MOLECULAR PHYLOGENETICS AND EVOLUTION Molecular Phylogenetics and Evolution 23 (2002) 357–400 www.academicpress.com One hundred and seventeen clades of euagarics Jean-Marc Moncalvo,a,* Rytas Vilgalys,a Scott A. Redhead,b James E. Johnson,a Timothy Y. James,a M. Catherine Aime,c Valerie Hofstetter,d Sebastiaan J.W. Verduin,e,f Ellen Larsson,g Timothy J. Baroni,h R. Greg Thorn,i Stig Jacobsson,g Heinz Cl
emencßon,d and Orson K. Miller Jr.c a b Department of Biology, Duke University, Durham, NC 27708, USA Systematic Mycology and Botany Section, Eastern Cereal and Oilseed Research, Agriculture and Agri-Food Canada, Ottawa, Ont., Canada K1A 0C6 c Department of Biology, Virginia Tech, Blacksburg, VA 24061, USA d Department of Ecology, Lausanne University, Lausanne, Switzerland e Nationaal Herbarium Nederland, Universiteit Leiden branch, P.O. Box 9514, 2300 RA Leiden, The Netherlands f Centraal Bureau voor Schimmelcultures, P.O. Box 85167, 3508 AD Utrecht, The Netherlands g Botanical Institute, G€oteborg University, SE 405 30 G€oteborg, Sweden h Department of Biological Sciences, SUNY College at Cortland, Cortland, NY 13045, USA i Department of Plant Sciences, University of Western Ontario, London, Ont., Canada N6A 5B7 Received 5 June 2001; received in revised form 7 December 2001 Abstract This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 50 end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a monophyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities. Ó 2002 Elsevier Science (USA). All rights reserved. Keywords: Nuclear large ribosomal subunit RNA; Phylogeny; Unequally weighted parismony; Agaricales; Homobasidiomycetes ‘‘As soon as it will be possible to delimit ‘mixed groups’ of this order, we shall see the Agaricales fall apart [and it will be] extremely difficult to define the * Corresponding author. Present address: Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON M5S 2C6, Canada. E-mail address: jeanmarc@duke.edu (J.-M. Moncalvo). limits of the groups obtained’’ (Singer, 1951, pp. 127– 128, footnote 51). The rapid development of DNA sequencing techniques, phylogenetic theory, and bioinformatics has enabled systematists to envision a phylogenetic classification of all the branches of the tree of life. Notable examples include the recently published phylogenies of vascular plants (Chase et al., 1993; Qiu et al., 1999; Soltis et al., 1997, 1998, 1999; Savolainen et al., 2000) 1055-7903/02/$ - see front matter Ó 2002 Elsevier Science (USA). All rights reserved. PII: S 1 0 5 5 - 7 9 0 3 ( 0 2 ) 0 0 0 2 7 - 1 358 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 and the ‘‘Deep Green’’ land plant phylogeny study (summarized in Brown, 1999). In fungi, the pace of discovery about natural relationships has also been greatly accelerated by new evidence from molecular systematics, mostly using ribosomal DNA sequence data. Based on molecular evidence, it is now believed that the Chytridiomycetes, Zygomycetes, Glomales, Ascomycetes, and Basidiomycetes form a monophyletic group sister to the Animals, whereas the myxomycetes and oomycetes, sometimes considered to be Fungi, should be classified outside the fungal kingdom (Bruns et al., 1992; Bowman et al., 1992; Wainright et al., 1993; Spiegel et al., 1995; Lipscomb et al., 1998; Tehler et al., 2000; James et al., 2000). rDNA phylogenies support monophyly of many traditional basidiomycete taxa, but have also demonstrated the existence of several clades composed of members of disparate traditional groups (Swann and Taylor, 1993, 1995; Hibbett et al., 1997; Begerow et al., 1997; Bruns et al., 1998). In the homobasidiomycetes, gilled mushrooms appear to have evolved multiple times from morphologically diverse ancestors (Hibbett et al., 1997; Thorn et al., 2000; Hibbett and Thorn, 2000), making the Agaricales polyphyletic. It has also been demonstrated that gasteromycetes (e.g., puffballs and sequestrate or secotioid fungi) have evolved several times from gilled or poroid ancestors (Baura et al., 1992; Bruns et al., 1989; Kretzer and Bruns, 1997; Hibbett et al., 1997; Peintner et al., 2001). These and other findings open the way to deconstruct artificial taxa (e.g., the Gasteromycetes) and redefine others in a phylogenetic context. In a preliminary outline for a major revision of the classification of the homobasidiomycetes based on phylogenetic principles, Hibbett and Thorn (2000) recognized eight major clades. The largest of these (with ca. 8400 known species), the euagarics clade, is the focus of this study. The core group of the euagarics clade is composed of gilled mushrooms. It corresponds largely to the Agaricineae of Singer (1986), but also includes taxa that were traditionally classified in the Aphyllophorales (e.g., Clavaria, Typhula, Fistulina, Schizophyllum, etc.) and several orders of Gasteromycetes (e.g., Hymenogastrales, Lycoperdales, Nidulariales). Phylogenetic relationships within the euagarics are still poorly known. However, an earlier molecular phylogenetic study that sampled rDNA sequences from 152 diverse agaricoid taxa showed that many families and genera of the Agaricales (e.g., K€ uhner, 1980; Singer, 1986) do not correspond to natural groups (Moncalvo et al., 2000). In this study we expand our previous sampling (Moncalvo et al., 2000) for the nuclear large ribosomal subunit gene (nLSU; or 25-28S rDNA) to include about one tenth of the total number of known species of euagarics. The nLSU region has been shown to be most useful to infer phylogenetic relationships in basidiomycetous fungi and allies at genus and family levels (Moncalvo et al., 2000; Fell et al., 2000; Weiss and Oberwinkler, 2001). Representatives of each of the eight major clades of homobasidiomycetes (as defined by Hibbett and Thorn, 2000) were also included in the analyses. The purpose of this large-scale analysis is to identify monophyletic groups (clades) of euagarics. 1. Materials and methods 1.1. Sampling of nucleotide sequences We sampled molecular data for 877 taxa representing 126 of the 192 Agaricineae genera recognized in Singer (1986) and members of each clade of homobasidiomycetes as defined in Hibbett and Thorn (2000). Nucleotide sequences produced in this study consist of about l000 bp located at the 50 end of the nuclear large ribosomal subunit gene, which encompass divergent domains D1– D3 (Michot et al., 1984). Sequences were produced in different laboratories using a variety of standard molecular methods. A total of 491 new sequences were produced for this study and were combined into a single data set with previously published sequences (Vilgalys and Sun, 1994; Chapela et al., 1994; Lutzoni, 1997; Binder et al., 1997; Pegler et al., 1998; Johnson and Vilgalys, 1998; Drehmel et al., 1999; Hopple and Vilgalys, 1999; Larsson and Larsson, 1998; Mitchell and Bresinsky, 1999; Thorn et al., 2000; Hwang and Kim, 2000; Moncalvo et al., 2000). The data matrix employed in Moncalvo et al. (2000) was used as a template for manual alignment of the other sequences. A small number of sequences were recoded to fit the template alignment (these sequences are labeled with an asterisk in the data matrix, which is available at http://www.biology.duke.edu/fungi/mycolab/agaricphylogeny_start.html). Recoding generally consisted in the removal of autapomorphic inserts located in otherwise highly conserved regions (these were phylogenetically uninformative, and some may also possibly be PCR-sequencing or editing errors). A sequence from the heterobasidiomycete Auricularia polytricha was used to root the homobasidiomycete phylogeny, as suggested in Hibbett et al. (1997). Collection data and GenBank accession numbers of the material used in this study are given in the Appendix. Authority names of the species used in this work can be found in the CABI Bioscience Database of Fungal Name (http://l94.131.255.3/cabipages/Names/ NAMES.ASP). Although a single sequence per species was used in the final analyses, taxonomic and sequence accuracy for several taxa were evaluated by sampling multiple collections from different sources. These taxa are identified in the Appendix A. J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 1.2. Phylogenetic analyses The 877 sequences sampled in this study were aligned in approximately 1000 positions. Hypervariable, indelrich regions with problematic alignment were excluded from the analyses. Unambiguously aligned gaps were treated as missing data. Phylogenetic analyses were conducted in PAUP* (Swofford, 1998) with Power Macintosh computers using maximum-parsimony as the optimality criterion. Unequally weighted parsimony was employed to account for biases in base composition and nucleotide substitution rates, using a stepmatrix estimated from a smaller, but similar data set (Moncalvo et al., 2000). It has been shown that unequally weighted parsimony can recover correct phylogenies with fewer characters than required by equally weighted parsimony (Hillis et al., 1994). Parsimony analyses of large data sets with high taxa/ characters ratio are impractical, and most parsimonious trees are not likely to be found (Rice et al., 1997). Therefore, only suboptimal searches could be conducted in this study. We performed an initial analysis using 100 heuristic searches of random addition sequence with TBR branch-swapping, MULPARS on, and MAXTREES set to 10, saving all trees in each replicate (the other settings in PAUP* were as follows: multistate taxa were interpreted as uncertainty, the steepest descent option was not in effect, and branches were collapsed if minimum branch length was zero). The shortest trees found in the initial searches were used as starting trees for a recurrent search with TBR branch-swapping and MAXTREES set to 5000. The Templeton (1983) test was used to evaluate whether the trees found in the initial and final searches differed statistically. Branch robustness was evaluated using 100 bootstrap (BS) replicates (Felsenstein, 1985) with TBR branch-swapping and MULPARS off. Fast bootstrap searches have been shown to reveal robust branches in large-scale phylogenies within a reasonable amount of computation time (Moncalvo et al., 2000). Several other searches using smaller data sets were also conducted for empirical examination of the sensitivity of the tree topologies in relation to taxon sampling, to test the robustness of certain clades. 2. Results 2.1. Phylogenetic analyses After removal of 123 redundant sequences (representing taxonomic duplicates) and regions with ambiguous nucleotide sequence alignment, the final data matrix was composed of 754 sequences and 781 characters: 211 characters were constant, 125 variable characters were parsimony uninformative, and 445 variable 359 characters were parsimony informative. The initial search produced 1000 trees ranging in size from 43988.7 to 44185.9. These trees were not significantly different from each other ðP > 0:05, Templeton test). When the shortest trees from the initial search were used as starting trees for TBR branch-swapping with MAXTREES set to 5000, the analysis yielded 5000 equally parsimonious trees of score 43985.2 (consistency index ¼ 0.1064, retention index ¼ 0.6611). To facilitate the discussion, we will refer to the strict consensus tree of the 5000 equally parsimonious trees found in the final analysis as the most parsimonious trees found (MPF tree). The MPF tree was carefully compared with the bootstrap tree and with slightly longer (but statistically not significantly different) trees produced in the initial searches to identify branches that were consistently recovered by maximum-parsimony and branches that were not. 2.2. Phylogenetic relationships Homobasidiomycetes clade. Both the MPF tree and the bootstrap tree support monophyly of six of the eight homobasidiomycetes clades recognized in Hibbett and Thorn (2000) and Binder and Hibbett (2002), i.e. (l) the euagarics clade, (2) the bolete clade, (3) the hymenochaetoid clade, (4) the thelephoroid clade, (5) the gomphoid–phalloid clade, and (6) the cantharelloid clade. The russuloid clade is recovered in the bootstrap tree (58% BS), but not in the MPF tree, whereas the polyporoid clade is recovered only in the MPF tree. A possible sister group relationship between the euagarics and the bolete clades (< 40% BS) and a basal position of the cantharelloid clade (< 41% BS) are also supported. Within the polyporoid clade, reciprocal monophyly of the polyporaceae and corticioid clades is supported in both the MPF and the bootstrap trees. These results are summarized in Figs. 1 and 2. Euagarics clade. Basal relationships within the euagarics clade were poorly resolved and several taxa remained as ‘‘orphans’’ (incertae sedis). Many branches present in the MPF tree collapsed in the bootstrap trees (Fig. 1). These branches were also generally not supported in trees slightly longer than the MPF tree (data not shown). Conversely, some branches recovered in the bootstrap tree were absent from the MPF tree but these branches generally had low statistical support (<40%; data not shown). For instance, the placement of the Amanita clade was inconsistent between different analyses: it is nested in a derived position of the Agaricaceae clade in the MPF tree and as sister group to Limacella in both the bootstrap tree and most of the suboptimal trees examined. To best summarize the results of the diverse analyses, we have edited the tree depicted in Fig. 2, as follows: branches that were not present in both the MPF tree and the bootstrap tree were collapsed, with the exception of some branches 360 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Fig. 1. Overall topologies of the strict consensus tree of 5000 equally most parsimonious trees found from heuristic searches (MPF tree) and the bootstrap 50% majority-rule consensus tree (BS tree). The placement in both trees of the eight major homobasidiomycetes groups (as defined in Hibbett and Thorn, 2000) is indicated by letters above corresponding branches. Trees are rooted with a sequence from the heterobasidiomycete Auricularia polytricha. that were present in either tree (as indicated in Fig. 2) which are useful for discussion. Within the euagarics, at least 117 clades revealed in the MPF tree (and generally also in slightly longer trees) have a bootstrap support >40% (Fig. 2) and/or are consistent with traditional groups based on morphology. Smaller clades often correspond to traditional genera (or part of them in cases of polyphyletic genera), J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 361 Fig. 2. Summary of the results of the phylogenetic analyses (see text). Branches in black lines were present in both the MPF tree and the bootstrap tree. Shaded branches were present in either the MPF (MP) or the BS tree, as indicated. Bootstrap values greater than 40% are shown above branches. In the tree depicted, Armillaria irazuensis should read A. affinis, Poromycena gracilis should read Fibboletus gracilis, and in /lichenomphalia Omphalia viridis should read O. hudsoniana. whereas several larger clades correspond to the core genera of traditional families, tribes, or subfamilies. Therefore, it is sometimes possible to label clades with existing names. Other clades, however, are composed of taxa for which a natural relationship was never sus- pected before or have no evident name associated with them. These clades are labeled with provisional names. To distinguish between clade names and traditional taxonomic names, clade names are written in lowercase, never italicized, and preceded with the symbol ‘‘/.’’ 362 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Fig. 2. (continued). 