DNA barcoding reveals mislabeling of endangered sharks sold as swordfish in New England fish markets

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Eppley, Thomas Coote This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4547946/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 15 Feb, 2025 Read the published version in Conservation Genetics → Version 1 posted 7 You are reading this latest preprint version Abstract Mislabeling of shark and swordfish meat poses a substantial challenge to conservation of rapidly declining pelagic shark populations in the North Atlantic, so routine market assessments are critical. New England’s southern region of Massachusetts, Connecticut, and Rhode Island has a historic reliance on fisheries and seafood consumption, including sharks and swordfish. The visual similarity of shark and swordfish meat is considerable, and as such, this study aimed to evaluate mislabeling of shark for swordfish meat collected from markets and grocery stores in New England in 2019. DNA barcoding was used on the mitochondrial cytochrome oxidase I (COI) gene to determine unambiguous identification of 38 collected samples, which were either labeled as Shortfin Mako shark ( Isurus oxyrinchus) , Common Thresher shark ( Alopias vulpinus ), or swordfish ( Xiphias gladius ) in market. Mako, an IUCN Red List Endangered species and Thresher, an IUCN Red List vulnerable species, are additionally listed on the CITES Appendix II List. Barcoding and phylogenetic analysis revealed four mislabeled samples for a total substitution rate of 10.5%. One substitution, labeled ‘Mako’ in the market, was identified as Thresher shark. Three further substitutions, labeled as ‘Swordfish’ in the market were identified as Mako, Alopias spp., and a Lamnid shark, all of which are endangered or threatened shark species. As samples were collected just before implementation of major import monitoring programs and a Mako fishing ban in the United States, this study has established a temporal baseline that can be used to determine if market mislabeling has decreased as a result of these conservation initiatives. Conservation Fisheries Mislabeling DNA Barcoding Sharks Endangered Figures Figure 1 Figure 2 Figure 3 Introduction The mislabeling of seafood products in markets is a principal issue for conservation efforts and consumer rights. Mislabeling of seafood products occurs when a product is substituted, accidentally or purposefully, to sell under an inaccurate name. Mislabeling occurs throughout the boat-to-market supply chain process, and is fueled by misidentification and profit ventures (e.g. selling lesser-value species under the name of high-value species). Accidental substitution occurs when unidentifiable cuts of fish or frozen filets are misidentified and given an incorrect label during distribution, shipping, purchase, or sale. Purposeful substitution occurs in favor of selling cheaper or more widely available species in the place of expensive or high-demand species. Elasmobranchs, including sharks and rays, are cartilaginous fish with long generation times, low fecundity, and low population growth rates which leave them extremely vulnerable to depletion by overfishing (Dulvy et al. 2021 ). Globally, the abundance of pelagic sharks declined by 71.1% between 1970 and 2018 due to overexploitation (Pacoureau et al. 2021 ). These dramatic declines of shark populations due to overfishing have received notable attention in the research literature (Baum et al. 2003 ; Myers et al. 2007 ; Ferretti et al. 2010 ) and spurred significant change in regulatory policy. However, despite these recent increases in protective regulation, including finning bans and stricter catch policies, global shark fishing mortality still continues to rise due to demand for shark products and through bycatch (Worm et al. 2024 ; Hammerschlag and Sims 2024 ). Mislabeling seafood products in markets disguises exploitation and poses an additional threat to shark population recovery. Visual species-level identification for sharks in markets is complicated because meat is often sold as headless and finless carcasses (Clarke et al. 2007 ; Rasmussen and Morrissey 2009 ). By removing the morphologically unique features such as the head and fins, it becomes a challenge to accurately identify the species visually (Almerón-Souza et al. 2018 ). These unidentifiable cuts of meat can create opportunities for accidental mislabeling or disguise purposeful mislabeling (Holmes et al. 2009 ). Research in both domestic and international markets has revealed extensive rates of mislabeling for numerous species of sharks and fish. In Brazil, 18 species of Elasmobranchs, including some IUCN Endangered species, were being sold under a single generic name in markets (Almerón-Souza et al. 2018 ). The shark market of Hong Kong - comprising 50% of the global fin trading industry - was found to sell 14 total shark species under only 11 names (Clarke et al. 2006 ). Globally, threatened shark species are mislabeled restaurants as prepared foods and unlabeled in consumer products such as pet food and makeup (Hobbs et al. 2019 ; Cardeñosa 2019 ). Geographically widespread studies also reveal that the severity and extent of current global seafood fraud is not limited to one country or region (Cawthorn et al. 2018 ). However, specific mislablings are more common, and these can be motivated by economic dynamics (Pincinato et al. 2022 ). For example, if catches of desired, high-demand, expensive species are low, purposeful mislabeling of cheaper, unwanted catches is a potential avenue to recoup economic losses (Donlan and Luque 2019 ). In markets, shark meat regularly attains only 20–60% of the price of Swordfish ( Xiphias gladius ), a high-value species (Rasmussen and Morrissey 2009 ; Pappalardo et al. 2011 ; Almerón-Souza et al. 2018 ). Pelagic sharks are low-value species which are frequently caught as unwanted bycatch in the swordfish fishery, making them common targets for mislabeling (Dufflocq et al. 2022 ). In Italy, the rate of shark being mislabeled for swordfish was found to exceed 15%, with a further 30%-80% of all shark meat samples mislabeled in some manner (Barbuto et al. 2010 ; Filonzi et al. 2010 ; Ferrito et al. 2019 ). In Spain, shark is more likely to be substituted for frozen or smoked swordfish than fresh swordfish (Herrero et al. 2011 ). The U.S. Food and Drug Administration (FDA) recently included shark for swordfish substitution on a report of commonly substituted seafood (Dufflocq et al. 2022 ; U.S. Food and Drug Administration 2024). Routine and accurate species-level identification of landed and marketed fish is integral to the development of sustainable fisheries and conservation of endangered species (Clarke et al. 2007 ). Relevant in this study, two species of pelagic shark, the Shortfin Mako ( Isurus oxyrinchus ) (hereafter: ‘Mako’), and the Common Thresher shark ( Alopias vulpinus ) (hereafter: ‘Thresher’) are of serious conservation concern. Mako is a globally endangered species, and Thresher is a vulnerable species with severe population fragmentation and continued decline of mature individuals (Rigby et al. 2019 , 2022 ). Mako and Thresher sharks are both listed on the CITES Appendix II list, which regulates their international trade because of extinction risk. Additionally, the International Commission for the Conservation of Atlantic Tuna (ICCAT), which recognizes that mako sharks are often caught as bycatch in ICCAT fisheries, has recommended that participating fishing entities should prohibit retention, shipping, and landing whole or partial North Atlantic Shortfin Mako shark. However, these protections and recommendations are not adequate. Current fishing of Shortfin Mako in the North Atlantic exceeds total allowable catch by nearly 6 times the limit required for population recovery (Sims et al. 2021 ). In the United States, the ICCAT recommendation was enforced by NOAA in 2022, and fishermen are no longer permitted to catch, land, or retain Atlantic Shortfin Mako. While promising, U.S. fishermen caught only 3% of the overall Shortfin Mako harvest in the North Atlantic in 2020 (NOAA 2024a ), so only a marginal effect on the larger population recovery of North Atlantic Shortfin Mako is expected from this ban. In this study, genetic barcoding is used to assess species-level identification of shark and Swordfish meat sold in New England markets. Genetic barcoding using a partial fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene (~ 650 bp) is a proven and accurate tool for identification to the species-level (Hebert et al. 2003 ; Ward et al. 2005 ) and has been globally developed as a quick, reliable, and relatively cost-efficient method for identifying animals through standardized reference databases. Genetic barcoding has been successfully used to identify fish (Ward et al. 2008 , 2009 ), high levels of mislabeling of sharks in markets (Marko et al. 2004 ; Griffiths et al. 2013 ; Melo Palmeira et al. 2013 ) and is the benchmark for seafood identification set by the U.S. FDA (Yancy et al. 2008 ; Khaksar et al. 2015 ). Materials and Methods Sample Collection Shark and swordfish meat sold under species-specific names such as: “Mako”, “Shortfin Mako”, “Thresher”, and “Swordfish” were collected from July to October 2019 in both fresh and frozen forms. Samples originated from fish markets (n = 13), chain grocery stores (n = 20), and small local markets (n = 7) in Massachusetts, Connecticut, and Rhode Island (Figure