CJ (2020) Consequences of seafood mislabeling for marine populations and fisheries management. Proceedings of the National Academy of Sciences of the United States of America 117(48), 30318-30323.
| Crossref | Google Scholar |
Lin T-C, Hsiao WV, Han S-J, Joung S-J, Shiao J-C (2021) A direct multiplex loop-mediated isothermal amplification method to detect three CITES-listed shark species. Aquatic Conservation: Marine and Freshwater Ecosystems 31(8), 2193-2203.
| Crossref | Google Scholar |
Munguia-Vega A, Terrazas-Tapia R, Dominguez-Contreras JF, Reyna-Fabian M, Zapata-Morales P (2022) DNA barcoding reveals global and local influences on patterns of mislabeling and substitution in the trade of fish in Mexico. PLoS ONE 17(4), e0265960.
| Crossref | Google Scholar |
Muñoz-Colmenero M, Blanco O, Arias V, Martinez JL, Garcia-Vazquez E (2016) DNA authentication of fish products reveals mislabeling associated with seafood processing. Fisheries 41(3), 128-138.
| Crossref | Google Scholar |
Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Research 28(12), e63.
| Crossref | Google Scholar |
O’Bryhim JR, Parsons ECM, Lance SL (2017) Forensic species identificaion of elasmobranch products sold in Costa Rican markets. Fisheries Research 186, 144-150.
| Crossref | Google Scholar |
Ogden R, Dawnay N, McEwing R (2009) Wildlife DNA forensics – bridging the gap between conservation genetics and law enforcement. Endangered Species Research 9(3), 179-195.
| Crossref | Google Scholar |
Pacoureau N, Rigby CL, Kyne PM, Sherley RB, Winker H, Carlson JK, Fordham SV, Barreto R, Fernando D, Francis MP, Jabado RW, Herman KB, Liu K-M, Marshall AD, Pollom RA, Romanov EV, Simpfendorfer CA, Yin JS, Kindsvater HK, Dulvy NK (2021) Half a century of global decline in oceanic sharks and rays. Nature 589, 567-571.
| Crossref | Google Scholar | PubMed |
Pérez-Jiménez JC (2014) Historical records reveal potential extirpation of four hammerhead sharks (Sphyrna spp.) in Mexican Pacific waters. Reviews in Fish Biology and Fisheries 24(2), 671-683.
| Crossref | Google Scholar |
Pérez-Jiménez JC, Wakida-Kusunoki A, Hernández-Lazo C, Mendoza-Carranza M (2020) Shark-catch composition and seasonality in the data-poor small-scale fisheries of the southern Gulf of Mexico. Marine and Freshwater Research 71(9), 1182-1193.
| Crossref | Google Scholar |
Pincinato RBM, Gasalla MA, Garlock T, Anderson JL (2022) Market incentives for shark fisheries. Marine Policy 139, 105031.
| Crossref | Google Scholar |
Powers SP, Fodrie FJ, Scyphers SB, Drymon JM, Shipp RL, Stunz GW (2013) Gulf-wide decreases in the size of large coastal sharks documented by generations of fishermen. Marine and Coastal Fisheries 5(2), 93-102.
| Crossref | Google Scholar |
Qu W, Shen Z, Zhao D, Yang Y, Zhang C (2009) MFEprimer: multiple factor evaluation of the specificity of PCR primers. Bioinformatics 25(2), 276-278.
| Crossref | Google Scholar |
Rasmussen RS, Morrissey MT (2008) DNA-based methods for the identification of commercial fish and seafood species. Comprehensive Reviews in Food Science and Food Safety 7(3), 280-295.
| Crossref | Google Scholar |
Rhodes KL, Tupper MH (2007) A preliminary market-based analysis of the Pohnpei, Micronesia, grouper (Serranidae:Epinephelinae) fishery reveals unsustainable fishing practices. Coral Reefs 26, 335-344.
