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Molecular identification methods of fish species: reassessment and possible applications

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Abstract

Fish species identification is traditionally based on external morphological features. Yet, in many cases fishes and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. This work intends to provide an updated and extensive overview on the PCR-methods for fish species identification. Among the ten main methods developed, three PCR-RFLP, PCR-FINS and PCR-specific primers have been the most used. Two other emerging methods, namely real-time PCR and microarray technology, offer new potential for quantification of DNA and simultaneous detection of numerous species, respectively. Almost 500 species have been targeted in the past decade, among which the most studied belong to gadoids, scombroids, and salmonids. The mitochondrial cytochrome b gene was by far the most targeted DNA markers. The most common applications belonged to the forensic, taxonomic, and ecological fields. At last, some key problems, such as the degradation of DNA, the reliability of sequences, and the use of scientific names, likely to be encountered during the development of molecular identification methods are described. In conclusion, the tremendous advances in molecular biology in the past 10 years has rendered possible the study of DNA from virtually any substrates, offering new perspectives for the development of various applications, which will likely continue to increase in the future.

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References

  • Ansfield M, Reaney SD, Jackman R (2000) Production of a sensitive immunoassay for detection of ruminant and porcine proteins, heated to >130°C at 2.7 bar, in compound animal feedstuffs. Food Agric Immunol 12:273–284. doi:10.1080/09540100020008146

    CAS  Google Scholar 

  • Antunes A, Ramos MJ (2005) Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes. Genomics 86:708–717. doi:10.1016/j.ygeno.2005.08.002

    PubMed  CAS  Google Scholar 

  • Aranishi F, Okimoto T, Ohkubo M (2005) Molecular identification of commercial spicy pollack roe products by PCR-RFLP analysis. J Food Sci 70:235–238

    Google Scholar 

  • Asensio L (2007) PCR-based methods for fish and fishery products authentication. Trends Food Sci Technol 18:558–566. doi:10.1016/j.tifs.2007.04.016

    Google Scholar 

  • Asensio L, Montero A (2008) Analysis of fresh fish labelling in Spanish fish retail shops. Food Control 19:795–799. doi:10.1016/j.foodcont.2007.08.005

    Google Scholar 

  • Asensio L, González I, García T et al (2008) Determination of food authenticity by enzyme-linked immunosorbent assay (ELISA). Food Control 19:1–8. doi:10.1016/j.foodcont.2007.02.010

    CAS  Google Scholar 

  • Babola O, Desvarenne S, Lacroix B et al (2004) L’identification des espèces animales dans l’alimentation humaine et animale: un exemple d’application de la technologie des puces à ADN. Bull Soc Fr Micr 19:30–36

    Google Scholar 

  • Balitzki-Korte B, Anslinger K, Bartsch C, Rolf (2005) Species identification by means of pyrosequencing the mitochondrial 12S rRNA gene. Int J Legal Med 119:291–294. doi:10.1007/s00414-005-0537-9

    PubMed  CAS  Google Scholar 

  • Bartlett S, Davidson W (1992) FINS (forensically informative nucleotide sequencing): a procedure for identifying the animal origin of biological specimens. Biotechniques 3:408–411

    Google Scholar 

  • Benesh DP, Hasu T, Suomalainen L-R et al (2006) Reliability of mitochondrial DNA in an acanthocephalan: the problem of pseudogenes. Int J Parasitol 36:247–254. doi:10.1016/j.ijpara.2005.09.008

    PubMed  CAS  Google Scholar 

  • Bensasson D, Zhang D, Hartl DL (2001) Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol 16:314–321. doi:10.1016/S0169-5347(01)02151-6

    PubMed  Google Scholar 

  • Birstein VJ, Doukakis P, Sorkin B et al (1998) Population aggregation analysis of three caviar-producing species of sturgeons and implications for the species identification of black caviar. Conserv Biol 12:766–775. doi:10.1046/j.1523-1739.1998.97081.x

    Google Scholar 

  • Blaxter M (2003) Molecular systematics: counting angels with DNA. Nature 421:122–124. doi:10.1038/421122a

    PubMed  CAS  Google Scholar 

  • Blaxter M (2004) The promise of a DNA taxonomy. Philos Trans R Soc Lond B Biol Sci 359:669–679. doi:10.1098/rstb.2003.1447

    PubMed  CAS  Google Scholar 

  • Bossier P (1999) Authentication of seafood products by DNA patterns. J Food Sci 64:189–193. doi:10.1111/j.1365-2621.1999.tb15862.x

    CAS  Google Scholar 

  • Bower MA, Spencer M, Matsumura S et al (2005) How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence? Nucleic Acids Res 33:2549–2556. doi:10.1093/nar/gki550

    PubMed  CAS  Google Scholar 

  • Bucciarelli G, Golani D, Bernardi G (2002) Genetic cryptic species as biological invaders: the case of a Lessepsian fish migrant, the hardyhead silverside Atherinomorus lacunosus. J Exp Mar Biol Ecol 273:143–149. doi:10.1016/S0022-0981(02)00138-7

    Google Scholar 

  • Byrkjedal I, Rees DJ, Willassen E (2007) Lumping lumpsuckers: molecular and morphological insights into the taxonomic status of Eumicrotremus spinosus (Fabricius, 1776) and Eumicrotremus eggvinii Koefoed, 1956 (Teleostei: Cyclopteridae). J Fish Biol 71:111–131. doi:10.1111/j.1095-8649.2007.01550.x

    CAS  Google Scholar 

  • Callejas C, Ochando MD (2001) Molecular identification (RAPD) of the eight species of the genus Barbus (Cyprinidae) in the Iberian Peninsula. J Fish Biol 59:1589–1599. doi:10.1111/j.1095-8649.2001.tb00223.x

    CAS  Google Scholar 

  • Carr SM, Kivlichan DS, Pepin P et al (1999) Molecular systematics of gadid fishes: implications for the biogeographic origins of Pacific species. Can J Zool 77:19–26. doi:10.1139/cjz-77-1-19

    Google Scholar 

  • Carrera E, García T, Céspedes A et al (2000) Differentiation of smoked Salmo salar, Oncorhynchus mykiss and Brama raii using the nuclear marker 5S rDNA. Int J Food Sci Technol 35:401–406. doi:10.1046/j.1365-2621.2000.00404.x

    CAS  Google Scholar 

  • Casper RM, Jarman SN, Deagle BE et al (2007) Detecting prey from DNA in predator scats: a comparison with morphological analysis, using Arctocephalus seals fed a know diet. J Exp Mar Biol Ecol 347:144–154. doi:10.1016/j.jembe.2007.04.002

    Google Scholar 

  • Chakraborty A, Aranishi F, Iwatsuki Y (2007) Polymerase chain reaction-restriction fragment length polymorphism analysis for species identification of hairtail fish fillets from supermarkets in Japan. Fish Sci 73:197–201. doi:10.1111/j.1444-2906.2007.01319.x

    CAS  Google Scholar 

  • Chapela MJ, Sotelo CG, Pérez-Martín RI et al (2007) Comparison of DNA extraction methods from muscle of canned tuna for species identification. Food Control 18:1211–1215. doi:10.1016/j.foodcont.2006.07.016

    CAS  Google Scholar 

  • Civera T (2003) Species identification and safety of fish products. Vet Res Commun 27:481–489. doi:10.1023/B:VERC.0000014205.87859.ab

    PubMed  Google Scholar 

  • Comesana AS, Abella P, Sanjuan A (2003) Molecular identification of five commercial flatfish species by PCR-RFLP analysis of a 12 rRNA gene fragment. J Sci Food Agric 83:752–759. doi:10.1002/jsfa.1368

    CAS  Google Scholar 

  • Comi G, Lacumi L, Rantsiou (2005) Molecular methods for the differentiation of species used in production of cod-fish can detect commercial frauds. Food Control 16:37–42. doi:10.1016/j.foodcont.2003.11.003

    CAS  Google Scholar 

  • Cooper A, Wayne R (1998) New uses for old DNA. Curr Opin Biotechnol 9:49–53. doi:10.1016/S0958-1669(98)80083-9

    PubMed  CAS  Google Scholar 

  • Dalmasso A, Civera T, Bottero MT (2006) Biomolecular approaches for the identification of tuna species. Vet Res Commun 30:179–181. doi:10.1007/s11259-006-0035-7

    Google Scholar 

  • Deagle B, Tollit D, Jarman S et al (2005) Molecular scatology as a tool to study diet: Analysis of prey DNA in scats from captive Steller sea lions. Mol Ecol 14:1831–1842. doi:10.1111/j.1365-294X.2005.02531.x