I). No retailers were sampled more than once, but a maximum of two samples from the same retailer were collected if they were labeled as different species. Data including retailer name, location and zip code, date, exact wording of market label (e.g. “Fresh Caught Wild Swordfish Steaks”), species designation, country of origin (Figure II), and price per pound were collected for each sample. Figure I Map of Southern New England with collection locations, images of collected samples, and a study timeline. Numbers in parentheses indicate the number of samples collected from each county. Thin lines denote county borders and bold lines denote state borders. Images of fresh shark and swordfish meat collected and analyzed in this study are pictured in their market conditions, some with prices and geographic information included. Pictures of (A) swordfish, (B) Thresher shark, and (C) Mako shark meat collected in this study are shown with market labels DNA Extraction & Molecular Protocols Samples were stored in 95% ethanol for preservation with frozen samples thawed before preservation. DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, USA) with a section of tissue (~ 100 mg) from each sample. A fragment of the mitochondrial DNA (mtDNA) COI gene was amplified by polymerase chain reaction (PCR) using fish primer sets FishF2 (5′ TCG ACT AAT CAT AAA GAT ATC GGC AC 3′) and FishR2 (5′ ACT TCA GGG TGA CCG AAG AAT CAG AA 3′) (Ward et al. 2005 ), and universal primer set LCO1490 (5′ GGT CAA CAA ATC ATA AAG ATA TTGG 3′) and HCO2198 (5′ TAA ACT TCA GGG TGA CCA AAA AAT CA 3′) (Folmer et al. 1994 ). Each 20 µL reaction contained ~ 50 ng extracted DNA, 10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2, 0.2 mM dNTPs, 25 units/mL Taq DNA Polymerase and 0.5 µL of each primer. Cycling conditions included an initial denaturation step of 94℃ for 4’, followed by 30 cycles at 94℃ for 4’, 50℃/58℃ for 1’, and 72℃ for 1’ with a final extension step of 72℃ for 4’. The amplification results were visualized on a 1.5% agarose gel run at 120 volts for 60 minutes, then stained with EtBr. PCR products were purified and sequenced by the Sanger method at the DNA Analysis Facility on Science Hill at Yale University. DNA sequencing was performed using both sets of primers on each of the 3’-5’ and 5’-3’ strands. Criteria for Genetic Identification To confirm unambiguous species-level genetic identification, a sequence was required to pass Criteria B (BOLD identification) or N (NCBI BLASTn identification), and P (Phylogenetic Analysis). Based on the length of the sequence, unambiguous criteria had different thresholds. In the case of ambiguous species-level identification, unambiguous genus-level identification was reported as the best identity. Criteria B : Sequences were entered into the BOLD (Barcode of Life Data System) Identification Engine ( https://boldsystems.org ) with the “All Barcode Records on BOLD” option (Ratnasingham and Hebert 2007 ). Records deposited in BOLD are validated for both DNA sequence and specimen data. For sequences > 600 bp, a threshold of > 97% Top Match Similarity was required for unambiguous identification. For sequences 90% Top Match Similarity was required for unambiguous species-level identification. For all sequences, a threshold of 100% Genus Composition was required for unambiguous genus-level identification. Criteria N : Sequences were blasted through NCBI (National Center for Biotechnology Information, Bethesda MD, USA) using the Basic Local Alignment Search Tool, Nucleotide (BLASTn) function in GenBank ( https://www.ncbi.nlm.nih.gov/ ) (Altschul et al. 1990 ). For sequences > 600 bp, a threshold of > 96% Percent Identity was required for unambiguous identification. For sequences 91% Percent Identity was required for unambiguous identification. Criteria P : To further confirm identification of putative mislabeling, samples categorized as “mislabeled” from Criteria B or N were additionally evaluated with phylogenetic analysis. Top hits from NCBI’s GenBank database with the highest query cover and maximum identical values (> 97%) for each species were chosen as reference sequences, downloaded, and added to the FASTA file of generated sequences from this study. Sequences were aligned with MUSCLE (Edgar 2004) and trees were constructed using the Maximum Likelihood (ML) method with the General Time Reversible (GTR) model using MEGA7 software ( Kumar et al. 2016 ; Stecher et al. 2020) . For unambiguous identification, the putatively substituted sample had to appropriately cluster within the expected taxonomic genus and species expected from Criteria B or N identification. Finally, all identified species were checked on the International Union for Conservation of Nature (IUCN) Red List ( https://www.iucnredlist.org ) and the conservation status was noted. Results Collected Samples Meat labeled ‘Swordfish’ accounted for 64.1% of all collected samples, and meat labeled ‘Mako’ comprised 28.2% of all collected sampled, indicating that these two species were the most readily sourced and available for consumption in New England. Meat labeled ‘Thresher’ was less common to find in markets and comprised 7.2% of the samples collected. No other shark species were detected. The majority of samples were sourced internationally for sale in the New England region, but nearly a quarter of markets had no origin location associated with their product (Figure II). The average price of swordfish meat collected for this study was $ 13.20/lb, and the average price of shark meat collected for this study was $ 9.49/lb. As such, shark meat attained only ~ 71% of the price of swordfish in market. Figure II Origins of shark and swordfish meat collected from markets in this study. Over a quarter of the samples (n, y-axis) collected were sourced domestically from the United States. Some markets had no source information about their product. Species identified in this study include the Common Thresher ( Alopias vulpinus ) in yellow, designated by the IUCN as a Vulnerable species, the Shortfin Mako ( Isurus oxyrinchus ), in gray, designated by the IUCN as an Endangered species, and the swordfish ( Xiphias gladius ), in blue, designated by the IUCN as a Near Threatened species Genetic Barcode Identification Analysis Out of 40 collected samples, 39 successfully amplified with PCR, a success rate of 97.5%. Unsuccessful PCR amplification may have been the result of inefficient primers (Marín et al. 2018 ) or degraded DNA. A total of 38 out of 39 amplified PCR products resulted in a sequence fragment of at least 220 bp, a success rate of 97.4%. Of the 38 sequences, 24 were considered full coverage (> 600 bp) and 14 were considered partial coverage ( 220 bp). Most pieces of collected meat were sold in markets on a cooled table or some amount of ice, but all meat was exposed to air for unknown durations, which leads to DNA degradation (Zimmermann et al. 2008 ). DNA degradation, common in seafood products, results in fragmented sequences like the partial coverage fragments that were observed in this study (Shokralla et al. 2015 ). Short fragments within the full-length COI barcode region have been proven effective at species-level identification (Marín et al. 2018 ), and all sequences were able to be evaluated for identity. Unambiguous species-level identification of all 38 sequences was successful (Supplementary Table I). Three samples (Sample 9, 13, 15) failed to pass Criteria N identification analysis. NCBI BLASTn Top Hit Percent Identity measures the fraction of the alignment that is identical between the blasted and reference sequence (Supplementary Table I). However, a query can share a low percent identity sequence and still be a significant hit. Regions of pelagic shark and swordfish COI mtDNA are particularly prone to intraspecific polymorphisms, which reduces Percent Identity value while still being a significant match (Pappalardo et al. 2011 ; Liu et al. 2013 ). Given this, the three partial coverage samples that failed Criteria N were still considered for unambiguous identification with the Criteria B requirements. All samples passed Criteria B identification analysis. BOLD Top Hit Similarity (Supplementary Table I) measures the percent of identical base pairs between the query and top hit reference sequence. Additionally, to ensure that a large number of consensus samples were considered, samples also had to pass the BOLD Taxonomic Genus Composition and BOLD Taxonomic Species Composition with a threshold of 100% match for genus-level or species-level identification (Supplementary Table I). These criteria represent the percent of reference sequences returned with consistent identity. To calculate this metric, the BOLD TaxonID Taxonomy Report was viewed for each sample and the Genus composition percent and Species composition percent were calculated based on the identity ratio of reference sequences returned. The threshold of 100% indicates that all returned reference sequences unanimously identified the same genus or species. Two samples returned a less than 100% confidence for species-level identification. Sample 6 was identified to the genus level and Sample 15 was identified to the family level for 100% confidence. Phylogenetic Analysis of Mislabeled Specimens Samples categorized as “mislabeled” from genetic barcode analysis were additionally evaluated in a phylogenetic tree to confirm putative mislabeling. The four samples (Sample 6, Sample 13, Sample 15, and Sample 27; Supplementary Table I) were visualized