Evaluation of ITS2-28S as a molecular marker for identification of calanoid copepods in the subtropical western North Pacific

Journal of Plankton Research

Volumn 35, Issue 3, 2013, Pages 644-656

  Hirai, Junya ^a   Shimode, Shinji ^b   Tsuda, Atsushi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b YOKOHAMA NATIONAL UNIVERSITY   (Japan)

Author keywords

calanoid copepods; DNA barcoding; ribosomal DNA; subtropical ocean

Indexed keywords

BIOMARKER; BODY SIZE; CRUSTACEAN; GENETIC ANALYSIS; GENETIC VARIATION; IDENTIFICATION KEY; MORPHOLOGY; PHYLOGENETICS;

PACIFIC OCEAN; PACIFIC OCEAN (NORTH);

EID: 84877264874     PISSN: 01427873     EISSN: 14643774     Source Type: Journal    
DOI: 10.1093/plankt/fbt016     Document Type: Article

References (54)

1. Adamowicz, S. J., Menu-Marque, S., Halse, S. A. et al. (2010) The evolutionary diversification of the Centropagidae (Crustacea, Calanoida): a history of habitat shifts. Mol. Phylogenet. Evol., 55, 418-430.
2. Andronov, V. N. (2001) On the taxonomy of the genus Nannocalanus Stars, 1925 (Crustacea, Copepoda: Calanidae). Zoosystematica Rossica, 9, 277-283.
3. Avise, J. C., Arnold, J., Ball, R. M. et al. (1987) Intraspecific phylogeo-graphy: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst., 18, 489-522.
4. Birky, C. W., Fuerst, P. and Maruyama, T. (1989) Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics, 121, 613-627.
5. Blanco-Bercial, L. and Alvarez-Marqués, F. (2007) RFLP procedure to discriminate between Clausocalanus Giesbrecht, 1888 (Copepoda, Calanoida) species in the Central Cantabrian Sea. J. Exp. Mar. Biol. Ecol., 344, 73-77.
6. Blanco-Bercial, L., Bradford-Grieve, J. and Bucklin, A. (2011) Molecular phylogeny of the Calanoida (Crustacea: Copepoda). Mol. Phylogenet. Evol., 59, 103-113.
7. Böttger-Schnack, R. and Machida, R. J. (2010) Comparison of morphological and molecular traits for species identification and taxonomic grouping of oncaeid copepods. Hydrobiologia, 666, 111-125.
8. Braga, E., Zardoya, R., Meyer, A. et al. (1999) Mitochondrial and nuclear rRNA based copepod phylogeny with emphasis on the Euchaetidae (Calanoida). Mar. Biol., 133, 79-90.
9. Bucklin, A. (2000) Methods for population genetic analysis of zoo-plankton. In Harris, R. P., Wiebe, P. H., Lenz, J. et al. (eds), ICES Zooplankton Methodology Manual. Academic Press, London, pp. 533-570.
10. Bucklin, A., Frost, B. W., Bradford-Grieve, J. et al. (2003) Molecular systematics and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae. Mar. Biol., 142, 333-343.
11. Bucklin, A., Frost, B. W. and Kocher, T. D. (1995) Molecular systema-tics of six Calanus and three Metridia species (Calanoida: Copepoda). Mar. Biol., 121, 655-664.
12. Bucklin, A., LaJeunesse, T. C., Curry, E. et al. (1996) Molecular diversity of the copepod, Nannocalanus minor: genetic evidence of species and population structure in the North Atlantic Ocean. J. Mar. Res., 54, 285-310.
13. Cepeda, G. D., Blanco-Bercial, L., Bucklin, A. et al. (2012) Molecular systematic of three species of Oithona (Copepoda, Cyclopoida) from the Atlantic Ocean: comparative analysis using 28S rDNA. Plos. One, 7, e35861.
14. Chihara, M. and Murano, M. (1997) An Illustrated Guide to Marine Plankton in Japan. Tokai University Press, Tokyo.
15. Dippenaar, S. M., Mathibela, R. B. and Bloomer, P. (2010) Cytochrome oxidase I sequences reveal possible cryptic diversity in the cosmopolitan symbiotic copepod Nesippus orientalis Heller, 1868 (Pandaridae: Siphonostomatoida) on elasmobranch hosts from the KwaZulu-Natal coast of South Africa. Exp. Parasitol., 125, 42-52.
16. Drummond, A. J., Ashton, B., Buxton, S. et al. (2010) Geneious v5.3. http://www.geneious.com./.
17. Elder, J. F. and Turner, B. J. (1995) Concerted evolution of repetitive DNA sequences in eukaryotes. Q. Rev. Biol., 70, 297-320.
18. Goetze, E. (2003) Cryptic speciation on the high seas; global phyloge-netics of the copepod family Eucalanidae. Proc. Roy. Soc. London. Series B, 270, 2321-2331.
19. Goetze, E. (2010) Species discovery in marine planktonic invertebrates through global molecular screening. Mol. Ecol., 19, 952-967.
20. Goetze, E. (2011) Population differentiation in the open sea: insights from the Pelagic Copepod Pleuromamma xiphias. Integr. Comp. Biol., 51, 580-597.
21. Gouy, M., Guindon, S. and Gascuel, O. (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol., 27, 221-224.
22. Folmer, O., Black, M., Hoeh, W. et al. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotech., 3, 294-299.
23. Hassouna, N., Michot, B. and Bachelleire, J. P. (1984) The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukar-yotes. Nucleic Acids Res., 12, 3563-3583.
24. Humes, A. G. (1994) How many copepods? Hydrobiologia, 292-293, 1-7.
25. Kiesling, T. L., Wilkinson, E., Rabalais, J. et al. (2002) Rapid identification of adult and naupliar stages of copepods using DNA hybridization methodology. Mar. Biotechnol., 4, 30-39.
26. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
27. Kosobokova, K. N. and Hirche, H. J. (2000) Zooplankton distribution across the Lomonosov Ridge, Arctic Ocean: species inventory, biomass and vertical structure. Deep-Sea Res. Pt. I, 47, 2029-2060.
28. Lee, C. E. (2000) Global phylogeography of a cryptic copepod species complex and reproductive isolation between genetically proximate 'populations'. Evolution, 54, 2014-2027.
29. Lee, C. Y., Liu, D. C. and Su, W. C. (2009) Seasonal and spatial variations in the planktonic copepod community of llan Bay and adjacent Kuroshio waters off northeastern Taiwan. Zool. Stud., 48, 151-161.
30. Llinas, L. (2008) Distribution, reproduction, and transport of zoo-plankton in the western Arctic. Ph.D. Dissertation. University of Miami, Coral Gables, FL.
31. Lindeque, P. K., Hay, S. J., Heath, M. R. et al. (2006) Integrating conventional microscopy and molecular analysis to analyse the abundance and distribution of four Calanus congeners in the North Atlantic. J. Plankton Res., 28, 221-238.
32. Long, E. O. and Dawid, B. (1980) Repeated genes in eukaryotes. Annu. Rev. Biochem., 49, 726-727.
33. Machida, R. J. and Tsuda, A. (2010) Dissimilarity of species and forms of planktonic Neocalanus copepods using mitochondrial COI, 12S, Nuclear ITS, and 28S Gene Sequences. Plos One, 5, e10278.
34. Malgorzata, A., Marszalek, M. A., Dayanandan, S. et al. (2009) Phylogeny of the genus Hesperodiaptomus (Copepoda) based on nu-cleotide sequence data of the nuclear ribosomal gene. Hydrobiologia, 624, 61-69.
35. Mauchline, J. (1998) The Biology of Calanoid Copepods. Academic Press, San Diego.
36. Minxiao, W., Song, S., Chaolun, L. et al. (2011) Distinctive mitochon-drial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies. BMC Genomics, 12, 73.
37. Nonomura, T., Machida, R. J. and Nishida, S. (2008) Stage-V copepo-dites of Calanus sinicus and Calanus jashnovi (Copepoda: Calanoida) in mesopelagic zone of Sagami Bay as identified with genetic markers, with special reference to their vertical distribution. Prog. Oceanogr., 77, 45-55.
38. Nylander, J. A. A. (2004) MrModeltest v2. Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University.
39. Rombouts, I., Beaugrand, G., Ibanez, F. et al. (2009) Global latitudinal variations in marine copepod diversity and environmental factors. Phil. Trans. R. Soc. Lond. B, 276, 3053-3062.
40. Rombouts, I., Beaugrand, G., Ibañez, F. et al. (2010) A multivariate approach to large-scale variation in marine planktonic copepod diversity and its environmental correlates. Limnol. Oceanogr., 55, 2219-2229.
41. Ronquist, F. and Huelsenbeck, J. P. (2003) MrBayes 3: Bayesian phylo-genetic inference under mixed models. Bioinformatics, 19, 1572-1574.
42. Schizas, N. V., Street, G. T., Coull, B. C. et al. (1997) An efficient DNA extraction method for small metazoans. Mol. Mar. Biol. Biotech., 6, 383-385.
43. Schnack-Schiel, S. B., Mizdalski, E. and Cornilis, A. (2010) Copepod abundance and species composition in the Eastern subtropical/tropical Atlantic. Deep-Sea Res. Pt. II, 57, 2064-2075.
44. Shimode, S., Toda, T. and Kikuchi, T. (2006) Spatio-temporal changes in diversity and community structure of planktonic copepods in Sagami Bay, Japan. Mar. Biol., 148, 581-597.
45. Song, Y., Wang, G. T., Yao, W. J. et al. (2008) Phylogeny of freshwater parasitic copepods in the Ergasilidae (Copepoda: Poecilostomatoida) based on 18S and 28S rDNA sequences. Parasitol. Res., 102, 299-306.
46. Sonnenberg, R., Nolte, A. W. and Tautz, D. (2007) An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Front. Zool., 4, 6.
47. Tamura, K., Peterson, D., Peterson, N. et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol., 28, 2731-2739.
48. Terazaki, M. and Tomatsu, C. (1997) A vertical multiple opening and closing plankton sampler. J. Adv. Mar. Sci. Technol. Soc., 3, 127-132.
49. Thompson, J. D., Gibson, T. J., Plewniak, F. et al. (1997) The Clustal-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
50. Tittensor, D. P., Mora, C., Jetz, W. et al. (2010) Global patterns and predictors of marine biodiversity across taxa. Nature, 466, 1098-1101.
51. Toda, T. (1986) Some problems in the classification of calanoid cope-pods. Aquabiology, 8, 182-192.
52. Woodd-Walker, R. S., Ward, P. and Clarke, A. (2002) Large-scale patterns in diversity and community structure of surface water cope-pods from the Atlantic Ocean. Mar. Ecol. Prog. Ser., 236, 189-203.
53. Wyngaard, G. A., Hoyńska, M. and Schulte, J. A. II. (2010) Phylogeny of the freshwater copepod Mesocyclops (Crustacea: Cyclopidae) based on combined molecular and morphological data, with notes on bio-geography. Mol. Phylogenet. Evol., 55, 753-764.
54. Xu, Z. H., Jiang, X. D., Wang, G. Z. et al. (2011) DNA extraction, amplification and analysis of the 28S rRNA portion in sediment-buried copepod DNA in the Great Wall Bay and Xihu Lake, Antarctica. J. Plankton Res., 33, 917-925.