Traditionally, fungi have been grouped into taxonomic hierarchies based on their reproductive characters. This has led to the establishment of two nomenclatures for one evolutionary past. One nomenclature recognizes the asexual states (anamorphs) and the other recognizing sexual states (teleomorphs). My primary interest has been the evaluation of anamorphic and teleomorphic characters and molecular data to reconstruct morphological evolution. The taxonomic group that I have done most of my work on is the family Clavicipitaceae in the order Hypocreales (Ascomycetes). Clavicipitaceae is a pantropical and subtropical group that are pathogens of arthropods, angiosperms, myxomycetes and other ascomycetes and symbionts of some angiosperms. The broad range of host substrates contained in this family have also provided me with the opportunity to study host shifts that have occurred during the evolutionary past. I am currently focusing on clavicipitaleans of the neotropics that I have collected in Costa Rica, Guyana, and Panama. My main research topics are:

• Morphological evolution of Clavicipitaceae – using morphological and sequence data to develop phylogenetic hypotheses and evaluate the phylogenetic information contained within each morphological character.

• Reconstruction of host substrate shifts in Clavicipitaceae – using morphological, sequence, host substrate and niche data to determine where in the family’s evolutionary past, host kingdom shifts have occurred and developed.

• Identification of molecular markers that may be diagnostic for monophyletic groups in Clavicipitaceae and other groups – using ribosomal secondary structure data to align ribosomal DNA (rDNA) sequences and investigate synapomorphic insertions and deletions (indels).

• Develop a phylogenetically based nomenclature – The previous three research topics provide the framework for the identification of diagnostic tools that will be used to recognize monophyletic fungal groups and develop a nomenclature that represents the common evolutionary past shared by anamorphic and teleomorphic fungi.

Morphological Evolution

Diehl had proposed three subfamilies in Clavicipitaceae. He further broke the subfamily Clavicipitoideae into three tribes based on based on the anamorphic states of species within each tribe. He considered species with a Sphecilia Lév. anamorphic state to belong to the tribe Clavicipitae. All species in this tribe belonged to the teleomorphic genus Claviceps Tul. The second tribe Balansiae, whose members produced an Ephelis Fr. anamorph were linked to the teleomorphic genera Balansia Speg. and Atkinsonella Diehl. The monophyly of both of these tribes have been supported by my data and previous investigators. Furthermore, my data support the monophyly of Diehl’s third tribe Ustilaginoideae (Bischoff et al., in prep).

While Diehl’s work in 1950 has influenced my own, I have tried to broaden its application. The most speciose genus in Clavicipitaceae is Cordyceps (Fr.) Link. Cordyceps is distinguished from other members of Clavicipitaceae based on an insect or fungal host substrate and a stipitate perithecial stroma. However, species in this genus have been linked to various anamorphic states and have been determined to be paraphyletic. My preliminary data suggests that stipitate perithecial stroma is a homoplastic character in the family and misleading when used as a diagnostic character. My investigations with large subunit (LSU) rDNA and morphological data suggest that anamorphic states may provide the additional informative characters needed for determining monophyletic groups in Clavicipitaceae. While investigating the anamorphic genus Polycephalomyces Kobayasi I found that the genus is likely monophyletic and can be linked to a particular clade containing Cordyceps insect pathogens (Bischoff et al., 2003).

I am currently studying other groups in Cordyceps, determining their anamorphic affinities and evaluating their phylogenetic placement. I intend to continue and expand this work to other groups in Clavicipitaceae and other Ascomycetes orders. Furthermore, I would be very interested in completely monographic works regarding Clavicipitaceae.

Host Substrate Shifts

The reconstruction of host substrate shifts that have occurred over the evolutionary past of Clavicipitaceae have been difficult to elucidate. This difficulty stems from the fact that particular fungal groups representing some of the host substrates utilized by clavicipitaleans are poorly represented in molecular databases. Furthermore, some hypotheses regarding their host specificity have been incorrectly identified. I have made an effort to collect and isolate species from these poorly represented groups. Careful study of these specimens in the field and evaluations of them upon returning to the laboratory have been informative. Previous studies have only tried to evaluate host shifting in Cordyceps between arthropod and fungal hosts. However, as stated above, Cordyceps is a paraphyletic group and the taxa only represent a portion of the diversity in the family. By including previously poorly represented taxa in analyses, my preliminary data suggests that their may have been one kingdom host jump from insect to plant substrates and one insect to fungal shift in pathogenicity. Furthermore, the host shifts appear to reflect the classic coevolution theory of pathogenic necrotrophs (kills the host) to pathogenic biotrophs (obligate) to symbiosis. Continued study of these groups and the addition of more collections will help us resolve these host shifting with greater confidence and may provide evidence as to what environmental niches provide the avenue for these shifts to occur.