3. Discussion This study is the first broad systematic treatment of the ‘‘euagarics’’ as they have recently emerged in phylogenetic systematics (summarized in Hibbett and Thorn, 2000). For the first time, this work presents the unambiguous systematic placement among the euagarics of many Gasteromycetes (Table 1) and reduced forms (Table 2) and reveals natural relationships of several taxa for which taxonomic position has been controversial in the past. Some clades revealed in this work correspond in full or in part with taxonomic groups recognized in the last century J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 363 Fig. 2. (continued). (e.g., in K€ uhner, 1980; Singer, 1986; Pegler, 1983; Bas et al., 1988; J€ ulich, 1981); however, many do not. The global taxonomic sampling of this study has allowed the identification of many distinct natural groups from which exemplar taxa could be selected to best represent both the euagarics and the homobasidiomycetes diversity in future phylogenetic studies. Data from other genes are still necessary both to examine to what extent the nLSU phylogeny shown in Figs. 1 and 2 does reflect organismal phylogeny (Doyle, 1992; Maddison, 1997) and to better resolve phylogenetic relationships both among and within clades. By sampling about one tenth of the total number 364 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Fig. 2. (continued). of known species of euagarics (Hawksworth et al., 1995; Hibbett and Thorn, 2000) and many other homobasidiomycetes taxa, this work should also significantly contribute to the development of a molecular database for the identification of new taxa and fungi from environmental samples (Bruns et al., 1998). 3.1. Large-scale phylogenies and higher clades of homobasidiomycetes A common question in molecular systematics concerns optimization of the sampling ratio between the number of taxa vs characters and the number of char- J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 365 Fig. 2. (continued). acters that are necessary to recover a correct phylogeny (Lecointre et al., 1994; Berbee et al., 2000). Both theoretical and empirical studies have demonstrated that increasing the taxa/characters ratio generally results in a decrease of statistical support in phylogenetic trees, especially at deeper nodes. However, it has also been shown that increasing taxon sampling increases accu- racy of phylogenetic reconstruction (Hillis, 1996, 1998). In this study, the number of taxa sampled (877) was about twice higher than the number of parsimony-informative characters sampled (445). Therefore, high statistical support for deeper nodes was unlikely to be attainable. In contrast, the recent homobasidiomycetes phylogeny of Binder and Hibbett (2002) used a much 366 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Fig. 2. (continued). lower taxa/characters ratio, consisting of 83 taxa and 1114 parsimony-informative characters (produced from sequence data from four ribosomal genes). It is therefore helpful to compare results from these two studies. Our analyses recover six of the eight homobasidiomycetes clades revealed in Binder and Hibbett (2002), but with lower bootstrap support. Both studies poorly resolve basal relationships between the homobasidiomycetes lineages, but both suggest a more basal position of the cantharelloid, gomphales–phallales, and thelephoroid clades. A major result in Binder and Hibbett (2002) was the strong bootstrap statistical support for a sister group relationship between the euagarics and the boletes (90% BS). This relationship J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 367 Fig. 2. (continued). was only weakly suggested in earlier studies that sampled fewer characters (Hibbett et al., 1997; Fig. 5 in Moncalvo et al., 2000) and in the large-scale analysis presented here (< 40% BS; Fig. 2). Another significant result in Binder and Hibbett (2002) was the well-supported placement of Hygrocybe and Humidicutis (Hygrophoraceae) at the base of the euagarics (85% BS), which in other studies were found either inside (Moncalvo et al., 2000) or outside (Bruns et al., 1998) the euagarics in phylogenetic reconstructions. Based on nLSU evidence, support for a monophyletic Hygrophoraceae is still lacking, and there is no indication of a possible placement of Hygrophorus/Humidicutis at the base of the euagarics clade. 368 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Fig. 2. (continued). At least three conclusions with regard to homobasidiomycetes phylogeny can be drawn from these and earlier studies: (1) a dense taxon sampling using a limited number of phylogenetic characters—as conducted here—can still recover deeper nodes in the phylogeny and reveal many terminal clades with high bootstrap statistical support; (2) a higher character/taxa ratio—as conducted in Binder and Hibbett (2002)—can boost bootstrap statistical support at deeper nodes, but not always; and (3) ribosomal genes alone are not sufficient to fully resolve natural relationships among higher clades of homobasidiomycetes. J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 369 Fig. 2. (continued). 3.2. Morphological and ecological insights derived from the euagarics phylogeny Gasteromycetization. The nesting of gasteromycetes taxa (e.g., puffballs and allies) among various groups of homobasidiomycetes was already indicated in earlier works (e.g., Baura et al., 1992; Bruns et al., 1989; Kretzer and Bruns, 1997; Hibbett et al., 1997; Peintner et al., 2001). However, as summarized in Table 1, this study is the first to unambiguously place several orders, families, and genera of gasteromycetes within the euagarics. Some of these relationships were already suggested by morphotaxonomists, including affinities between Torrendia and Amanita, between Thaxterogaster and Cortinarius, and between Longula and Agaricus (Malencon, 1931, 1955; Savile, 1955, 1968; Heim, 1971; Smith, 1973; Bas, 1975; Thiers, 1984; Miller and Walting, 1987; Reijnders, 2000), but others were not. For instance, the placement of the true puffballs (/lycoperdales; clade 83 in Fig. 2) and Tulostoma and Battarraea in /agaricaceae (clade 82) was not previously suspected by morphotaxonomists. However, it has already been shown that Agaricus mushrooms have many biochemical features in common with members of the Lycoperdales (see below). Gasteromycetization appears to have occurred more frequently in certain clades, in particular in /agaricaceae and brown-spored groups. Cyphelloid and reduced forms. Another syndrome of agaricoid fungi is the reduction of form or cyphellization, which has also occurred multiple times (Fig. 2 and 370 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Fig. 2. (continued). Table 2). For instance, we have identified Caripia as a reduced Gymnopus (in clade 5), Stigmatolemma as a cyphelloid Resupinatus (in clade 25), and Porotheleum as a cyphelloid member of /hydropoid (clade 27). Reduction and cyphellization are not unique to the euagarics, however, as shown by the placement of Podoscypha within the polyporoid clade and of Cotylidia within the hymenochaetoid clade. Polyphyletic origin and instability of the lamellate hymenium. Results from this study support earlier findings that demonstrate the multiple origins of the lamellate hymenium within the basidiomycetes (Hibbett et al., 1997; Thorn et al., 2000; Moncalvo et al., 2000) and reveal for the first time that the hymenochaetoid clade might also include gilled fungi (Rickenella, Cantharellopsis, and Omphalina pro parte; Fig. 2). A lamellate hymenium is also known in the bolete clade (Phylloporus; Bruns et al., 1998, Fig. 2), the polyporoid clade (Lentinus, Neolentinus, Heliocybe, and Faerberia; Hibbett and Vilgalys, 1993; Hibbett et al., 1997; Thorn et al., 2000, Fig. 2), the russuloid clade (Russulaceae; Hibbett et al., 1997; Moncalvo et al., 2000, Fig. 1), and the cantharelloid clade (Hibbett et al., 1997). Fig. 2 also indicates that transition from a gilled ancestor to a poroid hymenophore architecture has occurred at least three times within the euagarics: /fistulinoid (clade 117) in clade 115 and two times within /mycenaceae (clade 47). In the latter clade, Dictyopanus is in a derived position in /panelloid (clade 48), and /favolaschia and /porolaschia (clades 49 and 50) have probably both been derived from a common gilled ancestor. Ectomycorrhizal vs saprophyte habit. Most clades revealed in this study are only composed of either J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Table 1 Classification of gasteromycetoid taxa among the euagarics clade as indicated by molecular data Gasteromycete taxa Euagarics clade Lycoperdales Tulostoma Battarraea Podaxis /agaricaceae /agaricaceae /agaricaceae /agaricaceae Montagnea Longula Gyrophragmium Torrendia Thaxterogaster Protoglossum Hymenogaster pro parte Quadrispora Setchelliogaster References This work This work This work Hopple and Vilgalys, 1999 This work /agaricaceae/coprinus This work /agaricaceae/agaricus This work /agaricaceae/agaricus This work /amanita/caesareae This work /cortinarioid This work; Peintner et al., 2001 /cortinarioid Peintner et al., 2001 /cortinarioid Peintner et al., 2001 /cortinarioid Descolea spp. Descomyces Hymenogaster pro parte Gastrocybe Descolea spp. /hebelomatoid Leratiomyces smaragdina Leratiomyces similis /agrocybe /conocyboid Weraroa /stropharioid/ magnivelaris /stropharioid Nia Nidulariales /schizophylloid unresolved position Peintner et al., 2001 Martin and Raccabruna, 1999 Peintner et al., 2001 Peintner et al., 2001 Peintner et al., 2001 Hallen and Adams, 2000; this work This work Binder et al., 1997; This work Binder et al., 1997; this work Binder et al., 2001 Hibbett et al., 1997; this work Table 2 Classification of reduced forms among the euagarics clade as indicated by molecular data Reduced taxa Euagarics clade References Caripia Physalacria Lachnella Gloeostereum Calyptella Clavaria fusiformis Stigmatolemma Porotheleum Typhula phacorrhiza Stereopsis humphreyi Porodisculus Plicaturopsis /omphalotaceae/micromphale /physalacriaceae/physalacria euagarics /gloeostereae /hemimycena ? /tricholomopsis /resupinatus /hydropoid /phyllotopsis euagarics /fistulinoid euagarics; Clitocybe group? This This This This This This This This This This This This work work work work work work work work work work work work obligatory saprophytic or ectomycorrhizal taxa. For instance, all members of the larger /agaricaceae (clade 82), /mycenaceae (clade 47), /psathyrellaceae (clade 89), / stropharioid (clade 107), and the possibly monophyletic larger group that includes clades 1–26 are saprophytic. Clades composed only of putatively obligatorily ecto- 371 mycorrhizal taxa (Singer, 1986; Cl
emencßon, 1997; Norvell, 1998) include /tricholoma (clade 37), /amanita (clade 55), /hygrophorus (clade 65), /cortinarioid (clade 73), /phaeocollybia (clade 74), /hebeloma (clade 95), and /inocybe (clade 104). The existence of numerous, relatively large clades composed of either saprophytic or ectomycorrhizal fungi indicates that these two ecological habits have been relatively stable at least during the more recent radiation of the euagarics. Because of a lack of resolution of basal relationships, our phylogeny can neither fully support nor contradict results from a recent study by Hibbett et al. (2000) suggesting that the ancestor of the euagarics was ectomycorrhizal and that there have been multiple reversals to the saprophytic habit within this clade. However, there are several cases in our phylogeny that suggest that a transition from a saprophyte to a mycorrhizal habit is also possible. For instance, the putatively obligatorily ectomycorrhizal genus Descolea (Horak, 1971) is nested among saprophyte genera of clades 76–79, and both /amanita (clade 55) and /tricholoma (clade 37) also appear to be in derived, rather than basal, positions. All taxa in the Lyophylleae group are known to be saprophytes (Singer, 1986); therefore, the facultative mycorrhizal habit in Lyophyllum shimeji (Ohta, 1994; Agerer and Beenken, 1998), an ally to L. decastes (Moncalvo et al., 1993) in clade 34, is likely to be derived. Relationships with other cryptogams. Transition from a free-living to an obligatory lichenized habit has occurred at least three times independently within the homobasidiomycetes, as indicated from both anatomical (Oberwinkler, 1984; Redhead and Kuyper, 1987) and molecular (Gargas et al., 1995) evidence. It occurred at least once in the euagarics, with the radiation of /lichenomphalia (clade 64) from within the Arrhenia group. A second group of lichenized basidiomycetes, Dictyonema, may also possibly belong to the euagarics (Gargas et al., 1995); however, this taxon has not been sampled here and its phylogenetic affinities still remain unclear. The third known lichenization event in the homobasidiomycetes has occurred in the cantharelloid clade (Multiclavula), as indicated in both Fig. 2 and Hibbett et al. (1997). A suspected lichen parasite, Gamundia leucophylla (Bigelow, 1979), belongs to the euagarics and nests in a derived position in /fayodioid (clade 28). The biology of the association between agaric fungi and bryophytes is still not well known, but has been documented in several studies (e.g., Redhead, 1981, 1984). The phylogeny depicted in Fig. 2 reveals that transition to a facultative or an obligatory bryophilous habit has occurred several times independently, apparently always from a saprophyte ancestor. For instance, Lyophyllum palustris (parasite on Sphagnum; Redhead, 1981) is derived from within the Lyophylleae group (which encompasses clades 30–35). Galerina paludosa (also a parasite on Sphagnum; Redhead, 1981, 1984) is 372 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 possibly sister group to /gymnopilus (clade 98). The bryophilous or peat-inhabiting species Hypholoma ericaeum, Pholiota myosotis, and Pholiota henningsii (Noordeloos, 1999) are all independently derived from within /stropharioid (clade 107). Hypholoma uda and Phaeogalera stagnina (Redhead, 1979) are independently derived from psilocyboid taxa (at the base of clade 113 in Fig. 2). The fungus–bryophyte association does not appear to be evolutionarily very successful, judging from the limited radiation of bryophyte-associated clades. We observe only four instances of such radiations. (1) Psilocybe montana and P. chionophila are both often associated with mosses (Lamoure, 1977) and are uniquely derived from within /psilocybe (clade 113). (2) The / omphalina (clade 60) is composed of bryophilous species (Omphalina pyxidata and O. rivulicola; Lamoure, 1974) that are possibly a sister group of saprophytic species of Clitocybe and monophyletic with another bryophilous taxon, Rimbachia (Redhead, 1984) (Omphalina group in Fig. 2), hence representing one to two independent origins. (3) Nearly all members of /arrhenia (clade 63) are associated with bryophytes (Redhead, 1984). (4) All gilled taxa of /hymenochaete (Omphalina rosella, O. brevibasidita, O. marchantiae, Cantharellopsis prescottii, Rickenella mellea, and R. pseudogrisella) are bryophilous as are some Cotylidia species (S.A. Redhead et al., unpublished), and all may have a single origin (Fig. 2). Relationships with insects. Chapela et al. (1994) identified three groups of ant-associated fungi (labeled G1–G3). The phylogeny depicted in Fig. 2 indicates that two groups, G1 and G3, are independently derived from within /agaricaceae (clade 82), G3 being possibly monophyletic with members of the Leucocoprinus group (Johnson and Vilgalys, 1998). Group G2 is weakly supported (45% BS) as a sister group of /hydropoid (clade 27). The relatively large, obligatory termite-associate genus Termitomyces (Heim, 1977) forms clade 35 within the Lyophylleae group. The association between euagarics and insects has therefore developed independently several times. These associations appear to be evolutionarily stable, as indicated in our phylogeny by taxonomic radiation of the fungal partner and lack of observed reversal to a free-living habit. Overall, it appears that ecology supports many natural groups of euagarics better than morphology. It is therefore striking to observe that all earlier major treatments of the Agaricales focused primarily on morphology and microanatomy (e.g., K€ uhner, 1980; Singer, 1986; Pegler, 1983; Bas et al., 1988; J€ ulich, 1981; Cl
