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Fungi Phylogeny

Fungi Phylogeny

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Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha)
Meredith Blackwell
 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
Research in fungal phylogenetics andsystematics progressed rapidly in the past decadedue to advances in DNA sequencing technologies andanalytical methods. A newfound wealth of sequencedata acquired through community-wide initiatives hasadvanced the process of acquiring a stable phyloge-netic classification of many fungal taxa. Financialsupport from the National Science Foundation Re-search Coordination Networks: a phylogeny forkingdom Fungi (Deep Hypha) for 5 y enabled morethan 100 fungal systematists to assess the taxonsampling, molecular markers and analytical methodsnecessary to facilitate such a project. Later a secondNSF program provided financial support for the Assembling the Fungal Tree of Life (AFTOL) project to accomplish much of the research. Deep Hyphamay be viewed as an involved parent of AFTOL witha 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 arestable 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 insome terminal groups. The phylogenetic classificationin this issue of 
is a product of the AFTOLproject and many other independent research in-itiatives, and it is an initial synthesis of a workingclassification designed to be used for all majorpublications that require a phylogenetic classificationof fungi.
Key words: 
mycological community, mycota,systematicsFungi have a profound impact on global ecosys-tems. They modify our habitats and are essential formany ecosystem functions. Fungi form soil, recyclenutrients, decay wood, enhance plant growth and cullplants from their environment. They feed us, poisonus, parasitize us and cure us. They destroy our crops,homes and libraries, but they also produce valuablebiochemicals, such as ethanol and antibiotics. Forboth 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 ResearchCoordination Network, supported by the UnitedStates National Science Foundation (NSF), promotedand facilitated the cooperation necessary for themycological community to construct a comprehensivephylogeny of the Fungi. Although Deep Hypha didnot support data collection, it provided an essentialforum for fungal systematists to plan, coordinate andreport their activities. One initiative that grew out of Deep Hypha was the NSF-supported Assembling theFungal Tree of Life project (AFTOL), which providedmoney to develop multilocus molecular and morpho-logical datasets for the entire kingdom. As the articlesin this Deep Hypha issue of 
attest, AFTOLand other recent independent projects, helped di-rectly or indirectly by Deep Hypha, have dramaticallenhanced our understanding of fungal phylogeny. Inthis mission, Deep Hypha has been a success. Asa gauge of progress in the field one may consider thegrowth of fungal systematics through the latter half of the 20th century, as reflected in the successive volumes of 
Introductory Mycology 
by C.J. Alexopoulosand colleagues (Alexopoulos 1952, 1962; Alexopoulosand Mims 1979; Alexopoulos, Mims, Blackwell 1996).
The growth of fungal phylogenetics seen througAlexopoulos’s 
Introductory Mycolog
The intent of Alexopoulos’s
Introductory Mycology 
has alwaysbeen to be organized phylogenetically, as far aspossible. The first edition (Alexopoulos 1952) began with bacteria, including actinomycetes, and a modernconcept of prokaryotic cells and their structure waslacking. The second edition (Alexopoulos 1962)omitted bacteria but included for the first timeLabyrinthulales, Hyphochytridiomycetes [sic] andTrichomycetes. These groups are still included inthe latest edition of the text but mostly removed from
 Accepted for publication 12 November 2006.
Corresponding author. E-mail: mblackwell@lsu.edu
98(6), 2006, pp. 829–837.
