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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 |
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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 1952
, 1962
; Alexopoulos and Mims 1979
; Alexopoulos, Mims, Blackwell 1996
).
| The growth of fungal phylogenetics seen through Alexopouloss Introductory Mycology. |
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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 1995
, Taylor et al 1999
). 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 1992
, Bruns et al 1992
) with our understanding of major subkingdom relationships summarized as follows:
| Deep Hypha accomplishments. |
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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. |
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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 153238) in the EF-1
protein sequence (Baldauf and Palmer 1993
). Phylogenetic analysis of four combined nuclear protein-coding gene sequences includes opistokont protists as well as basal metazoans and fungi (Amaral-Zettler et al 2001
, Medina et al 2003
, Steenkamp 2006
) and provides evidence that Nuclearia is the sister taxon of Fungi (Steenkamp 2006
). 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 1987
). The data also reject other hypotheses, including groupings of plants and fungi (Philip et al 2005
), and animals and plants (Löytynoja and Milinkovitch 2001
).
Cienkowski (1865)
, 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 1984
). 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 2000
). Are we close to inferring the morphology of "first fungus"? If Steenkamp and colleagues (2006)
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 2004
). 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 2001
, Suh et al 2004
, 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 1997
, Fisher et al 2002, Kurtzman 2003
). 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 1996
, Moncalvo 2005
, Taylor et al 2000
).
| Classification. |
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| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Corresponding author. E-mail: mblackwell{at}lsu.edu
| LITERATURE CITED |
|---|
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|
|---|
. 1962. Introductory Mycology. New York: John Wiley & Sons.
, Mims CW. 1979. Introductory Mycology. New York: John Wiley & Sons.
, , Blackwell M. 1996. Introductory Mycology. New York: John Wiley & Sons. 869 p.
Amaral-Zettler LA, Nerad TA, OKelly CJ, Sogin ML. 2001. The nucleariid amoebae: more protists at the animal-fungal boundary. J Euk Microbiol 48:293297.[CrossRef][Medline]
Arnold AE, Maynard Z, Gilbert GS. 2001. Fungal endophytes in dicotyledonous neotropical trees: patterns of abundance and diversity. Mycol Res 105:15021507.[CrossRef]
Baldauf SL. 2003. The deep roots of eukaryotes. Science 300:17031706.
, Palmer JD. 1993. Animal and fungi are each others closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci USA 90:1155811562.
, Roger AJ, Wenk-Siefert I, Doolittle WF. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972977.[CrossRef][Medline]
Barr DJS. 1992. Evolution and kingdoms of organisms from the perspective of a mycologist. Mycologia 84:111.[CrossRef]
Bhattacharya D, Oliveira MC. 2000. The SSU rDNA coding region of a filose amoeba contains a Group I Intron lacking the universally conserved G at the 3'-terminus. J Eukaryot Microbiol 47:585589.[CrossRef][Medline]
Blackwell M, Jones KG. 1997. Taxonomic diversity and interactions of insect-associated ascomycetes. Biodiver Conserv 6:689699.[CrossRef]
Bowman BH, Taylor JW, Brownlee AG, Lee J, Lu S-D, White TJ. 1992. Molecular evolution of the fungi: relationship of the Basidiomycetes, Ascomycetes and Chytridiomycetes. Mol Biol Evol 9:285296.[Abstract]
Bruns TD, Vilgalys R, Barns SM, Gonzalez D, Hibbett DS, Lane DJ, Simon L, Stickel S, Szaro TM, Weisburg WG, Sogin ML. 1992. Evolutionary relationships within the Fungi: analyses of nuclear small subunit rRNA sequences. Mol Phylogen Evol 1:231241.[CrossRef][Medline]
Cassar SC, Blackwell M. 1996. Non-monophyly of ambrosia fungi in Ambrosiella. Mycologia 88:596601.[CrossRef]
Cavalier-Smith T. 1987. The origin of fungi and pseudo-fungi. In: Rayner ADM, Brasier CM, Moore D., eds. Evolutionary biology of fungi. Cambridge: Cambridge University Press. p 339353.
Cienkowski L. 1865. Beiträge zur Kenntnis der Monaden. Ark Microsk Anat I:203232. Pls. 1214.
Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature 440:623630.[CrossRef][Medline]
Fast NM, Keeling PJ. 2005. The fungal roots of microsporidian parasites. In: Vega FE, Blackwell M., eds. Insect-fungal associations. New York: Oxford Press. p 97118.
Fischer MC, Koenig GL, White TJ, Taylor JW. 2002. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia 94:7384.
Hawksworth DL. 2004. Fungal diversity and its implications for genetic resource collections. Stud Mycol 50:918.[Medline]
, Kirk PM, Sutton BC, Pegler DM. 1995. Ainsworth & Bisbys dictionary of the fungi. 8th ed. Egham: CAB International. 616 p.
