Study of the evolutionary relationships among Limonium species (Plumbaginaceae) using nuclear and cytoplasmic molecular markers

Molecular Phylogenetics and Evolution

Volumn 14, Issue 2, 2000, Pages 232-249

  Palacios, Carmen ^a,b   Rosselló, Josep A ^a,b   González Candelas, Fernando ^a,b  

^a UNIVERSITY OF VALENCIA   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPLAST DNA; CHROMOSOME NUMBER; EVOLUTION; GENETIC MARKER; GENETIC VARIANCE; HAPLOIDY; HAPLOTYPE; INTERNAL TRANSCRIBED SPACER; LIMONIUM; PHYLOGENY; POLYPHYLY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RIBOSOMAL DNA; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

EMBRYOPHYTA; LIMONIUM; LIMONIUM COSSONIANUM; LIMONIUM DELICATULUM; LIMONIUM FURFURACEUM; LIMONIUM MINUTUM; LIMONIUM NARBONENSE; LIMONIUM VULGARE; PLUMBAGINACEAE;

EID: 0034126432     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1999.0690     Document Type: Article

References (85)

1. Aimi T., Yamada T., Murooka Y. Nucleotide sequence and secondary structure of 5.8S rRNA from the unicellular green alga, Chlorella ellipsoidea. Nucleic Acids Res. 20:1992;6098-6098.
2. Albert V. A., Williams S. E., Chase M. W. Carnivorous plants: Phylogeny and structural evolution. Science. 257:1992;1491-1494.
3. Baker H. G. Dimorphism and monomorphism in the Plumbaginaceae. Ann. Bot (London). 17:1953;433-455.
4. Bakker F. T., Olsen J. L., Stam W. T. Evolution of nuclear rDNA ITS sequences in the Cladophora albida/sericea clade (Clorophyta). J. Mol. Evol. 40:1995;640-651.
5. Baldwin B. G., Sanderson M. J., Porter J. M., Wojciechowski M. F., Campbell C. S., Donoghue M. J. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on Angiosperm phylogeny. Ann. Missouri Bot. Gard. 82:1995;247-277.
6. Bloch W. A biochemical perspective of the polymerase chain reaction. Biochemistry. 30:1991;2735-2747.
7. Bobola M. S., Smith D. E., Klein A. S. Five major nuclear ribosomal repeats represent a large and variable fraction of the genomic DNA of Picea rubens and P. mariana. Mol. Biol. Evol. 9:1992;125-137.
8. Boissier J. P. The Candolle. A.P. Prodromus Systematics Naturalis Regni Vegetabilis. 1848;Masson, Paris.
9. Bokhari M. H. Variation and taxonomic importance of anatomical characters in Limonium. Notes R. Bot. Gard. Edinburgh. 32:1973;275-290.
10. Bremer B. Restriction data from chloroplast DNA for phylogenetic reconstruction: Is there only one accurate way of scoring. Plant Syst. Evol. 175:1991a;39-54.
11. Bremer B., Jansen R. K. Comparative restriction site mapping of chloroplast DNA implies new phylogenetic relationships within Rubiaceae. Am. J. Bot. 78:1991b;198-213.
12. Brunsfeld S. J., Soltis D. E., Soltis P. S. Evolutionary patterns and processes in Salix sect. Longifoliae: Evidence from chloroplast DNA. Syst. Bot. 17:1992;239-256.
13. Campbell C. S., Donoghue M. J., Baldwin B. G., Alice L. A., Wojciechowski M. F. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol. Biol. Evol. 14:1997;81-90.
14. Chase M. W., Soltis D. E., Olmstead R. G., Morgan D., Les D. H., Mishler B. D., Duvall M. R., Price R. A., Hills H. G., Qiu Y. L., Kron H. G., Rettig J. H., Conti E., Palmer J. D., Manhart J. R., Systma K. J., Michaels H. J., Kress W. J., Karol K. G., Clark W. D., Hedrén M., Gaut B. S., Jansen R. K., Kim K.-J., Wimpee C. F., Smith J. F., Furnier G. R., Xiang Q.-Y., Plunkett G. M., Soltis P. S., Swensen S. M., Williams S. E., Gadek P. A., Quinn C. J., Eguiarte L. E., Golenberg E., Learn G. H. Jr., Graham S. W., Barrett S. C. H., Dayanandan S., Albert V. A. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Missouri Bot. Gard. 80:1993;528-580.
