Molecular systematics of the Gelidiales: Inferences from separate and combined analyses of plastid rbcL and nuclear SSU gene sequences

European Journal of Phycology

Volumn 32, Issue 4, 1997, Pages 343-352

  Craig Bailey, J ^a,c   Wilson Freshwater, D ^b  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NORTH CAROLINA WILMINGTON   (United States)

^c BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

Author keywords

Gelidium; Phylogeny; Pterocladia; Pterocladiella; rbcL; SSU

Indexed keywords

EID: 2642619432     PISSN: 09670262     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0967026297001376     Document Type: Review

References (79)

1. ALBERT, V.A., BACKLUND, A. & BREMER, K. (1994). DNA characters and cladistics: the optimization of functional history. In Models in Phylogeny Reconstruction (Scotland, R.W., Siebert, D.J. & Williams, D.M., editors), Systematics Association Special Volume no. 52, 249-272. Clarendon Press, Oxford.
2. AKATSUKA, I. (1982) ('1981'). Comparative Morphology of the outermost cortical cells in the Gelidiaceae (Rhodophyta) of Japan. Nova Hedwigia, 35: 453-463.
3. AKATSUKA, I. (1986). Surface cell morphology and its relationship to other generic characters in non-parasitic Gelidiaceae (Rhodophyta). Bot. Mar., 29: 59-68.
4. BERNARDI, G. & BERNARDI, G. (1986). Compositional constraints and genome evolution. J. Mol. Evol., 24: 1-11.
5. BERNARDI, G. & BERNARDI, G. (1991). Compositional properties of nuclear genes from cold-blooded vertebrates. J. Mol. Evol., 33: 57-67.
6. BIRD, C.J., RICE, E.L., MURPHY, C.A. & RAGAN, M.A. (1992). Phylogenetic relationships in the Gracilariales (Rhodophyta) as determined by 18S rDNA sequences. Phycologia, 31: 510-522.
7. BIRD, C.J., RAGAN, M.A., CRITCHLEY, A. T., RICE, R.L. & GUTELL, R.R. (1994). Molecular relationships among the Gracilariaceae (Rhodophyta): further observation on some undetermined species. Eur. J. Phycol., 29: 195-202.
8. BREMER, K. (1988). The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution, 42: 795-803.
9. BULL, J.J., HUELSENBECK, J.P., CUNNINGHAM, C.W., SWOFFORD, D.L. & WADDELL, P.J. (1993). Partitioning and combining data in phylogenetic analysis. Syst. Biol., 42: 384-397.
10. CAMPBELL, J. & GOWRE, G. (1990). Codon usage in higher plants, green algae and cyanobacteria. Plant Physiol., 92: 1-11.
11. DIXON, P.S. & IRVINE, L.M. (1977). Seaweeds of the British Isles, vol. 1, Rhodophyta, part 1, Introduction, Nemaliales, Gigartinales. British Museum (Natural History), London.
12. DOYLE, J.J. (1992). Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Bot., 17: 144-163.
13. EDWARDS, S.V., ARCTANDER, P. & WILSON, A.C. (1991). Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc. R. Soc. Lond. B, 243: 99-107.
14. FAN, K.-C (1961). Morphological studies of the Gelidiales. Univ. Calif. Pub. Bot., 32: 315-368.
15. FELDMANN, J. & HAMEL, G. (1934). Observations sur quelques Gélidiacées. Rev. Gén. Bot., 46: 528-549.
16. FEISENSTEIN, J. (1978). Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool., 27: 401-410.
17. FELSENSTEIN, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
18. FELSENSTEIN, J. (1988). Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet., 22: 521-565.
