Mycologia
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DOI: 10.3852/mycologia.98.6.829
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Mycologia, 98(6), 2006, pp. 829-837.
© 2006 by The Mycological Society of America

Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha)


Meredith Blackwell 1

     Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803

David S. Hibbett

     Department of Biology, Clark University, Worcester, Massachusetts 01610

John W. Taylor

     Department of Plant and Microbial Biology, University of California, Berkeley, California 94720

Joseph W. Spatafora

     Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331

    ABSTRACT
 TOP
 ABSTRACT
 The growth of fungal...
 Deep Hypha accomplishments.--
 Work remaining.--
 Classification.--
 LITERATURE CITED
 

Research in fungal phylogenetics and systematics progressed rapidly in the past decade due to advances in DNA sequencing technologies and analytical methods. A newfound wealth of sequence data acquired through community-wide initiatives has advanced the process of acquiring a stable phylogenetic classification of many fungal taxa. Financial support from the National Science Foundation Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha) for 5 y enabled more than 100 fungal systematists to assess the taxon sampling, molecular markers and analytical methods necessary to facilitate such a project. Later a second NSF program provided financial support for the Assembling the Fungal Tree of Life (AFTOL) project to accomplish much of the research. Deep Hypha may be viewed as an involved parent of AFTOL with a continuing role as coordinator of likeminded workers. Many questions posed at the beginning of the Deep Hypha project have been addressed, at least in part, although some details remain to be clarified. Many of the main branches of the fungal tree are stable and well supported, often as a result of multigene analyses that involved collaboration of many laboratories. More work is necessary, however, to resolve certain branching events near the base of the tree, as well as to reconstruct relationships in some terminal groups. The phylogenetic classification in this issue of Mycologia is a product of the AFTOL project and many other independent research initiatives, and it is an initial synthesis of a working classification designed to be used for all major publications that require a phylogenetic classification of fungi.

Key words: mycological community, mycota, systematics

Fungi have a profound impact on global ecosystems. They modify our habitats and are essential for many ecosystem functions. Fungi form soil, recycle nutrients, decay wood, enhance plant growth and cull plants from their environment. They feed us, poison us, parasitize us and cure us. They destroy our crops, homes and libraries, but they also produce valuable biochemicals, such as ethanol and antibiotics. For both practical and intellectual reasons it is important to provide a phylogeny of Fungi on which a classification can be firmly based. The Deep Hypha Research Coordination Network, supported by the United States National Science Foundation (NSF), promoted and facilitated the cooperation necessary for the mycological community to construct a comprehensive phylogeny of the Fungi. Although Deep Hypha did not support data collection, it provided an essential forum for fungal systematists to plan, coordinate and report their activities. One initiative that grew out of Deep Hypha was the NSF-supported Assembling the Fungal Tree of Life project (AFTOL), which provided money to develop multilocus molecular and morphological datasets for the entire kingdom. As the articles in this Deep Hypha issue of Mycologia attest, AFTOL and other recent independent projects, helped directly or indirectly by Deep Hypha, have dramatically enhanced our understanding of fungal phylogeny. In this mission, Deep Hypha has been a success. As a gauge of progress in the field one may consider the growth of fungal systematics through the latter half of the 20th century, as reflected in the successive volumes of Introductory Mycology by C.J. Alexopoulos and colleagues (Alexopoulos 1952Go, 1962Go; Alexopoulos and Mims 1979Go; Alexopoulos, Mims, Blackwell 1996Go).


    The growth of fungal phylogenetics seen through Alexopoulos’s Introductory Mycology.—
 TOP
 ABSTRACT
 The growth of fungal...
 Deep Hypha accomplishments.--
 Work remaining.--
 Classification.--
 LITERATURE CITED
 
The intent of Alexopoulos’s Introductory Mycology has always been to be organized phylogenetically, as far as possible. The first edition (Alexopoulos 1952Go) began with bacteria, including actinomycetes, and a modern concept of prokaryotic cells and their structure was lacking. The second edition (Alexopoulos 1962Go) omitted bacteria but included for the first time Labyrinthulales, Hyphochytridiomycetes [sic] and Trichomycetes. These groups are still included in the latest edition of the text but mostly removed from a monophyletic concept of fungi with the exception of some Trichomycetes. As will be seen below some members of these of groups have come back into consideration as protists that are in a position basal to fungi and animals. Alexopoulos was concerned particularly about the placement of slime molds, and although they are excluded from fungi their position continues to be somewhat unsettled. The third edition (Alexopoulos and Mims 1979Go) had a new look with the addition of electron micrographs, the revolutionary technique of the time. Classification, still problematic, included slime mold groups within Fungi but separated them in a different subdivision. Oomycetes and chytrids also were placed in separate subdivisions, and Deuteromycotina was a group equal to but distinct from zygomycetes, ascomycetes and basidiomycetes.

