Abstract
Due to the morphological similarities among species, the International Commission for the Conservation of the Atlantic Tunas has recommended the use of diagnostic molecular tools to allow for robust species-level identifications of the billfishes. In this study, a protocol for the molecular identification of all six Atlantic billfishes was developed utilizing a PCR–RFLP approach, targeting the mitochondrial gene cytochrome c oxidase subunit 1. A survey of 28 restriction endonucleases identified two enzymes (TaqI and HaeIII) that produced species-specific banding patterns sufficient to distinguish species. The protocol was validated against billfishes captured across their Atlantic distributions.
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References
Beerkircher LR, Arocha F, Barse A, Prince ED, Restrepo V, Serafy JE, Shivji MS (2009) Effects of species misidentification on population assessment of overfished white marlin Tetrapturus albidus and roundscale spearfish T. georgii. Endanger Species Res 9:81–90
Collette BB, McDowell JR, Graves JE (2006) Phylogeny of recent billfishes (Xiphioidei). Bull Mar Sci 79:455–468
Ditton RB, Stoll JR (2003) Social and economic perspective on recreational billfish fisheries. Mar Freshw Res 54:545–554
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Hanner R, Floyd R, Bernard AM, Collette BB, Shivji MS (2011) DNA barcoding of billfishes. Mitochondrial DNA 22:27–36
ICCAT (2013) Report for biennial period, 2012–2013, part II vol 2. Madrid, Spain
Innes BH, Grewe PM, Ward RD (1998) PCR-based genetic identification of marlin and other billfish. Mar Freshw Res 49:383–388
Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23:1289–1291
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, William MC, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Little AG, Lougheed SC, Moyes CD (2010) Evolutionary affinity of billfishes (xiphiidae and istiophoridae) and flatfishes (plueronectiformes): independent and trans-subordinal origins of endothermy in teleost fishes. Mol Phylogenetics Evol 56:897–904
McDowell JR, Graves JE (2002) Nuclear and mitochondrial DNA markers for specific identification of istiophorid and xiphiid billfishes. Fish Bull 100:537–544
Shivji MS, Magnussen JE, Beerkircher LR, Hinteregger GF, Lee DW, Serafy JE, Prince ED (2006) Validity, identification, and distribution of the roundscale spearfish, Tetrapturus georgii (Teleostei: Istiophoridae): morphological and molecular evidence. Bull Mar Sci 79:483–491
Untergrasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40:e115
Uozumi Y (2003) Historical perspective of global billfish stock assessment. Mar Freshw Res 54:555–565
Vincze T, Posfai J, Roberts RJ (2003) NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 31:3688–3691
Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74:329–356
Acknowledgments
Funding was provided by the São Paulo Research Foundation (FAPESP No. 2009/54660-6) and the Guy Harvey Ocean Foundation.
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Domingues, R.R., Okuda, G., Bernard, A.M. et al. A DNA tool for the identification of heavily exploited Atlantic billfishes. Conservation Genet Resour 7, 807–809 (2015). https://doi.org/10.1007/s12686-015-0489-4
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DOI: https://doi.org/10.1007/s12686-015-0489-4