15. Clegg M. T. Plant molecular evolution. Am. Nat. 130:1987;s1-s5.
16. Crease T. J., Lynch M. Ribosomal DNA variation in Daphnia pulex. Mol. Biol. Evol. 5:1991;620-640.
17. Dixon M. T., Hillis D. M. Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analyses. Mol. Biol. Evol. 10:1993;256-267.
18. Dolcher T., Pignatti S. Un'ipotesi sull'evoluzione dei Limonium del bacino del Mediterraneo. Giorn. Bot. Ital. 105:1971;95-107.
19. Donoghue M. J., Cantino C. R. Paraphyly, ancestors, and the goals of taxonomy: A botanical defense of cladism. Bot. Rev. 54:1988;107-128.
20. Doyle J. DNA and higher plants systematics: Some examples from the legumes. Hewitt G. M. Molecular Techniques in Taxonomy. 1991;101-115 Springer-Verlag, Berlin.
21. Doyle J. J. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17:1992;144-163.
22. Doyle J. J., Doyle J. L. Chloroplast DNA phylogeny of the Papilionoid Legume Tribe Phaseoleae. Syst. Bot. 18:1993;309-327.
23. Doyle J. J., Doyle J. L., Brown A. H., Grace J. P. Multiple origins of polyploids in the Glycine tabacina complex inferred from chloroplast DNA polymorphism. Proc. Natl. Acad. Sci. USA. 87:1990;714-717.
24. Edelman, I, Olson, S, and, Devereux, J. 1995, Wisconsin sequence analysis package.
25. Erben M. Die gattung Limonium im Sudwestmediterranen raum. Mitt. Bot. München. 114:1978;361-631.
26. Erben M. Karyotype differentiation and its consequences in Mediterranean Limonium. Webbin. 34:1979;409-417.
27. Erben M. Limonium. Castroviejo S., Jedo C., Cirujano S., Lainz M., Montserrat P., Morales R., Muñoz F., Navarro C., Paiva J., Soriano C. Flora Iberica. 1993;2-143 Real Jardín Botánico Madrid-CSIC, Madrid.
28. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:1981;368-376.
29. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39:1985;783-791.
30. Felsenstein J. Phylogenies from restriction sites: A maximum-likelihood approach. Evolution. 46:1992;159-173.
31. Felsenstein, J. 1993, PHYLIP: Phylogenetic Inference Package, version 3.5c, Univ. of Washington, Seattle.
32. Fuertes J., Rosselló J. A., Nieto Feliner G. Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae). Syst. Biol. 1999.
33. Greuter W., Burdet H. M., Long G. Med-Checklist. 1989;Conservatoire et Jardin Botaniques de la Ville de Genève, Genève.
34. Harris S. A., Ingram R. Chloroplast DNA and biosystematics: The effects of intraspecific diversity and plastid transmission. Taxon. 40:1991;393-412.
35. Hershkovitz M. A., Zimmer E. A. Conservation patterns in angiosperm rDNA ITS-2 sequences. Nucleic Acids Res. 15:1996;2857-2867.
36. Hillis D. M. Discriminating between phylogenetic signal and random noise in DNA sequences. Miyamoto M. M., Cracraft J. Phylogenetic Analysis of DNA Sequences. 1991;278-294 Oxford Univ. Press, Oxford.
37. Hillis D. M., Huelsenbeck J. P. Signal, noise, and reliability in molecular phylogenetic analysis. J. Hered. 83:1992;189-195.
38. Hillis D. M., Moritz C., Porter C. A., Baker R. J. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science. 251:1991;308-310.
39. Holsinger K. E., Jansen R. K. Phylogenetic analysis of restriction site data. Methods Enzymol. 224:1993;439-455.
