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Biology Department, Clark University, Worcester, Massachusetts 01610
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ABSTRACT |
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 TOP ABSTRACT Introduction.--Prior phylogenetic...Multilocus perspectives.--Remaining problems.--LITERATURE CITED |
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The Agaricomycotina contains about one-third of the described species of Fungi, including mushrooms, jelly fungi and basidiomycetous yeasts. Recent phylogenetic analyses by P. Matheny and colleagues combining nuclear rRNA genes with the protein-coding genes rpb1, rpb2 and tef1 support the division of Agaricomycotina into Tremellomycetes, Dacrymycetes and Agaricomycetes. There is strong support for the monophyly of the Tremellomycetes, and its position as the sister group of the rest of the Agaricomycotina. Dacrymycetes and Agaricomycetes also are supported strongly, and together they form a clade that is equivalent to the Hymenomycetidae of Swann and Taylor. The deepest nodes in the Agaricomycetes, which are supported only by Bayesian measures of confidence, suggest that the Sebacinales, Cantharellales and Auriculariales are among the most ancient lineages. For the first time, the Polyporales are strongly supported as monophyletic and are placed as the sister group of the Thelephorales. The Agaricales, Boletales and Atheliales are united as the Agaricomycetidae, and the Russulales might be its sister group. There are still some problematical nodes that will require more loci to be resolved. Phylogenomics has promise for reconstructing these difficult backbone nodes, but current genome projects are limited mostly to the Agaricales, Boletales and Polyporales. Genome sequences from other major lineages, especially the early diverging clades, are needed to resolve the most ancient nodes and to assess deep homology in ecological characters in the Agaricomycotina.
Key words: Basidiomycota, heterobasidiomycetes, hymenomycetes, phylogeny, taxonomy, Wallemia
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Introduction.— |
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TOPABSTRACTIntroduction.--Prior phylogenetic...Multilocus perspectives.--Remaining problems.--LITERATURE CITED |
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). Molecular clock studies, reviewed by Taylor et al (2004), suggest that the Agaricomycotina could be anywhere from 380 000 000 to 960 000 000 y old. The Agaricomycotina contains large concentrations of wood decayers, litter decomposers and ectomycorrhizal fungi, along with relatively small numbers of important pathogens of timber (e.g. Phellinus weirii, Heterobasidion annosum), vegetable crops (Thanatephorus cucumeris) and humans (Filobasidiella neoformans). Some Agaricomycotina are highly poisonous (Amanita phalloides, Galerina autumnalis), while others are hallucinogenic (Psilocybe cubensis) or edible. The latter include cultivated saprotrophs (Agaricus bisporus, Lentinula edodes, Auricularia auriculajudae) and field-collected mycorrhizal species (Cantharellus cibarius, Boletus edulis, Tricholoma matsutake). Certain members of the Agaricomycotina produce the largest fruiting bodies (Bridgeoporus nobilissimus, Rigidoporus ulmarius) and the most extensive, long-lived mycelial networks in the Fungi (Armillaria gallica).
This article presents an overview of the higher-level phylogeny of the Agaricomycotina, with particular reference to recent multilocus studies by Matheny and colleagues (2006b, c) and the emerging AFTOL classification (http://www.clarku.edu/faculty/dhibbett/AFTOL/AFTOL.htm). For detailed information on specific clades, the reader is referred to the articles in the present volume that discuss the Agaricales, Boletales, Cantharellales, Hymenochaetales, Russulales and Phallomycetidae (Matheny et al 2006a, Binder and Hibbett 2006, Moncalvo et al 2006, Larsson et al 2006, Miller et al 2006, Hosaka et al 2006) and other recent works that survey major assemblages of Agaricomycotina (Binder et al 2005, Fell et al 2001, Hibbett unpublished, Hibbett and Thorn 2001, Larsson et al 2004, Moncalvo et al 2002, Sampaio 2004, Weiss et al 2004, Wells and Bandoni 2001). Representatives of groups of Agaricomycotina that are not the subject of individual articles in this volume are illustrated (FIG. 1).
