Original NSF Proposal
"From the genome to the tree of life"
NSF Proposal Body Bibliography Initial Core Participant's statements
1. Results from Prior Support 5. Examples: Research Integrating Genomics / Phylogenetics
2. Background: Phylogenetics / Evolution 6. Proposed Coordination Activities
3. Background: Genomics 7. Management / Coordination Mechanisms
4. Theme: Research Coordination Group 8. Significance

Section 1: Results from Prior Support

DOE/NSF/USDA Panel on Collaborative Research in Plant Biology
"The Origins and Phylogeny of Green Plants: A Research Coordination Group"
USDA grant 94-37105-0713, University of Tulsa, 1994-00, ($285,459)
Mark A. Buchheim, PI; Brent D. Mishler, co-PI; Russell L. Chapman, co-PI

Background on "Deep Green" and its goals

The green plants represent one of the six large clades of the crown eukaryotes -- more than 1/2 million species -- a clade at least 1 billion years old. Their morphological and chemical diversity, ecological dominance, and importance in human affairs are paramount among life's lineages. Reconstruction of the broad-scale phylogenetic relationships of green plants is important to our understanding of major evolutionary events such as the origin of multicellularity, diversification of life-history strategies, and the conquest of land (Graham, 1985; Mishler and Churchill, 1985). In addition, availability of a well-supported framework of relationships is necessary for practical purposes such as predicting useful chemicals for pharmacology, selecting promising genes for biotechnology studies, carrying out comparative functional and genomic studies, and setting conservation priorities.

The Green Plant Phylogeny Research Coordination Group (GPPRCG or "Deep Green"), through a series of meetings, workshops, and massive collaborative analyses, was organized to facilitate the production of a detailed phylogeny for this major branch of the tree of life. Considerable progress in understanding the phylogeny of green plants has been made, based on classical morphological characters, newly described ultrastructural features, and nucleotide sequence data from the nuclear, chloroplast, and mitochondrial genomes. The success of this effort has in turn generated exciting new opportunities for both applied and basic research and training. The more robust parts of the current cladogram, though clearly in need of support from future studies sampling more examplars and more character systems (morphological as well as molecular), can serve as a framework for some evolutionary interpretations currently, and also pinpoint key areas in need of further work. Addressing a phylogenetic study of this enormous scale has necessitated improvements in data handling and analysis that have broad applicability to phylogenetic studies of other organisms.

Coordination activities of the GPPRCG

Considerable preliminary data were available, and we were clearly poised back in 1994 for rapid progress in this area as a result of recent technological, theoretical, and computational improvements. However, several obstacles remained. No mechanism existed for attacking this major effort in a cooperative, coordinated manner. Certain groups were over-studied, other groups nearly unknown. Data sets derived from different molecules and different morphological character systems rarely included the same basic taxa, thus they could not be compared. Current analytical software, and the concepts behind it, needed improvements to handle analyses of this size and complexity, as did data storage and retrieval software. Standards for maintaining and adding to phylogenetic data bases, both morphological and molecular, needed to be discussed and then implemented. The GPPRCG was formed in 1994 in order to remedy these shortcomings by facilitating interactions between distinct research groups. A full account of the previous meetings and progress of the GPPRCG can be found at: http://ucjeps.berkeley.edu/bryolab/greenplantpage.html. The following is a brief synopsis.

The first meetings covered important, broad questions regarding taxon and data sampling. The group needed to establish a list of priorities for selecting exemplar taxa. Deliberations on questions of taxon sampling were divided into discussion sub-groups by taxonomic expertise. The group also had to identify types of characters, both morphological and molecular, that should or need to be sampled for each taxon. As with the question of taxon sampling, discussions of character sampling were broken down by expertise when appropriate (e.g., gross morphology vs. ultrastructure or chloroplast vs. nuclear genes). These decisions were publicized on the web site as a guide for future data gathering, in the form of data availability matrices (DAMs).
Later meetings emphasized two distinct topics, one theoretical and one empirical, i.e., methods for analysis of large, heterogeneous data sets, and phylogenetic analysis within the major clades of green plants. The general goal common to all meetings of the group has been to coordinate research across the community by openly providing standardized taxon and character information on our web site and developing new means of extracting phylogenetic information from these data.

Final meetings and workshops held in the last year of the grant enabled groups of researchers to get together and plan their specific collaborative analyses. These were in most cases accompanied by a series of talks for the public and preliminary presentations of research in preparation for the Botanical Congress. These included meetings of the green algal, fern, liverwort, moss, and seed plant subgroups. The data and other information shared at these workshops greatly increased the coordination and impact of the final presentations at the Congress.

Results of the GPPRCG to date were presented at a series of eight interlocking symposia at the XVI International Botanical Congress held in St. Louis, Missouri, 1-7 August, 1999. All the data sets and findings of these symposia are reflected on the GPPRCG web site, several series of papers in press in specialized professional journals, a review paper commissioned by Science, as well as in a book in progress on the phylogeny of green plants. This book will have two sections, one giving the details of competing phylogenetic hypotheses and the other discussing biological and evolutionary subjects in light of the phylogeny. There has also been considerable media attention to this effort, with more than 100 newspaper, radio, and magazine stories appearing since August 1999, giving us an opportunity to inform the public about the nature of phylogenetic reconstruction. The community of researchers in this area has been brought together, and a high level of communication and coordination achieved. In fact, the status of phylogenetic research on the green plants now serves as an example to all research groups interested in the other major branches of the tree of life.

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