Molecular phylogeny of the Siphonocladales (Chlorophyta: Cladophorophyceae)

Molecular Phylogenetics and Evolution

Volumn 44, Issue 3, 2007, Pages 1237-1256

  Leliaert, Frederik ^a   De Clerck, Olivier ^a   Verbruggen, Heroen ^a   Boedeker, Christian ^b   Coppejans, Eric ^a  

^a Centre for Molecular Phylogenetics and Evolution   (Belgium)

^b UNIVERSITEIT LEIDEN BRANCH   (Netherlands)

Author keywords

Benthic marine algae; Cladophorales; Cladophorophyceae; Convergent evolution; Doublet model; Long branch attraction; Molecular clock rooting; Molecular systematics; Morphological evolution; Outgroup rooting; Ribosomal DNA; RNA secondary structure; Segregative cell division; Siphonocladales; Taxonomy

Indexed keywords

ALGAL DNA; PRIMER DNA; RIBOSOME DNA;

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; CYTOLOGY; GENETICS; GEOGRAPHY; GREEN ALGA; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL; TIME;

ALGAE, GREEN; BASE SEQUENCE; DNA PRIMERS; DNA, ALGAL; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; TIME FACTORS;

ALGAE; CHLOROPHYTA; CLADOPHORA; CLADOPHORALES;

EID: 34547914805     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.04.016     Document Type: Article

References (101)

