Skip to main content
SpringerLink
Log in

DNA analysis methods for recognizing species invasion: the example of Codium, and generally applicable methods for algae

  • 1. Plenary lecture
  • Published:
Hydrobiologia Aims and scope Submit manuscript

Abstract

Analysis of DNA can help to distinguish those morphological characters indicative of species difference from those representing retained traits or parallel evolution. This can be of great value in detecting recent invaders. The choice of which DNA characters to examine not only dictates the methodology to be used but must also be appropriate for the detection level sought. Restriction endonuclease fragment comparisons of plastid DNA have been used to assess Codium species; the results show C. fragile subsp. tomentosoides from east and west coast North America to be identical while sympatric endemic Codium species each display their own unique set of fragments. For species of other algae, plastid DNA fragment patterns are not necessarily identical across a morphological species, e.g. Pandorina morum. Such repetitive element probes as M13 and the use of RAPDs are more appropriate for analysis of populations within species. DNA base sequence comparisons of nuclear rDNA genes often yield too few variant bases between closely related species for reliable identifications. Analysis of the more variable Internal Transcribed Spacer (ITS) region, lying between the small and large ribosomal subunit genes in nuclear DNA, yields more extensive base pair variation between species and relatively little within species; it may be an alternative choice for endonuclease restriction fragment analysis or for sequencing.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Adachi, M., Y. Sako & Y. Ishida, 1994. Restriction fragment length polymorphism of ribosomal DNA internal transcribed spacer and 5.8S regions in Japanese Alexandrium species (Dinophyceae). J. Phycol. 30: 857–863.

    Google Scholar 

  • Adams, C. R., K. A. Stamer, J. K. Miller, J. G. McNally, M. M. Kirk & D. L. Kirk, 1990. Patterns of organellar and nuclear inhiritance among progeny of two geographically isolated strains of Volvox carteri. Curr. Genet. 18: 141–153.

    Google Scholar 

  • Bakker, R. T., J. L. Olsen, W. T. Stam & C. vanden Hoek, 1992. Nuclear ribosomal DNA internal transcribed spacer regions (ITS 1 and ITS 2) define discrete biogeographic groups in Cladophora albida (Chlorophyta). J. Phycol. 28: 839–845.

    Google Scholar 

  • Baldwin, B. G., 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Mol. Phylogenet. Evol. 1: 3–16.

    Google Scholar 

  • Barrat, J., 1994. Ballast-water invasions of Chesapeake Bay studied by scientists. Smithsonian Inst. Res. Reports 76: 1–5.

    Google Scholar 

  • Bird, C. J., W. A. Nelson, E. L. Rice, K. G. Ryan & R. Villemur, 1990. A critical comparison of Gracilaria chilensis and G. sordida (Rhodophyta, Gracilariales). J. appl. Phycol. 2: 375–382.

    Google Scholar 

  • Bird, C. J., E. L. Rice, C. A. Murphy & M. A. Ragan, 1992. Phylogenetic relationships in the Gracilariales (Rhodophyta) as determined by 18S rDNA sequences. Phycologia 31: 510–522.

    Google Scholar 

  • Bird, C. J., M. A. Ragan, A. T. Critchley, E. L. Rice & R. R. Gutell, 1994. Molecular relationships among the Gracilariaceae (Rhodophyta): further observations on some undetermined species. Eur. J. Phycol. 29: 195–202.

    Google Scholar 

  • Buchheim, M. A. & R. L. Chapman, 1991. Phylogeny of the colonial green flagellates: a study of the 18S and 26S rRNA sequence data. BioSystems 25: 85–100.

    Google Scholar 

  • Buchheim, M. A. & R. L. Chapman, 1992. Phylogeny of Carteria (Chlorophyceae) inferred from molecular and organismal data. J. Phycol. 28: 362–374.

    Google Scholar 

  • Carlton, J. T. & J. A. Scanlon, 1985. Progression and dispersal of an introduced alga: Codium fragile ssp. tomentosoides (Chlorophyta) on the Atlantic coast of North America. Bot. mar. 28: 155–165.

    Google Scholar 

  • Coleman, A. W., 1995. Are the impacts of events in the earth's history discernable in the current distributions of freshwater algae? In J. Kristiansen (ed.), Biogeography of Freshwater Algae. (in press).

