Mycologia, 98(6), 2006, pp. 829–837.

# 2006 by The Mycological Society of America, Lawrence, KS 66044-8897

Issued 13 April 2007

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

Meredith Blackwell1 publications that require a phylogenetic classification

Department of Biological Sciences, Louisiana State of fungi.
University, Baton Rouge, Louisiana 70803 Key words: mycological community, mycota,
David S. Hibbett systematics
Department of Biology, Clark University, Worcester, Fungi have a profound impact on global ecosys-
Massachusetts 01610 tems. They modify our habitats and are essential for
many ecosystem functions. Fungi form soil, recycle
John W. Taylor nutrients, decay wood, enhance plant growth and cull
Department of Plant and Microbial Biology, University plants from their environment. They feed us, poison
of California, Berkeley, California 94720
us, parasitize us and cure us. They destroy our crops,
Joseph W. Spatafora homes and libraries, but they also produce valuable
Department of Botany and Plant Pathology, Oregon biochemicals, such as ethanol and antibiotics. For
State University, Corvallis, Oregon 97331 both practical and intellectual reasons it is important
to provide a phylogeny of Fungi on which a classifica-
tion can be firmly based. The Deep Hypha Research
Abstract: Research in fungal phylogenetics and Coordination Network, supported by the United
systematics progressed rapidly in the past decade States National Science Foundation (NSF), promoted
due to advances in DNA sequencing technologies and and facilitated the cooperation necessary for the
analytical methods. A newfound wealth of sequence mycological community to construct a comprehensive
data acquired through community-wide initiatives has phylogeny of the Fungi. Although Deep Hypha did
advanced the process of acquiring a stable phyloge- not support data collection, it provided an essential
netic classification of many fungal taxa. Financial forum for fungal systematists to plan, coordinate and
support from the National Science Foundation Re- report their activities. One initiative that grew out of
search Coordination Networks: a phylogeny for Deep Hypha was the NSF-supported Assembling the
kingdom Fungi (Deep Hypha) for 5 y enabled more Fungal Tree of Life project (AFTOL), which provided
than 100 fungal systematists to assess the taxon money to develop multilocus molecular and morpho-
sampling, molecular markers and analytical methods logical datasets for the entire kingdom. As the articles
necessary to facilitate such a project. Later a second in this Deep Hypha issue of Mycologia attest, AFTOL
NSF program provided financial support for the and other recent independent projects, helped di-
Assembling the Fungal Tree of Life (AFTOL) project rectly or indirectly by Deep Hypha, have dramatically
to accomplish much of the research. Deep Hypha enhanced our understanding of fungal phylogeny. In
may be viewed as an involved parent of AFTOL with this mission, Deep Hypha has been a success. As
a continuing role as coordinator of likeminded a gauge of progress in the field one may consider the
workers. Many questions posed at the beginning of growth of fungal systematics through the latter half of
the Deep Hypha project have been addressed, at least the 20th century, as reflected in the successive
in part, although some details remain to be clarified. volumes of Introductory Mycology by C.J. Alexopoulos
Many of the main branches of the fungal tree are and colleagues (Alexopoulos 1952, 1962; Alexopoulos
stable and well supported, often as a result of and Mims 1979; Alexopoulos, Mims, Blackwell 1996).
multigene analyses that involved collaboration of
many laboratories. More work is necessary, however, The growth of fungal phylogenetics seen through
to resolve certain branching events near the base of Alexopoulos’s Introductory Mycology.—The intent
the tree, as well as to reconstruct relationships in of Alexopoulos’s Introductory Mycology has always
some terminal groups. The phylogenetic classification been to be organized phylogenetically, as far as
in this issue of Mycologia is a product of the AFTOL possible. The first edition (Alexopoulos 1952) began
project and many other independent research in- with bacteria, including actinomycetes, and a modern
itiatives, and it is an initial synthesis of a working concept of prokaryotic cells and their structure was
classification designed to be used for all major lacking. The second edition (Alexopoulos 1962)
omitted bacteria but included for the first time
Labyrinthulales, Hyphochytridiomycetes [sic] and
Accepted for publication 12 November 2006. Trichomycetes. These groups are still included in
1
Corresponding author. E-mail: [email protected] the latest edition of the text but mostly removed from

829
830 MYCOLOGIA

a monophyletic concept of fungi with the exception removed with fungi and animals sharing common
of some Trichomycetes. As will be seen below some ancestors?
