Origin and Evolution of the Canal Raphe System in Diatoms

Protist

Volumn 162, Issue 5, 2011, Pages 723-737

  Ruck, Elizabeth C ^a   Theriot, Edward C ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Canal raphe; Diatom; Fibulae; Parallel evolution

Indexed keywords

ARTICLE; CELL WALL; CLASSIFICATION; DIATOM; EVOLUTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; MORPHOGENESIS; PHYLOGENY; ULTRASTRUCTURE;

BIOLOGICAL EVOLUTION; CELL WALL; DIATOMS; MOLECULAR SEQUENCE DATA; MORPHOGENESIS; PHYLOGENY;

BACILLARIALES; BACILLARIOPHYCEAE; BACILLARIOPHYTA; RAPHIDAE; RHOPALODIALES; SURIRELLALES;

EID: 80053096992     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2011.02.003     Document Type: Article

References (68)

1. Alverson A.J., Theriot E.C. Comments on the recent progress toward reconstructing the diatom phylogeny. J Nanosci Nanotechnol 2005, 5:57-62.
2. Alverson A.J., Jansen R.K., Theriot E.C. Bridging the Rubicon: Phylogenetic analysis reveals repeated colonization's of marine and fresh waters by thalassiosiroid diatoms. Mol Phylogenet Evol 2007, 45:193-210.
3. Alverson A.J., Cannone J.J., Gutell R.R., Theriot E.C. The evolution of elongate shape in diatoms. J Phycol 2006, 42:655-668.
4. Bruder K., Medlin L.K. Morphological and molecular investigations of naviculoid diatoms. II. Selected genera and families. Diatom Res 2008, 23:283-329.
5. Bruder K., Medlin L.K. Morphological and molecular investigations of naviculoid diatoms. III. Hippodonta and Navicula S.S. Diatom Res 2008, 23:331-347.
6. Czarnecki D.B. The freshwater diatom culture collection at Loras College, Dubuque, Iowa. Not Nat 1987, 465:1-16.
7. Daugbjerg N., Andersen R.A. A molecular phylogeny of the heterokont algae based on analyses of chloroplast-encoded rbcL sequence data. J Phycol 1997, 33:1031-1041.
8. DeYoe H., Lowe R.L., Marks J.C. Effects on nitrogen and phosphorus on the endosymbiont load of Rhopalodia gibba and Epithemia turgida (Bacillariophyceae). J Phycol 1992, 28:773-777.
9. Drum R.W., Pankratz S. Fine structure of an unusual cytoplasmic inclusion in the diatom genus Rhopalodia. Protoplasma 1965, 60:141-149.
10. Edgar S.M., Theriot E.C. Phylogeny of Aulacoseira (Bacillariophyta) based on molecules and morphology. J Phycol 2004, 40:772-788.
11. Floener L., Bothe H. Nitrogen Fixation in Rhopalodia gibba, a Diatom Containing Blue-greenish Inclusions Symbiotically. Endocytobiology, Endosymbiosis and Cell Biology 1980, 541-552. Walter de Gruyter & Co, Berlin. W. Schwemmler, H.E.A. Schenk (Eds.).
12. Geitler L. Zur Entwicklungsgeschichte der Epithemiaceen Epithemia, Rhopalodia und Denticula (Diatomophyceae) und ihre vermutlich symbiontischen Sphäroidkörper. Plant Syst Evol 1977, 128:259-275.
13. Goldman N., Anderson J.P., Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst Biol 2000, 49:652-670.
14. Guillard R.R.L. Culture of Phytoplankton for Feeding Marine Invertebrates. Culture of Marine Invertebrate Animals 1975, 26-60. Plenum Press, New York. W.L. Smith, M.H. Chanley (Eds.).
15. Guillard R.R.L., Ryther J.H. Studies of marine planktonic diatoms. I. Cyclotella nana Hustedt and Detonula confervacea (Cleve) Gran. Can J Microbiol 1962, 8:229-239.
16. Heath T.A., Hedtke S.M., Hillis D.M. Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 2008, 46:239-257.
17. Hedtke S.M., Stanger-Hall K., Baker R.J., Hillis D.M. All-male asexuality: Origin and maintenance of androgenesis in the Asian clam Corbicula. Evolution 2008, 62:1119-1136.
18. Hendey NI (1964) An Introductory Account of the Smaller Algae of British Coastal Waters, Part V: Bacillariophyceae (Diatoms). Fisheries Investigation Series IV: HMSO, London, pp 1-317.
