A new araphid diatom genus Psammoneis gen. nov. (Plagiogrammaceae, Bacillariophyta) with three new species based on SSU and LSU rDNA sequence data and morphology

REFERENCES

• Altekar G., Dwarkadas S., Huelsenbeck J.P. & Ronquist F. 2004. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407–415.
   PubMed Web of Science ®Google Scholar
• Alverson A.J. & Kolnick L. 2005. Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta). Journal of Phycology 41: 1248–1257.
   Web of Science ®Google Scholar
• Alverson A.J., Cannone J.J., Gutell R.R. & Theriot E.C. 2006. The evolution of elongate shape in diatoms. Journal of Phycology 42: 655–668.
   Web of Science ®Google Scholar
• Amato A., Kooistra W.H.C.F., Levialdi Ghiron J.H., Mann D.G., Pröschold T. & Montresor M. 2007. Reproductive isolation among sympatric cryptic species in marine diatoms. Protist 158: 193–207.
   PubMed Web of Science ®Google Scholar
• Anonymous. 1975. Proposals for a standardization of diatom terminology and diagnoses. Nova Hedwigia, Beiheft 53: 323–354.
   Google Scholar
• Behnke A., Friedl T., Chepurnov V.A. & Mann D.G. 2004. Reproductive compatibility and rDNA sequence analyses in the Sellaphora pupula species complex (Bacillariophyta). Journal of Phycology 40: 193–208.
   Web of Science ®Google Scholar
• Beszteri B., Ács É. & Medlin L.K. 2005. Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity. Protist 156: 317–333.
   PubMed Web of Science ®Google Scholar
• Beszteri B., John U. & Medlin L.K. 2007. An assessment of cryptic genetic diversity within the Cyclotella meneghiniana species complex (Bacillariophyta) based on nuclear and plastid genes, and amplified fragment length polymorphisms. European Journal of Phycology 42: 47–60.
   Web of Science ®Google Scholar
• Cahoon L.B. 1999. The role of benthic microalgae in neritic ecosystems. Oceanography and Marine Biology. An Annual Review 37: 47–86.
   Web of Science ®Google Scholar
• Capesius I. & Van De Peer Y. 1997. Secondary structure of the large ribosomal subunit RNA of the moss Funaria hygrometrica. Journal of Plant Physiology 151: 239–241.
   Web of Science ®Google Scholar
• Chepurnov V.A. & Mann D.G. 2004. Auxosporulation of Licmophora communis (Bacillariophyta) and a review of mating systems and sexual reproduction in araphid pennate diatoms. Phycological Research 52: 1–12.
   Web of Science ®Google Scholar
• Chepurnov V.A., Mann D.G., Sabbe K. & Vyverman W. 2004. Experimental studies on sexual reproduction in diatoms. International Review of Cytology 237: 91–154.
   PubMed Web of Science ®Google Scholar
• Coleman A.W. 2000. The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist 151: 1–9.
   PubMed Web of Science ®Google Scholar
• Coleman A.W. 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. TRENDS in Genetics 19: 370–375.
   PubMed Web of Science ®Google Scholar
• Cox E.J. & Ross R. 1981. The striae of pennate diatoms. In: Proceedings of the 6th International Diatom Symposium on Recent and Fossil Diatoms (Ed. by R. Ross), pp. 267–278. O. Koeltz, Koenigstein, Germany.
   Google Scholar
• De Toni G.B. 1890. Sulla Navicula aponina Kuetz. e sui due generi Brachysira Kuetz. e Libellus Cleve. Atti del Rale Instituto Veneto di Scienze, Lettere ed Arti 1890: 967–971.
   Google Scholar
• Elwood H.J., Olsen G.J. & Sogin M.L. 1985. The small subunit ribosomal DNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonichia pustulata. Molecular Biology and Evolution 2: 399–410.
   PubMed Web of Science ®Google Scholar
• Eppley R.W., Holmes R.W. & Strickland J.D.H. 1967. Sinking rates of the marine phytoplankton measured with a fluorochrometer. Journal of Experimental Marine Biology and Ecology 1: 191–208.
   Google Scholar
• Estes L. & Dute R.R. 1994. Valve abnormalities in diatom clones maintained in long-term culture. Diatom Research 9: 249–258.
   Google Scholar
• Evans K.M., Wortley A.H. & Mann D.G. 2007. An assessment of potential diatom “barcode” genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist 158: 349–364.
   PubMed Web of Science ®Google Scholar
• Guillou L., Chrétiennot-Dinet M.-J., Medlin L.K., Claustre H., Loiseaux-de Goër S. & Vaulot D. 1999. Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae class. nov. (Heterokonta). Journal of Phycology 35: 368–381.