members of these of groups have come back into
consideration as protists that are in a position basal to Phylogenetic status of kingdom Fungi at the time of
fungi and animals. Alexopoulos was concerned writing the Deep Hypha proposal. A monophyletic
particularly about the placement of slime molds, kingdom Fungi had been defined when Deep Hypha
and although they are excluded from fungi their began (Barr 1992, Bruns et al 1992) with our
position continues to be somewhat unsettled. The understanding of major subkingdom relationships
third edition (Alexopoulos and Mims 1979) had a new summarized as follows:
look with the addition of electron micrographs, the N Four phyla generally were accepted in kingdom
revolutionary technique of the time. Classification, Fungi: Chytridiomycota, Zygomycota, Basidiomy-
still problematic, included slime mold groups within cota and Ascomycota (Alexopoulos et al 1996, Barr
Fungi but separated them in a different subdivision. 1992, Bowman et al 1992, Bruns et al 1992,
Oomycetes and chytrids also were placed in separate Hawksworth et al 1995).
subdivisions, and Deuteromycotina was a group equal N The phyla Chytridiomycota and Zygomycota were
to but distinct from zygomycetes, ascomycetes and not supported as monophyletic and intergraded at
basidiomycetes. several points based on analyses of the SSU rDNA
In 1993 Charles Mims and Meredith Blackwell (Nagahama et al 1995, James et al 2000).
revised the text to provide a fourth edition (1996). N The Chytridiomycota was the only taxon within
For a book with a phylogenetic arrangement the kingdom Fungi to include representatives with
timing of the revision was arguably less than a flagellated stage at some point in their life cycle,
optimum, because results from DNA-based phyloge- and analyses agreed that some lineage of the
netic studies were just appearing. In fact the text was Chytridiomycota occupied the most basal branch
sent to the printer with a multitude of additions in the of kingdom Fungi, a finding consistent with
‘‘blue line’’ stage because of the appearance of new a choanoflagellate ancestor; however there was
papers and graciously contributed unpublished stud- conflict in the literature as to which group of the
ies that helped to establish the bare bones of Chytridiomycota was most basal ( James et al 2000).
a molecular phylogeny, which endured fairly well N The Chytridiomycota was paraphyletic, largely de-
despite heavy reliance on a single gene, SSU rDNA. A fined by the ancestral character state of a smooth
phylogeny was presented in a series of unresolved posterior flagellum. The Zygomycota was suspected
trees that required the use of informal names for of being polyphyletic with multiple origins within
numerous taxonomic groups. The text however did kingdom Fungi. Based on rDNA, at least one origin
use for the first time the term ‘‘phylum’’, newly was derived from within the Chytridiomycota,
sanctioned by the revised International Code of representing the loss of the flagellum; however
Botanical Nomenclature from the Tokyo Botanical this was contradicted by analysis of b-tubulin
Congress, and as such served as a transition between sequences (Keeling et al 2000, James et al 2000).
the old and the new, with hints of many changes to N At the other extreme, the Glomerales (until then
come. The monophyly of Fungi was established by considered a member of Zygomycota) appeared
separating four phyla from a number of excluded more closely related to the Ascomycota/Basidio-
groups (water molds, labyrinthulids and several types mycota clade (Simon et al 1993) based on rDNA.
of slime molds). Chytrids were placed firmly among N The larger clade comprising the Glomerales,
Fungi, and the heterokont flagellates were unques- Ascomycota and Basidiomycota was referred to as
tionably excluded. There were surprises: Pneumocystis ‘‘crown’’ fungi; ‘‘crown’’ fungi were supported as
was determined to be a fungus, Mixia was recognized a derived, higher monophyletic taxon within the
as a basidiomycete and Saccharomyces and Schizosac- Fungi, originated and diversified along with land
charomyces were shown to be widely separated. plants (Redecker et al 2000, Simon et al 1993,
Evidence was available to recognize the polyphyly of Taylor et al 1995).
