FGP Publications

2009

Chanderbali A.S., Albert, V.A., Leebens-Mack, J., Altman, N.S., Soltis, D.E. and Soltis, P.S. (2009) Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae). Proceedings of the National Academy of Sciences, USA, 106:8929-34. abstract

Duarte, J.M., Wall, P.K., Edger, P.P., Landherr, L.L., Ma, H., Pires, J.C., Leebens-Mack, J. and dePamphilis, C.W. (2009) Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology (In press).

Shan, H., Zahn, L., Guindon, S., Wall, P.K., Kong, H., Ma, H., dePamphilis, C.W., and Leebens-Mack, J. (2009) Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Molecular Biology and Evolution, 10:2229-2244. abstract (With support from the NSF Ancestral Angiosperm Genome Project.)

Wall, P.K., Leebens-Mack, J.H., Chanderbali, A., Barakat, A., Wolcott, E., Liang, H., Landherr, L., Tomsho, L.P., Hu, Y., Carlson, J.E., Ma, H., Schuster, S.C., Soltis, D.E., Soltis, P.S., Altman, N., and dePamphilis, C.W. (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics, 10:347. abstract (With support from the NSF Ancestral Angiosperm Genome Project.)

Warner, K.A., Rudall, P.J. and Frohlich, M.W. (2009) Environmental control of sepalness and petalness in perianth organs of waterlilies: a new Mosaic Theory for the evolutionary origin of a differentiated perianth. Journal of Experimental Botany, 60(12):3559-3574. abstract

2008

Chanderbali, A.S., Albert, V., Ashworth, V.E.T.M., Clegg, M.T., Litz, R.E., Soltis, D.E. and Soltis, P.S. (2008) Persea americana (avocado): bringing ancient flowers to fruit in the genomics era. Bioessays, 4:386-396. abstract

Duarte, J.M., Wall, P.K., Zahn, L.M., Soltis, P.S., Soltis, D.E., Leebens-Mack, J.H., Carlson, J.E., Ma, H., and dePamphilis, C.W. (2008) Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis. Taxon, 57(4):1110-1122. abstract

Hu, W., dePamphilis, C.W. and Ma, H. (2008) Phylogenetic analysis of the plant-specific Zinc Finger-Homeobox and Mini Zinc Finger gene families. Journal of Integrative Plant Biology, 50(8):1031-1045. abstract

Liang, H., Carlson, J.E., Leebens-Mack, J.H., Wall, P.K., Mueller, L.A., Buzgo, M., Landherr, L.L., Hu, Y., DiLoreto, D.S., Ilut, D.C., Field, D., Tanksley, S., Ma, H. and dePamphilis, C.W. (2008) An EST Database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics and Genomes, 4:419-433. abstract

Wall, P.K., Leebens-Mack, J., Muller, K., Field, D., Altman, N. and dePamphilis, C.W. (2008) PlantTribes: A gene and gene family resource for comparative genomics in plants. Nucleic Acids Research, 36:D970-976. abstract

Warner, K.A., Rudall, P.J. and Frohlich, M.W. (2008) Differentiation of perianth organs in Nymphaeales. Taxon 57(4):1096-1109. abstract

2007

Barakat, A., Wall, P.K., DiLoretto, S., dePamphilis, C.W. and Carlson, J.E. (2007) Conservation and divergence of microRNAs in Populus. BMC Genomics, 8:481. abstract

Barakat, A., Wall, P.K., Leebens-Mack, J.H., Wang, Y.J. and dePamphilis, C.W. (2007) Large scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. The Plant Journal, 51:991-1003. abstract

Buzgo, M., Chanderbali, A.S., Kim, S., Zheng, Z., Oppenheimer, D., Soltis, P.S. and Soltis, D.E. (2007) Floral developmental morphology of Persea americana (avocado, Lauraceae): the oddities of male organ identity. International Journal of Plant Sciences, 168(3):261-284. abstract

Gilbert, M.T., Binladen, J., Miller, W., Wiuf, C., Willerslev, E., Poinar, H., Carlson, J.E., Leebens-Mack, J.H. and Schuster, S.C. (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research, 31(5):1-10. abstract

Jansen, R.K., Cai, Z., Raubeson, L.A., Daniell, H., dePamphilis, C.W., Leebens-Mack, J.H., Müller, K.F., Guisinger-Bellian, M., Haberle, R.C., Hansen, A.K., Chumley, T.W., Lee, S.-B., Peery, R., McNeal, J., Kuehl, J.V. and Boore, J.L. (2007) Analysis of 81 genes from 64 chloroplast genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences, 104(49): 19369-19374. abstract

