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FISH-BOL, A Case Study for DNA Barcodes

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DNA Barcodes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 858))

Abstract

The FISH-BOL campaign was initiated in 2005, and currently has barcoded for the cytochrome c oxidase subunit I (COI) gene about 8,000 of the 31,000 fish species currently recognised. This includes the great majority of the world’s most important commercial species. Results thus far show that about 98% and 93% of marine and freshwater species, respectively, are barcode distinguishable. One important issue that needs to be more fully addressed in FISH-BOL concerns the initial misidentification of a small number of barcode reference specimens. This is unsurprising considering the large number of fish species, some of which are morphologically very similar and others as yet unrecognised, but constant vigilance and ongoing attention by the FISH-BOL community is required to eliminate such errors. Once the reference library has been established, barcoding enables the identification of unknown fishes at any life history stage or from their fragmentary remains. The many uses of the FISH-BOL barcode library include detecting consumer fraud, aiding fisheries management, improving ecological analyses including food web syntheses, and assisting with taxonomic revisions.

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References

  1. Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74:329–356

    Article  PubMed  CAS  Google Scholar 

  2. Eschmeyer WN, Fricke R, Fong JD, Polack DA (2010) Marine fish diversity: history of knowledge and discovery (Pisces). Zootaxa 2525:19–50

    Google Scholar 

  3. Ward RD, Zemlak TS, Innes BH et al (2005) Barcoding Australia’s fish species. Phil Trans R Soc London B 360:1847–1857

    Article  CAS  Google Scholar 

  4. 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

    Article  CAS  Google Scholar 

  5. Hubert N, Hanner R, Holm E et al (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3:e2490

    Article  PubMed  Google Scholar 

  6. Steinke D, Zemlak TS, Boutillier JA, Hebert PDN (2009) DNA barcoding Pacific Canada’s fishes. Mar Biol 156:2641–2647

    Article  Google Scholar 

  7. Steinke D, Zemlak TS, Hebert PDN (2009) Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS One 4: e6300

    Article  PubMed  Google Scholar 

  8. Valdez-Moreno M, Ivanova NV, Elias-Gutierrez M et al (2009) Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. J Fish Biol 74:377–402

    Article  PubMed  CAS  Google Scholar 

  9. Lakra WS, Verma WS, Goswami M et al (2010) DNA barcoding Indian marine fishes. Mol Ecol Resour 11:60–71

    Google Scholar 

  10. Dettai A, Lautredou AC, Bonillo C et al (2011) The actinopterygian diversity of the CEAMARC cruises: barcoding and molecular taxonomy as a multi-level tool for new findings. Deep-Sea Res II 58(Suppl 1):250–263

    Google Scholar 

  11. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, Hebert PDN (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes 6:959–964

    Article  CAS  Google Scholar 

  12. Meusnier I, Singer GAC, Landry J et al (2008) A universal DNA minibarcode for biodiversity analysis. BMC Genomics 9:214

    Article  PubMed  Google Scholar 

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

  14. Becker S, Hanner R, Steinke D (2011) Five years FISH-BOL—a brief status report. Mitochondrial DNA 22(Suppl 1):3–9

    Article  PubMed  CAS  Google Scholar 

  15. Williams A, Last PR, Gomon MF, Paxton JR (1996) Species composition and checklist of the demersal ichthyofauna of the continental slope off Western Australia (20–35°S). Record West Aust Mus 18:135–155

    Google Scholar 

  16. Smith PJ, McVeagh SM, Steinke D (2008) DNA barcoding for the identification of smoked fish products. J Fish Biol 72:464–471

    Article  CAS  Google Scholar 

  17. Wong EHK, Hanner R (2008) DNA barcoding detects market substitution in North American seafood. Food Res Int 41:828–837

    Article  CAS  Google Scholar 

  18. Rasmussen RS, Morrissey MT, Hebert PDN (2009) DNA barcoding of commercially important salmon and trout species (Oncorhynchus and Salmo) from North America. J Agric Food Chem 57:8379–8385

    Article  PubMed  CAS  Google Scholar 

  19. Dunn MR, Szabo A, McVeagh MS, Smith PJ (2010) The diet of deepwater sharks and the benefits of using DNA identification of prey. Deep-Sea Res I 57:923–930