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Prior phylogenetic classifications.— |
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TOPABSTRACTIntroduction.--Prior phylogenetic...Multilocus perspectives.--Remaining problems.--LITERATURE CITED |
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). Swann and Taylor (1993, 1995) performed pioneering studies with nuclear small subunit rRNA genes and divided the Basidiomycota into three major groups, the Hymenomycetes, Ustilaginomycetes and Urediniomycetes, which are called the Agaricomycotina, Ustilaginomycotina and Pucciniomycotina in the AFTOL classification, as recently formalized by Bauer et al (2006). Relationships among these three clades have proven difficult to resolve. The majority of analyses of nuclear rRNA genes have suggested that the Ustilaginomycotina is the sister group of the Agaricomycotina (e.g. Swann and Taylor 1995, Weiss et al 2004), which is consistent with ultrastructural characters (Lutzoni et al 2004, McLaughlin et al 1995), cell wall biochemistry (Prillinger et al 1993) and 5S rRNA secondary structure (Gottschalk and Blanz 1985). However, other analyses of rRNA genes as well as ß-tubulin sequences have suggested that the Pucciniomycotina is the sister group of the Agaricomycotina or have produced an unresolved trichotomy among the three clades (Begerow, John and Oberwinkler 2004; Nishida et al 1995).
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). Nevertheless, their choice of the name Hymenomycetes was not ideal because this term was used by Fries (1874) to refer to fungi that bear their spores on an exposed hymenium, as opposed to Gasteromycetes, which bear their spores internally. Long before Swann and Taylor’s publication it was well understood that the Hymenomycetes and Gasteromycetes of Fries are not monophyletic and these terms had come to be used in an informal, descriptive sense. The 9th edition of the Dictionary of the Fungi (Kirk et al 2001) referred to the Agaricomycotina as the Basidiomycetes, but this was also an unfortunate choice, because this term is used frequently to mean all fungi with a basidium (i.e. the Basidiomycota). In the AFTOL classification it was decided to use the name Agaricomycotina, because this name cannot be confused with informal terms and because it refers to Agaricus bisporus, which is perhaps the most widely recognized mushroom in the world.
The classification of major groups within the Agaricomycotina also has been unsettled. Taxa within the Agaricomycotina have been divided into heterobasidiomycetes (including species with mostly septate or tuning fork basidia, often with gelatinous fruiting bodies, yeast stages and spore repetition; approx. syn. Phragmobasidiomycetes; FIG. 1A–F) and homobasidiomycetes (mushroom-forming fungi, with undivided basidia; FIG. 1G–N). However, this basic division was shown to be artificial in the studies of Swann and Taylor (1995), who recognized two subclasses of Hymenomycetes, the Tremellomycetidae, containing Tremellales s.lat., and the Hymenomycetidae, containing homobasidiomycetes and the heterobasidiomycetous Auriculariales, Dacrymycetales and Thanatephorus cucumeris (Ceratobasidiales). Some workers recently have adopted the classification proposed by Swann and Taylor (e.g. Weiss et al 2004), but the classical heterobasidiomycete/homobasidiomycete dichotomy has remained influential. For example, the Mycota VIIb (McLaughlin et al 2001) contains separate chapters on heterobasidiomycetes (Wells and Bandoni 2001) and homobasidiomycetes (Hibbett and Thorn 2001) (although the latter chapter indicated that the homobasidiomycetes s.str. is not monophyletic). Similarly, the 9th edition of the Dictionary of the Fungi (Kirk et al 2001) contains two subclasses of "Basidiomycetes", the Tremellomycetidae, containing all the traditional heterobasidiomycetes, and the Agaricomycetidae, containing the homobasidiomycetes (TABLE I). The 16 orders within the Tremellomycetidae and Agaricomycetidae in the Dictionary classification largely parallel the orders of heterobasidiomycetes proposed by Wells and Bandoni (2001) and the informal clades of homobasidiomycetes proposed by Hibbett and Thorn (2001) (TABLE I). For the most part the orders recognized in the Dictionary are monophyletic based on current phylogenetic hypotheses, with the Polyporales and Tremellales being conspicuous exceptions.
