Advertisement

DNA Barcoding of Copepods

  • C. Rajthilak
  • P. Santhanam
  • P. Pachiappan
  • T. Veeramani
  • S. Ravikumar
Chapter

Abstract

Copepods are the most studied zooplankton focussing on diversity, morphology, taxonomy, phylogeny, distribution, life-cycle strategies, feeding behaviour and adaptation to various environmental conditions (Bradford-Grieve et al. 2010; Blanco-Bercial et al. 2011; Saiz and Calbet 2011). They are the most diverse taxon which extend over vast geographic ranges and are planktonic almost throughout their life cycle. Precise identification is based on our knowledge of morphological traits found among copepods. The common occurrence of spectacular ontogenetic changes and also higher levels of morphological plasticity persisted among copepods have remained a challenge for the species identification that can be readily addressed through the molecular level (McManus and Katz 2009). More recently, biodiversity assessments have been increasingly concentrated on molecular-based genetic methods (Bucklin et al. 2010a; Grant et al. 2011). The molecular taxonomical analysis has heralded a new era in solving the confusion caused by cryptic species (Goetze 2003, 2010; Miyamoto et al. 2010).

Notes

Acknowledgements

Authors are indebted to authorities of Alagappa University, Karaikudi, and Bharathidasan University, Tiruchirapalli, for facilities provided. One of the authors (CR) acknowledges the Science and Engineering Research Board (SERB), Govt. of India, New Delhi, for the financial support through National Post-Doctoral Fellowship (file number: PDF/2015/000407).