2006 by The Mycological Society of America, Lawrence, KS 66044-8897Issued 13 April 2007
a monophyletic concept of fungi with the exceptionof some Trichomycetes. As will be seen below somemembers of these of groups have come back intoconsideration as protists that are in a position basal tofungi and animals. Alexopoulos was concernedparticularly about the placement of slime molds,and although they are excluded from fungi theirposition continues to be somewhat unsettled. Thethird edition (Alexopoulos and Mims 1979) had a new look with the addition of electron micrographs, therevolutionary technique of the time. Classification,still problematic, included slime mold groups withinFungi but separated them in a different subdivision.Oomycetes and chytrids also were placed in separatesubdivisions, and Deuteromycotina was a group equalto but distinct from zygomycetes, ascomycetes andbasidiomycetes.In 1993 Charles Mims and Meredith Blackwellrevised the text to provide a fourth edition (1996).For a book with a phylogenetic arrangement thetiming of the revision was arguably less thanoptimum, because results from DNA-based phyloge-netic studies were just appearing. In fact the text wassent to the printer with a multitude of additions in the‘‘blue line’’ stage because of the appearance of new papers and graciously contributed unpublished stud-ies that helped to establish the bare bones of a molecular phylogeny, which endured fairly welldespite heavy reliance on a single gene, SSU rDNA. A phylogeny was presented in a series of unresolvedtrees that required the use of informal names fornumerous taxonomic groups. The text however diduse for the first time the term ‘‘phylum’’, newlsanctioned by the revised International Code of Botanical Nomenclature from the Tokyo BotanicalCongress, and as such served as a transition betweenthe old and the new, with hints of many changes tocome. The monophyly of Fungi was established by separating four phyla from a number of excludedgroups (water molds, labyrinthulids and several typesof slime molds). Chytrids were placed firmly amongFungi, and the heterokont flagellates were unques-tionably excluded. There were surprises:
 was determined to be a fungus,
was recognizedas a basidiomycete and
Schizosac- charomyces 
were shown to be widely separated.Evidence was available to recognize the polyphyly of groups such as gasteromycetes and polypores, andperhaps most important of all there was no phyloge-netically defensible use of the class Deuteromycetes(Taylor 1995, Taylor et al 1999). There were howevermany intriguing unresolved questions: Is it possiblethat 
is not a zygomycete? Are smuts andrusts not monophyletic? Do animals represent thesister group of fungi, or is the relationship moreremoved with fungi and animals sharing commonancestors?
Phylogenetic status of kingdom Fungi at the time of  writing the Deep Hypha proposal.
A monophyletickingdom Fungi had been defined when Deep Hyphabegan (Barr 1992, Bruns et al 1992) with ourunderstanding of major subkingdom relationshipssummarized as follows:
Four phyla generally were accepted in kingdomFungi: Chytridiomycota, Zygomycota, Basidiomy-cota and Ascomycota (Alexopoulos et al 1996, Barr1992, Bowman et al 1992, Bruns et al 1992,Hawksworth et al 1995).
The phyla Chytridiomycota and Zygomycota werenot supported as monophyletic and intergraded at several points based on analyses of the SSU rDNA (Nagahama et al 1995, James et al 2000).
The Chytridiomycota was the only taxon withinkingdom Fungi to include representatives witha flagellated stage at some point in their life cycle,and analyses agreed that some lineage of theChytridiomycota occupied the most basal branchof kingdom Fungi, a finding consistent witha choanoflagellate ancestor; however there wasconflict in the literature as to which group of theChytridiomycota was most basal (James et al 2000).
The Chytridiomycota was paraphyletic, largely de-fined by the ancestral character state of a smoothposterior flagellum. The Zygomycota was suspectedof being polyphyletic with multiple origins withinkingdom Fungi. Based on rDNA, at least one origin was derived from within the Chytridiomycota,representing the loss of the flagellum; howeverthis was contradicted by analysis of 
-tubulinsequences (Keeling et al 2000, James et al 2000).
At the other extreme, the Glomerales (until thenconsidered a member of Zygomycota) appearedmore closely related to the Ascomycota/Basidio-mycota clade (Simon et al 1993) based on rDNA.
The larger clade comprising the Glomerales, Ascomycota and Basidiomycota was referred to as‘‘crown’’ fungi; ‘‘crown’’ fungi were supported asa derived, higher monophyletic taxon within theFungi, originated and diversified along with landplants (Redecker et al 2000, Simon et al 1993,Taylor et al 1995).
The Basidiomycota and Ascomycota each weremonophyletic and together formed the mosderived fungal clade (Bowman et al 1992, Brunset al 1992) that comprised more than 95
of allknown fungi. Higher-level relationships withinboth the Ascomycota and Basidiomycota weretenuous.
The Ascomycota generally was recognized to in-830 M
clude the classes Euascomycetes (mostly filamen-tous, sporocarp-producing and mitosporic or co-nidial forms), Saccharomycetes (the true yeasts),and Archiascomycetes (a paraphyletic assemblageof basal taxa) (Nishida and Sugiyama 1994, Tayloret al 1993).
The Basidiomycota generally was recognized toinclude three classes: Urediniomycetes (rusts andrelatives), Ustilaginomycetes (smuts) and Hyme-nomycetes (mushrooms and relatives) (Swann andTaylor, 1995, Wells 1994).
