NSF Proposal - 11. Managment Plan

Coordination of the project. Six main institutions and two subcontractor institutions are involved in the proposed research. In addition, 19 collaborators are expected to play a significant role in the project. The roles of each PI and collaborator are spelled out below. This team represents an amazing range of expertise, and the research is multifaceted, thus the project will require careful coordination.

Charles O'Kelly will serve as Project Coordinator for the length of the grant. He will supervise our overall progress and interface with related research groups (see below). A Steering Committee (SC) for the project will be established, consisting of all the PIs. The SC will hold a conference call each month to review progress and activities. An email list will serve for routine communication across labs.

There will be continuous interaction, data-sharing, and cross-training activities among the eight institutions and beyond. The entire group, (SC, collaborators, and students) as well as relevant invitees, will meet at least once a year in association with national meetings (usually of the Botanical Society of America). These meetings will include progress reports as well as discussions and demonstrations of new techniques and approaches. Meeting proceedings and new data availability will be shared among labs, and broadly with the general botanical public, by posting to a Web page. Inclusion in the group's activities will be open to all who are interested in its activities, as with the GPPRCG collaboration (that had well over 200 participants). To encourage broader participation, letters of invitation to meetings will be sent to key labs and broadly advertised across the community, and information on the meeting will be posted on the group's Web site and the Web sites of other relevant groups and societies.

The proposed research in relation to the GPPRCG. The Green Plant Phylogeny Research Coordination Group (GPPRCG or "Deep Green"), through a series of meetings, workshops, and collaborative analyses, was organized in 1994 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. 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. The success of this effort generated exciting new opportunities for applied and basic research and training. A full account of progress of the GPPRCG can be found at: http://ucjeps.berkeley.edu/bryolab/greenplantpage.html. 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.

Even though the original grant to fund the GPPRCG has expired, the GPPRCG Executive Committee has continued to function as an overall coordinating mechanism for several successor grants. It is composed of six regular members (three-year terms) plus one student member (one-year terms). Principal Investigators of closely related grants are also appointed by vote of the Executive Committee to serve as ex officio members while their grant is active, thus ensuring smooth cooperation across all grants. If funded, this grant would be represented by PI O'Kelly as an ex officio member (note that a number of the other PIs and collaborators on this proposal also serve on the Committee). This assures sharing of information and resources and facilitates design of co-sponsored meetings and educational outreach activities. Every effort will continue to be made to facilitate efficient and open sharing across the community and participation by all interested parties.

Current members of the GPPRCG Executive Committee: (shown with the August they rotate off)

Elected members:
Dr. Charles F. Delwiche (2002)
Dr. Pam Soltis (2002)
Dr. Richard M. McCourt (2003)
Dr. Kathleen Pryer (2003)
Dr. Louise A. Lewis (2004)
Dr. Yin-Long Qiu (2004)

Ex officio members:
Dr. Brent D. Mishler, Chair (rotated off as elected member 2001; PI, Deep Gene)
Dr. Pam Soltis (current elected member; PI, Biocomplexity Grant on genome evolution)
Dr. Douglas Soltis (PI, Deep Time)
Dr. Claude dePamphilis (PI, Floral Genome Project)
Dr. Robert Jansen (PI, Comparative Chloroplast Genome Project)
Dr. Dina Mandoli (PI, The Green Plant BAC Library Project)
Dr. Mark A. Buchheim (rotated off as elected member 2000; PI, Chlorophyte algae project)
Graduate Student representative: Michael Zanis (2002)

Deep Green Research Coordination Networks. Two related Deep Green NSF RCN grants have recently begun operation to continue and extend the original Deep Green coordination -- one called "Deep Gene" Mishler, PI -- http://ucjeps.herb.berkeley.edu/bryolab/deepgene/index.html) to coordinate genomics and phylogenetics, the other ("Deep Time" D. Soltis, PI -- http://www.flmnh.ufl.edu/deeptime/) to coordinate paleontology and phylogenetics. The proposed research group will interface with both RCNs. Joint meetings of these networks will maintain communication and lead to joint sponsorships and colloquia (e.g., a joint workshop on phylogenetics for molecular biologists and paleobotanists). Through coordination among these RCNs and other groups, the network of interacting scientists will expand to include geologists, paleobotanists, morphologists, phylogeneticists, and genomic botanists.