19. FREDERICQ, S. & RAMÍREZ, M.E. (1996). Systematic studies of the antarctic species of the Phyllophoraceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis. Hydrobiologia, 326/327: 137-143.
20. FREDERICQ, S., HOMMERSAND, M.H. & FRESHWATER, D.W. (1996). The molecular systematics of some agar- and carrageenan-containing marine red algae based on rbcL sequence analysis. Hydrobiologia, 326/327: 125-135.
21. FRESHWATER, D.W. & RUENESS, J. (1994). Phylogenetic relationships of some European Gelidium (Gelidiales, Rhodophyta) species, based on rbcL nucleotide sequence analysis. Phycohgia, 33: 187-194.
22. FRESHWATER, D.W., FREDERICQ, S., BUTLER, B.S., HOMMERSAND, M.H. & CHASE, M.W. (1994). A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL. Proc. Natl. Acad. Sci. U.S.A., 91: 7281-7285.
23. FRESHWATER, D.W., FREDERICQ, S. & HOMMERSAND, M.H. (1995). A molecular phylogeny of the Gelidiales (Rhodophyta) based on analysis of plastid rbcL nucleotide sequences. J. Phycol., 31: 616-632.
24. GENETICS COMPUTER GROUP (1994). Program Manual for the GCG Package, UNIX v. 8.0. 575 Science Drive, Madison, WI 53711.
25. GERBI, S.A. (1985). Evolution of ribosomal DNA. In Molecular Evolutionary Genetics (MacIntyre, R.J., editor), 419-517. Plenum Press, New York.
26. GUIRY, M.D. & WOMERSLEY, H.B.S. (1992). Gelidiella minima sp. nov. (Rhodophyta) from Victoria, Australia: implications for the generic classification of the Gelidiaceae. Br. Phycol. J., 27: 165-176.
27. GUIRY, M.D. & WOMERSLEY, H.B.S. (1993). Capreolia implexa gen. et sp. nov. (Gelidiales, Rhodophyta) in Australia and New Zealand: an intertidal matforming alga with an unusual life history. Phycologia, 32: 266-277.
28. GUTELL, R.R., LARSEN, N., & WOESE, C.R. (1994). Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev., 58: 10-26.
29. HAMBY, R.K., SIMS, L., ISSEL, L. & ZIMMER, E.A. (1988). Direct ribosomal RNA sequencing: optimization of extraction and sequencing methods for work with higher plants. Plant Mol. Biol. Rep., 6: 175-192.
30. HOMMERSAND, M.H. & FREDERICQ., S. (1988). An investigation of cystocarp development in Gelidium pteridifolium with a revised description of the Gelidiales (Rhodophyta). Phycologia, 27: 254-272.
31. HOMMERSAND, M.H. & FREDERICQ, S. (1996). Vegetative and reproductive development of Pterocladia capillacea (Gelidiales, Rhodophyta) from La Jolla, California. Nova Hedwigia, 112: 147-160.
32. HOMMERSAND, M.H., FREDERICQ, S. & FRESHWATER, D.W. (1994). Phylogenetic systematics and biogeography of the Gigartinaceae (Gigartinales, Rhodophyta) based on sequence analysis of rbcL. Bot. Mar., 37: 193-203.
33. HUELSENBECK, J.P. & HILLIS, D.M. (1993). Success of phylogenetic methods in the four-taxon case. Syst. Biol., 42: 247-264.
34. IRWIN, D.M., KOCHER, T.D. & WILSON, A.C. (1991). Evolution of the cytochrome b of mammals. J. Mol. Evol., 32: 128-144.
35. JIN, L. & NEI, M. (1990). Limitations of the evolutionary parsimony method of phylogenetic analysis. Mot. Biol. Evol., 7: 82-102.
36. JOHANSEN, S., GUDDAL, P.H. & JOHANSEN, T. (1990). Organization of the mitochondrial genome of Atlantic cod, Gadus morhua. Nucleic Acids Res., 18: 411-419.
37. KAPRAUN, D.F., GANZON-FORTES, E., BIRD, K.T., TRONO, G. & BREDEN, C. (1994). Karyology and agar analysis of the agarophyte Gelidiella acerosa (Forsskål) Feldmann et Hamel from the Philippines. J. Appl. Phycol., 6: 545-550.
