The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods

LITERATURE CITED

• Barker FK, Lutzoni F. 2002. The utility of the incongruence length difference test. Syst Biol 51:625–637.
   Google Scholar
• Bianchinotti MV, Rajchenberg M, Greslebin AG. 2005. Parenthesome structure of some corticioid fungi. Mycol Res 109:923–926.
   Google Scholar
• Bidartondo MI, Bruns TD, Weiß M, Sergio C, Read DJ. 2003. Specialized cheating of the ectomycorrhizal symbiosis by an epiparasitic liverwort. Proc R Soc Lond B 270: 835–842.
   Google Scholar
• ———, Burghardt B, Gebauer G, Bruns TD, Read DJ. 2004. Changing partners in the dark: isotopic and molecular evidence of ectomycorrhizal liaisons between forest orchids and trees. Proc R Soc Lond B 271:1799–1806.
   Google Scholar
• Binder M, Hibbett DS. 2002. Higher-level phylogenetic relationships of homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions. Mol Phylogenet Evol 22:76–90.
   Google Scholar
• ———, ———, 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.
   Google Scholar
• Bininda-Emonds ORP, Sanderson MJ. 2001. Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst Biol 50:565–579.
   Google Scholar
• Bruns TD, Szaro TM, Gardes M, Cullings KW, Pan JJ, Taylor DL, Horton TR, Kretzer A, Garbelotto M, Li Y. 1998. A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis. Mol Ecol 7:257–272.
   Google Scholar
• Clémençon H. 1997. Anatomie der Hymenomyceten. Teufen: F. Flück-Wirth, Teufen.
   Google Scholar
• Corner EJH. 1950. A monograph of Clavaria and allied genera. London: Oxford University Press.
   Google Scholar
• ———. 1966. A monograph of cantharelloid fungi. London: Oxford University Press.
   Google Scholar
• Cunningham CW. 1997. Can three incongruence tests predict when data should be combined? Mol Biol Evol 14:733–740.
   Google Scholar
• ———, Zhu H, Hillis DM. 1998. Best-fit maximum-likelihood models for phylogenetic inference: empirical tests with known phylogenies. Evolution 52:978–987.
   Google Scholar
• Dahlman M, Danell E, Spatafora JW. 2000. Molecular systematics of Craterellus: cladistic analysis of nuclear LSU rDNA sequence data. Mycol Res 104:388–394.
   Google Scholar
• Darlu P, Lecointre G. 2002. When does the incongruence length difference test fail? Mol Biol Evol 19:432–437.
   Google Scholar
• Diederich P, Schultheis B, Blackwell M. 2003. Marchandiobasidium aurantiacum gen.sp.nov., the teleomorph of Marchandiomyces aurantiacus (Basidiomycota, Ceratobasidiales). Mycol Res 107:523–527.
   Google Scholar
• Donk MA. 1956. Notes on resupinate Hymenomycetes. II. The tulasnelloid fungi. Reinwardtia 3:363–379.
   Google Scholar
• ———. 1964. A conspectus of the families of Aphyllophorales. Persoonia 3:199–324.
   Google Scholar
• ———. 1972. The heterobasidiomycetes: a reconnaissance. II. Some problems connected with the restricted emendation. Proc K Ned Akad Wet Ser C, Biol Med Sci 75:376–390.
   Google Scholar
• Dunham SM, O’Dell TE, Molina R. 2003. Analysis of nrDNA sequences and microsatellite allele frequencies reveals a cryptic chanterelle species Cantharellus cascadensis sp. nov. from the American Pacific Northwest. Mycol Res 107:1163–1177.
   Google Scholar
• Eriksson J, Ryvarden L. 1973. The Corticiaceae of northern Europe. Vol 2: Aleurodiscus-Confertobasidium. Oslo, Norway: Fungiflora.
   Google Scholar
• ———, Hjortstam K, Ryvarden L. 1984. The Corticiaceae of northern Europe. Vol. 7. Schizophora-Suillosporium. Oslo, Norway: Fungiflora.
   Google Scholar
• Farris JS, Källersjö M, Kluge AG, Bult C. 1994. Testing significance of incongruence. Cladistics 10:315–319.
   Google Scholar
• Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410.
