DNA barcoding and molecular systematics of the benthic and demersal organisms of the CEAMARC survey

Polar Science

Volumn 5, Issue 2, 2011, Pages 298-312

  Dettai, Agnes ^a   Adamowizc, Sarah J ^b   Allcock, Louise ^c,d   Arango, Claudia P ^e   Barnes, David K A ^f   Barratt, Iain ^d   Chenuil, Anne ^g   Couloux, Arnaud ^h   Cruaud, Corinne ^h   David, Bruno ⁱ   Denis, Françoise ^j   Denys, Gael ^a   Díaz, Angie ^k   Eléaume, Marc ^a   Féral, Jean Pierre ^g   Froger, Aurélie ^a   Gallut, Cyril ^a   Grant, Rachel ^l   Griffiths, Huw J ^f   Held, Christoph ^m   Hemery, Lenaïg G ^a   Hosie, Graham ⁿ   Kuklinski, Piotr ^o,p   Lecointre, Guillaume ^a   Linse, Katrin ^f   Lozouet, Pierre ^a   Mah, Christopher ^q   Monniot, Françoise ^a   Norman, Mark D ^r   O'Hara, Timothy ^r   Ozouf Costaz, Catherine ^a   Piedallu, Claire ^a   Pierrat, Benjamin ⁱ   Poulin, Elie ^k   Puillandre, Nicolas ^a   Riddle, Martin ⁿ   Samadi, Sarah ^a   Saucède, Thomas ⁱ   Schubart, Christoph ^s   Smith, Peter J ^t   Stevens, Darren W ^t   Steinke, Dirk ^b   Strugnell, Jan M ^u   Tarnowska, K ^g   Wadley, Victoria ⁿ   Ameziane, Nadia ^a   more..

^a MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^b UNIVERSITY OF GUELPH   (Canada)

^c NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^d QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^e QUEENSLAND MUSEUM   (Australia)

^f BRITISH ANTARCTIC SURVEY   (United Kingdom)

^g AIX MARSEILLE UNIVERSITY   (France)

^h CENTRE NATIONAL DE SÉQUENÇAGE   (France)

ⁱ UNIVERSITÉ DE BOURGOGNE   (France)

^j UNIVERSITÉ DU MAINE   (France)

^k UNIVERSITY OF CHILE   (Chile)

^l UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^m ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

ⁿ AUSTRALIAN ANTARCTIC DIVISION   (Australia)

^o DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^p INSTITUTE OF OCEANOLOGY   (Poland)

^q DEPARTMENT OF PALEOBIOLOGY   (United States)

^r MUSEUM VICTORIA   (Australia)

^s UNIVERSITY OF REGENSBURG   (Germany)

^t NATIONAL INSTITUTE OF WATER AND ATMOSPHERIC RESEARCH   (New Zealand)

^u UNIVERSITY OF CAMBRIDGE   (United Kingdom)

more..

Author keywords

Barcode; CEAMARC; Cytochrome oxidase 1; Systematics; Taxonomy

Indexed keywords

BENTHOS; CEPHALOPOD; CYTOCHROME; DEMERSAL FISH; DIVERGENCE; ECHINODERM; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; MORPHOLOGY; NEW SPECIES; PHYLOGENETICS; PHYLOGEOGRAPHY; RESEARCH VESSEL; TAXONOMY; TELEOST;

ANTARCTIC PENINSULA; ANTARCTICA; DUMONT D'URVILLE SEA; ROSS SEA; SOUTHERN OCEAN; WEST ANTARCTICA;

CEPHALOPODA; ECHINOIDEA; PELMATOZOA; PYCNOGONIDA; RICE STRIPE VIRUS; TELEOSTEI;

EID: 79960657575     PISSN: 18739652     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.polar.2011.02.002     Document Type: Article

References (84)

