The actinopterygian diversity of the CEAMARC cruises: Barcoding and molecular taxonomy as a multi-level tool for new findings

Deep-Sea Research Part II: Topical Studies in Oceanography

Volumn 58, Issue 1-2, 2011, Pages 250-263

  Dettai, A ^a   Lautredou, A C ^a   Bonillo, C ^a   Goimbault, E ^a   Busson, F ^a   Causse, R ^a   Couloux, A ^b   Cruaud, C ^b   Duhamel, G ^a   Denys, G ^a   Hautecoeur, M ^a   Iglesias, S ^a   Koubbi, P ^c   Lecointre, G ^a   Moteki, M ^d   Pruvost, P ^a   Tercerie, S ^a   Ozouf, C ^a  

^a MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^c SORBONNE UNIVERSITÉ   (France)

^d TOKYO UNIVERSITY OF MARINE SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Antarctic zone; Barcode; Dumont d'Urville Sea; Ichthyology; Identification; Molecular taxonomy; Southern Ocean

Indexed keywords

ANTARCTIC ZONE; DUMONT D'URVILLE SEA; ICHTHYOLOGY; IDENTIFICATION; MOLECULAR TAXONOMY; SOUTHERN OCEAN;

BAR CODES; GENES;

TAXONOMIES;

CONTINENTAL SHELF; DATA SET; DATABASE; DIVERGENCE; GEOGRAPHICAL DISTRIBUTION; ICHTHYOFAUNA; IDENTIFICATION KEY; MOLECULAR ANALYSIS; MORPHOLOGY; SAMPLING; SPECIES DIVERSITY; TAXONOMY; TELEOST; TYPE SPECIMEN;

ADELIE COAST; ANTARCTICA; DUMONT D'URVILLE SEA; EAST ANTARCTICA; SOUTHERN OCEAN;

ARTEDIDRACONIDAE; CHANNICHTHYIDAE; CHIONODRACO; TELEOSTEI; TREMATOMUS; ZOARCIDAE;

EID: 79851491700     PISSN: 09670645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dsr2.2010.05.021     Document Type: Article

References (58)