40. Huelsenbeck J. P., Hillis D. M. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:1993;247-264.
41. Jukes T. H., Cantor C. R. Evolution of protein molecules. Munro H. N. Mammalian Protein Metabolism. 1969;21-132 Academic Press, New York.
42. Karvonen P., Savolainen O. Variation and inheritance of ribosomal DNA in Pinus sylvestris L. (Scots pine). Heredity. 71:1993;614-622.
43. Kim K.-J., Jansen R. K. Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. Plant Syst. Evol. 190:1994;157-185.
44. Ko K., Strauss N. A., Williams J. P. The localization and orientation of specific genes in the chloroplast chromosome of Vicia faba. Curr. Genet. 8:1984;359-367.
45. Kumar, S, Tamura, K, and, Nei, M. 1993, MEGA. Molecular Evolutionary Genetic Analysis version 1.0, The Pennsylvania State Univ.
46. Linczveski I. Tentamentum systematis ordinis Plumbaginalium Lindl. Novit. Syst. Plant. Vascul. 1968:1968;171-177.
47. Liu J. S., Schardl C. L. A conserved sequence in internal transcribed spacer-1 of plant nuclear RNA genes. Plant Mol. Biol. 26:1994;775-778.
48. Lledó M. D., Crespo M. B., Cameron K. M., Fay M. P., Chase M. W. Systematics of Plumbaginaceae based upon cladistic analysis of rbcL sequence data. Syst. Bot. 23:1998;21-29.
49. Maddison D. R. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 403:1991;315-328.
50. Maniatis T., Fristsh E. F., Sambrook J. Molecular Cloning: A Laboratory Manual. 1982;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
51. McDade L. A. Hybrids and phylogenetic systematics. II. The impact of hybrids on cladistic analysis. Evolution. 46:1992;1329-1346.
52. Mertens L. Origins of genotypic variation in North American dandelions inferred from ribosomal DNA and chloroplast DNA restriction enzyme analysis. Evolution. 47:1993;136-151.
53. Nei M. Molecular Evolutionary Genetics. 1987;Columbia Univ. Press, New York.
54. Nei M. Relative efficiencies of different tree-making methods for molecular data. Miyamoto M. M., Cracraft J. Phylogenetic Analysis of DNA Sequences. 1991;90-128 Oxford Univ. Press, New York.
55. Nei M., Miller J. C. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics. 125:1990;873-879.
56. Nicholas, K. B, and, Nicholas, H. B. Jr, 1997, GeneDoc: A tool for editing and annotating multiple sequence alignments. Software distributed by the author.
57. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:1994;41-48.
58. Olsthoorn R. C. L., Licis N., van Duin J. Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J. 13:1994;2660-2668.
59. Palmer J. D. Plastid chromosomes: Structure and evolution. Bogorad L., Vasil I. K. The Molecular Biology of Plastids: Cell Culture and Somatic Cell Genetics of Plants. 1991;5-53 Academic Press, New York.
60. Pau C. Noticia de algunas plantas curiosas o nuevas. Actas Soc. Esp. Hist. Nat. 27:1898;196-200.
61. Pax F. Statice: Die Natürlichen Pflanzenfamilien. 1897;Engler & Prantl, Leipzig.
62. Pignatti S. Limonium. Tutin T. G., Heywood J. S., Burges N. A., Moore D. M., Valentine S. M., Walters S. M., Webb D. A. Flora Europea. 1971;81-125 Cambridge Univ. Press. Cambridge.
63. Richards A. J. Plant Breeding Systems. 1986;Allen & Unwin, London.
64. Richards A. J., Kirschner J., Stepánek J., Marhold K. Apomixis and taxonomy: An introduction. Folia Geobot. Phytotax. 31:1996;281-282.
