Penn State Science
Claude dePamphilis

Claude dePamphilis

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Professor of Biology

405B Life Sciences
University Park, PA 16802
Phone: (814) 863-6412
Lab Address: 403 Life Sciences
Lab Phone: (814) 863-6413
Email:

Education

  1. PhD, University of Georgia

Research Interests

Plant Molecular Evolution and Systematics

I am a plant evolutionary biologist with broad interests in processes and patterns of evolution at both the molecular and organismal levels. My research is focused in three areas: (1) the evolution of the flower and the floral developmental program, (2) the study of parasitic plants, and (3) the chloroplast genome and phylogenomic evolution.

Evolutionary Genomics of the Flower

The sudden appearance of flowers in the fossil record over 100 million years ago represents a great mystery that has long puzzled plant and evolutionary biologists. Among the many key questions surrounding the origin and diversification of flowers are: (1) Did the earliest flowers possess the full complement of genetic information needed to assemble a modern flower? (2) Was genome duplication an important driver of the diversification of floral developmental pathways? (3) Are there genes that have conserved functions throughout much of flowering plant history? Recent studies in plant developmental genetics and genomics have identified more than 100 genes with specific roles in flower development in Arabidopsis and other model organisms. Other genes with critical roles may remain undiscovered, largely because of functional redundancy or lethality of loss-of-function mutations. This knowledge, along with the recently clarified phylogenetic relationships of flowering plants (see Leebens-Mack et al. 2005) and the availability of genome-scale data and bioinformatics analysis now make it possible to begin to understand how floral developmental pathways originated and diversified.

The Floral Genome Project (FGP), a multi-institutional, multi-collaborator study funded through the National Science Foundation’s (NSF’s) Plant Genome Research Project, was initiated to address these questions by studying the evolutionary diversification of floral regulatory genes and pathways throughout the major lineages of flowering plants. The study was designed to capture a large number of genes expressed during early flower development in 15 phylogenetically critical lineages of flowering plants and gymnosperms, and to determine their expression patterns at several levels of resolution. We then link the sequences and expression patterns through phylogenetic and molecular evolutionary analysis to infer the gene sets and expression patterns that may have been present in the earliest angiosperm lineages. As the principle investigator of the FGP, my group is involved in many aspects of the project, including library building, screening, and sequencing; studies of individual floral gene families; database construction; and a wide range of bioinformatic and molecular evolutionary studies.

Parasitic Plants

Another long-term focus of our research is the study of parasitic plants, including their phylogeny, biology, and molecular evolution. Although most plants are autotrophic, several thousand species of angiosperms obtain water, minerals, and fixed carbon heterotrophically, using specially modified roots (haustoria) that extract these materials directly from a host plant. In addition to their intrinsic interest as organisms with complex adaptations for direct feeding upon other plants, some parasitic plants are important crop plants and, thus, are of great economic significance. Furthermore, because some parasites have completely lost the ability to photosynthesize, these plants provide a powerful system for the investigation of the effects of drastically altered functional constraints on gene and genome evolution and function.

Chloroplast Genomes

Through a project funded by NSF’s Biocomplexity and Tree of Life programs, we are participating in the first large-scale chloroplast genome sequencing project focused on angiosperms and other seed plants. Our goal is to sequence, annotate, and analyze more than 55 chloroplast genomes that represent all major lineages of flowering plants and gymnosperms, with a special focus on evolutionarily interesting genomes that have undergone rearrangements or gene content changes. Within this larger study, our lab’s focus has been on the chloroplast genome evolution in parasitic plants, monocots, and basal angiosperms.

Selected Publications

  • Jiao, Y., N.J. Wickett, S. Ayyampalayam, A.S. Chanderbali, L. Landherr, P.E. Ralph, L. P. Tomsho, Y. Hu, H. Liang, P.S. Soltis, D.E. Soltis, S.W. Clifton, S.E. Schlarbaum, S.C. Schuster, H. Ma, J. Leebens-Mack, C.W. dePamphilis. Ancestral polyploidy in seed plants and angiosperms. Nature. Epub ahead of print, April 10, 2011.
  • Duarte, J.M., P.K. Wall, P.P. Edger, L.L. Landherr, H. Ma, J.C. Pires, J. Leebens-Mack, and C.W. dePamphilis. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology, 2010, 10:61.
  • Chanderbali, A.S., M.J. Yoo, L.M. Zahn, S.F. Brockington, P.K. Wall, M.A. Gitzendanner, V.A. Albert, J. Leebens-Mack, N.S. Altman, H. Ma, C.W. dePamphilis, D.E. Soltis, and P.S. Soltis. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proceedings of the National Academy of Science U S A., 2010, Dec 28;107(52):22570-22575.
  • Givnish, T.J., M. Ames, J.R. McNeal, M.R. McKain, P. R. Steele, C.W. dePamphilis, S.W. Graham, J.C. Pires, D.W. Stevenson, W.B. Zomlefer, B.G. Briggs, M.R. Duvall, M.J. Moore, J. M. Heaney, D.E. Soltis, P.S. Soltis, K. Thiele, and J.H. Leebens-Mack. Assembling the tree of the Monocotyledons: Plastome sequence phylogeny and evolution of Poales. Annals of the Missouri Botanical Gardens, 2010, 97:587-616.
  • Singh, R., A.L. Levitt, E.G. Rajotte, E.C. Holmes, N. Ostiguy, D. Vanengelsdorp, W.I. Lipkin, C.W. dePamphilis, A.L. Toth, and D.L. Cox-Foster. RNA viruses in hymenopteran pollinators: Evidence of inter-taxa virus transmission via pollen and potential impact on non-Apis hymenotpteran species. PLoS One, 2010, Dec. 22;5(12):e14357.
  • Westwood, J.H., J.I. Yoder, M.P. Timko, and C.W. dePamphilis. The evolution of parasitism in plants. Trends in Plant Science, 2010, Apr;15(4):227-235.
  • Zahn LM, Ma X, Altman NS, Zhang Q, Wall PK, Tian D, Gibas CJ, Gharaibeh R, Leebens-Mack JH, C.W. dePamphilis, Ma H. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biology, 2010 Oct 15;11(10):R101.

  • Selected Older Publications

  • Cui, L., J.H. Leebens-Mack, L-S. Wang, J. Tang, L. Rymarquis, D.B. Stern, and C.W. dePamphilis. 2006. Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evolutionary Biology, 6:13.
  • 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 Arabi
  • Leebens-Mack, J.H., L.A. Raubeson, L. Cui, J.V. Kuehl, M.H. Fourcade, T.W. Chumley, J.L. Boore, R.K. Jansen, and C.W. dePamphilis. 2005. Identifying the basal angiosperm node in chlorplast genome phylogenies: sampling one's way out of the Felsenstein zone
  • The Floral Genome Project Research Group: Soltis, D.E., P.S. Soltis, V.A. Albert, D.G. Oppenheimer, C.W. dePamphilis, H. Ma, W. Frohlich, and G. Theissen. 2002. Missing Links: The genetic architecture of the flower and floral diversification. Trends in
  • Bowe, L.M., G. Coat, and Claude W. dePamphilis. 2000. Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proceedings of the National Academy of S
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