   Google Scholar
• Fries EM. 1821. Systema Mycologicum, sistens fungorum ordines, genera et species huc usque cognitas. Vol. I. Berlin: Lund.
   Google Scholar
• Gatesy J, Baker RH, Hayashi C. 2004. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst Biol 53:342–355.
   Google Scholar
• Gonzalez D, Carling DE, Kuninaga S, Vilgalys R, Cubeta MA. 2001. Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs. Mycologia 93:1138–1150.
   Google Scholar
• Hallenberg N. 1984. A taxonomic analysis of the Sistotrema brinkmannii complex (Corticiaceae, Basidiomycetes). Mycotaxon 21:389–411.
   Google Scholar
• Henkel TW, Meszaros R, Aime MC, Kennedy A. 2005. New Clavulina species from the Pakaraima Mountains of Guyana. Mycol Prog 4:343–350.
   Google Scholar
• 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.
   Google Scholar
• ———, Gilbert LB, Donoghue MJ. 2000. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407:506–508.
   Google Scholar
• ———, Donoghue MJ. 2001. Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in homobasidiomycetes. Syst Biol 50:215–242.
   Google Scholar
• ———, 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.
   Google Scholar
• ———, Binder M. 2002. Evolution of complex fruiting-body morphologies in homobasidiomycetes. Proc R Soc Lond B Biol Sci 269:1963–1969.
   Google Scholar
• ———. 2003. Hymenomycetes, jelly fungi, yeasts, and mushrooms. http://tolweb.org/Hymenomycetes/20531/2003.09.22 in The Tree of Life Web Project, http://tolweb.org
   Google Scholar
• ———, Nilsson RH, Snyder M, Fonseca M, Costanzo J, Shonfeld M. 2005. Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom-forming fungi). Syst Biol 54:660–668.
   Google Scholar
• Hjortstam K, Larsson KH, Ryvarden L. 1988. The Corticia-ceae of northern Europe. Vol. 8. Phlebiella-Thanatephorus-Ypsilonidium. Oslo, Norway: Fungiflora.
   Google Scholar
• 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.
   Google Scholar
• Huelsenbeck JP. 1997. Is the Felsenstein zone a flytrap? Syst Biol 46:69–74.
   Google Scholar
• Jülich W. 1975. Studies in resupinate basidiomycetes. III. Persoonia 8:291–305.
   Google Scholar
• ———. 1981. Higher taxa of Basidiomycetes. Cramer, Lehre.
   Google Scholar
• Kottke I, Beiter A, Weiß M, Haug I, Oberwinkler F, Nebel M. 2003. Heterobasidiomycetes form symbiotic associations with hepatics: Jungermanniales have sebacinoid mycobionts while Aneura pinguis (Metzgeriales) is associated with a Tulasnella species. Mycol Res 107: 957–968.
   Google Scholar
• Kristiansen KA, Taylor DL, Kjøller R, Rasmussen HN, Rosendahl S. 2001. Identification of mycorrhizal fungi from single pelotons of Dactylorhiza majalis (Orchidaceae) using single-strand conformation polymorphism and mitochondrial ribosomal large subunit DNA sequences. Mol Ecol 10:2089–2093.
   Google Scholar
• Langer G. 1994. Die Gattung Botryobasidium Donk (Corticiaceae, Basidiomycetes). Bibl Mycol 158:1–459.
   Google Scholar
• Larsson E, Larsson KH. 2003. Phylogenetic relationships of russuloid basidiomycetes with emphasis on aphyllo-phoralean taxa. Mycologia 95:1037–1065.
   Google Scholar
• Larsson KH, Larsson E, Köljalg U. 2004. High phylogenetic diversity among corticioid homobasidiomycetes. Mycol Res 108:983–1002.
   Google Scholar
• Lemke PA. 1969. A reevaluation of homothallism, hetero-thallism and the species concept in Sistotrema brinkmanni. Mycologia 60:57–76.
   Google Scholar
• Lutzoni FM. 1997. Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets. Syst Biol 46:373–406.
   Google Scholar
• Lutzoni F, Kauff F, Cox JC, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Shcoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung GH, Lücking R, Lumbsch T, O’Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim YW, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R. 2004. Assembling the Fungal Tree of Life: progress, classification and evolution of subcellular traits. Am J Bot 91:1446–1480.