James TY, Porter D, Leander CA, Vilgalys R, Longcore JE. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can J Bot 78:336350.[CrossRef]
, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G-H, Johnson D, ORourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schüßler A, Longcore JE, ODonnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lücking R, Büdel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818822.[CrossRef][Medline]
Keeling PJ. 2003. Congruent evidence from a-tubulin and b-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet Biol 38:298309.[CrossRef][Medline]
, Luker MA, Palmer JD. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol Biol Evol 17:2331.
Kurtzman CP. 2003. Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora.. FEMS Yeast Res 4:233245.[CrossRef][Medline]
Liu Y, Whelen S, Hall BD. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:17991808.[Abstract]
Löytynoja A, Milinkovitch MC. 2001. Molecular phylogenetic analysis of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited. Proc Natl Acad Sci USA 98:1020210207.
Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Hambleton S, Crockett M, Shoemaker R, Sung GH, Lucking R, Lumbsch T, ODonnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim YW, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R. 2004. Assembling the Fungal Tree of Life: progress, classification and evolution of subcellular traits. Am J Bot 91:14461480.
Medina M, Collins AG, Taylor JW, Valentine JW, Lipps JH, Amaral-Zettler L, Sogin ML. 2003. Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa. Int J Astrobiol 2:203211.[CrossRef]
Moncalvo J-M. 2005. Molecular systematics: major fungal phylogenic groups and fungal species concepts. In: Xu JP, ed. Evolutionary genetics of Fungi. Norfolk: Horizon Scientific Press. p 133.
Nagahama T, Sato H, Shimazu M, Sugiyama J. 1995. Phylogenetic divergence of the entomophthoralean fungi: evidence from nuclear 18S ribosomal RNA gene sequences. Mycologia 87:203209.[CrossRef]
Nishida H, Sygiyama J. 1994. Archiascomycetes: detection of a major new lineage within the ascomycota. Mycoscience 35:361366.[CrossRef]
Patterson DJ. 1984. The genus Nuclearia (Sarcodina, Filosea) species composition and diagnoses of the taxa. Arch Protistenkd 128:127139.
Philip GK, Creevey CF, McInerney JO. 2005. The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol Biol Evol 22:11751184.
Philippe H, Snell EA, Bapteste E, Lopez P, Holland PWH, Casane D. 2004. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol 21: 17401752.
Ragan MA, Goggin CL, Cawthorn RJ, Cerenius L, Jamieson AVC, Plourd SM, Rand TG, Soderhall K, Gutell RR. 1996. A novel clade of protistan parasites near the animal-fungal divergence. Proc Natl Acad Sci USA 93: 1190711912.
Redecker D, Morton JB, Bruns TD. 2000. Ancestral lineages of arbuscular mycorrhizal fungi (Glomales). Mol Phylogenet Evol 14:276284.[CrossRef][Medline]
Schüßler A, Scwarzott D, Walker C. 2001. A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105:14141421.
Simon L, Bousquet L, Levesque RC, Lalonde M. 1993. Origin and diversification of endomycorrhizal fungi and coincidence with vascular plants. Nature 363:6769.[CrossRef]
Steenkamp ET, Wright J, Baldauf SL. 2006. The protistan origins of animals and fungi. Mol Biol Evol 23:93106.
Suh S-O, McHugh JV, Blackwell M. 2004. Expansion of the Candida tanzawaensis yeast clade: 16 novel Candida species from basidiocarp-feeding beetles. Int J Syst Evol Microbiol 54:24092429.
Swann EC, Taylor JW. 1995. Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot 73:S862S868.
Taylor JW. 1995. Making the Deuteromycota redundant: a practical integration of mitosporic and meiosporic fungi. Can J Bot 73S:S754S759.[CrossRef]
, Bowman B, Berbee ML, White TJ. 1993. Fungal model organisms: phylogenetics of Saccharomyces, Aspergillus and Neurospora. System Biol 42:440457.[CrossRef]
, Jacobson DJ, Fisher MC. 1999. The evolution of asexual fungi: reproduction, speciation and classification. An Rev Phytopathol 37:197246.[CrossRef]
, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and concepts in Fungi. Fungal Genet Biol 31:2132.[CrossRef][Medline]
Taylor TN, Remy W, Hass H, Kerp H. 1995. Fossil arbuscular mycorrhizae from the lower Devonian. Mycologia 87: 560573.[CrossRef]
Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPJW. 2002. Extensive fungal diversity in plant roots. Science 295:2051.
Wainwright PO, Hinkle G, Sogin ML, Stickel SK. 1993. Monophyletic origins of the Metazoa: an evolutionary link with the Fungi. Science 260:340342.
Wells K. 1994. Jelly fungi, then and now! Mycologia 86:1848.[CrossRef]
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