The campaign to DNA barcode all fishes, FISH-BOL.

FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.

[1]  A. Bortolus,et al.  Error Cascades in the Biological Sciences: The Unwanted Consequences of Using Bad Taxonomy in Ecology , 2008, Ambio.

[2]  H. Magalon,et al.  DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae) , 2007, Proceedings of the Royal Society B: Biological Sciences.

[3]  D. Janzen,et al.  DNA barcodes distinguish species of tropical Lepidoptera. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Robert Hanner,et al.  The problems and promise of DNA barcodes for species diagnosis of primate biomaterials , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[5]  C. Moritz,et al.  DNA barcoding will often fail to discover new animal species over broad parameter space. , 2006, Systematic biology.

[6]  R. Hanner,et al.  DNA barcoding detects market substitution in North American seafood , 2008 .

[7]  Paul D N Hebert,et al.  DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[8]  R. Hanner,et al.  Salvage of genetically valuable tissues following a freezer failure. , 2005, Molecular phylogenetics and evolution.

[9]  B. Deagle,et al.  Genetic screening for prey in the gut contents from a giant squid (Architeuthis sp.). , 2005, The Journal of heredity.

[10]  C. Strobeck,et al.  Forensic identification of ungulate species using restriction digests of PCR-amplified mitochondrial DNA. , 1995, Journal of forensic sciences.

[11]  A. Zhang,et al.  Inferring species membership using DNA sequences with back-propagation neural networks. , 2008, Systematic biology.

[12]  G. Wörheide,et al.  CO1 phylogenies in diploblasts and the 'Barcoding of Life' — are we sequencing a suboptimal partition? , 2006 .

[13]  L. Frézal,et al.  Four years of DNA barcoding: current advances and prospects. , 2008, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[14]  G. K. Yearsley Urolophus kapalensis sp. nov., a new stingaree (Myliobatiformes: Urolophidae) off eastern Australia , 2006 .

[15]  J. Choat,et al.  ACQUIRING REEF FISH DNA SEQUENCES FROM FORMALIN-FIXED MUSEUM SPECIMENS , 2003 .

[16]  P. Hebert,et al.  Identification of Birds through DNA Barcodes , 2004, PLoS biology.

[17]  Y. Iwatsuki,et al.  Museum fish specimens and molecular taxonomy: A comparative study on DNA extraction protocols and preservation techniques , 2006 .

[18]  S. Pääbo,et al.  Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes , 2004, Molecular ecology.

[19]  M. Sigler,et al.  Diet of Pacific Sleeper Shark, a Potential Steller Sea Lion Predator, in the North-East Pacific Ocean , 2006 .

[20]  Mehrdad Hajibabaei,et al.  A minimalist barcode can identify a specimen whose DNA is degraded , 2006 .

[21]  R. Ward,et al.  DNA barcoding Australia's fish species , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[22]  Jewell D Washington,et al.  Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia. , 2008, Journal of food protection.

[23]  William John Waugh,et al.  DNA barcoding in animal species: progress, potential and pitfalls. , 2007, BioEssays : news and reviews in molecular, cellular and developmental biology.

[24]  U. Jondelius,et al.  Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. , 2008, Molecular phylogenetics and evolution.

[25]  J. Sparks Molecular phylogeny and biogeography of the Malagasy and South Asian cichlids (Teleostei: Perciformes: Cichlidae). , 2004, Molecular phylogenetics and evolution.

[26]  D. Harris,et al.  Can you bank on GenBank , 2003 .

[27]  D. Steinke,et al.  DNA barcoding of shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species , 2008 .

[28]  Gaurav Vaidya,et al.  DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. , 2006, Systematic biology.

[29]  P. Hebert,et al.  DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. , 2007, Trends in genetics : TIG.

[30]  N. Mandrak,et al.  Identifying Canadian Freshwater Fishes through DNA Barcodes , 2008, PloS one.

[31]  D. Skibinski,et al.  A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes , 1994 .

[32]  Rob Ogden,et al.  Validation of the barcoding gene COI for use in forensic genetic species identification. , 2007, Forensic science international.

[33]  A. Antunes,et al.  Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes. , 2005, Genomics.

[34]  P. J. Smith,et al.  DNA barcoding discriminates spurdogs of the genus Squalus , 2007 .

[35]  J. Armstrong,et al.  DNA-based identification of salmonid prey species in seal faeces , 2005 .

[36]  P. Jambulingam,et al.  DNA Barcodes Can Distinguish Species of Indian Mosquitoes (Diptera: Culicidae) , 2007, Journal of medical entomology.