Kong, H., Landherr, L., Frohlich, M., Leebens-Mack, J.H., Ma, H., and dePamphilis, C.W. (2007) Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. The Plant Journal, 50:873-885. abstract

Morris, A.B., Bell, C.D., Judd, W.S., Soltis, D.E. and Soltis, P.S. (2007) Phylogeny and divergence time estimation in Illicium with implications for New World biogeography. Systematic Botany, 32:236-249. abstract

Soltis, D.E., Gitzendanner, M.A., and Soltis, P.S. (2007) 567-taxon data set for angiosperms: the challenges posed by Bayesian analyses of large data sets. International Journal of Plant Sciences, 168(2):137-157. abstract

Soltis, D.E., Chanderbali, A., Kim, S., Buzgo, M. and Soltis, P.S. (2007) The ABC model and its applicability to basal angiosperms. Annals of Botany, 100:155-163. abstract

Soltis D.E., Ma, H., Frohlich, M.W., Soltis, P.S., Albert, V.A., Oppenheimer, D.G., Altman, N.S., dePamphilis, C.W. and Leebens-Mack, J.H. (2007) The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends in Plant Science, 12(8):358-367. abstract

Wijeratne A.J., Zhang, W., Sun, Y., Liu, W., Albert, R., Zheng, Z., Oppenheimer, D.G., Zhao, D. and Ma, H. (2007) Differential gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networks. The Plant Journal, 52(1):14-29. abstract

2006

Altman, N. and Hua, J. (2006) Extending the loop design for 2-channel microarray experiments. Genetical Research, 3:153-163. abstract

Altman, N., Leebens-Mack, J.H., Zahn, L., Chanderbali, A., Tian, D., Werner, L., Ma, H. and dePamphilis, c.w. (2006) Behind the scenes: planning a multispecies microarray experiment. Chance, 19(3):28-39.

Buzgo, M., Soltis, D.E., Soltis, P.S., Ma, H., Hauser, B.A., Leebens-Mack, J.H. 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.

Cai, Z., Penaflor, C., Kuehl, J.V., Leebens-Mack, J.H., Carlson, J.E., dePamphilis, C.W., Boore, J.L. and Jansen, R.K. (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogenetic relationships of magnoliids. BMC Evol. Biol., 6:77. abstract

Carlson, J.E., Leebens-Mack, J.H., Wall, P.K., Zahn, L.M., Mueller, L.A., Landherr, L.L., Hu, Y., Ilut, D.C., Arrington, J.M., Choirean, S., Becker, A., Field, D., Tanksley, S.D., Ma, H. and dePamphilis, C.W. (2006) EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot. Plant Molecular Biology, 62:351-369. abstract

Chanderbali, A., S. Kim, M. Buzgo, P. Zheng, D.G. Oppenheimer, D.E. Soltis and P.S. Soltis. (2006) Genetic footprints of stamen ancestors guide perianth evolution in Persea (Lauraceae). International Journal of Plant Sciences, 167(6):1075-1089. abstract

Churchman, M.L., M.L. Brown, N.K. Kirik, M. Hülskamp, D. Inzé, L. De Veylder, J.D. Walker, Z. Zheng, D.G. Oppenheimer, T. Gwin, J. Churchman, and J.C. Larkin. (2006) SIAMESE, a novel plant-specific cell cycle regulator controls endoreplication onset in Arabidopsis thaliana. Plant Cell, 18(11):3145-3157. abstract

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. abstract

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 Research, 34: D692-D696. abstract

Cui, L., P.K. Wall, J.H. Leebens-Mack, B.G. Lindsay, D.E. Soltis, J.J. Doyle, P.S. Soltis, J.E. Carlson, K. Arumuganathan, A. Barakat, V.A. Albert, H. Ma and C.W. dePamphilis. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Research, 16: 738-749. (cover) abstract

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

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.

Frohlich, M. (2006) Recent developments regarding the evolutionary origin of flowers. In Developmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series Elsevier Limited, London, vol. 44, pp. 63-127.

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

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

Leebens-Mack, J.H., Vision, T., Brenner, E., Bowers, J.E., Cannon, S., Clement, M.J., Cunningham, C.W., dePamphilis, C.W., deSalle, R., Doyle, J.J., Eisen, J.A., Gu, X., Harshman, J., Jansen, R. K., Kellogg, E. A., Koonin, E.V., Mishler, B.D., Philippe, H., Pires, J.C., Qiu, Y-L., Rhee, S.Y., Sjölander, K., Soltis, D.E., Soltis, P.S., Stevenson, D.W., Wall, K., Warnow, T. and Zmasek, C. (2006) Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analysis (MIAPA). Omics 10(2): 231-237. abstract

Leebens-Mack, J.H., Wall, Duarte, J., K., Zheng, Z., Oppenheimer, D. and dePamphilis, C.W. (2006) A genomics approach to the study of ancient polyploidy and floral developmental genetics. In Developmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research series, Elsevier Limited, London, vol. 44, pp.527-549.