   Web of Science ®Google Scholar
• Hall T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
   Google Scholar
• Hasle G.R., von Stosch H.A. & Syvertsen E.E. 1983. Cymatosiraceae, a new diatom family. Bacillaria 6: 9–156.
   Google Scholar
• Honeywill C. 1998. A study of British Licmophora species and a discussion of its morphological features. Diatom Research 13: 221–271.
   Google Scholar
• Huelsenbeck J.P. & Ronquist F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17: 754–755.
   PubMed Web of Science ®Google Scholar
• Hustedt F. 1959. Die Kieselalgen Deutschlands, Österreichs und der Schweiz unter Berücksichtigung der übrigen Länder Europas Sowie der angrenzenden Meeresgebiete. Reprint 1977, Koeltz Science Publishers, Koenigstein, Germany. 845 pp.
   Google Scholar
• Jaworski G.H.M., Wiseman S.W. & Reynolds C.S. 1988. Variability in sinking rate of the freshwater diatom Asterionella formosa: the influence of colony morphology. British Phycological Journal 23: 167–176.
   Web of Science ®Google Scholar
• Kooistra W., De Stefano M., Mann D.G., Salma N. & Medlin L.K. 2003. Phylogenetic position of Toxarium, a pennate-like lineage within centric diatoms (Bacillariophyceae). Journal of Phycology 39: 185–197.
   Web of Science ®Google Scholar
• Kooistra W.H.C.F., Forlani G., Sterrenburg F.A.S. & De Stefano M. 2004. Molecular phylogeny and morphology of the marine diatom Talaroneis posidoniae gen. et sp. nov. (Bacillariophyta) advocate the return of the Plagiogrammaceae to the pennate diatoms. Phycologia 43: 58–67.
   Web of Science ®Google Scholar
• Kooistra W.H.C.F., Gersonde R., Medlin L.K. & Mann D.G. 2007. The origin and evolution of the diatoms: their adaptation to a planktonic existence. In: Evolution of primary producers in the sea (Ed. by P.G. Falkowski & A.H. Knoll), pp. 207–249. Academic Press, New York.
   Google Scholar
• Kooistra W.H.C.F., Sarno D., Balzano S., Gu H., Andersen R.A. & Zingone A. 2008. Global diversity and biogeography of Skeletonema species (Bacillariophyta). Protist 159: 177–193.
   PubMed Web of Science ®Google Scholar
• Lundholm N., Skov J., Pocklington R. & Moestrup O. 1997. Studies on the marine planktonic diatom Pseudo-nitzschia. 2. Autoecology of P. pseudodelicatissima based on isolates from Danish coastal waters. Phycologia 36: 381–388.
   Web of Science ®Google Scholar
• Mann D.G. & Evans K.M. 2007. Molecular genetics and the neglected art of diatomics. In: Unraveling the algae = the past, present and future of algal molecular systematics (Ed. by J. Brodie and J.M. Lewis), pp. 232–266. CRC Press, Boca Raton, FL.
   Google Scholar
• Marin B., Palm A., Klingberg M. & Melkonian M. 2003. Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparison and synapomorphic signatures in the SSU rRNA secondary structure. Protist 154: 99–145.
   PubMed Web of Science ®Google Scholar
• Mathews D.H., Disney M.D., Childs J.L., Schroeder S.J., Zuker M. & Turner D.H. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America 101: 7287–7292.
   PubMed Web of Science ®Google Scholar
• McBride S.A. & Edgar R.K. 1998. Janus cells unveiled: frustular morphometric variability in Gomphonema angustatum. Diatom Research 13: 293–310.
   Google Scholar
• Medlin L.K. & Kaczmarska I. 2004. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia 43: 245–270.
   Web of Science ®Google Scholar
• Medlin L., Elwood H.J., Stickel S. & Sogin M.L. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions. Gene 71: 491–499.
   PubMed Web of Science ®Google Scholar
• Medlin L.K., Kooistra W.H.C.F. & Schmid A.M.-M. 2000. A review of the evolution of the diatoms — a total approach using molecules, morphology and geology. In: The origin and early evolution of the diatoms: fossil, molecular and biogeographical approaches (Ed. by A. Witkowski & J. Sieminska), pp. 13–35. Szafer Institute of Botany, Polish Academy of Science, Cracow, Poland.
   Google Scholar
• Medlin L.K., Jung I., Bahulikar R., Mendgen K., Kroth P. & Kooistra W.H.C.F. 2008a. Evolution of the diatoms. VI. Assessment of the new genera in the araphids using molecular data. Nova Hedwigia 133: 81–100.
   Google Scholar
• Medlin L.K., Sato S., Mann D.G. & Kooistra W.H.C.F. 2008b. Molecular evidence confirms sister relationship of Ardissonea, Climacosphenia and Toxarium within the bipolar centric diatoms. Journal of Phycology. (in press).
