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REFERENCES

1. Litt, A., and Irish, V. F. (2003) Duplication and diversification in the APETALA1/FRUITFULL gene lineage: implications for the evolution of floral development. Genetics, 165, 821-833.

2. Small, R. L., Cronn, R. C. and Wendel, J. F. (2004) Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot., 17, 145-170.

3. Pflierger, S., Lefebvre, V. and Causse, M. (2001) The candidate gene approach in plant genetics: a review. Molec. Breeding, 7, 275-291.

4. Chee, P.W., Rong, J., Williams-Coplin, D., Schulze, S. R. and Paterson, A. H. (2004) EST derived PCR-based markers for functional gene homologues in cotton. Genome, 47, 449-462.

5. Mathews, S., Mason-Gamer, R. J., Spangler, R. E. and Kellogg, E. A. (2002) Phylogeny of the Andropogoneae inferred from phytochrome B, GBSSI, and ndhF. Int. J. Plant Sci., 163, 441-450.

6. Malcomber, S. T. and Kellogg, E. A. (2004) Heterogeneous expression patterns and separate roles of the SEPALLATA Gene LEAFY HULL STERILE1 in grasses. Plant Cell, 16, 1692-1706.

7. Koch, M., Haubold, B. and Mitchell-Olds, T. (2001) Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences Amer. J. Bot., 88, 534-544.

8. DeBry, R. W., and Seshadri, S. (2001) Nuclear intron sequences for phylogenetics of closely related mammals: An example using the phylogeny of Mus. J. Mammalogy, 82, 280-288.

9. Murphy, W. J., Eizirik, E., O'Brien, S. J., Madsen, O., Scally, M., Douady, C. J., Teeling, E., Ryder, O. A., Stanhope, M. J., de Jong, W. W. and Springer, M. S. (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science, 294, 2348-2351.

10. Barker, F. K., Cibois, A., Schikler, P., Feinstein, J. and Cracraft, J. (2004) Phylogeny and diversification of the largest avian radiation. Proc. Nat. Acad. Sci. USA, 101, 11040-11045.

11. Alvarez, I., and Wendel, J. F.. (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylog. Evol., 29, 417-434.

12. Rozen, S., and Skaletsky, H. J. (2000) Primer3 on the WWW for general users and for biologist programmers. In Krawetz, S. and Misener, S. (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386. Code available at http://www-genome.wi.mit.edu/genome_software/other/primer3.html

13. Rose, T. M., Schultz, E. R., Henikoff, J. G., Pietrokovski, S., McCallum, C. M. and Henikoff, S. (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly-related sequences. Nucleic Acids Res., 26, 1628-1635.

14. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876-4882.

15. Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Syst Biol., 46, 590-621.

16. Rice, P. Longden, I. and Bleasby, A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.

17. Felsenstein, J. (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

18. Vollbrecht, E., Veit, B., Sinha, N. and Hake, S. (1991) The developmental gene Knotted-1 is a member of a maize homeobox gene family. Nature, 350, 241-243.

19. Becker, A. and Theissen, G. (2003). The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol. Phylogenet. Evol., 29, 464-489.

20. Casano, L. M., Zapata, J. M., Martín, M. and Sabater, B. (2000) Chlororespiration and poising of cyclic electron transport: plastoquinone as electron transporter between thylakoid NADH dehydrogenase and peroxidase. J Biol. Chem., 275, 942-948.

21. Soltis, D. E., and Soltis, P. S. (1998) Choosing an approach and an appropriate gene for phylogenetic analysis. In Soltis, D. E., Soltis, P. S. and Doyle, J. J. (eds.) Molecular systematics of Plants II. DNA sequencing, Kluwer Academic Publishers, Boston, pp. 1-42.

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