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[A Phylogeny for Kingdom Fungi] [Proposal] [Correspondence] [Discussions] [Activities] [Participants]

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We welcome the participation of all systematists.  Please join us by sending in your name and address if you are interested in being a part of this project.
This material is based upon work supported by the National Science Foundation under Grant No. 0090301. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

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Table of Contents
PROJECT SUMMARY
PROJECT DESCRIPTION
 Previous results
 Introduction
      A Phylogeny for Fungi
      Phylogenetic status of Kingdom Fungi
 Goals
      Promote phylogenetics
      Create identification resources
      Make fungal phylogenetics more accessible
  Rationale
  Justification
RESEARCH COORDINATION ACTIVITIES
 Management plan
 Research coordination activities
 Increasing diversity
 Coordination between similar groups
 Information and material sharing
 Participants
BIBLIOGRAPHY
Budget
Summary Budget
BUDGET JUSTIFICATION
RESEARCH SUMMARIES OF PARTICIPANTS

A non-exclusive, gender (10 women of 31 participants) and age (27-80 years) diverse group of mycologists will form a research planning network for the execution of three goals: 1) promote fungal phylogenetics; 2) make available identification aids; and 3) provide a phylogeny and educational materials to mycologists and teachers. The participants will meet twice a year in each of the five years of funding to develop a set of exemplar taxa, choose morphological and molecular characters, discuss analysis methods appropriate to the characters, foster cooperation and collaboration for collection of large data sets, and coordinate educational initiatives. Most participants are currently or recently funded by NSF, and the participants bring exceptional expertise in fungal systematics, molecular biology, and data analysis to the project. We hope that new investigators, including post doctoral researchers, graduate students, and undergraduates will swell our ranks as they are brought into the group and included in its activities. Our goals are important for many fields: animal and plant pathology, food science, bioprospecting, environmental surveys of uncultivated fungi, evolutionary biology, and education. Rapid communication will be accomplished by electronic means and through public access of a web site. We will use self evaluation of the process in developing the phylogeny and related identification and educational materials. The phylogeny itself will be tested continually in the future as diverse exemplars of an estimated million new fungal taxa are discovered and included.

Fungal systematists will unite to face the problem of sheer fungal numbers and lack of even taxonomic coverage by forming a Research Coordination Network in Biological Sciences: A Phylogeny for Kingdom Fungi (Deep Hypha). Formation of the network forces us to face the gaps in our individual knowledge and to recognize that only by the development of large multigene data sets across diverse taxa can we produce a broad scale fungal phylogeny. The large number of species and relatively few scientists who study them (Table 1),will be transformed into a synergistic whole that will include exemplar taxa of many groups of fungi in a phylogenetic study based on multiple markers. Other evolutionary biologists have been attracted to fungi recently (e.g., fungus-growing ants and associated fungi; microsporidia); creation of Deep Hypha will be a focal point to attract other systematists who are needed in the phylogenetic effort.

Table 1. Numbers from Hawksworth et al (1995)1 are most likely gross underestimates. For example in his latest count, R.W. Lichtwardt used his intimate knowledge of Trichomycetes to count 55 genera and 226 species, and he is not finished counting yet (personal communication, 27 June 2000).

Phylogenetic status of Kingdom Fungi
Over the past ten to twenty years, researchers in fungal phylogenetics have made important advances in developing testable hypotheses on the evolution of fungi; the polyphyly of the organisms once considered to be "fungi" has been clearly and robustly demonstrated by recognition of several independent origins among the eukaryotes. A monophyletic Kingdom Fungi is well defined and supported (Barr 1992; Bruns et al 1992; Keeling et al 2000), and contemporary studies support the group as being most closely related to animals, possibly through a  choanoflagellate-like ancestor (fig 1) (Baldauf and Palmer 1993; Barr 1992; Ragan et al 1996; Wainright et al, 1993).

The "crown" fungi are supported as the most derived, higher monophyletic taxa within the Kingdom Fungi and may well correlate with the origin and diversification of land plants (Simon et al 1993, Taylor et al 1995).  The Ascomycota and Basidiomycota are the first and second largest phyla of the Kingdom Fungi, respectively, and together comprise over 95% of all known fungi (Table 1, see Hawksworth et al 1995).  Higher-level relationships within both the Ascomycota and Basidiomycota are tenuous. The Ascomycota generally is recognized to include the classes Euascomycetes (mostly filamentous, sporocarp-producing and mitosporic or conidial forms), Saccharomycetes (the true yeasts), and Archiascomycetes (a paraphyletic assemblage of basal taxa) (Nishida and Sugiyama 1994, Taylor et al 1994). The Basidiomycota generally is recognized to include the classes Urediniomycetes (the rusts and relatives), Ustilagniomycetes (the smuts) and Hymenomycetes (mushrooms and relatives) (Swann and Taylor, 1993; Wells 1994). The relationships of the classes within both the Ascomycota and Basidiomycota are controversial as are ordinal relationships within each of them (Berbee 1996; McLaughlin et al 1995; Spatafora 1995; Swann and Taylor 1993).

To date, the lion's share of phylogenetic studies has been performed on nucleotide data determined from the nuclear rDNA. While the utilization of SSU rDNA in fungal systematics proved to be a watershed event for mycologists, allowing us to answer many long-standing questions in fungal systematics, the continued use of single gene phylogenies has its obvious limitations. It is time that as a group, fungal systematists routinely perform multi-gene phylogenetic studies and do so in a coordinated manner in order to address questions that bridge individual research programs.

A robust phylogeney will allow us to clarify important questions about fungal evolution:

* Origin of the Fungi.  .  Is a choanoflagellate ancestor for fungi well supported? Where is the origin of DAP lysine biosynthesis in the fungal ancestry? Can character evolution (flagella, hyphae, etc.) be traced? Can we infer the general morphology of "first fungus"?

*Early diverging events within the Kingdom Fungi.   Limited molecular data do not support the monophyly of either the chytrids or the zygomyctes, suggesting multiple losses of the flagellum. In addition the association of many zygomycete groups with arthropods suggests the possibility of multiple origins of a terrestrial fungus. We should be able to address the paraphyly of the Chytridiomycota/Zygomycota clades, the origin of nonplant associated terrestrial fungi (i.e., multiple orgins of terrestrial fungi), character evolution (loss of flagella, modes of sexual reproduction, etc.), and realignment of major taxa of early diverging fungi.

*Phylogenetics of the "crown" fungi (crown fungi = Glomales, Basidiomycota and Ascomycota).  These taxa represent the terminal clade within the Kingdom Fungi and their origin appears to be correlated with the origin and diversification of land plants.  However, the relationship of the Glomales with the ascomycete/basidiomycete clade is tenuous and additional plant-associated zygomycetes have not been sampled.  Furthermore, the early divergences within the filamentous ascomycota (Euascomycetes) and macrosporocarp-producing basidiomycota (Hymenomycetes) are poorly understood. Could symbioses between green algae and fungi have evolved prior to the evolution of land plants and their mycorrhizal symbioses? What is the origin of dikaryotic fungi? When do we find the first organized sporocarps and plectenchyma (fungal tissue)?

2) Create identification resources for new fungi, including those that are difficult or impossible to cultivate. At a minimum, the Deep Hypha web site will provide an alignment of exemplar taxa ready for the inclusion of unknowns. The familial, generic, and subgeneric (e.g., species complex) identities of many fungi are unknown. Furthermore, many fungi are collected in a state in which identification is difficult (e.g., environmental samples, mycorrhizal root tips).  Molecular based identification has proven to be a powerful tool for mycorrhizae (Bruns et al, 1998), and the expanded use of this approach to other ecological groups of fungi will be of great benefit.  Also, a set of DNAs of exemplar taxa for distribution will be maintained at a central site, such as the Fungal Genetics Stock Center. Systematists could use the set of fungi for identifications, but also for development of new DNA regions. This goal is important to users in many fields: animal and plant pathology, food science, bioprospecting, environmental surveys of uncultivated fungi.

3) Make fungal phylogenetics more accessible to other biologists in the hopes of attracting them to study fungi and inducing them to include more about fungi in their teaching. Fungi are central organisms to life of earth, yet there are too few research programs on fungal biology and too little fungal biology included in general biology and evolutionary biology courses.  For example, a tree with an approximate geologic time scale would be valuable because time is a common currency of phylogeneticists working in different kingdoms and would provide a strong comparative foundation. Web-based materials will be developed to help accomplish this goal, and one meeting will emphasize web materials (see below, Information and Material Sharing).

Deep Hypha will need to address the following points in pursuing the goals: 1) If only 80,000 of an estimated 1.5 million fungi are known, we must discover missing diversity at higher taxonomic levels. Recently discovered taxa represent new family or order level diversity (Malloch and Blackwell 1989; Winka and Eriksson 2000). Deep Hypha will encourage global collecting in order to discover new lineages. Increasingly, fungal discovery and the development of molecular databases are becoming related processes with the realization that familiar taxa represent newly discovered diversity (Kohlmeyer et al 2000; Nishida and Sugiyama 1994; Redecker et al 2000). 2) The SSU rDNA gene database will be supplemented by other genes. Candidate genes will be developed early in the research planning. Some already have been tested by mycologists for limited sets of taxa, and these should be extended to additional taxa (Baldauf 1999; Kretzer and Bruns 1999; Liu and Hall 1999; Paquin et al 1997; Radford 1993). 3) Investigating methods of phylogenetic analysis suited to our data will recover the best trees. Mycologists often have been on the forefront of phylogenetic theory, and this project will improve communication of new methods of analysis among mycologists (Hibbett personal communication; Moncalvo et al 2000; Tehler et al. 2000). 4) Funding attempts will be strengthened by formation of Deep Hypha; members will encourage others in proposal writing, especially students who will write doctoral dissertation improvement proposals. 

Since the advent of PCR capabilities, mycologists have been able to study almost any fungi --those that cannot be grown in culture, those that are minute-- and the limiting factors usually have been discovery and acquisition of fungi, species level identifications, and dependence upon a single gene for which a relatively large database had been accumulated since before the time of PCR. Previous bottlenecks in production of sequences have been all but overcome by high throughput machines. The mycologists that have formed Deep Hypha recognize that the current phylogenetic picture of fungi overemphasizes the taxa that it depicts, and the greatest fungal diversity has yet to be included (fig 1, see also Table 1).

Because of the necessarily large number of Deep Hypha participants, extra effort is needed to attend to some details; two areas have been defined for which CoPIs will have key responsibilities. As fungal herbarium director at Oregon State University, Joseph W. Spatafora has a secure server, support services, and the experience needed to maintain the web site to be used for communication among the group members and to provide access to other interested biologists. He will have the primary responsibility for keeping the site functioning. Spatafora’s work in fungal systematics includes phylogenetic studies of clavicipitaceous ascomycetes and hypogeous basidiomycetes.  John W. Taylor, the second CoPI, is an organizing member of FungalWeb <http://webhotel.novo.dk/fungalweb/mainframe.asp> (see coordination plan, below); his duty will be to act as liaison between Deep Hypha and FungalWeb. Taylor is active in general and medical mycology, and he has established many of the basic techniques applied to fungal molecular systematics. In addition to his work in systematics he applies the new molecular tools to population genetics and studies of genetic recombination.

The PI and two CoPIs will act as steering committee members for Deep Hypha; two additional members will be elected by the core members present at the first meeting. The steering committee will hold discussions with network members if they are needed and can act as or appoint ad hoc committees, such as travel award committees; however, we plan to consult often with members and do not anticipate controversy. Funds are budgeted for two meetings per year for core group members. Postdoctoral associates and graduate students of core members will be included in at least one meeting per year, and funds are budgeted for this purpose (see Budget and Budget Justification). The two meetings for each of the five years will be thematic (Table 2), but the topics can be replaced at any time for one that the group feels is more timely. Invited speakers may be included for special expertise. In addition to thematic content each meeting will have adequate time devoted to the process of planning for the phylogeny. A highlight of each meeting will be the poster presentations of recent research results by members. It will be possible to provide demonstrations on the fungi organisms themselves. Meeting locations listed are tentative and may be changed if costs can be lowered appreciably or for some other reason.

Baton Rouge     Winter 2001 Getting started: selection of exemplar taxa, target molecules, and coordination
*establishing evaluation criteria
*defining target taxa
* defining hypotheses to test
* deciding on character sets
* make list of tools available for different taxa
* planning on development of tools for key under-studied taxa
* deciding on methods for generating data and analysis methods

The development of plans to produce a broad-scale phylogeny based on multiple markers can be evaluated routinely in discussions by the participants about the process and by providing questionnaires that can be filled out anonymously. Our aim is to form a nonexclusive communicative group to accomplish our goal, and open discussions of the process are required. Eventually, the process and its anticipated outcome, the phylogeny, will be evaluated every time we add a new taxon to the tree.

Increasing Diversity
The participants themselves are a diverse group of fungal taxonomists and systematists.  About one third of the group members are women; age diversity is exceptional, ranging from 27-80 years; members are employed by private and public research universities, governmental agencies, and three are retired from research universities. The diverse group is committed to maintaining and increasing diversity in their discipline as documented in the descriptions of their ongoing research programs (see below, Supplemental Materials).