The 9th edition of the Dictionary of the Fungi (Kirk et al 2001) contains the most comprehensive, detailed, and up-to-date classification of the Agaricomycotina in print. It represents a major overhaul of the classification in the 8th edition of the Dictionary (Hawksworth et al 1995) and is quite different from the classification currently employed by GenBank (http://www.ncbi.nlm.nih.gov/Taxonomy/; TABLE I). Nevertheless, there has been much recent progress in phylogenetic reconstruction that the current Dictionary classification does not reflect (Hibbett et al 2005). Many studies have reinforced the view that the Tremellomycetidae and Agaricomycetidae of the Dictionary are not monophyletic (Binder et al 2005, Moncalvo et al 2006, Weiss et al 2004) and the phylogenetic placements of many taxa formerly classified in the Polyporales, Tremellales and other orders have been resolved. In the process, five independent clades have been discovered that are not recognized in the Dictionary classification, including the heterobasidiomycetous Sebacinales (FIG. 1D) and four clades of homobasidiomycetes, the Atheliales, Corticiales, Gloeophyllales and Trechisporales (Binder et al 2005, Hibbett and Binder 2002, Larsson et al 2004, Lim 2001, Weiss et al 2004; FIG. 1G, I, J, N). These discoveries were based on analyses of rRNA genes, which generally provide weak bootstrap support for many deep nodes in the Agaricomycotina (Binder and Hibbett 2002). One of the major goals of the AFTOL project (http://aftol.org/) was to create multilocus datasets to resolve the deep nodes of the Agaricomycotina and other Fungi (Lutzoni et al 2004; Matheny et al 2006b, 2006c).
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Multilocus perspectives.— |
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TOPABSTRACTIntroduction.--Prior phylogenetic...Multilocus perspectives.--Remaining problems.--LITERATURE CITED |
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) represents a synthesis of recent studies of Agaricomycotina phylogeny and includes the 21 orders of Agaricomycotina in the forthcoming AFTOL classification as terminal taxa (some are not yet formally published, e.g. Gloeophyllales, Trechisporales). The backbone for the tree is taken from a study of higher-level phylogenetic relationships of Basidiomycota by Matheny and colleagues (2006c), which used sequences of rpb2, tef1 and nuclear 18S, 25S and 5.8S rRNA genes from 146 taxa, including 125 Agaricomycotina. The topology shown is from a Bayesian analysis of nucleotide characters (6603 positions, including 3318 parsimony informative positions). Sixteen orders of Agaricomycotina were represented in the dataset of Matheny et al, but the Cystofilobasidiales, Filobasidiales, Geastrales, Gloeophyllales and Hysterangiales were not included. Placements of these taxa (FIG. 2A) were based on other studies (Fell et al 2001, Hibbett and Donoghue 2001, Lutzoni et al 2004, Hosaka et al 2006). The trees (FIG. 2B) are derived from another study by Matheny et al (2006b), which used the three nuclear rRNA genes along with rpb1, rpb2 and tef1, and that was focused on the phylogenetic placement of Wallemia, an enigmatic group of apparently mitosporic Basidiomycota that has dolipore septa and colonizes dried and salted foods, and which is the sole genus of the Wallemiomycetes (Moore 1986, Zalar et al 2005).
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, c) the Ustilaginomycotina was resolved as being more closely related to the Agaricomycotina than the Pucciniomycotina (FIG. 2). It is too early, however, to state with confidence that the sister group of the Agaricomycotina has been identified, because analyses of protein-coding genes suggest that the closest relative of the Agaricomycotina might be Wallemia (FIG. 2B). This result appears to be driven primarily by the rpb2 data partition (Matheny et al 2006b). In contrast analyses that include rRNA genes place Wallemia as the sister group of the Ustilaginomycotina or as the sister group of Entorrhiza, which is a small group of root-inhabiting fungi that has been classified in the Entorrhizomycetidae, Ustilaginomycotina (Bauer et al 2001, Piepenbring 2004). Combined 18S, 25S and 5.8S rRNA gene sequences, which are the only molecular data currently available for Entorrhiza, consistently place this taxon as the sister group of the rest of the Basidiomycota, separate from other Ustilaginomycotina (FIG. 2B). However, additional loci are needed to resolve the phylogenetic placements of both Entorrhiza and Wallemia.