[37]  William S. Davidson,et al.  Identification of Thunnus Tuna Species by the Polymerase Chain Reaction and Direct Sequence Analysis of their Mitochondrial Cytochrome b Genes , 1991 .

[38]  P. Ikonomi,et al.  Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena. , 2007, International journal of systematic and evolutionary microbiology.

[39]  G. Sword,et al.  Double trouble for grasshopper molecular systematics: intra‐individual heterogeneity of both mitochondrial 12S‐valine‐16S and nuclear internal transcribed spacer ribosomal DNA sequences in Hesperotettix viridis (Orthoptera: Acrididae) , 2007 .

[40]  R. Ward,et al.  DNA barcoding reveals a likely second species of Asian sea bass (barramundi) (Lates calcarifer) , 2008 .

[41]  J. Avise Systematic Value of Electrophoretic Data , 1974 .

[42]  Gary R Carvalho,et al.  The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish , 2007, Genomics, society, and policy.

[43]  J. Gardner Hybridization in the Sea , 1997 .

[44]  A. Leviton,et al.  Standards in herpetology and ichthyology : Part I. Standard symbolic codes for institutional resource collections in herpetology and ichthyology , 1985 .

[45]  P. Hebert,et al.  DNA barcoding of Neotropical bats: species identification and discovery within Guyana , 2007 .

[46]  C. Cicero,et al.  Open access, freely available online Correspondence DNA Barcoding: Promise and Pitfalls , 2022 .

[47]  P. Hebert,et al.  Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes , 2004 .

[48]  Stephen Cameron,et al.  A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. , 2006, The Journal of heredity.

[49]  Michael J. Stanhope,et al.  Genetic Identification of Pelagic Shark Body Parts for Conservation and Trade Monitoring , 2002 .

[50]  F. Por,et al.  A "taxonomic affidavit": Why it is needed? , 2007, Integrative zoology.

[51]  J. Neigel,et al.  DNA barcoding as a tool for coral reef conservation , 2007, Coral Reefs.

[52]  Indra Neil Sarkar,et al.  DNA barcoding using chitons (genus Mopalia) , 2007 .

[53]  Brian D. Greene,et al.  Five new species of the damselfish genus Chromis (Perciformes: Labroidei: Pomacentridae) from deep coral reefs in the tropical western Pacific , 2008 .

[54]  J. Padial,et al.  Integrative taxonomists should use and produce DNA barcodes , 2007 .

[55]  D. Bellwood,et al.  Hybridization in coral reef fishes: introgression and bi-directional gene exchange in Thalassoma (family Labridae). , 2006, Molecular phylogenetics and evolution.

[56]  R. Zatorre,et al.  Fisheries: Mislabelling of a depleted reef fish , 2004, Nature.

[57]  A. Jensen LIFE HISTORY OF THE SPINY DOGFISH , 1965 .

[58]  S. Brenner,et al.  Fugu genome does not contain mitochondrial pseudogenes. , 2006, Genomics.

[59]  G. Saunders,et al.  Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[60]  M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[61]  Jeremy R. deWaard,et al.  An inexpensive, automation-friendly protocol for recovering high-quality DNA , 2006 .

[62]  C. Meyer,et al.  DNA Barcoding: Error Rates Based on Comprehensive Sampling , 2005, PLoS biology.

[63]  Woon Kee Paek,et al.  DNA barcoding Korean birds. , 2006, Molecules and cells.

[64]  P. Chakrabarty Systematics and historical biogeography of Greater Antillean Cichlidae. , 2006, Molecular phylogenetics and evolution.

[65]  Sujeevan Ratnasingham,et al.  Critical factors for assembling a high volume of DNA barcodes , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[66]  R. Vrijenhoek,et al.  DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. , 1994, Molecular marine biology and biotechnology.

[67]  D. Hartl,et al.  Mitochondrial pseudogenes: evolution's misplaced witnesses. , 2001, Trends in ecology & evolution.

[68]  R. I. Hill,et al.  Limited performance of DNA barcoding in a diverse community of tropical butterflies , 2007, Proceedings of the Royal Society B: Biological Sciences.

[69]  Marc Taconet,et al.  Integrating information on marine species identification for fishery purposes , 2006 .

[70]  I. Spies,et al.  DNA-based identification of Alaska skates (Amblyraja, Bathyraja and Raja: Rajidae) using cytochrome c oxidase subunit I (coI) variation , 2006 .

[71]  R. Hanner,et al.  Species identification in cell culture: a two-pronged molecular approach , 2007, In Vitro Cellular & Developmental Biology - Animal.

