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Hydrobiologia

, Volume 594, Issue 1, pp 19–32 | Cite as

Intra-specific rDNA-ITS restriction site variation and an improved protocol to distinguish species and hybrids in the Daphnia longispina complex

  • Morten SkageEmail author
  • Anders Hobæk
  • Štĕpánka Ruthová
  • Barbara Keller
  • Adam Petrusek
  • Jaromír Sed’a
  • Piet Spaak
Cladocera

Abstract

A collaborative research effort was undertaken to evaluate the robustness of a recently developed genetic tool for species identification of members in the morphologically variable Daphnia longispina species complex. This genetic method, based on restriction fragment length polymorphism (RFLP) of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA (rDNA) with restriction enzymes Mwo I and Sau96 I [Billiones et al., 2004. Hydrobiologia 526: 43–53], was applied to many different European populations. Results were compared with two or more independently obtained characters (morphology, allozymes, mitochondrial DNA (mtDNA), or cloned rDNA-ITS sequences). Individuals of most taxa were readily identified, but unexpected ITS-RFLP patterns were found in many individuals indicated by other markers to be D. galeata or one of its hybrids. Among 43 investigated D. galeata populations (902 specimen analysed by ITS-RFLP), deviant RFLP fragment patterns occurred in 26 (i.e., more than half) of the populations. The deviant patterns could be attributed to the loss of one single restriction site in the ITS2 region. This loss made the distinction of D. galeata from other species unreliable, and F1 hybrids could not be identified. Future users should be aware of this shortcoming of the Billions et al. [2004. Hydrobiologia 526: 43–53] protocol. As a solution to this problem, we present an improved genetic identification protocol based on a simple double digestion of the rDNA-ITS region with the restriction enzymes BsrB I and EagI. Sequence analyses of rDNA-ITS clones and preliminary testing indicate that the new protocol is unaffected by the rDNA variation which troubled the Mwo I/Sau96 I protocol. Further, the new protocol identifies all European species of the D. longispina complex, as well as their F1 hybrids. However, a wider screening is required to verify its general utility for all species, since yet unknown variation may occur.

Keywords

Daphnia longispina species complex ITS-RFLP Ribosomal DNA (rDNA) ITS Intragenomic Interspecific hybrids 

Notes

Acknowledgements

We thank Colleen Durkin, Piotr Madej, Marina Manca, Esther Keller, Christoph Tellenbach and Justyna Wolinska for help to obtain zooplankton samples of Swiss and Italian lakes and help in the laboratory. This study was supported by the University of Bergen, Norwegian Institute of Water Research, the Norwegian Research Council (Grant 121181/720), the Czech Science Foundation (project 206/04/0190), the Grant Agency of the Charles University (GA 114807) and the Czech Ministry of Education (MSM0021620828).