The combined rRNA, rpb2, tef1 dataset (Matheny et al 2006c) provides strong support for the earliest divergences in the Agaricomycotina. The Tremellomycetes are strongly supported as the sister group of the rest of the Agaricomycotina but are represented by only two isolates of Cryptococcus. Prior analyses with much more extensive sampling of Tremellomycetes using rRNA genes have found weak support for the monophyly of this group (Swann and Taylor 1995, Weiss et al 2004), or have resolved it as paraphyletic (Sampaio 2004) (Fell et al 2001 also sampled Tremellomycetes intensively, but their analyses did not test the monophyly of the Tremellomycetes because they did not include other groups of Agaricomycotina). Monophyly of Tremellomycetes was addressed in the second study by Matheny et al (2006b), which included representatives of Cystofilobasidiales, Filobasidiales and Tremellales. In analyses of rRNA genes alone the Tremellomycetes was resolved as a paraphyletic assemblage, with the Cystofilobasidiales placed as the sister group of the rest of the Agaricomycotina (FIG. 2B). These results are similar to those of Sampaio (2004), who analyzed partial 25S rRNA gene sequences. However analyses that used rpb1, rpb2, and tef1, either alone or in combination with the rRNA genes, provided strong support for the monophyly of Tremellales plus Cystofilobasidiales (Filobasidiales were not sampled for the protein-coding loci). These results highlight the importance of obtaining data from multiple loci for analyses of deep nodes in Agaricomycotina.
The Dacrymycetes (including only the Dacrymycetales) was strongly supported as monophyletic by both bootstrap and Bayesian criteria in the studies of Matheny and colleagues (2006b, c) as in other studies (Binder et al 2005, Weiss et al 2004). In addition, the Dacrymycetes was strongly supported as the sister group of the Agaricomycetes, which conflicts with placements of this group based on rRNA genes alone (Weiss et al 2004). The Dacrymycetes/Agaricomycetes clade is equivalent in composition to the Hymenomycetidae of Swann and Taylor (1995). Many Dacrymycetes and Tremellomycetes (as well as Auriculariales) form gelatinous, translucent fruiting bodies (FIG. 1A–C), and it is plausible that this could be the plesiomorphic condition of the Agaricomycotina as a whole. These two early diverging clades have very different ecological strategies, however. The Dacrymycetes are saprotrophs that produce a brown rot type of wood decay, whereas the Tremellomycetes include mycoparasites and pathogens of mammals (Wells and Bandoni 2001). Many Tremellomycetes have been cultured, but it is not known to what extent they are able to function saprotrophically in nature.
The Agaricomycetes also was supported strongly as monophyletic by both bootstrap and Bayesian measures (FIG. 2). Most of the terminal clades in the Agaricomycetes (FIG. 2A) have been discussed in previous studies and require little comment here (see the later articles in this volume). However, several nodes are resolved with confidence for the first time in the multilocus analyses of Matheny et al (2006c). One of these is the node that unites the Agaricales, Boletales and Atheliales, which is being proposed as the Agaricomycetidae in the AFTOL classification. The Atheliales is a small group of ephemeral resupinate forms (FIG. 1I), whereas the Agaricales and Boletales contain major concentrations of large pileatestipitate forms. The positioning of the Atheliales as the sister group of the Boletales, and the occurrence of resupinate taxa within early diverging clades of Boletales (Binder and Hibbett 2006) and Agaricales (Binder et al unpublished), is consistent with the view that resupinate forms make up a paraphyletic assemblage that has given rise to more elaborate forms many times within the Agaricomycetes (Hibbett and Binder 2002).
The Russulales is resolved as the sister group of the Agaricomycetidae, with strong Bayesian support and weak (66%) bootstrap support. If the Agaricales, Boletales and Russulales were found to form a monophyletic group, then that would be partly consistent with Singer’s (1986) conception of the Agaricales, which he divided into the suborders Agaricineae, Boletineae, and Russulineae. Of course, Singer’s suborders did not include many of the "aphyllophoraceous" and gasteroid taxa that are now known to be in the Agaricales, Boletales and Russulales.
