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Journal of Zhejiang University SCIENCE B 2008 Vol.9 No.10 P.779-786


Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses

Author(s):  Rui-lin ZHAO, Dennis E. DESJARDIN, Kasem SOYTONG, Kevin D. HYDE

Affiliation(s):  Faculty of Biology Conservation, Southwest Forestry University, Kunming 650224, China; more

Corresponding email(s):   kskasem@kmitl.ac.th

Key Words:  Gene, Molecular, Mushrooms, Phylogeny

Rui-lin ZHAO, Dennis E. DESJARDIN, Kasem SOYTONG, Kevin D. HYDE. Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses[J]. Journal of Zhejiang University Science B, 2008, 9(10): 779-786.

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author="Rui-lin ZHAO, Dennis E. DESJARDIN, Kasem SOYTONG, Kevin D. HYDE",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses
%A Rui-lin ZHAO
%A Kevin D. HYDE
%J Journal of Zhejiang University SCIENCE B
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%N 10
%P 779-786
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%D 2008
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B0860012

T1 - Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses
A1 - Rui-lin ZHAO
A1 - Dennis E. DESJARDIN
A1 - Kasem SOYTONG
A1 - Kevin D. HYDE
J0 - Journal of Zhejiang University Science B
VL - 9
IS - 10
SP - 779
EP - 786
%@ 1673-1581
Y1 - 2008
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B0860012

We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks (Agaricomycetes/Agaricomycotina/Basidiomycota) along with the most recent treatments of taxonomic systems in these taxa. Establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1] Ainsworth, G.C., Sparrow, F.K., Sussman, A.S. (Eds.), 1973. A Taxonomic Review with Keys: Basidiomycetes and Lower Fungi. In: The Fungi, an Advanced Treatise Volume IVB. Academic Press, New York and London.

[2] Antonin, V., Buyck, B., 2006. Marasmius (Basidiomycota, Marasmiaceae) in Madagascar and the Mascarenes. Fungal Diversity, 23:17-50.

[3] Baldauf, S.L., Palmer, J.D., 1993. Animals and fungi are each others closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA, 90(24):11558-11562.

[4] Barrasa, J.M., Esteve-Raventós, F., Dähncke, R.M., 2006. Clitocybula canariensis (Tricholomataceae), a new brown-rot fungus from the Canary Islands (Spain). Fungal Diversity, 22:1-11.

[5] Berbee, M.L., Carmean, D.A., Winka, K., 2000. Ribosomal DNA and resolution of branching order among the Ascomyceta: how many nucleotides are enough? Mol. Phyl. Evol., 17(3):337-344.

[6] Binder, M., Bresinsky, A., 2002. Derivation of a polymorphic lineage of Gasteromycetes from boletoid ancestors. Mycologia, 94(1):85-98.

[7] Binder, M., Hibbett, D.S., 2002. Higher-level phylogenetic relationships of homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions. Mol. Phyl. Evol., 22(1):76-90.

[8] Binder, M., Hibbett, D.S., Larsson, K.H., Larsson, E., Langer, E., Langer, G., 2005. The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes). Syst. Biodiv., 3(2):113-157.

[9] Blackwell, M., Hibbett, D.S., Taylor, J.W., Spatafora, J.W., 2006. Research coordination networks: a phylogeny for kingdom fungi (Deep Hypha). Mycologia, 98(6):829-837.

[10] Blanco-Dios, J.B., Wang, Z., Binder, M., Hibbett, D.S., 2006. A new Sparassis from Spain described using morphological and molecular data. Mycol. Res., 110(10):1227-1231.

[11] Bodensteiner, P., Binder, M., Agerer, R., Moncalvo, J.M., Hibbett, D.S., 2004. Phylogenetic diversity of cyphelloid forms in the homobasidiomycetes. Mol. Phyl. Evol., 33(2):501-515.

[12] Bruns, T.D., Vilgalys, R., Barns, S.M., Gonzalez, D., Hibbett, D.S., Lane, D.J., Simon, L., Stickel, S., Szaro, T.M., Weisburg, W.G., Sogin, M.L., 1992. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol. Phyl. Evol., 1(3):231-241.

[13] Bruns, T.D., Szaro, T.M., Gardes, M., Cullings, K.W., Pan, J.J., Taylor, D.L., Horton, T.R., Kretzer, A., Garbrlotto, M., Li, Y., 1998. A sequence database for the identification of ectomycorrhizal basidiamycetes by phylogenetic analysis. Mol. Ecol., 7(3):257-272.

[14] Burnett, J., 2003. Fungal Populations Species. Oxford University Press, London.