About half of the students (graduate and undergraduates) and postdoctoral associates of the core participants are women, and minority students are present in some laboratories, although in lower numbers. However, all participants welcome minority students and work toward the goal of increasing their numbers. Several examples include Petersen and Hughes at the University of Tennessee; they have trained African American and Hispanic undergraduates who are continuing in graduate programs; a Hispanic student currently is working on a PhD with them. Hughes has made a special effort at outreach by participating in several minority-based summer programs providing research experiences for minority teachers and students. Blackwell has worked through the advisors in the College of Basic Sciences and minority programs available at LSU to find qualified minority undergraduate students for year-around research opportunities in her lab but has been more successful in attracting minority students by seeking out their friends already doing research in the department. She also recently has approached the dean and is working for a new position in her department for a minority faculty member; a hiring of a single minority faculty member in the LSU chemistry department is credited with attracting more than twenty minority students to the physical chemistry group in less than five years. Others make similar efforts and are committed to these additional efforts to attract graduate students from underrepresented groups. The participants will continue to be active in the area of recruitment of underrepresented groups: seminars will be given at institutions with large underrepresented student populations; Deep Hypha will be publicized in historically black colleges and universities through personal contacts; participation in special minority research and tutoring programs in most of the participant  institutions, will be a priority.

The core members have been good at outreach to developing countries, many of which have large minority populations. These projects have been pursued on an ad hoc basis such as the workshop planned and executed by a number of NSF-funded researchers in conjunction with the Latin American Mycological Congress held in Caracas in October 1999. Members of Deep Hypha also are members of the Mycological Society of America, and this society has had a long history of gifts of journals and development of international representation within the society. These activities will continue, and in addition mycologists in developing nations will have access to our web based materials or when required, hard copies will be made available. 

Recently, a nascent international effort to make fungal phylogenetics available on the Internet,
FungalWeb, was initiated by an international group of mycologists <http://webhotel.novo.dk/fungalweb/mainframe.asp>. FungalWeb will be a web site to provide recent and accurate fungal taxonomy to a wide range of users. The plans are admirably ambitious. A combination of phenotypic and genotypic data will be used to provide a classification for all fungi to genera that can be accessed through direct links from FungalWeb on the Novo Nordisk web site outside the corporate fire wall. The classification will cover all fungi to genus level, and include the listing of fungal genera with links to Entrez and many other databases. The site already is useful for searching a variety of databases. FungalWeb will be useful to Deep Hypha, and there will be ample opportunity to cooperate with the group. Three members of our network, including Taylor, are members of the FungalWeb group. As CoPI Taylor will have the specific duty of coordinating between Deep Hypha and FungalWeb; however, it should be noted that our goals are more tightly focused and somewhat different from theirs in that our emphasis is on gathering geneotypic data for analysis in order to construct a phylogeny of fungi. However, the goals are complementary and our data should be of interest to FungalWeb, and FungalWeb should be of interest to us as an eventual site to make our work available. We plan to cooperate fully through Taylor and the personal contacts many of us have with the European group.

Another resource that will be useful to our network is the on line materials on ascomycetes posted and updated regularly by the mycology group at Umeå, Sweden, <http://www.umu.se/myconet/Myconet.html>.  While not a network as such, the group, under the leadership of Ove Eriksson, provides a variety of taxonomic resources, including extensive bibliographical materials and comments of the nomenclatural status of taxa.

1) Identification materials will include a set of aligned exemplar DNAs, accessible on the Internet, that can be used for identification of unknown fungi. An early priority will be for exemplars at higher taxonomic level because some fungi cannot immediately be placed in an order, especially if it is DNA from an environmental sample or immature specimen. Eventually, the taxonomic scale can be decreased to include low level taxa in the databases. We also will discuss more elaborate plans to include tools for phylogenetic analysis available on the Internet to facilitate such identifications. A second product to share with a broad community will be cultures of exemplar taxa that can be made available, perhaps through the Fungal Genetics Stock Center. The exemplars would represent wide taxonomic diversity and could be used as a basic "diversity" set to develop DNA regions for characters.  In fact several candidate molecules have been mentioned above, such as the RPB2 region used in the studies of Liu and Hall.

2) Educational materials will include notes of discussions and presentations held at our meetings.  These will be faithfully recorded and placed on the web site in a timely way so that they can be available to other mycologists and systematists within days of presentation. We will develop phylogenetic trees that will be placed on the Deep Hypha site as well as other sites interested in fungal phylogeny (FungalWeb, Tree of life). A large tree providing a framework for all fungi and correlated with other organisms and geologic events will be produced as our major contribution to education. Web site materials including meeting presentations and minutes of discussions will be immediately available and advertised widely in newsletters and websites of societies such as the Mycological Society of America, American Society of Microbiologists, American Phytopathological Society, Botanical Society of America, and National Association of Biology Teachers. FungalWeb and Tree of Life are additional outlets for completed products.

Deep Hypha intends to foster communication and promote collaboration through early sharing of data and other materials among participants. Within the project, data and other intellectual properties will remain the property of the person or laboratory group that collected them. This stipulation has not inhibited free exchange among us in the past, and the mycologists joined in this proposal have often shared data before publication (fig 2).  Whenever we share, the unpublished data will remain confidential until the owner releases them. Authorship in cases of publication of shared data should be determined by the collaborators, preferably at the beginning of the collaboration. Usually, the originator of an intellectual concept would be the first author, but individuals must come to terms on their own. As a community we already submit sequences to GenBank for release before or soon after acceptance of manuscripts, and our alignments are available through TreeBASE <http://herbaria.harvard.edu/treebase/ >; cultures and specimens usually are accessible as well. Many of the journals in which we publish require that these materials be made available to subsequent workers.

A short biographical sketch of each participant is found in the supplemental materials section at the end of the proposal. Most members of Deep Hypha are acquainted with each other, and many have had close interactions in research and publication, workshop organization, professional organizations, and student- and postdoctoral-teacher associations (fig. 2). As a group we are committed to maintaining and increasing diversity in our discipline as documented in the descriptions of ongoing research. Our common interests will serve to make us a close knit group that will accomplish its goals.
 

Baldauf, S. L. 1999. A search for the origins of animals and fungi: Comparing and combining molecular data. American Natruralist 154: S178-S188, Suppl.

Baldouf, S. L., and J. D. Palmer. 1993. Animal and fungi are each other's closest relatives: Congruent evidence from multiple proteins. PNAS 90: 11558-11562.

Barr, D. J. S. 1992. Evolution and kingdoms of organisms from the perspective of a mycologists - Presidential address, San Antonio, Texas, Aug. 6, 1991. Mycologia 84: 1-11.

Berbee, M. L. 1996. Loculoascomycete origins and evolution of filamentous ascomycete morphology from 18S rRNA gene sequence data. Mol. Biol. Evol. 13: 462-470.

Berbee, M. L., and J. W. Taylor. 1993. Dating the evolutionary radiations of the true fungi.  Canad. J. Bot. 71: 1114-1127.

Bowman, B. H., T. J. White, and J. W. Taylor. 1996. Human pathogenic fungi and their close nonpathogenic relatives. Mol. Phylogen. Evol. 6: 89-96.

Bowman, B. H., J. W. Taylor, A. G. Brownlee, J. Lee, S.-D. Lu, and T. J. White. 1992. Molecular evolution of the fungi: relationship of the Basidiomycetes, Ascomycetes and Chytridiomycetes. Mol. Biol. Evol. 9: 285-296.

Bruns, T. D., R. Vilgalys, S. M. Barns, D. Gonzalez, D. S. Hibbett, D. J. Lane, L. Simon, S. Stickel, T. M. Szaro, W. G. Weisburg, and M. L. Sogin. 1992. Evolutionary relationships within the Fungi: analyses of nuclear small subunit rRNA sequences.  Mol. Phylogen. Evol. 1: 231-241.

Bruns, T.D., T.M. Szaro, M. Gardes, K.W. Cullings, J.J. Pan, D.L. Taylor, T.R. Horton, A. Kretzer, M. Garbelotto and Y. Li. 1998.  A sequence database for the identification of ectomycorrhizal Basidiomycetes by phylogenetic analysis.  Molecular Ecology 7: 257-272.

de Hoog, G. S. 1997. Significance of fungal evolution for the understanding of their pathogenicity, illustrated with agents of phaeohyphomycosis. Mycoses 40: 5-8, Suppl. 2

Hawksworth, D. L., P. M. Kirk, B. C. Sutton, and D. M. Pegler. 1995. Ainsworth & Bisby’s Dictionary of the fungi. 8th ed. CAB International. Egham, UK. 616 p.

Hibbett, D. S., and M. J. Donoghue. 1998. Integrating phylogenetic analysis and classification in fungi. Mycologia 90: 347-356.

James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. E. Longcore. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Canad. J. Bot. 78: 336-350.

Keeling, P. J., M. A. Luker, and J. D. Palmer. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17: 23-31.

Kohlmeyer, J., J. W. Spatafora, and B. Volkmann-Kohlmeyer. 2000. Lulworthiales, a new order of marine Ascomycota. Mycologia 92: 453-458.

Kretzer, A. M., and T. D. Bruns. 1999. Use of atp6 in fungal phylogenetics: An example from the Boletales. Mol. Phylogen. Evol. 13: 483-492.

Malloch, D., and M. Blackwell. 1990. Kathistes, a new genus of pleomorphic ascomycetes.  Canad. J. Bot. 68: 1712-1721.

McLaughlin, D. J., M. E. Berres, L. J. Szabo. 1995. Molecules and morphology in basidiomycete phylogeny Canad. J. Bot. 73: S684-S692.

Moncalvo, J. M., F. M. Lutzoni, S. A. Rehner, J. Johnson, and R. Vilgalys. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst. Biol. 49: 278-305.

Nagahama, T., H. Sato, M. Shimazu, and J. Sugiyama. 1995. Phylogenetic divergence of the entomophthoralean fungi: Evidence from nuclear 18S ribosomal RNA gene sequences. Mycologia 87: 203-209.

Nishida, H., and J. Sygiyama. 1994. Archiascomycetes: Detection of a major new lineage within the ascomycota. Mycoscience 35: 361-366.

O'Donnell, K., H. C. Kistler, B. K. Tacke, and H. H. Casper. 2000. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. PNAS [In press].

Paquin, B., M.-J. Laforest, L. Forget, I. Roewer, W. Zhang, J. Longcore, and B. F. Lang. 1997. The Fungal Mitochondrial Genome Project: evolution of fungal mitochondrial genomes and their gene expression. Curr. Genet. 31: 380-395.

Radford, A. 1993. A fungal phylogeny based upon orotidine 5’-monophosphate decarboxylase. J. Mol. Evol. 36: 389-395.

Ragan, M. A., C. L. Goggin, R. J. Cawthorn, L. Cerenius, A. V. C. Jamieson, S. M. Plourd, T. G. Rand, K. Soderhall, R. R. Gutell.1996 A novel clade of protistan parasites near the animal-fungal divergence PNAS 93: 11907-11912.

Redecker, D., J. B. Morton, and T. D. Bruns. 2000. Ancestral lineages of arbuscular mycorrhizal fungi (Glomales). Mol. Phylogen. Evol. 14: 276-284.

Simon, L., L. Bousquet, R. C. Levesque, and M. Lalonde. 1993. Origin and diversification of endomycorrhizal fungi and coincidence with vascular plants. Nature 363: 67-69.

Spatafora, J. W. 1995. Ascomal evolution among filamentous ascomycetes: evidence from molecular data. Canad. J. Bot. 73: S811-S815.

Swann, E. C., and J. W. Taylor. 1995. Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Canad. J. Bot. 73: S862-S868.
Taylor, J. W., B. Bowman, M. L. Berbee, and T. J. White. 1993. Fungal model organisms: phylogenetics of Saccharomyces, Aspergillus and Neurospora. System. Biol. 42: 440-457.

Taylor, J. W., E. C. Swann , and M. L. Berbee. 1994. Molecular evolution of ascomycete fungi: phylogeny and conflict. p. 201-212.  In: Ascomycete Systematics: Problems and Perspectives in the Nineties.  Ed., Hawksworth, D.L. Plenum Press, New York.

Taylor, T. N., W. Remy, H. Hass, and H. Herp. 1995. Fossil arbuscular mycorrhizae from the lower Devonian. Mycologia 87: 560-573.

Tehler, A., J. S. Farris, D. L. Lipscomb, and M. Källersjö. 2000. Phylogenetic analyses of the fungi based on large rDNA data sets. Mycologia 92: 459-474.

Wainwright, P. O., G. Hinkle, M. L. Sogin, and S. K. Stickel. 1993. Monophyletic origins of the Metazoa: An evolutionary link with the Fungi. Science 260: 340-342.

Wells, K. 1994. Jelly fungi, than and now! Mycologia 86: 18-48.

Winka, K., and O. E. Eriksson. 2000. Papulosa amerospora accommodated in a new family (Papulosaceae, Sordariomycetes, Ascomycota) inferred from morphological and molecular data. Mycoscience 41: 96-104.

Blackwell has had equal numbers of men and women graduate students; however, the overwhelming majority of undergraduate researchers have been women. Five women, one an African American, are scheduled to do research in the coming fall semester. The Deep Hypha collaboration is important to Blackwell’s work, and she will be aided by collaboration with others.  She and her associates will have access to discussions of new techniques, especially in the area of data analysis and choice of new characters. Her interest in placing the Laboulbeniales and several other arthropod-associated ascomycetes among their close relatives will be aided by the development of new databases, because SSU rDNA data have not provided all the answers.

Selected publications
* Suh, S.-O., and M. Blackwell. 1999. Molecular phylogeny of the cleistothecial fungi placed in Cephalothecaceae and Pseudeurotiaceae.  Mycologia 91: 836-848.
* Jones, K. G., P. F. Dowd, and M. Blackwell. 1999. Polyphyletic origins of yeast-like endocytobionts from anobiid and cerambycid beetles.  Mycol. Res. 103: 542-546.
* Suh, S.-O., J. W. Spatafora, G. R. S. Ochiel, H. C. Evans, and M. Blackwell. 1998. Molecular phylogenetic study of a termite pathogen Cordycepioideus bisporus. Mycologia 90: 61-617.
* Blackwell, M., and K. G. Jones. 1997. Taxonomic diversity and interactions of insect-associated ascomycetes.  Biodiversity and Conservation 6: 689-699.
* Alexopoulos, C. J., C. W. Mims, and M. Blackwell. 1996. Introductory Mycology.  John Wiley & Sons, New York. 868 p. (first US printing), 869p. (successive US printings).  Translations in Spanish, Portuguese, German, Chinese.