1. Allcock A.L., Brierley A.S., Thorpe J.P., Rodhouse P.G. Restricted gene flow and evolutionary divergence between geographically separated populations of the Antarctic octopus Pareledone turqueti. Marine Biology 1997, 129:97-102.
2. Allcock A.L., Barratt I., Eléaume M., Linse K., Norman M.D., Smith P.J., Steinke D., Stevens D.W., Strugnell J.M. Cryptic speciation and the circumpolarity debate: a case study on endemic Southern Ocean octopuses using the COI barcode of life. Deep-sea Research II 2010, 10.1016/j.dsr2.2010.05.016.
3. Allcock A.L., Piatkowski U., Rodhouse P.G.K., Thorpe J.P. A study on octopodids from the Eastern Weddell Sea, Antarctica. Polar Biology 2001, 24:832-838.
4. Arango C.P., Soler Membrives A., Miller K.J. Genetic differentiation in the circum-antarctic sea spider Nymphon australe (Pycnogonida; Nymphonidae). Deep Sea Research II 2010, 10.1016/j.dsr2.2010.05.019.
5. Arnaud P.M. Contribution à la bionomie marine benthique des régions antarctiques et subantarctiques. Thétys 1974, 6(3):465-656.
6. 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.
7. Barratt I.M., Johnson M.P., Collins M.A., Allcock A.L. Female reproductive biology of two sympatric incirrate octopod species, Adelieledone polymorpha (Robson 1930) and Pareledone turqueti (Joubin 1905) (Cephalopoda: Octopodidae), from South Georgia. Polar Biology 2008, 31:583-594.
8. Beaman R.J., Harris P.T. Bioregionalisation of the George V shelf, East antarctica. Continental Shelf Research 2005, 25:1657-1691.
9. Beaman, R.J., O'Brien, P., 2009. Collaborative East antarctic marine census (CEAMARC): Post-survey Report, RSV Aurora Australis voyage 3, December 2007 - January 2008. Geoscience Australia record 2008/05, 61 pp.
10. Bely A., Weisblat D.A. Lessons from leeches: a call for DNA barcoding in the lab. Evolution and Development 2006, 8:491-501.
11. Bickford D., Lohman D.J., Sodhi N.S., Ng P.K.L., Meier R., Winker K., Ingram K.K., Das I. Cryptic species as a window on diversity and conservation. TRENDS in Ecology and Evolution 2007, 22(3):148-155.
12. Bortolus A. Error cascades in the biological Sciences: the unwanted consequences of using bad taxonomy in ecology. Ambio 2008, 37(2):114-118.
13. Bucklin A., Wiebe P.H., Smolenack S.B., Copley N.J., Beaudet J.G., Bonner K.G., Farber Lorda J., Pierson J.J. DNA barcodes for species identification of euphausiids (Euphausiacea, Crustacea). Journal of Plankton Research 2007, 29:483-493.
14. Bucklin A., Hopcroft R.R., Kosobokova K.S., Nigro L.M., Ortman B.D., Jennings R.M., Sweetman C.J. DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition. Deep-Sea Research II 2010, 57:40-48.
15. Bucklin A., Steinke D., Blanco-Bercial L. DNA barcoding of marine Metazoa. Annual Review of Marine Science 2011, 3:18.11-18.38.
16. Buhay J.E. " COI-like" sequences are becoming problematic in molecular systematic and DNA barcoding studies. Journal of Crustacean Biology 2009, 29(1):96-110.
17. Causse, R., Ozouf-Costaz, C., Koubbi, P., Lamy, D., Eléaume, M., Dettai, A., Duhamel, G., Busson, F., Pruvost, P., Post, A., Beaman, R. J., Riddle, M.J. Demersal ichtyofauna from the Dumont d'Urville Sea (East antarctica) during the CEAMARC surveys in 2007-2008. CEAMARC special issue of polar Science, submitted for publication.
18. Chenuil A., Egea E., Rocher C., Féral J.-P. Comparing Substitution Rates in Spatangoid Sea Urchins with Putatively Different Effective Sizes, and Other Echinoderm Datasets. Proceedings of the 12th International Echinoderm Conference 2009, P159-P161. Balkema.
19. Chenuil A., Hoareau T.B., Egea E., Penant G., Rocher C., Aurelle D., Mokhtar-Jamai K., Bishop J.D.D., Boissin E., Diaz A., Krakau M., Luttikhuizen P.C., Patti F.P., Blavet N., Mousset S. An efficient method to find potentially universal population genetic markers, applied to metazoans. BMC Evolutionary Biology 2010, 10:276.
20. Clarke A., Barnes D.K.A., Hodgson D.A. How isolated is Antarctica?. Trends in Ecology and Evolution 2005, 20:1-3.
