Baetscher DS, Locatelli NS, Won E, Fitzgerald T, McIntyre PB, Therkildsen NO (2023) Optimizing a metabarcoding marker portfolio for species detection from complex mixtures of globally diverse fishes. Environmental DNA 5:1589–1607

Article  CAS  Google Scholar 

Brandão JHSG, Bitencourt JA, Santos FB, Watanabe LA, Schneider H, Sampaio I, Affonso PRAM (2016) DNA barcoding of coastal ichthyofauna from Bahia, northeastern Brazil, South Atlantic: High efficiency for systematics and identification of cryptic diversity. Biochem Syst Ecol 65:214–224

Article  Google Scholar 

Briggs JC (1995) Global biogeography. Developments in paleontology and Stratigraphy, Vol. 14. Amsterdam: Elsevier.

Brígida NS, Lutz I, Martins T, Santana P, Barbosa A, Sampaio I, Vallinoto M, Evangelista-Gomes G (2024) Authentication of sushi and sashimi products from northeastern Pará, coastal Amazon, by DNA barcoding reveals commercial frauds and potential threats to human health and environment. Food Control 166:110724

Article  Google Scholar 

Carew ME, Yow WK, Robinson KL, Coleman RA, Hoffmann AA (2022) DNA barcoding and metabarcoding of highly diverse aquatic mites (Acarina) can improve their use in routine biological monitoring. Mar Freshw Res 73(7):900–914

Article  CAS  Google Scholar 

Collins RA, Cruickshank RH (2013) The seven deadly sins of DNA barcoding. Mol Ecol Resour 13:969–975

Article  CAS  PubMed  Google Scholar 

Craig MT, Graham RT, Torres RA, Hyde JR, Freitas MO, Ferreira BP, Hostim-Silva M, Gerhardinger LC, Bertoncini AA, Robertson DR (2009) How many species of goliath grouper are there? Cryptic genetic divergence in a threatened marine fish and the resurrection of a geopolitical species. Endanger Species Res 7:167–174

Article  Google Scholar 

Dayrat B (2005) Towards integrative taxonomy. Biol J Linn Soc 85:407–415

Article  Google Scholar 

Devi CBL (2004) Monograph On Bothid Larvae (Pleuronectiformes-Pisces). National Institute of Oceanography. http://drs.nio.org/drs/handle/2264/94. Accessed 10 February 2015.

Evseenko SA (2008) Distribution and routes of drift migrations in larvae of three species of flatfish Bothus (Bothidae) in open waters of the northern Atlantic. J Ichthyol 48:792–809

Article  Google Scholar 

Furey NB, Dance MA, Rooker JR (2013) Fine-scale movements and habitat use of juvenile Southern flounder Paralichthys lethostigma in an estuarine seascape. J Fish Biol 82:1453–1769

Article  Google Scholar 

Garcia-Vazquez E, Alvarez P, Lopes P, Karaiskou N, Perez J, Teia A, Martinez JL, Gomes L, Triantaphyllidis C (2006) PCR-SSCP of the 16S rRNA gene, a simple methodology for species identification of fish eggs and larvae. Sci Mar 70(2):13–21

Article  CAS  Google Scholar 

Gibson RN, Nash RD, Geffen AJ, Van der Veer HW (2014) Flatfishes: biology and exploitation, 2nd edn. John Wiley & Sons Ltd, New Jersey

Book  Google Scholar 

Hajibabaei M, Singer GA, Hebert PD, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23:167–172

Article  CAS  PubMed  Google Scholar 

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

CAS  Google Scholar 

Hebert PDN, Cywinska A, Ball SL, Dewaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc B 270:313–321

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–14817

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hendrich L, Morinière J, Haszprunar G, Hebert PD, Hausmann A, Köhler F, Balke M (2014) A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD. Mol Ecol Resour. http://onlinelibrary.wiley.com/enhanced/doi/10.1111/1755-0998.12354/. Accessed 11 March 2015.

Heracle BioSoft SRL (2014) DNA Baser Sequence Assembler 4.16. http://www.dnabaser.com/download/download.html. Accessed 21 January 2015.

