An evaluation of tribes and generic relationships in Melioideae (Meliaceae) based on nuclear ITS ribosomal DNA

Taxon

Volumn 57, Issue 1, 2008, Pages 98-108

  Muellner, Alexandra N ^a,b   Samuel, Rosabelle ^c   Chase, Mark W ^a   Coleman, Annette ^d   Stuessy, Tod F ^c  

^a JODRELL LABORATORY   (United Kingdom)

^b SENCKENBERG RESEARCH INSTITUTE   (Germany)

^c UNIVERSITY OF VIENNA   (Austria)

^d BROWN UNIVERSITY   (United States)

Author keywords

Internal transcribed spacer (ITS); Meliaceae; Melioideae; Molecular phylogenetics; rbcL

Indexed keywords

DICOTYLEDON; DNA; MAXIMUM LIKELIHOOD ANALYSIS; MOLECULAR ANALYSIS; NUCLEIC ACID ANALYSIS; OPTIMIZATION; PARSIMONY ANALYSIS; PHYLOGENETICS;

MELIACEAE; NAREGAMIA; QUIVISIANTHE; TURRAEA;

EID: 41349116552     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (32)

1. Chase, M.W. & Hills, H.G. 1991. Silica gel: an ideal desiccant for preserving field-collected leaves for use in molecular studies. Taxon 40: 215-220.
2. Chase, M.W., Morton, C.M. & Kallunki, J.A. 1999. Phylogenetic relationships of Rutaceae: a cladistic analysis of the subfamilies using evidence from rbcL and atpB sequence variation. Amer. J. Bot. 86: 1191-1199.
3. Cheek, M.R. 1990. A new species of Turraea (Meliaceae) from Madagascar and comments on the status of Naregamia. Kew Bull. 45: 711-715.
4. Cheek, M.R. 1996. The identity of Naregamia Wight & Arn. (Meliaceae). Kew Bull. 51: 716.
5. Coleman, A.W. 2007. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res. 35: 3322-3329.
6. Coleman, A.W., Preparata, R.M., Mehrotra, B. & Mai, J.C. 1998. Derivation of the secondary structure of the ITS-1 transcript in Volvocales and its taxonomic correlations. Protist 149: 135-146.
7. Felsenstein, J. 1985. Confidence limits on phylogenetics: an approach using the bootstrap. Evolution 39: 783-791.
8. Fitch, W.M. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20: 406-416.
9. Harms, H. 1940. Meliaceae. Pp. 1-172 in: Engler, A. & Prantl, K. (eds.), Die natürlichen Pflanzenfamilien, ed. 2, vol. 19 bI. W. Engelmann, Leipzig.
10. Hershkovitz, M.A. & Zimmer, E.A. 1996. Conservation patterns in angiosperm rDNA ITS2 sequences. Nucleic Acids Res. 24: 2857-2867.
11. Huelsenbeck, J.P. & Ronquist, F.R. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Biometrics 17: 754-755.
12. Jobes, D.V. & Thien, L.B. 1997. A conserved motif in the 5.8S ribosomal RNA (rRNA) gene is a useful diagnostic marker for plant internal transcribed spacer (ITS) sequences. Pl. Molec. Biol. Reporter 15: 326-334.
13. Liu, J.-S. & Schardl, C.L. 1994. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Pl. Molec. Biol. 26: 775-778.
14. Mabberley, D.J. 2000. The Plant-Book. Cambridge Univ. Press, Cambridge.
15. Mabberley, D.J., Pannell, C.M. & Sing, A.M. 1995. Meliaceae. Fl. Males., Ser. 1, Spermat. 12: 1-407.
16. Maggini, F., Marrocco, R., Gelati, M.T. & De Dominicis, R.I. 1998. Lengths and nucleotide sequences of the internal spacers of nuclear ribosomal DNA in gymnosperms and pteridophytes. Pl. Syst. Evol. 213: 199-205.
17. Mai, J.C. & Coleman, A.W. 1997. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J. Molec. Evol. 44: 258-271.
18. Mathews, D.H., Sabina, J., Zuker, M. & Turner D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Molec. Biol. 288: 911-940.
19. Muellner, A.N., Samuel, R., Chase, M.W., Pannell, C.M. & Greger, H. 2005. Aglaia (Meliaceae): an evaluation of taxonomic concepts based on DNA data and secondary metabolites. Amer. J. Bot. 92: 534-543.
20. Muellner, A.N., Samuel, R., Johnson, S.A., Cheek, M., Pennington, T.D. & Chase, M.W. 2003. Molecular phylogenetics of Meliaceae based on nuclear and plastid DNA sequences. Amer. J. Bot. 90: 471-480.
21. Muellner, A.N., Savolainen, V., Samuel, R. & Chase, M.W. 2006. The mahogany family "out-of-Africa": divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity. Molec. Phylog. Evol. 40: 236-250.
22. Pannell, C.M. 1992. A taxonomic monograph of the genus Aglaia Lour. (Meliaceae). Kew Bulletin, Additional Series 16. Her Majesty's Stationery Office, London.
23. Pennington, T.D. & Styles, B.T. 1975. A generic monograph of the Meliaceae. Blumea 22: 419-540.
24. Pennington, T.D., Styles, B.T. & Taylor, D.A.H. 1981. Meliaceae. Flora Neotropica Monographs 28. The New York Botanical Garden, Bronx.
25. Posada, D. & Crandall, K.A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
26. Posada, D. & Crandall, K.A. 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50: 580-601.
27. Soltis, D.E. & Soltis, P.S. 1998. Choosing an approach and an appropriate gene for phylogenetic analysis. Pp. 1-42 in: Soltis, D.E., Soltis, P.S. & Doyle, J.J. (eds.), Molecular Systematics of Plants II: DNA Sequencing. Kluwer, Boston.
28. Swofford, D.L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), version 4. Sinauer, Sunderland, Massachusetts.
29. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876-4882.
30. White, F. 1962. Geographic variation and speciation in Africa with particular reference to Diospyros. Publ. Syst. Assoc. 4: 71-103.
31. Whitten, W.M., Williams N.H. & Chase, M.W. 2000. Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopeinae: combined molecular evidence. Amer. J. Bot. 87: 1842-1856.
32. Zuker, M., Mathews, D.H. & Turner, D.H. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. Pp. 11-43 in: Barciszewski, J. & Clark, B.F.C. (eds.), RNA Biochemistry and Biotechnology. NATO ASI Series. Kluwer Academic Publishers, Boston.