JOSEPH W. SPATAFORA <http://www.orst.edu/dept/botany/mycology/index.html>
Spatafora, Co-PI for the proposal, conducts research on several different groups of fungi including members of both the Ascomycota and Basidiomycota. His PhD and postdoc training is in systematics of the Ascomycota.  Since joining the faculty of Oregon State University in 1995, he has expanded his research to include systematics and population genetics the Basidiomycota
with an emphasis on hypogeous ectomycorrhizal fungi.  His current work within the Ascomycota includes systematics of Cordyceps and the Clavicipitaceae, phylogenetic origins of marine ascomycetes, evolution of lichenization among the Ascomycota, and early evolutionary divergences among the Euascomycetes.  His current work within the Basidiomycota includes systematics and population genetics of Rhizopogon and systematics of Gomphales-Phallales clade.

Spatafora has actively collaborated with numerous mycologists and the result has been rich research experiences that have led to the discovery of a new order (Lulworthiales), recognition of the close relationship between morphologically dissimilar
(Gomphales-Phallales) and ecologically disparate groups of fungi (Microascales-Halosphaeriales), and the evolution of nonsexual lichens. A long-standing interest of Spatafora is the evolution of host affiliation of the insect and fungal pathogens of the genus Cordyceps and related fungi of the Clavicipitaceae. Spatafora's research program is related to the proposed project at many levels and across many taxonomic groups.  His major scientific contributions will be in the systematics of the Ascomycota and Basidiomycota, and he will greatly benefit from continued and enhanced collaborations with a diverse group of mycologists.  He is also committed to the development of additional genetic loci for use in molecular systematics of fungi.  He is currently developing a beta-tubulin dataset for the Clavicipitaceae and is interested in pursuing single copy genes (e.g., B subunit of vacuolar ATPase) for use at higher taxonomic levels. The development of such markers are paramount to many of Spatafora's research interests because rDNA -- while informative -- like any single gene has limited explanatory power.  Finally, Spatafora has been proactive in integrating web-based technology in the classroom  (http://www.bcc.orst.edu/~spatafoj/bot461/) and will contribute to and benefit from the  development of educational tools from the proposed Research Coordination Network.  Spatafora's past and current lab group includes two postdocs (2 women) and six graduate students, four undergraduates, and two international researchers, with half of each group being women.

Selected publications
* Kohlmeyer, J., J. W. Spatafora, and B. Volkmann-Kohlmeyer.  2000. Lulworthiales, a new order of marine Ascomycota. Mycologia 92: 453-458.
* Platt, J. L., and J. W. Spatafora. 2000. Evolutionary relationships of nonsexual lichenized fungi; molecular phylogenetic hypotheses for the genera Siphula and Thamnolia from SSU and LSU rDNA analyses. Mycologia 92: 475-487.
* Spatafora, J. W., B. Volkmann-Kohlmeyer,  and J. Kohlmeyer. 1998. Independent  terrestrial origins of the Halosphaeriales (marine Ascomycota).  Amer. J. Bot. 85: 1569-1580.
* Suh, S.-O., J. W. Spatafora, G. R. S. Ochiel, H. C. Evans, and M. Blackwell. 1998. Molecular phylogenetic study of a termite pathogen, Cordycepioideus bisporus.  Mycologia 90:  611-617.
* Spatafora, J. W. 1995. Ascomal evolution among filamentous ascomycetes: evidence from molecular data. Canad. J. Bot. 73: S811-S815.

JOHN W. TAYLOR < http://mollie.berkeley.edu/~taylor/index.html>
Taylor, a co-PI on this proposal, is an internationally known mycologist who has pioneered the use of molecular techniques in fungal systematics and population biology. The list of personnel and visitors to his laboratory provides a measure of Taylor's wide-ranging influence on modern mycology.  Taylor uses phylogenetic and population genetics methods to compare genetic variation and identify species and populations of fungi and to determine how they reproduce in nature. His studies have shown that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. The studies of Taylor and his colleagues also show that, although approximately one fifth of described fungi have been thought to be asexual and clonal, many of the pathogens appear to be undergoing recombination, depending upon factors relating to biology and distribution in space and time. One model fungus is the pathogen Coccidioides immitis, causative agent of coccidioidomycosis or Valley Fever, which was first isolated from the environment in 1932. It has been isolated on numerous occasions since then, but usually from clinical hosts. The morphology of C. immitis is indistinct from related species, thus, its identification hinges upon its ability to infect and produce spherules in a susceptible animal. Taylor and his associates now can isolate the fungus from soil samples without the use of a host. They identify the fungus in soil samples by using C. immitis specific primers based on the ITS sequence of ribosomal DNA.

Taylor is interested in the phylogenetic relationships of the Meliolaceae, an ascomycete group that had been of uncertain phylogenetic placement, but hypothesized some previous workers to be related to the powdery mildews. Cladisitc analysis shows that the two groups are not closely related and that the Meliolaceae is a group of unitunicate pyrenomycetes. The phylogenetic position of Meliolina is however, among the bitunicate ascomycetes. Other phylogenetic work in his lab includes studies of Penicillium, especially of terverticillate taxa; clades of Penicillium species sharing environmental characteristics are being identified, e.g., species growing on protein and lipid rich substrates, species prevalent in dry habitats, and those prevalent on carbohydrate rich substrates.

Taylor continues to have large numbers of successful students, postdoctoral researchers, and visitors in his laboratory all the time. He has been extremely collegial and has allowed many biologists from all over the world to be trained in his laboratory.  About half of the students and postdoctoral associates in Taylor’s lab are women, and he recently has trained two minority PhDs, an hispanic American and an African American. He has already collaborated with a number of core participants on this proposal, and this proposal will continue the tradition. He is committed to the planning and completion of phylogeny and to coordinating the effort with the other members of the FungalWeb project.

Selected publications
* Fisher, M. C., G. L. Koenig, T. J. White, and J. W. Taylor. 2000. Pathogenic clones versus environmentally driven population increase: analysis of an epidemic of the human fungal pathogen Coccidioides immitis. J. Clin. Microbiol. 38: 807-813.
* Saenz, G. S., and J. W. Taylor. 1999. Phylogenetic relationships of Meliola and Meliolina inferred from nuclear small subunit rRNA sequences. Mycol. Res. 103: 1049-1056.
* Greene, D. R., G. L. Koenig, and J. W. Taylor. 1999. Soil isolation and molecular identification of Coccidioides immitis. Abstracts of the General Meeting of the American Society for Microbiology 99: 494.
* Herr, R. A., A. Libero, J. W. Taylor, S. N. Arseculeratne, and L. Mendoza. 1999. Phylogenetic Analysis of Rhinosporidium seeberi's 18S Small-Subunit Ribosomal DNA groups this pathogen among members of the protoctistan Mesomycetozoa clade. J. Clin. Microbiol. 37: 2750-2754.
* Taylor, J. W., D. J. Jacobson, and M. Fisher. 1999. The evolution of asexual fungi: reproduction, speciation and classification. Ann. Rev. Phytopathol. 37:197-246.

MARGARET E. BARR
Barr probably works daily with far greater ascomycete diversity than many mycologists meet in a lifetime.  Using morphological characters derived from light microscopy, she provides broad scale coverage of pyrenomycetes and loculoascomycetes. She has been active in collaborations with other mycologists and on her own in describing not only many new species, but also higher taxa. However, it is her long works in which she provides diagrams and descriptions of thousands of forgotten fungi belonging to groups that few people know.  The two large works, one of loculoascomycetes and the other of pyrenomycetes, are the most detailed recent references we have available for these speciose groups of ascomycetes. After her retirement from the University of Massachusetts, she returned to her native British Columbia where she works regular hours daily on monographic studies of ascomycetes. She collaborates with a number of young mycologists, and especially offers her insights on taxon sampling for molecular studies; collectors from around the world send her specimens for identifications.

As an example of her work, during the last few years she has been interested in Loculoascomycetes that develop in plants of the Great Basin region of western USA, including three new species and the transferring of other species. She also collaborated in a study of forty-seven taxa of pyrenomycetes from southern Spain, providing new records from Spain and two new species. Her experience puts Barr in a unique position to make transfers and to describe new species. Barr trained several women PhDs at Massachusetts. She continues to collaborate with a number of other core participants on this proposal.

Selected publications
* Barr, M. E., and S. M. Huhndorf. 2000. Loculoascomycetes, pp. 283-305. Ch. 13 In: The Mycota, Vol. VII . Eds., D. J. McLaughlin and E. McLaughlin. Springer-Verlag.
* Réblová, M., M. E. Barr, and G. J. Samuels. 1999. Chaetophaeriaceae, a new family for Chaetophaeria and its relatives. Sydowia 51: 49-70.
* Barr, M. E. 1990. Melanommatales (Loculoascomycetes). N. Amer. Fl. Ser. II, 13: 1-129.
* Barr, M. E. 1990. Prodromus to nonlichenized, pyrenomycetous members of class Hymenoascomycetes. Mycotaxon  39:43-184.
* Barr, M. E. 1987. Prodromus to Class Loculoascomycetes. Publ. by the author, Amherst, MA 168 p.

MARY L. BERBEE  <http://www.botany.ubc.ca/maryb.html>
Berbee is investigating phylogeny and character evolution among loculoascomycetes.  Loculoascomycetes include fungi with diverse life strategies, varying from virulent plant pathogens to saprophytes, and from seemingly obligately asexual fungi to obligately sexual outcrossers. Phylogenetic research on loculoascomycetous fungi has practical applications; contributing, for example, to the detection of genes conditioning plant and animal pathogenicity.  It also is leading to increasingly comprehensive explanations for the origin of fungal life histories. Continuing projects in Berbee’s lab include phylogenetic analysis of two protein-coding genes, beta-tubulin and RPB2 (coding for the second largest subunit of DNA-dependent RNA polymerase II). Through collaboration with M. Barr, Berbee is progressing towards a comprehensive phylogenetic sampling of loculoascomycete lineages. This phylogenetic analysis is leading to the definition of monophyletic orders within the loculoascomycetes.

 About half the species of loculoascomycetes lack  known sexual states, and until recently, these 'asexual' fungi could not be linked with confidence to their closest sexual relatives. At the phylogenetic scale of genera and species, Berbee and her colleagues are integrating formerly unclassifiable asexual fungi with their closest sexual relatives. In collaboration with Turgeon (Cornell University),  Berbee is using funding from NSF to compare the evolution of mating type genes with the evolution of genes responsible for routine cellular housekeeping in sexual and asexual fungi.  With Berbee, Turgeon has discovered both phylogenetic and molecular genetic evidence for the multiple, independent origin of selfing species of the loculoascomycete genus Cochliobolus.  Using mating type gene distribution in natural populations, Berbee and Turgeon are distinguishing cryptic sex in species previously believed to be asexual from potentially truly clonal lineages.

Berbee's five former or continuing graduate students and three former postdocs represent seven countries and four continents.  A former woman Ph.D. student is of hispanic (Chilean) origin; she has a continuing position at Agri-food Canada.  Roughly equal numbers of young men and women undergraduates have worked in Berbee's laboratory.

Selected publications
* Landvik, S., O. E. Eriksson, and M. L. Berbee. 2000. Neolecta -- a fungal dinosaur? Evidence from beta-tubulin amino acid sequences. Submitted  to Mycologia.
* Inderbitzin, P., S. Landvik, M. Abdel-Wahab,  and M. Berbee. 2000. Aliquandostipitaceae, a new family for two new tropical pyrenomycetes (Ascomycota) with unusually wide hyphae. Am. J. Bot., in press.
* Yun, S.-H., M. L. Berbee, O. C. Yoder, and B. G. Turgeon. 1999. Evolution of fungal reproductive life style; self-fertility is derived from self-sterile ancestors. PNAS 96: 5592-5597.
* Berbee, M. L., M. Pirseyedi, and S. Hubbard. 1999. Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences. Mycologia  91: 964-977.
* Berbee, M. L. 1996. Loculoascomycete origins and evolution of filamentous ascomycete morphology from 18S rRNA gene sequence data. Mol. Biol. Evol. 13: 462-470.

THOMAS D. BRUNS < http://plantbio.berkeley.edu/~bruns/ >
Tom Bruns has made several major contributions to fungal systematics and ecology.  His early work with White, Taylor, and Lee on the development of primer sets for nuclear and mitochondrial rRNA genes and spacers made a lasting impact on the field of systematics, and the later fungal specific and basidiomycete specific ITS primers that he developed with Gardes have had a similar impact on the field of fungal ecology.  Understanding rates and modes of molecular evolution and incorporating this knowledge into the phylogenetic analysis has been one of his continuing concerns, and this was part of the first collaborative big-picture analyses of the fungal 18S data. Much of his systematic work has been focused at lower levels in the rust fungi, the suilloid fungi,  and the Glomales, or in using phylogenetic data for direct fungal identification from environmental samples.

Most of the current work in his lab is focused on the evolution and ecology of  mycorrhizal fungi.  This is work is based in part on applying the techniques of molecular systematics to dissect the composition of complex communities.  Some of the major findings have included:  1) there is a poor correspondence between above ground fruiting and below ground root colonization;  2) non-photosynthetic epiparasitic plants have unexpectedly specific fungal associations;  3) generalist fungi are numerically dominant in ectomycorrhizal systems and commonly connect dissimilar hosts; 4) a subset of ectomycorrhizal species dominate the sporebank and these are the main colonist of seedlings after severe fire.

