Phylogenetic relationships in Nicotiana (Solanaceae) inferred from multiple plastid DNA regions

Molecular Phylogenetics and Evolution

Volumn 33, Issue 1, 2004, Pages 75-90

  Clarkson, James J ^a,b   Knapp, Sandra ^c   Garcia, Vicente F ^d   Olmstead, Richard G ^d   Leitch, Andrew R ^b   Chase, Mark W ^a  

^a JODRELL LABORATORY   (United Kingdom)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^d UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Allopolyploidy; matK; ndhF; Phylogeny; trnL F; trnS G

Indexed keywords

PRIMER DNA;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; GEOGRAPHY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASTID; PLOIDY; TOBACCO;

BASE SEQUENCE; BAYES THEOREM; DNA PRIMERS; GEOGRAPHY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASTIDS; PLOIDIES; SEQUENCE ANALYSIS, DNA; TOBACCO;

MAGNOLIOPHYTA; NICOTIANA; SOLANACEAE; SYMONANTHUS;

EID: 4344572417     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.05.002     Document Type: Article

References (50)

1. Aoki S., Ito M. Molecular phylogeny of Nicotiana (Solanaceae) based on the nucleotide sequence of the matK gene. Plant Biol. 2:2000;316-324
2. Armstrong J.E. Comparative floral anatomy of Solanaceae: a preliminary survey. D'Arcy W.G. Solanaceae: Biology and Systematics. 1986;110-113 Columbia University Press, New York
3. Bennett M.D. The development and use of genomic in situ hybridization (GISH) as a new tool in plant biosystematics. Brandham P.E., Bennett M.D. Kew Chromosome Conference IV. 1995;167-183 Royal Botanic Gardens, Kew, Richmond
4. Bogani P., Lio P., Intrieri M.C., Buiatti M. A physiological and molecular analysis of the genus Nicotiana. Mol. Phylogenet. Evol. 7:1997;62-70
5. Bohs L., Olmstead R.G. Phylogenetic relationships in Solanum (Solanaceae) based on ndhF sequences. Syst. Bot. 22:1997;5-17
6. Carpenter J.M. Choosing among multiple equally parsimonious cladograms. Cladistics. 4:1988;291-296
7. Chase M.W., Hills H.G. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon. 40:1991;215-220
8. Chase M.W., Knapp S., Cox A.V., Clarkson J.J., Butsko Y., Joseph J., Savolainen V., Parokonny A. Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Ann. Bot. 92:2003;107-127
9. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:1987;11-15
10. Farris J.S. The retention index and the rescaled consistency index. Cladistics. 5:1989;417-419
11. Fay M.F., Olmstead R.G., Richardson J.E., Santiago J.E., Prance G.T., Chase M.W. Molecular data support the inclusion of Duckeodendron cestroides in Solanaceae. Kew Bull. 53:1997;203-212
12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:1985;783-791
13. Fitch W.M. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:1971;406-416
14. Fukuda T., Yokoyama J., Ohashi H. Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences. Mol. Phylogenet. Evol. 19:2001;246-258
15. Garcia V.F., Olmstead R.G. Phylogenetics of tribe Anthocercideae (Solanaceae) based on ndhF and trnL/F sequence data. Syst. Bot. 28:2003;609-615
16. Goodspeed T.H. The genus Nicotiana. Chronica Botanica. 16:1954;1-536
17. Greuter W. International Code of Botanical Nomenclature (Saint Louis code), Regnum Vegetabile 138. 2000;Koeltz, Königstein, Germany
18. Haegi L. The affinities of Anthocercis (Solanaceae) and related genera. D'Arcy W.G. Solanaceae: Biology and Systematics. 1986;27-40 Columbia University Press, New York
19. Hamilton M.B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol. Ecol. 8:1999;513-525
20. Holmgren P.K., Holmgren N.H., Barnett L.C. Index Herbariorum Part I: The Herbaria of The World, Regnum vegetabile 120. eighth ed.:1990;New York Botanical Garden, New York
21. Huelsenbeck J.P., Ronquist F. Mr Bayes: Bayesian inference of phylogeny. Bioinformatics. 17:2001;754-755
22. Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2001;2310-2314
23. Japan Tobacco Inc. 1994. The Genus Nicotiana Illustrated, Japan Tobacco Inc, Tokyo
24. Kelchner S.A. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann. Missouri. Bot. Gard. 87:2000;482-498
25. Kenton A., Parokonny A.S., Gleba Y.Y., Bennett M.D. Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Mol. Gen. Genet. 240:1993;159-169