emencßon, 1997), with limited attention being given to the taxonomic significance of physiological and ecological traits. This might explain why several taxonomic groups erected in the past are not natural. Redhead and Ginns (1985) were the first to introduce the idea of defining agaric genera based in part on their nutritional mode, but also supported by anatomical data, mating strategies, and nuclear status. Based upon wood rot capability, mycorrhizal formation, and nematophagy these authors refined several generic concepts (e.g., in Lentinula, Lentinus, Pleurotus, and Hypsizygus) and created new genera (e.g. Neolentinus and Ossicaulis) that are also supported by the molecular data presented here. For instance, our results support the distinction between Lentinula (in clade 8), Lentinus, and Neolentinus (the latter two being in /polyporaceae in the polyporoid clade; Fig. 2), in agreement with Thorn et al. (2000), and the segregation of Ossicaulis and Hypsizygus (both in the Lyophylleae group) from Pleurotus (in clade 59). 3.3. Clades of euagarics The reconstruction of a monophyletic euagarics results in the exclusion from that clade of several groups of gilled fungi traditionally classified in the Agaricales (e.g., the Russulaceae and Rickenella) and necessitates the inclusion in the clade of several clavaroid, poroid, secotioid, gasteroid, and reduced forms (Tables 1 and 2) that were traditionally classified in other orders of basidiomycetes or else controversially classified. Morphological, physiological, or ecological synapomorphies for the euagarics clade are unknown. Below, we list and briefly discuss the 117 euagarics clades recognized in Fig. 2. Many clades are directly rooted to the euagarics node. When a clade is not directly rooted to the euagarics node, its containing clade(s) is (are) indicated. For instance, to indicate that clade 3 (/omphalotus) nests in clade 2 (/omphalotoid), which is contained in clade 1 (/omphalotaceae), the following notation is used: /omphalotaceae/omphalotoid/omphalotus. These notations are practical. In future studies, it might be possible to reconcile phylogenetic systematic and traditional taxonomy. Clade 1 (87% BS): /omphalotaceae. Representative taxa: /lentinuloid and /omphalotoid. This clade includes several genera that were traditionally classified in various families or tribes of Agaricales (Singer, 1986) and one reduced form (Caripia montagnei) that was generally placed in the Stereales (Hawksworth et al., 1995). All / omphalotaceae are saprophytic or necrotrophic on wood or litter and have nonamyloid basidiospores that lack a germ pore. Clade 2 (64% BS): /omphalotoid. Containing clade: / omphalotaceae. Representative taxa: Anthracophyllum, Omphalotus, Lampteromyces, and Neonothopanus. The MPF tree indicates that /omphalotoid is possibly paraphyletic, but monophyly is relatively well supported by bootstrapping (64% BS) and by equally weighted parsimony analysis (data not shown). All members of this clade are lignicolous and have basidiomata with decurrent lamellae or that lack a well-formed central stipe. In general, the context tissues of the basidiomata are poorly differentiated and cystidia are absent. Anthraco- J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 phyllum, Lampteromyces, and Omphalotus species have all been shown to contain atromentin, as do other unrelated taxa (e.g., several boletes; Gill and Steglich, 1987). Lampteromyces and Omphalotus species also contain illudins and are luminescent and toxic (Singer, 1986). Neonothopanus nambi (reported as Pleurotus eugrammus; see Petersen and Krisai-Greilhuber, 1999) has also been reported to be luminescent (Corner, 1981), but this report needs confirmation. Clade 3 (75% BS): /omphalotus. Containing clades: / omphalotaceae/omphalotoid. Representative taxa: Omphalotus spp. and Lampteromyces japonicus. The tree topology in Fig. 2 suggests that these two generic names are possibly synonymous. Clade 4 (88% BS): /lentinuloid. Containing clade: / omphalotaceae. Representative taxa: Caripia, Gymnopus, Lentinula, Marasmiellus pro parte, Marasmius pro parte [excl. type], Micromphale, Rhodocollybia, and Setulipes. Close affinities between members of this clade have not been previously suggested. However, members of /lentinuloid share several characteristics. They all have pale, nonamyloid spores with a thin or secondarily thickened wall and no germ pore. Hyphae in the basidiomata often thicken and subsequently impart revivability to the carpophores. Several lentinuloideae taxa produce glutamyl–peptides which are precursors of compounds with a polysulfide smell (Gmelin et al., 1976). Clade 5 (76% BS): /micromphale. Containing clades: /omphalotaceae/lentinuloid. Representative taxa: Gymnopus pro parte, Caripia, Setulipes, and Micromphale. The type species of both Setulipes (S. androsaceus) and Micromphale (M. foetida) nest in this clade. Our results support segregation of Setulipes from Marasmius (Antonin, 1987) since the type of the latter genus, M. rotula, is in Clade 21. Micromphale is polyphyletic since M. perforans, although also belonging to this clade, does not cluster with M. foetida. Gymnopus sensu Halling (1983) and Antonin et al. (1997) is also polyphyletic, with its members nesting in both this clade and clade 7. Caripia, which produces highly reduced basidiomata, is apparently derived from Gymnopus species, which has not been previously suspected. Clade 6 (97% BS): /scorodonius. Containing clades: / omphalotaceae/lentinuloid. Representative taxa: Marasmius scorodonius and Marasmiellus opacus. A possible relationship between these two species has never been suspected before and is difficult to explain based on morphological or anatomical characters. Clade 7 (58% BS): /rhodocollybia. Containing clades: /omphalotaceae/lentinuloid. Representative taxa: Rhodocollybia maculata, Marasmiellus ramealis, and Gymnopus pro parte. Marasmiellus is polyphyletic, with M. ramealis clustering in /rhodocollybia and M. opacus in / scorodonius. It still remains unknown where its type species, M. juniperinus, belongs. 373 Clade 8 (89% BS): /lentinula. Containing clades: / omphalotaceae/lentinuloid. This clade corresponds to the genus Lentinula Earle. Clade 9 (71% BS): /physalacriaceae. Representative taxa: /physalacrioid and Armillaria. Although Physalacriaceae was originally conceived for clavaroid fungi (Corner, 1970), inclusion of Physalacria in the Agaricales in the vicinity of Gloiocephala by Singer (1951, 1986) is congruent with nLSU phylogeny. Physalacriaceae is apparently the oldest available family name for clade 9; however, it still remains to be demonstrated if the type species of Physalacria P. inflata belongs to this clade. Clade 10 (65% BS): /physalacrioid. Containing clade: /physalacriaceae. Representative taxa: Cyptotrama, Flammulina, Gloiocephala, Oudemansiella, Physalacria aff. orinocensis, Rhizomarasmius, Strobilurus, Xerula, and Oudemansiella. Several morphological similarities exist among these taxa. Most members of /physalacrioid have a hymeniform pileipellis composed of smooth and clavate cells that are often embedded in a gel, and several are characterized by the abundance of secretory, large, presumably multinucleate cystidia either in the hymenium, lamellar edges, pilear, and/or stipe surfaces. Strobilurins (antibiotics) are produced by Oudemansiella, Strobilurus, and Xerula, but also occur in other lineages (Anke, 1997). /Physalacrioid are primary colonizers of dead wood or leaves and do not demonstrate competitive ability of the mycelium to proliferate in soils and heavily colonized or rotten substrates. Flammulina, Rhizomarasmius, Strobilurus, and Xerula are also adapted for colonization of subterranean material. Our results also support the segregation of Marasmius pyrrhocephalus into Rhizomarasmius, as proposed by Petersen (2000), and indicate polyphyly of Gloiocephala sensu Singer (1986). Clade 11 (65% BS): /physalacria. Containing clades: / physalacriaceae/physalacrioid. Representative taxa: Physalacria aff. orinocensis and Gloiocephala spathularia. Both taxa are reduced agarics. Clade 12 (95% BS): /oudemansiella. Containing clades: /physalacriaceae/physalacrioid. Representative taxa: Oudemansiella and Xerula. The two names are sometimes considered synonyms (Singer, 1986). A close relationship of these two taxa is confirmed here. Clade 13 (97% BS): /armillaria. Containing clade: / physalacriaceae. This clade corresponds to the genus Armillaria (Fr.) Staude. Clade 14 (52% BS): /gloeostereae. Representative taxa: Gloeostereum and Cheimonophyllum. Both taxa are lignicolous, have fleshy and conchate pilei and inamyloid and white spores, and produce sequiterpene-based antibiotics (Takazawa and Kashino, 1991; Stadler et al., 1994). They have been classified together in the tribus Gloeostereae Ito & Imai (Parmasto, 1968) in the Stereales. Cheimonophyllum, but not Gloeostereum, was 374 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 placed in the Agaricales by Singer (1986). It was recently debated whether Gloeostereum is closer to Phlebia (/corticioid, in the polyporoid clade) or to the agarics (Petersen and Parmasto, 1993): this study indicates that it is phylogenetically related to the latter group. Clade 15 (56% BS): /baeosporoid. Representative taxa Baeospora and Hydropus scabripes. Both taxa have amyloid spores, cheilocystidia, dermatocystidia, and sarcodimitic tissues (Redhead, 1987) and form masses of simple conidia in culture (S.A. Redhead, pers. observ.). Hydropus scabripes was originally described in Mycena but based on nLSU data it is phylogenetically unrelated to either the type of Hydropus (H. fuliginarius, in clade 27) or Mycena (M. galericulata, in clade 47). /Baeosporoid is difficult to separate morphologically from /hydropoid (clade 27). Clade 16 (100% BS): /baeospora. Containing clade: / baeosporoid. This clade corresponds to the genus Baeospora Singer. Clade 17 (48% BS): /marasmiaceae. Representative taxa: /tetrapyrgoid and /marasmioid. All members of this clade have pale spores and are saprophytes. Clade 18 (100% BS): /tetrapyrgoid. Containing clade: /marasmiaceae. Representative taxa: Campanella and Tetrapyrgos. /Tetrapyrgoid is mostly composed of tropical species growing on woody debris. Basidiospores are hyaline, thin walled, smooth, inamyloid, and acyanophilous; the pilear trama is gelatinized (at least partly), inamyloid, with clamp connections; the epicutis has a well-developed or imperfect Rameales structure. Clade 19 (87% BS): /tetrapyrgos. Containing clades: / marasmiaceae/tetrapyrgoid. This clade corresponds to the genus Tetrapyrgos Horak. It differs from its sister group, /campanella, by having tetraradiate basidiospores and a centrally or laterally attached pileus. Clade 20 (61% BS): /campanella. Containing clades: / marasmiaceae/tetrapyrgoid. Representative taxa: Campanella spp. and an unidentified agaric. The two unidentified collections sampled from the mostly tropical genus Campanella exhibit the typical characters of the genus, as described in Singer (1986). The sister taxon (100% BS) of these two collections is another tropical, unidentified, centrally stipitate fungus with distant but well-developed gills connected with lower ridges or anastomoses (collection JMCR.34). Following Singer (1986), this collection would be classified as a Marasmiellus sensu lato, but its trama is similar to that of Campanella species. Clade 21 (85% BS): /marasmioid. Containing clades: /marasmiaceae. Representative taxa: Chaetocalathus, Crinipellis, Marasmius (incl. Hymenogloea). Clade 22 (71% BS): /crinipellis. Containing clades: / marasmiaceae/marasmioid. This clade corresponds to the genus Crinipellis Pat., which can be distinguished from other members of marasmioid by the presence of pseudoamyloid hairs on the pileus. Clade 23 (100% BS): /hemimycena. Representative taxa: Hemimycena spp. and Calyptella copula. Our results support the segregation of Hemimycena Singer from the bulk species of Mycena (clade 47) and indicate that the cyphelloid fungus Calyptella capula is derived from Hemimycena. Clade 24 (100% BS): /tricholomopsis. Representative species: Tricholomopsis rutilans, Collybia aurea, and Marasmius rhyssophyllus. A close relationship between the taxa of this clade has never been suspected before. All are saprophytic. Clade 25 (82% BS): /resupinatus. Representative taxa: Resupinatus and Stigmatolemma. Molecular data are in agreement with Singer (1986), who indicated a close relationship between Resupinatus and the reduced fungus Stigmatolemma. Our results additionally show that Stigmatolemma is derived from within Resupinatus, making the latter paraphyletic. Clade 26 (42% BS): /adonis. Representative species: Mycena aurantiidisca, M. adonis, and an unidentified marasmielloid, bioluminescent fungus from the neotropics. These species differ from Mycena sensu stricto (clade 47) by having inamyloid spores. Clade 27 (75% BS): /hydropoid. Representative taxa: Hydropus sensu stricto, Gerronema pro parte, Megacollybia, Clitocybula, and Porotheleum fimbriatum. The type of the genus Hydropus, H. fuliginarius, clusters here, whereas H. scabripes is in clade 16. Therefore, Hydropus sensu Singer (1986) is polyphyletic and should probably be restricted to species with amyloid spores, lacking pleurocystidia, and producing latex, as originally conceived by K€ uhner (1938). Our results also support K€ uhner’s (1980) placement of Megacollybia and Clitocybula close to Hydropus and indicate that the reduced fungus Porotheleum fimbriatum is derived from Hydropus species. Gerronema sensu Singer (1986) is polyphyletic (Lutzoni, 1997; Moncalvo et al., 2000), but is monophyletic as restricted by Norvell et al. (1994). Clade 28 (47% BS): /fayodioid. Representative taxa: Gamundia leucophylla, Caulorhiza hygrophoroides, Conchomyces bursaeformis, Myxomphalia maura, and Fayodia gracilipes. Although the presence of the latter taxon in this clade is moderately supported, there is good statistical support for the monophyly of the other taxa (75% BS). Singer (1986) already recognized affinities between some members of this clade as he considered Gamundia and Myxomphalia synonyms of Fayodia. However, a possible relationship between these taxa and Caulorhiza and Conchomyces has never been suspected before. Possible monophyly of clades 29–46. The MPF and slightly longer trees and trees produced with reduced data sets (data not shown) all consistently indicate the possible monophyly of a larger clade that includes the Collybia–Clitocybe (pro parte) group, the Lyophylleae group, /tricholomatoid, and Entolomataceae. However, J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 there is presently no statistical support to formally recognize this putative clade. Natural relationships between Tricholoma, Lyophylleae, and Entolomataceae have been speculated by Cl