To that date, the lion’s share of phylogeneticstudies had been performed on nucleotide datadetermined from nuclear rDNA (Alexopoulos et al1996).
 Deep Hypha accomplishments.— 
Mycologists wereprimed for the first NSF Assembling the Tree of Lifecompetition (2002) thanks to the community-widediscussions on taxon sampling and methodology that had been supported by Deep Hypha. Working withthe AFTOL consortium (and with much overlap inmembership) many Deep Hypha participants focusedon the same major loci, including the well character-ized nuclear rRNA genes, and the protein-coding loci
, which had been promoted asmolecular phylogenetic markers in Fungi by Hall andcolleagues (Liu et al 1999). The coordinated sam-pling enabled construction of kingdomwide multi-gene datasets (Lutzoni et al 2004, James et al 2006).Several Deep Hypha symposia and workshops wereheld in conjunction with other meetings during the AFTOL funding period. The symposia and workshopspromoted multigene, collaborative research in fungalphylogenetics, the use of state-of-the-art phylogeneticalgorithms and fungal biology in broader scientificand educational communities. This Deep Hypha issueof 
presents phylogenetic analyses of most major fungal clades, including many studies that wereaided by Deep Hypha and that use data obtained inthe AFTOL project. The articles included in this issueprovide summaries of the status of the phylogeneticreconstruction for most of the major fungal lineages,although some clades (e.g. Polyporales, Laboulbenio-mycetes) have been omitted. Some highlights follow.
Taylor and Berbee: Estimating the evolutionary ageof Fungi and the origin of its phyla and subphylaremains an elusive goal, but new fossil findings andimproved analytical methods support an origin of all extant phyla by the Devonian (Taylor et al1995).
Celio et al: Subcellular characters, especially associated with septal ultrastructure, while few innumber, are providing important synapomorphiesfor deep nodes that have proved problematical(e.g. monophyly of Agaricomycotina plus Ustilagi-nomycotina, and monophyly of Dimargaritales plusTrichomycetes s.s.).
James et al: The Chytridiomycota is not mono-phyletic. Fourteen clades, including a core groupof the traditional chytrids, are defined; theseclades have a paraphyletic relationship to otherflagellated fungi, notably Blastocladiales, many of  which have distinctive life cycles with sporicmeiosis.
also falls outside the otherchytrids.
White et al: The Zygomycota as previously recog-nized is not a monophyletic group. Two trichomy-cete groups no longer are considered to be fungiand the remaining traditional members havea paraphyletic relationship.
, tentative-ly suggested to be a chytrid by SSU rDNA data,appears as a sister of the Entomophthorales withincreased taxon sampling and use of a multigenedataset.
Redecker and Raab: Glomeromycota is accepted asa sister group of Basidiomycota
Ascomycota within kingdom Fungi on the basis of rDNA analysis (Schu¨ßler et al 2001). Some recent analyses including protein coding genes suppormonophyly of the phylum but also cast doubt onthe sister group relationship of these fungi withDikaryomycota. With a two-gene dataset the Glo-meromycota is upheld as a monophyletic taxon with six major clades.
Aime et al: Pucciniomycotina (
Urediniomycetes)comprises the rusts, Pucciniales (
Urediniales)and related teliospore-producing taxa (e.g. Septo-basidiales, Sporidiales, etc.). The subphylum isdefined with eight major clades ranked as classes(Agaricostilbomycetes, Atractiellomycetes, Classi-culomycetes, Cryptomycocolacomycetes, Cystobasi-diomycetes, Microbotryomycetes, Mixiomycetesand Pucciniomycetes) and eighteen orders.
Begerow et al: Ustilaginomycotina (
Ustilaginomy-cetes) comprisesthesmuts,Ustilaginales andrelatedtaxa. Based on morphological, ultrastructural andmolecular phylogenetic data, Ustilaginomycotina isdefined with three classes, Entorrhizomycetes, Usti-laginomycetes and Exobasidiomycetes, which collec-tively comprise 11 orders.
Hibbett: Agaricomycotina (
Hymenomycetes),one of the three main subphyla of Basidiomycota,includes Tremellomycetes, Dacrymycetes and Agar-icomycetes. Phragmobasidia are present in allthree classes with holobasidia restricted to the Agaricomycetes. The Agaricomycetes includeseight major subclades that are recognized assubclasses and orders and is characterized by highB

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