1. Aronson R.B., Moody R.M., Ivany L.C., Blake D.B., Werner J.E., Glass A. Climate change and trophic response of the Antarctic bottom fauna. PLoS One 2009, 4(2):e4385.
2. Balushkin A.V., Eakin R.R. A new toad plunderfish Pogonophryne fusca sp. nova (Fam. Artedidraconidae: Notothenioidei) with notes on species composition and species groups in the genus /Pogonophryne/Regan. Journal of Ichthyology 1998, 38:574-579.
3. Bely A., Weisblat D.A. Lessons from leeches: a call for DNA barcoding in the lab. Evolution and Development 2006, 8:491-501.
4. Bortolus A. Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology. Ambio 2008, 37:114-118.
5. Buhay J.E. "COI-like" sequences are becoming problematic in molecular systematic and DNA barcoding studies. Journal of Crustacean Biology 2009, 29:96-110.
6. Clarke A., Barnes D.K.A., Hodgson D.A. How isolated is Antarctica?. Trends in Ecology and Evolution 2005, 20:1-3.
7. DeSalle R., Egan M.G., Siddall M. The unholy trinity: taxonomy, species delimitation, and DNA barcoding. Philosophical Transaction of the Royal Society of London B Biological Science 2005, 360:1905-1916.
8. DeSalle R. Species discovery versus species identification in DNA barcoding efforts: Response to Rubinoff. Conservation Biology 2006, 20:1545-1547.
9. Dettai A., Lecointre G. In search of the Notothenioid relatives. Antarctic Science 2004, 16:71-85.
10. Eakin R.R. Artedidraconidae. Fishes of the Southern Ocean 1990, 332-356. J.L.B. Smith Institute of Ichthyology, Grahamstown, South Africa. O. Gon, P.C. Heemstra (Eds.).
11. Eakin R.R., Eastman J.T. New species of Pogonophryne (Pisces, Artedidraconidae) from the Ross Sea, Antarctica. Copeia 1998, 1998:1005-1009.
12. Eakin R.R., Eastman J.T., Jones C.D. Mental barbel variation in Pogonophryne scotti Regan (Pisces: Perciformes: Artedidraconidae). Antarctic Science 2001, 13:363-370.
13. Eastman J.T. Antarctic Fish Biology: Evolution in a Unique Environment 1993, Academic Press, San Diego, 322pp.
14. Eastman J.T., Clarke A. Radiations of Antarctic and non-Antarctic fish. Fishes of Antarctica: A Biological Overview 1998, 3-26. Springer Verlag, Milan. G. Di Prisco, E. Pisano, A. Clarke (Eds.).
15. Eastman J.T., Eakin R.R. An updated species list for notothenioid fish (Perciformes; Notothenioidei), with comments on Antarctic species. Archive of Fishery and Marine Research 2000, 48:11-20.
16. Eastman J.T., Eakin R.R. Fishes of the genus Artedidraco (Pisces, Artedidraconidae) from the Ross Sea, Antarctica, with the description of a new species and a colour morph. Antarctic Science 1999, 11:13-22.
17. Ekrem T., Willassen E., Stur E. A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetic and Evolution 2007, 43:530-542.
18. Eschmeyer, W.N., Fricke, R. (Eds.), 2009. Catalog of Fishes electronic version (9 September 2009). http://research.calacademy.org/ichthyology/catalog/fishcatmain.asp.
19. Formalin Workshop Summary, 2006. Path to effective recovering of DNA from formalin fixed biological samples in natural history collections. In: Tang, E.P.Y. (Ed.), The National Academies Press, http://www.nap.edu/openbook.php?record_id=11712.
20. Froese, R., Pauly, D. (Eds.), 2009. FishBase. World Wide Web electronic publication, version (10/2009). http://www.fishbase.org.
21. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Research Symposium Series 1999, 41:95-98.
22. Harris D.J. Can you bank on GenBank?. Trends in Ecology and Evolution 2003, 18:317-319.
23. Hebert P.D.N., Ratnasingham S., deWaard J.R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Philosophical Transactions of the Royal Society of London B Biological Science 2003, 270(suppl):S96-S99.
24. Hickerson M.J., Meyer C.P., Moritz C. DNA barcoding will often fail to discover new animal species over broad parameter space. Systematic Biology 2006, 55:729-739.
25. Hureau, J.-C., 1966. Biologie comparée de quelques Poissons antarctiques (Nototheniidae). Thèse, Muséum national d'Histoire naturelle, 1391p.
26. Johnson G.D., Paxton J.R., Sutton T.T., Satoh T.P., Sado T., Nishida M., Miya M. Deep-sea mystery solved: astonishing larval transformations and extreme sexual dimorphism unite three fish families. Biology Letters 2009, 5:235-239.
27. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 1980, 16:111-120.
28. Knudsen S.W., Møller P.R., Gravlund P. Phylogeny of the snailfishes (Teleostei: Liparidae) based on molecular and morphological data. Molecular Phylogenetics and Evolution 2007, 44:649-666.
29. Kon T., Yoshino T., Mukai T., Nishida M. DNA sequences identify numerous cryptic species of the vertebrate: a lesson from the gobioid fish Schindleria. Molecular Phylogenetics and Evolution 2007, 44:53-62.
30. Koubbi P., Duhamel G., Heck J.-H., Beans C., Loots C., Pruvost P., Tavernier E., Vacchi M., Vallet C. Ichthyoplankton in the neritic and coastal zone of Antarctica and Subantarctic islands: a review. Journal of Marine Systems 2009, 78:547-556.
