The Real maccoyii: Identifying Tuna Sushi with DNA Barcodes – Contrasting Characteristic Attributes and Genetic Distances

Abstract

BackgroundThe use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species.Methodology/Principal FindingsHere we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of “white tuna” were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus.Conclusions/SignificanceThe Convention on International Trade Endangered Species (CITES) requires that listed species must be identifiable in trade. This research fulfills this requirement for tuna, and supports the nomination of northern bluefin tuna for CITES listing in 2010.

DNA barcoding reveals high substitution rate and mislabeling in croaker fillets (Sciaenidae) marketed in Brazil: The case of “pescada branca” (Cynoscion leiarchus and Plagioscion squamosissimus)

“…of the labeling of fish and derived products, and a high rate of species substitution has been recorded (Barbuto et al, 2010;Carvalho et al, 2011b;Cawthorn et al, 2012;Filonzi, Chiesa, Vaghi, & Marzano, 2010;Kyle & Wilson, 2007;Lowenstein, Amato, & Kolokotronis, 2009;Maralit et al, 2013;Wong & Hanner, 2008;Yancy et al, 2008). The results of this study confirm the DNA barcode efficiency in the identification of fish because we unequivocally identified 90% of the fillets evaluated.…”

Genetic evidence reveals a unique lineage of Bryde’s whales in the northern Gulf of Mexico

“…Placement of these morphologically classified specimens was used to identify the clades corresponding to each of the 3 taxonomic groups. Finally, following Kershaw et al (2013), we applied characteristic attributes (CAs) diagnosis (Davis & N ixon 1992, Sarkar et al 2002, Lowenstein et al 2009) to controlregion sequences of B. e. edeni, B. e. brydei, B. omurai, and the haplotypes from the GOMx whales. We first used the 9 diagnostic sites identified by Kershaw et al (2013) to try to classify the GOMx Bryde's whales to the recognized subspecies.…”

Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genusLabeoas a case study

“…Secondly, the use of COI sequence diagnostics in concert with morphological characters in species descriptions (Amato et al 1999;Victor 2007) is recognized as an increasingly useful synergy. Incorporating gene sequences from type specimens (or retrospectively from topotypical material) optimizes the accuracy of future barcode identifications-which is particularly important when faunas are poorly understood taxonomically and geographical distributions undefined-while allowing for these data to be used as any other discrete character (DeSalle 2006) for unambiguously diagnosing species (DeSalle et al 2005;Lowenstein et al 2009). While comprehensive reference sequences from systematics-driven initiatives can be added to the Barcode of Life Data System (BOLD; Ratnasingham and Hebert 2007) with relative ease and can be used to generate species hypotheses or identifications, generating complete reference libraries in localities like the LCR is a far greater challenge.…”