The Polyporales (FIG. 1K–L) has been a particularly challenging group for basidiomycete systematists and were something of a garbage can taxon in the 9th edition of the Dictionary of the Fungi (Kirk et al 2001). Members of the Polyporales have been sampled in numerous studies, but the group has received weak bootstrap support (Binder and Hibbett 2002, Hibbett and Donoghue 2001) or has been resolved as paraphyletic (Binder et al 2005) or polyphyletic (Larsson et al 2004). The multilocus dataset of Matheny et al (2006c) included a diverse sample of 16 Polyporales, including white-rot and brown-rot species that represent the "core polyporoid clade", "phlebioid clade", "Antrodia clade" and "residual polyporoid clade", as delimited by Binder et al (2005). For the first time, the Polyporales was strongly supported as monophyletic, and the Thelephorales (FIG. 1H, M) was placed as its sister group, with moderately strong support (FIG. 2A). It is surprising to find that these two groups are closely related because the Thelephorales are exclusively mycorrhizal, as far as is known, whereas the Polyporales all are saprotrophic and include many decayers of large woody substrates. Evidently there was a transformation between saprotrophic and mycorrhizal life strategies early in the evolution of this clade.
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Remaining problems.— |
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TOPABSTRACTIntroduction.--Prior phylogenetic...Multilocus perspectives.--Remaining problems.--LITERATURE CITED |
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). This topological uncertainty will hinder efforts to understand the evolution of morphological and ecological characters or to localize shifts in diversification rates.
To resolve the remaining major phylogenetic questions in the Agaricomycotina it will be necessary to assemble and analyze large-scale molecular datasets that go far beyond the handful of loci that are the focus of the current AFTOL project. Complete genome sequences will be important to this effort because they can be used directly in phylogenomic analyses (e.g. Robbertse et al in press) and because they can guide the development of degenerate primers for amplifying orthologous genes across large numbers of taxa (e.g. Rokas et al 2005). Complete genomes also will be necessary to understand the genetic bases of ecological and physiological evolution, including switches between mycorrhizal and decayer life strategies, and the diversification of mechanisms for degradation of lignocellulose. Understanding the latter has potential applications in green technologies such as the production of alternative energy sources and therefore should be a priority.
Comparative genomics of Agaricomycotina is a young, rapidly expanding discipline. As of this writing, complete genome sequences have been produced for only four species, including multiple isolates of the human pathogen Cryptococcus neoformans, but there are at least nine other genome and expressed sequence tag (EST) sequencing efforts pending or in progress (a partial list of ongoing projects, with varying levels of activity, is listed in SUPPLEMENTARY TABLE I). Individually, a strong case can be made for each of the genome targets, but in aggregate they represent a phylogenetically skewed sample. Thus, in addition to the Cryptococcus projects, there are multiple projects in the Agaricales, Boletales and Polyporales and one ongoing project in the Gloeophyllales (which is important because Gloeophyllum trabeum is a model system for studies of brown-rot decay mechanisms). Having multiple genome sequences within these groups will be valuable because that will allow studies of genome evolution over a relatively short time. Nevertheless to resolve the backbone nodes of the Agaricomycotina phylogeny and to assess deep homology in ecological characters it will be necessary to obtain complete genome sequences from ecologically diverse species in clades that have yet to be sampled, including the Dacrymycetes, Sebacinales, Cantharellales, Auriculariales, Hymenochaetales and Russulales. (A dozen candidates, with brief rationales, are listed in SUPPLEMENTARY TABLE II).
Even if all the species in the supplementary information were sequenced, the available genomes still would represent a tiny fraction of the extant diversity of Agaricomycotina. Fortunately, as the articles in this volume attest, there has been tremendous recent progress in developing detailed phylogenetic hypotheses for terminal clades of Agaricomycotina. These studies increasingly are based on intensively sampled multilocus datasets (e.g. Hosaka et al 2006, Matheny et al 2006a) but there is still an excess of taxa for which there are only rRNA sequences, including those of the rapidly evolving ITS region. To achieve a comprehensive view of the phylogeny of Agaricomycotina, it will be necessary to integrate genome-scale information with the ever growing database of ITS and other highly variable regions, including sequences generated in molecular studies of fungal ecology.