in phylogenetic trees and confirmed instances of mislabeling as they clustered appropriately with the expected taxonomic genus and species from genetic barcode analysis (Figure III). In Figure IIIA, three minor clades of Mako samples are displayed with sequences generated in this study (Supplementary Table I) grouped with the reference sequences (NCBI, MG214784.1, MG837941.1, KT444008.1). Sample 13 was labeled ‘Wild Swordfish Steaks’ and Sample 27 was labeled ‘Wild Caught Swordfish Steak’. However, both samples are unambiguously identified as Shortfin Mako ( Isurus oxyrinchus ) and thus mislabeled. The reference outgroups were sourced from samples sequenced in this study ( Alopias Sample 7, Xiphias Sample 28). In Figure IIIB, one clade of Thresher samples is displayed with sequences generated in this study (Supplementary Table I) grouped with the reference sequence (NCBI, JF492809.1). Sample 6 was labeled ‘Fresh Mako Shark’, and Sample 15 was labeled ‘Swordfish Steak’. However, Sample 6 was unambiguously identified as a Thresher shark ( Alopias spp.) and Sample 15 was identified as family Lamnidae, and thus mislabeled. The reference outgroups were sourced from samples sequenced in this study ( Isurus Sample 5, Xiphias Sample 28). Figure III Phylogenetic analysis confirms the identity of mislabeled shark samples revealed in this study. Evolutionary history was inferred using the Maximum Likelihood method and General Time Reversible model. The trees with the highest log likelihood are shown. The percentage of trees in which associated taxa clustered together is shown next to the branches. The trees are drawn to scale, with branch lengths measured in the number of nucleotide substitutions per site. Sample numbers correspond to Supplementary Table I. Mislabeled samples cluster with elasmobranch taxa that were identified by NCBI and BOLD analysis and are highlighted in red Discussion Mislabeling as a Conservation Issue It has been well-documented that shark populations are declining globally, and conservation action must be taken immediately to ensure a reasonable chance for recovery. In the North Atlantic, the mortality rate for any individual mako shark in an annual period is 30% due to commercial fisheries alone (Byrne et al. 2017 ). While U.S. fishing of mako shark is illegal, the highly migratory mako shark swims through nearly 20 distinct management zones across the entire North Atlantic. Preventing this endangered species’ extirpation is contingent upon international cooperation for protection (Byrne et al. 2017 ) and elimination of opportunities for mislabeling in markets through systemic changes in fishery catch reporting (Cawthorn et al. 2018 ). This study is the first to evaluate the rate of shark mislabeling as swordfish meat in New England, a region heavily reliant on fisheries and seafood consumption. Sample analysis revealed four total instances of mislabeling, a 10.5% substitution rate for meat sold in southern New England markets. Of the four mislabeled samples, three had origin location data displayed in market. These three substitutions were all internationally sourced, with one each from Canada, Brazil, and Ecuador. It is possible that the distance these products were transported had an impact on the final outcome of the mislabeling. Markets selling only locally-caught fish showed no evidence of mislabeling in this study. Preventing Mislabeling Current market-level reporting programs may not be performing as well as they are intended. One large chain grocery store from which samples were collected advertised a “Random DNA Testing Service” that claimed to “set the innovation standard with DNA testing that ensures seafood labeling is accurate”. The information about the service, which is conducted regionally across their stores, was readily available on pamphlets which were distributed across their seafood counters to customers. Despite this advertised program, that chain grocery store was the source of one substitution in this study, where a slice of swordfish was unambiguously identified as Thresher shark. With mislabeling a threat at many stages of the supply chain, markets struggle to ensure they are selling accurately labeled products. Preventing mislabeling likely has to occur earlier in the supply chain, before fish products are processed into morphologically unidentifiable cuts. As the world’s largest seafood importer, the US has a responsibility to curb illegal fishing and seafood fraud (Williams et al. 2016 ; FAO 2018; He 2018 ). The Seafood Import Monitoring Program (SIMP) aims to do this by requiring seafood imports to be logged in the International Trade Data System (IDTS), which tracks all imports and exports for the entire US (NOAA 2024b ). Importers with intent to sell whole fish products in the US must provide data about the fish, catch location, type of fishing gear used, documentation of authorization to fish that particular species (NOAA 2024b ). As the samples from this study were collected very early on during SIMP implementation (SIMP started 2018, samples collected 2019), this study has established a temporal baseline that could be used to determine if market mislabeling has decreased. Future research should explore if rates of mislabeling across New England have been meaningfully reduced through effective SIMP monitoring and the U.S. mako fishing ban. While promising, SIMP program data is not yet available to public consumers in the US, but summary statistics are available in reports to congress compiled by NOAA. Allowing this database to be public so both US sellers of seafood and consumers are able to track the origins of their seafood would fundamentally change supply dynamics. Conclusions about New England’s Role in Global Shark Fisheries Despite the mislabeling found in this study, the regional shark fishery in New England may be an example of progress towards sustainable fisheries. While a 10.5% substitution rate in markets is not ideal, it is less than the substitution rates of 15–80% in reports from Asia, Brazil, and Italy (Melo Palmeira et al. 2013 ). This low substitution rate is undoubtedly influenced by the cultural demand in New England for locally sourced fish, which inhibits mislabeling opportunities from occurring. Additionally, the New England region, especially Massachusetts, is an important nursery area where the majority of sharks are catch-and-release (Skomal 2007 ). Due to the region’s investment in science education and communication, the local public recognizes sharks as ecologically valuable to New England and has advocated for their conservation by pushing back against lethal methods of shark management (Szczepaniak 2022 ). More broadly in the US, shark finning bans and total fishing bans have been enacted, setting the global standard for conservation actions for endangered marine species. Reflecting on the successes of shark management in New England has identified routes of action for global shark conservation. These actions include prioritizing local catch by reducing internationally-imported seafood in markets, establishing seafood import monitoring programs and making data publicly-available, routinely and randomly testing markets for commonly substituted seafood, and preventing endangered shark products from entering the market through catch, landing, and retention bans. Declarations Competing Interests Financial interests: Authors M.G.E and T.C. declare they have no relevant financial or non-financial interests to disclose. Funding Author M.G.E received funding support from Bard College at Simon’s Rock. The authors declare that no other funds, grants, or support was received during the preparation of this manuscript. Author Contribution Conceptualization, data curation, and formal analysis was performed by M.G.E. Both authors contributed to the study design. T.C. supervised the study. The first draft of the manuscript was written by M.G.E., and T.C. commented on all versions of the manuscript. Both authors read and approved the final manuscript. Acknowledgement The authors would like to thank Donald McClelland and Sarah Snyder for their helpful discussions on the project and feedback, Giulia de Gennaro for assistance with sample collection and feedback, Annabel Hughes for illustrations and comments on the manuscript, and Katie Lotterhos and Ally Swank for their comments on the manuscript. Data Availability Sequence data generated in this study were deposited as open data via the Northeastern University Digital Repository Service, available here: https://hdl.handle.net/2047/D20662827. All metadata supporting the findings of this study are available within the paper and its Supplementary Information. 