    PubMed  CAS  Google Scholar 

  • DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc B 360:1905–1916. doi:10.1098/rstb.2005.1722

    CAS  Google Scholar 

  • Doiron S, Bernatchez L, Blier P (2002) A comparative mitogenomic analysis of the potential adaptive value of Arctic charr mtDNA introgression in brook charr populations (Salvelinus fontinalis Mitchill). Mol Biol Evol 19:1902–1909

    PubMed  CAS  Google Scholar 

  • Ercolini D (2004) PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. J Microbiol Methods 56:297–314. doi:10.1016/j.mimet.2003.11.006

    PubMed  CAS  Google Scholar 

  • Etienne M, Jerome M, Fleurence J et al (2000) Identification of fish species after cooking by SDS–PAGE and urea IEF: a collaborative study. J Agric Food Chem 48:2653–2658. doi:10.1021/jf990907k

    PubMed  CAS  Google Scholar 

  • Forster P (2003) To err is human. Ann Hum Genet 67:2–4. doi:10.1046/j.1469-1809.2003.00002.x

    PubMed  CAS  Google Scholar 

  • Fox CJ, Taylor MI, Pereyra R et al (2005) TaqMan DNA technology confirms likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg-based methods. Mol Ecol 14:879–884. doi:10.1111/j.1365-294X.2005.02439.x

    PubMed  CAS  Google Scholar 

  • Froese R, Pauly P (eds) (2008) FishBase. World Wide Web electronic publication. www.fishbase.org, version (06/2008)

  • Gharrett AJ, Gray AK, Heifetz J (2001) Identification of rockfish (Sebastes spp.) by restriction site analysis of the mitochondrial ND-3/ND-4 and 12S/16S rRNA gene regions. Fish Bull (Wash D C) 99:49–62

    Google Scholar 

  • Gilbert MT, Bandelt H-J, Hofreiter M et al (2005) Assessing ancient DNA studies. Trends Ecol Evol 20:541–544. doi:10.1016/j.tree.2005.07.005

    PubMed  Google Scholar 

  • Granadeiro JP, Silva MA (2000) The use of otoliths and vertebrae in the identification and size-estimation of fish in predator-prey studies. Cybium 24:383–393

    Google Scholar 

  • Greig TW, Moore MK, Woodley CM (2005) Mitochondrial gene sequences useful for species identification of western North Atlantic Ocean sharks. Fish Bull (Wash D C) 103:516–523

    Google Scholar 

  • Hanner RH, Gregory TR (2007) Genomic diversity research and the role of biorepositories. Cell Pres Tech 5:93–103. doi:10.1089/cpt.2007.9993

    CAS  Google Scholar 

  • Harris DJ (2003) Can you bank on GenBank? Trends Ecol Evol 18:317–319. doi:10.1016/S0169-5347(03)00150-2

    Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL et al (2003) Biological identifications through DNA barcodes. Proc R Soc Lond Ser B Biol Sci 270:313–321. doi:10.1098/rspb.2002.2218

    CAS  Google Scholar 

  • Heist EJ, Gold JR (1999) Genetic identification of sharks in the U.S. Atlantic large coastal shark fishery. Fish Bull (Wash D C) 97:53–61

    Google Scholar 

  • Hoelzel AR (2001) Shark fishing in fin soup. Conserv Genet 2:69–72. doi:10.1023/A:1011590517389

    CAS  Google Scholar 

  • Horstkotte B, Rehbein H (2003) Fish species identification by means of restriction fragment length polymorphism and high-performance liquid chromatography. J Food Sci 68:2658–2666. doi:10.1111/j.1365-2621.2003.tb05785.x

    CAS  Google Scholar 

  • Hsieh HS, Hwang DF (2004) Molecular phylogenetic relationships of puffer fish inferred from partial sequences of cytochrome b gene and restriction fragment length polymorphism analysis. J Agric Food Chem 52:4159–4165. doi:10.1021/jf035462l

    PubMed  CAS  Google Scholar 

  • Hubalkova Z, Kralik P, Tremlova B et al (2007) Methods of gadoid fish species identification in food and their economic impact in the Czech Republic: a review. Vet Med 52:273–292

    CAS  Google Scholar 

  • Iff At F (2002) Mullets of Korangi Creek, Karachi. Rec Zool Surv Pak 14:11–18

    Google Scholar 

  • Janzen DH (2004) Now is the time. Philos Trans R Soc Lond B Biol Sci 359:731–732. doi:10.1098/rstb.2003.1444

    PubMed  Google Scholar 

  • Jarman S, Deagle B, Gales N (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Mol Ecol 13:1313–1322. doi:10.1111/j.1365-294X.2004.02109.x

    PubMed  CAS  Google Scholar 

  • Jérôme M, Lemaire C, Verrez-Bagnis V et al (2003) Direct sequencing method for species identification of canned sardine and sardine-type products. J Agric Food Chem 51:7326–7332. doi:10.1021/jf034652t

    PubMed  Google Scholar 

  • King RA, Read DS, Traugott M et al (2008) Molecular analysis of predation: a review of best practice for DNA-based approaches. Mol Ecol 17:947–963. doi:10.1111/j.1365-294X.2007.03613.x

    PubMed  CAS  Google Scholar 

  • Klossa-Kilia E, Papasotiropoulos V, Kilias G et al (2002) Authentication of Messolongi (Greece) fish roe using PCR-RFLP analysis of 16s RNA mtDNA segment. Food Control 13:169–172. doi:10.1016/S0956-7135(01)00097-4

    CAS  Google Scholar 

  • Kocher TD, Thomas WK, Meyer A et al (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86:6196–6200. doi:10.1073/pnas.86.16.6196

    PubMed  CAS  Google Scholar 

  • Kochzius M, Nölte M, Weber H et al (2008) DNA microarrays for identifying fishes. Mar Biotechnol 10:207–217. doi:10.1007/s10126-007-9068-3

    PubMed  CAS  Google Scholar 

  • Kon T, Yoshino T, Mukai T et al (2007) DNA sequences identify numerous cryptic species of vertebrate: a lesson from the gobioid fish Schindleria. Mol Phylogenet Evol 44:53–62. doi:10.1016/j.ympev.2006.12.007

    PubMed  CAS  Google Scholar 

  • Kvasnička F (2005) Capillary electrophoresis in food authenticity. J Sep Sci 28:813–825

    PubMed  Google Scholar 

  • Lakra WS, Goswami M, Mohindra V, Lal KK, Punia P (2007) Molecular identification of five Indian scianids (pisces: perciformes, sciaenidae) using RAPD markers. Hydrobiologia 583:359–363

    CAS  Google Scholar 

  • Li Z, Gray AK, Love MS et al (2006) A key to selected rockfishes (Sebastes spp.) based on mitochondrial DNA restriction fragment analysis. Fish Bull 104:182–196

    Google Scholar 

  • Lin W-F, Hwang D-F (2007) Application of PCR-RFLP analysis on species identification of canned tuna. Food Control 18:1050–1057

    CAS  Google Scholar 

  • Lipscomb D, Platnick N, Wheeler Q (2003) The intellectual content of taxonomy: a comment on DNA taxonomy. Trends Ecol Evol 18:65–66

    Google Scholar 

  • Lockley AK, Bardsley RG (2000) DNA-based methods for food authentication. Trends Food Sci Tech 11:67–77

    CAS  Google Scholar 

  • Ludwig A, Congiu L, Pitra C (2003) Nonconcordant evolutionary history of maternal and paternal lineages in Adriatic sturgeon. Mol Ecol 12:3253–3264

    PubMed  CAS  Google Scholar 

  • Mackie IM, Pryde SE, Gonzales-Sotelo C et al (1999) Challenges in the identification of species of canned fish. Trends Food Sci Tech 10:9–14

    CAS  Google Scholar 

  • Mafra I, Ferreira I, Beatriz M et al (2008) Food authentication by PCR-based methods. Eur Food Res Technol 227:649–665

    CAS  Google Scholar 

  • Maldini M, Marzano FN, Fortes GG et al (2006) Fish and seafood traceability based on AFLP markers: elaboration of a species database. Aquaculture 261:487–494

    CAS  Google Scholar 

  • Mallet J, Willmott K (2003) Taxonomy: renaissance or Tower of Babel? Trends Ecol Evol 18:57–59

    Google Scholar 

  • Maretto F, Reffo E, Dalvit C et al (2007) Finding 16S rRNA gene-based SNPs for the genetic traceability of commercial species belonging to Gadiformes. Ital J Anim Sci 6:161–163

    Google Scholar 

  • Marko PB, Lee SC, Rice AM (2004) Fisheries: mislabelling of a depleted reef fish. Nature 430:309–310