References

  1. Ashton, G.V., M.I. Stevens, M.C. Hart, D.H. Green, M.T. Burrows, E.J. Cook, and K.J. Willis. 2008. Mitochondrial DNA reveals multiple northern hemisphere introductions of Caprella mutica (Crustacea, Amphipoda). Molecular Ecology 17: 1293–1303.CrossRefGoogle Scholar
  2. Avise, J.C. 2009. Phylogeography: Retrospect and prospect. Journal of Biogeography 36: 3–15.CrossRefGoogle Scholar
  3. Blanco-Bercial, L., and F. Alvarez-Marques. 2007. RFLP procedure to discriminate between Clausocalanus Giesbrecht, 1888 (Copepoda, Calanoida) species in the Central Cantabrian Sea. Journal of Experimental Marine Biology and Ecology 344: 73–77.CrossRefGoogle Scholar
  4. Blanco-Bercial, L., J. Bradford-Grieve, and A. Bucklin. 2011. Molecular phylogeny of the Calanoida (Crustacea: Copepoda). Molecular Phylogenetics and Evolution 59: 103–113.CrossRefGoogle Scholar
  5. Bottger-Schnack, R., and R.J. Machida. 2010. Comparison of morphological and molecular traits for species identification and taxonomic grouping of oncaeid copepods. Hydrobiologia 666: 111–125.CrossRefGoogle Scholar
  6. Bradford-Grieve, J.M., G.A. Boxshall, S.T. Ahyong, and S. Ohtsuka. 2010. Cladistic analysis of the calanoid copepoda. Invertebrate Systematics 24: 291–321.CrossRefGoogle Scholar
  7. Braga, E., R. Zardoya, A. Meyer, and J. Yen. 1999. Mitochondrial and nuclear rRNA based copepod phylogeny with emphasis on the Euchaetidae (Calanoida). Marine Biology 133: 79–90.CrossRefGoogle Scholar
  8. Brown, W.M. 1985. The mitochondrial genome of animals. In Molecular evolutionary genetics, ed. R.J. Mclntyre, 95–130. New York: Plenum Press.CrossRefGoogle Scholar
  9. Bucklin, A. 2000. Methods for population genetic analysis of zooplankton, Chapter 11. In The zooplankton methodology manual, ed. R. Harris, P. Wiebe, J. Lenz, H.R. Skjoldal, and M. Huntley, 533–570. London: Academic.CrossRefGoogle Scholar
  10. Bucklin, A., and B.W. Frost. 2009. Morphological and molecular phylogenetic analysis of evolutionary lineages within Clausocalanus (Copepoda: Calanoida). Journal of Crustacean Biology 29: 111–120.CrossRefGoogle Scholar
  11. Bucklin, A., B.W. Frost, and T.D. Kocher. 1995. Molecular systematics of six Calanus and three Metridia species (Calanoida: Copepoda). Marine Biology 121: 655–664.CrossRefGoogle Scholar
  12. Bucklin, A., C.C. Caudill, and A.M. Bentley. 1998. Population genetics and phylogeny of marine planktonic copepods. In Molecular approaches to the study of the ocean, ed. K.C. Cooksey, 303–318. London: Chapman Hall.CrossRefGoogle Scholar
  13. Bucklin, A., M. Guarnieri, R.S. Hill, A.M. Bentley, and S. Kaartvedt. 1999. Taxonomic and systematic assessment of planktonic copepods using mitochondrial COI sequence variation and competitive, species-specific PCR. Hydrobiologia 401: 239–254.CrossRefGoogle Scholar
  14. Bucklin, A., B.W. Frost, J. Bradford-Grieve, L. Allen, and N. Copley. 2003. Molecular systematics and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae. Marine Biology 142: 333–343.CrossRefGoogle Scholar
  15. Bucklin, A., R.R. Hopcroft, K.N. Kosobokova, L.M. Nigro, B.D. Ortman, R.M.J. Jennings, and C.J. Sweetman. 2010a. DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition. Deep-Sea Research Part II 57: 40–48.CrossRefGoogle Scholar
  16. Bucklin, A., B.D. Ortman, R.M. Jennings, L.M. Nigro, C.J. Sweetman, N.J. Copley, T. Sutton, and P.H. Wiebe. 2010b. A Rosetta Stone for metazoan zooplankton: DNA barcode analysis of species diversity in the Sargasso Sea (Northwest Atlantic Ocean). Deep-Sea Research Part II 57: 2234–2247.CrossRefGoogle Scholar
  17. Burton, R.S. 1996. Molecular tools in marine ecology. Journal of Experimental Marine Biology and Ecology 200: 85–101.CrossRefGoogle Scholar
  18. Burton, R.S., R.J. Byrne, and P.D. Rawson. 2007. Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus. Gene 403: 53–59.CrossRefGoogle Scholar
  19. Cepeda, G.D., L. Blanco-Bercial, A. Bucklin, C.M. Beron, and M.D. Vinas. 2012. Molecular systematic of three species of Oithona (Copepoda, Cyclopoida) from the Atlantic Ocean: Comparative analysis using 28S Rdna. PLoS One 7: e35861.CrossRefGoogle Scholar
  20. Colgan, D.J., A. McLauchlan, G.D.F. Wilson, S.P. Livingston, G.D. Edgecombe, J. Macaranas, G. Cassis, and M.R. Gray. 1998. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Australian Journal of Zoology 46: 419–437.CrossRefGoogle Scholar