Diagnostic Molecular Markers

There has been a tremendous push in molecular systematics for the inclusion of more and more genes to be used for phylogenetic hypotheses. While the value of more data cannot be argued, I feel that this enormous influx has come at a price (beyond the financial cost) to systematic evaluations. Computer programs have been designed to align molecular data with the use of a gap to change cost ratio. A systematist can then push a few buttons and in a relatively short time have an alignment. Many systematists do not completely trust in these alignments (for good reason) and make manual adjustments by eye. However, by using ribosomal DNA (rDNA) and ribosomal secondary structure data I avoid the subjectivity that is inherent in alignment programs. By identifying stems and loops I properly delimit ambiguous regions and recognize indels (insertions and deletions). This evidence based method is currently the best way to be sure that you are comparing homologous characters. In addition, I have used this method to determine indel (insertion and deletion) locations that are specific to particular groups and may be used as diagnostic characters for monophyletic groupings. This has been very helpful in a project that is outside of my dissertation work regarding Phoma. Phoma is a paraphyletic anamorphic genus containing over 2000 species that have been linked to five families and four orders in Ascomycota. Other investigators have worked to determine morphological synapomorphies that can be used to place species of Phoma into distinct monophyletic groups. However, these methods require a great deal of morphological investigation including sectioning and ultrastructure studies. Preliminary evidence supports the use of particular ribosomal stems that can be used as diagnostic characters. I feel this method is especially important for groups that show a tremendous amount of morphological convergence making diagnosis extremely difficult. I will also investigate the occurrence of diagnostic indels for the determination of monophyletic groups in Clavicipitaceae.

Development of One Phylogenetically Based Nomenclature

Traditionally, fungi have been grouped into hierarchies based on their reproductive morphological characters. However, because many fungi, especially in the Ascomycetes, have both a sexual (teleomorphic) and asexual (anamorphic) state that may be separated by time and/or space mycology has two nomenclature. It is my intention during the course of my career to work towards the fusion these nomenclatures. This research interest is not mine alone and can not be accomplished by any one fungal systematist. The acceptance of one name for one organism must to be embraced by mycology as a whole if this is to be accomplished. However, the research interests that I have discussed above provide a framework for connecting these two nomenclatures into one phylogenetically based nomenclature. By linking the teleomorphic and anamorphic morphological characters that make up a fungal species we can recognize that organism in its complete life cycle. Definitive linkages are made through the isolation of one morph in culture and getting it to produce the other morph in the same culture. Another method of linking two morphs is by sequencing them (usually the internal transcribed sequences of the ribosomal DNA) and looking for congruence. If both morphs can not be found or developed in culture then the diagnostic sequence indels could be used as the characters needed to place the strain into the group with which it shares a most recent common ancestor. Furthermore, if we can determine how and where host substrate shifts are most likely to occur we may be able to avoid the taxonomic placement of organisms based on their host substrate as is often seen in fungal taxonomy. By taxonomically placing these organisms into monophyletic groups we will create a nomenclature that is based on the shared evolutionary history of these organisms.

Other Projects

There is a tremendous need for alpha taxonomy in mycology. It was conservatively estimated in 1991 that a mere 5% of the planet’s fungal diversity is known. This estimate was extrapolated from the ratio of fungi associated with plants and plant species known in the United Kingdom. This is likely an underestimate because it does not consider fungi associated with other organisms and does not represent the diversity that is found in the tropics. Barro Colorado Island (BCI) in Panama offers an excellent opportunity to develop estimates of fungal biodiversity. BCI is the most well study tropic forest in the world, complete with plant and animal (excluding arthropods) species lists.

Recently, I was awarded a grant to study the biodiversity of soil and detritus fungi of BCI. This initial study will certainly provide new species and likely new genera but will also be a step towards elucidating the fungal diversity of BCI. I intend to continue biodiversity studies at BCI and develop fungal diversity estimates that take these hyper-diverse ecosystems into consideration.