Major clades of Agaricales: a multilocus phylogenetic overview

Aanen DK, Eggleton P, Rouland-Lefevre C, Guldberg-Frøslev T, Rosendahl S, Boomsma J. 2002. The evolution of fungus-growing termites and their mutualistic fungal symbionts. Proc Nat Acad Sci, USA 99: 14887–14892.

Aime MC, Phillips-Mora. 2005. The causal agents of witches’ broom and frosty pod rot of cacao (chocolate,Theobroma cacao) form a new lineage of Marasmiaceae. Mycologia 97:1012–1022.

Altekar GS, Dwarkadas S, Huelsenbeck JP, Ronquist F. 2004. Parallel metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407–415.

Arnolds E. 1980. De oecologie en sociologie van Wasplaten (HygrophorussubgenusHygrocybe sensu lato). Natura 77:17–44.

———. 1986. Notes on Hygrophoraceae IXCamarophyllopsisHerink, an older name forHygrotramaSing. Mycotaxon 25:639–644.

———. 1990. Tribus Hygrocybeae. In: Bas C, Kuyper TW, Noordeloos ME, Vellinga EC, eds., Rotterdam: A.A. Balkema. p 70–111.

Bas C. 1998. Orders and families in agarics and boleti. In: Bas C, Kuyper TW, Noordeloos ME, Vellinga EC, eds. Flora agaracina neerlandica: critical monographs on families of agarics and boletii occurring in the Netherlands. Vol. 1. Rotterdam: A.A. Balkema. p 40–49.

Benjamin DR. 1995. Mushrooms: poisons and panaceas. New York: W.H. Freeman & Co. 422 p.

Bigelow HE. 1985. North American species ofClitocybe. Part II. Beih Nova Hedwigia 81:281–471.

Binder M, Besl H, Bresinsky A. 1997. Agaricales oder Boletales? Molekularbiologische Befunde zur Zuordnung einiger umstrittener Taxa. Z Mykol 63:189–196.

———, Bresinsky A. 2002. Derivation of a polymorphic lineage of Gasteromycetes from boletoid ancestors. Mycologia 94:85–98.

———, Hibbett DS. 2002. Higher-level Phylogenetic relationships of Homobasidiomycetetes (mushroom-forming fungi) inferred from four rDNA regions. Mol Phylogenet Evol 22:76–90.

———, ———, Larsson KH, Larsson E, Langer E, Langer G. 2005. The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes). Syst Biodivers 3:113–157.

———, ———, Wang Z, Farnham W. 2006. Evolutionary relationships ofMycaureola dilseae(Agaricales), a basidiomycete pathogen of a subtidal rhodophyte. Am J Bot 93:547–556.

Bodensteiner P, Binder M, Moncalvo JM, Agerer R, Hibbett DS. 2004. Phylogenetic relationships of cyphelloid homobasidiomycetes. Mol Phylogenet Evol 33:501–515.

Boertmann D. 1996. The genusHygrocybe. Fungi of Northern Europe 1:5–184.

Bougher NL, Malajczuk N. 1985. A new species ofDescolea(Agaricales) from Western Australia, and aspects of its ectomycorrhizal status. Aust J Bot 33:619–627.

———, Syme K. 1998. Fungi of southern Australia. Perth: University of Western Australia Press. 391 p.

Bresinsky A, Schneider G. 1975. Nitratreduktion durch Pilze und die Verwertbarkeit des Merkmals für die Systematik. Biochem System Ecol 3:129–135.

Bruns TD, Shefferson RP. 2004. Evolutionary studies of ectomycorrhizal fungi: recent advances and future directions. Can J Bot 82:1122–1132.

Chapela IH, Rehner SA, Schultz TR, Mueller UG. 1994. Evolutionary history of the symbiosis between fungus-growing ants and their fungi. Science 266:1691–1694.

Clémençon H. 1978. Siderophilous granules in the basidia of Hymenomycetes. Persoonia 10:83–96.

———. 2004. Cytology and plectology of the Hymenomycetes. Bibliothec Mycol 199:iii–488.

Czederpiltz DLL, Volk TJ, Burdsall HH. 2001. Field observations and inoculation experiments to determine the nature of the carpophoroids associated withEntoloma abortivumandArmillaria. Mycologia 93:841–851.

DeBry RW, Olmstead RG. 2000. A simulation study of reduced tree-search effort in bootstrap resampling analysis. Syst Biol 49:171–179.

De Román M, Claveria V, De Miguel AM. 2005. A revision of the descriptions of ectomycorrhizas published since 1961. Mycol Res 109:1063–1104.

Donk MA. 1964. Conspectus of the families of Aphyllophorales. Persoonia 3:199–324.