1. Andreakis N., Procaccini G., and Kooistra W.H.C.F. Asparagopsis taxiformis and Asparagopsis armata (Bonnemaisoniales, Rhodophyta): genetic and morphological identification of Mediterranean populations. Eur. J. Phycol. 39 (2004) 273-283
2. Bakker F.T., Olsen J.L., Stam W.T., and van den Hoek C. The Cladophora complex (Chlorophyta): new views based on 18S rRNA gene sequences. Mol. Phyl. Evol. 3 (1994) 365-382
3. Berger S., and Kaever M.J. Dasycladales (1992), Georg Thieme Verlag, Stuttgart
4. Bergsten J. A review of long-branch attraction. Cladistics 21 (2005) 163-193
5. Børgesen F. Contributions à la connaissance du genre Siphonocladus Schmitz. Overs. K. Dan. Vidensk. Selsk. Fosh. 1905 (1905) 259-291
6. Børgesen F. Some Chlorophyceae from the Danish West Indies. II. Bot. Tidskr. 32 (1912) 241-273
7. Børgesen F. The marine algae of the Danish West Indies. Part 1. Chlorophyceae. Dansk Bot. Ark. 1 4 (1913) 158
8. Børgesen F. Some marine algae from Mauritius. I. Chlorophyceae. Biol. Meddel. Kongel. Danske Vidensk. Selsk. 15 4 (1940) 81
9. Bot, P.V.M., 1992. Molecular relationships in the seaweed genus Cladophora. Ph.D. Thesis, University of Groningen, The Netherlands, 110 pp.
10. Buchheim M., Buchheim J., Carlson T., Braband A., Hepperle D., Krienitz L., Wolf M., and Hegewald E. Phylogeny of the Hydrodictyaceae (Chlorophyceae): inferences from rDNA data. J. Phycol. 41 (2005) 1039-1054
11. Butterfield N.J., Knoll A.H., and Swett K. Exceptional preservation of fossils in an Upper Proterozoic shale. Nature 334 (1988) 424-427
12. Cunningham C.W., Omland K., and Oakley T. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 13 (1998) 361-366
13. De Rijk P., Robbrecht E., de Hoog S., Caers A., Van de Peer Y., and De Wachter R. Database on the structure of large subunit ribosomal RNA. Nucleic Acids Res. 27 (1999) 174-178
14. De Rijk P., and De Wachter R. DCSE, an interactive tool for sequence alignment and secondary structure research. Comput. Appl. Biosci. 9 (1993) 735-740
15. Egerod L.E. An analysis of the siphonous Chlorophycophyta with special reference to the Siphonocladales, Siphonales, and Dasycladales of Hawaii. Univ. Calif. Publ. Bot. 25 (1952) 327-367
16. Egerod L.E. Marine algae of the Andaman Sea coast of Thailand: Chlorophyceae. Bot. Mar. 18 (1975) 41-66
17. Enomoto S., and Hirose H. On the septum formation of Microdictyon okamurai Setchell. Bull. Jap. Soc. Phycol. 19 (1971) 90-93
18. Enomoto S., and Okuda K. Culture studies of Dictyosphaeria (Chlorophyceae, Siphonocladales I). Life history and morphogenesis of Dictyosphaeria cavernosa. Jap. J. Phycol. 29 (1981) 225-236
19. Enomoto S., Hori T., and Okuda K. Culture studies of Dictyosphaeria (Chlorophyceae, Siphonocladales) II. Morphological analysis of segregative cell division in Dictyosphaeria cavernosa. Jap. J. Phycol. 30 (1982) 103-112
20. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Constructing a significance test for incongruence. Syst. Biol. 44 (1995) 570-572
21. Feau N., Hamelin R.C., and Bernier L. Attributes and congruence of three molecular data sets: inferring phylogenies among Septoria-related species from woody perennial plants. Mol. Phyl. Evol. 40 (2006) 808-829
22. Felicini G.P., and Perrone C. Segregative and pseudo-segregative cell division in Valonia utricularis (Siphonocladales-Cladophorales complex, Chlorophyta). Giorn. Bot. Ital. 128 (1994) 810-812
23. Felicini G.P., Perrone C., and Bottalico A. Endogenous and in vitro protoplasts of Valonia utricularis and Valonia aegagropila (Chlorophyta, Cladophorophyceae). Boll. Museo Region. Sci. Nat. Torino 15 (1997) 131-151
24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
25. Fritsch F.E. Cladophorella calcicola nov. gen. et sp., a terrestrial member of the Cladophorales. Ann. Bot. 8 (1944) 157-171
26. Goloboff P.A. Estimating character weights during tree search. Cladistics 9 (1993) 83-91
27. Gontcharov A.A., Marin B., and Melkonian M. Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). Mol. Biol. Evol. 21 (2004) 612-624
28. Graham S.W., Olmstead R.G., and Barrett S.C.H. Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots. Mol. Biol. Evol. 19 (2002) 1769-1781
29. Hanyuda T., Wakana I., Arai S., Miyaji K., Watano Y., and Ueda K. Phylogenetic relationships within Cladophorales (Ulvophyceae, Chlorophyta) inferred from 18S rRNA gene sequences, with special reference to Aegagropila linnaei. J. Phycol. 38 (2002) 564-571
30. Harvey J.B.J., and Goff L.J. A reassessment of species boundaries in Cystoseira and Halidrys (Phaeophyceae, Fucales) along the North American west coast. J. Phycol. 42 (2006) 707-720
31. Hillis D.M., and Huelsenbeck J.P. Signal, noise, and reliability in molecular phylogenetic analyses. J. Hered. 83 (1992) 189-195
32. Holland B.R., Penny D., and Hendy M.D. Outgroup misplacement and phylogenetic inaccuracy under a molecular clock - a simulation study. Syst. Biol. 52 (2003) 229-238
33. Huelsenbeck J.P., Bull J.J., and Cunningham C.W. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11 (1996) 152-158