In addition to a number of women PhD students and postdoctoral researchers, Bruns has trained a female Philippine student (MS) who is now a secondary school teacher. Bruns has trained many international workers, both students and visitors, who flock to his laboratory. Eleven undergraduates have done research in his lab in the last five years. The long-term goals of Bruns’ work are both compatible and complementary to those of the current proposal, and he thinks it would be a very synergistic interaction for all concerned. He is strongly committed to the current proposal. He already has collaborated with Taylor, Hibbett, Morton, Vilgalys, and O'Donnell.

Selected publications
* Redecker, D., J. B. Morton, and T. D. Bruns. 2000. Ancestral lineages of arbuscular mycorrhizal fungi (Glomales). Mol. Phylogen. Evol. 14: 276-284.
* Kretzer, A., and T. D. Bruns. 1999. Use of atp6 in fungal phylogenetics: an example from the Boletales. Mol. Phylogen. Evol. 13: 483-492.
* Bonello, P., T. D. Bruns, and M. Gardes. 1998. Genetic structure of a natural population of the ectomycorrhizal fungus Suillus pungens. New Phytol. 138: 533-542.
* Vogler, D. R. and T. D. Bruns. 1998.  Phylogenetic relationships among North American pine stem rusts (Cronartium and Peridermium spp.) Mycologia 90: 244-257.
* Roy, B. A., D. R. Vogler, T. D. Bruns, and T. M. Szaro. 1998 Cryptic species in the Puccinia monoica complex. Mycologia 90: 846-853.

PAULA T. DEPRIEST <http://www.mnh.si.edu/botany/projects/lichens/>
DePriest’s systematics research focuses on lichen-forming fungi and their fungal parasites. Presently she and her colleagues are examining phylogenetic relationships within the family Cladoniaceae (Cladonia, Cladina, etc.) of the Lecanoromycetes (the Lecanorales and related lichen-forming 'discomycetes'). Although the diverse and highly conspicuous reindeer lichens are ecologically and economically important, the generic status of some segregates is still contested. Through the use of rigorous phylogenetic analyses of nucleotide sequences from multiple genes to resolve the generic status of different genera, her research group is addressing the question. A data set of complete nucleotide sequences of the nuclear small subunit ribosomal DNA (SSU rDNA) from 45 species is being collected. Additionally, sequences from more variable genes may be needed to examine the relationships among lower taxa within Cladonia that have been linked to Cladina.

She and her colleagues continue to conduct phylogenetic research on many of the major groups of lichen-forming fungi in addition to the Lecanoromycetes, such as the Umbilicariaceae and Verricariales of the Eurotiomycetes/ Chaetothyriomycetes lineage, and she will contribute data on these and other appropriate groups of fungi as part of this network effort. DePriest also is studying the biological diversity of the Guyanas, a field-oriented program of the Department of Botany, National Museum of Natural History.

DePriest works with several Finnish associates on lichen projects including the phylogenetic studies of raindeer mosses, and in addition through the PEET program she is involved with Sam Hammer of Boston University in the training of undergraduates.

DePriest is enthusiastic about the coordinated plan to work toward a phylogeny of all fungi including lichens, and she looks forward to working with the other network members who will have the complete cooperation of herself and other members of her research group.

Selected publications
* Beard, K. H., and P. T. DePriest. 1996. Genetic variation within and among mats of the reindeer lichen, Cladina subtenuis (des Abb.) Hale and W. Culb. Lichenologist 28: 171-182.
* Gargas, A., P. T. DePriest, M. Grube, and A. Tehler. 1995. Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogenies. Science 268: 1492-1495.
* DePriest, P. T. 1993. Variation in the Cladonia chlorophaea complex I: Morphological and chemical variation in Southern Appalachian populations. Bryologist  96: 555-563.
* DePriest, P. T. 1994. Variation of the Cladonia chlorophaea complex II: Ribosomal DNA variation in a Southern Appalachian population. Bryologist  97: 117-126.
* DePriest, P. T. 1993. Small subunit rDNA variation in a population of lichen fungi due to optional group I introns. Gene 134: 67-74.

ANDREA GARGAS < http://www.wisc.edu/botany/gargas.html>
Gargas' work focuses on the evolution and molecular systematics of fungi in symbiotic relationships (lichens, mycorrhizae, and plant  pathogens). Previously, Gargas developed fungal-specific PCR primers and protocols for working with SSU rDNA from symbionts of lichen relationships and adapted these for sequencing other fungal DNAs, including rDNAs with insertions and Group I introns. Lichen associations arose several times within the fungi, yet until recently the closest relatives of lichen-forming fungi were not clear. With the inclusion of SSU rDNA sequences from additional lichen-forming fungi and from a diversity of fungal orders, she and her colleagues refined the resolution of hypotheses of relationships of lichen-forming fungi, and derived a comprehensive phylogeny for these fungi. DNA analyses showed at least three lichen origins within the basidiomycetes and at least two lichen origins within the ascomycetes, one within the apothecial ascomycetes (Lecanorales) and one within the perithecial ascomycetes (Arthoniales). Until now, the phylogenetic analyses have been limited to information from one or a few gene sequences, and this is expected to be expanded.

Lichen biogeography and fungal/algal coevolution also are being studied by applying molecular methods to the parmelioid lichens of the tropical genera Everniastrum, Cetrariastrum, and Concamerella. Inter-continental studies of lichen genetic diversity began in Costa Rica this summer with field collections. The research will test standard concepts of lichen biogeography and speciation, and will add information from the lichen photobionts to test for coevolution between the symbionts.

Gargas and her lab group are ready to participate and will benefit from the mycological knowledge of the group, especially from the diverse taxon sampling. She will join several other lichen and ascomycete systematists in the network. She has trained graduate students at the University of Copenhagen and currently has two students, one a woman, in her laboratory now.

Selected publications
* Jensen, A. B., A. Gargas, J. Eilenberg, S. Rosendahl. 1998. Relationships of the insect-pathogenic order entomophthorales (Zygomycota, Fungi) based on phylogenetic analyses of nuclear small subunit ribosomal DNA sequences (SSU rDNA). Fungal Genet. Biol. 24: 325-334
* Gargas, A., and P. T. DePriest. 1996. A nomenclature for fungal PCR primers with examples from intron-containing SSU rDNA. Mycologia 88: (5) 745-748
* Grube, M., A. Gargas, P. T. DePriest. 1996. A small insertion in the SSU rDNA of the lichen fungus Arthonia lapidicola is a degenerate group-I intron. Curr. Genet. 29: 582-586
* Gargas A, P. T. DePriest, M. Grube, and A. Tehler. 1995. Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268: 1492-1495
* Gargas, A., and J. W. Taylor. 1995. Phylogeny of discomycetes and early radiation of the apothecial ascomycetes inferred from SSU rDNA sequence data. Experimental Mycology 19: 7-15.

DAVID M. GEISER  <http://www.cas.psu.edu/docs/CASDEPT/PLANT/FACULTY/GEISER.html>
The research in Geiser’s laboratory focuses on the molecular population genetics and systematics of fungi, particularly cosmopolitan ascomycetes that exist both as pathogens and saprobes. In the past, his research centered on the genus Aspergillus. As Director of the Fusarium Research Center, he is now turning to the genus Fusarium as a focus of study. The Fusarium Research Center houses a culture collection with over 16,000 accessions, and serves the international research community by providing cultures and taxonomic expertise. Members of this genus present a wide variety of problems in agriculture and human health as plant pathogens, toxic food contaminants, and pathogens of mammals. His group is working to help combat the problems by figuring out basic aspects of Fusarium natural population biology. Specifically, they are 1) determining how species and populations are defined; 2) determining how important aspects such as mycotoxin production and pathogenicity are distributed among species and among populations within species; 3) inferring how toxin and pathogenicity traits evolve; and 4) producing a comprehensive database of molecular, morphological, toxicological, and pathogenicity data that
will be available to the Fusarium research community.

Analyzing the fungal genome provides a powerful means for making inferences about population biology and systematics. In fact, because of their small sizes and generally haploid nature, fungal genomes are particularly tractable. Geiser and his associates are employing both nucleic acid sequencing and robust genotyping methods such as amplification fragment length polymorphism analysis (AFLPs) to address basic issues, including whether or not they are sexual and how species are delimited, answers that are taken for granted in plants and animals.

Geiser is a new faculty member at Pennsylvania State University; he already is involved with students through the PEET project for which one of his departmental colleagues is PI.

This proposal is important for the work Geiser and his colleagues are doing, especially because the asexual ascomycetes they study need to be placed among their sexual relatives being studied by other members of Deep Hypha.  As a young mycologist in the first years of his career, he will benefit from the new contacts he will make within the group.

Selected publications
* Geiser, D. M., and K. F. LoBuglio. 1999. The monophyletic Plectomycetes: Ascosphaerales, Onygenales and Eurotiales. In: The Mycota, vol. VII, Eds., Lemke, P., D. J. McLaughlin, and E. McLaughlin. in press.
* Geiser, D. M., F. H. Harbinski, and J. W. Taylor. 1999. Molecular and analytical tools for characterizing Aspergillus and Penicillium species at the intra- and interspecific levels. In: Proceedings of the Third Aspergillus and Penicillium Workshop. Eds., Samson, R. A. and J. I. Pitt.
* Taylor, J. W., D. M. Geiser, V. Koufopanou, and A. Burt. 1999. The evolutionary biology and population genetics behind fungal strain typing. Clin. Microbiol. Rev. 12: 126-146.
* Geiser, D. M., J. C. Frisvad, and J. W. Taylor. 1998. Phylogenetic relationships in Aspergillus section Fumigati inferred from partial beta-tubulin and hydrophobin sequences. Mycologia 90: 831-845.
* Geiser, D. M., J. W. Taylor, K. B. Ritchie, and G. W. Smith. 1998. Cause of sea fan mortality in the West Indies. Nature 394: 137-138.

BENJAMIN D. HALL and YAJUAN LIU <http://depts.washington.edu/genetics/faculty/faculty.html>
Ben Hall has carried out research in the field of gene transcription since his days of graduate study. His experiments provided direct evidence for the complementary sequence relationship between messenger RNA and the genetic template. Coincident with a shift in his interests from macromolecular chemistry to the transfer of genetic information, Hall's group began work on the yeast Saccharomyces cerevisiae. They found three RNA polymerases in yeast with properties closely paralleling those of the RNA polymerases of mammalian cell nuclei. Subsequent research has made this yeast the system of choice for genetic exploration of eukaryotic RNA polymerase function. To facilitate molecular genetic studies in yeast, Hall's work first concentrated on developing methods to clone and characterize yeast genes of interest for the study of transcription. Those isolated include the CYC1 and mating-type loci, as well as several yeast suppresser tRNA genes. The initial work on these genes focused upon the promoter and terminator elements required for transcription by yeast RNA polymerases II and III. More recent research combines directed mutagenesis and in vivo screening for altered transcription with subsequent biochemical study of mutant polymerases to identify the location of specific functions within the yeast RNA polymerase III molecule. To a remarkable degree, the detailed positions of various catalytic motifs in this eukaryotic RNA polymerase mirror those recently determined for the E. coli enzyme.

Since 1994, Yajuan Liu and Hall, her PhD advisor, have collaborated on the use of RNA polymerase II to track the evolutionary history of the nuclear genome. Their studies suggest that analysis of sequences of a subunit of RNA polymerase II (RPB2) gives trees congruent with those of rDNA, but with somewhat better resolution for deeper branches. Major signatures in RPB2 that distinguish fungi from animals and plants and distinguish loculoascomycetes from other ascomycetes are currently under study by Liu to see what their relation is to the function of RNA Polymerase II.  She is doing this by making mutations in these signature regions and reintroducing them into S. cerevisiae in place of the wild type RPB2.  The question asked is then, what effect to the amino alterations have upon functions of the enzyme such as RNA chain elongation and transcription termination.

A graduate student in the Department of Botany is working out the intraspecies relationships in the Genus Inocybe and relationships to closely related genera.  For this, he is using sequences within RPB2, RPB1, and 28S rRNA.  The molecular work is being done in the Hall lab, in close cooperation with Liu. Another collaborative effort with Logsdon,  Doolittle and others, is using RPB2 to locate more precisely where microsporidians attach to the fungal clade.

Liu and Hall have shared sequences with about ten mycologists for the degenerate primers they developed for amplification and sequencing of the RPB2 gene long before publication of their work. More recently Liu and a Blackwell student have collaborated to design more effective primers, the sequences of which already have been distributed to several researchers. Several of the core members of the group have shared extracted DNA with Liu and Hall. These exchanges should continue and remain valuable in both directions, more so because Liu and Hall come to fungal phylogeny from the molecular biology side.

Selected publications
* Liu, Y. .J., S. Whelen, and B. D. Hall. 1999. Phylogenetic Relationships Among Ascomycetes: Evidence from an RNA Polymerse II Subunit. Mol. Biol. Evol. 16: 1799-1808.
* Stiller, J. W., and B. D. Hall. 1999. Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol. 16: 1270-1279.
* Denton, A. L., B. L. McConaughy, and B. D. Hall. 1998. Usefulness of RNA polymerase II coding sequences for estimation of green plant phylogeny. Mol. Biol. Evol. 15: 1082-1085.
* Liu, Y. J., S. O. Rogers, and J. F. Ammirati. 1997. Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal DNA internal transcribed spacers. Canad. J. Bot. 75: 519-532.
* Liu, Y. J., S. E. Whelen, and B. D. Hall. 1996. Sequencing studies of RPB2 genes in fungi and their phylogenetic implications. Mycological Society of America (Abstract #191M) Inoculum 47(3):110.