65. Rieseberg L. H., Brunsfeld S. J. Molecular evidence and plant introgression. Soltis P. S., Soltis D. E., Doyle J. J. Molecular Systematics of Plants. 1992;151-176 Chapman & Hall, New York.
66. Roelofs D., van Velzen J., Kuperus P., Bachmann K. Molecular evidence for an extinct parent of the tetraploid species Microseris acuminata and M. campestris (Asteraceae, Lactuceae). Mol. Ecol. 6:1997;641-649.
67. Saitou N., Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
68. Sang T., Crawford D. J., Stuessy T. F. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. Proc. Natl. Acad. Sci. USA. 92:1995;6813-6817.
69. Sankoff K. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28:1975;35-42.
70. Soltis D. E., Kuzoff R. K. Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution. 49:1995;727-742.
71. Soltis D. E., Soltis P. S., Milligan B. G. Intraspecific chloroplast DNA variation: Systematic and phylogenetic implications. Soltis P. S., Soltis D. E., Doyle J. J. Molecular Systematics of Plants. 1992;117-150 Chapman & Hall, New York.
72. Soltis D. E., Soltis P. S., Ranker T. A., Ness B. D. Chloroplast DNA variation in a wild plant, Tolmiea menziesii. Genetics. 121:1989;819-826.
73. Soltis K. E., Soltis P. S., Thompson J. N. Chloroplast DNA variation in Lithophragma (Saxifragaceae). Syst. Bot. 17:1992;607-619.
74. Sugiura M., Shinozaki K., Zaita N., Kusuda M., Kumano M. Clone bank of the tobacco (Nicotiana tabacum) chloroplast genome as a set of overlapping restriction endonuclease fragments: Mapping of eleven ribosomal protein genes. Plant Sci. 44:1986;211-216.
75. Suh Y., Thien L. B., Reeve H. E., Zimmer E. Z. Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae. Am. J. Bot. 80:1993;1042-1055.
76. Swofford, D. L. 1993, PAUP: Phylogenetic Analysis Using Parsimony, version 3.1, Laboratory of Molecular Systematics, Smithsonian Inst.
77. Swofford D. L., Olsen G. J., Waddell P. J., Hillis D. M. Phylogenetic inference. Hillis D. M., Moritz C., Mable B. K. Molecular Systematics. 1996;407-514 Sinauer, Sunderland.
78. Van der Sande C. A. F. M., Kwa M., van Nues R. W., van Heerikhuizen H., Raué H. A., Planta R. J. Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA. J. Mol. Biol. 223:1992;899-910.
79. van Houten W. H. J., Scarlett N., Bachmann K. Nuclear DNA markers of the Australian tetraploid Microseris scapigera and its North American diploid relatives. Theor. Appl. Genet. 87:1993;498-505.
80. Van Nues R. W., Rientjes J. M. J., van der Sande C. A. F. M., Zerp S. F., Sluiter C., Venema J., Planta R. J., Raué H. A. Separate structural elements within internal transcribed spacer 1 of Sacharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucleic Acids Res. 22:1994;912-919.
81. Wendel J. F., Schnabel A., Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA. 92:1995;280-284.
82. White T. J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Innis M. A., Golfand D. H., Sninsky J. J., White T. J. PCR Protocols: A Guide to Methods and Applications. 1990;315-322 Academic Press, New York.
83. Williams E. S., Albert V. A., Chase M. W. Relationships of Droseraceae: A cladistic analysis of rbcL sequence and morphological data. Am. J. Bot. 81:1994;1027-1037.
84. Yeh L. C. C., Lee J. C. Higher order structure of the 5.8S rRNA sequence within the yeast 35S precursor ribosomal RNA synthesized in vitro. J. Mol. Biol. 217:1991;649-659.
85. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.