34. Huelsenbeck J.P., Bollback J.P., and Levine A.M. Inferring the root of a phylogenetic tree. Syst. Biol. 51 (2002) 32-43
35. Jukes T.H., and Cantor C.R. Evolution of protein molecules. In: Munro H.N. (Ed). Mammalian Protein Metabolism (1969), Academic Press, New York 21-123
36. Kim G.H., and Klotchkova T.A. Development of protoplasts induced from wound-response in fifteen marine green algae. Jap. J. Phycol. 52 suppl. (2004) 111-116
37. Kim G.H., Klotchkova T.A., and West J.A. From protoplasm to swarmer: regeneration of protoplasts from disintegrated cells of the multicellular marine green alga Microdictyon umbilicatum (Chlorophyta). J. Phycol. 38 (2002) 174-183
38. Kjer K.M. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol. Phyl. Evol. 4 (1995) 314-330
39. Kraft G.T. Marine and estuarine benthic green algae (Chlorophyta) of Lord Howe Island, South-western Pacific. Aust. Syst. Bot. 13 (2000) 509-648
40. Kraft G.T., and Wynne M.J. Delineation of the genera Struvea Sonder and Phyllodictyon J.E. Gray (Cladophorales, Chlorophyta). Phycol. Res. 44 (1996) 129-143
41. Kützing F.T., 1843. Phycologia generalis. Leipzig.
42. La Claire II J.W. Cytomorphological aspects of wound healing in selected Siphonocladales (Chlorophyta). J. Phycol. 18 (1982) 379-384
43. Leliaert, F., 2004. Taxonomic and phylogenetic studies in the Cladophorophyceae (Chlorophyta). Ph.D. Dissertation, Ghent University, Belgium. 294 pp. (Available from: ).
44. Leliaert F., and Coppejans E. Crystalline cell inclusions: a new diagnostic character in the Cladophorophyceae (Chlorophyta). Phycologia 43 (2004) 189-203
45. Leliaert F., and Coppejans E. A revision of Cladophoropsis Børgesen (Siphonocladales, Chlorophyta). Phycologia 45 (2006) 657-679
46. Leliaert F., and Coppejans E. Systematics of two deep-water species from the Indo-West Pacific: Struvea gardineri A. Gepp & E. Gepp and Phyllodictyon orientale (A. Gepp & E. Gepp) Kraft & M.J. Wynne (Siphonocladales, Chlorophyta). Bot. J. Linn. Soc. 153 (2007) 115-132
47. Leliaert F., Rousseau F., de Reviers B., and Coppejans E. Phylogeny of the Cladophorophyceae (Chlorophyta) inferred from partial LSU rRNA gene sequences: is the recognition of a separate order Siphonocladales justified?. Eur. J. Phycol. 38 (2003) 233-246
48. Lindstrom S.C. The Bering Strait connection: dispersal and speciation in boreal macroalgae. J. Biogeogr. 28 (2001) 243-251
49. Littler D.S., and Littler M.M. Systematics of Anadyomene species (Anadyomenaceae, Chlorophyta) in the tropical western Atlantic. J. Phycol. 27 (1991) 101-118
50. López-Bautista J.M., and Chapman R.L. Phylogenetic affinities of the Trentepohliales inferred form small subunit ribosomal DNA. Int. J. Syst. Evol. Microbiol. 53 (2003) 2099-2106
51. Lyons-Weiler J., Hoelzer G.A., and Tausch R.J. Optimal outgroup analysis. Biol. J. Linn. Soc. 64 (1998) 493-511
52. Maddison, W.P., Maddison, D.R., 2006. Mesquite: a modular system for evolutionary analysis. Version 1.11. (Available from: ).
53. Maddison W.P., Donoghue M.J., and Maddison D.R. Outgroup analysis and parsimony. Syst. Zool. 33 (1984) 83-103
54. Mallet J. A species definition for the modern synthesis. Trends Ecol. Evol. 10 (1995) 294-299
55. McDonald K.L., and Pickett-Heaps J.D. Ultrastructure and differentiation in Cladophora glomerata. I. Cell division. Am. J. Bot. 63 (1976) 592-601
56. Murray S., Jorgensen M.F., Ho S.Y.W., Patterson D.J., and Jermiin L.S. Improving the analysis of dinoflagellate phylogeny based on rDNA. Protist 156 (2005) 269-286
57. Norris J.N., and Olsen J.L. Deep-water green algae from the Bahamas, including Cladophora vandenhoekii sp. nov. (Cladophorales). Phycologia 30 (1991) 315-328
58. Nylander, J.A.A., 2004. MrModeltest v2. Evolutionary Biology Centre, Uppsala University. (Available from: ).
59. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
60. Okuda K., Mine I., Morinaga T., and Kuwaki N. Cytomorphogenesis in cenocytic green algae: V. Segregative cell division and cortical microtubules in Dictyosphaeria cavernosa (Siphonocladales, Chlorophyceae). Phycol. Res. 45 (1997) 189-196
61. Olsen J.L., and West J.A. Ventricaria (Siphonocladales-Cladophorales complex, Chlorophyta), a new genus for Valonia ventricosa. Phycologia 27 (1988) 103-108
62. Olsen-Stojkovich, J.L., 1986. Phylogenetic studies of genera in the Siphonocladales-Cladophorales complex (Chlorophyta). Ph.D. Dissertation, University of California, Berkeley, 183 pp.
63. Olsen-Stojkovich J., West J.A., and Lowenstein J.M. Phylogenetics and biogeography in the Cladophorales complex (Chlorophyta): some insights from immunological distance data. Bot. Mar. 29 (1986) 239-249
64. O'Neil R.M., and La Claire II J.W. Mechanical wounding induces the formation of extensive coated membranes in giant algal cells. Science 255 (1984) 331-333
65. Oltmanns, F., 1922. Morphologie und Biologie der Algen. Ed. 2. vol. 1. Jena.
66. Papenfuss G.F., and Chihara M. The morphology and systematic position of the green algae Ernodesmis and Apjohnia. Phycologia 14 (1975) 309-316
67. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