emencßon (1978, 1997) from similarities in the cell walls of basidiospores and the presence of siderophilous granules in the basidia in Lyophylleae and some Entolomataceae taxa. The Collybia–Clitocybe group. In all our analyses / collybia, Clitocybe spp., Lepista spp., Dendrocollybia, Omphaliaster, and the reduced form Plicaturopsis crispa are recovered as a mono- or paraphyletic group attached to either the Lyophylleae group or /tricholomatoid. Clade 29 (70% BS): /collybia. This clade includes the type species of Collybia Kummer, C. tuberosa. Collybia should be restricted to its type and closely related taxa (including C. cirrhata and C. cookei; Fig. 2; Hughes et al., 2001). The Lyophylleae group. Both the MPF tree and the bootstrap tree produced in this study (Fig. 2) are in agreement with earlier studies that place Termitomyces in the Lyophylleae (Moncalvo et al., 2000; Hofstetter, 2000). Here we show that Ossicaulis may possibly also belong to this group (a sequence labeled Ossicaulis (GenBank Accession No. AF042625) that clustered with Macrocybe in Moncalvo et al. (2000) has been reidentified as a sequence of Callistosporium). However, statistical support for recognizing a larger, monophyletic Lyophylleae is weak. In particular, the exact positions of Ossicaulis (the only taxon of this clade lacking siderophilous granules) and Hypsizygus (which clusters outside the group in several suboptimal trees examined) remain unclear. The clades recognized below in the Lyophylleae group are in agreement with results of a broader, multigene systematic study of the Lyophylleae (Hofstetter, 2000). Clade 30 (98% BS): /asterophora. This clade belongs to the Lyophylleae group and corresponds to Asterophora Ditmar ex. Link (Redhead and Seifert, 2001). In Fig. 2, the sister group of /asterophora is Tricholomella constricta. Clade 31 (100% BS): /myochromella. This clade belongs to the Lyophylleae group. Representative species: Lyophyllum boudieri and L. inolens. /Myochromella is composed of small, collybioid species formerly classified in either Lyophyllum or Tephrocybe, which can be separated from these genera by having a striate and hygrophanous cap (Hofstetter, 2000). Clade 32 (74% BS): /lyophylloid. This clade belongs to the Lyophylleae group. Representative taxa: Lyophyllum leucophaeatum (type of Lyophyllum Karst.), L. favrei, L. ochraceum, and Calocybe spp. Clade 33 (63% BS): /calocybe. Containing clade: / lyophylloid, in the Lyophylleae group. This clade corresponds to the genus Calocybe sensu Singer (1986) with the exclusion of C. constricta and the inclusion of Lyophyllum favrei and L. ochraceum. Therefore, our results 375 support both the segregation of C. constricta in Tricholomella (Kalamees, 1992) and a close relationship between L. favrei and L. ochraceum with Calocybe species as indicated in K€ uhner and Romagnesi (1953). Clade 34 (62% BS): /paralyophyllum. This clade belongs to the Lyophylleae group. Representative taxa: Lyophyllum ambustum, L. decastes, L. semitale, L. caerulescens, L. anthracophilum, and L. atratrum. Clade 35 (100% BS): /termitomyces. This clade belongs to the Lyophylleae group. It corresponds to the termite-associated genus Termitomyces Heim (including Podabrella Singer), which is sister group to the type species of Tephrocybe (T. rancida) in Fig. 2. Clade 36 (40% BS): /tricholomatoid. Representative taxa: Tricholoma, Leucopaxillus, and Porpoloma. This clade is composed of fungi with a tricholomatoid habit and a white spore deposit. Our sampling of Porpoloma was restricted to a single, unidentified species; therefore a closer examination of this genus is still necessary to fully address its phylogenetic affinities. Tricholoma is held to be obligatorily ectomycorrhizal, whereas it is still controversial whether Porpoloma and Leucopaxillus are ectomycohrizal or saprophytic (Singer, 1986; Cl
emencßon (1997; G. Thorn, pers. obs.)). Clade 37 (68% BS): /tricholoma. Containing clade: / tricholomatoid. This clade corresponds to Tricholoma (Fr.) Staude, which is monophyletic only when restricted to ectomycorrhizal taxa (Pegler et al., 1998; Moncalvo et al., 2000). Clade 38 (82% BS): /leucopaxillus. Containing clade: /tricholomatoid. This clade corresponds to the genus Leucopaxillus Boursier as described in Singer (1986). In Fig. 2, Leucopaxillus is phylogenetically distinct from Tricholoma in contrast to a previous report (Moncalvo et al., 2000) that used a mislabeled sequence (L. albissimus SAR1-2-90, GenBank Accession No. AF042592, excluded from this study). Porpoloma is weakly supported as sister group of /leucopaxillus (Fig. 2). Clade 39 (100% BS): /catathelasma. This clade corresponds to Catathelasma Lovejoy, a taxon with problematic classification (K€ uhner, 1980; Singer, 1986). Analyses of nLSU sequence data consistently place it with two Rhodocybe species (Fig. 2), although without significant statistical support. We are not aware of any obvious anatomical, physiological, or ecological similarity between these taxa. Therefore, we consider /catathelasma to have unknown phylogenetic affinity in the euagarics. Entolomataceae (rhodocyboid and entolomatoid groups in Fig. 2). Modern agaricologists have agreed that the angular-pink-spored agarics (Entoloma sensu lato, Clitopilus, and Rhodocybe) represent a natural group, Entolomataceae (Singer, 1986; K€ uhner, 1980; Horak, 1980; Baroni, 1981; Baroni and Lodge, 1998). However, there is virtually no molecular support for a monophyletic Entolomataceae in our analyses, but this 376 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 hypothesis cannot be rejected from our data. In Fig. 2, the Entolomataceae segregates into two statistically weakly supported groups: a rhodocyboid group (Rhodocybe and Clitopilus) and an entolomatoid group (Entoloma sensu lato). Consistently nested in the former group is /catathelasma (clade 39), and frequently nested within the latter group is /callistosporoid (clade 41). Clade 40 (69% BS): /clitopilus. This clade belongs to the rhodocyboid group in the Entolomataceae. Representative taxa: Clitopilus spp. (including the type, C. prunulus) and Clitopilopsis hirneola. Clade 41 (97% BS): /callistosporoid. Representative taxa: Callistosporium, Macrocybe, and Pleurocollybia. This clade has not previously been recognized. All / callistosporoid are saprophytic and have a white spore print and hyaline, smooth, and inamyloid spores. Pigments are intracellular when present, and the epicutis is composed of filamentous hyphae that are either repent (Callistosporium and Pleurocollybia) or strongly interwoven (Macrocybe). Clade 42 (99% BS): /macrocybe. Containing clade: / callistosporoid. This clade corresponds to Macrocybe Pegler. Clade 43 (99% BS): /callistosporium. Containing clade: /callistosporoid. This clade corresponds to Callistosporium Singer. Its sister group is Pleurocollybia brunnescens (79% BS). Clade 44 (59% BS): /abortivum. This clade belongs to the entolomatoid group in the Entolomataceae. Representative species: Entoloma undatum, E. abortivum, E. sericeonitida, and Leptonia gracilipes. Clade 45 (< 40% BS): /nolanea. This clade belongs to the entolomatoid group in the Entolomataceae. It corresponds to the genus Nolanea (Fr.) Qu
elet, which may therefore warrant distinction from Entoloma. Clade 46 (59% BS): /inocephalus. This clade belongs to the entolomatoid group in the Entolomataceae. It corresponds to the genus Inocephalus (Noordeloos) P.D. Orton (Baroni and Hailing, 2000), with the inclusion of Entoloma canescens. Clade 47 (76% BS): /mycenaceae. Representative taxa: Mycena pro parte (including its type, M. galericulata), Resinomycena, Panellus stypticus (type of Panellus,) Dictyopanus, Favolaschia, Poromycena and Filoboletus spp., Prunulus, and Mycenoporella griseipora. Members of this clade of pale-spored agarics are morphologically very diverse, but amyloid spores are nearly always formed and dextrinoid tissues are frequent. Nearly all are primary colonizers of wood or leaves (they are rarely found on humus). Mycena sensu Singer (1986) is a polyphyletic genus with members clustering both in this clade and /adonis (clade26). It should therefore be restricted to taxa around its type species, M. galericulata. This study reveals a previously unsuspected relationship between Mycena and Panellus (including Dictyopanus). It also unambiguously places the tropical, poroid genus Favolaschia among the euagarics. Clade 48 (49% BS): /panelloid. Containing clade: / mycenaceae. Representative taxa: Resinomycena, Panellus, Dictyopanus, and Mycena viscidocruenta. A natural relationship between these taxa has never been suspected before. Clade 49 (<50% BS): /favolaschia. Containing clade: /mycenaceae. This clade corresponds to the genus Favolaschia (Pat.) Pat. Clade 50 (76% BS): /porolaschia. Containing clade: / mycenaceae. Representative taxa: Poromycena and Filoboletus spp. and Mycenoporella griseipora. All members of this clade have a poroid hymenium. However, it also appears that additional sampling of mycenaceae from the tropics breaks down generic distinction between poroid and gilled mycenoid taxa (J. M. Moncalvo, pers. obs.). Clade 51 (90% BS): prunulus. Containing clade:/ mycenaceae. This clade corresponds to Mycena sect. Purae in Singer (1986), for which the generic name Prunulus S.F. Gray is available (Redhead et al., 2001). Clade 52 (64% BS): /phyllotopsis. Representative taxa: Phyllotopsis nidulans, Pleurocybella porrigens, and Typhula phacorrhiza. Typhula was previously classified in the Cantharellales (Hawksworth et al., 1995), but shown to be among the euagarics by Hibbett et al. (1997). Relationships between taxa of this clade have not been previously suspected, and we are still unaware of any morphological or anatomical character that could unify them. Clade 53 (90% BS): /pluteus. This clade corresponds to Pluteus Fries. At least two well-supported clades can be distinguished within this genus: one clade (63% BS) includes only species of section Pluteus, and one clade (92% BS) is composed of members of both sections Hispidoderma Fayod and Celluloderma Fayod. Clade 54 (98% BS): /melanoleuca. This clade corresponds to Melanoleuca Pat. This genus can be distinguished by several unique characters, but its relationships with other pale-spored agarics have never been clear (see for instance Singer, 1986). In our analyses, Melanoleuca clusters with Pluteus but with weak bootstrap support (<40%). The two taxa share similar stature and pigments, but differ significantly in their microanatomy. Clade 55 (97% BS): /amanita. This clade corresponds to the genus Amanita Persoon. Monophyly of the ectomycorrhizal Amanita taxa is strongly supported (97% BS); a potentially nonectomycorrhizal species, A. armillariformes (Miller et al., 1990), clusters weakly with / amanita in the bootstrap tree and is not monophyletic with other Amanita species in the MPF tree. There is a good agreement between molecular and morphological data for infrageneric segregation of the genus, as shown in Fig. 2 and in earlier studies (Drehmel et al., 1999; Weiss et al., 1998; Moncalvo et al., 2000b). This work J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 shows for the first time that the secotioid fungus Torrendia belongs to Amanita subsection Caesareae (99% BS). Clade 56 (<40% BS): /limacella. This clade corresponds to the genus Limacella Earle, with inclusion of the monotypic genus Catatrama (Franco-Molano, 1991). The two taxa share a bilateral lamellar trama. viscid pilei, and amyloid spores. A sister group relationship between Limacella and Amanita (Amanitaceae) is weakly supported in our analyses. Clade 57 (91% BS): /pleurotaceae. Representative taxa: Hohenbuehlia (including its Nematoctonus anamorphs) and Pleurotus. The production of nematodetrapping organs and nematophagy are synapomorphies for this clade (Moncalvo et al., 2000; Thorn et al., 2000). Clade 58 (94% BS): /hohenbuehlia. Containing clade: /pleurotaceae. This clade corresponds to the genus Hohenbuehlia Schulzer, including its Nematoctonus anamorphs. Clade 59 (93% BS): /pleurotus. Containing clade: / pleurotaceae. This clade corresponds to the genus Pleurotus (Fr.) Qu
elet. Omphalinoid and hygrophoroid taxa. Most members of Omphalina sensu lato and Hygrophoraceae sensu singer (1986) are intermixed in clades 60–71 and related groups. These taxa have white, generally smooth, thinwalled spores; pilei are generally brightly pigmented and often have attached or decurrent gills. Many omphalinoid and hygrophoroid taxa form obligatory or facultative association with bryophytes or algae (see above). Three groups can be recognized in Fig. 2, although statistical support for each group remains weak: they are the Omphalina group, the Arrhenia group, and the Hygrophoraceae group. Clade 60 (81% BS): /omphalina. Representative taxa: Omphalina pyxidata and O. rivulicola. Both species are bryophilous (Lamoure, 1974). The former species is the conserved type for Omphalina (Greuter et al., 2000). Omphalina s.s. Singer (1986) has already been shown to be polyphyletic (Lutzoni, 1997; Moncalvo et al., 2000). In Fig. 2, Omphalina species sensu lato are in this clade and in the Arrhenia group and the hymenochaetoid clade. Both the MPF tree and the bootstrap (<50% BS) tree indicate possible monophyly of /omphalina with another bryophyte-associate taxon, Rimbachia (see above), and saprophyte Clitocybe species (Omphalina group; Fig. 2). Clade 61 (70% BS): /neohygrophoroid. Representative taxa: Neohygrophorus angelesianus and Pseudoomphalina felloides. A close phylogenetic relationship between these two species has never been suspected before. The Arrhenia group (clades 61–64). Both the MPF tree and the bootstrap (<50% BS) tree indicate possible monophyly of the core Omphalina (excluding the type species) with members of Arrhenia, Cantharellula, 377 Pseudoarmillariella, and Gliophorus. Several taxa in this group are associated with cryptogams (see above). Clade 62 (49% BS): /cantharelluloid. This clade belongs to the Arrhenia group. Representative taxa: Cantharellula umbonata and Pseudoarmillariella ectypoides. Affinities between these two taxa were already suspected by Singer, who first recognized Pseudoarmillariella as a subgenus of Cantharellula before recognizing it at the genus level (Singer, 1986). Clade 63 (77% BS): /arrhenia. This clade belongs to the Arrhenia group. Representative taxa: Arrhenia auriscalpium, A. lobata, Omphalina velutipes, O. epichysium, O. sphagnicola, O. philonotis, O. obscurata, O. griseopallidus, and O. viridis. Clade 63 includes the type species of Arrhenia (A. auriscalpium) and the core of the nonlichenized Omphalina species. Clade 64 (71% BS): /lichenomphalia. This clade belongs to the Arrhenia group. Representative taxa: Omphalina luteovitellina, O. hudsoniana, O. velutina, and O. grisella. Lichenization is a synapomorphy for this clade. Monophyly of /lichenomphalia with another lichenized fungus, O. ericetorum, is not evident in Fig. 2 but has been shown in Lutzoni (1997). These species correspond to ‘‘Phytoconis ’’ sensu Redhead and Kuyper (1987). The Hygrophoraceae group (clades 65–68). There is virtually no support for a monophyletic Hyrophoraceae sensu auth. in our analyses, as indicated by the placement of Gliophorus laeta in the Arrhenia group and the possible relationship between Hygrophorus and Chrysomphalina species (the latter being traditionally classified in the Tricholomataceae). However, the core genera of Hygrophoraceae (Hygrophorus, Hygrocybe, Humidicutis, and Cuphophyllus) cluster together in the bootstrap tree (<40% BS). Clade 65 (97% BS): /hygrophorus. This clade belongs to the Hygrophoraceae group and corresponds to Hygrophorus Fr., a genus that can be distinguished by its ectomycorrhizal habit and the presence of a bilateral lamellar trama. Clade 66 (66% BS): /chrysomphalina. This clade belongs to the Hygrophoraceae group. It corresponds to the genus Chrysomphalina Cl