Duncan EG, Galbraith MH. 1972. Post-meiotic events in the Homobasidiomycetidae. Trans Br Mycol Soc 58:387–392.

Fayod V. 1889. Prodrome d’une histoire naturelle des Agaricinées. Annls Sci Nat Bot Sér 7,9:181–411.

Fries E. 1821–1832. Systema mycologicum, sistens fungorum ordines, genera et species hucusque cognitas. Gryphiswaldiae.

———. 1828. Elenchus fungorum. Vols. I & II. Germany: Greifswald.

———. 1857–63. Monographia hymenomycetum sueciae. Vols. I & II. Uppsala: C.A. Leffler.

———. 1874. Hymenomycetes europaei. Uppsala: Berling. 755 p.

Frøslev TG, Matheny PB, Hibbett DS. 2005. Lower level relationships in the mushroom genusCortinarius(Basidiomycota, Agaricales): a comparison of RPB1, RPB2, and ITS phylogenies. Mol Phylogenet Evol 37: 602–618.

Gulden G, Stensrud Ø, Shalchian-Tabrizi K, Kauserud H. 2005.GalerinaEarle: a polyphyletic genus in the consortium of dark-spored agarics. Mycologia 97:823–837.

Hacskaylo E. 1971. The role of mycorrhizal associations in the evolution of the higher basidiomycetes. In: Petersen RH, ed. Evolution in the higher basidiomycetes: an international symposium. Knoxville: University of Tennesee Press. p 217–237.

Hallen HE, Watling R, Adams GC. 2003. Taxonomy and toxicity ofConocybe lacteaand related species. Mycol Res 107:969–979.

Harmaja H. 1978. The division of the genusLepista. Karstenia 18:49–54.

———. 2002.Amylolepiota,ClavicybeandCystodermella, new genera of Agaricales. Karstenia 42:39–48.

———. 2003. Notes onClitocybe s. lato(Agaricales). Ann Bot Fennici 40:213–218.

Heim R. 1971. The interrelationships between the Agaricales and Gasteromycetes. In: Petersen RH, ed. Evolution in the higher basidiomycetes. Knoxville: University of Tennessee Press. p 505–534.

Hesler LR, Smith AH. 1963. North American species ofHygrophorus. Knoxville: University of Tennessee Press. 416 p.

Hibbett DS, Pine EM, Langer E, Langer G, Donoghue MJ. 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc Natl Acad Sci USA 94:12002–12006.

———, Gilbert LB, Donoghue MJ. 2000. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407:506–508.

———, Thorn RG. 2001. Basidiomycota: Homobasidiomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA, eds. The Mycota. VIIB. Systematics and Evolution. Berlin: Springer-Verlag. p 121–168.

———, Binder M. 2002. Evolution of complex fruiting-body morphologies in homobasidiomycetes. Proc R Soc Lond B 269:1963–1969.

———. 2004. Trends in morphological evolution in homobasidiomycetes inferred using maximum likelihood: a comparison of binary and multistate approaches. Syst Biol 53:889–903.

Hofstetter V, Clémençon H, Vilgalys R, Moncalvo JM. 2002. Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences. Mycol Res 106:1043–1059.

Horak E. 1968. Synopsis generum Agaricalium (Die Gattungstypen der Agaricales). Beiträge zur Kryptogamenflora der Schweiz 13:1–741.

———. 1990. Monograph of the New Zealand Hygrophoraceae (Agaricales). NZ J Bot 28:255–309.

Hsiang T, Wu C. 2000. Genetic relationships of pathogenicTyphulaspecies assessed by RAPD, ITS-RFLP and ITS sequencing. Mycol Res 104:16–22.

Hughes KW, Petersen RH, Johnson JE, Moncalvo JM, Vilgalys R, Redhead SA, Thomas T, McGhee LL. 2001. Infrageneric phylogeny ofCollybia s. str.based on sequences of ribosomal ITS and LSU regions. Mycol Res 105:164–172.

Jülich W. 1981. Higher taxa of basidiomycetes. Bibliothec Mycol 85:5–485.

Kirk PM, Cannon PF, David JC, Stalpers JA. 2001. Ainsworth & Bisby’s dictionary of the fungi. 9th ed. Surrey, UK: CAB International. 655 p.

Kobayashi H, Degawa Y, Yamada A. 2003. Two new records of entolomatoid fungi associated with rosaceous plants from Japan. Mycoscience 44:331–333.

———, Yamada A, Tokumasu S, Kakishima M. 2005. Mycorrhizal morphology in Rosaceae and Ulmaceae produced by entolomatoid fungi in Japan. Abstract from the Mycological Society of American and Mycological Society of Japan Joint Meeting, Hilo, Hawaii, 30 Jul–5 Aug 2005. 144 p.