21. Clarke A., Griffiths H.J., Barnes D.K.A., Meredith M.P., Grant S.M. Spatial variation in seabed temperatures in the Southern Ocean: implications for benthic ecology and biogeography. Journal of Geophysical Research 2009, 114:G03000.
22. Collins M.A., Allcock A.L., Belchier M. Cephalopods of the South Georgia slope. Journal of the Marine Biological Association of the United Kingdom 2004, 84:415-419.
23. David B., Choné T., Mooi R., De Ridder C. Antarctic echinoidea. Synopses of the Antarctic Benthos 2005, Vol. 10:274. Koeltz Scientific Books, Königstein.
24. SCAR-MarBIN: The Antarctic Marine Biodiversity Information Network World Wide Web Electronic Publication. 2009, Available online at. http://www.scarmarbin.be/, C. De Broyer, B. Danis (Eds.).
25. Dettai A., Lautredou A.-C., Bonillo C., Goimbault E., Busson F., Causse R., Couloux A., Cruaud C., Duhamel G., Denys G., Hautecoeur M., Iglesias S., Koubbi P., Lecointre G., Moteki M., Pruvost P., Tercerie S., Ozouf C. The actinopterygian diversity of the CEAMARC cruises: barcoding and molecular taxonomy as a multi level tool for new findings. Deep Sea Research II 2010, 10.1016/j.dsr2.2010.05.021.
26. Diaz A., Féral J.-P., David B., Saucède T., Poulin E. Evolutionary pathways among shallow and deep sea echinoids of the genus Sterechinus in the Southern Ocean. Deep Sea Research II 2010, 10.1016/j.dsr2.2010.10.012.
27. Doyle J.J. Gene trees and species trees: molecular systematics as one-character taxomony. Systematic Botany 1992, 17:144-163.
28. Duhamel G., Hautecoeur M., Dettai A., Causse R., Pruvost P., Busson F., Couloux A., Koubbi P., Williams R., Ozouf-Costaz C., Nowara G. Liparids from the Eastern sector of Southern Ocean and first information from molecular studies. Cybium 2010, 34:319-343.
29. Eastman J.T., McCune A.R. Fishes on the Antarctic continental shelf: evolution of a marine species flock?. Journal of Fish Biology 2000, 57(suppl. A):84-102.
30. Ekrem T., Willassen E., Stur E. A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution 2007, 43:530-542.
31. Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 1994, 3:294-299.
32. Galtier N., Nabholtz B., Glémin S., Hurst G.D.D. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 2009, 18:4541-4550.
33. González Wevar C.A., Nakano T., Cañete J.I., Poulin E. Molecular phylogeny and historical biogeography of Nacella (Patellogastropoda: Nacellidae) in the Southern ocean. Molecular Phylogenetics and Evolution 2010, 56:115-124.
34. González-Wevar C.A., David B., Poulin E. Phylogeography and demographic inference in Nacella (Patinigera) concinna (Strebel, 1908) in the western antarctic Peninsula. Deep Sea research II 2010, 10.1016/j.dsr2.2010.05.026.
35. Grant R.A., Linse K. Barcoding Antarctic biodiversity; current status and the CAML initiative, a case study of marine invertebrates. Polar Biology 2009, 32(11):1629-1637.
36. Grant R.A., Griffiths H., Steinke D., Wadley V., Linse K. Antarctic DNA barcoding; a drop in the ocean?. Polar Biology 2010, 10.1007/s00300-010-0932-7.
37. Hajibabaei M., deWaard J.R., Ivanova N.V., Ratnasingham S., Dooh R.T., Kirk S.L., Mackie P.M., Hebert P.D. Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society London B: Biological Sciences. 2005, 360(1462):1959-1967.
38. Harris D.J. Can you bank on GenBank?. Trends in Ecology and Evolution 2003, 18:317-319.
39. Hayward P.J. The Antarctic Cheilostomatous Bryozoa 1995, Oxford University Press.
40. 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.
41. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., Francis C.M. Identification of birds through DNA barcodes. PLoS Biology 2004, 2:e312.
42. Hoareau T.B., Boissin E. Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata. Molecular Ecology Ressources 2010, 10(6):960-967.
43. Hunt B., Strugnell J., Bednarsek N., Linse K.R., Nelson J., Pakhomov E., Seibel B., Steinke D., Würzberg L. Poles apart: the ''bipolar'' pteropod species Limacina helicina is genetically distinct between the Arctic and Antarctic oceans. PloS ONE 2010, 5(3):e9835.