References

  1. Anderson, I. C., S. M. Chambers & J. W. G. Cairney, 2001. ITS-RFLP and ITS sequence diversity in Pisolithus from central and eastern Australian sclerophyll forests. Mycological Research 105: 1304–1312.Google Scholar
  2. Aranishi, F., 2005. Rapid PCR-RFLP method for discrimination of imported and domestic mackerel. Marine Biotechnology 7: 571–575.PubMedCrossRefGoogle Scholar
  3. Arnheim, N., 1983. Concerted evolution of multigene families. In Nei, M. & R. K. Koehen (eds), Evolution of Genes and Proteins. Sinauer, Sundeland, Mass: 38–61.Google Scholar
  4. Benzie, J. A. H., 2005. The genus Daphnia (including Daphniopsis): (Anomopoda, Daphniidae) In Dumont, H. J. F. (ed.), Guides to the Identification of the Microinvertebrates of the Continental Waters of the World, No 21. Backhuys Publishers, Leiden: 376.Google Scholar
  5. Billiones, R., M. Brehm, J. Klee & K. Schwenk, 2004. Genetic identification of Hyalodaphnia species and interspecific hybrids. Hydrobiologia 526: 43–53.CrossRefGoogle Scholar
  6. Buckler E. S., A. Ippolito & T. P. Holtsford, 1997. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145: 821–832.PubMedGoogle Scholar
  7. Brede, N., A. Thielsch, C. Sandrock, P. Spaak, B. Keller, B. Streit & K. Schwenk, 2006. Microsatellite markers for European Daphnia. Molecular Ecology Notes 6: 536–539.CrossRefGoogle Scholar
  8. Burgermeister, W., K. Metge, H. Braasch & E. Buchbach, 2005. ITS-RFLP patterns for differentiation of 26 Bursaphelenchus species (Nematoda: Parasitaphelenchidae) and observations on their distribution. Russian Journal of Nematology 13: 29–42.Google Scholar
  9. Colbourne, J. K. & P. D. N. Hebert, 1996. The systematics of North American Daphnia (Crustacea: Anomopoda): a molecular phylogenetic approach. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 351: 349–360.CrossRefGoogle Scholar
  10. Coleman, A. W., 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics 19: 370–375.PubMedCrossRefGoogle Scholar
  11. Cousyn, C., L. De Meester, J. K. Colbourne, L. Brendonck, D. Verschuren & F. Volckaert, 2001. Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes. Proceedings of the National Academy of Sciences USA 98: 6256–6260.Google Scholar
  12. Crease, T. J. & M. Lynch, 1991. Ribosomal DNA Variation in Daphnia pulex. Molecular Biology and Evolution 8: 620–640.Google Scholar
  13. Fernández, A., T. Garcia, L. Asensio, M. A. Rodriguez, I. Gonzalez, P. E. Hernandez & R. Martin, 2001. PCR-RFLP analysis of the internal transcribed spacer (ITS) region for identification of 3 clam species. Journal of Food Science 66: 657–661.CrossRefGoogle Scholar
  14. Flössner, D., 2000. Die Haplopoda und Cladocera (ohne Bosminidae) Mitteleuropas. Backhuys Publishers, Leiden: 428.Google Scholar
  15. Giessler, S., 1997. Analysis of reticulate relationships within the Daphnia longispina species complex. Allozyme phenotype and morphology. Journal of Evolutionary Biology 10: 87–105.CrossRefGoogle Scholar
  16. Hall, T., 1999. BioEdit sequence alignment editor. Department of Microbiology, North Carolina State University.Google Scholar
  17. Harris, D. J. & K. A. Crandall, 2000. Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): Implications for phylogenetic and microsatellite studies. Molecular Biology and Evolution 17: 284–291.PubMedGoogle Scholar
  18. Hebert, P. D. N. & M. J. Beaton, 1988. Methodologies for Allozyme Analysis using Cellulose Acetate Electrophoresis. Helena Laboratories, Beaumont, TX.Google Scholar
  19. Hobæk, A., M. Skage & K. Schwenk, 2004. Daphnia galeata × D. longispina hybrids in western Norway. Hydrobiologia 526: 55–62.CrossRefGoogle Scholar
  20. Jankowski, T. & D. Straile, 2004. Allochronic differentiation among Daphnia species, hybrids and backcrosses: the importance of sexual reproduction for population dynamics and genetic architecture. Journal of Evolutionary Biology 17: 312–321.PubMedCrossRefGoogle Scholar
  21. Keller, B. & P. Spaak, 2004. Nonrandom sexual reproduction and diapausing egg production in a Daphnia hybrid species complex. Limnology and Oceanography 49: 1393–1400.Google Scholar