    PubMed  CAS  Google Scholar 

  • Martin AP, Palumbi SR (1993) Protein evolution in different cellular environments: cytochrome b in sharks and mammals. Mol Biol Evol 10:873–891

    PubMed  CAS  Google Scholar 

  • Masri S, Rast H, Ripley T et al (2002) Detection of genetically modified coho salmon using polymerase chain reaction (PCR) amplification. J Agric Food Chem 50:3161–3164

    PubMed  CAS  Google Scholar 

  • Matejusová I, Doig F, Middlemas SJ et al (2008) Using quantitative real-time PCR to detect salmonid prey in scats of grey Halichoerus grypus and harbour Phoca vitulina seals in Scotland—an experimental and field study. J Appl Ecol 45:632–640

    Google Scholar 

  • McDowell JR, Graves JE (2002) Nuclear and mitochondrial DNA markers for specific identification of istiophorid and xiphiid billfishes. Fish Bull 100:537–544

    Google Scholar 

  • Methven DA, McGowan C (1998) Distinguishing small juvenile Atlantic cod (Gadus morhua) from Greenland cod (Gadus ogac) by comparing meristic characters and discriminant function analysis of morphometric data. Can J Zool 76:1054–1062

    Google Scholar 

  • Michelini E, Cevenini L, Mezzanotte L et al (2007) One-step triplex-polymerase chain reaction assay fot the authentication of yellowfin (Thunnus albacares), bigeye (Thunnus obesus), and skipjack (Katsuwonus pelamis) tuna DNA from fresh, frozen, and canned tuna samples. J Agric Food Chem 55:7638–7647

    PubMed  CAS  Google Scholar 

  • Millar CD, Huynen L, Subramanian S et al (2008) New developments in ancient genomics. Trends Ecol Evol 23:386–393

    PubMed  Google Scholar 

  • Miraglia M, Berdal KG, Brera C (2004) Detection and traceability of genetically modified organisms in the food production chain. Food Chem Toxicol 42:1157–1180

    PubMed  CAS  Google Scholar 

  • Moretti VM, Turchini GM, Bellagamba F et al (2003) Traceability issues in fishery and aquaculture products. Vet Res Comm 27:497–505

    Google Scholar 

  • Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLoS Biol 2:1529–1531

    CAS  Google Scholar 

  • Nilsson RH, Ryberg M, Kristiansson E (2006) Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE 1:e59

    PubMed  Google Scholar 

  • Pääbo S, Irwin DM, Wilson AC (1990) DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718–4721

    PubMed  Google Scholar 

  • Pääbo S, Poinar H, Serre D et al (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38:645–679

    PubMed  Google Scholar 

  • Paterlini M (2007) There shall be order. The legacy of Linnaeus in the age of molecular biology. EMBO Rep 8:814–816

    PubMed  CAS  Google Scholar 

  • Pegg GH, Sinclair B, Briskey L et al (2006) MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia. Sci Mar 70:7–12

    CAS  Google Scholar 

  • Pepe T, Trotta M, Di Marco I et al (2007) Fish species identification in surimi-based products. J Agric Food Chem 55:3681–3685

    PubMed  CAS  Google Scholar 

  • Pierce GJ, Boyle PR (1991) A review of methods for diet analysis in piscivorous marine mammals. Oceanogr Mar Biol Ann Rev (Lond) 29:409–486

    Google Scholar 

  • Poinar HN (2002) The genetic secrets some fossils hold. Acc Chem Res 35:676–684

    PubMed  CAS  Google Scholar 

  • Politov D, Gordon N, Afanasiev K et al (2000) Identification of palearctic coregonid fish species using mtDNA and allozyme genetic markers. J Fish Biol 74:51–71

    Article  Google Scholar 

  • Quinteiro J, Sotelo CG, Rehbein H et al (1998) Use of mtDNA direct polymerase chain reaction (PCR) sequencing and PCR-restriction fragment length polymorphism methodologies in species identification of canned tuna. J Agric Food Chem 46:1662–1669

    CAS  Google Scholar 

  • Rasmussen RS, Morrissey MT (2008) DNA-based methods for the identification of commercial fish and seafood species. Compr Rev Food Sci Food Saf 7:280–295

    CAS  Google Scholar 

  • Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of Life Data systems (www.barcodinglife.org). Mol Ecol Notes 7:355–364

  • Redenbach Z, Taylor EB (2003) Evidence for bimodal hybrid zones between two species of charr (Pisces: Salvelinus) in northwestern North America. J Evol Biol 16:1135–1148

    PubMed  CAS  Google Scholar 

  • Rehbein H (1990) Electrophoretic techniques for species identification of fishery products. Z Lebensm Unters Forsch 191:1–10

    Google Scholar 

  • Rehbein H, Mackie I, Pryde S et al (1999) Fish species identification in canned tuna by PCR-SSCP: validation by a collaborative study and investigation of intra-species variability of the DNA-patterns. Food Chem 64:263–268

    CAS  Google Scholar 

  • Reid SM, Wilson CC (2006) PCR-RFLP based diagnostic tests for Moxostoma species in Ontario. Conserv Genet 7:997–1000

    CAS  Google Scholar 

  • Richardson D, Vanwye J, Exum A et al (2007) High-throughput species identification: from DNA isolation to bioinformatics. Mol Ecol Notes 7:199–207

    CAS  Google Scholar 

  • Roelfsema JH, Peters DJ (2005) Denaturing gradient gel electrophoresis (DGGE). In: Walker JM, Rapley R (eds) Medical biomethods handbook. Humana Press, New York, pp 79–86

    Google Scholar 

  • Ronaghi M (2001) Pyrosequencing sheds light on DNA sequencing. Genome Res 11:3–11

    PubMed  CAS  Google Scholar 

  • Ruedas LA, Salazar-Bravo J, Dragoo JW (2000) The importance of being earnest: what, if anything, constitutes a “specimen examined? Mol Phylogenet Evol 17:129–132

    PubMed  CAS  Google Scholar 

  • Sanjuan A, Raposo-Guillan J, Comesana A (2002) Genetic identification of Lophius budegassa and L. piscatorius by PCR-RFLP analysis of a mitochondrial tRNAGLU/Cytochrome b segment. J Food Sci 67:2644–2648

    Google Scholar 

  • Schander C, Willassen E (2005) What can biological barcoding do for marine biology? Mar Biol Res 1:79–83

    Google Scholar 

  • Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature 435:17

    PubMed  CAS  Google Scholar 

  • Schlick-Steiner BC, Seifert B, Stauffer C et al (2007) Without morphology, cryptic species stay in taxonomic crypsis following discovery. Trends Ecol Evol 22:391–392

    PubMed  Google Scholar 

  • Seberg O, Humphries CJ, Knapp S et al (2003) Shortcuts in systematics? A commentary on DNA-based taxonomy. Trends Ecol Evol 18:63–65

    Google Scholar 

  • Sevilla R, Diez A, Noren M et al (2007) Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes. Mol Ecol Notes 7:730–734

    CAS  Google Scholar 

  • Sheppard SK, Harwood JD (2005) Advances in molecular ecology: tracking trophic links through predator-prey food-webs. Funct Ecol 19:751–762

    Google Scholar 

  • Sites JW, Marshall JC (2003) Delimiting species: a renaissance issue in systematic biology. Trends Ecol Evol 18:462–470

    Google Scholar 

  • Smith P, MCveagh S, Allain V et al (2005) DNA identification of gut contents of large pelagic fishes. J Fish Biol 67:1178–1183

    Google Scholar 

  • Strange R, Stepien C (2007) Yellow (Perca flavescens) and Eurasian (P. fluviatilis) perch distinguished in fried fish samples by DNA analysis. Fish Bull 105:292–295

    Google Scholar 

  • Strauss RE, Bond CE (1990) Taxonomic methods: morphology. In: Schreck CB, Moyle PB (eds) Methods for fish biology. American Fisheries Society, Maryland, pp 109–140

    Google Scholar 

  • Takeyama H, Chow S, Tsuzuki H et al (2001) Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification. J Fish Biol 58:1646–1657

    CAS  Google Scholar 

  • Tautz D, Arctander P, Minelli A et al (2003) A plea for DNA taxonomy. Trends Ecol Evol 18:70–74

    Google Scholar 

  • Teletchea T, Maudet C, Hänni C (2005) Food and forensic molecular identification: update and challenges. Trends Biotech 23:359–366

    CAS  Google Scholar 

  • Teletchea T, Laudet V, Hänni C (2006) Phylogeny of the Gadidae (sensu Svetovidov, 1948) based on their morphology and two mitochondrial genes. Mol Phyl Evol 38:189–199