  21. Engelmann, J.C., S. Rahmann, M. Wolf, J. Schultz, E. Fritzilas, S. Kneitz, T. Dandekar, and T. Müller. 2009. Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources 9: 83–93.CrossRefGoogle Scholar
  22. Figueroa, D.F. 2011. Phylogenetic analysis of Ridgewayia (Copepoda: Calanoida) from the Galapagos and of a new species from the Florida Keys with a reevaluation of the phylogeny of Calanoida. Journal of Crustacean Biology 31: 153–165.CrossRefGoogle Scholar
  23. Folmer, O.M., W. Black, R. Hoen, R. Lutz, and R. Vrijenhoek. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294–299.Google Scholar
  24. Fuentes-Reines, J.M., and E. Suarez-Morales. 2014. A new subspecies of Nitokra affinis Gurney, 1927 (Copepoda, Harpacticoida) from the Caribbean coast of Colombia. ZooKeys 378: 1–15.CrossRefGoogle Scholar
  25. Geller, J., C. Meyer, M. Parker, and H. Hawk. 2013. Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Molecular Ecology Resources 13: 851–861.CrossRefGoogle Scholar
  26. Goetze, E. 2003. Cryptic speciation on the high seas; global phylogenetics of the copepod family Eucalanidae. Proceedings of the Royal Society of London – Series B: Biological Sciences 270: 2321–2331.CrossRefGoogle Scholar
  27. ———. 2005. Global population genetic structure and biogeography of the oceanic copepods Eucalanus hyalinus and E. spinifer. Evolution 59: 2378–2398.Google Scholar
  28. ———. 2010. Species discovery in marine planktonic invertebrates through global molecular screening. Molecular Ecology 19: 952–967.CrossRefGoogle Scholar
  29. ———. 2011. Population differentiation in the Open Sea: Insights from the pelagic copepod Pleuromamma xiphias. Integrative and Comparative Biology 51: 580–597.CrossRefGoogle Scholar
  30. Goetze, E., and J. Bradford-Grieve. 2005. Genetic and morphological description of Eucalanus spinifer T. Scott, 1894 (Calanoida: Eucalanidae), a circumglobal sister pecies of the copepod E. hyalinus S.S. (Claus, 1866). Progress in Oceanography 65: 55–87.CrossRefGoogle Scholar
  31. Grant, R.A., H.J. Griffiths, D. Steinke, V. Wadley, and K. Linse. 2011. Antarctic DNA barcoding; a drop in the ocean? Polar Biology 34: 775–780.CrossRefGoogle Scholar
  32. Halanych, K.M., J.D. Bacheller, A.M.A. Aguinaldo, S.M. Liva, D.M. Hillis, and J.A. Lake. 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 267: 1641–1643.CrossRefGoogle Scholar
  33. Halanych, K.M., R.A. Lutz, and R.C. Vrijenhoek. 1998. Evolutionary origins and age of vestimentiferan tube-worms. Cahiers de Biologie Marine 39: 355–358.Google Scholar
  34. Hassanin, A. 2006. Phylogeny of Arthropoda inferred from mitochondrial sequences: Strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Molecular Phylogenetics and Evolution 38: 100–116.CrossRefGoogle Scholar
  35. Hassouna, N., B. Michot, and J.P. Bachelleire. 1984. The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Research 12: 3563–3583.CrossRefGoogle Scholar
  36. Hebert, P.D.N., A. Cywinska, S.L. Ball, and J.R. deWaard. 2003a. Biological identifications through DNA barcodes. Proceedings of the Biological Sciences 270: 313–322.CrossRefGoogle Scholar
  37. Hebert, P.D.N., S. Ratnasingham, and J.R. deWaard. 2003b. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings- Royal Society of London [Biol] 270: S96–S99.CrossRefGoogle Scholar
  38. Hebert, P.D.N., E.H. Penton, J.M. Burns, D.H. Janzen, and W. Hallwachs. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America 101: 14812–14817.CrossRefGoogle Scholar
  39. Hill, R.S., L.D. Allen, and A. Bucklin. 2001. Multiplexed species-specific PCR protocol to discriminate four N. Atlantic Calanus species, with an mtCOI gene tree for ten Calanus species. Marine Biology 139: 279–287.CrossRefGoogle Scholar
  40. Hillis, D.M., and M.T. Dixon. 1991. Ribosomal DNA: Molecular evolution and phylogenetic inference. The Quarterly Review of Biology 66: 411–453.CrossRefGoogle Scholar
  41. Ki, J., K. Lee, H.G. Park, S. Chullasorn, H. Dahms, and J. Lee. 2009. Phylogeography of the copepod Tigriopus japonicus along the Northwest Pacific rim. Journal of Plankton Research 31: 209–221.CrossRefGoogle Scholar
  42. Laakmann, S., G. Gerdts, R. Erler, T. Knebelsberger, P. Martinez Arbizu, and M.J. Raupach. 2013. Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences. Molecular Ecology Resources 13: 862–876.CrossRefGoogle Scholar