[15] Buyck, B., Mitchell, D., Parrent, J., 2006. Russula parvovirescens sp. nov., a common but ignored species in the eastern Unoted States. Mycologia, 98(4):612-615.

[16] Callac, P., Guinberteau, J., 2005. Morphological and molecular characterization of two novel species of Agaricus section Xanthodermatei. Mycologia, 97(2):416-424.

[17] Capelari, M., Rosa, L.H., Lachance, M.A., 2006. Description and affinities of Agaricus martineziensis, a rare species. Fungal Diversity, 21:11-18.

[18] Celio, G.J., Padamsee, M., Dentinger, B.T.M., Bauer, R., McLaughlin, D.J., 2006. Assembling the fungal tree of life: constructing the structural and biochemical database. Mycologia, 98(6):850-859.

[19] Dai, Y.C., Wang, Z., Binder, M., Hibbett, D.S., 2006. Phylogeney and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genes. Mycologia, 98(4):584-592.

[20] Desjardin, D.E., Wang, Z., Binder, M., Hibbett, D.S., 2004. Sparassis cystidiosa sp. nov. from Thailand is described using morphological and molecular data. Mycologia, 96(5):1010-1014.

[21] Doyle, J.J., 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Bot., 17(1):144-163.

[22] Garibay-Orijel, R., Cifuentes, J., Estrada-Torres, A., Caballero, J., 2006. People using macro-fungal diversity in Oaxaca, Mexico. Fungal Diversity, 21:41-67.

[23] Hallen, H.E., Watling, R., Adams, G.C., 2003. Taxonomy and taxicity of Conocybe lacteal and related species. Mycol. Res., 107(8):969-979.

[24] Harrison, G.R., 1998. Linking evolutionary pattern and process. In: Howard, D.J., Berlocher, S.H. (Eds.), Endless Forms. Oxford University Press, Oxford.

[25] Hibbett, D.S., 2004. Trends in morphological evolution in homobasidiomycetes inferred using maximum likelihood a comparison of binary and multistate approaches. Syst. Biol., 53(6):889-903.

[26] Hibbett, D.S., 2006. A phylogenetic overview of the Agaricomycotina. Mycologia, 98(6):917-925.

[27] Hibbett, D.S., Donoghue, M.J., 1996. Implications of phylogenetic studies for conservation of genetic diversity in shiitake mushrooms. Cons. Biol., 10(5):1321-1327.

[28] Hibbett, D.S., Thorn, R.G., 2001. Basidiomycota: Homobasidiomycetes. In: McLaughlin, D.J., McLaughlin, E.G., Lemke, R.A. (Eds.), The Mycota, Vol. 7B. Systematics and Evolution. Springer-Verlag, New York, p.121-168.

[29] Hibbett, D.S., Binder, M., 2002. Evolution of complex fruiting body morphologies in homobasidiomycetes. Proc. Roy. Soc. B Biol. Sci., 269(1504):1963-1969.

[30] Hibbett, D.S., Tsuneda, A., Fukumasa-Nakai, Y., Donoghue, M.J., 1995. Phylogenetic diversity in shiitake inferred from nuclear ribosomal DNA sequences. Mycologia, 87(5):618-638.

[31] Hibbett, D.S., Pine, E.M., Langer, E., Langer, G., Donoghue, M.J., 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc. Natl. Acad. Sci. USA, 94(22):12002-12006.

[32] Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M., Lücking, R., et al., 2007. A higher-level phylogenetic classification of the fungi. Mycol. Res., 111(5):509-548.

[33] Huelsenbeck, J.P., Rannala, B., 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science, 276(5310):227-232.

[34] Hughey, B.D., Adams, G.C., Bruns, T.D., Hibbett, D.S., 2000. Phylogeny of Calostoma, the gelatinous stalked puffball, based on nuclear and mitochondrial ribosomal DNA sequences. Mycologia, 92(1):94-104.

[35] James, T.Y., Kauff, F., Schoch, C., Matheny, P.B., Hofstetter, V., Cox, C., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., et al., 2006. Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature, 443(7113):818-822.

[36] Kasuga, T., White, T.J., Taylor, J.W., 2002. Estimation of nucleotide substitution rates in eurotiomycetes fungi. Mol. Biol. Evol., 19:2318-2324.

[37] Kaul, T.N., 1997. Introduction to Mushroom Science (Systematics). Science Publishers Inc., New Hampshire.

[38] Kendrick, B., 2000. The Fifth Kingdom, 3rd Ed. Focus Publishing, USA.

[39] Kirk, P.M., Cannon, P.F., David, J.C., Stalpers, J.A., 2001. Dictionary of the Fungi, 9th Ed. CAB International, London.