    CAS  Google Scholar 

  • Teletchea F, Bernillon J, Duffraisse M et al (2008) Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples. J Appl Ecol 45:967–975

    CAS  Google Scholar 

  • Tinti F, Ungaro N, Pasolini P et al (2003) Development of molecular and morphological markers to improve species-specific monitoring and systematics of Northeast Atlantic and Mediterranean skates (Rajiformes). J Exp Mar Biol Ecol 288:149–165

    Google Scholar 

  • Tsai Y-H, Hsieh H, Chen H-C et al (2007) Histamine level and species identification of billfish meats implicated in two food-borne poisonings. Food Chem 104:1366–1371

    CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    PubMed  CAS  Google Scholar 

  • Ward RD, Zemlak TS, Innes BH et al (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci 360:1847–1857

    PubMed  CAS  Google Scholar 

  • Waugh J (2007) DNA barcoding in animal species: progress, potential and pitfalls. BioEssays 29:188–197

    PubMed  CAS  Google Scholar 

  • Weder JKP, Rehbein H, Kaiszer KP (2001) On the specificity of tuna-directed primes in PCR-SSCP analysis of fish and meat. Eur Food Res Technol 213:139–144

    CAS  Google Scholar 

  • Wheeler QD, Raven PH, Wilson EO (2004) Taxonomy: impediment or expedient? Science 303:285

    PubMed  CAS  Google Scholar 

  • Will KW, Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20:47–55

    Google Scholar 

  • Will KW, Mishler BD, Wheeler QD (2005) The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol 54:844–851

    PubMed  Google Scholar 

  • Willerslev E, Cooper A (2005) Ancient DNA. Proc R Soc Lond Ser B Biol Sci 272:3–16

    CAS  Google Scholar 

  • Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63:3741–3751

    PubMed  CAS  Google Scholar 

  • Wolf C, Hübner P, Lüthy J (1999) Differentiation of sturgeon species by PCR-RFLP. Food Res Int 32:699–705

    CAS  Google Scholar 

  • Woolfe M, Primrose S (2004) Food forensics: using DNA technology to combat misdescription and fraud. Trends Biotechnol 22:222–226

    PubMed  CAS  Google Scholar 

  • Yang D, Cannon A, Saunders S (2004) DNA species identification of archaeological salmon bone from the Pacific Northwest Coast of North America. J Archaeol Sci 31:619–631

    Google Scholar 

  • Zhang J, Huang L, Huo H (2004) Larval identification of Lutjanus Bloch in Nansha coral reefs by AFLP molecular method. J Exp Mar Biol Ecol 298:3–20

    CAS  Google Scholar 

Download references

Acknowledgements

I thank two anonymous reviewers that helped to improve the manuscript.

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Authors and Affiliations

  1. UR AFPA, Nancy Université, MAN 34 Rue Sainte Catherine, 54000, Nancy, France

    Fabrice Teletchea

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Appendix: List of the studies reviewed

Appendix: List of the studies reviewed

  1. 1.

    Akasaki T, Yanagimoto T, Yamakami K, et al. (2006) Species identification and PCR-RFLP analysis of cytochrome b gene in cod fish (Order Gadiformes) products. J Food Sci 71:190–195.

  2. 2.

    Aoyama J, Ishikawa S, Otake T, et al. (2001) Molecular approach to species identification of eggs with respect to determination of the spawning site of the Japanese eel Anguilla japonica. Fish Sci 67:761–763. doi:10.1046/j.1444-2906.2001.00288.x.

  3. 3.

    Aranishi F (2005) PCR-RFLP analysis of nuclear nontranscribed spacer for mackerel species identification. J Agric Food Chem 53:508–511. doi:10.1021/jf0484881.

  4. 4.

    Aranishi F (2005) Rapid PCR-RFLP method for discrimination of imported and domestic mackerel. Mar Biotechnol 7:571–575. doi:10.1007/s10126-004-4102-1.

  5. 5.

    Aranishi F (2006) Single fish egg DNA extraction for PCR amplification. Cons Gen 7:153–156. doi:10.1007/s10592-005-5387-y.

  6. 6.

    Aranishi F, Okimoto T, Izumi S (2005) Identification of gadoid fishes (Pisces, Gadidae) by PCR-RFLP analysis. J Appl Genet 46:69–73.

  7. 7.

    Aranishi F, Okimoto T, Ohkubo M (2006) A short-cut DNA extraction from cod caviar. J Sci Food Agric 86:425–428. doi:10.1002/jsfa.2370.

  8. 8.

    Aranishi F, Okimoto T, Ohkubo M, et al. (2005) Molecular identification of commercial spicy pollack roe products by PCR-RFLP analysis. J Food Sci 70:235–238.

  9. 9.

    Asahida T, Yamashita Y, Kobayashi T (1997) Identification of consumed stone flounder, Kareius bicoloratus (Basilewsky), from the stomach contents of sand shrimp, Crangon affinis (De Haan) using mitochondrial DNA analysis. J Exp Mar Biol Ecol 217:153–163. doi:10.1016/S0022-0981(97)00039-7.

  10. 10.

    Asensio L, Gonzalez I, Fernandez A, et al. (2001) PCR-SSCP: A simple method for the authentification of grouper (Epinephelus guaza), werck fish (Polyprion americanus), and nile perch (Lates niloticus) fillets. J Agric Food Chem 49:1720–1723. doi:10.1021/jf001185w.

  11. 11.

    Asensio L, González I, Rodríguez M et al. (2004) PCR-ELISA for the semiquantitative detection of Nile perch (Lates niloticus) in sterilized fish muscle mixtures. J Agric Food Chem 52:4419–4422. doi:10.1021/jf0350010.

  12. 12.

    Babola O, Desvarenne S, Lacroix B, et al. (2004) L’identification des espèces animales dans l’alimentation humaine et animale: un exemple d’application de la technologie des puces à ADN. Bull Soc Fr Micr 19:30–36.

  13. 13.

    Balitzki-Korte B, Anslinger K, Bartsch C, et al. (2005) Species identification by means of pyrosequencing the mitochondrial 12S rRNA gene. Int J Legal Med 119:291–294. doi:10.1007/s00414-005-0537-9.

  14. 14.

    Birstein VJ, Doukakis P, Sorkin B, et al. (1998) Population aggregation analysis of three caviar-producing species of sturgeons and implications for the species identification of black caviar. Conserv Biol 12:766–775. doi:10.1046/j.1523-1739.1998.97081.x.

  15. 15.

    Bottero MT, Civera T, Nucera D, et al. (2003) Design of universal primers for the detection of animal tissues in feedstuff. Vet Res Commun 27:667–669. doi:10.1023/B:VERC.0000014243.75976.cd.

  16. 16.

    Bottero MT, Dalmasso A, Cappelletti M, et al. (2007) Differentiation of five tuna species by a multiplex primer-extension assay. J Biotechnol 129:575–580. doi:10.1016/j.jbiotec.2007.01.032.

  17. 17.

    Bucciarelli G, Golani D, Bernardi G (2002) Genetic cryptic species as biological invaders: the case of a Lessepsian fish migrant, the hardyhead silverside Atherinomorus lacunosus. J Exp Mar Biol Ecol 273:143–149. doi:10.1016/S0022-0981(02)00138-7.

  18. 18.

    Byrkjedal I, Rees DJ, Willassen E (2007) Lumping lumpsuckers: molecular and morphological insights into the taxonomic status of Eumicrotremus spinosus (Fabricius, 1776) and Eumicrotremus eggvinii Koefoed, 1956 (Teleostei: Cyclopteridae). J Fish Biol 71:111–131. doi:10.1111/j.1095-8649.2007.01550.x.

  19. 19.

    Callejas C, Ochando MD (1998) Identification of Spanish barbel species using the RAPD technique. J Fish Biol 53:208–215. doi:10.1111/j.1095-8649.1998.tb00121.x.

  20. 20.

    Callejas C, Ochando MD (2001) Molecular identification (RAPD) of the eight species of the genus Barbus (Cyprinidae) in the Iberian Peninsula. J Fish Biol 59:1589–1599. doi:10.1111/j.1095-8649.2001.tb00223.x.

  21. 21.

    Calo-Mata P, Sotelo CG, Pérez-Martín RI, et al. (2003) Identification of gadoid fish species using DNA-based techniques. Eur Food Res Technol 217:259–264. doi:10.1007/s00217-003-0735-y.

  22. 22.

    Carrera E, García T, Céspedes A et al. (2000) Differentiation of smoked Salmo salar, Oncorhynchus mykiss and Brama raii using the nuclear marker 5S rDNA. Int J Food Sci Technol 35:401–406. doi:10.1046/j.1365-2621.2000.00404.x.