  43. Landis, F.C., and A. Gargas. 2007. Using ITS2 secondary structure to create species-specific oligonucleotide probes for fungi. Mycologia 99: 681–692.CrossRefGoogle Scholar
  44. Lee, C.E. 2000. Global phylogeography of a cryptic copepod species complex and reproductive isolation between genetically proximate “populations”. Evolution 54: 2014–2027.CrossRefGoogle Scholar
  45. Machida, R.J., and A. Tsuda. 2010. Dissimilarity of species and forms of planktonic Neocalanus copepods using mitochondrial COI, 12S, nuclear ITS, and 28S gene sequences. PLoS One 5: e10278.CrossRefGoogle Scholar
  46. Machida, R.J., M.U. Miya, M. Nishida, and S. Nishida. 2002. Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Marine Biotechnology 4: 406–417.CrossRefGoogle Scholar
  47. ———. 2004. Large-scale gene rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea), with notes on new versatile primers for the srRNA and COI genes. Gene 332: 71–78.CrossRefGoogle Scholar
  48. Mackie, J., M. Keough, and L. Christidis. 2006. Invasion patterns inferred from cytochrome oxidase I sequences in three bryozoans, Bugula neritina, Watersipora subtorquata, and Watersipora arcuata. Marine Biology 149: 285–295.CrossRefGoogle Scholar
  49. McManus, G.B., and L.A. Katz. 2009. Molecular and morphological methods for identifying plankton: What makes a successful marriage? Journal of Plankton Research 31: 1119–1129.CrossRefGoogle Scholar
  50. Merrit, T.J.S., L. Shi, M.C. Chase, M.A. Rex, and R.J. Etter. 1998. Universal cytochrome b primers facilitate intraspecific studies in molluscan taxa. Molecular Marine Biology and Biotechnology 7: 7–11.Google Scholar
  51. Miyamoto, H., R.J. Machida, and S. Nishida. 2010. Genetic diversity and cryptic speciation of the deep sea chaetognath Caecosagitta macrocephala (Fowler, 1904). Deep-Sea Research Part II 57: 2211–2219.CrossRefGoogle Scholar
  52. Nuwer, M., B. Frost, and E.V. Armbrust. 2008. Population structure of the planktonic copepod Calanus pacificus in the North Pacific Ocean. Marine Biology 156: 107–115.CrossRefGoogle Scholar
  53. Ortman, B.D. 2008. DNA Barcoding the Medusozoa and Ctenophora. Disseration, University of Connecticut, Storrs, 121pp.Google Scholar
  54. Palumbi, S.R. 1996. Nucleic acids II. The polymerase chain re- action. In Molecular systematics, ed. D.M. Hillis, C. Moritz, and B.K. Mable, 2nd ed., 205–247. Sunderland: Sinauer Associates.Google Scholar
  55. Papadopoulos, L.N., K.T.C.A. Peijnenburg, and P.C. Luttikhuizen. 2005. Phylogeography of the calanoid copepods Calanus helgolandicus and C. euxinus suggests Pleistocene divergences between Atlantic, Mediterranean, and Black Sea populations. Marine Biology 147: 1353–1365.CrossRefGoogle Scholar
  56. Park, J.K., B.L. Choe, and K.S. Eom. 2004. Two mitochondrial lineages in Korean freshwater Corbicula (Corbiculidae: Bivalvia). Molecules and Cells 17: 410–414.Google Scholar
  57. Place, A.R., X.J. Feng, C.R. Steven, H.M. Fourcade, and J.L. Boore. 2005. Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. Journal of Experimental Marine Biology and Ecology 319: 15–27.CrossRefGoogle Scholar
  58. Rajthilak, C., P. Santhanam, M. Raja, T. Suman, S. Rajasree, R. Ramkumar, and P. Perumal. 2015. First distributional record of Nitokra affinis Gurney, 1927 (Copepoda: Harpacticoida: Ameiridae) from Vellar estuary (south-east India): Structural and molecular evidence. Marine Biodiversity Records 8: 1–9.CrossRefGoogle Scholar
  59. Raupach, M.J., C. Mayer, M. Malyutina, and J.W. Wegele. 2009. Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data. Proceedings of the Royal Society of London – Series B: Biological Sciences 276: 799–808.CrossRefGoogle Scholar
  60. Rocha-Olivares, A., J.W. Fleeger, and W. Foltz. 2001. Decoupling of molecular and morphological evolution in deep lineages of a meiobenthic harpacticoid copepod. Molecular Biology and Evolution 18: 1088–1102.CrossRefGoogle Scholar
  61. Saiz, E., and A. Calbet. 2011. Copepod feeding in the ocean: Scaling patterns, composition of their diet and the bias of estimates due to microzooplankton grazing during incubations. Hydrobiologia 666: 181–196.CrossRefGoogle Scholar
  62. Schizas, N.V., G.T. Street, B.C. Coull, G.T. Chandler, and J.M. Quattro. 1999. Molecular population structure of the marine benthic copepod Microarthridion littorale along the southeastern and Gulf coasts of the USA. Marine Biology 135: 399–405.CrossRefGoogle Scholar