THOMAS C. HARRINGTON <http://www.public.iastate.edu/~tcharrin/homepage.html>
Tom Harrington uses morphological and ecological characters upon which to base hypotheses and carries through with molecular studies of scolytid beetle-associated ascomycetes and other forest pathogens. His interests in the systematics of a broad range of taxa, including bark endophytes of Pinus radiata, the ascomycete genera Ophiostoma and Ceratocystis, and the basidiomycetes Armillaria and Heterobasidion, has contributed to elucidation of their taxonomic and phylogenetic status throughout their ranges.

Harrington recently has taken a lead in using mating gene sequences in ascomycete taxonomy (MAT-2 gene). Harrington has a number of international collaborators, including a group of forest mycologists in the Republic of South Africa, Brazilians interested in beetle-associated fungi and tree pathogens, New Zealand and Korean specialists in insect-dispersed ascomycetes, and Finnish specialists interested in Heterobasidion evolution.  Through these collaborations he has collected widely and has a knowledge of the taxa he studies, which encompasses the entire world.

In the last five years Harrington has had six graduate students, three of whom are currently studying with him. Of the five undergraduates in his lab doing independent study, one was a African-American woman, who may have entered graduate school; another undergraduate women is a technician for Pioneer Hybrid, and a third women is entering graduate school in microbiology.

Harrington is a collaborative scientist with many international colleagues, but the project is important to him because he will be able to work with sytematists who are interested in the broader groups to which the forest pathogens he studies belong and to place them within a broader context.

Selected publications
* Coetzee, M. P. A., B. D. Wingfield, T. C. Harrington, D. Dalevi, T. A. Coutinho, and M. J. Wingfield. 2000. Geographic diversity of Armillaria mellea s. s. based on phylogenetic analysis. Mycologia 92: 105-113.
* Witthuhn, R. C., B. D. Wingfield, M. J. Wingfield, and T. C. Harrington. 1999. PCR-based identification and phylogeny of species of Ceratocystis sensu stricto. Mycol. Res. 103: 743-749.
* Witthuhn, R. C., B. D. Wingfield, M. J. Wingfied, M. Wolfaardt, and T. C. Harrington. 1998. Monophyly of the conifer species in the Ceratocystis coerulescens complex using DNA sequence data. Mycologia 90: 96-101.
* Maijala, P., T. C. Harrington, and M. Raudaskoski. 1998. Peroxidase gene structure and gene trees in Heterobasidion. Pp. 62-70 In: Preceedings of the Fourth Meeting on the Genetics and Cellular Biology of Basidiomycetes. Eds.,  L.J.L.D. Van Griensven , and J. Visser. The Netherlands.
* Harrington, T. C., J. Stenlid, and K. Korhonen. 1998. Evolution in the genus Heterobasidion. In: Root and Butt Rots of Forest Trees. 9th Intern. Conf. on Root and Butt Rots. Eds., Delatour, C., J. J. Guillaumin, B. Lung-Escarmant, and B. Marcais. INRA Editions (France), Les Colloques 89: 63-74.

DAVID S. HIBBETT <http://www.clarku.edu/~biol/faculty/Hibbett/hibbett.html>
Hibbett recognizes the fact that fungi are an important, understudied group of eukaryotes. In nature, they function as decomposers, pathogens, and partners in diverse symbioses, such as lichens and mycorrhizae. Fungal morphology encompasses a spectrum of forms, including mushrooms, coral fungi, puffballs, and many others. Despite their morphological variability,
fungi are anatomically simple, and they have a notoriously poor fossil record. Consequently, the evolutionary relationships of the kingdom members are poorly understood.

Recently, Hibbett developed a preliminary phylogenetic classification for the homobasidiomycetes, a major result of the work he is doing. He uses comparative analyses of DNA sequences to infer the phylogenetic relationships of fungi, concentrating on basidiomycetes, and he is working on broad sampling of many agarics, boletes, and polypores. He is interested in using phylogenetic trees to understand the pathways by which fungal forms and ecological strategies have evolved. In this regard he is looking at basidiomycetes including some that belong within the large order, Aphyllophorales, as well as mushroom groups and is tracking the dramatic morphological changes that occur in the divergence of certain groups. For example he is studying cantherelloid species and has verified that the clade is supported by a synapomorphy of a common type of nuclear division.  In addition finds that morphologically diverse fungi that have been called stinkhorns, earth stars, other gasteromycetes, and cannon-ball fungi, are in fact members of a clade containing clavarioid fungi. Although he finds extensive convergence in fruiting body morphology, certain anatomical and biochemical features appear to be phylogenetically informative.

He has interest in fungal morphology and paleontology as well. His studies in these areas make use of an evolutionary perspective gained through molecular studies. Hibbett is interested in using phylogenetic trees to assess conservation priorities; in his study of Lentinula he found many that many geographical regions remain unsampled, and he suggests that certain areas might have particularly high levels of diversity and should be targeted for further study and conservation. Finally, Hibbett promotes translating phylogenetic trees into classifications to create classifications insuring that taxonomy reflects up-to-date phylogenetic hypotheses.

Hibbett worked with undergraduate and graduate students while he was a postdoctoral associate.  This opportunity helped him to appreciate the importance of collaboration in broad research topics and in training of students. He will make important contributions to the network members, while he will benefit from group interactions as he begins his career in a relatively new position where he is somewhat isolated from other taxonomic mycologists.

Selected publications
* Hibbett, D. S., and R. G. Thorn. 2000. Basidiomycota: Homobasidiomycetes.  Pp. 121-168, In: The Mycota, VII Part B. Eds., McLaughlin, D. J., E. G. McLaughlin, and P. A. Lemke. Springer-Verlag.
* Pine, E. M., D. S. Hibbett, and M. J. Donoghue. 1999. Phylogenetic relationships of cantharelloid and clavarioid Homobasidiomycetes based on mitochondrial and nuclear rDNA sequences. Mycologia 91: 944-963.
* Hibbett, D. S., and M. J. Donoghue. 1998. Integrating phylogenetic analysis and classification in fungi. Mycologia  90:347-356.
* Hibbett, D. S., E. M. Pine, E. Langer, G. Langer, and M. J. Donoghue. 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. PNAS 94: 12002-12006.
* Hibbett, D. S., D. Grimaldi, and M. J. Donoghue. 1995. Cretaceous mushrooms in amber. Nature 377: 487.

SABINE M. HUHNDORF <http://www.fmnh.org./research_collections/botany/staff_cv_huhndorf.htm>
Huhndorf's research on fungi focuses on ascomycetes, especially loculoascomycetes and pyrenomycetes, organisms which are plant pathogens and agents of decomposition. Her research has floristic and monographic components, and she currently is working on worldwide monographs of Lasiosphaeria and Chaetosphaeria, two genera that occur on woody hosts. A detailed assessment of the relationship among families in the Sordariales and among the genera in the Lasiosphaeriaceae using morphological and molecular data is also being undertaken.  Her other recent monographic studies include works on the cosmopolitan genera Jobellisia and Leptosphaeria and the tropical genera, Lasiosphaeriella, Xenolophium, and Ostropella. These systematic studies are leading to improved classification and a better understanding of generic relationships in these groups and test theories of speciation and biogeography. Her work involves the microscopic examination and assessment of herbarium specimens along with laboratory in vitro culture studies of fresh specimens to determine growth and reproductive characteristics.

Her floristic work is focused in the West Indies, in Costa Rica and in French Guiana. In general, ascomycetes are not well-known and have not been widely collected from many tropical habitats. Areas like the tropical, lowland, rainforest in Saul, French Guiana, the Osa Peninsula in Costa Rica and the Caribbean National Forest in Puerto Rico, offer the possibility to survey and inventory the ascomycete mycota and ask questions about biology, ecology, distribution and host specificity. These projects involve an active field work program as well as laboratory studies, and the surveys will serve as models for assessing ascomycete biodiversity in other tropical forests and ultimately, the information on fungal biodiversity will lead to a manual for identifying tropical ascomycetes. Huhndorf has developed effective methods for recording and entering fungal records and electronic illustrations in databases to document her taxonomic work.

Huhndorf is training a PhD student and a Venezuelan postdoctoral associate at The Field Museum. In her capacity as a PEET PI, Huhndorf has collaborated with a number of other mycologists, and the network will ensure that collaborations continue to be fruitful. She is excited about this proposal and will bring her databasing skills to the group in exchange for discussions, especially, those in which the topic is collection of additional databases.

Selected publications
* Courtecuisse, R., G. J. Samuels, M., A. Y. Rossman, G. Cremers, S. M. Huhndorf, and S. L. Stephenson. 1996. Check-list of fungi from French Guiana. Mycotaxon 57: 1-85.
* Huhndorf, S. M., and F. A. Fernández. 1999. Neotropical Ascomycetes 8. New species of Lasiosphaeriella. Mycologia 91: 544-552.
* Huhndorf, S. M., F. A. Fernández, and D. J. Lodge. 1999. Neotropical Ascomycetes 9.  Jobellisia species from Puerto Rico and elsewhere. Sydowia 51: 183-196.
* Huhndorf, S. M. 1997. A preliminary survey of loculoascomycetes and pyrenomycetes of Saul, French Guiana. Chapter 19. pp. 327-339. In Symposium on Tropical Mycology. Ed., Hyde, K.D. University of Hong Kong Press.
* Huhndorf, S. M. 1993. Neotropical Ascomycetes 3. Reinstatement of the genus Xenolophium and two new species from French Guiana. Mycologia 85: 490-502.

CLETUS P. KURTZMAN <http://wdcm.nig.ac.jp/kurtzman.html>
Kurtzman and his colleague Fell recently completed the fourth edition revision of the compendium, The Yeasts, the “Bible” for yeast workers.  This edition of the book is the first to introduce molecular methods for identification and classification. Because yeasts as a group are particularly important in industrial processes and medicine and as model organisms, the work is essential to many users. In addition Kurtzman and his associates have provided taxonomic tools that allow many new workers to be able to study yeasts. Their database of a 600pb region of the LSU rRNA gene, which includes the variable D1/D2 loop, now makes it possible to place any of over 600 ascomycetous yeasts among the nearest relatives by using sequences for comparison. Ongoing research in his laboratory investigates molecular systematics of ascomycetous yeasts employing phylogenetic analysis of rDNA and other gene sequences. His goal is to understand species and other taxonomic boundaries and to use this information for a phylogenetic system of classification for the yeasts. In addition, numerous new species are being discovered and described, many from species-poor areas of the phylogenetic tree. These habitats include old basidiocarps, insects, fruits, leaves, flowers, and other plant parts.

Kurtzman is active in international circles, and occupies leadership roles in several international mycological groups, culture collection policy, and medical mycology research. Kurtzman continues to promote unification of mycologists by holding joint meetings. He brings his collegial attitude to the group and he will benefit from his exposure to the wide variety of fungi to which yeasts are related.

Although he is not affiliated with a university, Kurtzman has helped to train visiting scientists, and in the last five years Mexican and Dutch scientists were included.

Selected publications
* Kurtzman, C. P. 2000. Four new yeasts in the Pichia anomala clade. Int. J. Syst. Evol. Microbiol. 50: 395-404.
* Kurtzman, C. P. 2000. Three new ascomycetous yeasts from insect-associated arboreal habitats. Canad. J. Microbiol. 46: 50-58.
* Kurtzman, C. P. 1998. Discussion of teleomorphic and anamorphic ascomycetous yeasts and a key to genera. p 111-121. In: The Yeasts, a taxonomic study. 4th ed. Eds., Kurtzman, C. P., and J. W. Fell. Elsevier Science, Amsterdam.
* Kurtzman, C. P., and C. J. Robnett. 1998. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73:331-371.
* Kurtzman C. P., J. W. Fell, eds. 1998. The yeasts, a taxonomic study. 4th ed. Amsterdam: Elsevier Science. p 111-121.

ROBERT W. LICHTWARDT <http://www.nhm.ukans.edu/~fungi/>
Fungi and insects constitute large, species-rich groups for which there are few taxonomic specialists, the more so for those organismal groups in aquatic or marine environments. This study concentrates on an intriguing group of fungi that are symbiotic in the guts of primitive flies like Chironomidae and in crustaceans and millipedes. Lichtwardt is the world’s authority on trichomycete fungi, and he and his students and colleagues, including a number of international collaborators pursue research on the taxonomy, phylogeny, and potential coevolution of gut-inhabiting fungi and their insect hosts. Most of the fungi appear to have little negative effect on the hosts, but a few are known to be lethal to mosquito larvae; another reduces reproductive output in blackflies when they invade the ovarian tissue of the host insect, and subsequently are dispersed as "cysts" during egg-laying.

Lichtwardt’s research concentrates on fungi that are associated with mostly aquatic insects and crustaceans.  A large collection of these species-rich assemblages which are studied by few people in the world, have been amassed by Lichtwardt.  He remains active after retirement from the University of Kansas and occupies his original laboratory where he trains students under PEET funding. Lichtwardt also is active in collecting, and he continues to build his extensive worldwide collection of these organisms. He makes good use of the Internet by posting valuable materials for the study of these fungi, such as a primer “An Overview of Trichomycete Systematics” and “World Literature on Trichomycetes,” “New Genera and Species of Trichomycetes,”  “Cultured Species of Trichomycetes,” “Cultures Deposited With the American Type Culture Collection, “ and “Keys to Orders and Genera of Trichomycetes.”

The training of both graduate and postdoctoral students emphasizes laboratory and museum work as well as field collecting, and includes visits to the USDA-Peoria laboratory for training in modern DNA sequencing of fungi. Computerization of all aspects of research, including specimen databasing and construction of interactive identification keys, will enhance the timely dissemination of results from the University of Kansas' World Wide Web server.