Krüger D, Binder M, Fischer M, Kreisel H. 2001. The Lycoperdales. A molecular approach to the systematics of some gasteroid mushrooms. Mycologia 93:947–957.

Kühner R. 1977. Variation of nuclear behaviour in the homobasidiomycetes. Trans Br Mycol Soc 68:1–16.

———. 1980. Les Hyménomycètes agaricoïdes. Bull Soc Linn Lyon 49: Numéro spécial. 1027 p.

———. 1984. Some mainlines of classification in the gill fungi. Mycologia 76:1059–1074.

———, Romagnesi H. 1953. Flore analytique des champignons supérieurs (agarics, bolets, chanterelles). Paris: Masson. 556 p.

Kuyper TW. 1995. 5.Clitocybe. In: Bas C, Kuyper TW, Noordeloos ME, Vellinga EC, eds. Flora agaricina neerlandica. Vol. 3. Rotterdam: A.A. Balkema. p 42–62.

Largent DL. 1994. Entolomatoid fungi of the western United States and Alaska. Eureka, California: Mad River Press. 277 p.

Larsson KH, Larsson E, Kõljalg U. 2004. High phylogenetic diversity among corticioid basidiomycetes. Mycol Res 108:983–1002.

Maddison DR, Maddison WP. 2000. MacClade 4: analysis of phylogeny and character evolution. Sunderland, Massachusetts: Sinauer Associates.

Malloch DW. 1987. The evolution of mycorrhizae. Can J Plant Path 9:398–402.

———, Pirozynski KA, Raven PH. 1980. Ecological and evolutionary significance of mycorrhizal symbioses in vascular plants (a review). Proc Natl Acad Sci USA 77: 2113–2118.

Mata JL, Hughes KW, Petersen RH. 2004. Phylogenetic placement ofMarasmiellus juniperinus. Mycoscience 45:214–221.

Matheny PB. 2005. Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). Mol Phylogenet Evol 35:1–20.

———, Bougher NL. 2006. The new genusAuritellafrom Africa and Australia (Inocybaceae, Agaricales): molecular systematics, taxonomy and historical biogeography. Mycol Prog 5:2–17.

———, Liu YJ, Ammirati JF, Hall BD. 2002. Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am J Bot 89:688–698.

Moncalvo JM, Lutzoni FM, Rehner SA, Johnson J, Vilgalys R. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst Biol 49:278–305.

———, Vilgalys R, Redhead SA, Johnson JE, Jame TY, Aime MC, Hofstetter V, Verduin SJW, Larsson E, Baroni TJ, Thorn RG, Jacobsson S, Clémençon H, Miller Jr OK. 2002. One hundred seventeen clades of euagarics. Mol Phylogenet Evol 23:357–400.

Moser MM. 1983. Keys to agarics and boleti. London: Roger Phillips. 535 p.

Mueller GM, Ammirati JF. 1993. Cytological studies inLaccaria(Agaricales). II. Assessing phylogenetic relationships amongLaccaria,Hydnangiumand other Agaricales. Am J Bot 80:322–329.

Mueller UG, Rehner SA, Schultz TR. 1998. The evolution of agriculture in ants. Science 281:2034–2038.

Munkacsi AB, Pan JJ, Villesen P, Mueller UG, Blackwell M, McLaughlin DJ. 2004. Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants. Proc R Soc Lond B 271:1777–1782.

Norvell LL. 1998. Observations on the development, morphology and biology ofPhaeocollybia. Mycol Res 102:615–630.

———. 2001. An informal poll for MSA members: should the type ofCoprinusbe changed? Inoculum 52:5.

———, Redhead SA, Ammirati JF. 1994.Omphalina sensu latoin North America 1–2. 1:Omphalina wynniaeand the genusChrysomphalina. 2:Ompahlina sensuBigelow. Mycotaxon 50:379–407.

Oberwinkler F. 1984. Fungus-alga interactions in basidiolichens. Beih Nova Hedwig 79:739–774.

Okabe I, Matsumoto N. 2003. Phylogenetic relationships ofSclerotium rolfsii(teleomorphAthelia rolfsii) andS. delphiniibased on ITS sequences. Mycol Res 107:164–168.

Pegler DN, Young TWK. 1969. Ultrastructure of basidiospores in Agaricales in relation to taxonomy and spore discharge. Trans Br Mycol Soc 52:491–513.

———, ———. 1971. Basidiospore morphology in the Agaricales. Beih Nova Hedwig 35:1–210.

———, ———. 1979. Spore form and phylogeny of Entolomataceae (Agaricales). Sydow Beih. 8:290–303.

Peintner U, Bougher NL, Castellano MA, Moncalvo JM, Moser MM, Trappe JM, Vilgalys R. 2001. Multiple origins of sequestrate fungi related toCortinarius(Cortinariaceae). Am J Bot 88:2168–2179.