38. KLUGE, A.G. (1989). A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool., 38: 7-25.
39. KLUGE, A.G. & FARRIS, J.S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool., 18: 1-32.
40. KRAFT, G.T. (1976). The morphology of Beckerella scalaramosa, a new species of Gelidiales (Rhodophyta) from the Philippines. Phycologia, 15: 85-91.
41. KUHNER, M.K. & FELSENSTEIN, J. (1994). A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol., 11: 459-468.
42. LANYON, S.M. (1988). The stochastic mode of molecular evolution: what consequences for systematic investigations? The Auk, 105: 565-573.
43. LEE, H.-B. (1994). Some species of Gelidium (Gelidiales, Rhodophyta) from Korea. In Taxonomy of Economic Seaweeds..., Vol. IV (Abbott, I.A., editor), 67-79. California Sea Grant College Program, La Jolla, CA.
44. LI, W.-H. & GRAUR, D. (1991). Fundamentals of Molecular Evolution. Sinauer, Sunderland, MA.
45. LIAO, L.M. (1995). A morphological study and taxonomic re-assessment of some genera and species of the Gracilariaceae (Gracilariales, Rhodophyta). PhD dissertation, University of North Carolina at Chapel Hill, Chapel Hill, NC.
46. LOCKHART, P.J., STEEL, M.A., HENDY, M.D. & PENNY, D. (1994). Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 1: 605-412.
47. + oxidoreductase of Cyanophora paradoxa upon translocation from cyanoplast to nucleus. Gene, 146: 123-127.
48. MEYER, A. (1993). Evolution of mitochondrial DNA in fishes. In Biochemistry and Molecular Biology of Fishes, 2, Molecular Biology Frontiers (Hochachka, P.W. & Mommsen, T.P., editors), 1-38. Elsevier, Amsterdam.
49. NEI, M. (1991). Relative efficiencies of different tree-making methods for molecular data. In Phylogenetic Analysis of DNA Sequences (Miyamoro, M.M. & Cracraft, J., editors), 90-128. Oxford University Press, New York.
50. NORRIS, R.E. (1987). A re-evaluation of Ptilophora Kützing and Beckerella Kylin (Gelidiales, Rhodophyceae) with a review of South African species. Bot. Mar., 30: 243-258.
51. NORRIS, R.E. (1992). The marine red algae of Natal South Africa: order Gelidiales (Rhodophyta). Mem. Bot. Surv. South Africa, 61: 1-43.
52. OKAMURA, K. (1900) Illustrations of the Marine Algae of Japan, vol. 1(1). Tokyo, ii + 14 pp., 5 pls.
53. OLSEN, G.J., LARSEN, N. & WOESE, C. R. (1991). The ribosomal database project. Nucleic Acids Res., 19: 2017-2021.
54. OLSEN, G.J., MATSUDA, H., HAGSTROM, R. & OVERBEEK, R. (1994). fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Biol. Sci., 10: 41-48.
55. RAGAN, M.A., BIRD, C.J., RICE, E.L., GUTELL, R.R., MURPHY, C.A. & SIMGH, R.K. (1994). A molecular pbylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc. Natl. Acad. Sci. U.S.A., 91, 7276-7280.
56. RAO, P.S. (1974). Some observations on the cytology of Gelidiella acerosa (Forsskal) Feldmann et Hamel. Cytologia, 39: 391-395.
57. RAO, P.S. & TRIVEDI, M.K. (1980). Reproduction in Gelidiella. In Taxonomy of Algae (Desikachary, T.V. & Raja Rao, V.N., editors), 255-260.
58. RIESEBERG, L.H., BECKSTROM-STERNBERG, J.H.S. & DOAN, K. (1990). Helianthus annuus ssp. texanus has chloroplast DNA and nuclear ribosomal RNA genes of Helianthus debilis ssp. cucumerifolius. Proc. Natl. Acad. Sci. U.S.A. 87: 593-597.