Lichtwardt has three PhD students and an undergraduate working in his laboratory currently.  He has trained two women graduate students and a postdoctoral associate in the last five years. In addition to the PEET trainees at the University of Kansas, Lichtwardt has additional trainees involved in the grant off campus.

Lichtwardt will benefit from the group association for increased taxon sampling; he will better be able to place the trichomyetes among their relatives and determine if the three groups currently recognized constitute a monophyletic group.

Selected publications
* Lichtwardt, R. W., C. L. Lastra, and M. G. Mazzucchelli. 2000. Fungi living in the guts of larval aquatic insects in northwestern Argentina. Mycologia 92: 332-340.
* Lichtwardt, R. W., L. C. Ferrington, and C. L. Lastra. 1999. Trichomycetes in Argentinean aquatic insect larvae. Mycologia  91: 1060-1082.
* Lichtwardt, R. W., and M. C. Williams. 1999. Three Harpellales that live in one species of aquatic chironomid larva. Mycologia 91: 396-399.
* Lichtwardt, R. W., and R. D. Grigg. 1998. Four new Smittium species inhabiting the hindgut of Chironomidae larvae. Mycologia  90: 427-433.
* Lichtwardt, R. W. 1997. Costa Rican gut fungi (Trichomycetes) infecting lotic insect larvae. Rev. Biol. Trop. 45: 1349-1383.

FRANÇOIS LUTZONI <http://www.fmnh.org./research_collections/botany/staff_cv_lutzoni.htm>
Lutzoni’s research interests are centered on lichens and symbiosis, and in particular, the following major topics: 1) Floristics and systematics of lichens using both morphological and molecular data. 2) Requirements and consequences for a transition to mutualism during the evolution of fungi; this work is done on a model system including both lichen-forming and closely related non-lichenized Omphalina species. Data from this model system are gathered through in vitro experiments and molecular evolutionary studies. The data generated are analyzed using comparative methods. 3) Macroevolutionary studies of lichenized and non-lichenized ascomycetes; this research project is aimed toward a better understanding of the relationships among orders of ascomycetes using molecular and morphological data sets. 4) Phylogenetic reconstruction theory is another topic of  interest, especially the combinability testing methods and problems associated with resolving phylogenetic relationships among many taxa. As Lutzoni and his collaborators try to solve phylogenetic relationships among larger numbers of taxa, the need for multiple data sets becomes increasingly acute. Combinability testing is not only a way to determine if data sets should be combined in their entirety, but is also a tool for exploring the specific characteristics of each data set that causes phylogenetic incongruence. 5) Cospeciation between lichen-forming fungal species and their algal symbiont Coccomyxa (Chlorophyta) is currently being addressed by sequencing the same genes in both the fungal and algal partners of distinct lichen populations for different lichen species.

Lutzoni is has worked with undergraduate and graduate students, and in addition he has participated with PI Huhndorf and Mueller on a PEET project. The gathering of large amounts of data by the group will be of interest to Lutzoni in his effort to test combinability of data sets.

Selected publications
* Lutzoni, F., P. Wagner, and V. Reeb. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst. Biol. 49: in press.
* Moncalvo, J. M., F. M. Lutzoni, S. A. Rehner, J. Johnson, and R. Vilgalys. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst. Biol. 49: 278-305.
* Fernandez, A., F. Lutzoni, and S. M. Huhndorf. 1999. Teleomorph-anamorph connections: the new pyrenomycetous genus Carpoligna and its Pleurothecium anamorph. Mycologia 91: 251-262.
* Lutzoni, F. 1997. Phylogeny of lichen- and non lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets. Syst. Biol. 46: 373-406 (journal cover).
* Lutzoni, F., and R. Vilgalys. 1995. Integration of morphological and molecular data sets in estimating fungal phylogenies. Canad. J. Bot. 73: S649-S659.

DAVID J. McLAUGHLIN < http://biosci.cbs.umn.edu/plantbio/faculty/mclaughlin.htm>
Basidiomycetes are an ecologically important group of fungi. Their systematics and phylogeny are undergoing major revision with guidance from molecular and subcellular characters. McLaughlin’s research focuses on basidiomycete evolution, phylogeny, systematics, and biodiversity. His current projects include 1) consolidation and computerization of the two Minnesota fungal herbaria to provide an on-line database for Minnesota fungi; 2) analysis of the ectomycorrhizal basidiomycetes in oak savannah above- and below-ground to determine biodiversity and the influence of fire and nitrogen on fungal community structure; 3) analysis of two species complexes in the very large mushroom genus Psathyrella, using light microscopic and molecular data, to assess the value of morphological characters in separating species; and 4) analysis of phylogeny in the core group of clavarioid fungi to assess generic relationships and the value of subcellular characters in establishing relationships in hymenomycetes, i.e., mushrooms and their relatives. These projects all depend on phylogenetic data, including the biogeographic studies and the identification of ectomycorrhizal fungi from roots.

His research group has a particular focus on clavarioid fungi, which are pivotal in many evolutionary schemes of the development of complex mushrooms. The clavarioid fungi produce their spore-forming cells unprotected on the surface of club-shaped or branched fruitbodies. Initial molecular analysis suggests that these fungi are an artificial assemblage of taxa with superficially similar fruitbodies, but the extent to which they are an artificial group is still unknown because few taxa have been investigated. McLaughlin and his colleagues have as a goal to evaluate the core groups of clavarioid fungi, Clavariaceae and Pterulaceae, using molecular and structural characters. They also want to make an in-depth analysis of the Pterulaceae, because it appears to be important in tropical forest ecosystems, is poorly understood systematically, and is amenable to study. A additional objective is to begin an ultrastructural assessment of the systematic significance of specialized cells (cystidia) and differentiated hyphae in clavarioid fungi and their relatives.

In their recent work they have demonstrated that molecular and subcellular characters are effective in establishing phylogenetic relationships in the Urediniomycetes, i.e., the basidiomycete class that includes the rust fungi and their relatives. Morphological characters have thus far failed to provide synapomorphies for the major mushroom clades established with molecular data, i.e., for the Hymenomycetes. Ultrastructural characters have been little investigated in this class. To carry out an analysis of the utility of subcellular characters for phylogenetic analysis of Hymenomycetes, McLaughlin and his collaborators need to identify the close relatives of the core group of clavariod fungi among the mushrooms, as well as to establish the monophyletic nature of these families, so that valid structural comparisons can be made between clavarioid fungi and other mushrooms.

McLaughlin has had six graduate students in the last five years; three of whom are still in school. In addition he has had undergraduate students and a postdoctoral associate in the lab. Of the individuals trained in his lab during this time four were women and three were Asians.

The fungal research coordination network is important to his research for a variety of reasons. Establishing a valid phylogeny involves data from all fruiting body morphologies, but, since each type is frequently the specialty of a particular scientist, access to this range of organisms is most effectively achieved through group planning. Since the technical demands permit very few organisms to be surveyed, subcellular analysis requires coordination to decide on the taxa to be analyzed and on the characters to be surveyed to make a comparable data set. In addition, taxonomic and biogeographic questions arising from his studies often require fresh or recent specimens from other parts of the country or elsewhere for molecular analysis, and this material may be best obtained as part of a group effort.

Selected publications
* McLaughlin, D. J., E. G. McLaughlin, and P. A. Lemke  (eds.). 2000. The Mycota. VIIA and VIIB. Systematics and Evolution. Springer Verlag. (In press).
* Swann, E. C., E. M. Frieders, and D. J. McLaughlin. 2000. Urediniomycetes. In: The Mycota. VII. Systematics and Evolution. Eds., McLaughlin, D.J., E. G. McLaughlin, and P. A. Lemke. Springer Verlag. (In press).
* Swann, E. C., E. M. Frieders, and D. J. McLaughlin. 1999. Microbotryum, Kriegeria, and the changing paradigm in basidiomycete classification. Mycologia 91: 51-66.
* McLaughlin, D. J., E. M. Frieders, M. E. Berres, J. C. Doublès, and S. M. Wick. 1996. Immunofluorescence analysis of the microtubule cytoskeleton in the yeast phase of the basidiomycetes Kriegeria eriophori and Septobasidium carestianum. Mycologia 88: 339-349.
* McLaughlin, D. J., E. M. Frieders, and H. S. Lu. 1995. A microscopist's view of heterobasidiomycete phylogeny. Stud. Mycol. 38: 91-109.

JOSEPH B. MORTON  <http://invam.caf.wvu.edu/Myc_Lab/Joe/joe.htm>
Morton has worked 18 years on the taxonomy, biology, ecology, and evolutionary biology of arbuscular endomycorrhizal fungi (Glomales, Zygomycota).  During the past decade, he also has built up and managed the largest international living stock collection of these fungi (INVAM), which consists of over 1200 accessions from six continents.  With almost 40% of the species in this collection putatively undescribed, much research has focused on developing morphological criteria that unambiguously differentiated species.  Numerous comparative developmental studies have helped to define characters and generate a predictive model for robust diagnoses. With more confident species delimitation, comparisons then were generated using other character sets to examine phylogenetic relationships.  Immunological studies led to production of monoclonal antibodies, of which one clone specific for two taxa that have since been shown using DNA sequences to belong to a distant ancestral group and another clone that is Glomales-specific for and iron-rich glycoprotein important in soil aggregation.  Fatty acid profiles also were used to complement morphology in resolving phylogenetic relationships in one suborder of Glomales.  More recently, small subunit rDNA sequences revealed that morphologically-atypical species (including several with dimorphism spanning families) are ancient relative to other glomalean taxa and are more closely related to a nonmycorrhizal zygomycete fungus, Geosiphon pyriforme.  Since this fungus is a symbiont with a Nostoc cyanobacterium, valuable clues as to the origin of mycorrhizal fungi may reside in this association.  Since arbuscular fungi are obligate symbionts, research also has focused on methodology to measure fungal community structure using trapping methods, relationships between fungal and plant community structure in habitat extremes (arid vs. wetlands), and biogeographic analyses.

Morton has had near equal numbers of male and female graduate students, of which one was Asian and another hispanic.  He has trained post-doctoral associates and research technicians. Undergraduate students involved in the laboratory were largely (70%).

This proposal is important to Morton’s research program in that it will help him to solidify phylogenetic hypotheses within Glomales and the relationship of Glomales to other crown fungal taxa (Ascomycota and Basidiomycota). Currently, small subunit sequence data are conflicting:  amongst ancestral taxa these data are strongly concordant with other molecular, ecological, and morphological characters, yet among more recent taxa they are strongly contradictory.  Other molecular data are needed to resolve these conflicts and establish some measure of a true phylogeny, and it is hoped the collaborations in this project will stimulate this research in Morton’s laboratory and in other labs with whom Morton collaborates (Bruns and associates).  It is critical, at this juncture, to establish levels of resolution for known molecular data sets and new ones that are in the process of being discovered.

Selected publications
* Redecker, D., J. B. Morton, and T. D. Bruns. 2000. Ancestral lineages of arbuscular mycorrhizal fungi (Glomales).  Mol. Phylogen. Evol. 14: 276-284.
* Morton, J. B. 1999. Evolution of endophytism in arbuscular mycorrhizal fungi of Glomales. pp. 121-140. In: Microbial Endophytes. Eds., Bacon,  C. W. and J. H. White. Marcel Dekker, Inc., New York.
* Bentivenga, S. P., and J. B. Morton. 1996. Congruence of fatty acid methyl ester profiles and morphological characters of arbuscular mycorrhizal fungi in Gigasporaceae.  PNAS 93: 5659-5662.
* Morton, J. B. 1990.  Evolutionary relationships among arbuscular mycorrhizal fungi in the Endogonaceae.  Mycologia 82:192-207.
* Morton, J. B., and G. L. Benny. 1990. Revised classification of arbuscular mycorrhizal fungi (Zygomycetes):  a new order, Glomales, two new suborders, Glomineae and Gigasporineae, and two new families, Acaulosporaceae and Gigasporaceae, with an emendation of Glomaceae.  Mycotaxon 37: 471-491.

GREGORY M. MUELLER <http://www.fmnh.org./research_collections/botany/staff_cv_mueller.htm>
Mueller’s research program centers on the systematics, ecology and evolution of higher fungi and the mutualistic mycorrhizal symbiosis that some of them form. Four long-term projects are currently receiving most of his attention: 1) A survey of mushrooms and related fungi of the Costa Rican tropical oak forests. Goals of the study are to: a) develop the first comprehensive survey of higher fungi from the neotropics; b) build scientific infrastructure in Costa Rica through training of graduate students and improving facilities; and, c) screen fungi for anti-AIDS and anti-cancer compounds. 2) A survey of mushrooms and related fungi occurring in northern Illinois and Indiana to determine species composition, distribution and host specificity and to assess the effect of air pollution on fungi in the region. 3) Comparison of biogeographic relationships between macrofungi of eastern North America and temperate eastern Asia. Goals of this study are to document macrofungal diversity in China and to determine the taxonomic similarity of the two regions based on detailed morphological analyses and analysis of DNA sequence data of selected taxa. 4) A monographic study of the genera Hydnangium, Laccaria, and Podohydnangium. This work is designed to test various theories of speciation, coevolution (with their obligate tree symbionts) and biogeography of fungi that form ectomycorrhizae. These projects entail an active field work component as well as laboratory studies that include micromorphological analyses  (computer-aided light microscopy, SEM and TEM), examination of in vitro culture morphology, pairing studies and DNA sequencing. These interrelated projects are providing information on fungal ecology and biology that are crucial to temperate and tropical forest management and conservation.

Mueller has been active in outreach to mycologists in Latin America through his neotropical studies. He has trained a number of Costa Ricans and helped to put on a teaching workshop in Venezuela in conjunction with the Latin American Congress in Caracas.  He has trained several graduate students. He has been an effective mentor, including for high school students; one notable woman student was the grand prize winner in the Westinghouse Science Talent Search several years ago.