groups such as gasteromycetes and polypores, and N The Basidiomycota and Ascomycota each were
perhaps most important of all there was no phyloge- monophyletic and together formed the most
netically defensible use of the class Deuteromycetes derived fungal clade (Bowman et al 1992, Bruns
(Taylor 1995, Taylor et al 1999). There were however et al 1992) that comprised more than 95% of all
many intriguing unresolved questions: Is it possible known fungi. Higher-level relationships within
that Basidiobolus is not a zygomycete? Are smuts and both the Ascomycota and Basidiomycota were
rusts not monophyletic? Do animals represent the tenuous.
sister group of fungi, or is the relationship more N The Ascomycota generally was recognized to in-
 BLACKWELL ET AL: A PHYLOGENY FOR FUNGI 831

clude the classes Euascomycetes (mostly filamen- for deep nodes that have proved problematical
tous, sporocarp-producing and mitosporic or co- (e.g. monophyly of Agaricomycotina plus Ustilagi-
nidial forms), Saccharomycetes (the true yeasts), nomycotina, and monophyly of Dimargaritales plus
and Archiascomycetes (a paraphyletic assemblage Trichomycetes s.s.).
of basal taxa) (Nishida and Sugiyama 1994, Taylor N James et al: The Chytridiomycota is not mono-
et al 1993). phyletic. Fourteen clades, including a core group
N The Basidiomycota generally was recognized to of the traditional chytrids, are defined; these
include three classes: Urediniomycetes (rusts and clades have a paraphyletic relationship to other
relatives), Ustilaginomycetes (smuts) and Hyme- flagellated fungi, notably Blastocladiales, many of
nomycetes (mushrooms and relatives) (Swann and which have distinctive life cycles with sporic
Taylor, 1995, Wells 1994). meiosis. Olpidium also falls outside the other
N To that date, the lion’s share of phylogenetic chytrids.
studies had been performed on nucleotide data N White et al: The Zygomycota as previously recog-
determined from nuclear rDNA (Alexopoulos et al nized is not a monophyletic group. Two trichomy-
1996). cete groups no longer are considered to be fungi
and the remaining traditional members have
Deep Hypha accomplishments.— Mycologists were a paraphyletic relationship. Basidiobolus, tentative-
primed for the first NSF Assembling the Tree of Life ly suggested to be a chytrid by SSU rDNA data,
competition (2002) thanks to the community-wide appears as a sister of the Entomophthorales with
discussions on taxon sampling and methodology that increased taxon sampling and use of a multigene
had been supported by Deep Hypha. Working with dataset.
the AFTOL consortium (and with much overlap in N Redecker and Raab: Glomeromycota is accepted as
membership) many Deep Hypha participants focused a sister group of Basidiomycota + Ascomycota
on the same major loci, including the well character- within kingdom Fungi on the basis of rDNA
ized nuclear rRNA genes, and the protein-coding loci analysis (Schüßler et al 2001). Some recent
tef1 and rpb1 and rpb2, which had been promoted as analyses including protein coding genes support
molecular phylogenetic markers in Fungi by Hall and monophyly of the phylum but also cast doubt on
colleagues (Liu et al 1999). The coordinated sam- the sister group relationship of these fungi with
pling enabled construction of kingdomwide multi- Dikaryomycota. With a two-gene dataset the Glo-
gene datasets (Lutzoni et al 2004, James et al 2006). meromycota is upheld as a monophyletic taxon
Several Deep Hypha symposia and workshops were with six major clades.
held in conjunction with other meetings during the N Aime et al: Pucciniomycotina (5Urediniomycetes)
AFTOL funding period. The symposia and workshops comprises the rusts, Pucciniales (5 Urediniales)
promoted multigene, collaborative research in fungal and related teliospore-producing taxa (e.g. Septo-
phylogenetics, the use of state-of-the-art phylogenetic basidiales, Sporidiales, etc.). The subphylum is
algorithms and fungal biology in broader scientific defined with eight major clades ranked as classes
and educational communities. This Deep Hypha issue (Agaricostilbomycetes, Atractiellomycetes, Classi-
of Mycologia presents phylogenetic analyses of most culomycetes, Cryptomycocolacomycetes, Cystobasi-
diomycetes, Microbotryomycetes, Mixiomycetes
major fungal clades, including many studies that were
and Pucciniomycetes) and eighteen orders.