19. Hillis D.M. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 1998, 47:3-8.
20. Hillis D.M., Mable B.K., Moritz C. Applications of Molecular Systematics: The State of the Field and a Look into the Future. Molecular Systematics 1996, 1-655. Sinauer Associates, Sunderland, Massachusetts, USA. D.M. Hillis, C. Moritz, B.K. Mable (Eds.).
21. Hillis D.M., Pollock D.D., McGuire J.A., Zwickl D.J. Is sparse taxon sampling a problem for phylogenetic inference?. Syst Biol 2003, 52:124-126.
22. Huelsenbeck J.P., Hillis D.M., Jones R. Parametric Bootstrapping in Molecular Phylogenetics: Applications and Performance. Molecular Zoology: Advances, Strategies and Protocols 1996, 19-45. Wiley-Liss, New York. J.D. Ferraris, S.R. Palumbi (Eds.).
23. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
24. Hustedt F. Untersuchungen über den Bau der Diatomeen. IV. Zur Morphologie und Systematik der Gattungen Denticula und Epithemia. Ber Deutsch Bot Ges 1928, 46:148-157.
25. Hustedt F. Untersuchungen über den Bau der Diatomeen. VII-VIII. VII. Weitere Untersuchungen über die Kanalraphe der Nitzschioideae. VIII. Untersuchungen über die Kanalraphe der Gattung Surirella. Ber Deutsch Bot Ges 1929, 47:101-111.
26. Hustedt F. Bacillariophyta (Diatomae). Die Süsswasser-Flora Mitteleuropas 1930, 1-466. Gustav Fischer Verlag, Jena. A. Pascher (Ed.).
27. Jones H.M., Simpson G.E., Stickle A.J., Mann D.G. Life history and systematics of Petroneis (Bacillariophyta), with special reference to British waters. Eur J Phycol 2005, 40:61-87.
28. Kilham S.S., Kreeger D.A., Goulden C.E., Lynn S. COMBO: A defined freshwater culture medium for algae and zooplankton. Hydrobiologia 1998, 377:147-159.
29. Krammer K. Valve morphology and taxonomy in the genus Stenopterobia (Bacillariophyceae). Br Phycol J 1989, 24:237-243.
30. Krammer K., Lange-Bertalot H. Bacillariophyceae. 2. Teil. Bacillariaceae, Epithemiaceae, Surirellaceae. Süsswasserflora von Mitteleuropa. Band 2/2 1988, 1-596. Gustav Fischer Verlag, Stuttgart, New York. H. Ettl, J. Gerloff, H. Heynig (Eds.).
31. Lange-Bertalot H., Krammer K. Bacillariaceae, Epithemiaceae. Surirellaceae. Biblioth Diatomol 1987, 15:1-289.
32. Lange-Bertalot H., Krammer K. Observations on Simonsenia and some small species of Denticula and Nitzschia. Nova Hedwigia 1993, 106:121-131.
33. Mann D.G. Auxospore formation and neoteny in Surirella angusta (Bacillariophyta) and a modified terminology for cells of Surirellaceae. Nova Hedwigia 2000, 71:165-183.
34. Maddison W.P., Maddison D.R. MacClade 4: Analysis of Phylogeny and Character Evolution 2005, Sinauer Associates, Sunderland, Massachusetts.
35. Medlin L.K., Kaczmarska I. Evolution of the diatoms V: Morphological and cytological support for the major clades and a taxonomic revision. Phycologia 2004, 43:245-270.
36. Medlin L.K., Kooistra W.C.H.F., Schmid A.-M.M. A Review of the Evolution of the Diatoms - a Total Approach Using Molecules, Morphology and Geology. The Origin and Early Evolution of the Diatoms: Fossil, Molecular and Biogeographical Approaches 2000, 13-35. W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow. A. Witkowski, J. Sieminska (Eds.).
37. Medlin L.K., Elwood H.J., Stickel S., Sogin M.L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 1988, 71:491-499.
38. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Bioinformatics 2008, 24:581-583.
39. Paddock T.B.B., Sims P.A. A preliminary survey of the raphe structure of some advanced groups of diatoms (Epithemiaceae-Surirellaceae). Nova Hedwigia Beih 1977, 54:291-322.
40. Paddock T.B.B., Sims P.A. Observations on the marine diatom genus Auricula and two new genera, Undatella and Proboscidea. Bacillaria 1980, 3:161-196.