26. Kitamura S., Inoue M., Shikazono N., Tanaka A. Relationships among Nicotiana species revealed by the 5S rDNA spacer sequence and fluorescence in situ hybridization. Theor. Appl. Genet. 103:2001;678-686
27. Knapp S., Stafford P., Persson V. Pollen morphology in the Anthocercideae (Solanaceae). Kurtziana. 28:2000;7-18
28. Knapp S., Chase M.W., Clarkson J.J. Nomenclatural changes and a new sectional classification in Nicotiana (Solanaceae). Taxon. 52:2004;73-82
29. Komarnitsky S.I., Komarnitsky I.K., Cox A., Parokonny A.S. Evolution of sequences of internal transcribed spacer of nuclear ribosomal DNA of American species of the genus Nicotiana. Cytol. Genet. 32:1998;61-67
30. Komarnitsky S.I., Komarnitsky I.K., Cox A., Parokonny A.S. Molecular phylogeny of the 5.8S ribosomal RNA genes in 37 species of Nicotiana genus. Genetika. 34:1998;883-889. in Russian with an English summary
31. Lim Y.K., Matyáçek R., Lichtenstein C.P., Leitch A.R. Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma. 109:2000;245-258
32. Lin T.Y., Kao Y.Y., Lin S., Lin R.F., Chen C.M., Huang C.H., Wang C.K., Lin Y.Z., Chen C.C. A genetic linkage map of Nicotiana plumbaginifolia Nicotiana longiflora based on RFLP and RAPD markers. Theor. Appl. Genet. 103:2001;905-911
33. Linnaeus C. Species Plantarum. first ed.:1753;Salvius, Stockholm
34. Merxmüller H., Buttler K.P. Nicotiana in der Afrikanischen namib - ein pflanzengeographisches und phylogenetisches Rätsel. Mitt. Bot. Staatssamml. München. 12:1975;91-104
35. Murad L., Lim K.Y., Christopodulou V., Matyasek R., Lichtenstein C.P., Kovarik A., Leitch A. The origin of tobacco's T genome is traced to a particular lineage within Nicotiana tomentosiformis (Solanaceae). Am. J. Bot. 89:2002;921-928
36. LYS (UUU) gene from mustard. Curr. Genet. 11:1987;251-257
37. Olmstead R.G., Palmer J.D. Chloroplast DNA and systematics of the Solanaceae. Hawkes J.G., Lester R.N., Nee M. Solanaceae III, Taxonomy, Chemistry, Evolution. 1991;161-168 Royal Botanic Gardens, Kew, Richmond
38. Olmstead R.G., Palmer J.D. Chloroplast DNA phylogeny of the Solanaceae: subfamilial relationships and character evolution. Ann. Missouri Bot. Gard. 79:1992;346-360
39. Olmstead R.G., Sweere J.A. Combining data in phylogenetic systematics: an empirical approach using three molecular datasets in the Solanaceae. Syst. Biol. 43:1994;467-481
40. Olmstead R.G., Sweere J.A., Spangler R.E., Palmer J.D. Phylogeny and provisional classification of the Solanaceae based on chloroplast DNA. Nee M., Lester R.N., Hawkes J.G. Solanaceae IV. 1999;111-137 Royal Botanic Gardens, Kew, Richmond
41. Parokonny A.S., Kenton A.Y. Comparative physical mapping and evolution of the Nicotiana tabacum karyotype. Brandham P.E., Bennett M.D. Kew Chromosome Conference IV. 1995;301-320 Royal Botanical Gardens, Kew
42. Purdie R.W., Symon D.E., Haegi L. Solanaceae. Flora Aust. 29:1982;1-208
43. Reeves G., Chase M.W., Goldblatt P., Rudall P., Fay M.F., Cox A.V., Lejeune B., Souza-Chies T. Molecular systematics of Iridaceae: evidence from four plastid DNA regions. Amer. J. Bot. 88:2000;2074-2087
44. Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K., Ohto C., Torazawa K., Meng B.Y., Sugita M., Deno H., Kamogashira T., Yamada K., Kusuda J., Takaiwa F., Kato A., Tohdoh N., Shimada H., Suguira M. The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:1986;2043-2049
45. Suzuki Y., Glazko G.V., Nei M. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA. 99:2002;16138-16143
46. Swofford, D.L., 2001. PAUP*: Phylogenetic Analysis Using Parsimony (* and other methods), Version 4. Computer Program distributed by Sinauer Associates, Sunderland, MA
47. Taberlet P.L., Gielly G., Pautou, Bouvet J. Universal primers for amplification of three non-coding regions of chlorplast DNA. Plant Mol. Biol. 17:1991;1105-1109
48. Wendel J.F., Schinabel A., Seelanan T. An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol. Phylogenet. Evol. 4:1995;298-313
49. Whitten W.M., Williams N.H., Chase M.W. Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopeinae: combined molecular evidence. Amer. J. Bot. 87:2000;1842-1856
50. Wells P.V. Variation in section Trigonophyllae of Nicotiana. Madroño. 15:1960;148-151