aided by Deep Hypha and that use data obtained in
the AFTOL project. The articles included in this issue N Begerow et al: Ustilaginomycotina (5Ustilaginomy-
provide summaries of the status of the phylogenetic cetes) comprises the smuts, Ustilaginales and related
reconstruction for most of the major fungal lineages, taxa. Based on morphological, ultrastructural and
molecular phylogenetic data, Ustilaginomycotina is
although some clades (e.g. Polyporales, Laboulbenio-
defined with three classes, Entorrhizomycetes, Usti-
mycetes) have been omitted. Some highlights follow.
laginomycetes and Exobasidiomycetes, which collec-
N Taylor and Berbee: Estimating the evolutionary age tively comprise 11 orders.
of Fungi and the origin of its phyla and subphyla N Hibbett: Agaricomycotina (5Hymenomycetes),
remains an elusive goal, but new fossil findings and one of the three main subphyla of Basidiomycota,
improved analytical methods support an origin of includes Tremellomycetes, Dacrymycetes and Agar-
all extant phyla by the Devonian (Taylor et al icomycetes. Phragmobasidia are present in all
1995). three classes with holobasidia restricted to the
N Celio et al: Subcellular characters, especially Agaricomycetes. The Agaricomycetes includes
associated with septal ultrastructure, while few in eight major subclades that are recognized as
number, are providing important synapomorphies subclasses and orders and is characterized by high
832 MYCOLOGIA

levels of homoplasy associated with all major teoid and plicaturopsidoid. Ectomycorrhizae ap-
basidioma morphologies (e.g. mushrooms, crusts, pear to have evolved at least 11 times in the
etc.) Agaricales, nine of them in the agaricoid/tricho-
N Larsson et al: The Hymenochaetales (hymenochae- lomatoid clade. A family-based phylogenetic classi-
toid clade) is dominated by wood-decaying species fication is outlined for the six major clades in
previously classified in the artificial families Corti- which 30 families, four autonomous tribes and two
ciaceae, Polyporaceae and Stereaceae. The major- informally named clades are recognized.
ity of these species cause white rots. No unequiv- N Sugiyama et al: The earliest diverging lineages of
ocal morphological synapomorphies are known for the Ascomycota include Neolectomycetes, Pneu-
the hymenochaetoid clade. However, almost all mocystidiomycetes, Schizosaccharomycetes and
species examined ultrastructurally have dolipore Taphrinomycetes. These taxa were classified for-
septa with continuous parenthesomes. merly in the Taphrinomycotina (5Archiascomy-
N Moncalvo et al: The Cantharellales (cantharelloid cetes), and while increased taxon and character
clade) includes the genera Cantharellus, Crater- sampling have resulted in increased support, the
ellus, Hydnum, Clavulina, Membranomyces, Multi- monophyly of the subphylum is debatable and its
clavula, Sistotrema, Botryobasidium, the family use remains controversial.
Ceratobasidiaceae and possibly Tulasnella. Numer- N Suh et al: Subphylum Saccharomycotina consists of
ous taxa within the clade are characterized by fast a single order, Saccharomycetales. Although many
molecular evolution, especially rDNA sequences, close relatives of Saccharomyces cerevisiae are known
which continue to complicate phylogenetic in- from whole genome sequences, few protein-coding
ference of this group. gene sequences are available for other species,
N Hosaka et al: Phallomycetidae is proposed for the especially basal members of the group. At least 12
gomphoid-phalloid clade, which includes four well clades based on rDNA analyses are strongly
supported major subclades. Three of the four supported.