Petersen RH, ed. 1971. Evolution in the higher basidiomycetes. Knoxville: University of Tennessee Press. 562 p. 13 pl.

Pine EM, Hibbett DS, Donoghue MJ. 1999. Phylogenetic relationships of cantharelloid and clavarioid Homobasidiomycetes based on mitochondrial and nuclear rDNA sequences. Mycologia 91:944–963.

Redhead SA. 1981. Parasitism of bryophytes by agarics. Can J Bot 59:63–67.

———. 1985. Proposal to conserveMycena(Tricholomataceae, Agaricales). Taxon 34:303–307.

———, Ginns JH. 1985. A reappraisal of agaric genera associated with brown rots of wood. Trans Mycol Soc Jap 26:349–381.

———, Ammirati JF, Norvell LL, Seidl MT. 2000. Notes on western North American snowbank fungi. Mycotaxon 76:321–328.

———, Vilgalys R, Moncalvo JM, Johnson J, Hopple JS. 2001a.CoprinusPers. and the disposition ofCoprinusspeciessensu lato. Taxon 50:203–241.

———, ———, ———, ———, ———. 2001b. Proposals to conserve or reject. Proposals to conservePsathyrella(Fr.) Quél. with a conserved type and to reject the namePselliophoraP. Karst. (Basidiomycetes: Psathyrellaceae). Taxon 50:275–277.

———, Moncalvo JM, Vilgalys R, Lutzoni F. 2002a. Phylogeny of agarics: partial systematics solutions for bryophilus omphalinoid agarics outside of the Agaricales (euagarics). Mycotaxon 82:151–168.

———, Lutzoni F, Moncalvo JM, Vilgalys R. 2002b. Phylogeny of agarics: partial systematics solutions for core omphalinoid genera in the Agaricales (euagarics). Mycotaxon 83:19–57.

Rihs JD, Padhye AA, Good CB. 1996. Brain abscess caused bySchizophyllum commune: an emerging basidiomycete pathogen. J Clin Microbiol 34:1628–1632.

Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574.

Rouland-Lefevre C, Diouf MN, Brauman A, Neyra M. 2002. Phylogenetic relationships inTermitomyces(family Agaricaceae) based on the nucleotide sequence of ITS: a first approach to elucidate the evolutionary history of the symbiosis between fungus-growing termites and their fungi. Mol Phylogenet Evol 22:423–429.

Salamin N, Chase MW, Hodkinson TR, Savolaine V. 2003. Assessing internal support with large phylogenetic matrices. Mol Phylogenet Evol 27:528–539.

Sigler L, Bartley JR, Parr DH, Morris AJ. 1999. Maxillary sinusitis caused by medusoid form ofSchizophyllum commune. J Clin Microbiol 37:3395–3398.

Singer R. 1986. The Agaricales in modern taxonomy. 4th ed. Koenigstein, Germany: Koeltz Scientific Books. 981 p. 88 pl.

———. 1991. Toward a definition of the genus in mycological taxonomy. Mycol Helvetica 6:92–94.

Smith AH, Smith HV, Weber NS. 1979. How to know the gilled mushrooms. Dubuque, Iowa: Wm. C. Brown Publishers. 334 p.

———, Stuntz DE. 1950. New or noteworthy fungi from Mt Rainier National Park. Mycologia 62:80–134.

Swofford DL. 2003. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, Massachusetts: Sinauer Associates.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acid Res 25:4876–4882.

Thorn RG, Moncalvo JM, Reddy CA, Viglays R. 2000. Phylogenetic analysis and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoidlentinoid fungi. Mycologia 92:241–252.

Vellinga EC. 2004. Ecology and distribution of lepiotaceous fungi (Agaricaceae)—a review. Nova Hedwig 78:273–299.

Vizzini A, Girlanda M. 1997.Squamanita umbonata(Sums.) Bas, a mycoparasite ofInocybe oblectabilis(Britz.) Sacc.—preliminary note. Allionia 35:171–175.

Watling R, Gregory NM. 1987. 5 / Strophariaceae & Coprinaceae pp. In: Gregory NM, Watling R, eds. British fungus flora: agarics and boleti. Edinburgh: Royal Botanic Garden. p 1–121.

Weiss M, Selosse MA, Rexer KH, Urban A, Oberwinkler F. 2004. Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential. Mycol Res 108:1003–1010.

White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenies. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. San Diego: Academic Press. p 315–322.

Wiens JJ. 2006. Missing data and the design of phylogenetic analyses. J Biomed Inform 39:34–42.

Wilson AW, Desjardin DE. 2005. Phylogenetic relationships in the gymnopoid and marasmioid fungi (Basidiomycetes, euagarics clade). Mycologia 97:667–679.