  23. 23.

    Carrera E, García T, Céspedes A et al. (1999) PCR-RFLP of the mitochondrial cytochrome oxidase gene: a simple method for the discrimination between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). J Sci Food Agric 79:1654–1658. doi:10.1002/(SICI)1097-0010(199909)79:12<1654::AID-JSFA414>3.0.CO;2-S.

  24. 24.

    Carrera E, García T, Céspedes A et al. (1999) Salmon and trout analysis by PCR-RFLP for identity authentication. J Food Sci 64:410–413. doi:10.1111/j.1365-2621.1999.tb15053.x.

  25. 25.

    Casper RM, Jarman SN, Deagle BE, et al. (2007) Detecting prey from DNA in predator scats: a comparison with morphological analysis, using Arctocephalus seals fed a known diet. J Exp Mar Biol Ecol 347:144–154. doi:10.1016/j.jembe.2007.04.002.

  26. 26.

    Céspedes A, García T, Carrera E, et al. (2000) Genetic differentiation between sole (Solea solea) and Greenland halibut (Reinhardtius hippoglossoides) by PCR-RFLP analysis of a 12S rRNA gene fragment. J Sci Food Agric 80:29–32. doi:10.1002/(SICI)1097-0010(20000101)80:1<29::AID-JSFA470>3.0.CO;2-4.

  27. 27.

    Céspedes A, García T, Carrera E, et al. (1999) Identification of Sole (Solea solea) and Greenland Halibut (Reinhardtius hippoglossoides) by PCR Amplification of the 5S rDNA Gene. J Agric Food Chem 49:1046–1050. doi:10.1021/jf9810970.

  28. 28.

    Céspedes A, García T, Carrera E, et al. (1998) Identification of flatfish species using polymerase chain reaction (PCR) amplification and restriction analysis of the cytochrome b gene. J Food Sci 63:206–209.

  29. 29.

    Chakraborty A, Aranishi F, Iwatsuki Y (2005) Molecular identification of hairtail species (Pisces: Trichiuridae) based on PCR-RFLP analysis of the mitochondrial 16S rRNA gene. J Appl Genet 46:381–385.

  30. 30.

    Chakraborty A, Aranishi F, Iwatsuki Y (2007) Polymerase chain reaction-restriction fragment length polymorphism analysis for species identification of hairtail fish fillets from supermarkets in Japan. Fish Sci 73:197–201. doi:10.1111/j.1444-2906.2007.01319.x.

  31. 31.

    Chan RWK, Dixon PI, Pepperell JG, et al. (2003) Application of DNA-based techniques for the identification of whaler sharks (Carcharhinus spp.) caught in protective beach meshing and by recreational fisheries off the coast of New South Wales. Fish Bull (Wash D C) 101:910–914.

  32. 32.

    Chapela MJ, Sanchez A, Suarez MI, et al. (2007) A rapid methodology for screening hake species (Merluccius spp.) by single-stranded conformation polymorphism analysis. J Agric Food Chem 55:6903–6909. doi:10.1021/jf070132c.

  33. 33.

    Chapela MJ, Sotelo CG, Pérez-Martín RI, et al. (2007) Comparison of DNA extraction methods from muscle of canned tuna for species identification. Food Contr 18:1211–1215. doi:10.1016/j.foodcont.2006.07.016.

  34. 34.

    Chapman DD, Abercrombie DL, Douady CJ, et al. (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. Cons Gen 4:415–425. doi:10.1023/A:1024771215616.

  35. 35.

    Cheng C-A, Hsieh Y-W, Noguchi T, et al. (2001) Effect of processing on sequence of cytochrome b gene and its restriction site in the meat of puffer Takifugu rubripes. J Food Drug Anal 9:232–237.

  36. 36.

    Cocolin I, D’Agaro E, Manzano M, et al. (2000) Rapid PCR-RFLP method for the identification of marine fish fillets (Seabass, Seabream, Umbrine, and Dentex). J Food Sci 65:1315–1317. doi:10.1111/j.1365-2621.2000.tb10604.x.

  37. 37.

    Colombo F, Mangiagalli G, Renon P (2005) Identification of tuna species by computer-assisted and cluster analysis of PCR-SSCP electrophoretic patterns. Food Contr 16:51–53. doi:10.1016/j.foodcont.2003.11.006.

  38. 38.

    Comesana AS, Abella P, Sanjuan A (2003) Molecular identification of five commercial flatfish species by PCR-RFLP analysis of a 12 rRNA gene fragment. J Sci Food Agric 83:752–759. doi:10.1002/jsfa.1368.

  39. 39.

    Comi G, Iacumin L, Rantsiou K, et al. (2005) Molecular methods for the differentiation of species used in the production of cod-fish can detect commercial frauds. Food Contr 16:37–42. doi:10.1016/j.foodcont.2003.11.003.

  40. 40.

    Dalmasso A, Civera T, Bottero MT (2006) Biomolecular approaches for the identification of tuna species. Vet Res Commun 30:179–181. doi:10.1007/s11259-006-0035-7.

  41. 41.

    Dalmasso A, Fontanella E, Piatti P, et al. (2007) Identification of four tuna species by means of real-time PCR and melting curve analysis. Vet Res Commun 31:355–357. doi:10.1007/s11259-007-0036-1.

  42. 42.

    Das P, Prasad H, Meher PK, et al. (2005) Evaluation of genetic relationship among six Labeo species using randomly amplified polymorphic DNA (RAPD). Aquacult Res 36:564–569. doi:10.1111/j.1365-2109.2005.01254.x.

  43. 43.

    Dawnay N, Ogden R, McEwing R, et al. (2007) Validation of the barcoding gene COI for use in forensic genetic species identification. Forensic Sci Int 173:1–6. doi:10.1016/j.forsciint.2006.09.013.

  44. 44.

    de los Angeles Barriga-Sosa I, Pérez-Ramírez M, Soto-Aguirre F, et al. (2005) Inter-specific variation of the mitochondrial r16S gene among silversides, “Peces Blancos” (Atherinopsidae: Menidiinae) and its utilization for species identification. Aquaculture 250:637–651. doi:10.1016/j.aquaculture.2005.05.003.

  45. 45.

    Deagle B, Tollit D, Jarman S, et al. (2005) Molecular scatology as a tool to study diet: Analysis of prey DNA in scats from captive Steller sea lions. Mol Ecol 14:1831–1842. doi:10.1111/j.1365-294X.2005.02531.x.

  46. 46.

    Di Finizio A, Guerriero G, Russo GL, et al. (2007) Identification of gadoid species (Pisces, Gadidae) by sequencing and PCR-RFLP analysis of mitochondrial 12S and 16S rRNA gene fragments. Eur Food Res Technol 225:337–344. doi:10.1007/s00217-006-0420-z.

  47. 47.

    Dooley J, Sage H, Brown H, et al. (2005) Improved fish species identification by use of lab-on-a-chip technology. Food Contr 16:601–607. doi:10.1016/j.foodcont.2004.06.022.

  48. 48.

    Dooley J, Sage H, Clarke M-A, et al. (2005) Fish species identification using PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis: application to detect white fish species in food products and an interlaboratory study. J Agric Food Chem 53:3348–3357. doi:10.1021/jf047917s.

  49. 49.

    Fox CJ, Taylor MI, Pereyra R, et al. (2005) TaqMan DNA technology confirms likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg-based methods. Mol Ecol 14:879–884. doi:10.1111/j.1365-294X.2005.02439.x.

  50. 50.

    Gagnaire PA, Tsukamoto K, Aoyama J, et al. (2007) RFLP and semi-multiplex PCR-based identification of four eel species from the south-western Indian Ocean region. J Fish Biol 71:279–287. doi:10.1111/j.1095-8649.2007.01605.x.

  51. 51.

    Garcia-Vazquez E, Izquierdo JI, Perez J, et al. (2006) Genetic variation at ribosomal genes supports the existence of two different European subspecies in the megrim Lepidorhombus whiffiagonis. J Sea Res 56:59–64. doi:10.1016/j.seares.2006.04.001.

  52. 52.

    Gharrett AJ, Gray AK, Heifetz J (2001) Identification of rockfish (Sebastes spp.) by restriction site analysis of the mitochondrial ND-3/ND-4 and 12S/16S rRNA gene regions. Fish Bull (Wash D C) 99:49–62.

  53. 53.

    Greig TW, Moore MK, Woodley CM (2005) Mitochondrial gene sequences useful for species identification of western North Atlantic Ocean sharks. Fish Bull (Wash D C) 103:516–523.

  54. 54.