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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1 E-mail: dhibbett{at}clarku.edu
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LITERATURE CITED |
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TOPABSTRACTIntroduction.--Prior phylogenetic...Multilocus perspectives.--Remaining problems.--LITERATURE CITED |
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———, ———, Sampaio JP, Weiß M, Oberwinkler F. 2006. The simple-septate basidiomycetes: a synopsis. Mycol Progress 5:41–66.[CrossRef]
Begerow D, John B, Oberwinkler F. 2004. Evolutionary relationships among ß-tubulin gene sequences of basidiomycetous fungi. Mycol Res 108:1257–1263.[CrossRef][Medline]
Binder M, Hibbett DS. 2002. Higher-level phylogenetic relationships of homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions. Mol Phylogenet Evol 22:76–90.[CrossRef][Medline]
———, ———. 2006. Molecular systematics and biological diversification of Boletales. Mycologia 98(6):917–925.
———, ———, Larsson KH, Larsson E, Langer E, Langer G. 2005. The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (homobasidiomycetes). Syst Biodiv 3:113–157.[CrossRef]
Fell JW, Boekhout T, Fonseca A, Sampaio JP. 2001. Basidiomycetous yeasts. In: McLaughlin DJ, McLaughlin EG, Lemke PA, eds. Systematics and evolution. Part B. Berlin: Springer-Verlag. The Mycota VII:1–36.
Fries EM. 1874. Hymenomycetes europaei. Uppsala: Berling. 755 p.
Gottschalk M, Blanz PA. 1985. Untersuchungen an 5S ribosomalen Ribonucleinsäuren als Beitrag zur Klärung von Systematik und Phylogenie der Basidiomyceten. Z Mycol 51:205–243.
Hawksworth DL, Kirk PM, Sutton BC, Pegler DN. 1995. Ainsworth and Bisby’s Dictionary of the Fungi. 8th ed. Wallingford, UK: CAB International. 616 p.
Hibbett DS, Binder M. 2002. Evolution of complex fruiting-body morphologies in homobasidiomycetes. Proc R Soc Lond B 269:1963–1969.[Medline]
———, Donoghue MJ. 2001. Analysis of correlations among wood decay mechanisms, mating systems, and substrate ranges in homobasidiomycetes. Syst Biol 50:215–242.[Medline]
———, Nilsson RH, Snyder M, Fonseca M, Costanzo J, Shonfeld M. 2005. Automated phylogenetic taxonomy: an example in the Homobasidiomycetes (mushroom-forming Fungi). Syst Biol 54:660–668.
———, Thorn RG. 2001. Homobasidiomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA, eds. Systematics and evolution. Part B. Berlin: Springer-Verlag. The Mycota VII:121–170.
Hosaka K, Bates ST, Beever RE, Castellano MA, Colgan W, Domínguez LS, Nouhra ER, Geml J, Giachini AJ, Kenney SR, Simpson NB, Trappe JM. 2006. Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders. Mycologia 98:949–959.
Kirk PM, Cannon PF, David JC, Stalpers JA. 2001. Ainsworth and Bisby’s Dictionary of the Fungi. 9th ed. Cambridge, United Kingdom: CAB International University Press.
Larsson KH, Larsson E, Kõljalg U. 2004. High phylogenetic diversity among corticioid homobasidomycetes. Mycol Res 108:983–1002.[CrossRef][Medline]
———, Parmasto E, Langer E, Nakasone KK, Redhead SA. 2006. Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade. Mycologia 98:926–936.
Lim YW. 2001. Systematic study of corticioid fungi based on molecular sequence analyses [Doctoral dissertation]. School of Biological Sciences, Seoul National University, Seoul, Korea. 228 p.
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, Sung G-H, Lücking R, Lumbsch T, O’Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim Y-W, Matheny PB, 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 91:1446–1480.
Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo J-M, Ge Z-W, Yang Z-L, Slot JC, Ammirati JF, Baroni TJ, Bougher NL, Hughes KW, Lodge DJ, Kerrigan RW, Seidl MT, Aanen DK, DeNitis M, Daniele GM, Desjardin DE, Kropp BR, Norvell LL, Parker A, Vellinga EC, Vilgalys R, Hibbett DS. 2006a. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:984–997.
———, Gossman JA, Zalar P, Arun Kumar TK, Hibbett DS. 2006b. Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota. Can J Bot (In press).
———, Wang Z, Binder M, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Petersen RH, Hofstetter V, Ammirati JF, Schoch C, Langer GE, McLaughlin DJ, Wilson AW, Crane PE, Frøslev T, Ge ZW, Kerrigan RW, Slot JC, Vellinga EC, Liang ZL, Aime MC, Baroni TJ, Fischer M, Hosaka K, Matsuura K, Seidl MT, Vaura J, Hibbett DS. 2006c. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phyl Evol (In press).