  • Coleman, A. W. & L. J. Goff, 1991. DNA analysis of eukaryotic algal species. J. Phycol. 27: 463–473.

    Google Scholar 

  • Coleman, A. W., A. Suarez & L. J. Goff, 1994. Molecular delineation of species and syngens in Volvocacean green algae (Chlorophyta). J. Phycol. 30: 80–90.

    Google Scholar 

  • Coleman, A. W., W. F. Thompson & L. J. Goff, 1991. Identification of the mitochondrial genome in the chrysophyte alga Ochromonas danica. J. Protozool. 38: 129–135.

    Google Scholar 

  • Coyer, J. A., D. L. Robertson & R. S. Alberte, 1994. Genetic variability within a population and between diploid/haploid tissue of Macrocystis pyrifera (Phaeophyceae). J. Phycol. 30: 545–552.

    Google Scholar 

  • Destombe, C. & S. E. Douglas, 1991. Rubisco spacer sequence divergence in the rhodophyte alga Gracilaria verrucosa and closely related species. Curr. Genetics 19: 395–398.

    Google Scholar 

  • Fain, S. R., 1992. Interpopulation chloroplast DNA sequence variation in the giant kelp, Macrocystis. J. Phycol. 28 (Suppl.): 16.

    Google Scholar 

  • Fain, S. R., L. D. Druehl & D. L. Baillie, 1988. Repeat and single copy sequences are differentially conserved in the evolution of kelp chloroplast DNA. J. Phycol. 24: 292–302.

    Google Scholar 

  • Goff, L. J. & A. W. Coleman, 1988. The use of plastid DNA restriction endonuclease patterns in delineating red algal species and populations. J. Phycol. 24: 357–368.

    Google Scholar 

  • Goff, L. J. & D. A. Moon, 1993. Amplification of nuclear and plastid genes from algal herbarium specimens and algal spores. J. Phycol. 29: 381–384.

    Google Scholar 

  • Goff, L. J., L. Liddle, P. C. Silva, M. Voytek & A. W. Coleman, 1992. Tracing species invasion in Codium, a siphonous green alga, using molecular tools. Am. J. Bot. 79: 1279–1285.

    Google Scholar 

  • Goff, L. J., D. A. Moon & A. W. Coleman, 1994. Molecular delineation of species and species relationships in the red algal agarophytes Gracilariopsis and Gracilaria (Gracilariales). J. Phycol. 30: 521–537.

    Google Scholar 

  • Harris, E. H., J. E. Boynton, N. W. Gillham, B. D. Burkhart & S. M. Newman, 1991. Chloroplast genome organization in Chlamydomonas. Arch. Protistenk. 139: 183–192.

    Google Scholar 

  • Hommersand, M. H., S. Fredericq & D. W. Freshwater, 1994. Phylogenetic systematics and biogeography of the Gigartinaceae (Gigartinales, Rhodophyta) based on sequence analysis of rbcL. Bot. mar. 37: 193–203.

    Google Scholar 

  • Jupe, E. R., R. L. Chapman & E. A. Zimmer, 1988. Nuclear ribosomal RNA genes and algal phylogeny: the Chlamydomonas example. BioSystems 21: 223–230.

    Google Scholar 

  • Kooistra, W. H. C. R., W. T. Stam, J. L. Olsen & C. van den Hoek, 1992. Biogeography of Cladophoropsis membranacea (Chlorophyta) based on comparisons of nuclear rDNA ITS sequences. J. Phycol. 28: 660–668.

    Google Scholar 

  • Kowallik, K. R., 1989. Molecular aspects and phylogenetic implications of plastid genomes of certain chromophytes. In J. C. Green, B. S. C. Leadbeater & W. L. Diver (eds) The Chromophyte Algae. Systematics Association 38: 101–124.

  • Larson, A., M. M. Kirk & D. L. Kirk, 1992. Molecular phylogeny of the volvocine flagellates. Mol. Biol. Evol. 9: 85–105.

    Google Scholar 

  • Lewis, L. A., L. W. Wilcox, P. A. Fuerst & G. L. Floyd, 1992. Concordance of molecular and ultrastructural data in the study of zoosporic chlorococcalean green algae. J. Phycol. 28: 375–380.