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Food Control 34:249–252. https://doi.org/10.1016/j.foodcont.2013.04.017 Myers RA, Baum JK, Shepherd TD et al (2007) Cascading effects of the loss of apex predatory sharks from a coastal ocean. Science 315:1846–1850. https://doi.org/10.1126/science.1138657 NOAA (2024a) Atlantic Shortfin Mako Shark. In: NOAA Fisheries Species Directory. https://www.fisheries.noaa.gov/species/atlantic-shortfin-mako-shark . Accessed 6 May 2024 NOAA (2024b) Seafood Import Monitoring Program. In: NOAA. https://www.fisheries.noaa.gov/international/international-affairs/seafood-import-monitoring-program-facts-and-reports . Accessed 7 May 2024 Pacoureau N, Rigby CL, Kyne PM et al (2021) Half a century of global decline in oceanic sharks and rays. Nature 589:567–571. https://doi.org/10.1038/s41586-020-03173-9 Pappalardo AM, Guarino F, Reina S et al (2011) Geographically widespread swordfish barcode stock identification: a case study of its application. PLoS ONE 6:e25516. https://doi.org/10.1371/journal.pone.0025516 Pincinato RBM, Gasalla MA, Garlock T, Anderson JL (2022) Market incentives for shark fisheries. Mar Policy 139:105031. https://doi.org/10.1016/j.marpol.2022.105031 Rasmussen RS, Morrissey MT (2009) Application of DNA-based methods to identify fish and seafood substitution on the commercial market. Compr Rev Food Sci Food Saf 8:118–154. https://doi.org/10.1111/j.1541-4337.2009.00073.x Ratnasingham S, Hebert PDN (2007) bold: The Barcode of Life Data System. Mol Ecol Notes 7:355–364. http://www.barcodinglife.org https://doi.org/10.1111/j.1471-8286.2007.01678.x Rigby CL, Barreto R, Carlson J et al (2019) Isurus oxyrinchus. The IUCN Red List of Threatened Species e. https://doi.org/10.2305/IUCN.UK.2019-1.RLTS.T39341A2903170.en . .T39341A2903170. Rigby CL, Barreto R, Fernando D et al (2022) Alopias vulpinus (amended version of 2019 assessment). The IUCN Red List of Threatened Species e. https://doi.org/10.2305/IUCN.UK.2022-1.RLTS.T39339A212641186.en . .T39339A212641186. Shokralla S, Hellberg RS, Handy SM et al (2015) A DNA Mini-Barcoding System for Authentication of Processed Fish Products. Sci Rep 5:15894. https://doi.org/10.1038/srep15894 Sims DW, Mucientes G, Queiroz N (2021) Shortfin mako sharks speeding to the brink. Science 371:355. https://doi.org/10.1126/science.abg2355 Skomal G (2007) Shark nursery areas in the coastal waters of Massachusetts. Am Fish Soc Symp Szczepaniak GP (2022) Protecting Beaches from Bites: Shark Management Programs in New England. Ocean Coastal LJ 27:233–266 Food US (2024) and Drug Administration Seafood Species Substitution and Economic Fraud. In: U.S. Food and Drug Administration. https://www.fda.gov/food/seafood-guidance-documents-regulatory-information/seafood-species-substitution-and-economic-fraud . Accessed 6 May 2024 Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74:329–356. https://doi.org/10.1111/j.1095-8649.2008.02080.x Ward RD, Holmes BH, White WT, Last PR (2008) DNA barcoding Australasian chondrichthyans: results and potential uses in conservation. Mar Freshw Res 59:57–71. https://doi.org/10.1071/MF07148 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. https://doi.org/10.1098/rstb.2005.1716 Williams R, Burgess MG, Ashe E et al (2016) U.S. seafood import restriction presents opportunity and risk. Science 354:1372–1374. https://doi.org/10.1126/science.aai8222 Worm B, Orofino S, Burns ES et al (2024) Global shark fishing mortality still rising despite widespread regulatory change. Science 383:225–230. https://doi.org/10.1126/science.adf8984 Yancy HF, Zemlak TS, Mason JA et al (2008) Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia. J Food Prot 71:210–217. https://doi.org/10.4315/0362-028x-71.1.210 Zimmermann J, Hajibabaei M, Blackburn DC et al (2008) DNA damage in preserved specimens and tissue samples: a molecular assessment. Front Zool 5:18. https://doi.org/10.1186/1742-9994-5-18 Additional Declarations No competing interests reported. Supplementary Files SupplementaryTable1ConsGenetics.xlsx Cite Share Download PDF Status: Published Journal Publication published 15 Feb, 2025 Read the published version in Conservation Genetics → Version 1 posted Editorial decision: Revision requested 28 Oct, 2024 Reviews received at journal 10 Sep, 2024 Reviewers agreed at journal 31 Aug, 2024 Reviewers invited by journal 17 Jun, 2024 Editor assigned by journal 08 Jun, 2024 Submission checks completed at journal 08 Jun, 2024 First submitted to journal 07 Jun, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4547946","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":316401183,"identity":"dc0196f1-0834-40bd-bb91-3a0f6c401388","order_by":0,"name":"Madeline G. Eppley","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABC0lEQVRIie3RsUoDMRjA8e84uClya4qUvkIk69k+iIslcFMPnES3g0Imq2tKhXuFgCCOCYFM2vnADoJPULo4KDU5KAg20tEh/yGE8P0gIQCx2P8sUX7Nu23947jeM7urIz0/of2SHUqIOpTkxzOl1hzO6OvUbtZPxWDQuM0FFH2p9pPe/fJczzlUjyvLhH4uT6TN2EJASUOEtBNijjxpJxQ0N4nMEE0RmHGIjDz5cuRBdGQ7ani+cWQbJAQ7kjgicUfUuLYodUQFCV65t9wscSXaksELZ0za0l2MMDoPkHwx028fl0V1J5iBaz48babmPUVXw/5tgABG7gsy/OvCgfEdgc8/BmKxWCz2DRUoZbsk87UrAAAAAElFTkSuQmCC","orcid":"","institution":"Northeastern University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Madeline","middleName":"G.","lastName":"Eppley","suffix":""},{"id":316401185,"identity":"03508ad1-eaa8-4a34-a9f8-d40d84807ff3","order_by":1,"name":"Thomas Coote","email":"","orcid":"","institution":"Bard College at Simon's Rock","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Thomas","middleName":"","lastName":"Coote","suffix":""}],"badges":[],"createdAt":"2024-06-07 20:08:22","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4547946/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4547946/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s10592-025-01675-5","type":"published","date":"2025-02-15T15:58:04+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":58804903,"identity":"89a0b334-706c-4db7-9cd6-ad8cb26675ca","added_by":"auto","created_at":"2024-06-21 10:40:36","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1150578,"visible":true,"origin":"","legend":"\u003cp\u003eMap of Southern New England with collection locations, images of collected samples, and a study timeline. Numbers in parentheses indicate the number of samples collected from each county. Thin lines denote county borders and bold lines denote state borders. Images of fresh shark and swordfish meat collected and analyzed in this study are pictured in their market conditions, some with prices and geographic information included. Pictures of (A) swordfish, (B) Thresher shark, and (C) Mako shark meat collected in this study are shown with market labels\u003c/p\u003e","description":"","filename":"Figure1ConsGenetics.png","url":"https://assets-eu.researchsquare.com/files/rs-4547946/v1/c49672528c0ea87383eeee83.png"},{"id":58804901,"identity":"188f54ca-233f-4447-b481-11eab64be587","added_by":"auto","created_at":"2024-06-21 10:40:36","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":164470,"visible":true,"origin":"","legend":"\u003cp\u003eOrigins of shark and swordfish meat collected from markets in this study. Over a quarter of the samples (n, y-axis) collected were sourced domestically from the United States. Some markets had no source information about their product. Species identified in this study include the Common Thresher (\u003cem\u003eAlopias vulpinus\u003c/em\u003e) in yellow, designated by the IUCN as a Vulnerable species, the Shortfin Mako (\u003cem\u003eIsurus oxyrinchus\u003c/em\u003e), in gray, designated by the IUCN as an Endangered species, and the swordfish (\u003cem\u003eXiphias gladius\u003c/em\u003e), in blue, designated by the IUCN as a Near Threatened species\u003c/p\u003e","description":"","filename":"Figure2ConsGenetics.png","url":"https://assets-eu.researchsquare.com/files/rs-4547946/v1/7f65e3dc239c7e202d5009e6.png"},{"id":58804904,"identity":"04bce254-62d9-4660-9667-290e6a9e6eee","added_by":"auto","created_at":"2024-06-21 10:40:36","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":181241,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic analysis confirms the identity of mislabeled shark samples revealed in this study. Evolutionary history was inferred using the Maximum Likelihood method and General Time Reversible model. The trees with the highest log likelihood are shown. The percentage of trees in which associated taxa clustered together is shown next to the branches. The trees are drawn to scale, with branch lengths measured in the number of nucleotide substitutions per site. Sample numbers correspond to Supplementary Table I. Mislabeled samples cluster with elasmobranch taxa that were identified by NCBI and BOLD analysis and are highlighted in red\u003c/p\u003e","description":"","filename":"Figure3ConsGenetics.png","url":"https://assets-eu.researchsquare.com/files/rs-4547946/v1/ed31aab3d140e20117f1844f.png"},{"id":76488386,"identity":"464462ff-0824-461d-a480-dafb63684060","added_by":"auto","created_at":"2025-02-17 16:14:08","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1994460,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4547946/v1/3f3daead-8463-458a-ab71-f1b2166aca82.pdf"},{"id":58805631,"identity":"8bf08a9b-4007-40bd-8b90-a9b4c66cc8a6","added_by":"auto","created_at":"2024-06-21 10:48:36","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":12773,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryTable1ConsGenetics.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-4547946/v1/2241f280fffb9bc4393d1dc4.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"DNA barcoding reveals mislabeling of endangered sharks sold as swordfish in New England fish markets","fulltext":[{"header":"Introduction","content":"\u003cp\u003eThe mislabeling of seafood products in markets is a principal issue for conservation efforts and consumer rights. Mislabeling of seafood products occurs when a product is substituted, accidentally or purposefully, to sell under an inaccurate name. Mislabeling occurs throughout the boat-to-market supply chain process, and is fueled by misidentification and profit ventures (e.g. selling lesser-value species under the name of high-value species). \u003cem\u003eAccidental substitution\u003c/em\u003e occurs when unidentifiable cuts of fish or frozen filets are misidentified and given an incorrect label during distribution, shipping, purchase, or sale. \u003cem\u003ePurposeful substitution\u003c/em\u003e occurs in favor of selling cheaper or more widely available species in the place of expensive or high-demand species.