FGP Publications

2006

Buzgo, M., Soltis, D.E., Soltis, P.S., Ma, H., Hauser, B.A., Leebens-Mack, J., and Johansen, B. (2006) Perianth development in the basal monocot Triglochin maritima (Juncaginaceae). In: Monocots: comparative biology and evolution, 2 vols., Rancho Santa Ana Botanic Gardens, CA. (In Press).

Cui, L., Leebens-Mack, J.H., Wang, L-S., J. Tang, Rymarquis, L., Stern, D., and dePamphilis, C.W. (2006) Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evolutionary Biology. 6:13.

Cui, L., Veeraraghavan, N., Richter, A., Wall, K., Jansen, R. K., Leebens-Mack, J., Makalowska, I., and dePamphilis, C.W. (2006) ChloroplastDB: the chloroplast genome database. Nucleic Acids Res. 34: D692-D696.

Duarte, J. M., Cui, L., Wall, K., Zhang, Q., Zhang, X., Leebens-Mack, J.H., Ma, H., Altman, N., and dePamphilis, C.W. (2006) Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol. 23:469-478.

Frohlich M. (2006) Recommendations and goals for evo-devo research: scenarios, genetic constraint, and developmental homeostasis. In: Monocots: comparative biology and evolution, 2 vols., Rancho Santa Ana Botanic Gardens, CA. (In Press).

Hu, W., and Ma, H. 2006. Characterization of a novel putative zinc-finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development. Plant J. 45: 399-422. (cover)

Kim, S., Soltis, P.S., Wall, K., and Soltis, D. E. (2006) Phylogeny and domain evolution in the APETALA2-like gene family. Mol. Biol. Evol. 23:107-120.

Ma, H. 2006. A molecular portrait of Arabidopsis meiosis. In The Arabidopsis Book. Eds. C.R. Somerville, E.M. Meyerowitz, J. Dangl, and M. Stitt, American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0009, http://www.aspb.org/publications/arabidopsis/

Soltis, D. E., Soltis, P. S., and Leebens-Mack, J.H. (eds.). (2006) Developmental Genetics of the Flower. Advances in Botanical Research series Elsevier Limited, London. (In Press)

Soltis, P.S., Soltis, D.E., Kim, S., Chanderbali, A., and Buzgo, M. (2006) Modifications of the ABC model based on analyses of basal angiosperms. In Developmental Genetics of the Flower, D.E. Soltis, P.S. Soltis and J.H. Leebens-Mack eds. Advances in Botanical Research series Elsevier Limited, London. (In Press)

Zahn, L. M., Feng, B., and Ma, H. (2006) Beyond the ABC model: regulation of floral homeotic genes. In Developmental Genetics of the Flower, D.E. Soltis, P.S. Soltis and J.H. Leebens-Mack eds. Advances in Botanical Research series Elsevier Limited, London. (In Press)

Zahn, L.M., Leebens-Mack, J., Arrington, J.M., Hu, Y., Landherr, L., dePamphilis, C., Becker, A., Theissen, G., and Ma, H. (2006) Conservation and divergence in the AGAMOUS Subfamily of MADS-Box Genes: evidence of independent sub- and neofunctionalization events. Evol. Develop. 8:30-45. (cover)

2005

Albert, V.A., Soltis, D.E., Carlson, J.E., Farmerie, W.G., Wall, P.K., Ilut, D.C., Solow, T.M., Mueller, L.A., Landherr, L.L., Hu,Y., Buzgo, M., Kim, S., Yoo, M.-J., Frohlich, M.W., Perl-Treves, R., Schlarbaum, S.E., Bliss, B.J., Zhang, X., Tanksley, S.D., Oppenheimer, D.G., Soltis, P.S., Ma, H., dePamphilis, C.W., and Leebens-Mack, J.H. (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biology 5(1):5

Albert, V. A., ed. (2005) Parsimony, Phylogeny, and Genomics. Oxford Univ. Press.

Albert, V. A. (2005) Parsimony and phylogenetics in the genomic age. Pp. 1-11 in Parsimony, Phylogeny, and Genomics, ed. V. A. Albert, Oxford Univ. Press.

Buzgo, M., Soltis, D.E., Soltis, P.S., Ma, H., Hauser, B.A., Leebens-Mack, J., and Johansen, B. (2005) Perianth development in the basal monocot Triglochin maritima (Juncaginaceae).  In: Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons (Monocot III), Rancho Santa Ana Botanic Gardens, CA, 2003. (In Press).