subclades (Geastrales, Hysterangiales and Phal- N Spatafora et al: Pezizomycotina includes the
lales) are represented entirely by gastroid taxa. majority of filamentous, sporocarp-producing and
While the gastroid morphology is derived from mitosporic or conidial species of Ascomycota. The
epigeous, nongastroid taxa (e.g. Ramaria) in the apothecial classes Pezizomycetes and Orbiliomy-
Gomphales, the topology of the Phallales indicates cetes are supported as being the two most basal
that the truffle-like form is an ancestral morphol- taxa of the subphylum. The remaining taxa form
ogy of the stinkhorn fruiting bodies. a well supported clade that includes the Arthonio-
N Miller et al: The Russulales contains a remarkable mycetes plus Dothideomycetes, Eurotiomycetes,
variety of sporophore forms, including resupinate, Lecanoromycetes plus Lichinomycetes and Leotio-
discoid, effused-reflexed, clavarioid, pileate or mycetes plus Sordariomycetes.
gasteroid. Based on molecular and morphological N Hansen and Pfister: Pezizomycetes comprise all
data, 12 families and approximately 80 genera have Ascomycota that form operculate asci with the
been identified, although placement of many taxa majority of species forming apothecial ascomata.
has not yet been determined. Presence of gloeo- The class includes three well supported subclades,
plerous hyphae containing fluid that stains black in all of which are classified currently in the Pezizales.
sulfoaldehyde compounds is a synapomorphy for N Schoch et al: Dothideomycetes includes the ma-
the Russulales, but amyloid reactions in spore or jority of bitunicate ascostromatic species, excluding
hyphal walls is an inconsistent trait for the order. Chaetothyriales and related taxa. Support for the
N Binder and Hibbett: Boletales includes six major monophyly of the class and its sister group
lineages recognized at the subordinal level, Bole- relationship with Arthoniomycetes is strengthened
tineae, Paxillineae, Sclerodermatineae, Suillineae, by the acquisition of protein coding data, and two
Tapinellineae and Coniophorineae. Analyses of new subclasses, Pleosporomycetidae and Dothideo-
the multigene dataset confirmed sister group mycetidae, are described.
relationships among Boletales, Agaricales and N Geiser et al: Eurotiomycetes includes two sub-
Atheliales, and ancestral state reconstruction sug- classes, Eurotiomycetidae and Chaetothyriomyceti-
gests that the ancestor of the Boletales was a brown- dae, which collectively include prototunicate,
rotting, resupinate or polyporoid, saprotrophic bitunicate and lichenized species. The monophyly
basidiomycete. of Eurotiomycetes has been debated, but new data
N Matheny et al: Multigene analyses support Agar- provide strong support for the class as defined
icales comprising six major clades, the agaricoid, herein and for the inclusion of the Coryneliales in
tricholomatoid, marasmioid, hygrophoroid, plu- the Eurotiomycetidae.
 BLACKWELL ET AL: A PHYLOGENY FOR FUNGI 833

N Wang et al: Leotiomycetes contains the majority of in a phylogenetic context. Members of Opistokontia
the inoperculate, apothecial fungi with the excep- (Animalia, Fungi and four protist allies, including
tion of Geoglossaceae, which is shown to represent Choanoflagellata, Ichthyosporea, Mesomycetozoea
a separate origin of the earth tongue morphology. and Corallochytrea, Nuclearia and Ministeria) share
Leotiomycetes contains the Helotiales, Rhytisma- an insertion of about 12 amino acids (positions 153–
tales, Erysiphales, Cyttariales and Myxotrichaceae, 238) in the EF-1a protein sequence (Baldauf and
and proves to be one of the most diverse classes of Palmer 1993). Phylogenetic analysis of four combined
Ascomycota with respect to ascomatal morpholo- nuclear protein-coding gene sequences includes
gies. opistokont protists as well as basal metazoans and
N Zhang et al: Sordariomycetes includes all non- fungi (Amaral- Zettler et al 2001, Medina et al 2003,
lichenized perithecial species and related cleis- Steenkamp 2006) and provides evidence that Nucle-
tothecial and anamorphic taxa. Multigene analyses aria is the sister taxon of Fungi (Steenkamp 2006).
support the recognition of three subclasses (Hy- Furthermore the establishment of the monophyly of
pocreomycetidae, Sordariomycetidae and Xylario- Choanoflagellata indicates that these organisms could
mycetidae), but placement of additional lineages not have been an ancestor shared by animals and
within the class is undetermined. fungi, as has been suggested (Cavalier-Smith 1987).