    Heist EJ, Gold JR (1999) Genetic identification of sharks in the U.S. Atlantic large coastal shark fishery. Fish Bull (Wash D C) 97:53–61.

  55. 55.

    Hird HJ, Hold GL, Chisholm J, et al. (2005) Development of a method for the quantification of haddock (Melanogrammus aeglefinus) in commercial products using real-time PCR. Eur Food Res Technol 220:663–637.

  56. 56.

    Hoelzel AR (2001) Shark fishing in fin soup. Cons Gen 2:69–72. doi:10.1023/A:1011590517389.

  57. 57.

    Hold GL, Russell VJ, Pryde SE, et al. (2001) Validation of a PCR-RFLP based method for the identification of salmon species in food products. Eur Food Res Technol 212:385–389. doi:10.1007/s002170000237.

  58. 58.

    Hold GL, Russell VJ, Pryde SE, et al. (2001) Development of a DNA-Based method aimed at identifying the fish species present in food products. J Agric Food Chem 49:1175–1179. doi:10.1021/jf001149x.

  59. 59.

    Horstkotte B, Rehbein H (2003) Fish species identification by means of restriction fragment length polymorphism and high-performance liquid chromatography. J Food Sci 68:2658–2666. doi:10.1111/j.1365-2621.2003.tb05785.x.

  60. 60.

    Hsieh HS, Chai T, Cheng CA, et al. (2004) Application of DNA technique for identifying the species of different processed products of swordfish meat. J Food Sci 69:FCT1–FCT6. doi:10.1111/j.1365-2621.2004.tb17847.x.

  61. 61.

    Hsieh HS, Chai T, Hwang DF (2005) Rapid PCR-RFLP method for the identification of 5 billfish species. J Food Sci 70:246–249.

  62. 62.

    Hsieh HS, Chai T, Hwang DF (2007) Using the PCR-RFLP method to identify the species of different processed products to billfish meats. Food Contr 18:369–374. doi:10.1016/j.foodcont.2005.11.002.

  63. 63.

    Hsieh HS, Hwang DF (2004) Molecular phylogenetic relationships of puffer fish inferred from partial sequences of cytochrome b gene and restriction fragment length polymorphism analysis. J Agric Food Chem 52:4159–4165. doi:10.1021/jf035462l.

  64. 64.

    Hsieh YW, Hwang PA, Pan HH, et al. (2003) Identification of tetradotoxin and fish species in an adulterated dried mullet roe implicated in food poisoning. J Food Sci 68:142–146. doi:10.1111/j.1365-2621.2003.tb14130.x.

  65. 65.

    Hsieh YW, Shiu YC, Cheng CA, et al. (2002) Identification of toxin and fish species in cooked fish liver implicated in food poisoning. J Food Sci 67:948–952. doi:10.1111/j.1365-2621.2002.tb09433.x.

  66. 66.

    Hwang D-F, Jen H–C, Hsieh Y-W, et al. (2004) Applying DNA techniques to the identification of the species of dressed toasted eel products. J Agric Food Chem 52:5972–5977. doi:10.1021/jf034525x.

  67. 67.

    Imsiridou A, Minos G, Katsares V, et al. (2007) Genetic identification and phylogenetic inferences in different Mugilidae species using 5S rDNA markers. Aquacult Res 38:1370–1379. doi:10.1111/j.1365-2109.2007.01808.x.

  68. 68.

    Infante C, Catanese G, Ponce M, et al. (2004) Novel method for the authentication of frigate tunas (Auxis thazard and Auxis rochei) in commercial canned products. J Agric Food Chem 52:7435–7443. doi:10.1021/jf0492868.

  69. 69.

    Infante C, Crespo A, Zuasti E, et al. (2006) PCR-based methodology for the authentication of the atlantic mackerel Scomber scombrus in commercial canned products. Food Res Int 39:1023–1028. doi:10.1016/j.foodres.2006.02.006.

  70. 70.

    Itoi S, Nakaya M, Kaneko G, et al. (2005) Rapid identification of eels Anguilla japonica and Anguilla anguilla by polymerase chain reaction with single nucleotide polymorphism-based specific probes. Fish Sci 71:1356–1364. doi:10.1111/j.1444-2906.2005.01102.x.

  71. 71.

    Ivanova N, Zemlak T, Hanner R, et al. (2007) Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes 7:544–548. doi:10.1111/j.1471-8286.2007.01748.x.

  72. 72.

    Jarman S, Deagle B, Gales N (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Mol Ecol 13:1313–1322. doi:10.1111/j.1365-294X.2004.02109.x.

  73. 73.

    Jérôme M, Lemaire C, Bautista JM, et al. (2003) Molecular phylogeny and species identification of sardines. J Agric Food Chem 51:43–50. doi:10.1021/jf020713w.

  74. 74.

    Jérôme M, Lemaire C, Verrez-Bagnis V, et al. (2003) Direct sequencing method for species identification of canned sardine and sardine-type products. J Agric Food Chem 51:7326–7332. doi:10.1021/jf034652t.

  75. 75.

    Karaiskou N, Apostolidis AP, Triantafyllidis A, et al. (2003) Genetic identification and phylogeny of three species of the genus Trachurus based on mitochondrial DNA analysis. Mar Biotechnol 5:493–504. doi:10.1007/s10126-002-0099-5.

  76. 76.

    Karaiskou N, Triantafyllidis A, Alvarez P, et al. (2007) Horse mackerel egg identification using DNA methodology. Mar Ecol (Berl) 28:429–434. doi:10.1111/j.1439-0485.2007.00190.x.

  77. 77.

    Karaiskou N, Triantafyllidis A, Margaroni M, et al. (2005) A double DNA approach for identifying Macrorhamphosus scolopax (Pisces, Centriscidae). ICES J Mar Sci 62:1683–1690. doi:10.1016/j.icesjms.2005.05.011.

  78. 78.

    Karaiskou N, Triantafyllidis A, Triantaphyllidis C (2003) Discrimination of three Trachurus species using both mitochondrial-and nuclear-based DNA approaches. J Agric Food Chem 51:4935–4940. doi:10.1021/jf034063n.

  79. 79.

    Kitano T, Umetsu K, Tian W, et al. (2007) Two universal primer sets for species identification among vertebrates. Int J Legal Med 121:423–427. doi:10.1007/s00414-006-0113-y.

  80. 80.

    Klossa-Kilia E, Papasotiropoulos V, Kilias G, et al. (2002) Authentication of Messolongi (Greece) fish roe using PCR-RFLP analysis of 16s rRNA mtDNA segment. Food Contr 13:169–172. doi:10.1016/S0956-7135(01)00097-4.

  81. 81.

    Kon T, Yoshino T, Mukai T, et al. (2007) DNA sequences identify numerous cryptic species of vertebrate: a lesson from the gobioid fish Schindleria. Mol Phylogenet Evol 44:53–62. doi:10.1016/j.ympev.2006.12.007.

  82. 82.

    Kyle CJ, Wilson CC (2007) Mitochondrial DNA identification of game harvested freshwater fish species. Forensic Sci Int 166:68–76. doi:10.1016/j.forsciint.2006.03.025.

  83. 83.

    Lakra WS, Goswami M, Mohindra V, et al. (2007) Molecular identification of five indian sciaenids (Pisces: Perciformes, Sciaenidae) using RAPD markes. Hydrobiologia 585:359–363. doi:10.1007/s10750-006-0480-x.

  84. 84.

    Li Z, Gray AK, Love MS, et al. (2006) A key to selected rockfishes (Sebastes spp.) based on mitochondrial DNA restriction fragment analysis. Fish Bull (Wash D C) 104:182–196.

  85. 85.

    Li Z, Nishimoto MM, Love MS, et al. (2006) Comparing the identification of southern California juvenile rockfish (genus Sebastes spp.) by restriction site analysis of the mitochondrial ND3/ND4 region and by morphological characteristics. Fish Bull (Wash D C) 104:376–382.

  86. 86.

    Lin W–F, Hwang D-F (2007) Application of PCR-RFLP analysis on species identification of canned tuna. Food Contr 18:1050–1057. doi:10.1016/j.foodcont.2006.07.001.

  87. 87.

    Lin Y-S, Poh Y-P, Lin S-M, et al. (2002) Molecular techniques to identify freshwater eels: RFLP analyses of PCR-amplified DNA fragments and allele-specific PCR from mitochondrial DNA. Zool Stud 41:421–430.

  88. 88.

    Lindstrom D (1999) Molecular species identification of newly hatched Hawaiian amphidromous gobioid larvae. Mar Biotechnol 1:167–174. doi:10.1007/PL00011764.

  89. 89.