    Article  CAS  Google Scholar 

  20. Barnett A, Redd KS, Frusher SD et al (2010) Non-lethal method to obtain stomach samples from a large marine predator and the use of DNA analysis to improve dietary information. J Exp Mar Biol Ecol 393:188–192

    Article  Google Scholar 

  21. Cooper JK, Sykes G, King S et al (2007) Species identification in cell culture: a two-pronged molecular approach. In Vitro Cell Dev Biol Anim 43:344–351

    Article  PubMed  CAS  Google Scholar 

  22. Lakra WS, Swaminathan TR, Rathore G et al (2010) Development and characterization of three new diploid cell lines from Labeo rohita (Ham.). Biotechnol Prog 26:1008–1013

    PubMed  CAS  Google Scholar 

  23. Victor BC (2007) Coryphopterus kuna, a new goby (Perciformes: Gobiidae: Gobinae) from the western Caribbean, with the identification of the late larval stage and an estimate of the pelagic larval duration. Zootaxa 1526:51–61

    Google Scholar 

  24. De Astarloa JMD, Mabragana E, Hanner R, Figueroa DE (2008) Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding. Zootaxa 1921:35–46

    Google Scholar 

  25. Eschmeyer WN (2010) Catalog of fishes electronic version. http://research.calacademy.org/ichthyology/catalog/fishcatmain.asp. Accessed 25 Oct 2010

  26. Ward RD, Woodwark M, Skibinski DOF (1994) A comparison of genetic diversity levels in marine, freshwater and anadromous fish. J Fish Biol 44:213–232

    Article  Google Scholar 

  27. Ward RD (2009) DNA barcode divergence among species and genera of birds and fishes. Mol Ecol Resour 9:1077–1085

    Article  PubMed  CAS  Google Scholar 

  28. Steinke D, Hanner R, Hebert PDN (2009) Rapid high-quality imaging of fishes using a flat-bed scanner. Ichthyol Res 56:210–211

    Article  Google Scholar 

  29. Ivanova NV, Dewaard JR, Hebert PDN (2006) An inexpensive automation-friendly protocol for recovering high-quality DNA. Mol Ecol Notes 6:998–1002

    Article  CAS  Google Scholar 

  30. Klanten SO, van Herwerden L, Choat JH (2003) Acquiring reef fish DNA sequences from formalin-fixed museum specimens. Bull Mar Sci 73:771–776

    Google Scholar 

  31. Bucklin A, Allen LD (2004) MtDNA sequencing from zooplankton after long-term preservation in buffered formalin. Mol Phylogent Evol 30:879–882

    Article  CAS  Google Scholar 

  32. Zhang J (2010) Exploiting formalin-preserved fish specimens for resources of DNA barcoding. Mol Ecol Resour 10:935–941

    Article  PubMed  CAS  Google Scholar 

  33. Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081–1084

    Article  PubMed  CAS  Google Scholar 

  34. Antunes A, Ramos MJ (2005) Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes. Genomics 86:708–717

    Article  PubMed  CAS  Google Scholar 

  35. Venkatesh B, Dandona N, Brenner S (2006) Fugu genome does not contain mitochondrial pseudogenes. Genomics 87:307–310

    Article  PubMed  CAS  Google Scholar 

  36. Teletchea F, Laudet V, Hanni C (2006) Phylogeny of the Gadidae (sensu Svetovidov, 1948) based on their morphology and two mitochondrial genes. Mol Phylogent Evol 38:189–199

    Article  CAS  Google Scholar 

  37. Knudsen SW, Moller PR, Gravlund P (2007) Phylogeny of the snailfishes (Teleostei: Liparidae) based on molecular and morphological data. Mol Phylogent Evol 44:649–666

    Article  CAS  Google Scholar 

  38. Moore ABM, White WT, Ward RD et al (2011) Rediscovery and redescription of the smoothtooth blacktip shark Carcharhinus leiodon (Carcharhinidae) from Kuwait, with notes on its ecology and conservation. Mar Freshw Res 62:528–539

    Article  CAS  Google Scholar 

  39. Scribner KT, Page KS, Bartron ML (2000) Hybridization in freshwater fishes: a review of case studies and cytonuclear methods of biological inference. Rev Fish Biol Fish 10: 293–323