N Miadilkowska et al: Lecanoromycetes includes The data also reject other hypotheses, including
most of the lichen-forming fungal species (.13 groupings of plants and fungi (Philip et al 2005),
500). Three subclasses are recognized, including and animals and plants (Löytynoja and Milinkovitch
Acarosporomycetidae, Ostropomycetidae and Le- 2001).
canoromycetidae, but support for Lecanoromyce- Cienkowski (1865), who studied a number of
tidae is tenuous. Monophyly of several orders and problematic organisms, including species of Amoebi-
families is not supported, and traditional use of dium and labyrinthulids, also described Nuclearia.
ascus morphology in systematics of the class cannot This is a genus of amoeboid protists with spherical
be applied consistently. bodies and radiating, rigid, filose pseudopodia; many
species form walled cysts (Patterson 1984). These
The works described above will have a large impact
species are known from freshwater where they ingest
on future textbooks and continuously updated Web-
based educational materials, which will continue to algae and might be associated with aquatic animals,
increase in importance. Toward this end, Deep including fish. Environmental DNA samples indicate
Hypha participants are involved in the Tree of Life that members of the genus also might be present in
Project ,http://tolweb.org/tree/., where biological marine environments (Bhattacharya and Oliveira
information, including phylogenetic trees, soon will 2000). Are we close to inferring the morphology of
be available for each of the major fungal taxa ‘‘first fungus’’? If Steenkamp and colleagues (2006)
discussed in this issue of Mycologia. are correct, we are getting close. One superficial
problem however is the absence of a flagellum in
Work remaining.— The base of the tree and the Nuclearia, an apparent loss such as the one that has
bare branches. Questions about the base of the fungal occurred within the main fungal lineage, or could the
tree remain, but fungi usually have been proposed to flagellum be present in an unconnected missing
have a close relationship with animals (Baldauf et al morphological state? Both possibilities were sug-
2000, Baldauf 2003, Baldauf and Palmer 1993, Embley gested.
and Martin 2006, Keeling 2003, Keeling et al 2000, Fast The branch tips of the current tree are fairly bare
and Keeling 2005, Phillipe et al 2004, Ragan et al 1996, and many taxa remain to be discovered and included
Steenkamp et al 2006, Wainright et al 1993), although in analyses. If the conservative estimate of 1 500 000
the details of the basal radiation are not clear. When fungal taxa is used, as it continues to be, less than
Deep Hypha began the major questions included: Is a 10th of the taxa in the kingdom have been
a choanoflagellate ancestor for fungi well supported? discovered (Hawksworth 2004). Many of these taxa
Where is the origin of DAP lysine biosynthesis in the will come from field studies. Fungi from rapid
fungal ancestry? Can character evolution (flagella, radiations into a multitude of habitats continue to
hyphae, etc.) be traced? Can we infer the general be discovered in large numbers in geographically
morphology of ‘‘first fungus’’? Are microsporidians distant localities or undercollected hidden habitats
fungi or merely closely related organisms? (Arnold et al 2001, Suh et al 2004, Vanderkoornhuyse
Five years later these questions are only partially et al 2002). Other taxa from previously described all
answered, largely because of long branches and inclusive taxa, especially those with few distinctive
incomplete taxon sampling. In addition, studies of morphological traits, will be dissected out as cryptic
physiology and biochemistry have not been addressed taxa (Blackwell and Jones 1997, Fisher et al 2002,
834 MYCOLOGIA

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.
 BLACKWELL ET AL: A PHYLOGENY FOR FUNGI 835

Kurtzman 2003). One other way we are increasing ———, Mims CW. 1979. Introductory Mycology. New York:
numbers of taxa is by applying phylogenetic species John Wiley & Sons.
concepts. Use of this concept results in a better ———, ———, Blackwell M. 1996. Introductory Mycology.
understanding of the biology of organisms, including New York: John Wiley & Sons. 869 p.