The network would involve Mueller with more potential collaborators who will help to round out the worldwide taxon sampling of the taxa in which he is interested and to place them in higher level taxonomic groups.

Selected publications
* Halling, R. E., G. M. Mueller, and M. J. Dallwitz. 1999. A new Phylloporus (Basidiomycetes, Boletaceae) with a key to species in Colombia and Costa Rica. Mycotaxon 73: 63-67.
* Halling, R. E., and G. M. Mueller. 1999. A new species and a new record for the genus Xerula (Agaricales) from Costa Rica. Mycotaxon 71: 105-110.
* Aruguete, D. M., J. H. Aldstadt, and G. M. Mueller. 1998. Accumulation of several heavy metals and lanthanides in mushrooms (Agaricales) from the Chicago region. Sci. Total Environ. 224: 43-56.
* Wu, Q. X., and G. M. Mueller. 1997. Biogeographic relationships between the macrofungi of temperate eastern Asia and eastern North America. Canad. J. Bot. 75: 2108-2116.
* Albee, S. R., G. M Mueller, and B. R Kropp. 1996. Polymorphisms in the large intergenic spacer of the nuclear ribosomal repeat identify Laccaria proxima strains. Mycologia 88: 970-976.

KERRY O’DONNELL <http://nrrl.ncaur.usda.gov/the_collection3.htm#The curators>
Research in O’Donnell’s laboratory focuses primarily on molecular evolutionary genetics of Fusarium, a genus of plant pathogenic and toxigenic ascomycetous fungi.  Collectively, the fusaria represent the most important genus of phytopathogenic and mycotoxigenic fungi.  Scientists who encounter these pathogens have had to rely on cultural characteristics and microscopic morphology for their identifications.  To address this problem, we are constructing an electronically portable DNA sequence database to investigate species boundaries and to serve as a systematic tool for the rapid identification of all fusaria.  These data allow the identification of strains to known taxa, and also assist in the identification of new taxa.  To date, these systematic tools have advanced our knowledge of the evolution, biogeography and species limits of several of the most important plant pathogenic and toxigenic lineages within Fusarium.  In addition, O’Donnell’s group is using phylogenetics of DNA sequence data to study the evolution of other fungal groups including the Zygomycota (especially the Mucorales) and Morchella, the highly prized genus of true morels. O’Donnell is widely published, however, we decided to cite one of his manuscripts that is under review to emphasize the importance of his work to zygomycetes, a group few systematists throughout the world are working on. O’Donnell’s work is essential to an understanding of the phylogeny of this entire phylum that is proported to be polyphyletic in early studies that included few taxa.

O’Donnell is not in a university and has little opportunity to work with students; however, he is extremely interactive and works with other mycologists.  He has collaborated with Lutzoni and Bruns of one project and has been involved in training Lichtwardt PEET students inn molecular techniques. The network will enhance and formalize such associations and facilitate the development of new interactions.

Selected publications
* O'Donnell, K., F. M. Lutzoni, T. W. Ward, and G. L. Benny. 2000. Evolutionary relationships among mucorlaean Fungi (Zygomycota): Evidence for family polyphyly on a large scale. Mycologia [in review].
* O'Donnell, K., H. C. Kistler, B. K. Tacke, and H. H. Casper. 2000. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. PNAS [In press].
* O'Donnell, K., E. Cigelnik, and H. I. Nirenberg. 1998. Molecular systematics and phylogeography of the Gibberella fujikuroi complex of Fusarium. Mycologia 90: 465-493.
* O'Donnell, K., E. Cigelnik, and G. L. Benny. 1998. Phylogenetic relationships among the Harpellales (Trichomycetes) and Kickxellales (Zygomycetes), two orders of Zygomycota that form regularly septate hyphae. Mycologia 90: 624-639.
* O'Donnell, K., E. Cigelnik, N. S. Weber, and J. M. Trappe. 1997. Phylogenetic relationships among ascomycetous truffles and the true and false morels inferred from 18S and 28S ribosomal DNA sequence analysis. Mycologia 89: 48-65.

RONALD H. PETERSON and KAREN W. HUGHES <http://fp.bio.utk.edu/mycology/>
Petersen and Hughes have combined their research interests (mycology and genetics respectively) to collaborate on studies and graduate student training involving the larger basidiomycete fungi (fungi which often have conspicuous fruiting bodies, usually mushrooms and their allies).  Their worldwide approach, broad taxonomic coverage, and combination of techniques, including mating type studies, morphological analyses (including culture characters), protein electrophoresis, and DNA markers, make their studies both thorough and unique. The multidisciplinary approach has been used to circumscribe species within a genus, to examine species  biogeographical distributions and ecology, and to suggest patterns of fungal evolution. In some studies, the number of species within a genus has been reduced, recognition that many species have been named on the basis of morphological variation in a phenotypically plastic group (e.g., Pholiota and the Pleurotus djamor complex).  Other investigations have found reproductively-isolated cryptic and often sympatric species that differ in only subtle morphological characters or substrate preference (Xeromphalina).   Surprisingly, even in economically important genera such as Flammulina, a number of species with distinct morphology, substrate preference and distributions, were unknown and physiological and medicinal studies carried out by previous workers were attributed to incorrect species epithets.  Current studies give primary emphasis to monographic treatments of the genera Clavicorona, Lentinellus and Auriscalpium, all members of the Auriscalpiaceae with a view towards family-level circumscription.  They maintain an extensive herbarium and culture collection (currently 5,300 dikaryon cultures) in conjunction with their studies, and train graduate students and postdoctoral associates in laboratory and museum work, as well as providing field collecting experiences in the United States and abroad.  They host a 2-3 foreign mycologists annually for collaborative research funded by the University of Tennessee Hesler endowment.  They also host "Highlands Week," an annual meeting of mycology students and visiting scientists at Highlands, North Carolina, for purposes of training and collecting.

Petersen and Hughes already know the benefits of this kind of collaborative effort through their participation in NSF PEET programs.  Among this group they expect to provide expertise on the identification of basidiomycetes and taxon sampling and to help with developing a large DNA database for basidiomycetes. They and their associates will benefit especially from the discussions of analysis techniques.  Of special benefit for taxon sampling is proximity to the Southern Appalachians including the Great Smoky Mountains National Park (GSMNP) and to the highlands of North Carolina.  These regions are high in species diversity and endemism.  The GSMNP is the site for the "All Taxon Biological Inventory"

They have trained large numbers of students, including several African American and Hispanic undergraduates, several of whom are pursuing graduate programs and a current Hispanic Ph.D. student. In addition Hughes has participated in a number of minority-based summer programs including an NIH-sponsored program (research experience for minority teachers and students) and the McNair Program directed towards pre-doctoral research experiences for minority students. She also participates in the Threshold Program which provides research experiences for outstanding undergraduates at the University of Tennessee.

Selected publications
* Redhead, S. A., and R. H. Petersen. 1999. New species, varieties and combinations in the genus Flammulina. Mycotaxon 71:285-294.
* Gordon, S. A., and R. H. Petersen. 1998. Infraspecific variation among geographically separated collections of Marasmius scorodonius. Mycotaxon 69: 453-466.
* Petersen, R.H., and J. Cifuentes-Blanco. 1998. Mating systems of three Mexican Aphyllophorales. Folia Cryptog. Estonica 23: 111-117.
* Wise, K., and R. H. Petersen. 1998. A Natural History of Mt. LeConte. Univ. Tennessee Press. 179 pp.
* Petersen, R. H., D. B. G. Nicholl, and K. W. Hughes. 1997 Mating systems of some putative polypore-agaric relatives. Plant Syst. Evol. 207: 135-158.

* Hughes, K. W., L. L. McGhee, A. S. Methven, J. E. Johnson, and R. H. Petersen. 1999.  Patterns of geographic speciation in the genus Flammulina based on sequences of the ribosomal ITS1-5.8S-ITS2 area. Mycologia 91: 978-986.
* Petersen, R. H., and K. W. Hughes 1999. Species and speciation in mushrooms. BioScience (June).
* Hughes, K. W., T. Toyahara, and R. H. Petersen. 1998. Disjunct populations of Pleurotopsis longinqua. Mycologia 90: 595-600.
* Hughes, K. W., and R. H. Petersen. 1997. Relationships between Omphalotus species based on RFLP patterns of the ribosomal ITS1-5.8S-ITS2 region. Plant Syst. Evol. 211: 213-237.
* Petersen, R. H., and K. W. Hughes. 1997. Mating systems in Omphalotus (Paxillaceae, Agaricales). Syst. Evol. 211: 217-229.

DONALD H. PFISTER < http://www.herbaria.harvard.edu/discomycetes/ >
Pfister focuses his work on the Discomycetes including members both of the Pezizales and Helotiales.  In the Pezizales he has done monographic and phylogenetic work most particularly recently on the suborder Sarcoscyphineae.  This suborder was established to circumscribe a group of cup-fungi with operculate asci in which the ascus morphology was thought to delimit a monophyletic group.  Recent work has indicated that the Sarcoscyhineae is not monophyletic.  A monographic and phylogenetic of the genus Phillipsia has shown that character evaluation is an important part of forming a taxonomy of this group.  A monograph of the genus Cookeina is due to be published in the fall of 2000.  Other studies in Pfister’s research group involve the biogeographical and populational studies (Chorioactis and Cyttaria), phylogenetic and monographic studies of the Pezizaceae, and phylogenetic studies in the Helotiales, focusing on the core group of the Helotiales and the Orbiliaceae. The Orbiliaceae (Helotiales, Ascomycota), is a large family of inoperculate discomycetes.  Members of the family are interesting because many produce anamorphs (asexual, vegetative states) that represent a variety of life histories and interactions with other organisms. Some trap and consume nematodes and other small animals; others produce conidia that are adapted to dispersal in water. Some anamorphs are produced about which we know little biologically yet their anatomy, morphology, and physiology suggest interactions with other organisms. The diversity of anamorphic form is not completely mirrored in teleomorphic (sexual state) diversity and Pfister and his students are expanding upon previous work on the diversity of anamorphs in this family. The position of the Orbiliaceae among the filamentous ascomycetes also is problematic, and a phylogeny is being completed for these fungi. Pfister and his colleagues also are studying the phylogenetic placement of a number of other discomycetes:  Cookeina, Cyttaria, Medeolaria farlowii, Chorioactis, Wynnea, Geoglossum, Trichoglossum, and Leotia.

Pfister teaches mycology and plant science courses and is director of the Farlow Herbarium (FH) which houses nearly 1,400,000 specimens of lichenized and non-lichenized fungi, bryophytes, and algae. The collections are world-wide in scope. He is the Interim Director of the Harvard University Herbaria. Pfister has had excellent colleagues including postdoctoral researchers (both men and women), graduate students (3 are women) and many recent undergraduates of whom two were hispanic and one a woman, now a graduate student at the University of California, Berkeley. In addition he has encouraged three recent women PhDs, one from South American, by including them in his studies.

Selected publications
* Hansen, K., D. H. Pfister, and D. S. Hibbett. 1999. Phylogenetic relationships among species of Phillipsia inferred from molecular and morphological data. Mycologia 91: 299-314.
* Harrington, F. A., D. H. Pfister, D. Potter, and M. J. Donoghue. 1999. Phylogenetic studies within the Pezizales. I. 18S rRNA sequence data and classification. Mycologia 91: 41-50.
* Hansen, K, D. H. Pfister, and D. S. Hibbett. 1999. Phylogenetic relationships among species of Phillipsia inferred from molecular and morphological data. Mycologia 91: 299-314.
* Plotnikova , J. M., T. L. Reuber, F. M. Ausubel, and D. H. Pfister. 1998. Powdery mildew pathogenesis of Arabidopsis thaliana. Mycologia 90: 1009-1016.
* Pfister, D. H. 1997. Castor, Pollux and life histories of fungi. Mycologia 89: 1-23.

MARTHA J. POWELL <http://www.as.ua.edu/biology/faculty/faculty/mp.html>
DAVID PORTER <http://dogwood.botany.uga.edu/~porter/porter.html>
JOYCE E. LONGCORE <http://www.aewc.um.maine.edu/Science/dept/plantbio/facresch.htm#longcore>

Powell, Porter, and Longcore are joined by a PEET project to study the microscopic aquatic fungi known as chytrids. Controversy exists still about whether the group is monophyletic and the number of times flagella were lost among the group. The recent discovery that a chytrid may be implicated in amphibian decline on several continents, emphasized the confusion over the status and role of this organism and has highlighted the poor state of taxonomic knowledge of these fungi in general. The members of the chytrid consortium bring their individual expertise to this chytrid study.

Powell focuses her work on gathering and analyzing ultrastructural characters of the chytrid zoospores. Before the advent of molecular methods to study fungi, microscopists were able to use zoospore characters not only to distinguish chytrids from other flagellated organisms, but to define groups within the chytrid lineages.  In addition the suggestion of a choanoflagellate relationship to chytrids was first suggested by ultrastructural morphology.

The work of Porter focuses on the systematics of chytrids using molecular characters. Recent molecular phylogenetic analyses of 18S ribosomal DNA sequences from various members of the traditionally recognized "phycomycetes" have upheld the morphological data demonstrating the polyphyletic nature of this group, and have helped delimit a more natural assemblage of chytrid fungi. Porter and his colleagues now are working to define lineages within the group.

Longcore's strengths are her ability to isolate and culture members of the Chytridiomycota into pure culture, and her understanding of morphological and ultrastructural characters, which she has
gained from working with a number of colleagues, including Franz Lang and his associates, as a member of the Fungal Mitochondrial Genome Project. Her role lies in her ability to isolate and identify chytrids, essential for taxon sampling in studies that address questions on phylogeny by the application of molecular and ultrastructural characters.