  63. Schizas, N.V., B.C. Coull, G.T. Chandler, and J.M. Quattro. 2002. Sympatry of distinct mitochondrial DNA lineages in a copepod inhabiting estuarine creeks in the southeastern USA. Marine Biology 140: 585–594.CrossRefGoogle Scholar
  64. Selkoe, K.A., C.M. Henzler, and S.D. Gaines. 2008. Seascape genetics and the spatial ecology of marine populations. Fish and Fisheries 9: 363–377.CrossRefGoogle Scholar
  65. Shao, R., and S.C. Barker. 2007. Mitochondrial genomes of parasitic arthropods: Implications for studies of population genetics and evolution. Parasitology 134: 153–167.CrossRefGoogle Scholar
  66. Simon, C., F. Frati, A. Beckenbach, B. Crespi, H. Liu, and P. Flook. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved PCR primers. Annals of the Entomological Society of America 87: 651–701.CrossRefGoogle Scholar
  67. Simon, C., T.R. Buckley, F. Frati, J.B. Stewart, and A.T. Beckenbach. 2006. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics 37: 545–579.CrossRefGoogle Scholar
  68. Smith, P.J., D. Steinke, M.S. McVeagh, A.L. Stewart, C.D. Struthers, and C.D. Roberts. 2008. Molecular analysis of Southern Ocean skates (Bathyraja) reveals a new species of Antarctic skate. Journal of Fish Biology 73: 1170–1182.CrossRefGoogle Scholar
  69. Soh, Y., S.W. Kwon, W. Lee, and Y.H. Yoon. 2012. A new Pseudodiaptomus (Copepoda, Calanoida) from Korea supported by molecular data. Zootaxa 3368: 229–244.Google Scholar
  70. Sonnenberg, R., A.W. Nolte, and D. Tautz. 2007. An evaluation of LSU rDNA D1–D2 sequences for their use in species identification. Frontiers in Zoology 4: 6.CrossRefGoogle Scholar
  71. Spears, T., L.G. Abele, and W. Kim. 1992. The monophyly of brachyuran crabs: A phylogenetic study based on 18S rRNA. Systematic Biology 41: 446–461.CrossRefGoogle Scholar
  72. Staton, J.L., L.C. Wickliffe, L. Garlitska, S.M. Villanueva, and B.C. Coull. 2005. Genetic isolation discovered among previously described sympatric morphs of a meiobenthic copepod. Journal of Crustacean Biology 25: 551–557.CrossRefGoogle Scholar
  73. Steinke, D., T.S. Zemlak, and P.D.N. Hebert. 2009. Barcoding nemo: DNA-based identifications for the ornamental fish trade. PLoS One 4: e6300.CrossRefGoogle Scholar
  74. Takenaka, Y., A. Yamaguchi, N. Tsuruoka, M. Torimura, T. Gojobori, and Y. Shigeri. 2012. Evolution of bioluminescence in marine planktonic copepods. Molecular Biology and Evolution 29: 1669–1681.CrossRefGoogle Scholar
  75. Tautz, D., P. Arctander, A. Minelli, R.H. Thomas, and A.P. Vogler. 2003. A plea for DNA taxonomy. Trends in Ecology & Evolution 18: 70–74.CrossRefGoogle Scholar
  76. Thum, R.A. 2004. Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: An example with the North American genera. Hydrobiologia 519: 135–141.CrossRefGoogle Scholar
  77. Thum, R.A., and R.G. Harrison. 2009. Deep genetic divergences among morphologically similar and parapatric Skistodiaptomus (Copepoda: Calanoida: Diaptomidae) challenge the hypothesis of Pleistocene speciation. Biological Journal of the Linnean Society 96: 150–165.CrossRefGoogle Scholar
  78. White, T.J., T. Bruns, S. Lee, and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols, ed. M.A. Innis, D.H. Gelfand, and J.J. Sninsky, 315–322. New York: Academic Press.Google Scholar
  79. Wolstenholme, D.R. 1992. Animal mitochondrial-DNA – Structure and evolution. International Review of Cytology 141: 173–216.CrossRefGoogle Scholar
  80. Wyngaard, G.A., M. Hołynska, and J.A. Schulte. 2010. Phylogeny of the freshwater copepod Mesocyclops (Crustacea: Cyclopidae) based on combined molecular and morphological data, with notes on biogeography. Molecular Phylogenetics and Evolution 55: 753–764.CrossRefGoogle Scholar
  81. Zardoya, R., E. Costas, V. Lopez-Rodas, A. Garrido-Pertierra, and J.M. Bautista. 1995. Revised dinoflagellate phylogeny inferred from molecular analysis of large-subunit ribosomal RNA gene sequences. Journal of Molecular Evolution 41: 637–645.Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • C. Rajthilak
    • 1
  • P. Santhanam
    • 2
  • P. Pachiappan
    • 3
  • T. Veeramani
    • 2
  • S. Ravikumar
    • 1
  1. 1.Department of Oceanography and Coastal Area Studies, School of Marine SciencesAlagappa UniversityThondiIndia
  2. 2.Department of Marine Science, School of Marine SciencesBharathidasan UniversityTiruchirappalliIndia
  3. 3.Department of Biotechnology, School of BiosciencesPeriyar UniversitySalemIndia

Personalised recommendations