59. RODRÍGUEZ, D. & SANTELICES, B. (1987). Patterns of apical structure in the genera Gelidium and Pteroclodia (Getidiaceae, Rhodophyta). Hydrobiologia, 151/152: 199-203.
60. RODRÍGUEZ, D. & SANTELICES, B. (1988). Separation of Gelidium and Pterocladia on vegetative characters. In Taxonomy of Economic Seaweeds..., vol. II (Abbott, I.A., editor), 115-125. California Sea Grant College Program, La Jolla, CA.
61. RODRÍCUEZ, D. & SANTELICES, B. (1996). Medullary structure differences in Gelidium and Pterocladia (Gelidiales, Rhodophycea): taxonomic meaning. Phycol. Res., 44: 223-232.
62. SAMBROOK, J., FRITSCH, E.F. & MANIATIS, T. (1989). Molecular Cloning: A Laboratory Manual, vols. 1-3, 2nd edition. Cold Spring Harbor Laboratory Press, New York.
63. SANTELICES, B. (1990). New and old problems in the taxonomy of the Gelidiales (Rhodophyta). Hydrobiologia, 204/205: 125-135.
64. SANTELICES, B. & HOMMERSAND, M.H. (1997). Pterocladiella, a new genus in the Gelidiaceae (Gelidiales, Rhodophyta). Phycologia, 36: 114-119.
65. SAS (1989). SAS/STAR User's Guide, Version 6.0, 4th edition. SAS Institute, Cary,NC.
66. SAUNDERS, G.W. & KRAFT. G.T. (1994). Small-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). I. Evidence for the Plocamiales ord. nov. Can. J. Bot., 72: 1250-1263.
67. SAUNDERS, G.W. & KRAFT, G.T. (1996). Sall-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 2. Recognition of the Halymeniales ord. nov. Can. J. Bot., 74: 694-707.
68. SOKAL, R.R. & ROHLF, F.J. (1981). Biometry, 2nd edition. W.H. Freeman, New York.
69. SOLTIS, D.E. & KUZOFF, R.K. (1995). Discordance between nuclear and chloroplast phytogenies in the Heuchera group (Saxifragaceae). Evolution, 49, 727-742.
70. SOLTIS, D.E., SOLTIS, P.S., COLLIER, T.G. & EDGERTON, M.L. (1991). Chloroplast DNA variation within and among genera of the Heuchera group: evidence for chloroplast capture and paraphyly. Am. J. Bot., 78: 1091-1112.
71. SOLTIS, D.E., SOLTIS, P.S., THOMPSON, J.N. & PELLMYR, O. (1992). Chloroplast DNA variation in Lithophragma (Saxifragaceae). Syst. Bot., 17: 607-619.
72. SOLTIS, D.E., JOHNSON, L.A. & LOONEY, C. (1996). Discordance between ITS and chloroplast topologies in the Boykinia group (Saxifragaceae). Syst. Bot., 21: 169-185.
73. SORHANNUS, U. (1996). Higher ribosomal RNA substitution rates in Bacillariophyceae and Dasycladales than in Mollusca, Echinodermata, and Actinistia - Tetrapoda. Mol. Biol. Evol., 13: 1032-1038.
74. STEEL, M., LOCKHART, P.J. & PENNY, D. (1995). A frequency-dependent significance test for parsimony. Mol. Phylogenet. Evol., 4: 64-71.
75. SWOFFORD, D.L. (1993). PAUP: Phylogenetic Analysis Using Parsimony, version 3.1.1. Computer Program distributed by the Illinois Natural History Survey, Champaign, IL.
76. VAWTER, L. & BROWN, W.M. (1993). Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics, 134: 597-608.
77. WAKELY, J. (1994). Substitution-rate variation among sites and the estimation of transition bias. Mol. Biol. Evol., 11: 436-442.
78. WENDEL, J.F., STEWART, J.M. & RETTING, J.H. (1991). Molecular evidence for homoploid reticulate evolution among Australian species of Gossypium. Evolution, 45: 694-711.
79. WOLFE, K.H., Li, W.-H. & SHARP, P.M. (1987). Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc. Natl. Acad. Sci. U.S.A., 84: 9054-9058.