Powell and Porter have been active in training students, more than half of whom are women. Both the graduate and undergraduate students trained remain active in biology.  Their current students include three African-American women, two of whom are graduate students, and Asian-American undergraduates. Longcore currently has two students, one of whom is a woman.

This proposal is important to the program of these chytrid workers, especially because of the basal position of some chytrids in Kingdom Fungi; the apparent polyphyly of the chytrids and interdigitation with zygomycete groups in the trees produced thus far requires that taxon sampling include zygomycete groups.

Selected publications
* Blackwell, W. H., and M. J. Powell. 1999. The nomenclatural propriety of Rhizophlyctis rosea. Mycotaxon 70: 213-218.
* Powell, M. J. 1993. Looking at mycology with a Janus face: A glimpse at Chytridiomycetes active in the environment.  Mycologia 85: 1-20.
* Powell, M. J., and S. Roychoudhury. 1992. Ultrastructural organization of Rhizophlyctis harderii zoospores and redefinition of the type 1 microbody-lipid globule complex.  Canad. J. Bot. 70: 750-761.
* Roychoudhury,  S., and M. J. Powell. 1992. Precise flagellar configuration of the Rhizophlyctis harderii zoospore. Canad. J. Bot. 70: 762-771.
* Powell, M. J. 1978. Phylogenetic implications of the microbody lipid globule complex in zoosporic fungi. BioSystems 10: 167-180.

* James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. Longcore. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Canad. J. Bot. 78:336-350.
* James, T. Y., D. Porter, J. L. Hamrick, and R. Vilgalys. 1999. Evidence for limited inter-   continental gene flow in the cosmopolitan mushroom, Schizophyllum commune. Evolution 53: 1665-1677.
* Doggett, M. S., and D. Porter. 1996. Fungal parasitism of Synedra acus (Bacillariophyceae) and the significance of parasite life history.  Euro. J. Protistol. 32: 490-497.
* Doggett, M. S., and D. Porter. 1996. Sexual reproduction in the fungal parasite Zygorhizidium planktonicum. Mycologia 88: 720-732.
* Leipe, D. D., P. Wainright, J. H. Gunderson, D. Porter, D. J. Patterson, F. Valois, S. Himmerich, and M. L. Sogin. 1994. The stramenopiles from a molecular perspective: 16S like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 33: 369-377.

* James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. E. Longcore. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Canad. J. Bot. 78: 336-350.
* Longcore, J. E. 1999. Batrachochytrium dendrobatidis gen. et sp. nov., a chytrid pathogenic to amphibians. Mycologia 91: 219-227.
* Nyvall, P., M. Pedersèn, and J. E. Longcore. 1999. Thalassochytrium gracilariopsidis (Chridiomycota), gen. et sp. nov., endosymiotic in Gracilariopsis sp. (Rhodophyceae). J. Phycol. 35: 176-185.
* Paquin, B., M.-J. Laforest, L. Forget, I. Roewer, W. Zhang, J. Longcore, and B. F. Lang. 1997. The Fungal Mitochondrial Genome Project: evolution of fungal mitochondrial genomes and their gene expression. Curr. Genet. 31: 380-395.
* Longcore, J. E. 1995. Morphology and zoospore ultrastructure of Entophlyctis luteolus sp. nov. (Chytridiales): implications for chytrid taxonomy. Mycologia 87: 25-33.

JACK D. ROGERS <http://plantpath.wsu.edu/person/rogers.htm#Rogers>
Rogers’ current studies entail mycobiotic, revisionary, and monographic studies in the Xylariaceae (Xylariales, Ascomycetes). Specific studies are: 1)  Field and laboratory work that will lead to a treatment of xylariaceous and some other pyrenomycetes in the Hawaiian Islands. 2)  A monograph of Nemania (with Y.-M. Ju). 3) Monographic studies in Xylaria. 4) Cooperative studies with Marc Stadler (Bayer Co., Germany) on secondary metabolites and their role in taxonomy of Xylariaceae. 5) Cooperative studies with Fernando Pelaez (Merck, Sharpe, & Dohme, Spain) on molecular aspects of systematics of Xylariaceae.

Rogers has worked all of his career on xylariaceous fungi based on morphological concepts, and he has numerous hypotheses based on his long-term research on the group.  The network will be important to him, because he would welcome the opportunity of cooperating with molecular-oriented and molecular-competent students to test the hypotheses.  He sees his role in a network as one who would furnish hypotheses, and morphological and field data; more importantly he has material already selected to test hypotheses in various ways, especially by molecular means.

Rogers has had an excellent record of training PhDs in plant pathology and mycology. He has trained at least five women who hold positions in agricultural departments in North America.  In addition he has trained several male hispanic students.

Selected publications
* Rogers, J. D., Y. M. Ju, and F. Candoussau. 1999. Biporispora europaea gen. et sp. nov., a new pyrenomycete from France. Nova Hedwegia 68: 421-424.
* Ju, Y. M., and J. D. Rogers. 1999. The Xylariaceae of Taiwan (excluding anthostomella). Mycotaxon 73: 343-440.
* Ju, Y. M., and J. D. Rogers. 1996. A revision of the genus Hypoxylon. APS Press. 365 pp.
* Rogers, J. D. 1994. Problem genera and family interfaces in the Eupyrenomycetes. p. 321-331. In: Ascomycete systematics: problems and perspectives in the nineties. Ed., Hawksworth, D. L. Plenum Press, NY.
* Rogers, J. D. 1979. The Xylariaceae: systematic, biological, and evolutionary aspects. Mycologia 71: 1-42.

GARY J. SAMUELS <http://nt.ars-grin.gov/SBMLweb/About/Staff/IndivInfo/Gary.htm>
Samuels is working on monographic studies of the Hypocreales (Ascomycetes). These fungi comprise some of the most conspicuous and common ascomycetes observed in natural forests at all latitudes, and they also are involved in diseases and toxicoses of plants and animals. The emphasis is on a monograpic study of one of the most speciose clades of this order that includes Hypocrea and Hypomyces. A major component of the group’s research is phylogenetic analysis using molecular characters in combination with characters derived from phenotype.

Development of a network of active researchers will be an important step in beginning to understand the phylogeny of all fungi, and only can a collaborative, committed group even consider such a feat. Samuels feels that from the point of view of integrating the taxonomy of 'fungi imperfecti' into the botanical system by the group, such an endeavor will reinforce the illogicality of maintaining separate systems and may guide us in modifying the International Code of Botanical Nomenclature to allow naming species in a single genus regardless of which morph, the sexual or the asexual morph, is represented in the type specimen.

Through an adjunct appointment at Pennsylvania State University and involvement in a PEET project, Samuels has helped to train three postdoctoral researchers, three graduate students, and an undergraduate student.  Among these trainees have been five women including an hispanic; one woman is from a former Soviet Block country.

Samuels is committed to the collaboration of the network and feels he will benefit through more interaction with those who use the techniques that he has recently begun to use.  Also, because he has interest in ascomycetes that parasitize basidiomycetes, that expertise will be readily available to identify hosts.

Selected publications
* Dodd, S., R.N. Crowhurst, A.G. Rodrigo, G.J. Samuels, R.A. Hill, and A. Stewart. 2000. Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data.  Mycol. Res. 104: 23-34.
* Samuels, G.J., O. Petrini, K. Kuhls, E. Lieckfeldt, and C.P. Kubicek. 1998. The Hypocrea schweinitzii complex and Trichoderma sect. Longibrachiatum. Stud. Mycol. 41: 1-54.
* Kindermann J, El-Ayouti Y, Samuels GJ, Kubicek CP. 1998. Phylogeny of the Genus Trichoderma Based on Sequence Analysis of the Internal Transcribed Spacer Region 1 of the rDNA Cluster.  Fungal. Genet. Biol. 24:298-309.
* Kuhls, K., E. Lieckfeldt, G.J. Samuels, T. Börner, W. Meyer, and C.P. Kubicek. 1997. Revision of Trichoderma sect. Longibrachiatum including related teleomorphs based on analysis of ribosomal DNA internal transcribed spacer sequences. Mycologia 89: 442-460.
* Rehner, S.A., and G.J. Samuels.  1995. Molecular systematics of the Hypocreales: a teleomorph gene phylogeny and the status of their anamorphs. Canad. J. Bot. 73: S816-S823.

EMORY G. SIMMONS <http://www.wabash.edu/magazine/1999/FallWinter/answers/emory_simmons.htm>
Simmons was former head of mycology, U.S. Army Natick Research Laboratory, who later was at the University of Massachusetts. He works daily from his home to produce detailed descriptions and identification materials of microscopic fungi.  For example he currently is devoting himself to Alternaria, a group of asexual spinoffs of some of the loculoascomycetes.  As can be judged from the number of themes and variations of his papers, there are many many names in Alternaria. Although Simmons’ sole-authored papers might lead one to believe he has few colleagues, the opposite is true. He has many colleagues and correspondents that contribute cultures or material from which he isolates alternarias for study.

He will benefit from the group by being involved with mycologists who use molecular techniques, and he would be able to provide well characterized material for DNA extraction.  Simmons has participated in teaching workshops, most recently the NSF sponsored workshop held in conjunction with the Latin American Mycological Congress in Caracas.

Selected publications
* Simmons, E. G. 1999. Alternaria themes and variations (236-243) - Host-specific toxin producers. Mycotaxon 70: 325-369.
* Simmons, E. G. 1999. Alternaria themes and variations (226-235) - Classification of citrus pathogens. Mycotaxon 70: 263-323.
* Simmons, E. G. 1998. Multiplex conidium morphology in species of the Ulocladium atrum group. Canad. J. Bot. 76: 1533-1539.
* Simmons, E. G. 1998. Alternaria themes and variations (224-225). Mycotaxon 68: 417-427.
* Simmons, E. G. 1997. Alternaria themes and variations (151-223). Mycotaxon 65: 1-91.

RYTAS VILGALYS <http://www.botany.duke.edu/fungi/mycolab/default.htm>
Vilgalys uses the techniques of molecular biology as well as more conventional approaches (culturing, mating studies, etc.) to answer questions about the natural history of fungi. His current research is focused on three areas:  1) phylogenetic biology and systematics, especially of the Agaricales (mushrooms);  2) the genetics of speciation, including patterns of morphological vs. genetic divergence, and analysis of the genetic factors underlying development of intersterility between related species; and 3) population biology of fungi, estimation of breeding systems and measurement of gene flow in natural populations. Fungi currently under investigation include the oyster mushroom (Pleurotus ostreatus) as well as several species of medically important fungi (Candida albicans and Cryptococcus neoformans)

The major research effort in his laboratory for the last ten years has been aimed at understanding molecular evolution of ribosomal RNA genes in fungi, and their use for estimating evolutionary relationships of the higher Basidiomycotina. Vilgalys and his colleagues are surveying rDNA sequence variation from various families of the Agaricales (mushrooms) and related fungi.
Saprobic basidiomycetes also offer an excellent system for studying the meaning of "what is a species" in fungi. This research combines the study of morphology, mating behavior, genetics and molecular systematics to try and understand how species differ and how they evolve. Mating compatibility studies have repeatedly demonstrated strong intersterility barriers among most species. Previous studies on DNA-level variation in the mushroom Collybia dryophila revealed a surprisingly high degree of genetic divergence associated with speciation among intersterility groups. More recently, Vilgalys’ studies of speciation in the oyster mushroom genus Pleurotus have examined the importance of biogeography as a primary factor associate with speciation.

At the molecular level, genomes of mushroom species also appear to 'turn over' more rapidly than other eukaryotes. Vilgalys employs molecular approaches to study genetic mechanisms which may operate during speciation. These methods include the use of DNA restriction fragment polymorphisms (RFLPs) and Amplified Fragment Length Polymorphisms (AFLP) to estimate genetic diversity and along with electrophoretic karyotyping, as well as more conventional methods based on mating compatibility studies. One of the current objectives of this research will be to develop a generalized model for genome evolution in Basidiomycotina and its role in the development of intersterility barriers (speciation). Unique features of fungal life histories have profound relevance for their population biology. They have been investigating the significance of mating systems and life history for determining genetic structure using molecular markers, both in wild mushroom species (Pleurotus ostreatus and Schizophyllum commune) as well as in several human pathogenic fungi (Candida albicans and Cryptococcus neoformans, in collaboration with Dr. Thomas G. Mitchell of the Duke University Medical Center). A variety of approaches and markers are being employed to addresses questions ranging from how far do spores disperse, to how much clonality vs. recombination occurs in natural populations.

Vilgalys has trained a number of students and postdoctoral associates, including several women. Undergraduate students often are included in the research.

The network is important to Vilgalys and his colleagues because they work on a wide variety of taxa, and the additional breadth supplied by the other members within the broad taxonomic categories would be especially helpful for several of the current students. He collaborates with a number of the other network members, including Porter, Hibbett, and Bruns.

Selected publications
* Moncalvo, J. M., F. M. Lutzoni, S. A. Rehner, J. Johnson, and R. Vilgalys. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst. Biol. 49: 278-305.
* James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. Longcore. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Canad. J. Bot. 78: 336-350.
* James, T. Y., D. Porter, J. L. Hamrick, and R. Vilgalys. 1999. Evidence for limited inter-   continental gene flow in the cosmopolitan mushroom, Schizophyllum commune. Evolution 53: 1665-1677.
* Pringle, A., J. M. Moncalvo, and R. Vilgalys. 2000. High levels of variation in ribosomal DNA sequences within and among spores of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica. Mycologia 92: 259-268.
* Hopple, J. S., and R. Vilgalys. 1999. Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: Divergent domains, outgroups, and monophyly. Mol. Phylogenet. Evol. 13: 1-19.