41. Peragallo H, Peragallo M (1897-1908) Diatomées marines de France et des districts maritimes voisins. Micrographe-Editeur, M.J. Tempère, Grez-sur-Loing, pp 1-491.
42. Pickett-Heaps J.D. Valve morphogenesis and the microtubule center in three species of the diatom Nitzschia. J Phycol 1983, 19:269-281.
43. Pickett-Heaps J.D., Kowalski S.E. Valve morphogenesis and the microtubule center of the diatom Hantzschia amphioxys. Eur J Cell Biol 1981, 25:150-170.
44. Posada D., Buckley T.R. Model selection and model averaging in phylogenetic: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 2004, 53:793-808.
45. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
46. Prechtl J., Kneip C., Lockhart P., Wenderoth K., Maier U.-G. Intracellular spheroid bodies of Rhopalodia gibba have nitrogen-fixing apparatus of cyanobacterial origin. Mol Biol Evol 2004, 21:1477-1481.
47. Rambaut A, Drummond AJ (2007) Tracer v1.4, Available at (last accessed 6 October 2010). http://beast.bio.ed.ac.uk/Tracer.
48. Rambaut A., Grassly N.C. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 1997, 13:235-238.
49. Ross R., Cox E.J., Karayeva N.I., Mann D.G., Paddock T.B.B., Simonsen R., Sims P.A. An amended terminology for the siliceous components of the diatom cell. Nova Hedwigia 1979, 64:513-533.
50. Round F.E., Crawford R.M., Mann D.G. The Diatoms: Biology & Morphology of the Genera 1990, Cambridge University Press, Cambridge, pp 1-747.
51. Ruck E.C., Kociolek J.P. Preliminary phylogeny of the family Surirellaceae (Bacillariophyta). Biblioth Diatomol 2004, 50:1-236.
52. Schmid A.-M.M. The development of structure in the shells of diatoms. Nova Hedwigia Beih 1979, 64:219-236.
53. Schrader H.-J. Types of raphe structures in the diatoms. Nova Hedwigia 1973, 45:195-230.
54. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002, 51:492-508.
55. Shimodaira H., Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
56. Simonsen R. The diatom system: Ideas on phylogeny. Bacillaria 1979, 2:9-71.
57. Sims P.A., Paddock T.B.B. The fenestral fibula: A new structure in the diatoms. Bacillaria 1982, 5:7-42.
58. Sims P.A., Mann D.G., Medlin L.K. Evolution of the diatoms: insights from fossil, biological and molecular data. Phycologia 2006, 45:361-402.
59. Sorhannus U. Diatom phylogenetics inferred based on direct optimization of nuclear-encoded SSU rDNA sequences. Cladistics 2004, 20:487-497.
60. Sorhannus U. A nuclear-encoded small-subunit ribosomal RNA timescale for diatom evolution. Mar Micropaleontol 2007, 65:1-12.
61. Stamatakis A. RaxML-VI-HPC; Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
62. Swofford D.L. PAUP: Phylogenetic Analysis Using Parsimony (and other methods) 2002, Sinauer Associates, Sunderland, Massachusetts.
63. Theriot E.C., Cannone J.J., Gutell R.R., Alverson A.J. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. Eur J Phycol 2009, 44:277-290.
64. Theriot E.C., Ashworth M., Ruck E.C., Nakov T., Jansen R.K. A preliminary multigene phylogeny of the diatoms (Bacillariophyta): Challenges for future research. Plant Ecol Evol 2010, 143:278-296.
65. Verbruggen H., Theriot E.C. Building trees of algae: some advances in phylogenetic and evolutionary analysis. Eur J Phycol 2008, 43:229-252.
66. Wilcox T (2004) SG Runner vers. 1.5.3: a MAC OSX shell-wrapper for Seq-Gen. Published by the author, available at (last accessed 6 October 2010). http://homepage.mac.com/tpwilcox/.
67. Zwickl DJ (2006) Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Ph.D. Dissertation, The University of Texas at Austin, pp 1-115.
68. Zwickl D.J., Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 2002, 51:588-598.