| Crossref | Google Scholar |
Rigby CL, Barreto R, Carlson J, Fernando D, Fordham S, Francis MP, Herman K, Jabado RW, Jones GCA, Liu KM, Lowe CG, Marshall A, Pacoureau N, Romanov E, Sherley RB, Winker H (2022) Carcharodon carcharias (amended version of 2019 assessment). The IUCN Red List of threatened species 2022: e.T3855A212629880. Available at https://dx.doi.org/10.2305/IUCN.UK.2022-1.RLTS.T3855A212629880.en
Roheim CA, Bush SR, Asche F, Sanchirico JN, Uchida H (2018) Evolution and future of the sustainable seafood market. Nature Sustainability 1, 392-398.
| Crossref | Google Scholar |
Saldaña-Ruiz LE, Sosa-Nishizaki O, Cartamil D (2017) Historical reconstruction of Gulf of California shark fishery landings and species composition, 1939–2014, in a data-poor fishery context. Fisheries Research 195, 116-129.
| Crossref | Google Scholar |
Sherman CS, Digel ED, Zubick P, Eged J, Haque AB, Matsushiba JH, Simpfendorfer CA, Sant G, Dulvy NK (2023) High overexploitation risk due to management shortfall in highly traded requiem sharks. Conservation Letters 16(2), e12940.
| Crossref | Google Scholar |
Shivji M, Clarke S, Pank M, Natanson L, Kohler N, Stanhope M (2002) Genetic identification of pelagic shark body parts for conservation and trade monitoring. Conservation Biology 16(4), 1036-1047.
| Crossref | Google Scholar |
Smart U, Cihlar JC, Budowle B (2021) International wildlife trafficking: a perspective on the challenges and potential forensic genetics solutions. Forensic Science International: Genetics 54, 102551.
| Crossref | Google Scholar | PubMed |
Spaet JLY, Berumen ML (2015) Fish market surveys indicate unsustainable elasmobranch fisheries in the Saudi Arabian Red Sea. Fisheries Research 161, 356-364.
| Crossref | Google Scholar |
Steadman D, Appleby T, Hawkins J (2014) Minimising unsustainable yield: Ten failing European fisheries. Marine Policy 48, 192-201.
| Crossref | Google Scholar |
Sultana S, Ali ME, Hossain MAM, Asing , Naquiah N, Zaidul ISM (2018) Universal mini COI barcode for the identification of fish species in processed products. Food Research International 105, 19-28.
| Crossref | Google Scholar | PubMed |
Tatulli G, Cecere P, Maggioni D, Galimberti A, Pompa PP (2020) A rapid colorimetric assay for on-site authentication of cephalopod species. Biosensors 10(12), 190.
| Crossref | Google Scholar |
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25(24), 4876-4882.
| Crossref | Google Scholar | PubMed |
Travaille KLT, Lindley J, Kendrick GA, Crowder LB, Clifton J (2019) The market for sustainable seafood drives transformative change in fishery social-ecology systems. Global Environmental Change 57, 101919.
| Crossref | Google Scholar |
Wang Y, Feng J, Tian X (2019) Application of loop-mediated isothermal amplification (LAMP) for rapid detection of Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus) and haddock (Melanogrammus aeglefinus). Molecular and Cellular Probes 47, 101420.
| Crossref | Google Scholar | PubMed |
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360, 1847-1857.
| Crossref | Google Scholar |
Ward RD, Hanner R, Herbert PDN (2009) The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74(2), 329-356.
| Crossref | Google Scholar | PubMed |
Wells RS, Natoli A, Braulik G (2019) Tursiops truncatus. The IUCN Red List of threatened species 2019: e.T22563A156932432. Available at https://dx.doi.org/10.2305/IUCN.UK.2019-1.RLTS.T22563A156932432.en
Wilwet L, Shakila RJ, Sivaraman B, Nayak BB, Kumar HS, Jaiswar AK, Jeyasekaran G (2021) Rapid detection of fraudulence in seven commercial shrimp products by species-specific PCR assays. Food Control 124, 107871.
| Crossref | Google Scholar |
Worm B, Davis B, Kettemer L, Ward-Paige CA, Chapman D, Heithaus MR, Kessel ST, Gruber SH (2013) Global catches, exploitation rates, and rebuilding options for sharks. Marine Policy 40, 194-204.
| Crossref | Google Scholar |