emencßon. Our results support the segregation of this genus from both Gerronema and Omphalina, as discussed in Cl
emencßon (1982). Clade 67 (98% BS): /hygrocybe. This clade belongs to the Hygrophoraceae group. It corresponds to the genus Hygrocybe Kummer, including Pseudohygrocybe Kovalenko. In Fig. 2, species of Pseudohygrocybe (61% BS) are separated from Hygrocybe sensu stricto (95% BS). Clade 68 (90% BS): /cuphophylloid. This clade belongs to the Hygrophoraceae group. Representative taxa: Chromosera cyanophylla and Cuphophyllus citrinopallidus. These two genera were segregated from Hygrocybe (see Redhead et al., 1995). Results of our analysis indicate that /cuphophylloid could be sister group of / hygrocybe, but statistical support is weak (<40% BS). 378 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Clade 69 (76% BS): /xeromphalinoid. Representative taxa: Xeromphalina and Heimiomyces. A close relationship between these two genera was already recognized by Singer (1986), who considered Heimiomyces a subgenus of Xeromphalina. Clade 70 (<40% BS): /xeromphalina. Containing clade: /xeromphalinoid. This clade corresponds to Xeromphalina K€ uhner & Maire. Clade 71 (86% BS): /heimiomyces. Containing clade: /xeromphalinoid. This clade corresponds to Heimiomyces Singer. Clade 72 (99% BS): /laccaria. This clade corresponds to Laccaria Berk. & Br. Monophyly of this ectomycorrhizal, white-spored genus is strongly supported by nLSU sequence data. However, its phylogenetic relationships are still unresolved. In earlier studies (Bruns et al., 1998; Moncalvo et al., 2000) Laccaria clustered with brown-spored taxa, but statistical support was weak. Clade 73 (0% BS): /cortinarioid. Representative taxa: Cortinarius, Rozites, Dermocybe, Rapacea, and the gasteromycete Thaxterogaster. All members of this clade are obligatorily ectomycorrhizal. Monophyly of these taxa is weakly supported in our analyses. However, the MPF tree is consistent with the multigene phylogeny of U. Peintner et al. (unpublished). Clade 74 (98% BS): /phaeocollybia. This clade corresponds to Phaeocollybia Heim. Clade 75 (85% BS): /squamanita. This clade corresponds to Squamanita Imbach. Clade 76(<40% BS): /bolbitiaceae. Representative taxa: /bolbitioid and /conocyboid. This clade corresponds in part to the family Bolbitiaceae in Singer (1986). It is possibly a sister group of /panaeoloideae. Descolea, included in Bolbitiaceae by Singer (1986), nests in an unresolved position between /bolbitiaceae and /panaeoloideae (Fig. 2). Clade 77 (100% BS): /conocyboid. Containing clade: / bolbitiaceae. Representative taxa: Gastrocybe and Conocybe. Gastrocybe appears to be a secotioid Conocybe (Hallen and Adams, 2000; Fig. 2). Clade 78 (82% BS): /bolbitioideae. Containing clade: /bolbitiaceae. Representative taxa: Bolbitius and Pholiotina subnuda. Pholiotina has an overall morphology closer to Conocybe (Singer, 1986) but P. subnuda appears to be phylogenetically closer to Bolbitius. Clade 79 (95% BS): /panaeoloideae. Representative taxa: Panaeolina, Panaeolus, and Copelandia. This clade corresponds to Panaeoloideae Singer (1986) in Coprinaceae ( ¼ Psathyrellaceae; Redhead et al., 2001), but our results indicate that it is possibly closer to /bolbitiaceae. Clade 80 (<40% BS): /agrocybe. This clade corresponds to the genus Agrocybe Fayod with the inclusion of the gasteromycete Leratiomyces smaragdina. Leratiomyces appears to be polyphyletic, with L. similis nesting in clade 113. Clade 81 (<40% BS): /nidulariaceae. Representative taxa: Crucibulum laeve and Cyathus stercoreus. The placement of the bird nest fungi (Nidulariales) in the euagarics was first demonstrated by Hibbett et al. (1997) and is supported in this study. However, its exact position among the euagarics remains unknown. Clade 82 (52% BS): /agaricaceae. Representative taxa: /lycoperdales, /agaricus, /leucocoprinus, /coprinoid, /macrolepiota, Podaxis, Lepiota, Leucoagaricus, Melanophyllum, Chlorophyllum, Cystolepiota, Battarraea, Tulostoma, and two groups of attine fungi. This clade represents a morphologically highly diverse assemblage of taxa, including traditional orders and genera of gasteromycetes and hymenomycetes. However, virtually all the taxa in the clade occur on the soil (none are primary wood decay organisms and none are known to be ectomycorrhizal) and fairy ring formation is a common feature in the Agaricaceae. The true puffballs (Lycoperdales) have many biochemical features in common with Agaricus, such as formation of urea, concentration of silver, mercury, selenium, and arsenic, and biosynthesis of methylmercury and arsenobetaine (Byrne et al., 1979; Slejkovec et al., 1997; Tjakko Stijve, pers. comm. to H.C.). Clade 83 (56% BS): /lycoperdales. Containing clade: / agaricaeae. This clade corresponds to the traditional gasteromycete order Lycoperdales. Clade 84 (96% BS): /agaricus. Containing clade: / agaricaeae. This clade corresponds to Agaricus Fries, with the inclusion of the secotioid genera Gyrophragmium and Longula. Clade 85 (77% BS): /coprinoid. Containing clade: / agaricaeae. Representative taxa: /coprinus and Montagnea. A close affinity between Coprinus sensu stricto (Redhead et al., 2001) and the secotioid genus Montagnea is established here. Clade 86 (53% BS): /coprinus. Containing clade: / agaricaeae. This clade corresponds to Coprinus Persoon as emended by Redhead et al. (2001). Clade 87 (<40% BS): /macrolepiota Containing clade: /agaricaeae. This clade corresponds to Macrolepiota Singer. Clade 88 (81% BS): /cystoderma. Containing clade: / agaricaeae. Representative taxa: Cystoderma amianthinum (type of Cystoderma Fayod) and C. chocoanum. The separate placement of Cystoderma granulosum, which clusters with Ripartitella (Johnson and Vilgalys, 1998; Fig. 2) remains unexplained and needs further scrutiny. The placement of Floccularia as sister group to /cystoderma is weakly supported by bootstrapping (<50% BS), and there is no obvious morphological character to explain this relationship. Clade 89 (55% BS): /psathyrellaceae. Representative taxa: Psathyrella, Lacrymaria, /coprinopsis, /coprinellus, and /parasola. This clade corresponds to the family Psathyrellaceae as defined in Redhead et al. (2001). J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Clade 90 (<40% BS): /coprinopsis. Containing clade: /psathyrellaceae. This clade corresponds to the genus Coprinopsis as described in Redhead et al. (2001). Clade 91 (98% BS): /parasola. Containing clade: / psathyrellaceae. This clade corresponds to the genus Parasola as described in Redhead et al. (2001). Clade 92 (41% BS): /coprinellus. Containing clade: / psathyrellaceae. This clade corresponds to the genus Coprinellus as described in Redhead et al. (2001). Clade 93 (56% BS): /psathyrella. Containing clade: / psathyrellaceae. Representative species: Psathyrella gracilis (type species of Psathyrella). The results in Fig. 2 question monophyly of the large genus Psathyrella. Clade 94 (<40% BS): /hebelomatoid. Representative taxa: Naucoria, and /hebeloma. This large-scale analysis supports a close relationship between the ectomycorrhizal genera Hebeloma and Naucoria and indicates that the latter genus is probably not monophyletic. These results are in agreement with other molecular studies (Aanen et al., 2000; E. Horak et al., unpublished; U. Peintner et al., unpublished). The placement in this clade of Pholiota lignicola is suspect and needs confirmation. Clade 95 (60% BS): /hebeloma. Containing clade: / hebelomatoid. This clade corresponds to Hebeloma Kummer. Clade 96 (73% BS): /hemipholiota. This clade corresponds to Hemipholiota (Singer) Romagn. ex Bon. Clade 97 (69% BS): /gymnopiloid. Representative taxa: /gymnopilus and Galerina paludosa. Galerina appears to be a polyphyletic genus, with its members clustering here and close to /panaeolideae (clade 79). Clade 98 (99% BS): /gymnopilus. Containing clade: / gymnopiloid. This clade corresponds to the saprophytic genus Gymnopilus Karsten with the inclusion of Hebelomina Maire. Hebelomina was erected for taxa that resemble Hebeloma but are distinguished by having smooth and hyaline spores (Singer, 1986). This study confirms a close affinity of Hebelomina with dark-spored taxa, but indicates that the taxon is derived from within Gymnopilus rather than being close to Hebeloma (in clade 95). The ecology of Hebelomina is unclear. Singer (1986) wrote that the taxon is ‘‘probably ectomycorrhizal.’’ Because natural groups revealed by rDNA phylogenies are generally largely congruent with ecology and Gymnopilus is known not to be ectomycorrhizal, our results would suggest that Hebelomina is probably not ectomycorrhizal. Clade 99 (46% BS): /tubarioid. Representative taxa: Tubaria and Phaeomarasmius. Singer (1986) classified the former genus in Crepidotaceae and the latter in Strophariaceae; however, a close relationship between these two taxa was already indicated by K€ uhner (1980). Clade 100 (99% BS): /tubaria. Containing clade: / tubarioid. This clade corresponds to Tubaria (W.G. Smith) Gillet, as described in Singer (1986). 379 Clade 101 (<40% BS): /crepidotoid. Representative taxa: Crepidotus and Simocybe. These two genera are reciprocally monophyletic in the bootstrap analysis, but not in the MPF tree. Reciprocal monophyly is also supported from an independent phylogenetic analysis in Aime (2001). A close relationship between Crepidotus and Simocybe is also apparent from morphology (Singer, 1986; K€ uhner, 1980). Clade 102 (<40% BS): /crepidotus. Containing clade: /crepidotoid. This clade corresponds to Crepidotus Kummer. Clade 103 (<40% BS): /simocybe. Containing clade: / crepidotoid. This clade corresponds to Simocybe Karsten. Clade 104 (53% BS): /inocybe. This clade corresponds to the genus Inocybe Fries. In both the MPF tree and the bootstrap tree /inocybe comes close to /crepidotoid, but with weak statistical support (<40% BS). Clade 105 (100% BS): /pleuroflammula. This clade corresponds to Pleuroflammula Singer. Clade 106(<40% BS): /psychedelia. Representative taxa: Psilocybe cubensis, P. semilanceata, P. stuntzii, P. flmetaria, P. liniformans, P. cyanescens, and P. subaeruginosa. This clade is composed only of psilocybincontaining (hallucinogenic) species of Psilocybe, whereas nonhallucinogenic Psilocybe species are in clade 112. Psilocybin is also produced in other mushrooms, for instance in Copelandia and Panaeolus (in clade 79) and several Pluteus species (in clade 53) (Stijve and Bonnard, 1986; Stamets, 1996). /Psychedelia is monophyletic with /stropharioid in the MPF tree, but this relationship is not supported by bootstrapping. Clade 107 (<40% BS): /stropharioid. Representative taxa: /stropharia, /pholiota, /semiglobata /magnivelaris, Phaeonematoloma, Hypholoma spp, and the secotioids Weraroa spp. and Leratiomyces similis. Chrysocystidia are present in all members of this clade, except in some species in /magnivelaris (e.g., in Stropharia magnivelaris). They are also absent in Pachylepyrium, the putative sister group of /stropharioid (Fig. 2). Clade 108 (73% BS): /semiglobata. Containing clade: /stropharioid. Representative taxa: Stropharia semiglobata and S. umbonatescens. These two Stropharia species may not be monophyletic with the type of the genus, S. aeruginosa. Clade 109 (<40% BS): /hypholoma. Containing clade: /stropharioid. Representative taxa: Hypholoma sublateritium. H. capnoides, H. subviride, H. fasciculare, and H. ericaeum. This clade is composed of the core species of Hypholoma Kummer. However, this genus is probably polyphyletic: in our analyses H. subericaeum clusters with Pholiota subochracea, H. aurantiacum is in clade 111, and H. udum is basal to Psilocybe spp. in clade 113. H. udum is the only species with chrysocystidia that classifies outside /stropharioid; the placement of this species therefore needs further scrutiny. 380 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Clade 110 (<40% BS): /stropharia. Containing clade: /stropharioid. Representative taxa: Stropharia aeruginosa, S. rugosoannulata, S. coronilla, S. hardii, and S. hornemannii. This clade includes the type of the genus Stropharia, S. aeruginosa, and closely related species. Our results suggest that Stropharia magnivelaris (in clade 112), S. albocrenulata (in an isolated position outside /stropharioid), and possibly also S. semiglobata and S. umbonatescens (both in clade 108) should be excluded from this genus. Clade 111 (<40% BS): /pholiota. Containing clade: / stropharioid. This clade corresponds to the core of the genus Pholiota Kummer, including its type species (P. squarrosa). Our results support the separation of Hemipholiota (clade 96) from Pholiota and suggest the exclusion from Pholiota of P. oedipus (close to clade 99), P. tuberculosa (in an isolate position between clades 103 and 104 in Fig. 2), and possibly P. subochracea (which clusters with Hypholoma subericaeum in /stropharioid) and P. lignicola (in a doubtful position in clade 94). Clade 112 (74% BS): /magnivelaris. Containing clade: /stropharioid. Representative taxa: Stropharia magnivelaris, Hypholoma aurantiacum, and the secotioids Leratiomyces similis and Weraroa erythrocephala. Clade 113 (61% BS): /psilocybe. Representative taxa: Psilocybe montana (type of Psilocybe in Singer, 1986) and related non-psilocybe-containing species (as listed in Fig. 2), including Melanotus. Monophyly of Psilocybe is questioned by nLSU data: hallucinogenic species are separated in clade 106, and Psilocybe subcoprophila clusters with Phaeogalera stagnina at the base of clade 113. Based on Fig. 2, /psilocybe may possibly also include Kuehneromyces, Phaeogalera, and Hypholoma udum. Clade 114 (98% BS): /volvariella. This clade corresponds to Volvariella Spegazzini. In the results depicted in Fig. 2 and other analyses (data not shown) /volvariella consistently clusters with /schizophylloid but always with a weak statistical support. Clade 115 (54% BS): /schizophylloid. Representative taxa: Schizophyllum, Fistulina, and Porodisculus pendulus. This study supports the findings by Hibbett et al. (1997) showing that Schizophyllum and Fistulina are closely related and belong to the euagarics. Clade 116 (100% BS): /schizophyllum. Containing clade: /schizophylloid. Clade 116 corresponds to Schizophyllum Fr. Clade 117 (100% BS): /fistulinoid. Containing clade: / schizophylloid. Representative taxa: Fistulina and the reduced fungus Porodisculus pendulus. A possible affinity of Fistulina with both agarics and reduced forms was already indicated by Singer (1986, p. 843) who stated that ‘‘the gelatinizing of the trama of Fistulina and the acanthophysoid hairs of Pseudofistulina suggest [...] strong similarities with cyphelloid reduced agarics [...]. I am not at present ready to introduce Fistulinaceae as a family of the Agaricales, because I believe that additional studies will be required to substantiate this position.’’ Euagarics Incertae Sedis. Natural relationships of several species included in this study remain unresolved. However, our results support the placement in the euagarics of the following taxa: Clavaria fusiformis (possibly related to Tricholomopsis in clade 24), Pleurotopsis longinqua, Lachnella alboviolascens, Tectella patellaris, Stereopsis humphreyi, Cantharocybe gruberi, Camarophyllus pratensis, Pseudoclitocybe cyathiformis, Stropharia albocrenulata, Ripartites, Flammula alnicola, Phaeolepiota aurea, Macrocystidia cucumis, Floccularia albolanaripes, Pholiota oedipus, Pholiota tuberculosa, Laccaria, Squamanita, Phaeocollybia, Descolea, Galerina spp. (this genus does not appear to be monophyletic), Agrocybe, Cystoderma, Ripartitella, Mythicomyces, Stagnicola, Hemipholiota, Flammulaster, Inocybe, Pleuroflammula, and Nidulariaceae. 4. Conclusions Ribosomal DNA systematics has become a standard method in fungal taxonomy. It is therefore expected that in the coming years rDNA sequence data for the large majority of homobasidiomycetes will be produced. In nearly all studies published to date, rDNA data have been useful but not entirely sufficient for reconstructing fully resolved, well-supported phylogenies, for at least two reasons: (1) rDNA genes cannot always resolve relationships at every taxonomic level (Bruns et al., 1991) and (2) rDNA cannot provide the number of molecular characters needed to provide statistical support at all taxonomic levels (Berbee et al., 2000). In consequence, several laboratories are beginning to develop primers for PCR amplification and sequencing of additional mitochondrial and nuclear protein-coding genes in fungi (e.g., Thon and Royse, 1999; Kretzer and Bruns, 1999). Eventually, combining phylogenetic data from this work and others into a ‘‘supertree’’ (Sanderson et al., 1998) may boost our understanding of evolutionary relationships in the euagarics and other fungi and contribute to Darwin’s dream (as cited in Burkhardt and Smith, 1990;, p. 456): ‘‘The time will come [...] though I shall not live to see it, when we shall have fairly true genealogical trees of each kingdom of nature.’’ Acknowledgments The authors are grateful to the following persons who provided material and taxonomic expertise for this study: Duur Aanen, Jean B