   Google Scholar
• Nagumo T. & Kobayashi H. 1990. The bleaching method for gently loosening and cleaning a single diatom frustule. Diatom 5: 45–50.
   Google Scholar
• Posada D. & Crandall K.A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817–818.
   PubMed Web of Science ®Google Scholar
• R Development Core Team. 2005. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: http://www.R-project.org.
   Google Scholar
• Ronquist F. & Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
   PubMed Web of Science ®Google Scholar
• Round F.E. 1993. A Synedra (Bacillariophyta) clone after several years in culture. Nova Hedwgia, Beiheft 106: 353–359.
   Google Scholar
• Round F.E., Crawford R.M. & Mann D.G. 1990. The diatoms: biology and morphology of the genera. Cambridge University Press, Cambridge, UK. 747 pp.
   Google Scholar
• Sabbe K. & Vyverman W. 1995. Taxonomy, morphology and ecology of some widespread representatives of the diatom genus Opephora. European Journal of Phycology 30: 235–249.
   Web of Science ®Google Scholar
• Sarno D., Kooistra W.C.H.F., Medlin L.K., Percopo I. & Zingone A. 2005. Diversity in the genus Skeletonema (Bacillariophyceae). II. An assessment of the taxonomy S. costatum-like species, with the description of four new species. Journal of Phycology 41: 151–176.
   Web of Science ®Google Scholar
• Sato S., Watanabe T., Kooistra W.H.C.F. & Medlin L.K. 2008a. Morphology of four plagiogrammacean diatoms; Dimeregramma minor var. nana, Neofragilaria nicobarica, Plagiogramma atomus and Psammogramma vigoensis gen. et sp. nov., and their phylogenetic relationship inferred from partial 28S rDNA. Phycological Research. (in press).
   Google Scholar
• Sato S., Mann D.G., Nagumo T., Tanaka J., Tadano T. & Medlin L.K. 2008b. Auxospore fine structure and variation in modes of cell size changes in Grammatophora marina (Bacillariophyta). Phycologia 47: 12–27.
   Web of Science ®Google Scholar
• Simonsen R. 1972. Ideas for a more natural system of the centric diatoms. Nova Hedwigia, Beiheft 39: 37–54.
   Google Scholar
• Simonsen R. 1979. The diatom system: ideas on phylogeny. Bacillaria 2: 9–71.
   Google Scholar
• Sims P.A., Mann D.G. & Medlin L.K. 2006. Evolution of the diatoms: insights from fossil, biological and molecular data. Phycologia 45: 361–402.
   Web of Science ®Google Scholar
• Sinninghe-Damste J.S., Muyzer G., Abbas B., Rampen S.W., Masse G., Allard W.G., Belt S.T., Robert J.-M., Rowland S.J., Moldowan J.M., Barbanti S.M., Fago F.J., Denisevich P., Dahl J., Trindade L.A.F. & Schouten S. 2004. The rise of the rhizosolenoid diatoms. Science 304: 584–587.
   PubMed Web of Science ®Google Scholar
• Snoeijs P. 1992. Studies in the Tabularia fasciculata complex. Diatom Research 7: 313–344.
   Google Scholar
• Snoeijs P. & Kuylenstierna M. 1991. Two new diatom species in the genus Tabularia from the Swedish coast. Diatom Research 6: 351–365.
   Google Scholar
• Sorhannus U. 2007. A nuclear-encoded small-subunit ribosomal RNA timescale for diatom evolution. Marine Micropaleontolog 65: 1–12.
   Web of Science ®Google Scholar
• Stamatakis A., Ludwig T. & Meier H. 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456–463.
   PubMed Web of Science ®Google Scholar
• Stoermer E.F. 1967. Polymorphism in Mastogloia. Journal of Phycology 3: 73–77.
   PubMed Web of Science ®Google Scholar
• Swofford D.L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10. Sinauer Associates, Sunderland, MA, USA.
   Google Scholar
• Sullivan M.J. & Currin C.A. 2000. Community structure and functional dynamics of benthic microalgae in salt marshes. In: Concepts and controversies in tidal marsh ecology (Ed. by M.P. Weinstein & D.A. Kreeger), pp. 81–106. Kluwer Academic Publishers, Dordrecht, Germany.
   Google Scholar
• Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F. & Higgins D.G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24: 4876–4882.
   Web of Science ®Google Scholar
• Underwood G.J.C. & Kromkamp J. 1999. Primary production by phytoplankton and microphytobenthos in estuaries. Advances in Ecological Research 29: 93–153.
   Web of Science ®Google Scholar
• Van de Peer Y., Caers A., De Rijk P. & De Wachter R. 1998. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Research 26: 179–182.
   Web of Science ®Google Scholar
• Williams D.M. & Round F.E. 1986. Revision of the genus Synedra Ehrenb. Diatom Research 1: 313–339.
   Google Scholar