44. Hunter R.L., Halanych K.M. Evaluating connectivity in the brooding brittle star Astrotoma agassizii across the drake passage in the southern ocean. Journal of Heredity 2008, 99:137-148.
45. Irwin D.E., Bensch S., Irwin J.H., Price T.D. Speciation by distance in a ring species. Science 2005, 307:414-416.
46. Ivanova N.V., Dewaard J.R., Hebert P.D.N. An inexpensive, automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes 2006, M6:998-1002.
47. Koubbi P., Ozouf-Costaz C., Hureau J.-C., Lecointre G., Pisano E., Vacchi M., Razouls S., White M., Le Guilloux E. Le sous-ordre des Notothenioidei (Ostéichthyens, Perciformes), modèle unique de radiation adaptative en milieu isolé 2001, /Rapport d'activité 2000/, Campagne d'été 2000-20016 fig, Institut Français pour la Recherche et la Technologie Polaires, 64-70.
48. Koubbi P., Ozouf-Costaz C., Hosie G. L'ichtyofaune de la mer de Dumont D'Urville: apports du Census of Antarctic Marine Life au programme d'Ichtyologie Côtière en Terre Adélie (ICOTA) 2009, IPEV, Rapport d'activité 2008. Campagnes D'été 2008-2009: 44-45.
49. Koubbi P., Ozouf-Costaz C., Moteki M., Goarant A., Hulley P.A., Dettai A., Duhamel G., Pruvost P., Causse R., Tavernier E., Post A., Beaman R.J., Rintoul S., Hirawake T., Hirano D., Ishimaru T., Riddle M., Hosie G. Estimating the biodiversity of the East Antarctic shelf and oceanic zone for ecoregionalisation: example of the ichthyofauna of the CEAMARC (Collaborative East Antarctic Marine Census) CAML surveys. Polar Science 2010, 4(2):115-133.
50. Krabbe K., Leese F., Mayer C., Tollrian R., Held C. Cryptic mitochondrial lineages in the widespread pycnogonid Colossendeis megalonyx Hoek, 1881 from Antarctic and Subantarctic waters. Polar Biology 2010, 33(3):281-292.
51. Lautredou A.-C., Bonillo C., Denys G., Cruaud C., Lecointre G., Dettai A. Molecular taxonomy and identification of genus Trematomus (Notothenioidei, Teleostei): how good is barcoding with COI?. Polar Science 2010, 4(2):333-352.
52. Lecointre, G., Gallut, C., Bonillo, C., Couloux, A., Ozouf-Costaz, C., Dettai, A. The antarctic fish genus Artedidraco is paraphyletic (Teleostei, Notothenioidei, Artedidraconidae). Polar Biology, in press.
53. Lee Y., Song M., Lee S., Leon R., Godoy S., Cañete I. Molecular phylogeny and divergence time of the Antarctic sea urchin (Sterechinus neumayeri) in relation to the South American sea urchins. Antarctic Science 2004, 1:29-36.
54. Leese F., Held C. Identification and characterization of microsatellites from the Antarctic isopod Ceratoserolis trilobitoides - nuclear evidence for cryptic species. Conservation Genetics 2008, 9:1369-1372.
55. Linse K., Cope T., Lorz A.N., Sands C. Is the Scotia Sea a centre of Antarctic marine diversification? Some evidence of cryptic speciation in the circum-Antarctic bivalve Lissarca notorcadensis (Arcoidea: Philobryidae). Polar Biology 2007, 30:1059-1068.
56. Lockhart, S.J., 2006. Molecular evolution, phylogenetics and parasitism and in antarctic cidaroid echinoids. PhD Thesis. University of California (Santa Cruz).
57. Maddison M.P. Gene trees in species trees. Systematic Biology 1997, 46:523-536.
58. Madon, C., 1998. Disparité morphologique et architecturale des Schizasteridae incubants (Echinoidea, Spatangoida) des régions australes = Morphological and architectural disparity of brooding Schizasterids (Echinoidea, Spatangoida) from south polar regions. PhD, Université de Dijon.
59. Mahon A.R., Arango C.P., Halanych K.M. Genetic diversity of Nymphon (Arthropoda: Pycnogonida: Nymphonidae) along the Antarctic Peninsula with a focus on Nymphon australe Hodgson 1902. Marine Biology 2008, 155:315-323.
60. Monniot, F., Dettai, A., Eleaume, M., Cruaud, C., Ameziane, N. Antarctic ascidians (Tunicata) of the French-Australian survey CEAMARC in Terre Adélie. Zootaxa, in press.