\u003c/p\u003e \u003cp\u003eElasmobranchs, including sharks and rays, are cartilaginous fish with long generation times, low fecundity, and low population growth rates which leave them extremely vulnerable to depletion by overfishing (Dulvy et al. \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). Globally, the abundance of pelagic sharks declined by 71.1% between 1970 and 2018 due to overexploitation (Pacoureau et al. \u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). These dramatic declines of shark populations due to overfishing have received notable attention in the research literature (Baum et al. \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2003\u003c/span\u003e; Myers et al. \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e2007\u003c/span\u003e; Ferretti et al. \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2010\u003c/span\u003e) and spurred significant change in regulatory policy. However, despite these recent increases in protective regulation, including finning bans and stricter catch policies, global shark fishing mortality still continues to rise due to demand for shark products and through bycatch (Worm et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2024\u003c/span\u003e; Hammerschlag and Sims \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2024\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eMislabeling seafood products in markets disguises exploitation and poses an additional threat to shark population recovery. Visual species-level identification for sharks in markets is complicated because meat is often sold as headless and finless carcasses (Clarke et al. \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2007\u003c/span\u003e; Rasmussen and Morrissey \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e2009\u003c/span\u003e). By removing the morphologically unique features such as the head and fins, it becomes a challenge to accurately identify the species visually (Almer\u0026oacute;n-Souza et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). These unidentifiable cuts of meat can create opportunities for accidental mislabeling or disguise purposeful mislabeling (Holmes et al. \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2009\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eResearch in both domestic and international markets has revealed extensive rates of mislabeling for numerous species of sharks and fish. In Brazil, 18 species of Elasmobranchs, including some IUCN Endangered species, were being sold under a single generic name in markets (Almer\u0026oacute;n-Souza et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). The shark market of Hong Kong - comprising 50% of the global fin trading industry - was found to sell 14 total shark species under only 11 names (Clarke et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2006\u003c/span\u003e). Globally, threatened shark species are mislabeled restaurants as prepared foods and unlabeled in consumer products such as pet food and makeup (Hobbs et al. \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Carde\u0026ntilde;osa \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Geographically widespread studies also reveal that the severity and extent of current global seafood fraud is not limited to one country or region (Cawthorn et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2018\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eHowever, specific mislablings are more common, and these can be motivated by economic dynamics (Pincinato et al. \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). For example, if catches of desired, high-demand, expensive species are low, purposeful mislabeling of cheaper, unwanted catches is a potential avenue to recoup economic losses (Donlan and Luque \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). In markets, shark meat regularly attains only 20\u0026ndash;60% of the price of Swordfish (\u003cem\u003eXiphias gladius\u003c/em\u003e), a high-value species (Rasmussen and Morrissey \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e2009\u003c/span\u003e; Pappalardo et al. \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Almer\u0026oacute;n-Souza et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). Pelagic sharks are low-value species which are frequently caught as unwanted bycatch in the swordfish fishery, making them common targets for mislabeling (Dufflocq et al. \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). In Italy, the rate of shark being mislabeled for swordfish was found to exceed 15%, with a further 30%-80% of all shark meat samples mislabeled in some manner (Barbuto et al. \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2010\u003c/span\u003e; Filonzi et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2010\u003c/span\u003e; Ferrito et al. \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). In Spain, shark is more likely to be substituted for frozen or smoked swordfish than fresh swordfish (Herrero et al. \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). The U.S. Food and Drug Administration (FDA) recently included shark for swordfish substitution on a report of commonly substituted seafood (Dufflocq et al. \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; U.S. Food and Drug Administration 2024). Routine and accurate species-level identification of landed and marketed fish is integral to the development of sustainable fisheries and conservation of endangered species (Clarke et al. \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2007\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eRelevant in this study, two species of pelagic shark, the Shortfin Mako (\u003cem\u003eIsurus oxyrinchus\u003c/em\u003e) (hereafter: \u0026lsquo;Mako\u0026rsquo;), and the Common Thresher shark (\u003cem\u003eAlopias vulpinus\u003c/em\u003e) (hereafter: \u0026lsquo;Thresher\u0026rsquo;) are of serious conservation concern. Mako is a globally endangered species, and Thresher is a vulnerable species with severe population fragmentation and continued decline of mature individuals (Rigby et al. \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e2019\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Mako and Thresher sharks are both listed on the CITES Appendix II list, which regulates their international trade because of extinction risk. Additionally, the International Commission for the Conservation of Atlantic Tuna (ICCAT), which recognizes that mako sharks are often caught as bycatch in ICCAT fisheries, has recommended that participating fishing entities should prohibit retention, shipping, and landing whole or partial North Atlantic Shortfin Mako shark. However, these protections and recommendations are not adequate. Current fishing of Shortfin Mako in the North Atlantic exceeds total allowable catch by nearly 6 times the limit required for population recovery (Sims et al. \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). In the United States, the ICCAT recommendation was enforced by NOAA in 2022, and fishermen are no longer permitted to catch, land, or retain Atlantic Shortfin Mako. While promising, U.S. fishermen caught only 3% of the overall Shortfin Mako harvest in the North Atlantic in 2020 (NOAA \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e2024a\u003c/span\u003e), so only a marginal effect on the larger population recovery of North Atlantic Shortfin Mako is expected from this ban.\u003c/p\u003e \u003cp\u003eIn this study, genetic barcoding is used to assess species-level identification of shark and Swordfish meat sold in New England markets. Genetic barcoding using a partial fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene (~\u0026thinsp;650 bp) is a proven and accurate tool for identification to the species-level (Hebert et al. \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2003\u003c/span\u003e; Ward et al. \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2005\u003c/span\u003e) and has been globally developed as a quick, reliable, and relatively cost-efficient method for identifying animals through standardized reference databases. Genetic barcoding has been successfully used to identify fish (Ward et al. \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e2008\u003c/span\u003e, \u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e2009\u003c/span\u003e), high levels of mislabeling of sharks in markets (Marko et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2004\u003c/span\u003e; Griffiths et al. \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Melo Palmeira et al. \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2013\u003c/span\u003e) and is the benchmark for seafood identification set by the U.S. FDA (Yancy et al. \u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e2008\u003c/span\u003e; Khaksar et al. \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2015\u003c/span\u003e).