    Lockley A, Bardsley R (2000) Novel Method for the Discrimination of Tuna (Thunnus thynnus) and Bonito (Sarda sarda) DNA. J Agric Food Chem 48:4463–4468. doi:10.1021/jf000387p.

  90. 90.

    Lopez I, Pardo M (2005) Application of relative quantification TaqMan Real-Time polymerase chain reaction technology for the identification and quantification of Thunnus alalunga and Thunnus albacares. J Agric Food Chem 53:4554–4560. doi:10.1021/jf0500841.

  91. 91.

    Ludwig A, Debus L, Jenneckens I (2002) A molecular approach to Controlol the international trade in black caviar. Inter Rev Hydrobiol 87:661–674. doi:10.1002/1522-2632(200211)87:5/6<661::AID-IROH661>3.0.CO;2-S.

  92. 92.

    Luthy SA, Cowen RK, Serafy JE, et al. (2005) Toward identification of larval sailfish (Istiophorus platypterus), white marlin (Tetrapterus albidus), and blue marlin (Makaira nigricans) in the western North Atlantic Ocean. Fish Bull (Wash D C) 103:588–600.

  93. 93.

    Maldini M, Marzano F, Fortes G, et al. (2006) Fish and seafood traceability based on AFLP markers: elaboration of a species database. Aquaculture 261:487–494. doi:10.1016/j.aquaculture.2006.07.010.

  94. 94.

    Maretto F, Reffo E, Dalvit C, et al. (2007) Finding 16S rRNA gene-based SNPs for the genetic traceability of commercial species belonging to Gadiformes. Ital J Anim Sci 6:161–163.

  95. 95.

    Masri S, Rast H, Ripley T, et al. (2002) Detection of genetically modified coho salmon using polymerase chain reaction (PCR) amplification. J Agric Food Chem 50:3161–3164. doi:10.1021/jf011606p.

  96. 96.

    McDowell JR, Graves JE (2002) Nuclear and mitochondrial DNA markers for specific identification of istiophorid and xiphiid billfishes. Fish Bull (Wash D C) 100:537–544.

  97. 97.

    Michelini E, Cevenini L, Mezzanotte L, et al. (2007) One-step triplex-polymerase chain reaction assay fot the authentication of yellowfin (Thunnus albacares), bigeye (Thunnus obesus), and skipjack (Katsuwonus pelamis) tuna DNA from fresh, frozen, and canned tuna samples. J Agric Food Chem 55:7638–7647. doi:10.1021/jf070902k.

  98. 98.

    Nam YK, Park JE, Kim KK, et al. (2003) A rapid and simple PCR-based method for the analysis of transgenic fish using a restricted amount of fin tissue. Transgenic Res 12:523–525. doi:10.1023/A:1024274508052.

  99. 99.

    Pardo M, Pérez-Villareal B (2004) Identification of commercial canned tuna species by restriction site analysis of mitochondrial DNA products obtained by nested primer PCR. Food Chem 86:143–150. doi:10.1016/j.foodchem.2003.09.024.

  100. 100.

    Parsons K, Piertney S, Middlemas S, et al. (2005) DNA-based identification of salmonid prey species in seal faeces. J Zool (Lond) 266:275–281. doi:10.1017/S0952836905006904.

  101. 101.

    Pegg GH, Sinclair B, Briskey L, et al. (2006) MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia. Sci Mar 70:7–12.

  102. 102.

    Pepe T, Trotta M, Di Marco I, et al. (2007) Fish species identification in surimi-based products. J Agric Food Chem 55:3681–3685. doi:10.1021/jf063321o.

  103. 103.

    Perez J, Alvarez P, Martinez J, et al. (2005) Genetic identification of hake and megrim eggs in formaldehyde-fixed plankton samples. ICES J Mar Sci 62:908–914. doi:10.1016/j.icesjms.2005.04.001.

  104. 104.

    Perez M, Vieites J, Presa P (2005) ITS1-rDNA-based methodology to identify world-wide hake species of the genus Merluccius. J Agric Food Chem 53:5239–5247. doi:10.1021/jf048012h.

  105. 105.

    Politov D, Gordon N, Afanasiev K, et al. (2000) Identification of palearctic coregonid fish species using mtDNA and allozyme genetic markers. J Fish Biol 74:51–71.

  106. 106.

    Purcell M, Mackey G, LaHood E (2004) Molecular methods for the genetic identification of salmonid prey from Pacific harbor seal (Phoca vitulina richardsi) scat. Fish Bull (Wash D C) 102:213–220.

  107. 107.

    Quinteiro J, Sotelo CG, Rehbein H, et al. (1998) Use of mtDNA direct polymerase chain reaction (PCR) sequencing and PCR-restriction fragment length polymorphism methodologies in species identification of canned tuna. J Agric Food Chem 46:1662–1669. doi:10.1021/jf970552+.

  108. 108.

    Quinteiro J, Vidal R, Izquierdo M, et al. (2001) Identification of hake species (Merluccius genus) using sequencing and PCR-RFLP analysis of mitochondrial DNA Controlol region sequences. J Agric Food Chem 49:5108–5114. doi:10.1021/jf010421f.

  109. 109.

    Rehbein H (2005) Identification of the fish species of raw or cold-smoked salmon and salmon caviar by single-strand conformation polymorphism (SSCP) analysis. Eur Food Res Technol 220:625–632. doi:10.1007/s00217-004-1067-2.

  110. 110.

    Rehbein H, Kress G, Schmidt T (1997) Application of PCR-SSCP to species identification of fishery products. J Sci Food Agric 74:35–41. doi:10.1002/(SICI)1097-0010(199705)74:1<35::AID-JSFA765>3.0.CO;2-2.

  111. 111.

    Rehbein H, Mackie I, Pryde S, et al. (1999) Fish species identification in canned tuna by PCR-SSCP: validation by a collaborative study and investigation of intra-species variability of the DNA-patterns. Food Chem 64:263–268. doi:10.1016/S0308-8146(98)00125-3.

  112. 112.

    Rehbein H, Sotelo C, Perez-Martin R, et al. (2002) Differentiation of raw and processed eel by PCR-based techniques: restriction fragment length polymorphism analysis (RFLP) and single strand conformation polymorphism analysis (SSCP). Eur Food Res Technol 214:171–177. doi:10.1007/s00217-001-0457-y.

  113. 113.

    Reid SM, Wilson CC (2006) PCR-RFLP based diagnostic tests for Moxostoma species in Ontario. Conserv Genet 7:997–1000. doi:10.1007/s10592-006-9113-1.

  114. 114.

    Renshaw M, Saillant E, Broughton R, et al. (2006) Application of hypervariable genetic markers to forensic identification of ‘wild’ from hatchery-raised red drum, Sciaenops ocellatus. Forensic Sci Int 156:9–15. doi:10.1016/j.forsciint.2005.05.038.

  115. 115.

    Richardson D, Vanwye J, Exum A, et al. (2007) High-throughput species identification: from DNA isolation to bioinformatics. Mol Ecol Notes 7:199–207. doi:10.1111/j.1471-8286.2006.01620.x.

  116. 116.

    Robertson M, Ovenden J, Barker S (2007) Identification of small juvenile scombrids from northwest tropical Australia using mitochondrial DNA cytochrome b sequences. Ichthyol Res 54:246–252. doi:10.1007/s10228-007-0397-z.

  117. 117.

    Rocha-Olivares A (1998) Multiplex haplotype-specific PCR: a new approach for species identification of the early life stages of rockfishes of the species-rich genus Sebastes Cuvier. J Exp Mar Biol Ecol 231:279–290. doi:10.1016/S0022-0981(98)00098-7.

  118. 118.

    Rocha-Olivares A, Moser H, Stannard J (2000) Molecular identification and description of pelagic young of the rockfishes Sebastes constellatus and Sebastes ensifer. Fish Bull (Wash D C) 98:353–363.

  119. 119.

    Rosel P, Kocher T (2002) DNA-based identification of larval cod in stomach contents of predatory fishes. J Exp Mar Biol Ecol 267:75–88. doi:10.1016/S0022-0981(01)00359-8.

  120. 120.

    Russell V, Hold G, Pryde S, et al. (2000) Use of restriction fragment length polymorphism to distinguish between salmon species. J Agric Food Chem 48:2184–2188. doi:10.1021/jf991213e.

  121. 121.

    Ruzainah A, Siti Azizah M, Patimah I, et al. (2003) RAPD fingerprinting of the eel-loaches Pangio filinaris and Pangio piperata: preliminary evaluation. Aquacult Res 34:959–965. doi:10.1046/j.1365-2109.2003.00951.x.

  122. 122.