[40] Kretzer, A.M., Bruns, T.D., 1999. Use of atp6 in fungal phylogenetics: an example from the boletales. Mol. Phyl. Evol., 13(3):483-492.

[41] Kropp, B.P., Matheny, P.B., 2004. Basidiospore homoplasy and variation in the lnocybe chelanensis group in North America. Mycologia, 96(2):295-309.

[42] Larsson, K.H., Larsson, E., Köljalg, U., 2004. High phylogenetic diversity amony corticioid basidiomycetes. Mycol. Res., 108(9):983-1002.

[43] Le, H.T., Nuytinck, J., Verbeken, A., Lumyong, S., Desjardin, D.E., 2007a. Lactarius in northern Thailand: 1. Lactarius subgenus Piperites. Fungal Diversity, 24:173-224.

[44] Le, H.T., Stubbe, D., Verbeken, A., Nuytinck, J., Lumyong, S., Desjardin, D.E., 2007b. Lactarius in northern Thailand:2. Lactarius subgenus Plinthogali. Fungal Diversity, 27:61-94.

[45] Lechner, B.E., Wright, J.E., Popoff, E., 2006. New taxa and new records of fungi for Argentina from Iguazú National Park, Misiones. Fungal Diversity, 21:131-139.

[46] Liu, Y.J., Hall, B.D., 2004. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc. Natl. Acad. Sci. USA, 101(13):4507-4512.

[47] Liu, Y.J., Whelen, S., Hall, B.D., 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol. Biol. Evol., 16:1799-1808.

[48] Maddison, W.P., 1997. Gene trees in species trees. Syst. Biol., 46(3):523-536.

[49] Matheny, P.B., 2005. Improving phylogenetic inference of mushrooms with RBP1 and RBP2 nucleotide sequences Inocybe, Agaricales. Mol. Phyl. Evol., 35(1):1-20.

[50] Matheny, P.B., Bougher, N.L., 2006. The new genus Auritella from Africa and Australia (Inocybaceae, Agaricales): molecular systematics, taxonomy and historical biogeography. Mycol. Prog., 5(1):2-17.

[51] Matheny, P.B., Liu, Y.J., Ammirati, J.F., Hall, B.D., 2002. Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocebe, Agaricales). Am. J. Bot., 89(4):688-698.

[52] Matheny, P.B., Curtus, J.M., Hofstetter, V., Aime, M.C., Moncalvo, J.M., Ge, Z.W., Yang, Z.L., Slot, J.C., Ammirati, J.F., Baroni, T.L., et al., 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia, 98(6):982-995.

[53] Matheny, P.B., Wang, Z., Binder, M., Curtis, J.M., Lim, Y.W., Nilsson, R.H., Hughes, K.W., Hofstetter, V., Ammirati, J.F., Schoch, C., et al., 2007. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol. Phyl. Evol., 43(2):430-451.

[54] Mayden, R.L., 1997. A Hierarchy of Species Concepts: The DENOUEMENt in the Saga of the Species Problem. In: Claridge, M.F., Dawah, H.A., Wilson, M.P. (Eds.), The Units of Biodiversity. Chapman & Hall, London, p.381-424.

[55] Mayr, E., 1940. Speciation phenomena in birds. Am. Nat., 74(752):249-278.

[56] Mayr, E., 1968. The role of systematics in biology. Science, 159(3815):595-599.

[57] Mayr, E., 1982. The Growth of Biological Thought. Harvard University Press, Cambridge, MA.

[58] Mayr, E., Ashlock, P.D., 1991. Principles of Systematic Zoology, 2nd Ed. McGraw-Hill, New York.

[59] Miller, A.N., Huhndorf, S.M., 2004. Using phylogenetic species recognition to delimit species boundaries within Lasiosphaeria. Mycologia, 96(5):1106-1127.

[60] Minnis, A.M., Sundberg, W.J., Nelsen, S.F., 2006. Pluteus aurantipes sp. nov. from Wisconsin, United States. Mycologia, 98(4):659-661.

[61] Moncalvo, J.M., 2005. Molecular Systematics: Major Fungal Phylogenetic Groups and Fungal Species Concepts. In: Xu, J.P. (Ed.), Evolutionary Genetics of Fungi. Horizon Scientific Press, Norfolk.

[62] Moncalvo, J.M., Lutzoni, F.M., Rehner, S.A., Johnson, J., Vilgalys, R., 2000. Phylogenetic relationships of Agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst. Biol., 49(2):278-305.

[63] Moncalvo, J.M., Vilgalys, R., Redhead, S.A., Johnson, J.E., James, T.Y., Aime, M.C., Hofstetter, V., Verduin, S.J.W., Larsson, E., Baroni, T.J., et al., 2002. One hundred and seventeen clades of euagarics. Mol. Phyl. Evol., 23(3):357-400.