68. Posada D., and Crandall K.A. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50 (2001) 580-601
69. Posada D., and Buckley T.R. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53 (2004) 793-808
70. Rindi F., Lopez-Bautista J.M., Sherwood A.R., and Guiry M.D. Morphology and phylogenetic position of Spongiochrysis hawaiiensis gen. et sp. nov., the first known terrestrial member of the order Cladophorales (Ulvophyceae, Chlorophyta). Int. J. Syst. Evol. Microbiol. 56 (2006) 913-922
71. Ronquist F., and Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
72. Russo C.A.M., Takezaki N., and Nei M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13 (1996) 525-536
73. Schöniger M., and von Haeseler A. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol. 3 (1994) 240-247
74. Scott J.L., and Bullock K.W. Ultrastructure of cell-division in Cladophora-pre-gametangial cell-division in haploid generation of Cladophora flexuosa. Can. J. Bot. 54 (1976) 1546-1560
75. Silva P.C., Basson P.W., and Moe R.L. Catalogue of the Benthic Marine Algae of the Indian Ocean (1996), University of California Press, Berkeley
76. *and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
77. Swofford D.L., Olsen G.J., Waddell P.J., and Hillis D.M. Phylogenetic inference. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics. second ed. (1996), Sinauer, Sunderland, MA 407-514
78. Tappan H. The Paleobiology of Plant Protists (1980), W.H. Freeman and Co., San Fransisco
79. Taylor W.R. The marine algae of Florida with special reference to the Dry Tortugas. Publ. Carnegie Inst. Wash. 379 (1928) 219
80. Taylor W.R. Plants of Bikini and Other Northern Marshall Islands (1950), University of Michigan Press, Ann Arbor
81. Taylor W.R. Marine Algae of the Eastern Tropical and Subtropical Coasts of the Americas (1960), The University of Michigan Press, Ann Arbor
82. Telford M.J., Wise M.J., and Gowri-Shankar V. Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria. Mol. Biol. Evol. 22 (2005) 1129-1136
83. van den Hoek C. Revision of the European Species of Cladophora (1963), Brill E.J., Leiden
84. van den Hoek C. A taxonomic revision of the American species of Cladophora (Chlorophyceae) in the North Atlantic Ocean and their geographic distribution. Verh. Kon. Ned. Akad. Wetensch., Afd. Natuurk., Tweede Sect. 78 (1982) 236
85. van den Hoek C. The systematics of the Cladophorales. In: Irvine D.E.G., and John D.M. (Eds). Systematics of the Green Algae (1984), Academic Press, London 157-178
86. van den Hoek C., and Chihara M. A taxonomic revision of the marine species of Cladophora (Chlorophyta) along the coasts of Japan and the Russian Far-east National Science Museum (Tokyo). Monographs 19 (2000) 242
87. van den Hoek C., Mann D.G., and Jahns H.M. Algae. An Introduction to Phycology (1995), Cambridge University Press, Cambridge
88. van der Strate H.J., Boele-Bos S.A., Olsen J.L., van de Zande L., and Stam W.T. Phylogeographic studies in the tropical seaweed Cladophoropsis membranaceae (Chlorophyta, Ulvophyceae) reveal a cryptic species complex. J. Phycol. 38 (2002) 572-582
89. Verbruggen H., De Clerck O., Kooistra W.H.C.F., and Coppejans E. Molecular and morphometric data pinpoint species boundaries in Halimeda section Rhipsalis (Bryopsidales, Chlorophyta). J. Phycol. 41 (2005) 606-621
90. Wagner H.P., and Zaneveld J.S. The Xanthophyceae and Chlorophyceae of the western Ross Sea, Victoria land, Antarctica and Macquarie Island collected under the direction of Zaneveld, J.S. (1963-1967). Blumea 33 (1988) 141-180
91. Weber-van Bosse, A., 1913. Liste des algues du Siboga. I. Myxophyceae, Chlorophyceae, Phaeophyceae avec le concours de M. Th. Reinbold. Siboga-Expeditie Monographie 59a. Leiden, 186 pp.
92. Wheeler W.C. Nucleic-acid sequence phylogeny and random outgroups. Cladistics 6 (1990) 363-367
93. Womersley H.B.S. The Marine Benthic Flora of Southern Australia. Part I (1984), Government Printer, South Australia, Adelaide
94. Womersley H.B.S., and Bailey A. Marine algae of the Solomon Islands. Philos. Trans. R. Soc. Lond. B 259 (1970) 257-352
95. Wortley A.H., Rudall P.J., Harris D.J., and Scotland R.W. How much data are needed to resolve a difficult phylogeny? Case study in Lamiales. Syst. Biol. 54 (2005) 697-709
96. Wray J.L. Calcareous algae. In: Haq B.U., and Boersma A. (Eds). Introduction to Marine Micropaleontology (1978), Elsevier, New York 171-187
97. Wuyts J., De Rijk P., Van de Peer Y., Winkelmans T., and De Wachter R. The European large subunit ribosomal RNA database. Nucleic Acids Res. 29 (2001) 175-177
98. Wysor, B., 2002. Biodiversity and biogeography of marine green algae of the Republic of Panama. Ph.D. Dissertation, University of Louisiana at Lafayette.
99. Xia X., and Xie Z. DAMBE: data analysis in molecular biology and evolution. J. Hered. 92 (2001) 371-373
100. Zechman F.W., Theriot E.C., Zimmer E.A., and Chapman R.L. Phylogeny of the Ulvophyceae (Chlorophyta): cladistic analysis of nuclear-encoded rRNA sequence data. J. Phycol. 26 (1990) 700-710
101. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415