The proposed research in relation to other research groups. The scale of the proposed research plus its relationship with other current and planned research projects dictate effective coordination and collaboration. For taxon sampling and research progress we are coordinating other groups beyond the GPPRCG including those of Mitsuyasu Hasebe (Japan), Michael Gray (Organelle Genome Mega- sequencing Project, Canada), Sean Graham (Canada). Broad collaboration among these groups minimizes redundancy in sequencing while increasing the efficiency of dissemination and analysis of results. Sequenced genomes will be of more utility than the scope of the project and it will be essential to provide detailed information to the research community, beyond deposition of data in the public domain.

Active phylogenetic projects to be coordinated with this project
In addition to a large body of published literature, there is a large number of active phylogenetic projects ongoing in the more "shallow" branches of green plants. The concatenation analyses proposed here will link together the topologies being produced by these "local" phylogenetic studies. These studies are thus complementary to the research proposed here, and will be coordinated by means of the GPPRCG and representative collaborators from these projects included in this proposal.

Information & material sharing. Part of the success of Deep Green was the clear and repeated commitment of its organizers to individual ownership of data prior to publication and proper attribution of contributions by collaborators. We will continue this commitment. Therefore, on our Web site we will indicate the availability of data rather than distribute any unpublished data of individual investigators. We will indicate what resources and data are available and from whom. Our previous experience suggests that this will prevent duplication of research effort and suggest possible collaborations by allowing everyone to see who is doing what. Contribution of data to collaborative analyses will not required by participants in the group, although we anticipate that those who participate will be interested in exploring such collaborations.

The Web site will also link to related sites, including "Deep Gene" RCN, "Deep Green" and Plant and Algal BAC (planned) Web sites, as well as Web sites developed by the PIs to disseminate information on particular green plants (e.g., Land Plants Online http://www.science.siu.edu/landplants/index.html). Sharing of information reduces undue overlap of data, and provides up-to-date information on genomics and organismal resources (e.g., culture collections, data archiving, extracted DNAs, etc). Educational tools such as teaching modules for K-12 are featured on the "Deep Gene" Website. These will be further developed as results are accumulated from the Tree of Life Initiative.

Morphological Data Archive. One major problem in morphological systematics is the scattering and loss of physical materials (such as permanent slides, mounted blocks, photographs, etc.) and data as researchers retire. Some of the most important materials in green algal phylogeny have already been lost this way. Thus we will develop an archive for a wide variety of data and materials, hosted at the University and Jepson Herbaria, UC Berkeley. This will include culture collections, and morphological and ultrastructural data from deceased and retired scientists. In addition, a major effort will be made to integrate unpublished archived data made available by our collaborators into our studies (e.g., see attached letters from Brown, Duckett and Ligrone).

Training. The GPPRCG has always placed a heavy emphasis on student involvement and training. All of our workshops have included graduate students who are active in the field. The present proposal will continue that tradition, but will expand training activities from workshops and symposia into the laboratory. Where possible, students will visit among the laboratories of one of the collaborators. Additional training activities will be facilitated by the workshops sponsored jointly with the RCNs. These include the general annual workshops as well as workshops focused on specific topics and on cross- training between disciplines. Much of this cross- training will be funded through related RCN projects ("Deep Gene" & "Deep Time"), which award summer lab internships for undergraduates and laboratory exchange experiences for graduate students. Teacher workshops through "Deep Gene" are designed to disseminate information on plant genomics and to assist teachers in developing the best practices to teach this information.

Increasing diversity. The proposed RCN will welcome participation by a diverse array of scientists and will encourage participation by underrepresented groups and those individuals in diverse types of institutions. The best way to increase the participation of under-represented groups in science is through public outreach and opportunities/information for students. The proposed K-12 teacher workshops, workshops at professional meetings, as well as learning modules on the web site, will effect knowledge transfer to younger students as well as undergraduate and graduate students. These activities will increase the visibility of exciting science to all potential future scientists, including those in under- represented groups. Notices of the web site and workshops will be sent to biology and science departments at colleges and universities across the country as well as to associations such as the National Association of Science Teachers and the National Biology Teachers Association. We will actively seek out minority-serving institutions, In each competition for student awards, a portion will be reserved for deserving women and ethnic minority students. We will also encourage the participation of individuals from primarily undergraduate institutions (PUIs) by earmarking some awards for these students and faculty.

Assessment of research coordination activities. At the conclusion of each workshop, symposium, meeting, or other group event, a questionnaire will be distributed to all participants to gauge their satisfaction with the operation and productivity of the session. The SC will consider the suggestions in the survey and make appropriate changes in the operation of future meetings. Our past experience with Deep Green strongly suggests that this will be a positive and productive experience for all participants.

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