Amaral-Zettler LA, Nerad TA, O’Kelly CJ, Sogin ML. 2001.
dispersal and geographical and host relations (Cassar
The nucleariid amoebae: more protists at the animal-
and Blackwell 1996, Moncalvo 2005, Taylor et al fungal boundary. J Euk Microbiol 48:293–297.
2000). Arnold AE, Maynard Z, Gilbert GS. 2001. Fungal endo-
phytes in dicotyledonous neotropical trees: patterns of
Classification.—The goal of synthesizing a uniform abundance and diversity. Mycol Res 105:1502–1507.
classification for kingdom Fungi was initiated at the Baldauf SL. 2003. The deep roots of eukaryotes. Science
Deep Hypha Arizona 2004 meeting and was designed 300:1703–1706.
as a collaborative effort with a number of mycolo- ———, Palmer JD. 1993. Animal and fungi are each other’s
gists. The authors of the Dictionary of the Fungi, closest relatives: congruent evidence from multiple
individual authors of pages of the Tree of Life Web proteins. Proc Natl Acad Sci USA 90:11558–11562.
Project, the anticipated revision of the Alexopoulos ———, Roger AJ, Wenk-Siefert I, Doolittle WF. 2000.
textbook, GenBank and Myconet (www.fieldmuseum. A kingdom-level phylogeny of eukaryotes based on
combined protein data. Science 290:972–977.
org/myconet/) have agreed to use the classification.
Barr DJS. 1992. Evolution and kingdoms of organisms from
Many of the naming conventions applied to the
the perspective of a mycologist. Mycologia 84:1–11.
classification of all fungi were those of Eriksson for Bhattacharya D, Oliveira MC. 2000. The SSU rDNA coding
Myconet. The overall goal of the classification was to region of a filose amoeba contains a Group I Intron
produce a higher level phylogenetic classification of lacking the universally conserved G at the 39-terminus.
the Fungi by naming well supported clades. To do so, J Eukaryot Microbiol 47:585–589.
available higher level names sanctioned by the Blackwell M, Jones KG. 1997. Taxonomic diversity and
International Code of Botanical Nomenclature are interactions of insect-associated ascomycetes. Biodiver
employed for as many well supported clades as Conserv 6:689–699.
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TJ. 1992. Molecular evolution of the fungi: relationship
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of the Basidiomycetes, Ascomycetes and Chytridiomy-
Basidiomycota). The tree diagram (FIG. 1) is based on cetes. Mol Biol Evol 9:285–296.
this classification and represents a working or draft Bruns TD, Vilgalys R, Barns SM, Gonzalez D, Hibbett DS,
consensus classification of the Fungi. A more com- Lane DJ, Simon L, Stickel S, Szaro TM, Weisburg WG,
plete classification is in preparation and will be Sogin ML. 1992. Evolutionary relationships within the
published as a multi-authored manuscript (http://www. Fungi: analyses of nuclear small subunit rRNA se-
clarku.edu/faculty/dhibbett/AFTOL/AFTOL.htm). quences. Mol Phylogen Evol 1:231–241.
The classification presented here (FIG. 1) can be used as Cassar SC, Blackwell M. 1996. Non-monophyly of ambrosia
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ACKNOWLEDGMENTS Ark Microsk Anat I:203–232. Pls. 12–14.
We thank all our collaborators who participated in the Deep Embley TM, Martin W. 2006. Eukaryotic evolution, changes
Hypha project. We acknowledge financing from the and challenges. Nature 440:623–630.
National Science Foundation (Research Coordination Net- Fast NM, Keeling PJ. 2005. The fungal roots of microspo-
ridian parasites. In: Vega FE, Blackwell M., eds. Insect-
works in Biological Sciences: a phylogeny for Kingdom
fungal associations. New York: Oxford Press. p 97–118.
Fungi, NSF- 0090301 to M. Blackwell, J.W. Spatafora and
Fischer MC, Koenig GL, White TJ, Taylor JW. 2002.
J.W. Taylor. We appreciate the commitment of James E.
Molecular and phenotypic description of Coccidioides
Rodman to promote systematics and encourage mycology
posadasii sp. nov., previously recognized as the non-
for the past 25 y. We dedicate this paper to him.
California population of Coccidioides immitis. Mycolo-
gia 94:73–84.
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