Hobern DBIOSCAN (2021) DNA barcoding to accelerate taxonomy and biogeography for conservation and sustainability. Genome 64(3):161–164

Article  PubMed  Google Scholar 

Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes 7:544–548

Article  CAS  Google Scholar 

Joyeux JC, Floeter SR, Ferreira CEL, Gasparini JL (2001) Biogeography of tropical reef fishes: the South Atlantic puzzle. J Biogeogr 28:831–841

Article  Google Scholar 

Keenan C (1994) Recent evolution of population structure in Australian barramundi, Lates calcarifer (Bloch): an example of isolation by distance in one dimension. Aust J Mar Freshwat Res 45:1123–1148

Article  Google Scholar 

Kekkonen M, Hebert PD (2014) DNA barcode-based delineation of putative species: efficient start for taxonomic workflows. Mol Ecol Resour 14:706–715

Article  PubMed  PubMed Central  Google Scholar 

Kerr KC, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PD (2007) Comprehensive DNA barcode coverage of North American birds. Mol Ecol Notes 7:535–543

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kochzius M, Seidel C, Antoniou A, Botla SK, Campo D, Cariani A, Vazquez EG, Hauschild J, Hervet C, Hjörleifsdottir S, Hreggvidsson G, Kappel K, Landi M, Magoulas A, Marteinsson V, Nölte M, Planes S, Tinti F, Turan C, Venugopal MN, Weber H, Blohm D (2010) Identifying fishes through DNA barcodes and microarrays. PLoS ONE 5:e12620

Article  PubMed  PubMed Central  Google Scholar 

Menezes NA, Buckup PA, Figueiredo JL, Moura RL (2003) Catálogo das espécies de peixes marinhos do Brasil. Museu de Zoologia USP, São Paulo.

Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLOS Biol 2:e354

Article  PubMed  PubMed Central  Google Scholar 

Moura RL, Figueiredo JL, Sazima I (2001) A new parrotfish (Scaridae) from Brazil, and revalidation of Sparisoma amplum (Ranzani, 1842), Sparisoma frondosum (Agassiz, 1831), Sparisoma axillare (Steindachner, 1878) and Scarus trispinosus Valenciennes, 1840. Bull Mari Sci 68:505–524

Google Scholar 

Oliveira LS, Bitencourt JA, Galdino JH, Sampaio I, Carneiro PLS, Affonso PRAM (2023) Genetic diversity in natural populations of the near-threatened species Lignobrycon myersi (Characiformes, Triportheidae): implications for species conservation. Zebrafish 20(6):271–279. https://doi.org/10.1089/zeb.2023.0036

Article  CAS  Google Scholar 

Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In: Hills D, Moritz C, Mable B (eds) Molecular Systematics. Sinauer Associates, Massachusetts, pp 205–248

Google Scholar 

Pereira LHG, Hanner R, Foresti F, Oliveira C (2013) Can DNA barcoding accurately discriminate megadiverse neotropical freshwater fish fauna? BMC Genet 14:20. https://doi.org/10.1186/1471-2156-14-20

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rambaut A (2014) FigTree, a graphical view of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree. Accessed 21 January 2015.

Ratnasingham S, Hebert PD (2013) A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS ONE 8:e66213

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ribeiro ADO, Caires RA, Mariguela TC, Pereira LHG, Hanner R, Oliveira C (2012) DNA barcodes identify marine fishes of São Paulo State. Brazil Mol Ecol Resour 12(6):1012–1020

Article  CAS  PubMed  Google Scholar 

Rocha LA, Craig MT, Bowen BW (2007) Phylogeography and the conservation of coral reef fishes. Coral Reefs 26:501–512

Article  Google Scholar 

Saavedra-Diaz LM, Acero A, Navas GR (2000) Lenguados de la familia paralichthyidae (Pisces: Pleuronectiformes) conocidos del caribe colombian. Dieciocho 295:310

Google Scholar 

Sanger F, Nichlen S, Coulson AR (1977) DNA Sequencing with chain-termination inhibitors. P Natl Acad Sci 74:5463–5468

Article  CAS  Google Scholar 

Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21(8):2045–2050

Article  CAS  PubMed  Google Scholar 

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

Article