In 1993 Charles Mims and Meredith Blackwell revised the text to provide a fourth edition (1996). For a book with a phylogenetic arrangement the timing of the revision was arguably less than optimum, because results from DNA-based phylogenetic studies were just appearing. In fact the text was sent to the printer with a multitude of additions in the "blue line" stage because of the appearance of new papers and graciously contributed unpublished studies that helped to establish the bare bones of a molecular phylogeny, which endured fairly well despite heavy reliance on a single gene, SSU rDNA. A phylogeny was presented in a series of unresolved trees that required the use of informal names for numerous taxonomic groups. The text however did use for the first time the term "phylum", newly sanctioned by the revised International Code of Botanical Nomenclature from the Tokyo Botanical Congress, and as such served as a transition between the old and the new, with hints of many changes to come. The monophyly of Fungi was established by separating four phyla from a number of excluded groups (water molds, labyrinthulids and several types of slime molds). Chytrids were placed firmly among Fungi, and the heterokont flagellates were unquestionably excluded. There were surprises: Pneumocystis was determined to be a fungus, Mixia was recognized as a basidiomycete and Saccharomyces and Schizosaccharomyces were shown to be widely separated. Evidence was available to recognize the polyphyly of groups such as gasteromycetes and polypores, and perhaps most important of all there was no phylogenetically defensible use of the class Deuteromycetes (Taylor 1995Go, Taylor et al 1999Go). There were however many intriguing unresolved questions: Is it possible that Basidiobolus is not a zygomycete? Are smuts and rusts not monophyletic? Do animals represent the sister group of fungi, or is the relationship more removed with fungi and animals sharing common ancestors?

Phylogenetic status of kingdom Fungi at the time of writing the Deep Hypha proposal. – A monophyletic kingdom Fungi had been defined when Deep Hypha began (Barr 1992Go, Bruns et al 1992Go) with our understanding of major subkingdom relationships summarized as follows:


    Deep Hypha accomplishments.—
 TOP
 ABSTRACT
 The growth of fungal...
 Deep Hypha accomplishments.--
 Work remaining.--
 Classification.--
 LITERATURE CITED
 
Mycologists were primed for the first NSF Assembling the Tree of Life competition (2002) thanks to the community-wide discussions on taxon sampling and methodology that had been supported by Deep Hypha. Working with the AFTOL consortium (and with much overlap in membership) many Deep Hypha participants focused on the same major loci, including the well characterized nuclear rRNA genes, and the protein-coding loci tef1 and rpb1 and rpb2, which had been promoted as molecular phylogenetic markers in Fungi by Hall and colleagues (Liu et al 1999Go). The coordinated sampling enabled construction of kingdomwide multigene datasets (Lutzoni et al 2004Go, James et al 2006Go). Several Deep Hypha symposia and workshops were held in conjunction with other meetings during the AFTOL funding period. The symposia and workshops promoted multigene, collaborative research in fungal phylogenetics, the use of state-of-the-art phylogenetic algorithms and fungal biology in broader scientific and educational communities. This Deep Hypha issue of Mycologia presents phylogenetic analyses of most major fungal clades, including many studies that were aided by Deep Hypha and that use data obtained in the AFTOL project. The articles included in this issue provide summaries of the status of the phylogenetic reconstruction for most of the major fungal lineages, although some clades (e.g. Polyporales, Laboulbeniomycetes) have been omitted. Some highlights follow.

The works described above will have a large impact on future textbooks and continuously updated Web-based educational materials, which will continue to increase in importance. Toward this end, Deep Hypha participants are involved in the Tree of Life Project <http://tolweb.org/tree/>, where biological information, including phylogenetic trees, soon will be available for each of the major fungal taxa discussed in this issue of Mycologia.


    Work remaining.—
 TOP
 ABSTRACT
 The growth of fungal...
 Deep Hypha accomplishments.--
 Work remaining.--
 Classification.--
 LITERATURE CITED
 
The base of the tree and the bare branches. – Questions about the base of the fungal tree remain, but fungi usually have been proposed to have a close relationship with animals (Baldauf et al 2000Go, Baldauf 2003Go, Baldauf and Palmer 1993Go, Embley and Martin 2006Go, Keeling 2003Go, Keeling et al 2000Go, Fast and Keeling 2005Go, Phillipe et al 2004, Ragan et al 1996Go, Steenkamp et al 2006Go, Wainright et al 1993), although the details of the basal radiation are not clear. When Deep Hypha began the major questions included: 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"? Are microsporidians fungi or merely closely related organisms?