McLaughlin DJ, Frieders EM, Lü H. 1995. A microscopist’s view of heterobasidiomycete phylogeny. Stud Mycol 38: 91–109.
———, McLaughlin EG, Lemke PA. 2001. Systematics and evolution. Part B. Berlin: Springer-Verlag. The Mycota VII:121–170.
Miller SL, Larsson E, Larsson K-H, Verbeken A, Nuytinck J. 2006. Perspectives in the new Russulales. Mycologia 98: 960–970.
Moncalvo JM, Vilgalys R, Redhead SA, Johnson JE, James TY, Aime MC, Hofstetter V, Verduin SJW, Larsson E, Baroni TJ, Thorn RG, Jacobsson S, Clémençon H, Miller Jr OK. 2002. One hundred and seventeen clades of euagarics. Mol Phyl Evol 23:357–400.[CrossRef][Medline]
———, Nilsson RH, Koster B, Dunham SM, Bernaruer T, Matheny PB, McLenon T, Margaritescu, Weiß M, Garnica S, Danell E, Langer G, Langer E, Larsson E, Larsson K-H, Vilgalys R. 2006. The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. Mycologia 98:937–948.
Moore RT. 1986. A note on Wallemia sebi. Antonie van Leeuwenhoek 52:183–187.[CrossRef][Medline]
Nishida H, Ando K, Ando Y, Hirata A, Sugiyama J. 1995. Mixia osmundae: transfer from the Ascomycota to the Basidiomycota based on evidence from molecules and moprhology. Can J Bot 73:S660–S666.[CrossRef]
Piepenbring M. 2004. Comparative morphology of galls formed by smut fungi and discussion of generic concepts. In: Agerer R, Piepenbring M, Blanz P, eds. Frontiers in basidiomyocte mycology. Eching, Germany: IHW-Verlag. p 117–164.
Prillinger H, Oberwinkler F, Umile C, Tlachac K, Bauer R, Dörfler C, Taufratzhofer E. 1993. Analysis of cell wall carbohydrates (neutral sugars) from ascomycetous and basidiomycetous yeasts with and without derivatization. J Gen Appl Microbiol 39:1–34.[CrossRef]
Robbertse B, Reeves J, Schoch C, Spatafora JW. 2006. A phylogenomic analysis of the Ascomycota. Fungal Genetics and Biology (In press).
Rokas A, Krüger D, Carroll SB. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933–1938.
Sampaio JP. 2004. Diversity, phylogeny and classification of basidiomycetous yeasts. In: Agerer R, Piepenbring M, Blanz P, eds. Frontiers in basidiomyocte mycology. Eching, Germany: IHW-Verlag. p 49–80.
Singer R. 1986. The Agaricales in modern taxonomy. 4th ed. Königstein, Germany: Koeltz Scientific Books. 981 p.
Swann EC, Taylor JW. 1993. Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycologia 85:923–936.[CrossRef]
———, ———. 1995. Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot 73:S862–S868.[CrossRef]
Taylor JW, Spatafora J, O’Donnell K, Lutzoni F, James T, Hibbett DS, Geiser D, Bruns TD, Blackwell M. 2004. The Fungi. In: Cracraft J, Donoghue M, eds. Assembling the tree of life. New York: Oxford University Press. p 171–194.
Weiß M, Bauer R, Begerow D. 2004. Spotlights on heterobasidiomycetes. In: Agerer R, Piepenbring M, Blanz P, eds. Frontiers in basidiomyocte mycology. Eching, Germany: I HW-Verlag. p 7–48.
Wells K, Bandoni RJ. 2001. Heterobasidiomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA, eds. Systematics and evolution. Part B. Berlin: Springer-Verlag. The Mycota VII:85–120.
Zalar P, de Hoog GS, Schroers HJ, Frank JF, Gunder-Cimerman N. 2005. Taxonomy and phylogeny of the xerophilic genus Wallemia (Wallemiomycetes and Wallemiales, cl. et ord. nov.). Antonie van Leeuwenhoek 87:311–328.[CrossRef][Medline]
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