    Article  Google Scholar 

  40. Gardner JPA (1997) Hybridization in the sea. In: Blaxter JHS, Southward AJ (eds) Advances in marine biology, vol 31. Academic, New York, pp 2–78

    Google Scholar 

  41. Bengtson P (1988) Open nomenclature. Palaeontology 31:223–227

    Google Scholar 

  42. Lowenstein JH, Amato G, Kolokotronis SO (2009) The real maccoyii: identifying tuna sushi with DNA barcodes—contrasting character attributes and genetic distances. PLoS One 4:e7866

    Article  PubMed  Google Scholar 

  43. Wong EHK, Shivji MS, Hanner RH (2009) Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resour 9(Suppl 1):243–256

    Article  PubMed  CAS  Google Scholar 

  44. Elias M, Hill RI, Willmott KR, Dasmahapatra KK, Brower AVZ, Mallet J, Jiggins CD (2007) Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proc R Soc B Biol Sci 274:2881–2889

    Article  CAS  Google Scholar 

  45. Abdo Z, Golding GB (2007) A step towards barcoding life: a model-based, decision-theoretic method to assign genes to pre-existing species groups. Syst Biol 56:44–56

    Article  PubMed  CAS  Google Scholar 

  46. Zhang AB, Sikes DS, Muster C, Li SQ (2008) Inferring species membership using DNA sequences with back propagation neural networks. Syst Biol 57:202–215

    Article  PubMed  CAS  Google Scholar 

  47. Seo T-K (2010) Classification of nucleotide sequences using support vector machines. J Mol Evol 71:250–267

    Article  PubMed  CAS  Google Scholar 

  48. Filonzi L, Chiesa S, Vaghi M, Marzano FN (2010) Molecular barcoding reveals mislabelling of commercial fish products in Italy. Food Res Int 43:1383–1388

    Article  CAS  Google Scholar 

  49. Ardura A, Pola IG, Ginuino I, Gomes V, Garcia-Vasquez E (2010) Application of barcoding to Amazonian commercial fish labelling. Food Res Int 43:1549–1552

    Article  Google Scholar 

  50. Barbuto M, Galimberti A, Ferri E, Labra M, Malandra R, Galli P, Casiraghi M (2010) DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo” (Mustelus spp.). Food Res Int 43:376–381

    Article  CAS  Google Scholar 

  51. Holmes BH, Steinke D, Ward RD (2009) Identification of shark and ray fins using DNA barcoding. Fish Res 95:280–288

    Article  Google Scholar 

  52. Neira FJ, Keane JP (2008) Ichthyoplankton-based spawning dynamics of blue mackerel (Scomber australasicus) in south-eastern Australia: links to the East Australian Current. Fisheries Oceanogr 17:281–298

    Article  Google Scholar 

  53. Victor BC, Hanner R, Shivji M, Hyde J, Caldow C (2009) Identification of the larval and juvenile stages of the Cubera snapper, Lutjanus cyanopterus, using DNA barcoding. Zootaxa 2215:24–36

    Google Scholar 

  54. Pegg GG, Sinclair B, Briskey L, Aspden WJ (2006) MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia. Sci Mar 70(Suppl 2):7–12

    CAS  Google Scholar 

  55. Richardson DE, Vanwye JD, Exum AM et al (2007) High-throughput species identifications: from DNA isolation to bioinformatics. Mol Ecol Notes 7:199–207

    Article  CAS  Google Scholar 

  56. Valdez-Moreno M, Vasquez-Yeomans L, Elias-Gutierrez M et al (2010) Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula, Mexico: potential in fisheries management. Mar Freshw Res 61:665–671

    Article  CAS  Google Scholar 

  57. Hubert N, Deirieu-Trottin E, Irisson JO et al (2010) Identifying coral reef fish larvae through DNA barcoding: a test case with the families Acanthuridae and Holocentridae. Mol Phylogent Evol 55:1195–1203

    Article  CAS  Google Scholar 

  58. Ward RD, Holmes BH, Yearsley GK (2008) DNA barcoding reveals a likely second species of Asian seabass (barramundi) (Lates calcarifer). J Fish Biol 72:458–463

    Article  Google Scholar 

  59. Ward RD, Costa FO, Holmes BH, Steinke D (2008) DNA barcoding shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa but a likely two species for both Zeus faber (John dory) and Lepidopus caudatus (silver scabbardfish). Aquat Biol 3:71–78