[72]  D. Janzen,et al.  Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[73]  P. Hebert,et al.  bold: The Barcode of Life Data System (http://www.barcodinglife.org) , 2007, Molecular ecology notes.

[74]  A. Cywinska,et al.  Identifying Canadian mosquito species through DNA barcodes , 2006, Medical and veterinary entomology.

[75]  R. Hanner,et al.  Genomic Diversity Research and the Role of Biorepositories , 2007 .

[76]  K. Scribner,et al.  Hybridization in freshwater fishes: a review of case studies and cytonuclear methods of biological inference , 2000, Reviews in Fish Biology and Fisheries.

[77]  M. Oppen,et al.  Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria) , 2002, Molecular ecology.

[78]  J. F. Caddy,et al.  Apparent changes in the trophic composition of world marine harvests: the perspective from the FAO capture database , 2000 .

[79]  G. Carvalho,et al.  DNA barcodes of fish of the Scotia Sea, Antarctica indicate priority groups for taxonomic and systematics focus , 2008, Antarctic Science.

[80]  P. Arctander,et al.  A new species of living bovid from Vietnam , 1993, Nature.

[81]  A. Meyer,et al.  Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[82]  V. Savolainen,et al.  Towards writing the encyclopaedia of life: an introduction to DNA barcoding , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[83]  Jos Houbraken,et al.  Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case , 2007, Proceedings of the National Academy of Sciences.

[84]  D. Gledhill,et al.  A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepede) , 2007 .

[85]  F. Cipriano,et al.  Species identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation. , 1998, The Journal of heredity.

[86]  John C. Avise,et al.  Molecular Markers, Natural History and Evolution , 1993, Springer US.

[87]  A. Mitchell DNA barcoding demystified , 2008 .

[88]  John C. Avise Molecular Markers, Natural History and Evolution , 1994, Springer US.

[89]  Howard A Ross,et al.  Testing the reliability of genetic methods of species identification via simulation. , 2008, Systematic biology.

[90]  S. Ratnasingham,et al.  Biological identifications through DNA barcodes: the case of the Crustacea , 2007 .

[91]  M. Gouy,et al.  Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. , 2006, Molecular phylogenetics and evolution.

[92]  R. Ward,et al.  DNA barcoding Australasian chondrichthyans: results and potential uses in conservation , 2008 .

[93]  W. Davidson,et al.  FINS (forensically informative nucleotide sequencing): A procedure for identifying the animal origin of biological specimens. , 1992, BioTechniques.

[94]  G. Pegg,et al.  MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia , 2006 .

[95]  R DeSalle,et al.  Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata , 2007, Proceedings of the Royal Society B: Biological Sciences.

[96]  B. Victor Coryphopterus kuna , a new goby (Perciformes: Gobiidae: Gobiinae) from the western Caribbean, with the identification of the late larval stage and an estimate of the pelagic larval duration , 2007 .

[97]  T. Yates,et al.  The importance of being earnest: what, if anything, constitutes a "specimen examined?". , 2000, Molecular phylogenetics and evolution.

[98]  Amanda D. Roe,et al.  Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding. , 2007, Molecular phylogenetics and evolution.

[99]  Dario Leister,et al.  NUMTs in sequenced eukaryotic genomes. , 2004, Molecular biology and evolution.

[100]  Dirk Steinke,et al.  DNA barcoding for the identification of smoked fish products , 2008 .

[101]  C. Baker,et al.  A SIBLING SPECIES OF SEA CUCUMBER DISCOVERED BY STARCH GEL ELECTROPHORESIS. , 1963, Comparative biochemistry and physiology.

[102]  A. Hoffmann,et al.  DNA identification of urban Tanytarsini chironomids (Diptera:Chironomidae) , 2007, Journal of the North American Benthological Society.

[103]  R. Ward,et al.  An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes , 2007 .

[104]  Natalia Ivanova,et al.  Universal primer cocktails for fish DNA barcoding , 2007 .

[105]  B. Victor Redescription of Coryphopterus tortugae (Jordan) and a new allied species Coryphopterus bol (Perciformes: Gobiidae: Gobiinae) from the tropical western Atlantic Ocean , 2008 .

[106]  J. Graves,et al.  Specific identification of western Atlantic Ocean scombrids using mitochondrial DNA cytochrome C oxidase subunit I (COI) gene region sequences , 2007 .

[107]  S. France,et al.  DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa) , 2002, Hydrobiologia.

[108]  E. Willassen,et al.  A comprehensive DNA sequence library is essential for identification with DNA barcodes. , 2007, Molecular phylogenetics and evolution.