\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eSample Collection\u003c/h2\u003e \u003cp\u003eShark and swordfish meat sold under species-specific names such as: \u0026ldquo;Mako\u0026rdquo;, \u0026ldquo;Shortfin Mako\u0026rdquo;, \u0026ldquo;Thresher\u0026rdquo;, and \u0026ldquo;Swordfish\u0026rdquo; were collected from July to October 2019 in both fresh and frozen forms. Samples originated from fish markets (n\u0026thinsp;=\u0026thinsp;13), chain grocery stores (n\u0026thinsp;=\u0026thinsp;20), and small local markets (n\u0026thinsp;=\u0026thinsp;7) in Massachusetts, Connecticut, and Rhode Island (Figure I). No retailers were sampled more than once, but a maximum of two samples from the same retailer were collected if they were labeled as different species. Data including retailer name, location and zip code, date, exact wording of market label (e.g. \u0026ldquo;Fresh Caught Wild Swordfish Steaks\u0026rdquo;), species designation, country of origin (Figure II), and price per pound were collected for each sample.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eFigure I\u003c/b\u003e Map of Southern New England with collection locations, images of collected samples, and a study timeline. Numbers in parentheses indicate the number of samples collected from each county. Thin lines denote county borders and bold lines denote state borders. Images of fresh shark and swordfish meat collected and analyzed in this study are pictured in their market conditions, some with prices and geographic information included. Pictures of (A) swordfish, (B) Thresher shark, and (C) Mako shark meat collected in this study are shown with market labels\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eDNA Extraction \u0026amp; Molecular Protocols\u003c/h2\u003e \u003cp\u003eSamples were stored in 95% ethanol for preservation with frozen samples thawed before preservation. DNA was isolated using the Qiagen DNeasy Blood \u0026amp; Tissue Kit (Qiagen, USA) with a section of tissue (~\u0026thinsp;100 mg) from each sample. A fragment of the mitochondrial DNA (mtDNA) COI gene was amplified by polymerase chain reaction (PCR) using fish primer sets FishF2 (5\u0026prime; TCG ACT AAT CAT AAA GAT ATC GGC AC 3\u0026prime;) and FishR2 (5\u0026prime; ACT TCA GGG TGA CCG AAG AAT CAG AA 3\u0026prime;) (Ward et al. \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2005\u003c/span\u003e), and universal primer set LCO1490 (5\u0026prime; GGT CAA CAA ATC ATA AAG ATA TTGG 3\u0026prime;) and HCO2198 (5\u0026prime; TAA ACT TCA GGG TGA CCA AAA AAT CA 3\u0026prime;) (Folmer et al. \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e1994\u003c/span\u003e). Each 20 \u0026micro;L reaction contained\u0026thinsp;~\u0026thinsp;50 ng extracted DNA, 10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2, 0.2 mM dNTPs, 25 units/mL Taq DNA Polymerase and 0.5 \u0026micro;L of each primer.\u003c/p\u003e \u003cp\u003eCycling conditions included an initial denaturation step of 94℃ for 4\u0026rsquo;, followed by 30 cycles at 94℃ for 4\u0026rsquo;, 50℃/58℃ for 1\u0026rsquo;, and 72℃ for 1\u0026rsquo; with a final extension step of 72℃ for 4\u0026rsquo;. The amplification results were visualized on a 1.5% agarose gel run at 120 volts for 60 minutes, then stained with EtBr. PCR products were purified and sequenced by the Sanger method at the DNA Analysis Facility on Science Hill at Yale University. DNA sequencing was performed using both sets of primers on each of the 3\u0026rsquo;-5\u0026rsquo; and 5\u0026rsquo;-3\u0026rsquo; strands.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eCriteria for Genetic Identification\u003c/h2\u003e \u003cp\u003eTo confirm unambiguous species-level genetic identification, a sequence was required to pass \u003cem\u003eCriteria B\u003c/em\u003e (BOLD identification) or \u003cem\u003eN\u003c/em\u003e (NCBI BLASTn identification), and \u003cem\u003eP\u003c/em\u003e (Phylogenetic Analysis). Based on the length of the sequence, unambiguous criteria had different thresholds. In the case of ambiguous species-level identification, unambiguous genus-level identification was reported as the best identity.\u003c/p\u003e \u003cp\u003e \u003cem\u003eCriteria B\u003c/em\u003e: Sequences were entered into the BOLD (Barcode of Life Data System) Identification Engine (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://boldsystems.org\u003c/span\u003e\u003cspan address=\"https://boldsystems.org\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e with the \u0026ldquo;All Barcode Records on BOLD\u0026rdquo; option (Ratnasingham and Hebert \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2007\u003c/span\u003e). Records deposited in BOLD are validated for both DNA sequence and specimen data. For sequences\u0026thinsp;\u0026gt;\u0026thinsp;600 bp, a threshold of \u0026gt;\u0026thinsp;97% Top Match Similarity was required for unambiguous identification. For sequences\u0026thinsp;\u0026lt;\u0026thinsp;600 bp, a threshold of \u0026gt;\u0026thinsp;90% Top Match Similarity was required for unambiguous species-level identification. For all sequences, a threshold of 100% Genus Composition was required for unambiguous genus-level identification. \u003cem\u003eCriteria N\u003c/em\u003e: Sequences were blasted through NCBI (National Center for Biotechnology Information, Bethesda MD, USA) using the Basic Local Alignment Search Tool, Nucleotide (BLASTn) function in GenBank (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ncbi.nlm.nih.gov/\u003c/span\u003e\u003cspan address=\"https://www.ncbi.nlm.nih.gov/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e (Altschul et al. \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e1990\u003c/span\u003e). For sequences\u0026thinsp;\u0026gt;\u0026thinsp;600 bp, a threshold of \u0026gt;\u0026thinsp;96% Percent Identity was required for unambiguous identification. For sequences\u0026thinsp;\u0026lt;\u0026thinsp;600 bp, a threshold of \u0026gt;\u0026thinsp;91% Percent Identity was required for unambiguous identification. \u003cem\u003eCriteria P\u003c/em\u003e: To further confirm identification of putative mislabeling, samples categorized as \u0026ldquo;mislabeled\u0026rdquo; from Criteria B or N were additionally evaluated with phylogenetic analysis. Top hits from NCBI\u0026rsquo;s GenBank database with the highest query cover and maximum identical values (\u0026gt;\u0026thinsp;97%) for each species were chosen as reference sequences, downloaded, and added to the FASTA file of generated sequences from this study. Sequences were aligned with MUSCLE \u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e(Edgar 2004)\u003c/span\u003e and trees were constructed using the Maximum Likelihood (ML) method with the General Time Reversible (GTR) model using MEGA7 software \u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e(\u003c/span\u003eKumar et al. \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; \u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eStecher et al. 2020)\u003c/span\u003e. For unambiguous identification, the putatively substituted sample had to appropriately cluster within the expected taxonomic genus and species expected from Criteria B or N identification. Finally, all identified species were checked on the International Union for Conservation of Nature (IUCN) Red List (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.iucnredlist.org\u003c/span\u003e\u003cspan address=\"https://www.iucnredlist.org\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e and the conservation status was noted.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003eCollected Samples\u003c/h2\u003e \u003cp\u003eMeat labeled \u0026lsquo;Swordfish\u0026rsquo; accounted for 64.1% of all collected samples, and meat labeled \u0026lsquo;Mako\u0026rsquo; comprised 28.2% of all collected sampled, indicating that these two species were the most readily sourced and available for consumption in New England. Meat labeled \u0026lsquo;Thresher\u0026rsquo; was less common to find in markets and comprised 7.2% of the samples collected. No other shark species were detected. The majority of samples were sourced internationally for sale in the New England region, but nearly a quarter of markets had no origin location associated with their product (Figure II). The average price of swordfish meat collected for this study was \u003cspan\u003e$\u003c/span\u003e13.20/lb, and the average price of shark meat collected for this study was \u003cspan\u003e$\u003c/span\u003e9.49/lb. As such, shark meat attained only\u0026thinsp;~\u0026thinsp;71% of the price of swordfish in market.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eFigure II\u003c/b\u003e Origins of shark and swordfish meat collected from markets in this study. Over a quarter of the samples (n, y-axis) collected were sourced domestically from the United States. Some markets had no source information about their product. Species identified in this study include the Common Thresher (\u003cem\u003eAlopias vulpinus\u003c/em\u003e) in yellow, designated by the IUCN as a Vulnerable species, the Shortfin Mako (\u003cem\u003eIsurus oxyrinchus\u003c/em\u003e), in gray, designated by the IUCN as an Endangered species, and the swordfish (\u003cem\u003eXiphias gladius\u003c/em\u003e), in blue, designated by the IUCN as a Near Threatened species\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eGenetic Barcode Identification Analysis\u003c/h2\u003e \u003cp\u003eOut of 40 collected samples, 39 successfully amplified with PCR, a success rate of 97.5%. Unsuccessful PCR amplification may have been the result of inefficient primers (Mar\u0026iacute;n et al. \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2018\u003c/span\u003e) or degraded DNA. A total of 38 out of 39 amplified PCR products resulted in a sequence fragment of at least 220 bp, a success rate of 97.4%. Of the 38 sequences, 24 were considered full coverage (\u0026gt;\u0026thinsp;600 bp) and 14 were considered partial coverage (\u0026lt;\u0026thinsp;600 bp and \u0026gt;\u0026thinsp;220 bp). Most pieces of collected meat were sold in markets on a cooled table or some amount of ice, but all meat was exposed to air for unknown durations, which leads to DNA degradation (Zimmermann et al. \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2008\u003c/span\u003e). DNA degradation, common in seafood products, results in fragmented sequences like the partial coverage fragments that were observed in this study (Shokralla et al. \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Short fragments within the full-length COI barcode region have been proven effective at species-level identification (Mar\u0026iacute;n et al. \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2018\u003c/span\u003e), and all sequences were able to be evaluated for identity. Unambiguous species-level identification of all 38 sequences was successful (Supplementary Table I).