    Google Scholar 

  • Maggs, C. A., S. E. Douglas, J. Fenety & C. J. Bird, 1992. A molecular and morphological analysis of the Gymnogongrus devoniensis (Rhodophyta) complex in the North Atlantic. J. Phycol. 28: 214–232.

    Google Scholar 

  • Manhart, J. R. & R. M. McCourt, 1992. Molecular data and species concepts in the algae. J. Phycol. 28: 730–737.

    Google Scholar 

  • Mayr, E., 1948. The bearing of the new systematics on genetical problems. The nature of species. Adv. in Genet. 2: 205–237.

    Google Scholar 

  • Moore, L. J., 1990. An examination of the chloroplast and mitochondrial DNAs of sexually isolated populations of Pandorina morum Bory de St. Vincent. Ph.D. Thesis, Brown University, Providence, RI. pp. 140.

    Google Scholar 

  • Olmstead, R. G. & J. D. Palmer, 1994. Chloroplast DNA systematics: a review of methods and data analysis. Am. J. Bot. 81: 1205–1224.

    Google Scholar 

  • Olsen, J. L., W. T. Stam, S. Berger & D. Menzel, 1994. 18S rDNA and evolution in the Dasycladales (Chlorophyta): modern living fossils. J. Phycol. 30: 729–744.

    Google Scholar 

  • Palmer, J. E., R. K. Jansen, H. J. Michaels, M. W. Chase & J. R. Manhart, 1988. Chloroplast DNA variation and plant phylogeny. Ann. Missouri bot. Gard. 75: 1180–1206.

    Google Scholar 

  • Patwary, M. U., R. M. MacKay & J. P. van der Meer, 1993. Revealing genetic markers in Gelidium vagum (Rhodophyta) through the random amplified polymorphic DNA (RAPD) technique. J. Phycol. 29: 216–222.

    Google Scholar 

  • Rice, E. L. & C. J. Bird, 1990. Relationships among geographically distant populations of Gracilaria verrucosa (Gracilariales. Rhodophyta) and related species. Phycologia 29: 501–510.

    Google Scholar 

  • Silva, P. C., 1955. The dichotomous species of Codium in Britain. J. mar. biol. Ass. U.K. 2: 7–9.

    Google Scholar 

  • Silva, P. C., 1957. Codium in Scandinavian waters. Svensk Bot. Tidsk. 51: 117–134.

    Google Scholar 

  • Stabile, J. E., J. C. Gallagher & E. T. Wurtzel, 1990. Molecular analysis of intraspecific variation in the marine diatom Skeletonema costatum. Biochem. Syst. Ecol. 18: 5–9.

    Google Scholar 

  • Stabile, J. E., E. T. Wurtzel & J. C. Gallagher, 1992. Comparison of chloroplast DNA and allozyme variation in winter strains of the marine diatom Skeletonema costatum (Bacillariophyta). J. Phycol. 28: 90–94.

    Google Scholar 

  • Van Oppen, M. J. H., O. E. Dickmann, C. Wiencke, W. T. Stam & J. L. Olsen, 1994. Tracking dispersal routes: phylogeography of the arctic-antarctic disjunct seaweed Acrosiphonia arcta (Chlorophyta). J. Phycol. 30: 67–80.

    Google Scholar 

  • Wilcox, L. W., L. A. Lewis, P. A. Fuerst & G. L. Floyd, 1992. Assessing the relationships of autosporic and zoosporic chlorococcalean green algae with 18S rDNA sequence data. J. Phycol. 28: 381–386.

    Google Scholar 

  • Zechman, F. W., E. A. Zimmer & E. C. Theriot, 1994. Use of ribosomal DNA internal transcribed spacers for phylogenetic studies in diatoms. J. Phycol. 30: 507–512.

    Google Scholar 

  • Zimmer, E. A., S. L. Martin, S. M. Beverley, Y. W. Kan & A. C. Wilson, 1980. Rapid duplication and loss of genes coding for the alpha chains of hemoglobin. Proc. Natl. Acad. Sci. USA 77: 2158–2162.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Biology and Medicine, Brown University, 02912, Providence, RI, USA

    Annette W. Coleman

Authors
  1. Annette W. Coleman
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Coleman, A.W. DNA analysis methods for recognizing species invasion: the example of Codium, and generally applicable methods for algae. Hydrobiologia 326, 29–34 (1996). https://doi.org/10.1007/BF00047784

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00047784

Key words

Search

Navigation