    Saitoh K, Takagaki M, Yamashita Y (2003) Detection of Japanese flounder-specific DNA from gut contents of potential predators in the field. Fish Sci 69:473–477. doi:10.1046/j.1444-2906.2003.00647.x.

  123. 123.

    Sanjuan A, Raposo-Guillan J, Comesana A (2002) Genetic identification of Lophius budegassa and L. piscatorius by PCR-RFLP analysis of a mitochondrial tRNAGLU/Cytochrome b segment. J Food Sci 67:2644–2648. doi:10.1111/j.1365-2621.2002.tb08792.x.

  124. 124.

    Santaclara F, Cabado A, Vieites J (2006) Development of a method for genetic identification of four species of anchovies: E. encrasicolus, E. anchoita, E. ringens, and E. japonicus. Eur Food Res Technol 223:609–614. doi:10.1007/s00217-005-0241-5.

  125. 125.

    Sebastio P, Zanelli P, Neri T (2001) Identification of Anchovy (Engraulis encrasicholus L.) and gilt sardine (Sardinella aurita) by polymerase chain reaction, sequence of their mitochondrial cytochrome b gene, and restriction analysis of polymerase chain reaction products in semipreserves. J Agric Food Chem 49:1194–1199. doi:10.1021/jf000875x.

  126. 126.

    Sevilla R, Diez A, Noren M, et al. (2007) Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes. Mol Ecol Notes 7:730–734. doi:10.1111/j.1471-8286.2007.01863.x.

  127. 127.

    Sezaki K, Itoi S, Watabe S (2005) A simple method to distinguish two commercially valuable eel species in Japan Anguilla japonica and A. anguilla using polymerase chain reaction strategy with a species-specific primers. Fish Sci 71:414–421. doi:10.1111/j.1444-2906.2005.00979.x.

  128. 128.

    Shivji M, Clarke S, Pank M, et al. (2002) Genetic identification of pelagic shark body parts for conservation and trade monitoring. Conserv Biol 16:1036–1047. doi:10.1046/j.1523-1739.2002.01188.x.

  129. 129.

    Smith P, MCveagh S, Allain V et al. (2005) DNA identification of gut contents of large pelagic fishes. J Fish Biol 67:1178–1183. doi:10.1111/j.0022-1112.2005.00804.x.

  130. 130.

    Sotelo C, Calo-Mata P, Chapela M, et al. (2001) Identification of flatfish (Pleuronectiforme) species using DNA-based techniques. J Agric Food Chem 49:4562–4569. doi:10.1021/jf010452a.

  131. 131.

    Spies IB, Gaichas S, Stevenson D, et al. (2006) DNA-based identification of Alaska skates (Amblyraja, Bathyraja and Raja: Rajidae) using cytochrome c oxydase subunit I (coI) variation. J Fish Biol 69:283–292. doi:10.1111/j.1095-8649.2006.01286.x.

  132. 132.

    Strange R, Stepien C (2007) Yellow (Perca flavescens) and Eurasian (P. fluviatilis) perch distinguished in fried fish samples by DNA analysis. Fish Bull (Wash D C) 105:292–295.

  133. 133.

    Tagliavini J, Conterio F, Gandolfi G, et al. (1999) Mitochondrial DNA sequences of six sturgeons species and phylogenetic relationships within Acipenseridae. J Appl Ichthyology 15:17–22. doi:10.1111/j.1439-0426.1999.tb00198.x.

  134. 134.

    Takeyama H, Chow S, Tsuzuki H, et al. (2001) Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification. J Fish Biol 58:1646–1657. doi:10.1111/j.1095-8649.2001.tb02319.x.

  135. 135.

    Taylor M, Fox C, Rico C (2002) Species-specific TaqMan probes for simultaneous identification of (Gadus morhua L.), haddock (Melanogrammus aeglefinus L.) and whithing (Merlangius merlangus L.). Mol Ecol Notes 2:599–601. doi:10.1046/j.1471-8286.2002.00269.x.

  136. 136.

    Terol J, Mascarell R, Fernandez-Pedrosa V, et al. (2002) Statistical validation of the identification of tuna species: bootstrap analysis of mitochondrial DNA sequences. J Agric Food Chem 50:963–969. doi:10.1021/jf011032o.

  137. 137.

    Tinti F, Ungaro N, Pasolini P, et al. (2003) Development of molecular and morphological markers to improve species-specific monitoring and systematics of Northeast Atlantic and Mediterranean skates (Rajiformes). J Exp Mar Biol Ecol 288:149–165. doi:10.1016/S0022-0981(03)00021-2.

  138. 138.

    Trotta M, Schönhuth S, Pepe T, et al. (2005) Multiplex PCR method for use in real-time PCR for identification of fish fillets from Grouper (Epinephelus and Mycteroperca species) and common substitute species. J Agric Food Chem 53:2039–2045. doi:10.1021/jf048542d.

  139. 139.

    Tsai Y-H, Hsieh H, Chen H–C, et al. (2007) Histamine level and species identification of billfish meats implicated in two food-borne poisonings. Food Chem 104:1366–1371. doi:10.1016/j.foodchem.2007.01.052.

  140. 140.

    Tzeng CH, Chen CS, Chiu TS (2007) Analysis of morphometry and mitochrodrial DNA sequences from two Trichiurus species in waters of the western North Pacific: taxonomic assessment and population structure. J Fish Biol 70:165–176. doi:10.1111/j.1095-8649.2007.01368.x.

  141. 141.

    Von Der Heyden S, Lipinski M, Matthee C (2007) Species-specific genetic markers for identification of early-life history stages of Cape hakes, Merluccius capensis and Merluccius paradoxus in the southern Benguela current. J Fish Biol 70:262–268. doi:10.1111/j.1095-8649.2007.01409.x.

  142. 142.

    Ward R, Zemlak T, Innes B, et al. (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc B-Biol Sci 360:1847-1857.

  143. 143.

    Watanabe S, Minegishi Y, Yoshinaga T, et al. (2004) A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys. Mar Biotechnol 6:566–574. doi:10.1007/s10126-004-1000-5.

  144. 144.

    Weder J, Rehbein H, Kaiser K–P (2001) On the specificity of tuna-directed primers in PCR-SSCP analysis of fish and meat. Eur Food Res Technol 213:139–144. doi:10.1007/s002170100339.

  145. 145.

    Whithler R, Candy J, Beacham T, et al. (2004) Forensic DNA analysis of Pacific salmonid samples for species and stock identification. Environ Biol Fishes 69:275–285. doi:10.1023/B:EBFI.0000022901.26754.0b.

  146. 146.

    Wolf C, Burgener M, Lüthy J (2000) PCR-RFLP Analysis of Mitochondrial DNA: Differentiation of Fish Species. LWT-Food Sci. Technol 33:144–150.

  147. 147.

    Wolf C, Hübner P, Lüthy J (1999) Differentiation of sturgeon species by PCR-RFLP. Food Res Int 32:699–705. doi:10.1016/S0963-9969(99)00150-7.

  148. 148.

    Wuertz S, Belay M, Kirschbaum F (2007) On the risk of criminal contamination in caviar trade by intended contamination of caviar with PCR products. Aquaculture 269:130–134. doi:10.1016/j.aquaculture.2007.05.027.

  149. 149.

    Yang D, Cannon A, Saunders S (2004) DNA species identification of archaelogical salmon bone from the Pacific Northwest Coast of North America. J Archaeol Sci 31:619–631. doi:10.1016/j.jas.2003.10.008.

  150. 150.

    Zhang J, Huang H, Cai Z, et al. (2007) Species identification in salted products of red snappers by semi-nested PCR-RFLP based on the mitochondria 12S rRNA gene sequence. Food Contr 18:1331–1336. doi:10.1016/j.foodcont.2005.01.001.

  151. 151.

    Zhang J, Huang H, Cai Z, et al. (2006) Species identification in salted products of red snappers by semi-nested PCR-RFLP based on the mitochondrial 12S rRNA gene sequence. Food Contr 17:557–563. doi:10.1016/j.foodcont.2005.01.011.

  152. 152.

    Zhang J, Huang L, Huo H (2004) Larval identification of Lutjanus Bloch in Nansha coral reefs by AFLP molecular method. J Exp Mar Biol Ecol 298:3–20. doi:10.1016/S0022-0981(03)00341-1.

  153. 153.

    Zhang J, Wang H, Cai Z (2007) The application of DGGE and AFLP-derived SCAR for discrimination between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Food Contr 18:672–676. doi:10.1016/j.foodcont.2006.02.015.

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Teletchea, F. Molecular identification methods of fish species: reassessment and possible applications. Rev Fish Biol Fisheries 19, 265–293 (2009). https://doi.org/10.1007/s11160-009-9107-4

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