\u003c/p\u003e \u003cp\u003eThree samples (Sample 9, 13, 15) failed to pass Criteria N identification analysis. NCBI BLASTn Top Hit Percent Identity measures the fraction of the alignment that is identical between the blasted and reference sequence (Supplementary Table I). However, a query can share a low percent identity sequence and still be a significant hit. Regions of pelagic shark and swordfish COI mtDNA are particularly prone to intraspecific polymorphisms, which reduces Percent Identity value while still being a significant match (Pappalardo et al. \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Liu et al. \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Given this, the three partial coverage samples that failed Criteria N were still considered for unambiguous identification with the Criteria B requirements.\u003c/p\u003e \u003cp\u003eAll samples passed Criteria B identification analysis. BOLD Top Hit Similarity (Supplementary Table I) measures the percent of identical base pairs between the query and top hit reference sequence. Additionally, to ensure that a large number of consensus samples were considered, samples also had to pass the BOLD Taxonomic Genus Composition and BOLD Taxonomic Species Composition with a threshold of 100% match for genus-level or species-level identification (Supplementary Table I). These criteria represent the percent of reference sequences returned with consistent identity. To calculate this metric, the BOLD TaxonID Taxonomy Report was viewed for each sample and the Genus composition percent and Species composition percent were calculated based on the identity ratio of reference sequences returned. The threshold of 100% indicates that all returned reference sequences unanimously identified the same genus or species. Two samples returned a less than 100% confidence for species-level identification. Sample 6 was identified to the genus level and Sample 15 was identified to the family level for 100% confidence.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003ch2\u003ePhylogenetic Analysis of Mislabeled Specimens\u003c/h2\u003e \u003cp\u003eSamples categorized as \u0026ldquo;mislabeled\u0026rdquo; from genetic barcode analysis were additionally evaluated in a phylogenetic tree to confirm putative mislabeling. The four samples (Sample 6, Sample 13, Sample 15, and Sample 27; Supplementary Table I) were visualized in phylogenetic trees and confirmed instances of mislabeling as they clustered appropriately with the expected taxonomic genus and species from genetic barcode analysis (Figure III).\u003c/p\u003e \u003cp\u003eIn Figure IIIA, three minor clades of Mako samples are displayed with sequences generated in this study (Supplementary Table I) grouped with the reference sequences (NCBI, MG214784.1, MG837941.1, KT444008.1). Sample 13 was labeled \u0026lsquo;Wild Swordfish Steaks\u0026rsquo; and Sample 27 was labeled \u0026lsquo;Wild Caught Swordfish Steak\u0026rsquo;. However, both samples are unambiguously identified as Shortfin Mako (\u003cem\u003eIsurus oxyrinchus\u003c/em\u003e) and thus mislabeled. The reference outgroups were sourced from samples sequenced in this study (\u003cem\u003eAlopias\u003c/em\u003e Sample 7, \u003cem\u003eXiphias\u003c/em\u003e Sample 28).\u003c/p\u003e \u003cp\u003eIn Figure IIIB, one clade of Thresher samples is displayed with sequences generated in this study (Supplementary Table I) grouped with the reference sequence (NCBI, JF492809.1). Sample 6 was labeled \u0026lsquo;Fresh Mako Shark\u0026rsquo;, and Sample 15 was labeled \u0026lsquo;Swordfish Steak\u0026rsquo;. However, Sample 6 was unambiguously identified as a Thresher shark (\u003cem\u003eAlopias\u003c/em\u003e spp.) and Sample 15 was identified as family Lamnidae, and thus mislabeled. The reference outgroups were sourced from samples sequenced in this study (\u003cem\u003eIsurus\u003c/em\u003e Sample 5, \u003cem\u003eXiphias\u003c/em\u003e Sample 28).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eFigure III\u003c/b\u003e Phylogenetic analysis confirms the identity of mislabeled shark samples revealed in this study. Evolutionary history was inferred using the Maximum Likelihood method and General Time Reversible model. The trees with the highest log likelihood are shown. The percentage of trees in which associated taxa clustered together is shown next to the branches. The trees are drawn to scale, with branch lengths measured in the number of nucleotide substitutions per site. Sample numbers correspond to Supplementary Table I. Mislabeled samples cluster with elasmobranch taxa that were identified by NCBI and BOLD analysis and are highlighted in red\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eMislabeling as a Conservation Issue\u003c/h2\u003e \u003cp\u003eIt has been well-documented that shark populations are declining globally, and conservation action must be taken immediately to ensure a reasonable chance for recovery. In the North Atlantic, the mortality rate for any individual mako shark in an annual period is 30% due to commercial fisheries alone (Byrne et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). While U.S. fishing of mako shark is illegal, the highly migratory mako shark swims through nearly 20 distinct management zones across the entire North Atlantic. Preventing this endangered species\u0026rsquo; extirpation is contingent upon international cooperation for protection (Byrne et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2017\u003c/span\u003e) and elimination of opportunities for mislabeling in markets through systemic changes in fishery catch reporting (Cawthorn et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2018\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThis study is the first to evaluate the rate of shark mislabeling as swordfish meat in New England, a region heavily reliant on fisheries and seafood consumption. Sample analysis revealed four total instances of mislabeling, a 10.5% substitution rate for meat sold in southern New England markets. Of the four mislabeled samples, three had origin location data displayed in market. These three substitutions were all internationally sourced, with one each from Canada, Brazil, and Ecuador. It is possible that the distance these products were transported had an impact on the final outcome of the mislabeling. Markets selling only locally-caught fish showed no evidence of mislabeling in this study.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003ePreventing Mislabeling\u003c/h2\u003e \u003cp\u003eCurrent market-level reporting programs may not be performing as well as they are intended. One large chain grocery store from which samples were collected advertised a \u0026ldquo;Random DNA Testing Service\u0026rdquo; that claimed to \u0026ldquo;set the innovation standard with DNA testing that ensures seafood labeling is accurate\u0026rdquo;. The information about the service, which is conducted regionally across their stores, was readily available on pamphlets which were distributed across their seafood counters to customers. Despite this advertised program, that chain grocery store was the source of one substitution in this study, where a slice of swordfish was unambiguously identified as Thresher shark. With mislabeling a threat at many stages of the supply chain, markets struggle to ensure they are selling accurately labeled products.\u003c/p\u003e \u003cp\u003ePreventing mislabeling likely has to occur earlier in the supply chain, before fish products are processed into morphologically unidentifiable cuts. As the world\u0026rsquo;s largest seafood importer, the US has a responsibility to curb illegal fishing and seafood fraud (Williams et al. \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; FAO 2018; He \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). The Seafood Import Monitoring Program (SIMP) aims to do this by requiring seafood imports to be logged in the International Trade Data System (IDTS), which tracks all imports and exports for the entire US (NOAA \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2024b\u003c/span\u003e). Importers with intent to sell whole fish products in the US must provide data about the fish, catch location, type of fishing gear used, documentation of authorization to fish that particular species (NOAA \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2024b\u003c/span\u003e). As the samples from this study were collected very early on during SIMP implementation (SIMP started 2018, samples collected 2019), this study has established a temporal baseline that could be used to determine if market mislabeling has decreased. Future research should explore if rates of mislabeling across New England have been meaningfully reduced through effective SIMP monitoring and the U.S. mako fishing ban. While promising, SIMP program data is not yet available to public consumers in the US, but summary statistics are available in reports to congress compiled by NOAA. Allowing this database to be public so both US sellers of seafood and consumers are able to track the origins of their seafood would fundamentally change supply dynamics.