    Article  Google Scholar 

  60. Lara A, de Leon JLP, Rodriguez R, Casnae D, Cote G, Bernatchez L, Garcia-Machado E (2010) DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts. Mol Ecol Resour 10:421–430

    Article  PubMed  CAS  Google Scholar 

  61. Zemlak TS, Ward RD, Connell AD et al (2009) DNA barcoding reveals overlooked marine fishes. Mol Ecol Resour 9(Suppl 1):237–242

    Article  PubMed  CAS  Google Scholar 

  62. Sriwattanarothai N, Steinke D, Ruenwongsa P et al (2010) Molecular and morphological evidence supports the species status of the Mahachai fighter Betta sp. Mahachai and reveals new species of Betta from Thailand. J Fish Biol 77:414–424

    Article  PubMed  CAS  Google Scholar 

  63. Ward RD, Holmes BH, Zemlak TS, Smith PJ (2007) DNA barcoding discriminates spurdogs of the genus Squalus. In: Last PR, White WT, Pogonoski JJ (eds) Descriptions of new dogfishes of the genus Squalus (Squaloidea: Squalidae). CSIRO Marine and Atmospheric Research Paper 014, Hobart, Australia, pp 117–130

    Google Scholar 

  64. Victor BC (2008) Redescription of Coryphopterus tortugae (Jordan) and a new allied species Coryphopterus bol (Perciformes: Gobiidae: Gobiinae) from the tropical western Atlantic Ocean. J Ocean Sci Found 1:1–19

    Google Scholar 

  65. Pyle RL, Earle JL, Greene BD (2008) Five new species of the damselfish genus Chromis (Perciformes: Labroidei: Pomacentridae) from deep coral reefs in the tropical western Pacific. Zootaxa 1671:3–31

    Google Scholar 

  66. Lin HC, Galland GR (2010) Molecular analysis if Acanthemblemaria macrospilus (Teleostei: Chaenopsidae) with description of a new species from the Gulf of California, Mexico. Zootaxa 2525:51–62

    Google Scholar 

  67. Ebert DA, White WT, Goldman KJ et al (2010) Resurrection and redescription of Squalus suckleyi (Girard, 1854) from the North Pacific, with comments on the Squalus acanthias subgroup (Squaliformes: Squalidae). Zootaxa 2612: 22–40

    Google Scholar 

  68. Baldwin CC, Mounts JH, Smith DG, Weight LA (2009) Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx. Zootaxa 2008:1–22

    Google Scholar 

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

    Article  CAS  Google Scholar 

  70. Messing J (1983) New M13 vectors for cloning. Methods Enzymol 101:20–78

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

I thank William White and Peter Last (CSIRO Marine and Atmospheric Research) for discussions on aspects of this paper, and Bronwyn Holmes and Dan Gledhill (also of CSIRO) for comments on an early draft. I also thank Paul Hebert (co-chair of FISH-BOL) and Bob Hanner (campaign coordinator of FISH-BOL) for their great work in helping to make FISH-BOL a success, and the many FISH-BOL participants who have collected, identified and barcoded many thousands of specimens. A special thanks goes to the team at the Canadian Centre for DNA Barcoding for barcoding the majority of fish specimens sequenced to date.

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  1. Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research, Tasmania, Australia

    Robert D. Ward

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  1. Robert D. Ward
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Correspondence to Robert D. Ward .

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Editors and Affiliations

  1. National Museum of Natural History, Dept. Botany, Smithsonian Institution, 10th St. & Constitution Ave. NW.,, Washington, 20560-0166, District of Columbia, USA

    W. John Kress

  2. National Museum of Natural History, Dept. Botany, Smithsonian Institution, 10th St. & Constitution Ave. NW.,, Washington, 20560-0166, District of Columbia, USA

    David L. Erickson

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Ward, R.D. (2012). FISH-BOL, A Case Study for DNA Barcodes. In: Kress, W., Erickson, D. (eds) DNA Barcodes. Methods in Molecular Biology, vol 858. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-591-6_21

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  • DOI: https://doi.org/10.1007/978-1-61779-591-6_21

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-590-9

  • Online ISBN: 978-1-61779-591-6

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