61. Moore S. Fluid Preservation. Care and Conservation of Natural History Collections 1999, 92-132. Butterworth Heinemann, Oxford. D. Carter, A.K. Walker (Eds.).
62. 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(2):832-840.
63. Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.-H., Koljalg U. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PloS ONE 2006, 1:e59.
64. Padial J.M., Miralles A., De la Riva I., Vences M. The integrative future of taxonomy. Frontiers in Zoology 2010, 25(7):16.
65. Palero F., Hall S., Clark P.F., Johnston D., Mackenzie-Dodds J., Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina 2010, 74(3):465-470.
66. Pearse J.S., Mooi R., Lockhart S.J., Brandt A. Brooding and species diversity in the southern ocean: selection for brooders or speciation within brooding clades?. Smithsonian at the Poles: Contributions to International Polar Year Science 2009, 181-196. I.A. Krupnik, M.A. Lang, S.E. Miller (Eds.).
67. Post A.L., Beaman R.J., O'Brien P.E., Eléaume M., Riddle M.J. Community structure and benthic habitats across the George V shelf, East Antarctica: trends through space and time. Deep Sea Res. II 2010, 10.1016/j.dsr2.2010.05.020.
68. Puillandre N., Strong E.E., Bouchet P., Boisselier M.-C., Couloux A., Samadi S. Identifying gastropod spawn from DNA barcodes: possible but not yet practicable. Molecular Ecology Ressources 2009, 9(5):1311-1321.
69. Ratnasingham S., Hebert P.D.N. BOLD: the barcode of life data system. Molecular Ecology Notes 2007, 7:355-364.
70. Smith P.J., Steinke D., Mcveagh S.M., Stewart A.L., Struthers C.D., Roberts C.D. Molecular analysis of Southern Ocean skates (Bathyraja) reveals a new species of Antarctic skate. Journal of Fish Biology 2008, 73:1170-1182.
71. Stefaniak L.M., Lambert G., Gittenberger A., Zhang H., Lin S., Whitlatch R.B. Genetic conspecificity of the worldwide populations of Didemnum vexillum Kott, 2002. Aquatic Invasions 2009, 4(1):29-44.
72. 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.
73. Strugnell J.M., Cherel I., Cooke I.R., Gleadall I.G., Hochberg F.G., Ibáñez C.M., Jorgensen E., Laptikhovsky V.V., Linse K., Norman M., Vecchione M., Voight J.R., Allcock A.L. The Southern Ocean: source and sink?. Deep Sea Research II 2010, 10.1016/j.dsr2.2010.05.015.
74. Teletchea F. Molecular identification methods of fish species: reassessment and possible applications. Reviews in Fish Biology and Fisheries 2009, 19(3):265-293.
75. Thatje S. The future fate of the Antarctic marine biota?. Trends in Ecology and Evolution 2005, 20:418-419.
76. Undheim E.A.B., Norman J.A., Thoen H.H., Fry B.G. Genetic identification of southern ocean octopod samples using mtCOI. Comptes Rendus Biologies 2010, 333:395-404.
77. Valdez-Moreno M., Vasquez-Yeomans L., Elias-Gutierrez M., Ivanova N.V., Hebert P.D.N. Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula, Mexico: potential in fisheries management. Marine and Freshwater Research 2010, 61(6):665-671.
78. Valentini A., Pompanon F., Taberlet P. DNA barcoding for ecologists. Trends in Ecology and Evolution 2009, 24(2):110-117.
79. 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.
80. Ward R.D., Bronwyn H.H., O'Hara T.D. DNA barcoding discriminates echinoderm species. Molecular Ecology Resources 2008, 8:1202-1211.
81. Ward R.D., Hanner R., Hebert P.D. The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 2009, 74:329-356.
82. Webb K.E., Barnes D.K.A., Clark M.S., Bowden D.A. DNA barcoding: a molecular tool to identify Antarctic marine larvae. Deep Sea Research II 2006, 53:1053-1060.
83. Wilson N.G., Belcher R.L., Lockhart S.J., Halanych K.M. Multiple lineages and an absence of panmixia in the 'circumpolar' crinoid Promachocrinus kerguelensis in the Atlantic sector of Antarctica. Marine Biology 2007, 152(4):895-904.
84. Zhang J. Exploiting formalin-preserved fish specimens for resources of DNA barcoding. Molecular Ecology Resources 2010, 10:935-941.