NSF Proposal - 10. Results from Prior Support

Jeffrey Boore. NSF 9807100. "A Phylogeny of Major Metazoan Radiations". 1998-2001, $200,000.
We determined complete mitochondrial genome sequences for 25 phylogenetically diverse invertebrates. Several contentious higher level relationships were robustly reconstructed using mitochondrial gene arrangement characters: Pogonophora are a family within Annelida; Platyhelminthes and lophophorates fall within Eutrochozoa; Sipuncula are more closely related to Annelida than to Mollusca; insects evolved within Crustacea, not from myriapods. We have also developed models for gene order rearrangements and explored many aspects of mitochondrial DNA structure as well as their impact on phylogeny reconstruction. 16 publications to date.

Michael J. Donoghue. NSF 9806937, "Duplicate genes and plant phylogeny: phytochromes and the rooting of the seed plants, angiosperms, and eudicots", 1998-2001, $180,200.
A series of phytochrome gene duplications were used to root the seed plants, the angiosperms, and the eudicots. CHR (3): Three undergraduate women. Four publications to date.

Dina Mandoli. NSF 9630618, "Cell biology & genetics of Acetabularia phenotypes that are arrested in development", 1996-2000, $200,000.
We completed all 3 Aims: 1) we finished inbreeding near isogenic lines proving that we can perform genetic manipulations; 2) we demonstrated that high- throughput transformation and selection work well; and 3) we studied development, compensation and genetics of developmentally arrested phenotypes. This research makes development of insertional mutagenesis of A. acetabulum feasible. 16 publications to date. CHR (29): 1 postdoctoral fellow (NSF), 4 graduate and 24 undergraduate students. Includes 17 women, 10 minorities, 2 learning disabled, 8 Gates or Hughes Fellows. 24 out of 29 plan or have careers in science.

Brent Mishler. USDA 94-37105-0713 (DOE/NSF/USDA Collaborative Research in Plant Biology), "The Origins and Phylogeny of Green Plants: A Research Coordination Group"; 1994-2000, $285,459; NSF 0090227, "Beyond 'Deep Green': Towards an Integration of Plant Phylogenetics and Plant Genomics"; 2001-2006, $496,434.
The Green Plant Phylogeny Research Coordination Group (GPPRCG; "Deep Green"), has been working since 1994 to facilitate the reconstruction of an ever more resolved phylogeny. See full progress report at: http://ucjeps.berkeley.edu/bryolab/greenplantpage.html. Preliminary results of the GPPRCG were presented in a series of eight symposia at the XVI International Botanical Congress in 1999 and published in a series of papers in specialized professional journals, as well as numerous reviews. Progress of a new effort of this group, supported by an RCN grant "Deep Gene", can be found at: http://ucjeps.herb.berkeley.edu/bryolab/deepgene/index.html. Many professional workshops, research visits, and student training activities have already been supported.

Charles J. O'Kelly. DEB-0075601, "Towards a Monograph of the Ulvellaceae (Ulvophyceae, Chlorophyta) and related green algae", 2000-2004, $320,000.
We are finding: (1) numerous new species (at least 15) within this assemblage; (2) significant lack of support for generic concepts based on morphology, some genera are polyphyletic at the class level (Friedl and O'Kelly 2002) while others (especially those in the Ulvellaceae sensu stricto) cannot be sustained; (3) assortment of these algae among five putative clades, including the Cladophorales, the Ulotrichales, the Ulvaceae and Kornmanniaceae of the Ulvales, and a clade, previously unrecognized at the molecular level, basal to other Ulvales and possibly identical with the "Ctenocladaceae" of some morphological classifications. One publication to date. CHR (3): one postdoc and 2 research technicians.

Richard Olmstead. DEB-9727025, ?Chloroplast DNA Phylogeny of Basal Angiosperms?, 1998- 2001, $205,000; DEB- 0090313; "Chloroplast DNA Phylogeny of Seed Plants and Basal Angiosperms", 2001-2004, $240,000.
We identified 17 chloroplast genes (Graham and Olmstead 2000a) that permit resolution of ancient land plant radiations (e.g., low synonymous substitution rates and low site-to-site rate heterogeneity) to analyze ~15kb of data. Our evidence suggests that full resolution of the basal angiosperm radiation is possible with high levels of confidence. My current NSF grant expands this work to include more extensive sampling in seed plants and other major land plant lineages in collaboration with Sean Graham (U. Alberta). Chara and Coleochaete are included as outgroups. Four publications to date. CHR (10): one postdoc, 2 research technicians, 3 grad students (partial support), and 6 undergrads on REU suppl., including 2 minorities.

Karen Renzaglia: DEB-9527735. °Spermatogenesis in "pteridophytes": ultrastructure, differentiation and phylogeny.° 1996-2001, $140,000.
Our major research findings fall into two categories: (1) comparative information on cellular development and structure in land plants and (2) contributions to clarifying evolutionary trends and resolving phylogenetic relationships among basal embryophytes. We have provided detailed descriptions of sperm cell architecture and cellular development in pteridophytes, bryophytes, green algae and seed plants. Our work reveals that structural and developmental complexity in plant sperm cells are unsurpassed in any other group of organisms. We have generated new data, assembled published data and analyzed one of the most comprehensive data bases of both morphological and molecular data associated with the phylogeny of land plants. 27 publications to date, 6 with undergraduate co-authors. Nine undergraduates, one doctoral student and three master's students have worked on plant spermatogenesis since 1995.

Alan Smith: DEB-9616260 "Collaborative research: Phylogeny, character evolution, and diversification of extant ferns", 1997-2002, $25,619 (with K. M. Pryer and P. G. Wolf). DEB-9807053 "Morphological and molecular systematics of the Polypodiaceae and Grammitidaceae", 1998-2002 $55,939, (with T. A. Ranker and C. H. Haufler).
The first of these awards supported phylogenetic studies on the ca. 10 basalmost families of extant ferns. By virtue of the results obtained, as well as some previous work, we expanded our study to include Psilotaceae and Equisetaceae, two groups traditionally thought to be fern allies, but now believed to be nested in the fern clade. Altogether, ca. 65 examplars (genera) from the basal clade were sequenced for four genes plus morphology. A similar approach has been applied to the study to the Polypodiaceae and Grammitidaceae, generally acknowledged to be the most recently derived of the higher leptosporangiate ferns.

Paul G. Wolf. DEB-9707087 ?Collaborative Research: Phylogeny, character evolution, and diversification of extant ferns?. 1997-2000, $94,990.
We used data from 4 genes and morphology from over 60 taxa to resolve phylogeny of vascular plants. Our data indicate that horsetails and ferns together are the sister to seed plants. Five publications to date.

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