erub
e, Jacqueline Bonnard, Hal Burdsall, Phillippe Callac, Cony Decock, Dennis Desjardin, Roy Halling, David Hibbett, Terry Henkel, Egon Horak, Omon Isikhuemhen, Rick Kerrigan, J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Thomas Kuyper, Jean Lodge, Lorelei Norvell, Ursula Peintner, Ron Petersen, Beatrice Senn-Irlet, and Roy Watling. We thank Sean Li and Omon Isikhuemhen for help in the laboratory, Gonzalo Platas for providing us with a sequence of Torrendia, and Ursula Reintner, Manfred Binder and Dave Hibbett for sharing unpublished results. This work was supported by NSF Grant DEB-9708035 to R.V. and J.M.M. A grant from the 381 Biotic Surveys and Inventories Program of NSF, DEB9525902, to D.J. Lodge and T.J.B. provided the opportunity to include several neotropical species in this study. S.J.W.V. and V.H. are grateful to, respectively, the NWO Research Council for Life Sciences in The Netherlands and the Soci
et
e Acad
emique Vaudoise in Switzerland for travel grants to visit Duke University in the course of this study. Appendix A. List of strains used with their sources and GeneBank accession numbers Taxon GenBank Accession No. Source: Strain No.a Anthracophyllum lateritium Neonothopanus nambi AF261324 AF042577 AF135175 AF261325 AF042621 AF042010 AF135172 AF042008 AF042596 AF042595 AF223172 AF261326 AF261327 AF261585 AF261328 AF261329 AF261330 AF261331 AF261332 AF261333 AF261334 AF261335 AF261336 AF042597 AF042626 AF042650 AF223173 AF042579 AF261557 AF261558 AF261559 AF261560 AF261561 AF261562 AF042628 AF042651 AF261337 AF042629 AF261338 AF261339 AF261340 AF261341 This work: (T) CULTENN4419 Moncalvo et al., 2000 (as Nothopanus eugrammus) This work: (D) RVPR27 This work: (V) VT645.7 Moncalvo et al., 2000 Binder et al., 1997 Moncalvo et al., 2000 Binder et al., 1997 Moncalvo et al., 2000 (as Collybia) Moncalvo et al., 2000 (as Collybia) This work: CBS174.48 This work: (J) JEJ.PR.213 This work: (D) JMCR.143 This work: (D) HN4730 This work: (J) JEJ.VA.567 This work: (J) JEJ.574 This work: (D) HN2270 This work: (J) JEJ.586 This work: DAOM175382 This work: (D) RVPR98.46 This work: (D) RV.PR.98.08 This work: (D) RVPR98.13 This work: (D) RV98/32 Moncalvo et al., 2000 (as Collybia) Moncalvo et al., 2000 Moncalvo et al., 2000 This work: CBS426.79 Moncalvo et al., 2000 This work: (G) TMI1941 This work: (G) RGT960624 This work: (D) HN2002 This work: (D) R38 This work: (G)TMI1172 This work: (G) TMI1485 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: DAOM186918 Moncalvo et al., 2000 (as Campanella) This work: (T) TENN7373 This work: (D) RV-PR075 This work: (D) RV98/79 This work: (D) JMCR.34 Omphalotus olivascens Omphalotus nidiformis Omphalotus olearius Lampteromyces japonicus Gymnopus polyphyllus Gymnopus dryophilus Gymnopus acervatus Gymnopus sp. Caripia montagnei Setulipes androsaceus Micromphale foetidum Marasmiellus opacus Marasmius scorodonius Gymnopus sp Gymnopus sp. Gymnopus biformis Rhodocollybia maculata Marasmiellus ramealis Gymnopus peronatus Lentinula edodes Lentinula boryana Lentinula novaezelandieae Lentinula lateritia Micromphale perforans Tetrapyrgos nigripes Tetrapyrgos subdendrophora Tetrapyrgos sp. Campanella sp. Campanella sp. Unidentified agaric 382 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Marasmius delectans Marasmius sp. Marasmius cladophyllus Hymenogloea papyracea Marasmius capillaris Marasmius rotula Marasmius fulvoferrugineus Chaetocalathus liliputianus Chaetocalathus sp. Crinipellis campanella Crinipellis maxima Crinipellis sp. Gloiocephala spathularia Physalacria aff.orinocensis Rhodotus palmatus Xerula megalospora Xerula furfuracea Oudemansiella canarii Flammulina velutipes Strobilurus trullisatus Rhizomarasmius pyrrhocephalus U11922 AF261342 AF261343 AF261344 AF042631 AF261345 AF261584 AF261346 AF261347 U11916 AF042630 AF261348 AF261349 AF261350 AF042565 AF042649 AF042566 AF261351 AF042641 AF042633 AF261352 AF042605 AF261353 AF042642 AF042632 AF261354 AF042593 AF261355 AF261356 AF261357 AF141637 AF261358 AF261359 AF261379 AF261360 AF261361 AF261362 AF042604 AF042634 AF261363 AF042635 U66433 AF261364 U66434 AF261365 AF261366 AF261367 AF261368 AF261369 AF261370 AF261371 U11901 U11890 Chapela et al., 1994 This work: (J) JEJ.PR.256 This work: (D)JMCR. 121 This work: HALLING.5013 Moncalvo et al., 2000 This work: (J) JEJ.VA.595 This work: (D) HN2346 This work: DAOM175886 This work: (T) TENN3572 Chapela et al., 1994 Moncalvo et al., 2000 This work: (D) RV.PR98/75 This work: (D) JMCR.115 This work: (T) TENN9134 Moncalvo et al., 2000 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (D) RV.PR100 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (J) JEJ.596 Moncalvo et al., 2000 (as Marasmius) This work: (D) RV98/78 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (T) TENN7573 Moncalvo et al., 2000 This work: (B) GC17 This work: (D) JMCR.126 This work: DAOM187959 Hallenberg and Parmasto (GenBank) This work: DAOM187554 This work: DAOM214662 This work: (J) JAN.SW.21835 This work: DAOM216791 This work: DAOM174885 This work: (D) JMCR.32 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (T) TENN4256 Moncalvo et al., 2000 Lutzoni, 1997 This work: (J) JEJ580 Lutzoni, 1997 This work: (V) OKM27143 This work: DAOM195782 This work: DAOM195995 This work: DAOM196062 This work: (D) RV98/43 This work: (S) HC.10/11/98.C This work: (J) FP102067 Chapela et al., 1994 Chapela et al., 1994 Cyptotrama asprata Gloiocephala menieri Gloiocephala sp. Armillaria tabescens Armillaria ‘‘NABS1’’ Armillaria affinis Cheimonophyllum candidissimum Gloeostereum incarnatum Hemimycena delicatella Hemimycena ignobilis Calyptella capula Mycena aurantiidisca Mycena adonis bioluminescent agaric Pleurotopsis longinqua Baeospora myriadophylla Baeospora myosura Hydropus scabripes Gerronema strombodes Gerronema subclavatum Gerronema sp. Megacollybia platyphylla Clitocybula oculus Hydropus fuliginarius Hydropus sp. Porotheleum fimbriatum ¼ Stromatoscypha fimbriata attine fungus G2 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon Resupinatus sp. Resupinatus alboniger Resupinatus dealbatus Stigmatolemma poriaeforme cyphelloid sp. Phyllotopsis nidulans Pleurocybella porrigens Typhula phacorrhiza Gamundia leucophylla Caulorhiza hygrophoroides Conchomyces bursaeformis Fayodia gracilipes Myxomphalia maura Floccularia albolanaripes Mythicomyces corneipes Stereopsis humphreyi Pseudoclitocybe cyathiformis Collybia tuberosa Collybia cirrhata Collybia cookei Dendrocollybia racemosa Clitocybe dealbata Clitocybe connata Lepista nuda Lepista nuda Clitocybe ramigena Clitocybe glacialis Clitocybe odorata Lepista nebularis Plicaturopsis crispa Omphaliaster borealis Tricholoma atroviolaceum Tricholoma imbricatum Tricholoma focale Tricholoma myomyces Tricholoma vernaticum Tricholoma pardinum Tricholoma venenatum Tricholoma portentosum Tricholoma intermedium Tricholoma subaureum Tricholoma caligatum Tricholoma matsutake Tricholoma cf. flavovirens Tricholoma vaccinum Leucopaxillus albissimus Leucopaxillus gentianeus GenBank Accession No. Source: Strain No.a U11905 AF042599 AF042600 AF139944 AF261372 AF261373 AF042578 AF042594 AF261374 AF261375 AF042640 AF042603 AF261376 AF261377 AF261378 AF261380 AF261381 AF261382 AF261383 AF261384 AF261385 AF261386 AF261387 AF261388 AF042598 AF042589 AF223175 AF042590 AF042624 AF139963 AF042648 AF261389 AF261390 AF223217 AF261586 AF261391 U76457 U76458 U76460 U76459 U76461 U76462 U76463 U76464 U76465 U76466 U76467 AF261392 U62964 U86672 U86443-4 AF261393 AF261394 Chapela et al., 1994 Moncalvo et al., 2000 Moncalvo et al., 2000 Thorn et al., 2000 (as Asterotus) This work: (J)RLG1156sp This work: HHB3534sp Moncalvo et al., 2000 Moncalvo et al., 2000 This work: DAOM195241 This work: DAOM192749 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (D) RV95/695 This work: DAOM187531 This work: DAOM187839 This work: DAOM214667 This work: DAOM178138 This work: DAOM185795 This work: DAOM191063 This work: (D) DUKE1424 This work: DAOM191061 This work: (T) TENN53630 This work: (T) TENN53540 This work: (T) TENN55143 Moncalvo et al., 2000 (as Collybia) Moncalvo et al., 2000 This work: (S) HC95/cp3 Moncalvo et al., 2000 Moncalvo et al., 2000 (as Clitocybe) Thorn et al., 2000 Moncalvo et al., 2000 This work: DAOM208590 This work: (D) RV98/145 This work: CBS362.65 This work: (D) RV98/1 This work: DAOM189775 Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) Shank and Vilgalys (GenBank) This work: (D) SAR1/2/88 Hwang and Kim, 2000. Pegler et al., 1998 Nakasone and Rentmeester (GenBank) This work: DAOM182713 This work: (T) TENN5616 383 384 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Porpoloma sp. Hypsizygus ulmarius Ossicaulis lignatilis AF261395 AF042584 AF261396 AF261397 n.a. AF139964 AF223193 AF223194 AF223192 AF223195 AF223198 AF223196 AF223197 AF223200 AF223199 AF223203 AF223187 AF223186 AF223189 AF223188 AF223206 AF223205 AF223204 AF223201 AF223215 AF223216 AF223214 AF223211 AF223212 AF223213 AF042582 AF223210 AF042583 AF223209 AF223208 AF042581 AF042585 AF261398 AF042586 AF042587 AF261399 AF223174 AF223202 AF223185 AF223183 AF223184 AF223182 AF223179 AF223180 AF223181 AF261400 AF223176 AF223177 This work: JLPR3395 Moncalvo et al., 2000 This work: DAOM188196 This work: (D, V) D604 This work: DAOM211765 Thorn et al., 2000 This work: (S) SAG5/271yo9 This work: (S) SAG5/27.11 This work: CBS362.80 This work: BSI92/245 This work: CBS320.80 This work: CBS321.80 This work: CBS328.50 This work: CBS717.87 This work: CBS714.87 This work: CBS204.47 This work: (S) HC80/148 This work: CBS660.87 This work: CBS320.85 This work: (S) HC84/75 This work: (S) HC78U This work: CBS379.88 This work: BSI96/84 This work: CBS330.85 This work: CBS451.87 This work: CBS452.87 This work: CBS450.87 This work: BSI94/88 This work: (S) HC79/132 This work: CBS156.44 Moncalvo et al., 2000 This work: CBS709.87 Moncalvo et al., 2000 This work: (S) HC80/140 This work: IFO30978 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (D) JMleg.MUID Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (D) JJs.n. This work: BSI93/3 This work: (S) HAe251/97 This work: BSI94/cp1 This work: (S) HAe.251.97 This work: (S) HC96/cp4 This work: BSI94/cp2 This work: (S) HC77/33 This work: (S) HC80/103 This work: (S) HC79/181 This work: (D) RVPR10 June 97 This work: (S) HC80/99 This work: (S) HC78/64 Lyophyllum tylicolor Lyophyllum gibberosum Lyophyllum palustris Tephrocybe rancida Tricholomella constricta Lyophyllum boudieri Lyophyllum inolens Lyophyllum ambustum Lyophyllum anthracophilum Lyophyllum atratum Lyophyllum decastes Lyophyllum caerulescens Lyophyllum sykosporum Lyophyllum semitale Termitomyces cylindricus Termitomyces clypeatus Termitomyces heimii Termitomyces microcarpus Termitomyces sp. Termitomyces subhyalinus Lyophyllum leucophaeatum Lyophyllum ochraceum Lyophyllum favrei Calocybe Calocybe Calocybe Calocybe Calocybe Calocybe ionides naucoria obscurissima cyanea persicolor gambosa J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon Calocybe carneum Asterophora lycoperdoides Asterophora parasitica Catathelasma ventricosa Catathelasma imperialis Rhodocybe fallax Rhodocybe truncata Rhodocybe caelata Rhodocybe mundula Rhodocybe popinalis Clitopilus ‘‘flaviphyllus’’ Clitopilus apalus Clitopilus scyphoides Clitopilus prunulus Clitopilopsis hirneola Entoloma bloxamii Trichopilus porphyrophaeus Leptonia subserrulata Alboleptonia stylophora Inopilus entolomoides Entoloma lividum Entoloma nidorosum Entoloma bicolor Entoloma rhodopolium Entoloma flavifolium Entoloma alpicola Inocephalus quadratus Inocephalus lactifluus Inocephalus murraii Entoloma canescens Pouzarella nodospora Entoloma haastii Entoloma odorifer Entoloma unicolor Leptonia carnea Entoloma undatum Entoloma abortivum Entoloma sericeonitida Leptonia gracilipes Nolanea conica Nolanea cetrata Nolanea hirtipes Nolanea conferenda Nolanea strictia Nolanea sericea GenBank Accession No. Source: Strain No.a U86441/2 AF223178 AF223190 AF223191 AF261401 AF261402 AF223166 AF223165 AF261283 AF223168 AF223167 AF261282 AF261284 AF261285 AF261286 AF261287 AF261288 AF042645 AF223164 AF223163 AF261289 AF261290 AF261291 AF261292 AF261293 AF261294 AF261295 AF261296 AF261297/8 AF261299 AF261301 AF261302 AF261303 AF261304 AF261305/6 AF261307 AF261308 AF261309 AF261310 AF261311/2 AF261313 AF261314 AF223169 AF261315 AF261316 AF261317 AF261319 AF261320 AF261321 AF042620 AF261318 AF223170 AF223171 Nakasone and Rentmeester (GenBank) This work: CBS552.50 This work: CBS170.86 This work: CBS683.82 This work: DAOM221514 This work: DAOM225247 This work: CBS129.63 This work: CBS605.79 This work: (V) OKM25668 This work: CBS604.76 This work: CBS482.50 This work: (C) TB5890 This work: (C) TB4698 This work: (C) TB6378 This work: (C) TB8067 This work: (C) M536 This work: (C) T777 Moncalvo et al., 2000 This work: CBS576.87 This work: CBS577.87 This work: (C) TB6117 This work: (C) TB6957 This work: (C) TB6993 This work: (C) TB8475 This work: (C) TB8507 This work: (C) TB5034 This work: (C) TB6807 This work: (C) TB6263 This work: (C) TB4967 This work: (C)TB6221 This work: (C) TB6215 This work: (C) TB6415 This work: (C) TB7695 This work: (C) TB7962 This work: (C) TB6038 This work: (C) TB5657 This work:(C) TB5716 This work: (C) BY21 This work: (C) TB6366 This work: (C) TB5520 This work: (C) TB5812 This work: (C) TB6398 This work: CBS143.34 This work: (C) TB7144 This work: (C) TB6033 This work: (C) MB6 This work: (C) TB7382 This work: (C) K1171992 This work: (C) TB7660 Moncalvo et al., 2000 (as Entoloma) This work: (C) TB6506 This work: CBS237.50 This work: CBS153.46 385 386 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Entoloma sp. Claudopus depluens Collybia aurea