  22. Long, E. O. & I. B. David, 1980. Repeated genes in Eukaryotes. Annual review in Biochemistry 49: 727–764.CrossRefGoogle Scholar
  23. Márquez, L. M., D. J. Miller, J. B. MacKenzie & M. J. H. van Oppen, 2003. Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora. Molecular Biology and Evolution 20: 1077–1086.PubMedCrossRefGoogle Scholar
  24. Nilssen, J. P., A. Hobæk, A. Petrusek & M. Skage, 2007. Restoring Daphnia lacustris G.O. Sars, 1862 (Crustacea, Anomopoda) – a cryptic species in the Daphnia longispina group. doi:  10.1007/s10750-007-9076-3
  25. Palapala, V. A., T. Aimi, S. Inatomi & T. Morinaga, 2002. ITS-PCR-RFLP method for distinguishing commercial cultivars of edible mushroom, Flammulina velutipes. Journal of Food Science 67: 2486–2490.CrossRefGoogle Scholar
  26. Petrusek, A., F. Bastiansen & K. Schwenk, 2005. European Daphnia Species (EDS) – Taxonomic and genetic keys. http://www.natur.cuni.cz/ekologie/EDS/. [Build 2006-01-12 beta]. CD-ROM, distributed by the authors. Department of Ecology and Evolution, J.W. Goethe-University, Frankfurt am Main, Germany & Department of Ecology, Charles University, Prague, Czechia.Google Scholar
  27. Ruggiero M. V. & G. Procaccini, 2004. The rDNA ITS region in the marine angiosperm Halophila stipulacea (Hydrocharitaceae): intra-genomic variability and putative pseudogenic sequences. Journal of Molecular Evolution 58: 115–121.PubMedCrossRefGoogle Scholar
  28. Schwenk, K. & P. Spaak, 1995. Evolutionary and ecological consequences of interspecific hybridization in Cladocerans. Experientia 51: 465–481.CrossRefGoogle Scholar
  29. Schwenk, K., P. Junttila, M. Rautio, F. Bastiansen, A. Knapp, O. Dove, R. Billiones & B. Streit, 2004. Ecological, morphological, and genetic differentiation of Daphnia (Hyalodaphnia) from the Finnish and Russian subarctic. Limnology and Oceanography 49: 532–539.Google Scholar
  30. Schwenk, K., D. Posada & P. D. N. Hebert, 2000. Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species. Proceedings of the Royal Society of London Series B-Biological Sciences 267: 1833–1842.Google Scholar
  31. Smith, G. P., 1976. Evolution of Repeated DNA Sequences by Unequal Crossover. Science 191: 528–535.PubMedCrossRefGoogle Scholar
  32. Taylor, D. J., C. R. Ishikane & R. A. Haney. 2002. The systematics of Holarctic bosminids and a revision that reconciles molecular and morphological evolution. Limnology and Oceanography 47: 1486–1495.CrossRefGoogle Scholar
  33. Taylor, D. J., H. L. Sprenger & S. Ishida, 2005. Geographic and phylogenetic evidence for dispersed nuclear introgression in a daphniid with sexual propagules. Molecular Ecology 14: 525–537.PubMedCrossRefGoogle Scholar
  34. Thompson, J. D., D. G. Higgins & T. J. Gibson, 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680.PubMedCrossRefGoogle Scholar
  35. Vollmer S. V. & S. R. Palumbi, 2005. Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Molecular Ecology 13: 2763–2772.CrossRefGoogle Scholar
  36. Wolf, H. G. & M. A. Mort, 1986. Interspecific hybridization underlies phenotypic variability in Daphnia populations. Oecologia 68: 507–511.CrossRefGoogle Scholar
  37. Wörheide, G., S. Nichols & J. Goldberg, 2004. Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies. Molecular Phylogenetics and Evolution, 33: 816–830.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Morten Skage
    • 1
    Email author
  • Anders Hobæk
    • 2
  • Štĕpánka Ruthová
    • 3
  • Barbara Keller
    • 4
    • 5
  • Adam Petrusek
    • 3
  • Jaromír Sed’a
    • 6
  • Piet Spaak
    • 4
    • 5
  1. 1.Department of BiologyUniversity of BergenBergenNorway
  2. 2.Norwegian Institute of Water ResearchRegional office BergenBergenNorway
  3. 3.Department of EcologyCharles University in Prague, Faculty of SciencePrague 2Czechia
  4. 4.Eawag, Swiss Federal Institute of Aquatic Science and TechnologyDubendorfSwitzerland
  5. 5.Institute of Integrative BiologyZurichSwitzerland
  6. 6.Biological Centre ASCRInstitute of HydrobiologyCeske BudejoviceCzechia

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