   Google Scholar
• Martin GW. 1948. New or noteworthy tropical fungi. IV. Lloydia 11:111–122.
   Google Scholar
• Miadlikowska J, Lutzoni F. 2004. Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits. Am J Bot 91:449–464.
   Google Scholar
• Parmasto E. 1968. Conspectus systematis Corticearum. Tartu. 261 p.
   Google Scholar
• ———, Nilsson RH, Larsson KH. 2004. Cortbase version 2. Extensive updates of a nomenclatural database for corticioid fungi (Hymenomycetes). Phyloinformatics 1:5.
   Google Scholar
• Persoon CH. 1825. Mycologia Europaea. Erlanga.
   Google Scholar
• Petersen RH. 1971. Interfamilial relationships in the clavarioid and cantharelloid fungi. In: Petersen RH, ed. Evolution in the higher Basidiomycetes. Knoxville, Tennessee: The University of Tennessee Press. p 345–374.
   Google Scholar
• Petersen R. 1988. The clavarioid fungi of New Zealand. Wellington: DSIR Science Information Publishing Centre. 170 p.
   Google Scholar
• 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.
   Google Scholar
• Poe S, Swofford DL. 1999. Taxon sampling revisited. Nature 398:299–300.
   Google Scholar
• Rasmussen HN. 1995. Terrestrial orchids from seed to mycotrophic plant. Cambridge, UK: Cambridge University Press.
   Google Scholar
• Roberts P. 1999. Rhizoctonia-forming fungi. Kew, UK: Royal Botanic Gardens.
   Google Scholar
• Sanderson MJ, Purvis A, Henze C. 1998. Phylogenetic supertrees: assembling the trees of life. Trend Ecol Evol 13:105–109.
   Google Scholar
• Setaro S, Weiß M, Oberwinkler F, Kottke I. 2006. Sebacinales form ectendomycorrhizas with Cavendishia nobilis, a member of the Andean clade of Ericaceae, in the mountain rain forest of southern Ecuador. New Phytologist 169:355–365.
   Google Scholar
• Shefferson RP, ———, Kull T, Taylor DL. 2005. High specificity generally characterizes mycorrhizal association in rare lady’s slipper orchids, genus Cypripedium. Mol Ecol 14:613–626.
   Google Scholar
• Sikaroodi M, Lawrey JD, Hawksworth DL, DePriest PT. 2001. The phylogenetic position of selected lichenicolous fungi: Hobsonia, Illosporium and Marchandiomyces. Mycol Res 105:453–460.
   Google Scholar
• Taylor DL, Bruns TD, Szaro TM, Hodges SA. 2003. Divergence in mycorrhizal specialization within Hex-alectris spicata (Orchidaceae), a nonphotosynthetic desert orchid. Am J Bot 90:1168–1179.
   Google Scholar
• Thacker JR, Henkel TW. 2004. New species of Clavulina from Guyana. Mycologia 96:650–657.
   Google Scholar
• Ullrich RC, Raper JR. 1975. Primary homothallism-relation to heterothallism in the regulation of sexual morphogenesis in the wood-rotting basidiomycete, Sistotrema brinkmannii. Genetics 80:311–321.
   Google Scholar
• Weiß M, Oberwinkler F. 2001. Phylogenetic relationships in Auriculariales and related groups—hypotheses derived from nuclear ribosomal DNA sequences. Mycol Res 105:403–415.
   Google Scholar
• ———, Bauer R, Begerow D. 2004a. Spotlights on hetero-basidiomycetes. In: Agerer R, Piepenbring M, Blanz P, eds. Frontiers in Basidiomycote Mycology, Eching: IHW-Verlag. p 7–48.
   Google Scholar
• ———, Selosse MA, Rexer KH, Urban A, Oberwinkler F. 2004b. Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential. Mycol Res 108:1003–1010.
   Google Scholar
• Wells K, Oberwinkler F. 1982. Tremelloscypha gelatinosa, a species of a new family Sebacinaceae. Mycologia 74: 325–331.
   Google Scholar
• Wiens JJ. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst Biol 47:625–640.
   Google Scholar
• ———. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol 52:528–538.
   Google Scholar