Tricholomopsis rutilans Marasmius rhyssophyllus Clavaria fusiformis Macrocybe gigantea Macrocybe titans Callistosporium luteoolivaceum Callistosporium xanthophyllum Pleurocollybia brunnescens Mycena rorida Mycena leaiana Mycena inclinata Mycena galericulata Mycena clavicularis Mycena insignis ‘‘Cotobrusia calostomoides’’ cf. Poromycena Mycena viscidocruenta Resinomycena acadiensis Resinomycena rhododendri Dictyopanus pusillus Dictyopanus sp. Panellus stypticus Favolaschia cinnabarina Favolaschia calocera Favolaschia cf. calocera Favolaschia cf. calocera Favolaschia cf. sprucei Poromycena sp. Filoboletus gracilis Poromycena manipularis Mycenoporella griseipora Prunulus rutilantiformis Prunulus pura cplx Prunulus pura cplx Tectella patellaris Macrocystidia cucumis Hohenbuehelia sp. Hohenbuehelia cf. atrolucida Hohenbuehelia grisea Hohenbuehelia petaloides Nematoctonus geogenius Hohenbuehelia sp. Hohenbuehelia portegna Nematoctonus robustus Hohenbuehelia tristis AF261322 AF261323 AF261403 AF261404 n.a. n.a. AF042591 U86437 AF261405 AF261406 AF261407 AF261408 AF261411 AF042636 AF261412 AF042637 AF261413 AF261424 AF261429 AF261414 AF042638 AF261415 AF261425 AF261426 AF261427 AF261416 AF261417 AF261418 AF261419 AF261420 AF261421 AF261422 AF261423 AF261428 AF042606 AF261409 AF261410 AF261430 AF261431 AF139960 AF042603 AF139954/5 AF139956 AF139957/8 AF139950/1 AF139959 AF139952/3 AF042602 AF135171 U04140 U04160 U04143 U04144 This work: (D) JM98/123 This work: (C) TB7522 This work: (D) RV.PR98/27 This work: DAOM225484 This work: JLPR5831 This work: (D) RV.98.143 Moncalvo et al., 2000 Pegler et al., 1998 This work: (D) JM99/124 This work: IB19770276 This work: DAOM34832 This work: DAOM215019 This work: DAOM167618 Moncalvo et al., 2000 (as M. galericulata) This work: (T) TENN7495 Moncalvo et al., 2000 This work: DAOM208539 This work: (D)JMCR.100 This work: (D) JM98/128 This work: DUKE3411 Moncalvo et al., 2000 This work: (J) JEJ.VA.599 This work: (D) RV.PR98/36 This work: (T) CULTENN7699 This work: (J) CMC5 This work: (D) RVPR82 This work: (J) SR.KEN.346 This work: (D) JM98/186 This work: (D) JM98/372 This work: (D) TH6418 This work: (D) RV.PR114 This work: (J) JEJ.PR.253 This work: (D) JM98/217 This work: (D) JM98/156 Moncalvo et al., 2000 (as Mycena) This work: (D) JMCR.101 This work: (D) JM98/136 This work: (D) TH6346 This work: DAOM181084 Thorn et al., 2000 Moncalvo et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Moncalvo et al., 2000 Thorn et al., 2000 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Pleurotus ostreatus J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon Pleurotus pulmonarius Pleurotus populinus Pleurotus eryngii Pleurotus abieticola Pleurotus australis Pleurotus cornucopiae Pleurotus djamor Pleurotus calyptratus Pleurotus cystidiosus Pleurotus smithii Pleurotus laevis Pleurotus dryinus Pleurotus tuberregium Pleurotus purpureoolivaceus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus Pluteus petasatus primus brunneoradiatus pouzarianus pallidus cervinus pellitus atromarginatus salicinus ephebeus ‘‘white’’ sp. romellii admirabilis Pluteus aurantiorugosus Pluteus umbrosus Pluteus chrysophlebius Melanoleuca cognata Melanoleuca alboflavida Amanita muscaria Amanita roseitincta GenBank Accession No. Source: Strain No.a U04147 U04142 U04157 U04152 U04141 U04151 U04153 U04159 U04136 U04137 U04155 U04154 AF135176 AF261432 U04146 U04135 AF042575 U04139 U04138 AF135177 U04148 U04149 U04150 U04156 U04158 AF139968 AF135178 AF135180 AF042576 AF135179 AF042611 AF042610 AF261567 AF261568 AF261569 AF261570 AF261571 AF261572 AF261573 AF261574 AF042612 AF261576 AF261575 AF261577 AF261578 AF261579 AF261580 AF261581 AF261433 AF261434 AF139965 AF042643 AF097369 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Thorn et al., 2000 This work: (D) RV95/568 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Moncalvo et al., 2000 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Thorn et al., 2000 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Vilgalys and Sun, 1994 Thorn et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Moncalvo et al., 2000 Thorn et al., 2000 This work: (S) JB91/21 This work: (S) JB94/24 This work: (S) JB97/3 This work: (S) JB94/26 This work: (S) JB90/27 This work: (S) JB97/19 This work: (S) JB93/3 This work: (S)JB97/14 This work: (S) JB97/6 This work: (S) JB97/23 Moncalvo et al., 2000 This work: (S) JMCR.124 This work: (S) JB97/26 This work: DAOM193532 This work: DAOM197226 This work: DAOM197369 This work: DAOM197235 This work: DAOM 190194 This work: DAOM210221 This work: DAOM215874 Thorn et al., 2000 Moncalvo et al., 2000 Drehmel et al., 1999 387 388 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Amanita farinosa Amanita gemmata Amanita ceciliae Amanita fulva Amanita vaginata Amanita jacksonii Torrendia pulchella Amanita citrina Amanita brunnescens Amanita flavoconia Amanita rubescens Amanita flavorubescens Amanita franchetii Amanita bisporigera Amanita phalloides Amanita virosa Amanita rhoadsii Amanita solitariiformis Amanita peckiana AF097370 AF097371 AF097372 AF097373 AF097375 AF097376 AF261566 AF041547 AF097379 AF042609 AF042607 AF042609 AF097381 AF097384 AF261435 AF097386 AF097391 AF097390 AF042608 AF097387 AF097388 AF097393 AF261436 AF261437 U85301 AF261438 AF261439 AF261440 AF261441 AF261442 AF261443 AF261444 U66455 U66442 U66453 U66449 U66456 U66429 U66428 U66448 U66436 U66447 U66454 U66443 U66446 U66445 AF261445 AF261446 U66450 U66451 U66431 AF042564 AF261447 Drehmel et al., 1999 Drehmel et al., 1999 Drehmel et al., 1999 Drehmel et al., 1999 Drehmel et al., 1999 Drehmel et al., 1999 This work: G.Platas Hopple and Vilgalys, 1999 Drehmel et al., 1999 Moncalvo et al., 2000 Moncalvo et al., 2000 Moncalvo et al., 2000 Drehmel et al., 1999 Drehmel et al., 1999 This work: UPS2701 Drehmel et al., 1999 Drehmel et al., 1999 Drehmel et al., 1999 Moncalvo et al., 2000 Drehmel et al., 1999 Drehmel et al., 1999 Drehmel et al., 1999 This work: DAOM216919 This work: DAOM184734 Johnson and Vilgalys, 1998 This work: (V) VT(L18) This work: (V) VT8.9.96 This work: DAOM211663 This work: DAOM208569 This work: DAOM11115 This work: DAOM198740 This work: DAOM191921 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 (as Phaeotellus) Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 (as O. grisella) Lutzoni, 1997 Lutzoni, 1997 This work: DAOM180811 This work: DAOM196394 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Moncalvo et al., 2000 This work: (J) JEJ.VA.587 Amanita volvata Amanita rhopalopus Amanita armillariiformis Limacella glischra Limacella glioderma Limacella illinata Catatrama costaricensis Neohygrophorus angelesianus Pseudoomphalina felloides Cantharellula umbonata Pseudoarmillariella ectypoides Omphalina velutipes Omphalina epichysium Omphalina sphagnicola Omphalina philonotis Omphalina viridis Arrhenia lobata Arrhenia auriscalpium Omphalina obscurata Omphalina griseopallidus Omphalina luteovitellina Omphalina velutina Omphalina velutina Omphalina hudsoniana Omphalina ericetorum Gliophorus laeta Omphalina pyxidata Omphalina rivulicola Clitocybe lateritia Clitocybe clavipes J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon Clitocybe sp. Rimbachia bryophila Humidicutis marginata Hygrophorus sordidus Hygrophorus bakerensis Chrysomphalina chrysophylla Chrysomphalina grossula Hygrocybe conica Hygrocybe spadicea Hygrocybe miniata Hygrocybe sp. Hygrocybe cantharellus Cuphophyllus citrinopallidus Chromosera cyanophylla ¼ Mycena lilacifolia Camarophyllus pratensis Cotylidia alba Cotylidia diaphina Cotylidia aurantiaca Cantharellopsis prescotii Omphalina brevibasidiata Omphalina rosella Rickenella mellea Rickenella pseudogrisella Omphalina marchantiae Xeromphalina cauticinalis Xeromphalina campanelloides Xeromphalina cornui Xeromphalina fraxinophila Xeromphalina helbergeri Xeromphalina austroandina Xeromphalina kauffmanii Xeromphalina brunneola Xeromphalina campanella Heimiomyces fulvipes Heimiomyces tenuipes Heimiomyces sp. Ripartitella brasiliensis Cystoderma granulosum Cystoderma chocoanum Cystoderma amianthinum Phaeolepiota aurea Lachnella alboviolascens Melanophyllum haematospermum Melanophyllum echinatum Lepiota clypeolaria Lepiota acutesquamosa Lepiota cristata Lepiota humei Lepiota flammeotincta Lepiota felina GenBank Accession No. Source: Strain No.a U86439/40 AF261448 AF261449 AF042580 AF042562 AF042623 U66430 U66444 U66457 AF261450 AF261451 AF261452 AF261453 AF261454 U66435 AF261455 AF261456 AF261457 AF261458 AF261459 AF261460 AF261461 U66441 U66452 U66438 U66437 U66432 AF042639 AF261462 AF261463 AF261464 AF261465 AF261466 AF261467 AF261468 AF261469 AF261470 AF261471 AF261472 U85300 U85299 U85302 AF261473 AF261474 AF261475 AF261476 AF059231 U85291 U85293 U85292 U85284 U85296 U85295 Nakasone et al., (GenBank) This work: (J) JEJ.VA.581 This work: DAOM192811 Moncalvo et al., 2000 Moncalvo et al., 2000 Moncalvo et al., 2000 Lutzoni, 1997 Lutzoni, 1997 (as Omphalina) Lutzoni, 1997 (as Omphalina wynniae) This work: DAOM190581 This work: DAOM171030 This work: DAOM169729 This work: (D) JM98/368 This work: (D) JM98/369 Lutzoni, 1997 (as Hygrocybe) This work: DAOM208603 This work: (D) DUKE1645 This work: DAOM215543 This work: (D) RV.PR98/28 This work: DAOM182136 This work: (D) JMCR.33 This work: DAOM225483 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 Lutzoni, 1997 (as Gerronema) Moncalvo et al., 2000 This work: (T) TENN6368 This work: (T) TENN6397 This work: (T) TENN6398 This work: (T) TENN6255 This work: (T) TENN7392 This work: (T) TENN6906 Thiswork: (T)TENN1179 This work: (T) TENN7250 This work: (T) TENN5864 This work: (T) TENN6908 This work: (D) RV95/396 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 This work: DAOM188121 This work: DAOM178195 This work: DAOM223321 This work: DAOM197183 Mitchell and Bresinsky, 1999 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 389 390 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Lepiota subincarnata Cystolepiota cystidiosa Cystolepiota cystophora Macrolepiota caperatus U85294 U85298 U85297 U85277 U11923 U85304 U85275 U85278 U85279 U85276 U85286 U85305 U85306 AF041540 U85289 U11920 U85288 AF041541 U85290 U85287 U85281 U11921 U85280 U85285 U85283 U85282 U11915 U85274 U85303 U11902 U11893 U11895 U11906 U11911 AF059227 AF059218 AF059220 AF059225 AF059226 AF059217 AF059215 AF041542 U85273 AF059221 AF059222 AF059219 U11910 AF059223 AF059228 AF059229 AF059230 AF059224 AF261477 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Chapela et al., 1994 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Hopple and Vilgalys, 1999 Johnson and Vilgalys, 1998 Chapela et al., 1994 Johnson and Vilgalys, 1998 Hopple and Vilgalys, 1999 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Chapela et al., 1994 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Chapela et al., 1994 Johnson and Vilgalys, 1998 Johnson and Vilgalys, 1998 Chapela et al., 1994 Chapela et al., 1994 Chapela et al., 1994 Chapela et al., 1994 Chapela et al., 1994 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Hopple and Vilgalys, 1999 Johnson and Vilgalys, 1998 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Chapela et al., 1994 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 Mitchell and Bresinsky, 1999 This work: (D) JMCR.50 Macrolepiota procera Macrolepiota excoriata Macrolepiota gracilenta Macrolepiota colombiana Leucocoprinus cepaestipes Leucocoprinus fragilissimus Leucocoprinus luteus Leucocoprinus birnbaumii Leucocoprinus Leucocoprinus Leucoagaricus Leucoagaricus cf. brebissonii longistriatus rubrotinctus naucinus Leucoagaricus sp. Leucoagaricus hortensis Leucoagaricus americanus Chlorophyllum molybdites attine fungus G1 attine fungus G1 attine fungus G3 attine fungus G3 Agaricus bisporus Agaricus Agaricus Agaricus Agaricus Agaricus Agaricus Agaricus spissicaulis devoniensis impudicus bitorquis bernardii pocillator campestris Agaricus xanthoderma Agaricus silvaticus Agaricus arvensis Agaricus silvicola Agaricus abruptibulbus Agricus lanipes Agaricus maskae Agaricus semotus Agaricus sp. J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Gyrophragmium dunalii Longula texensis Battarraea laciniata Coprinus sterquilinus Coprinus comatus Montagnea arenaria Montagnea radiosus Montagnea candollii Podaxis pistillaris Calvatia sp. Bovista sp. Lycoperdon coloratum Lycoperdon marginatum Tulostoma simulans Crucibulum laeve Cyathus stercoreus Coprinopsis atramentaria Coprinopsis acuminata Coprinopsis romagnesiana Coprinopsis lagopides Coprinopsis lagopus Coprinopsis luteocephala Coprinopsis xenobia Coprinopsis phlyctidospora Coprinopsis macrocephala Coprinopsis cf. erythrocephala Coprinopsis scobicola Coprinopsis cf. Pseudoochraceovela Coprinopsis radiata Coprinopsis cf. Impexi Coprinopsis trispora Coprinopsis narcotica Coprinopsis semitalis Coprinopsis cf. americana Coprinopsis quadrifida Coprinopsis cinerea Coprinopsis sclerotiger Coprinopsis cf. dictyocalyptrata Coprinopsis kimurae Coprinopsis gonophylla Coprinopsis friesii Coprinopsis utrifer Coprinopsis cothurnata Coprinopsis latispora Parasola nudiceps Parasola megasperma Parasola auricoma ‘‘Coprinus’’ cf. cordisporus Coprinellus curtus Coprinellus heterosetulosus Coprinellus cf. sclerocystidiosus Coprinellus bisporus Coprinellus congregatus AF261478 AF261479 AF208534 AF041530 AF041529 AF041538 AF261480 AF261481 AF041539 AF261482 AF261483 AF261484 AF261485 AF261486 AF261582 AF261583 AF041484 AF041485 AF041486 AF041488 AF041490 AF041505 AF041498 AF041499 AF041489 AF041496 AF041491 AF041492 AF041493 AF041495 AF041504 AF041506 AF041508 AF041487 AF139945 AF041494 AF041509 AF041497 AF041500 AF041502 AF041503 AF041501 AF041507 AF041510 AF041517 AF041518 AF041519 AF041511 AF041527 AF041520 AF041521 AF041523 AF041528 This work: leg.CALLAC This work: (V) OKM19301 This work: (V) OKM22810 Hopple and Vilgalys, 1999 Hopple and Vilgalys, 1999 Hopple and Vilgalys, 1999 This work: (V) EK13 This work: (V) EK7 Hopple and Vilgalys, 1999 This work: (J) JRT008 This work: (D) DUKE2395 This work: (D) TYJ This work: (J) JEJ.NC.60 This work: (D) DUKE3733 This work: (G) T816 This work: (G) T815 Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Thorn et al., 2000 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) Hopple and Vilgalys, 1999 (as Coprinus) 391 392 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Coprinellus callinus Coprinellus aokii Coprinellus flocculosus Coprinellus xanthothrix Coprinellus micaceus Coprinellus domesticus Coprinellus radians Coprinellus disseminatus Coprinellus heptemerus Psathyrella gracilis Psathyrella sp. Psathyrella candolleana Psathyrella delineata Psathyrella aff. vanhermanii Psathyrella camptopoda Lacrymaria velutina AF041524 AF041526 AF041515 AF041512 AF041513 AF041514 AF041516 AF041525 AF041522 AF041533 AF261488 AF041531 AF041532 AF261487 AF261489 AF041534 AF139972 AF139946 AF205670 AF205672 AF205671 AF205673 AF205674 n.a. AF205675 AF205676 AF205677 AF205702 AF205703 AF205704 AF205705 AF205678 AF205683 AF205684 AF205685 AF205681 AF205682 AF205686 AF205669 AF205679 AF205680 AF205690 AF205687 AF205688 AF205708 AF205709 AF205707 AF205706 AF208533 AF261490 AF261491 AF205710 AF205689 Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 (as Hopple and Vilgalys, 1999 This work: (D) JMCR.119 Hopple and Vilgalys, 1999 Hopple and Vilgalys, 1999 This work: (D) JMCR.31 This work: DAOM214256 Hopple and Vilgalys, 1999 Thorn et al., 2000 Thorn et al., 2000 This work: (V) MCA 189 This work: (V) OKM27048 This work: (V) MCA386 This work: (V)MCA188 This work: (V) MCA343 This work: DAOM196391 This work: (V) MCA258 This work: (V) OKM26739 This