Buzgo, M., Soltis, P. S., and Soltis, D. E.  (2005) Floral developmental morphology of Amborella trichopoda (Amborellaceae).  International Journal of Plant Sciences, 165: 925-947.

Buzgo, M., Soltis, P.S., Kim, S., and Soltis, D.E. (2005) The making of a flower. The Biologist. 52(3):149-154.

Frohlich M. (2005) In: Proceedings of the Third International Conference on the Comparative Biology of the Monocotyledons (Monocot III), Rancho Santa Ana Botanic Gardens, CA, 2003. (In Press).

Kim, S., Koh, J., Ma, H., Hu, Y., Endress, P., Hauser, B., Soltis, P.S., and Soltis, D.E. (2005). Sequence and expression studies of A-, B-, and E-class MADS-box genes in Eupomatia (Eupomatiaceae):  Support for the bracteate origin of the calyptra. Intl. J. Plant Sci. 166(2):185-198

Kim, S., J. Koh , M-J.Yoo, H. Kong, Y. Hu, H. Ma, P.S. Soltis and D.E. Soltis. (2005). Expression of floral MADS-box genes in basal angiosperms: Implications for the evolution of floral regulators. Plant J. 43(5):724-744. (cover)

Kirik, V., Lee, M.M., Wester, K., Herrmann, U., Zheng, Z., Oppenheimer, D., Schiefelbein, J. and Hlskamp, M. (2005) Functional diversification of MYB23 and GL1 genes in trichome morphogenesis and initiation. Development 132(7):1477-1485

Kuhl, J.C., Havey, M.J., Martin, W.J., Cheung, F., Yuan, Q., Landherr, L., Hu, Y., Leebens-Mack, J., Town, C.D., and Sink, K.C. Comparative genomic analyses of Asparagus officinalis L. Genome 48:1052-1060.

Leebens-Mack, J.H., Raubeson, L. A., Cui, L., Kuehl, J. V., Fourcade, M. H., Chumley, T. W., Boore, J. L., Jansen, R. K., and dePamphilis, C. W. (2006) Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol. Biol. Evol. 22(10):1948-1963.

Leebens-Mack, J.H., Soltis, D.E., and Soltis, P.S.  (2005) Plant reproductive genomics at the Plant and Animal Genome Conference.  Comparative and Functional Genomics 6: 159-169.

Ma, H. (2005). Molecular genetic analysis of microsporogenesis and microgametogenesis. 2005. Annu. Rev. Plant Biol. (In Press).

Park, S.O., Zheng, Z., Oppenheimer, D.G., and Hauser, B.A. (2005). The PRETTY FEW SEEDS 2 gene encodes an Arabidopsis homeodomain protein that regulates ovule development. Development 132(4):841-849.

Soltis, D. E., Soltis, P. S., Chase, M. W., and Endress, P. (2005) Phylogeny, evolution, and classification of flowering plants. Sinauer Associates, Sunderland, MA.

Wang, J., B.G. Lindsay, L. Cui, P.K. Wall, J. Marion, J. Zhang, and dePamphilis, C. W. (2005) Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. BMC Bioinformatics, 6:300.

Yoo, M., Bell, C. D., Soltis, P. S., and Soltis, D. E. (2005). Estimation of divergence times and biogeography in Nymphaeales.  Systematic Botany. (In Press).

Zahn, L. M., Kong, H., Leebens-Mack, J., Kim, S., Soltis, P.S., Landherr, L.L., Soltis, D.E., dePamphilis, C. W., and Ma, H. (2005). The evolution of the SEPALLATA subfamily of MADS-box genes: A pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics (In Press).

Zahn, L. M., Leebens-Mack, J., dePamphilis, C. W., Ma, H., and Theissen, G. (2005). To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. J. Hered. 96(3):225-240.

Zhang, X., Feng, B., Zhang, Q., Zhang, D., Altman, N., and Ma, H. (2005) Genome-wide analysis of Arabidopsis early floral gene expression and comparison with vegetative and later reproductive stages. Plant Mol. Biol. 58: 401-419.

2004

Buzgo, M., Soltis, D. E., Soltis, P. S., and Ma, H.  (2004) Towards a comprehensive integration of morphological and genetic studies of floral development. Trends in Plant Science. 9: 164-173.

Jobson R.W., Nielsen R., Laakkonen L., Wikstrom M., and Albert V.A.  2004.  Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation. 101(52):18064-18068

Kim, S, Yoo, M-J., Albert, V. A., Farris, J. S., Soltis, P. S., and Soltis, D. E. (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. American Journal of Botany 91:2102-2118.