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eConclusions about New England\u0026rsquo;s Role in Global Shark Fisheries\u003c/h2\u003e \u003cp\u003eDespite the mislabeling found in this study, the regional shark fishery in New England may be an example of progress towards sustainable fisheries. While a 10.5% substitution rate in markets is not ideal, it is less than the substitution rates of 15\u0026ndash;80% in reports from Asia, Brazil, and Italy (Melo Palmeira et al. \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). This low substitution rate is undoubtedly influenced by the cultural demand in New England for locally sourced fish, which inhibits mislabeling opportunities from occurring. Additionally, the New England region, especially Massachusetts, is an important nursery area where the majority of sharks are catch-and-release (Skomal \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2007\u003c/span\u003e). Due to the region\u0026rsquo;s investment in science education and communication, the local public recognizes sharks as ecologically valuable to New England and has advocated for their conservation by pushing back against lethal methods of shark management (Szczepaniak \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). More broadly in the US, shark finning bans and total fishing bans have been enacted, setting the global standard for conservation actions for endangered marine species. Reflecting on the successes of shark management in New England has identified routes of action for global shark conservation. These actions include prioritizing local catch by reducing internationally-imported seafood in markets, establishing seafood import monitoring programs and making data publicly-available, routinely and randomly testing markets for commonly substituted seafood, and preventing endangered shark products from entering the market through catch, landing, and retention bans.\u003c/p\u003e \u003c/div\u003e"},{"header":"Declarations","content":"\u003cp\u003e \u003ch2\u003eCompeting Interests\u003c/h2\u003e \u003cp\u003eFinancial interests: Authors M.G.E and T.C. declare they have no relevant financial or non-financial interests to disclose.\u003c/p\u003e \u003ch2\u003eFunding\u003c/h2\u003e \u003cp\u003eAuthor M.G.E received funding support from Bard College at Simon\u0026rsquo;s Rock. The authors declare that no other funds, grants, or support was received during the preparation of this manuscript.\u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eConceptualization, data curation, and formal analysis was performed by M.G.E. Both authors contributed to the study design. T.C. supervised the study. The first draft of the manuscript was written by M.G.E., and T.C. commented on all versions of the manuscript. Both authors read and approved the final manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eThe authors would like to thank Donald McClelland and Sarah Snyder for their helpful discussions on the project and feedback, Giulia de Gennaro for assistance with sample collection and feedback, Annabel Hughes for illustrations and comments on the manuscript, and Katie Lotterhos and Ally Swank for their comments on the manuscript.\u003c/p\u003e\u003ch2\u003eData Availability\u003c/h2\u003e\u003cp\u003eSequence data generated in this study were deposited as open data via the Northeastern University Digital Repository Service, available here: https://hdl.handle.net/2047/D20662827. All metadata supporting the findings of this study are available within the paper and its Supplementary Information.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eAlmer\u0026oacute;n-Souza F, Sperb C, Castilho CL et al (2018) Molecular Identification of Shark Meat From Local Markets in Southern Brazil Based on DNA Barcoding: Evidence for Mislabeling and Trade of Endangered Species. Front Genet 9:138. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fgene.2018.00138\u003c/span\u003e\u003cspan address=\"10.3389/fgene.2018.00138\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAltschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. 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Front Zool 5:18. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/1742-9994-5-18\u003c/span\u003e\u003cspan address=\"10.1186/1742-9994-5-18\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"conservation-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"coge","sideBox":"Learn more about [Conservation Genetics](https://www.springer.com/journal/10592)","snPcode":"10592","submissionUrl":"https://submission.nature.com/new-submission/10592/3","title":"Conservation Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Conservation, Fisheries, Mislabeling, DNA Barcoding, Sharks, Endangered","lastPublishedDoi":"10.21203/rs.3.rs-4547946/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4547946/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eMislabeling of shark and swordfish meat poses a substantial challenge to conservation of rapidly declining pelagic shark populations in the North Atlantic, so routine market assessments are critical. New England\u0026rsquo;s southern region of Massachusetts, Connecticut, and Rhode Island has a historic reliance on fisheries and seafood consumption, including sharks and swordfish. The visual similarity of shark and swordfish meat is considerable, and as such, this study aimed to evaluate mislabeling of shark for swordfish meat collected from markets and grocery stores in New England in 2019. DNA barcoding was used on the mitochondrial cytochrome oxidase I (COI) gene to determine unambiguous identification of 38 collected samples, which were either labeled as Shortfin Mako shark (\u003cem\u003eIsurus oxyrinchus)\u003c/em\u003e, Common Thresher shark (\u003cem\u003eAlopias vulpinus\u003c/em\u003e), or swordfish (\u003cem\u003eXiphias gladius\u003c/em\u003e) in market. Mako, an IUCN Red List Endangered species and Thresher, an IUCN Red List vulnerable species, are additionally listed on the CITES Appendix II List. Barcoding and phylogenetic analysis revealed four mislabeled samples for a total substitution rate of 10.5%. One substitution, labeled \u0026lsquo;Mako\u0026rsquo; in the market, was identified as Thresher shark. Three further substitutions, labeled as \u0026lsquo;Swordfish\u0026rsquo; in the market were identified as Mako, \u003cem\u003eAlopias\u003c/em\u003e spp., and a Lamnid shark, all of which are endangered or threatened shark species. As samples were collected just before implementation of major import monitoring programs and a Mako fishing ban in the United States, this study has established a temporal baseline that can be used to determine if market mislabeling has decreased as a result of these conservation initiatives.\u003c/p\u003e","manuscriptTitle":"DNA barcoding reveals mislabeling of endangered sharks sold as swordfish in New England fish markets","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-06-21 10:40:31","doi":"10.21203/rs.3.rs-4547946/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-10-28T13:06:12+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-09-10T17:46:31+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"262478531592216545127612822768375526186","date":"2024-08-31T16:15:12+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-06-17T12:25:36+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-06-08T07:38:45+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-06-08T07:37:21+00:00","index":"","fulltext":""},{"type":"submitted","content":"Conservation Genetics","date":"2024-06-07T19:54:41+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"conservation-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"coge","sideBox":"Learn more about [Conservation Genetics](https://www.springer.com/journal/10592)","snPcode":"10592","submissionUrl":"https://submission.nature.com/new-submission/10592/3","title":"Conservation Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"e25887f4-85b8-47f6-92f8-3cd5d0393f6b","owner":[],"postedDate":"June 21st, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-02-17T16:12:33+00:00","versionOfRecord":{"articleIdentity":"rs-4547946","link":"https://doi.org/10.1007/s10592-025-01675-5","journal":{"identity":"conservation-genetics","isVorOnly":false,"title":"Conservation Genetics"},"publishedOn":"2025-02-15 15:58:04","publishedOnDateReadable":"February 15th, 2025"},"versionCreatedAt":"2024-06-21 10:40:31","video":"","vorDoi":"10.1007/s10592-025-01675-5","vorDoiUrl":"https://doi.org/10.1007/s10592-025-01675-5","workflowStages":[]},"version":"v1","identity":"rs-4547946","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4547946","identity":"rs-4547946","version":["v1"]},"buildId":"cBFmMYwuxLRRLfASyISRj","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}