31. Kuhn K.L., Near T.J. Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences. Antarctic Science 2009, 21:565-570.
32. Lautredou, A.-C., Bonillo, C., Denys, G., Cruaud, C., Ozouf-Costaz, C., Lecointre, G., Dettai, A., in press. Molecular taxonomy and identification within the Antarctic genus Trematomus (Notothenioidei, Teleostei): How valuable is barcoding with COI? Polar Science.
33. Leclerc M.C., Barriel V., Lecointre G., De Reviers B. Low divergence in rDNA ITS sequences among five species of Fucus (Phaeophyta) suggests a very recent radiation. Journal of Molecular Evolution 1998, 46:115-120.
34. Lockley A., Bardsley R. DNA-based methods for food authentication. Trends in Food Science Technology 2000, 11:67-77.
35. Meier R., Zhang G., Ali F. The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Systematic Biology 2008, 57:809-813.
36. Meyer C.P., Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 2005, 3(12):e422.
37. Moore S. Fluid preservation. Care and Conservation of Natural History Collections 1999, 92-132. Butterworth Heinemann, Oxford. D. Carter, A.K. Walker (Eds.).
38. Mueller R.L. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in bayesian phylogenetic analysis. Systematic Biology 2006, 55:289-300.
39. Naish T., Powell R., Levy R., Wilson G., Scherer R., Talarico F., Krissek L., Niessen F., Pompilio M., Wilson T., Carter L., DeConto R., Huybers P., McKay R., Pollard D., Ross J., Winter D., Barrett P., Browne G., Cody R., Cowan E., Crampton J., Dunbar G., Dunbar N., Florindo F., Gebhardt C., Graham I., Hannah M., Hansaraj D., Harwood D., Helling D., Henrys S., Hinnov L., Kuhn G., Kyle P., Läufer A., Maffioli P., Magens D., Mandernack K., McIntosh W., Millan C., Morin R., Ohneiser C., Paulsen T., Persico D., Raine I., Reed J., Riesselman C., Sagnotti L., Schmitt D., Sjunneskog C., Strong P., Taviani M., Vogel S., Wilch T., Williams T. Obliquity-paced Pliocene West Antarctic ice sheet oscillations. Nature 2009, 458:322-328.
40. Near T.J., Cheng C.H. Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences. Molecular Phylogenetics and Evolution 2008, 47:832-840.
41. North, A.W., Kellermann, A., 1990. Identification key and catalogue of larval antarctic fish. In: Kellermann, A. (Ed.), Ber. Polarforsch. 67. and BIOMASS Scientific Series 10.
42. Orti G., Meyer A. The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences. Systematic Biology 1997, 46:75-100.
43. Ozouf-Costaz C., Hureau J.C., Beaunier M. Chromosome studies on fish of the suborder Notothenioidei collected in the Weddell Sea during EPOS 3 cruise. Cybium 1991, 15(4):275-290.
44. Pisano E., Ozouf-Costaz C. Cytogenetics and evolution in extreme environment: the case of Antarctic fishes. Fish Adaptation 2002, 311-338. Oxford IBH Publishing, New Delhi. A. Val, G. Kapoor (Eds.).
45. Ratnasingham S., Hebert P.D.N. BOLD: the barcode of life data system. Molecular Ecology Notes 2007, 7:355-364.
46. Rock J., Costa F.O., Walker D.I., North A.W., Hutchinson W.F., Carvalho G.R. DNA barcodes of fish of the Scotia Sea, Antarctica indicate priority groups for taxonomic and systematics focus. Antarctic Science 2008, 20:253-262.
47. Rubinoff D., Cameron S., Will K. A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. Journal of Heredity 2006, 97:581-594.
48. Steig E.J., Schneider D.P., Rutherford S.D., Mann M.E., Comiso J.C., Shindell D.T. Warming of the Antarctic ice-sheet surface since the 1957 International Geophysical Year. Nature 2009, 457:459-462.
49. Steinke D., Zemlak T.S., Boutillier J.A., Hebert P.D.N. DNA barcoding of Pacific Canada's fishes. Marine Biology 2009, 156:2641-2647.
50. Swofford D. PAUP. Phylogenetic Analysis Using Parsimony (and other Methods), Version 4.0b10 2002, Sinauer Associates, Sunderland, MA.
51. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 2007, 24:1596-1599.
52. Thatje S. The future fate of the Antarctic marine biota?. Trends in Ecology and Evolution 2005, 20:418-419.
53. Van de Putte A.P., Van Houdt J.K.J., Maes G.E., Janko K., Koubbi P., Rock J., Volckaert F.A.M. Species identification in the trematomid family using nuclear genetic markers. Polar Biology 2009, 32:1731-1741.
54. Ward R.D., Zemlak T.S., Innes B.H., Last P.R., Hebert P.D. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London B Biological Science 2005, 360:1847-1857.
55. Ward R.D., Hanner R., Hebert P.D. The campaign to DNA barcode all fishes. FISH-BOL. Journal of Fisheries Biology 2009, 74:329-356.
56. Winnepenninckx B., Backeljau T., De Wachter R. Extraction of high molecular weight DNA from molluscs. Trends in Genetics 1993, 9(1993):407.
57. Wong H.K., Hanner R.H. DNA barcoding detects market substitution in North American seafood. Food Research International 2008, 41:828-837.
58. Zemlak T.S., Ward R.D., Connell A.D., Holmes B.H., Hebert P.D. DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources 2009, 9(Suppl. 1):237-242.