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 support monophyly 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
LACKWELL ET AL