Molecular Evolution and Phylogenetic Utility of the Chloroplastrpl16Intron inChusqueaand the Bambusoideae (Poaceae)

Molecular Phylogenetics and Evolution

Volumn 8, Issue 3, 1997, Pages 385-397

  Kelchner, Scot A ^a   Clark, Lynn G ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE PROTEIN; YRPL16 PROTEIN, PETUNIA HYBRIDA;

ARTICLE; CHLOROPLAST; CLASSIFICATION; GENETICS; INTRON; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PLANT;

CHLOROPLASTS; EVOLUTION, MOLECULAR; INTRONS; PHYLOGENY; PLANT PROTEINS; PLANTS;

EID: 0031306828     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1997.0432     Document Type: Article

References (66)

1. Aldrich J., Cherney B. W., Merlin E., Christopherson L. The role of insertions/deletions in the evolution of the intergenic region betweenpsbAtrnH. Curr. Genet. 14:1988;137-146.
2. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution. 42:1988;795-803.
3. Bremer K. Combinable component consensus. Cladistics. 6:1990;369-372.
4. Calderón C. E., Soderstrom T. R. The genera of Bambusoideae (Poaceae) of the American continent: Keys and comments. Smithsonian Contr. Bot. 44:1980;1-27.
5. Chase M. W., Hills H. H. Silica gel: An ideal material for field preservation of leaf samples for DNA studies. Taxon. 40:1991;215-220.
6. L. G. Clark, 1986, Systematics ofChusqueaChusquea,Swallenochloa,Verticillatae,Serpentes,Longifoliae, Iowa State University, Ames.
7. Clark L. G. Systematics ofChusqueaSwallenochloa,Verticillatae,Serpentes,Longifoliae. Syst. Bot. Monographs. 27:1989;1-127.
8. Clark L. G. ChusqueaLongiprophyllae. Syst. Bot. 15:1990;615-634.
9. Clark L. G. ChusqueaSwallenochloa. Brittonia. 44:1992;387-422.
10. Clark L. G. Diversity and distribution of the Andean woody bamboos (Poaceae: Bambusoideae). Biodiversity and Conservation of Neotropical Montane Forests. 1995;The New York Botanical Garden, New York. p. 501-512.
11. Clark L. G. Four new species ofChusquea. Brittonia. 48:1996;250-262.
12. Clark L. G. Diversity, biogeography, and evolution inChusquea. Chapman G. The Bamboos. 1997;33-44 Academic Press, London.
13. Clark L. G., Davidse G., Ellis R. P. Natural hybridization in bamboos: Evidence fromChusqueaSwallenochloa. Natl. Geogr. Res. 5:1989;459-476.
14. Clark L. G., Zhang W., Wendel J. F. A phylogeny of the grass family (Poaceae) based onndhF. Syst. Bot. 20:1995;436-460.
15. W. D. Clayton, S. A. Renvoize, 1986, Genera Graminum, Her Majesty's Stationery Office, London.
16. Donoghue M. J., Olmstead R. G., Smith J. F., Palmer J. D. Phylogenetic relationships of Dipsacales based onrbcL. Ann. Missouri Bot. Gard. 79:1992;333-345.
17. Downie S. R., Palmer J. D. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. Soltis D. E. Molecular Systematics of Plants. 1992;14-35 Chapman and Hall, New York.
18. Downie S. R., Katz-Downie D. S., Cho K-J. Phylogenetic analysis of Apiaceae subfamily Apioideae using nucleotide sequences from the chloroplastrpoC1. Mol. Phyl. Evol. 6:1996a;1-18.
19. Downie S. R., Llanas E., Katz-Downie D. S. Multiple independent losses of therpoC1. Syst. Bot. 21:1996b;135-151.
20. Doyle J. J., Doyle J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:1987;11-15.
21. Doyle J. J., Doyle J. L., Palmer J. D. Multiple independent losses of two genes and one intron from legume chloroplast genomes. Syst. Bot. 20:1995;272-294.
22. Dransfield S., Widjaja E. A. Plant Resources of South-East Asia No. 7: Bamboos. 1995;Backhuys, Leiden.
23. Ferris C., Oliver R. P., Davy A. J., Hewitt G. M. Using chloroplast DNA to trace postglacial migration routes of oaks into Britain. Mol. Ecol. 4:1995;731-738.
24. Gaut B. S., Clark L. G., Wendel J. F., Muse S. V. Comparison of the molecular evolutionary process atrbcLndhF. Mol. Biol. Evol. 14:1997;769-777.
25. Gentry A. H. Neotropical floristic diversity: Phytogeographical connections between Central and South America, pleistocene climatic fluctuations, or an accident of the Andean orogeny? Ann. Missouri Bot. Gard. 69:1982;557-593.
26. Gielly L., Taberlet P. The use of chloroplast DNA to resolve plant phylogenies: Non-coding versusrbcL. Mol. Biol. Evol. 11:1994;769-777.
27. Golenberg E. M., Clegg M. T., Durbin M. L., Doebley J., Ma D. P. Evolution of a non-coding region of the chloroplast genome. Mol. Phyl. Evol. 2:1993;52-64.
28. Hancock J. M. The contribution of slippage-like processes to genome evolution. J. Mol. Evol. 41:1995;1038-1047.
29. Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C.-R., Meng B.-Y., Li Y.-Q., Kanno A., Nishizawa Y., Hirai A., Shinozaki K., Sugiura M. The complete sequence of the rice (Oryza sativa. Mol. Gen. Genet. 217:1989;185-194.
30. Hodges S. A., Arnold M. L. Columbines: A geographically widespread species flock. Proc. Natl. Acad. Sci. USA. 91:1994;5129-5132.