work: (V) OKM26279 This work: (V) MCA672 This work: (V) MCA604 This work: (V) MCA638 This work: (V)MCA163 This work: (V) OKM26 This work: (V)MCA381 This work: (V) OKM26899 This work: (V) OKM27300 This work: (V) OKM26976 This work: (V) OKM270 This work: (V) MCA387 This work: (V) OKM27270 This work: (V) MCA384 This work: (V) OKM26827 This work: (V) TJB8699 This work: (V) MCA424 This work: (V) OKM27046 This work: (V) MCA682 This work: (V) VTMH3760 This work: (V) MCA393 This work: (V) MCA750 This work: (V) OKM24609 This work: DAOM194781 This work: DAOM198223 This work: (V) MCA391 This work: (V) MCA385 Crepidotus crocophyllus Crepidotus nephrodes Crepidotus distortus Crepidotus applanatus v. globigera Crepidotus malachius Crepidotus herbarum Crepidotus sp. Crepidotus fraxinicola Crepidotus mollis Crepidotus uber Crepidotus cf. subaffinis Crepidotus inhonestus Crepidotus lundelli Crepidotus amygdalosporus Crepidotus versutus Crepidotus sp. Crepidotus aureus Crepidotus cesatii Crepidotus sphaerosporus Crepidotus cinnabarinus Crepidotus sp. Crepidotus betula Crepidotus antillarum Crepidotus nyssicola Simocybe sp. Simocybe sumptuosa Simocybe amara Simocybe americana Simocybe centuncula Simocybe sp. Pleuroflammula sp. Pleuroflammula flammea Tubaria furfuracea Tubaria hiemalis Coprinus) Coprinus) Coprinus) Coprinus) Coprinus) Coprinus) Coprinus) Coprinus) Coprinus) J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Tubaria rufo-fulva Tubaria sp. Phaeomarasmius erinaceus AF205712 AF205711 AF261492 AF261594 AF261493 AF042588 AF261494 AF261495 AF261496 AF261497 AF042615 AF195592 AF042613 AF042614 AF261595 AF261498 AF261499 AF261500 AF261501 AF261550 AF261549 AF261551 AF261552 AF261502 AF261503 AF261504 AF261505 AF261506 AF261507 AF261508 AF261509 AF261510 AF042616 AF042617 AF042618 AF261596 AF261597 AF261598 AF261599 AF261600 AF261601 AF261602 AF261603 AF261604 n.a. AF261605 AF261606 AF261607 AF261608 AF261511 AF261609 AF261610 AF261611 This work: (V) OKM24681 This work: (V) OKM24351 This work: DAOM153741 This work: (L) SV.H4 ¼ ECV934 This work: DAOM182559 Moncalvo et al., 2000 This work: (D) JM96/46 This work: (D)JMCR.127 This work: ZT4339 This work: (D) G96/3 Moncalvo et al., 2000 This work: SJ940 Moncalvo et al., 2000 Moncalvo et al., 2000 This work: (D) SV.S6 This work: DAOM209287 This work: DAOM216796 This work: DAOM212213 This work: DAOM174626 This work: DAOM225303 This work: IB19951102 This work: (D) HN3036 This work: DAOM198883 This work: NORVELL1981111.C2.5 This work: DAOM215609 This work: NORVELL1981104.01.3 This work: NORVELL1981111.C2.6 This work: DAOM221500 This work: DAOM225481 This work: DAOM199323 This work: DAOM191293 This work: DAOM174733 Moncalvo et al., 2000 Moncalvo et al., 2000 Moncalvo et al., 2000 (as P. silvatica) This work: (L) v220 ¼ CBS102746 This work: (L) v226 ¼ CBS101990 This work: (L) v188 ¼ CBS102740 This work: (D) D580 This work: (L) v189 ¼ CBS101972 This work: (L) v221 ¼ CBS101989 This work: (L) v200 ¼ CBS101979 This work: (L) v078 ¼ CBS101835 This work: (L) v212 ¼ CBS101983 This work: (L) v069 ¼ CBS101829 This work: c659 ¼ CBS659.87 (type) This work: (L) v026 ¼ CBS101811 This work: (L) v113 ¼ CBS101867 This work: (L) v077 ¼ CBS101833 This work: (D) RV.PR64 This work: (L) v208 ¼ CBS101982 This work: (L) v145 ¼ CBS101873 This work: (D) D2402 (AnnePringle) Flammulaster rhombisporus Laccaria bicolor Laccaria ochropurpurea Laccaria vulcanica Rapacea mariae Rozites caperatus Dermocybe marylandensis Cortinarius subbalustinus Cortinarius iodes Cortinarius sp. Cortinarius distans Cortinarius vibratilis Cortinarius violaceus Cortinarius traganus Cortinarius speciosissimus Thaxterogaster pingue Thaxterogaster porphyreum Thaxterogaster violaceus Phaeocollybia attenuata Phaeocollybia redheadii Phaeocollybia kauffmanii Phaeocollybia dissiliens Phaeocollybia jennyae Squamanita odorata Squamanita umbonata Stagnicola perplexa Inocybe petiginosa Inocybe geophylla var. lilacea Inocybe sp. Psilocybe sp. Psilocybe phyllogena Psilocybe micropora Psilocybe inquilinus Psilocybe subviscida Psilocybe pratensis Psilocybe xeroderma Psilocybe schoeneti Psilocybe crobula Psilocybe montana v. macrospora Psilocybe montana Psilocybe chionophila Psilocybe aff. apelliculosa Psilocybe apelliculosa Melanotus phillipsii Melanotus subcuneiformis Melanotus horizontalis Psilocybe pseudobullacea Psilocybe pseudobullacea 393 394 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Psilocybe coprophila AF139971 AF261612 AF261613 AF261614 AF261615 AF261512 AF042619 AF042567 U11917 AF261616 AF261617 AF261618 AF261619 AF261620 AF261621 AF261622 AF261513 AF261623 AF261514 U11918 AF261515 AF195594 AF195588 AF261516 AF261517 AF261624 AF261625 AF261626 AF261518 AF195598 AF195599 AF261627 AF261628 AF261629 AF261630 AF042570 AF261631 AF195595 AF042569 AF041544 AF139976 AF261632 AF261633 AF195600 AF042009 AF261634 AF261635 AF059232 AF261636 AF261637 AF195597 AF195596 AF261638 Thorn et al., 2000 This work: (L) v254 ¼ CBS101998 This work: (L) v121 ¼ CBS101859 This work: (L) v120 ¼ CBS101858 This work: (L) v135 This work: DAOM187559 This work: (S) DSM1684 This work: (V)VT 1263 Chapela et al., 1994 This work: (L) v112 ¼ CBS101853 This work: (L) v051 ¼ CBS101814 This work: (L) v185 This work: (L) v141 This work: (L) v199 ¼ CBS10197 This work: (D) RV95/502 ( ¼ HN2883) This work: (D) RV95/448 ( ¼ HN3408) This work: (T) TENN6030 This work: (L) SV.S2 This work: AANEN540 Chapela et al., 1994 This work: DAOM176597 This work: SJ90025 This work: SJ86071 This work: AANEN-M29 This work: DAOM174734 This work: (L) v253 This work: (L) v166 ¼ CBS102729 This work: (D) D602 This work: (D) JMCR.99 This work: SJ85066 This work: SJ97002 This work: (L) v038 (as Psilocybe uda) This work: (L) H16(HB7) ¼ CB6321 This work: (L) H15(HB8) ¼ GHP996 This work: CBS810.87 Moncalvo et al., 2000 This work: (L) SV.S4 This work: SJ84170 Moncalvo et al., 2000 Hopple and Vilgalys, 1999 Thorn et al., 2000 This work: (L) v001 ¼ CBS101784 This work: (L) H17(HB5) ¼ Daams This work: SJ85098 Binder et al., 1997 This work: (D) RV95/656 ¼ HN3037 This work: (L) v073 Mitchell and Bresinsky, 1999 This work: (L) SV.S3 This work: (L) SV.S7 This work: SJ76247 This work: SJ92047 This work: CBS838.87 Psilocybe merdaria Psilocybe moelleri Psilocybe subcoprophila Phaeogalera stagnina Kuehneromyces mutabilis Psilocybe stuntzii Psilocybe Psilocybe Psilocybe Psilocybe Psilocybe Psilocybe semilanceata fimetaria liniformans cubensis cyanescens subaeruginosa Pachylepyrium funariophilum Unidentified agaric Hebeloma sp. Hebeloma crustuliniforme Hebeloma longicaudum cf. Pholiota lignicola Flammula alnicola Naucoria escharoides Stropharia semiglobata Stropharia umbonatescens cf. Stropharia Pholiota subochracea Phaeonematoloma myosotis Hypholoma udum Hypholoma ericaeum Hypholoma subericaeum Hypholoma fasciculare Hypholoma subviride Hypholoma capnoides Hypholoma sublateritium Stropharia rugosoannulata Hypholoma aurantiacum Stropharia magnivelaris Leratiomyces similis Weraroa erythrocephala Stropharia coronilla Stropharia hardii Stropharia aeruginosa Stropharia hornemannii J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Weraroa virescens AF042013 AF261639 AF042568 AF261641 AF261642 AF195608 AF261643 AF195609 AF261644 AF261645 AF195607 AF195602 AF195603 AF195604 AF195605 AF195606 AF195601 AF261646 AF261647 AF195593 AF042644 AF041545 AF139941 AF139942 AF261648 AF261519 U11913 AF041543 AF261520 AF041546 AF261521 AF261522 AF261523 AF042011 AF195590 AF261524 U11924 AF041537 AF041535 AF261525 AF041536 AF261526 AF261649 AF195589 AF195587 AF042012 AF261650 AF261651 AF195591 AF261652 AF261527 AF261528 AF261653 Binder et al., 1997 This work: (D) RV95/669 ¼ HN3050 Moncalvo et al., 2000 This work: (L) SV.S1 This work: (L) H24(HB17) ¼ MEN This work: SJ12894 This work: CBS185.53 This work: SJ96022 This work: (L) v027 This work: CBS710.84 This work: (E) LL950724 This work: (E) NH9200 This work: SJ84131 This work: SJ83118 This work: SJ84095 This work: SJ96017 This work: SJ86074 This work: (L) H26(HB12) ¼ GHP1817 This work: (L) H18(HB16) ¼ CB This work: SJ94086 Moncalvo et al., 2000 Hopple and Vilgalys, 1999 Thorn et al., 2000 Thorn et al., 2000 This work: (L) v228 This work: DAOM167564 Chapela et al., 1994 Hopple and Vilgalys, 1999 This work: (D) JMCR.137 Hopple and Vilgalys, 1999 This work: DAOM208660 This work: DAOM174734 This work: (D) DUKE3001 Binder et al., 1997 This work: (E) RM3225 This work: DAOM208552 Chapela et al., 1994 Hopple and Vilgalys, 1999 Hopple and Vilgalys, 1999 This work: (D) JM98/6 Hopple and Vilgalys, 1999 This work: (D) JM98/10 This work: (L) H19(HB6) ¼ GHP1469 This work: (E) KGN94 This work: SJ86019 Binder et al., 1997 This work: CBS296.36 This work: CBS489.90 This work: SJ84074 This work: CBS168.79 This work: CBS169.79 This work: DAOM197244 This work: CBS388.88 Pholiota squarrosoides Pholiota squarrosa Pholiota lenta Pholiota mixta Pholiota highlandensis Pholiota henningsii Pholiota lundbergii Pholiota limonella Pholiota aurivella Pholiota jahnii Pholiota gummosa Pholiota conissans Pholiota flammans Hemipholiota lucifera Hemipholiota destruens Hemipholiota populnea Agrocybe praecox Agrocybe semiorbicularis Agrocybe dura Gastrocybe lateritia Bolbitius vitellinus Bolbitius demangei Conocybe rickenii Pholiotina subnuda Naucoria bohemica Descolea gunnii Leratiomyces smaragdina Galerina marginata Galerina nana Panaeolina foenisecii Panaeolus acuminatus Panaeolus sp. Panaeolus semiovatus Copelandia cyanescens Pholiota oedipus Stropharia albocrenulata Pholiota tuberculosa Ripartites metrodii Gymnopilus aeruginosus Gymnopilus spectabilis Gymnopilus junonius Gymnopilus penetrans Hebelomina neerlandica Galerina paludosa 395 396 J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Cantharocybe gruberi AF261529 AF261530 AF261531 AF261532 AF261587 AF261588 AF261589 AF261590 AF261591 AF261592 AF261593 U11925 U11914 AF042622 AF042007 AF042015 AF261533 AF042571 U11926 AF041548 AF042572 U11919 AF042573 AF042574 AF042646 AF139949 AF261281 AF139947 AF135174 AF261534 AF261535 X78776 X78780 n.a. AF261536 AF135173 AF261563 AF261564 AF261565 AF261537 AF261538 AF135181 AF261539 AF261540 AF261541 AF261542 AF261543 AF261544 AF261545 AF139948 AF139961 AF139967 AF139966 This work: DAOM225482 This work: DED6609 This work: (D) JMleg.SRL This work: (D) JMleg.AIME This work: (D) TYJ.Belize1 This work: CBS301.32 This work: CBS267.60. This work: (D) FL02.1 This work: (D) RGT-970618/01 This work: (D) DSH93-183 This work: DAOM198417 Chapela et al., 1994 Chapela et al., 1994 Moncalvo et al., 2000 Binder et al., 1997 Binder et al., 1997 This work: (D) JMCR.77 Moncalvo et al., 2000 Chapela et al., 1994 Hopple and Vilgalys, 1999 Moncalvo et al., 2000 Chapela et al., 1994 Moncalvo et al., 2000 Moncalvo et al., 2000 (as L. volemus) Moncalvo et al., 2000 Thorn et al., 2000 This work: (E) F799 Thorn et al., 2000 Thorn et al., 2000 This work: DAOM171399 This work: (D) PR10 june 97 Moncalvo et al., 1995 Moncalvo et al., 1995 This work: (D) MUCL4027 This work: DAOM72065 Thorn et al., 2000 This work: (D) Neda C500 This work: (D) E.Kay88/65 This work: (D) RV95/37 This work: (H) DAOM196328 This work: (H) DAOM129034 Thorn et al., 2000 This work: (H) FPL11801 This work: (H) DSH93/195 This work: (H) DAOM211792 This work: (H) DAOM180 496 This work: (H) DAOM180504 This work: (H) DAOM79978 This work: (H) DAOM212269 Thorn et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Thorn et al., 2000 Volvariella volvacea Volvariella hypopithys Schizophyllum commune Schizophyllum radiatum Schizophyllum fasciatum Schizophyllum umbrinum Schizophyllum amplum Fistulina hepatica Porodisculus pendulus Phylloporus rhodoxanthus Boletus retipes Suillus luteus Hygrophoropsis aurantiaca Boletus satanas Scleroderma columnare Russula earlei Russula mairei Russula virescens Russula romagnesii Lactarius corrugis Lactarius piperatus Lactarius sp. Bondarzewia mesenterica Heterobasidion annosum Auriscalpium vulgare Faerberia carbonaria Neolentinus dactyloides Podoscypha parvula Beenakia sp. Ganoderma lucidum gr. Ganoderma australe gr. Amauroderma omphalodes Pycnoporus cinnabarinus Lentinus tigrinus Lentinus squarrosulus Panus sp. Panus sp. Trametes suaveolens Fomes fomentarius Polyporus squamosus Dentocorticium sulphurellum Polyporus varius Datronia mollis Daedaleopsis confragosa Lenzites betulina Polyporus tuberaster Polyporus melanopus Gloeophyllum trabeum Irpex lacteus Phanerochaete chrysorhiza Phanerochaete chrysosporium J.-M. Moncalvo et al. / Molecular Phylogenetics and Evolution 23 (2002) 357–400 397 Appendix A. (continued) Taxon GenBank Accession No. Source: Strain No.a Ceraceomyces serpens Ceraceomyces microsporus Ceraceomyces eludens Phlebia lilascens GR.2 Phlebia nitidula Phlebia centrifuga Phlebia acerina Phlebia lindtneri Phlebia livida Pseudotomentella ochracea Phlebiopsis gigantea Gelatoporia pannocincta Hyphodontia radula Phlebia bresadolae Phlebia deflectens Phlebia griseoflavescens Phlebia lilascens GR.3 Phlebia queletii Phlebia radiata Phlebia rufa Phlebia subochracea Phlebia subserialis Phlebia tremellosa Phlebia tristis Phlebia uda Resinicium bicolor Trichaptum abietinum Postia placenta Lentaria michneri Ramaria eumorpha Gomphus novaezelandia Gloeocantharellus okapaensis Protubera sp. Aseroe arachnoidea Multiclavula vernalis Multiclavula corynoides Clavulina cristata Serpula lacrimans Sphaerobolus stellatus Auricularia polytricha AF090882 AF090874 AF090881 AF141621 AF141625 AF141618 AF141615 AF141623 AF141624 AF092847 AF141634 AF141612 AF141613 AF141617 AF141619 AF141620 AF141622 AF141626 AF141627 AF141628 AF141630 AF141631 AF141632 AF141633 AF141614 AF141635 AF141636 AF139970 AF261546 AF139973 AF261547 AF261548 AF261555/233 AF139943 U66439 U66440 AF261553 AF139974 AF139975 AF261554 Larsson and Larsson, 1998 Larsson and Larsson, 1998 Larsson and Larsson, 1998 Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Hallenberg and Parmasto (GenBank) Thorn et al., 2000 This work: (D) RV98/147 This work: (G) T798 This work: ZT68-657 This work: ZT7135 This work: (D) JM98/351 This work: (G) TMI50070 Lutzoni, 1997 Lutzoni, 1997 This work: (D) RV98/144 Thorn et al., 2000 This work: (G) T800 This work: (D) HN4076 a Origin of material as follows: AANEN, Duur Aanen, Netherlands; (B), Jean B
erub
e, Canada; BSI, B
eatrice Senn-Irlet, Switzerland; (C), SUNY Cortland, U.S.A.; CALLAC, Philippe Callac, France; CBS, Centraalbureau voor Schimmelcultures, Netherlands; (D), Duke University, U.S.A.; DAOM, National Mycological Herbarium, Canada; DED, Dennis Desjardin, San Franciso State University, U.S.A.; (E), Ellen Larsson; (G), Greg Thorn; G. Platas, sequence provided by Gonzala Platas, MERK, Spain; (H), DNA provided by David Hibbett, Clark University, U.S.A.; HALLING, Roy Halling, New York Botanical Garden, U.S.A.; HHB, Hal Burdsall, U.S.A.; IB, University of Innsbruck, Austria; IFO, Institute for fermentation, Japan; (J), James Johnson; JLPR, Jean Lodge, Puerto Rico; (L), University of Leiden, Netherlands; NORVELL, Lorelei Norvell, Portland, U.S.A.; (S), University of Lausanne, Switzerland; SJ, Stig Jacobsson; (T), University of Tennessee, U.S.A.; UPS, Uppsala Herbarium Sweden; (V), Virginia Tech, U.S.A.; ZT, ETH Z€ urich, Switzerland. * Strain not used in the final analysis (cluster with the taxon listed above in preliminary analyses). References Aanen, D.K., Kuyper, T.W., Boekhout, T., Hoekstra, R.F., 2000. Phylogenetic relationships in the genus Hebeloma based on ITS 1 and 2 sequences, with special emphasis on the Hebeloma crustuliniforme complex. Mycologia 92, 269–281. Agerer, R., Beenken, L., 1998. 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