Five years later these questions are only partially answered, largely because of long branches and incomplete taxon sampling. In addition, studies of physiology and biochemistry have not been addressed in a phylogenetic context. Members of Opistokontia (Animalia, Fungi and four protist allies, including Choanoflagellata, Ichthyosporea, Mesomycetozoea and Corallochytrea, Nuclearia and Ministeria) share an insertion of about 12 amino acids (positions 153–238) in the EF-1{alpha} protein sequence (Baldauf and Palmer 1993Go). Phylogenetic analysis of four combined nuclear protein-coding gene sequences includes opistokont protists as well as basal metazoans and fungi (Amaral-Zettler et al 2001Go, Medina et al 2003Go, Steenkamp 2006Go) and provides evidence that Nuclearia is the sister taxon of Fungi (Steenkamp 2006Go). Furthermore the establishment of the monophyly of Choanoflagellata indicates that these organisms could not have been an ancestor shared by animals and fungi, as has been suggested (Cavalier-Smith 1987Go). The data also reject other hypotheses, including groupings of plants and fungi (Philip et al 2005Go), and animals and plants (Löytynoja and Milinkovitch 2001Go).

Cienkowski (1865)Go, who studied a number of problematic organisms, including species of Amoebidium and labyrinthulids, also described Nuclearia. This is a genus of amoeboid protists with spherical bodies and radiating, rigid, filose pseudopodia; many species form walled cysts (Patterson 1984Go). These species are known from freshwater where they ingest algae and might be associated with aquatic animals, including fish. Environmental DNA samples indicate that members of the genus also might be present in marine environments (Bhattacharya and Oliveira 2000Go). Are we close to inferring the morphology of "first fungus"? If Steenkamp and colleagues (2006)Go are correct, we are getting close. One superficial problem however is the absence of a flagellum in Nuclearia, an apparent loss such as the one that has occurred within the main fungal lineage, or could the flagellum be present in an unconnected missing morphological state? Both possibilities were suggested.

The branch tips of the current tree are fairly bare and many taxa remain to be discovered and included in analyses. If the conservative estimate of 1 500 000 fungal taxa is used, as it continues to be, less than a 10th of the taxa in the kingdom have been discovered (Hawksworth 2004Go). Many of these taxa will come from field studies. Fungi from rapid radiations into a multitude of habitats continue to be discovered in large numbers in geographically distant localities or undercollected hidden habitats (Arnold et al 2001Go, Suh et al 2004Go, Vanderkoornhuyse et al 2002). Other taxa from previously described all inclusive taxa, especially those with few distinctive morphological traits, will be dissected out as cryptic taxa (Blackwell and Jones 1997Go, Fisher et al 2002, Kurtzman 2003Go). One other way we are increasing numbers of taxa is by applying phylogenetic species concepts. Use of this concept results in a better understanding of the biology of organisms, including dispersal and geographical and host relations (Cassar and Blackwell 1996Go, Moncalvo 2005Go, Taylor et al 2000Go).


    Classification.—
 TOP
 ABSTRACT
 The growth of fungal...
 Deep Hypha accomplishments.--
 Work remaining.--
 Classification.--
 LITERATURE CITED
 
The goal of synthesizing a uniform classification for kingdom Fungi was initiated at the Deep Hypha Arizona 2004 meeting and was designed as a collaborative effort with a number of mycologists. The authors of the Dictionary of the Fungi, individual authors of pages of the Tree of Life Web Project, the anticipated revision of the Alexopoulos textbook, GenBank and Myconet (www.fieldmuseum.org/myconet/) have agreed to use the classification. Many of the naming conventions applied to the classification of all fungi were those of Eriksson for Myconet. The overall goal of the classification was to produce a higher level phylogenetic classification of the Fungi by naming well supported clades. To do so, available higher level names sanctioned by the International Code of Botanical Nomenclature are employed for as many well supported clades as possible, and these names are used more consistently across the major phyla of Fungi (e.g. Ascomycota and Basidiomycota). The tree diagram (FIG. 1Go) is based on this classification and represents a working or draft consensus classification of the Fungi. A more complete classification is in preparation and will be published as a multi-authored manuscript (http://www.clarku.edu/faculty/dhibbett/AFTOL/AFTOL.htm). The classification presented here (FIG. 1Go) can be used as a guide to the groups discussed in this issue with the goal of producing a stable higher-level phylogenetic classification of Fungi.


Figure 1
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FIG 1. Phylogenetic tree diagram of members of kingdom Fungi. This tree is based on the phylogenetic studies of a number of mycologists. The project was originated by AFTOL and represents a first effort to provide an ordinal level phylogenetic classification to be used by all mycological publications. An expanded discussion of the classification is in preparation and will be published elsewhere. The most recent and archived earlier versions can be accessed at <http://www.clarku.edu/faculty/dhibbett/AFTOL/AFTOL.htm>. Also see the site for rules used in its construction.

 


    ACKNOWLEDGMENTS
 
We thank all our collaborators who participated in the Deep Hypha project. We acknowledge financing from the National Science Foundation (Research Coordination Networks in Biological Sciences: a phylogeny for Kingdom Fungi, NSF- 0090301 to M. Blackwell, J.W. Spatafora and J.W. Taylor. We appreciate the commitment of James E. Rodman to promote systematics and encourage mycology for the past 25 y. We dedicate this paper to him.


    FOOTNOTES
 
Accepted for publication November 12, 2006.

1 Corresponding author. E-mail: mblackwell{at}lsu.edu


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