31. Horn S. P., Clark L. G. Pollen viability inChusquea subtessellata. Biotropica. 24:1992;577-579.
32. Johnson L. A., Soltis D. E. matKs. str. Syst. Bot. 19:1994;143-156.
33. Jordan W. C., Courtney M. W., Neigel J. E. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). Am. J. Bot. 83:1996;430-439.
34. Kelchner S. A., Wendel J. F. Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr. Genet. 30:1996;259-262.
35. S. Kumar, K. Tamura, M. Nei, 1993, MEGA: Molecular Evolutionary Genetics Analysis, version 1.0, Pennsylvania State University, University Park.
36. Levinson G., Gutman G. A. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:1987;203-221.
37. Marshall C. R., Raff E. C., Raff R. A. Dollo's law and the resurrection of genes. Proc. Natl. Acad. Sci. USA. 91:1994;12283-12287.
38. Morton B. R. Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast non-coding regions. Proc. Natl. Acad. Sci. USA. 92:1995;9717-9721.
39. Morton B. R., Clegg M. T. A chloroplast DNA mutational hotspot and gene conversion in a non-coding region nearrbcL. Curr. Genet. 24:1993;357-365.
40. Ogihara Y., Terachi T., Sasakuma T. Molecular analysis of the hot-spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot-spot region. Genetics. 129:1991;873-884.
41. Pohl R. W. Flora costaricensis: Family number 15, Gramineae. Fieldiana Bot n.s. 4:1980;1-608.
42. Pohl R. W., Clark L. G. New chromosome counts forChusqueaAulonemia. Am. J. Bot. 79:1992;478-480.
43. Posno M., van Vliet A., Groot G. S. P. The gene forSpirodella oligorhizaE. coli. Nucleic Acids Res. 14:1986;3181-3195.
44. Prance G. T. A review of the phytogeographic evidences for Pleistocene climate changes in the neotropics. Ann. Missouri Bot. Gard. 69:1982;594-624.
45. Rigaa A., Monnerot M., Sello D. Molecular cloning and complete nucleotide sequence of the repeated unit and flanking gene of the scallopPecten maximus. J. Mol. Evol. 41:1995;189-195.
46. Rychlik W., Rhoads R. E. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res. 17:1989;8543-8551.
47. Shimada H., Sugiura M. Fine structural features of the chloroplast genome: Comparison of the sequenced chloroplast genomes. Nucleic Acids Res. 19:1991;983-995.
48. Simpson B. B. Pleistocene changes in the flora of the high tropical Andes. Paleobiology. 1:1975;273-294.
49. Soderstrom T. R. Some evolutionary trends in the Bambusoideae (Poaceae). Ann. Missouri Bot. Gard. 68:1981;15-47.
50. Soderstrom T. R., Calderón C. E. The species ofChusquea. Brittonia. 30:1978a;154-164.
51. Soderstrom T. R., Calderón C. E. ChusqueaSwallenochloa. Brittonia. 30:1978b;297-312.
52. Soderstrom T. R., Ellis R. The position of bamboo genera and allies in a system of grass classification. Soderstrom T. R., Hilu K., Campbell C., Barkworth M. E. Grass Systematics and Evolution. 1987;225-238 Smithsonian Institution Press, Washington.
53. T. R. Soderstrom, E. J. Judziewicz, L. G. Clark, 1988, Distribution patterns of neotropical bamboos, Proceedings of a Workshop on Neotropical Distribution Patterns, W. R. HeyerP. E. Vanzolini, 121, 157, Academia Brasileira de Ciencias, Rio de Janeiro.
54. 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 and Hall, New York.
55. M. Sugiura, 1989, Oryza sativa, Nagoya University, Center for Gene Research, Nagoya, Japan.
56. D. L. Swofford, 1993, PAUP: Phylogenetic Analysis Using Parsimony, Illinois Natural History Survey, Champaign.
57. Takaiwa F., Sugiura M. Nucleotide sequence of the16S-23S. Nucleic Acids Res. 10:1982;2665-2676.
58. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
59. van Ham R. C. H. J., t'Hart H., Mes T. H. M., Sandbrink J. M. Molecular evolution of non-coding regions of the chloroplast genome in the Crassulaceae and related species. Curr. Genet. 25:1994;558-566.
60. vom Stein J., Hachtel W. Deletions/insertions, short inverted repeats, sequences resemblingattOenotheraMunzia. Mol. Gen. Genet. 213:1988;513-518.
61. Whittemore A. T., Schaal B. A. Interspecific gene flow in sympatric oaks. Proc. Natl. Acad. Sci. USA. 88:1991;2540-2544.
62. Widmer Y., Clark L. G. New species ofChusquea. Ann. Missouri Bot. Gard. 78:1991;164-171.
63. Wolfson R., Higgins K. G., Sears B. B. Evidence for replication slippage in the evolution ofOenothera. Mol. Biol. Evol. 8:1991;709-720.
64. W. Zhang, 1996, Phylogeny and Classification of the Bamboos (Poaceae: Bambusoideae), Iowa State University, Ames.
65. Zurawski G., Clegg M. T. Evolution of higher-plant chloroplast DNA-encoded genes: Implications for structure-function and phylogenetic studies. Annu. Rev. Plant Physiol. 38:1987;398-418.
66. Zurawski G., Clegg M. T., Brown A. H. D. The nature of nucleotide sequence divergence between barley and maize chloroplast DNA. Genetics. 106:1984;735-749.