[64] Moncalvo, J.M., Nilsson, R.H., Koster, B., Dunbam, S.M., Bernaruer, T., Matheny, P.B., Porter, T.M., Margaritescu, S., Weiß, M., Garnica, S., et al., 2006. The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. Mycologia, 98(6):937-948.

[65] Noordeloos, M.E., Hausknecht, A., 2007. The genus Entoloma (Basidiomycetes, Agaricales) of the Mascarenes and Seychelles. Fungal Diversity, 27:111-144.

[66] Noordeloos, M.E., Vrinda, K.B., Manimohan, P., 2007. On two remarkable brown-spored agarics from Kerala State, India. Fungal Diversity, 27:145-155.

[67] Nuytinck, J., Wang, X.H., Verbeken, A., 2006. Descriptions and taxonomy of the Asian representatives of Lactarius sect. Deliciosi. Fungal Diversity, 22:171-203.

[68] O′Donnell, K., Lutzoni, F., Ward, T.J., Benny, G.L., 2001. Evolutionary relationships among mucoralean fungi (Zygomecota): evidence for family polyphyly on a large scale. Mycologia, 93(2):286-296.

[69] Ortiz-Santana, B., Lodge, D.J., Baroni, T.J., Both, E.E., 2007. Boletes from Belize and the Dominican Republic. Fungal Diversity, 27:247-416.

[70] Ovrebo, C.L., Baroni, T.J., 2007. New taxa of Tricholomataceae and Entolomataceae (Agaricales) from Central America. Fungal Diversity, 27:157-170.

[71] Peintner, U., Bougher, N.L., Castellano, M.A., Moncalvo, J.M., Moser, M.M., Trappe, J.M., Vilgalys, R., 2001. Multiple origins of sequestrate fungi related to Cortinatius (Cortinatiaceae). Am. J. Bot., 88(12):2168-2179.

[72] Petersen, R.H., Hughes, K.W., 1999. Species and speciation in mushrooms. BioScience, 49(6):440-452.

[73] Reeb, V., Lutzoni, F., Roux, C., 2004. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special enphasis on the lichen-forming Acarosporaceae and evolution of pilyspory. Mol. Phyl. Evol., 32(3):1036-1060.

[74] Rehner, S.A., Buckley, E., 2005. A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia, 97(1):84-98.

[75] Robison, M.M., Chiang, B., Horgen, P.A., 2001. A phylogeny of the genus Agaricus based on mitochondrial atp6 sequences. Mycologia, 93(1):30-37.

[76] Simpson, G.G., 1961. Principles of Animal Taxonomy. Columbia University Press, New York.

[77] Singer, R., 1962. The Agaricales in Modern Taxonomy, 2th Ed. Weinheim, J. Cramer, Germany, p.916.

[78] Singer, R., 1986. The Agaricales in Modern Taxonomy, 4th Ed. Koeltz Scientific Books, Koenigsternm, Germany, p.981.

[79] Sugiyama, J., 1998. Relatedness, phylogeny, and evolution of the fungi. Mycoscience, 39(4):487-511.

[80] Swann, E.C., Taylor, J.W., 1993. Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycologia, 85(6):923-936.

[81] Swann, E.C., Taylor, J.W., 1995. Phylogenetic perspective on basidiomycetes systematics: evidence from the 18S rRNA gene. Can. J. Bot., 73(Suppl. 1):S862-S868.

[82] Tan, Y.S., Desjardin, D.E., Vikineswary, S., Abdullah, N., 2007. New species and mating studies of Marasmius from Malaysia. Fungal Diversity, 25:187-217.

[83] Taylor, J.W., Jacobson, D.J., Kroken, S., Kasuga, T., Geiser, D.M., Hibbett, D.S., Fisher, M.C., 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol., 31(1):21-32.

[84] Tehler, A., Farris, J.S., Lipscomb, D.L., Källersjo, M., 2000. Phylogenetic analyses of the fungi based on large rDNA data sets. Mycologia, 92(3):459-474.

[85] Wang, Z., Binder, M., Hibbett, D.S., 2002. A new species of Cudonia based on morphological and molecular data. Mycologia, 94(4):641-650.

[86] Wang, Z., Binder, M., Dai, Y.C., Hibbett, D.S., 2004. Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and a protein-coding gene (rpb2). Mycologia, 96(5):1013-1027.

[87] Wiley, E.O., 1978. The evolutionary species concept reconsidered. Syst. Zool., 27(1):17-26.

[88] Zhang, N., Blackwell, M., 2002. Molecular phylogeny of Melanospora and similar pyrenomycetous fungi. Mycol. Res., 106(2):148-155.

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