Liang, H., Fang, E.G., Tomkins, J.P., Luo, M., Kudrna, D., Arumuganathan, K., Zhao, S., Schlarbaum, S.E., Banks, J.A., dePamphilis, C.W., Mandoli, D.F., Wing, R.A. and Carlson, J.E. (2006) Development of a BAC library resource for yellow poplar (Liriodendron tulipifera) and the identification of genomic regions associated with flower development and lignin biosynthesis. Tree Genetics and Genomes, 3(3):215-225. abstract

Lindqvist, C., Scheen, A.-C., Yoo, M.-J., Grey, P., Oppenheimer, D.G., Leebens-Mack, J.H., Soltis, D.E., Soltis, P.S. and Albert, V.A. (2006) An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers. BMC Plant Biology 6:16. abstract

Ma, H. (2006) A molecular portrait of Arabidopsis meiosis. In The Arabidopsis Book, C.R. Somerville, E.M. Meyerowitz, J. Dangl, and M. Stitt, eds. American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0095. abstract

McNeal, J.R., Leebens-Mack, J.H., Arumuganathan, K., Kuehl, J.V., Boore, J.L. and dePamphilis, C.W. (2006) Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques 41(1):69-73. abstract

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, vol. 44, 594 pp.

Soltis, P.S., Soltis, D.E., Kim, S., Chanderbali, A. and Buzgo, M. (2006) Expression of floral regulators in basal angiosperms and the origin and evolution of ABC-function. In Devlopmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research: Incorporating Advances in Plant Pathology, vol. 44, pp.484-506.

Teeri, T.H., Kotilainen, M., Uimari, A., Ruokolainen, S., Ng, Y.P., Malm, U., Pöllänen, E., Broholm, S., Laitinen, R., Elomaa, P. and Albert, V.A. (2006) Floral developmental genetics of Gerbera (Asteraceae). In Devlopmental Genetics of the Flower, D.E. Soltis, J.H. Leebens-Mack and P.S. Soltis, eds. Advances in Botanical Research, vol. 44, pp.324-351.

Tuskan, G.A., S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R.R. Bhalerao, R.P. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G.-L. Chen, D. Cooper, P.M. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Déjardin, C. dePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jorgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J.-C. Leplé, P. Locascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D. R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C.-J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. Van de Peer, D. Rokhsar. (2006) The genome of black cottonwood, Populus trichcarpa (Torr. & Gray ex Brayshaw). Science, 313:1556-1604. abstract

Yoo, M.J., Albert, V.A., Soltis, P.S. and Soltis, D.E. (2006) Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants. BMC Plant Biology, 6:3-12. abstract

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, vol. 44, pp.164-207.

Zahn, L.M., Leebens-Mack, J.H., Arrington, J.M., Hu, Y., Landherr, L., dePamphilis, C.W., 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. Evolution and Development, 8:30-45. (cover) abstract

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. abstract

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

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. abstract

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) abstract

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

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. abstract

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. abstract

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. abstract

Ma, H. (2005). Molecular genetic analysis of microsporogenesis and microgametogenesis. 2005. Annual Review of Plant Biology. 56:393-434. abstract

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. abstract

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. abstract

Yoo, M., Bell, C. D., Soltis, P. S. and Soltis, D. E. (2005). Divergence times and historical biogeography in Nymphaeales.  Systematic Botany, 30:693-704. abstract

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, 169(4):2209-2223.abstract

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. abstract

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. abstract

2004

Buzgo, M., Soltis, P.S., and Soltis, D.E. (2004) Floral developmental morphology of Amborella trichopoda (Amborellaceae).  International Journal of Plant Sciences, 165: 925-947. abstract

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. abstract

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. Proceedings of the National Academy of Sciences, USA 101(52):18064-18068. abstract

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. abstract

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. abstract

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. abstract

Soltis, P.S., Soltis, D.E., Chase, M.W., Endress, P.K., and Crane, P.R. (2004) The diversification of flowering plants. In Assembling 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. abstract

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. Proceedings of the National Academy of Sciences, USA 101(44):15817-22. abstract

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 Physiology 135:1084-1099. abstract

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. abstract

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: 1831-1842. abstract

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

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. abstract

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. abstract

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. abstract

Soltis, D.E. and Soltis, P.S. (2003) The role of phylogenetics in comparative genetics. Plant Physiology 132: 1790-1800. full text

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

2002

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

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. abstract