Kong, H.-Z., Leebens-Mack, J., Ni, W., dePamphilis, C. W., and Ma, H. (2004) Highly heterogeneous rates of evolution in the SKP1 gene family in animals and plants: functional and evolutionary implications. Molecular Biology and Evolution. 21:117-128.

Ni, W., Li, W., Zhang, X., Hu, W., Zhang, W., Wang, G., Han, T., Zahn, L. M., Zhao, D.-Z., and Ma, H. (2004)  Genetic control of reproductive development in flowering plants.  In Molecular Plant Physiology. Ed. R. P. Sharma.  Haworth Press, New York. In press

Soltis, D. E., Albert, V. A., Kim, S., Yoo, M.-J. Soltis, P. S., Frohlich, M. W., Leebens-Mack, J., Kong, H., Wall, K., Ma, H., and dePamphilis, C.W. (2004) Evolution of the Flower. In R. Henry (ed.) Diversity and Evolution of Plants, CABI Publishers.

Soltis, D. E. and Soltis, P. S. (2004) Amborella not a basal angiosperm? Not so fast. American Journal of Botany. 91: 997-1001

Soltis, D. E. and Soltis, P. S. (2004) The role of phylogenetics in comparative genetics. Plant Physiology 132: 1790-1800.

Soltis, D. E., Soltis, P. S., Chase, M. W., and Endress, P. (2004)  Phylogeny, evolution, and classification of flowering plants.  Smithsonian Press.  (In press).

Soltis, P. S., Soltis, D. E., Chase, M. W., Endress, P. K., and Crane, P. R. (2004) The diversification of flowering plants. In The Tree of Life (J. Cracraft and M. Donoghue, eds.). pp. 154-167. Oxford University Press, New York.

Soltis, P. S. and Soltis, D. E.  (2004)  Origin and diversification of angiosperms.  American Journal of Botany 91: 1614-1626.

Uimari, A., Kotilainen, M., Elomaa, P., Yu, D., Albert, V.A., and Teeri, T.H. 2004.  Integration of reproductive meristem fates by a SEPALLATA-like MADS-box gene. 101(44):15817-22

Wang, G., Kong, H., Sun, Y., Zhang, X., Zhang, W., Altman, N., dePamphilis, C. W., and Ma, H. (2004) Genome-wide analysis of cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins.  Plant Physiol. 135:1084-1099.

Wang, J-P.Z. Lindsay, B.G., Leebens-Mack, J, Cui, L., Wall, K, Miller, W.C. and dePamphilis, C.W.  (2004) EST Clustering Error Evaluation and Correction. Bioinfomatics 20:2973-84.

2003

Albert, V. A. (2003)  Genetics of flower morphology.  In Yearbook of Science and Technology McGraw-Hill. Pp. 151-153.

Elomaa, P., Uimari, A., Mehto, M., Albert, V. A., Laitinen, R. A. E., and Teeri, T. H.  (2003) Activation of anthocyanin biosynthesis in Gerbera hybrida (Asteraceae) suggests conserved protein-protein and protein-promoter interactions between the anciently diverged monocots and eudicots.  Plant Physiology 133: 1-12.

Frohlich, M.W. (2003)  An evolutionary scenario for the origin of flowers. Nature Reviews Genetics 4:559-556.

Hu, W., Wang, Y., Bowers, C., and Ma, H.  (2003) Isolation, sequence analysis, and expression studies of florally expressed genes in Arabidopsis. Plant Molecular Biology. 53: 545-563.

Ronse de Craene, L., Soltis, D. E., and Soltis P.S. (2003) Evolution of floral structures in basal angiosperms. International Journal of Plant Sciences 164: S329-363.

Soltis, D.E., Fishbein, M., and Kuzoff R. K.  (2003) Reevaluating the evolution of epigyny: data from phylogenetics and floral ontogeny.  International Journal of Plant Sciences 164: S251-S264.

Soltis, P. S. and Soltis, D.E. (2003) Applying the bootstrap in phylogeny reconstruction. Statistical  Science 18: 1-12.

2002

Albert, V.A., Oppenheimer, D.G. and Lindqvist, C. (2002) Pliotropy, redundancy, and the evolution of flowers.  Trends in Plant Science 7: 297-300.

Soltis, D. E., Soltis, P. S., Albert, V. A., Oppenheimer, D. G., dePamphilis, C.W., Ma, H., Frohlich, M. W. and Theissen, G.  (2002) Missing links: the genetic architecture of flower and floral diversification.  Trends in Plant Science 7:22-31