New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

LITERATURE CITED

• Andersen HL, Ekman S. 2004. Phylogeny of Micareaceae inferred from nrSSU DNA sequences. Lichenologist 36: 27–35.
   Google Scholar
• ———,———. 2005. Disintegration of the Micareaceae (lichenized Ascomycota): a molecular phylogeny based on mitochondrial rDNA sequences. Mycol Res 109:21–30.
   Google Scholar
• Beck A, Friedl T, Rambold G. 1998. Selectivity of photobiont choice in a defined lichen community: inferences from cultural and molecular studies. New Phytol 139: 709–720.
   Google Scholar
• ———, Kasalicky T, Rambold G. 2002. Myco-photobiontal selection in a Mediterranean cryptogam community with Fulgensia fulgida. New Phytol 153:317–326.
   Google Scholar
• Blanco O, Crespo A, Divakar PK, Esslinger TH, Hawksworth DL, Lumbsch HT. 2004a. Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data. Mycol Res 108:873–884.
   Google Scholar
• ———, ———, Elix JA, Hawksworth DL, Lumbsch HT. 2004b. A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota, Lecanorales). Taxon 53:959–975.
   Google Scholar
• ———, ———, Divakar PK, Elix JA, Lumbsch HT. 2005. Molecular phylogeny of parmotremoid lichens (Ascomycota, Parmeliaceae). Mycologia 97:150–159.
   Google Scholar
• ———, ———, Ree RH, Lumbsch HT. 2006. Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity. Mol Phyl Evol 39:52–69.
   Google Scholar
• Brodo IM, Henssen A. 1995. A new isidiate crustose lichen in northwestern North America. Bibl Lichen 58:27–41.
   Google Scholar
• Buschbom J, Mueller G. 2004. Resolving evolutionary relationships in the lichen-forming genus Porpidia and related allies (Porpidiaceae, Ascomycota). Mol Phyl Evol 32:66–82.
   Google Scholar
• Chadefaud M, Letrouit-Galinou MA, Favre MC. 1968. Sur l’origine phylogénétique et l’évolution des Ascomycètes des lichens. Bull Soc Bot Fr Mém Colloq Lich 1968:79–111.
   Google Scholar
• Clauzade G, Diederich P, Roux C. 1989. Nelikeniĝintaj fungoj likenloĝaj. Ilustrita determinlibro. Bull Soc linn Provence, num spec 1:1–142.
   Google Scholar
• Cordeiro LMC, Reis RA, Cruz LM, Stocker-Wörgötter E, Grube M, Iacomini M. 2005. Molecular studies of photobionts of selected lichens from the coastal vegetation of Brazil. FEMS Microbiol Ecol 54:381–390.
   Google Scholar
• Crespo A, Blanco O, Hawksworth DL. 2001. The potential of mitochrondrial DNA for establishing phylogeny and stabilizing generic concepts in the parmelioid lichens. Taxon 50:807–819.
   Google Scholar
• Culberson CF. 1986. Biogenetic relationships of the lichen substances in the framework of systematics. Bryologist 89:91–98.
   Google Scholar
• Culberson WL, Culberson CF. 1994. Secondary metabolites as a tool in ascomycete systematics: lichenized fungi. In: Hawksworth DL, ed. Ascomycete Systematics: problems and perspective in the nineties. New York: Plenum Press. p 155–163.
   Google Scholar
• Ekman S. 2001. Molecular phylogeny of the Bacidiaceae. Mycol Res 105:783–797.
   Google Scholar
• ———, Tønsberg T. 2002. Most species of Lepraria and Leproloma form a monophyletic group closely related to Stereocaulon. Mycol Res 106:1262–1276.
   Google Scholar
• Elix JA. 1993. Progress in the generic delimitation of Parmelia sensu lato lichens (Ascomycotina: Parmeliaceae) and a synoptic key to the Parmeliaceae. Bryologist 96:359–383.
   Google Scholar
• ———. 1996. Biochemistry and secondary metabolites. In: Nash III TH, ed. Lichen biology. Cambridge, UK: University Press. p 154–180.
   Google Scholar
• Eriksson OE. 1981. The families of bitunicate ascomycetes. Opera Bot 60:1–209.
   Google Scholar
• ———, ed. 2006. Outline of Ascomycota—2006. Myconet 12:1–82.
   Google Scholar
• Gaya E. 2006. Revisió morfològica I molecular dels tàxons lobulats del gènere Caloplaca (Teloschistaceae, Líquens), amb especial èmfasi en el grup de C. saxicola [Doctoral dissertation]. Barcelona, Spain: Universitat de Barcelona. 423 p.
   Google Scholar
• ———, Lutzoni F, Zoller S, Navarro-Rosinés P. 2003. Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming Ascomycota). Am J Bot 90:1095–1103.
   Google Scholar
• Geiser DM, Gueidan C, Miadlikowska J, Lutzoni F, Kauff F, Hofstetter V, Fraker E, Schoch CL, Tibell L, Untereiner WA, Aptroot A. 2006. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. Mycologia 98(6):1055–1066.
   Google Scholar
• Grube M, Baloch E, Lumbsch T. 2004. The phylogeny of Porinaceae (Ostropomycetidae) suggests a neotenic origin of perithecia in Lecanoromycetes. Mycol Res 108:1111–1118.
   Google Scholar
• Hafellner J. 1978. Catolechia Flotow ex Massalongo emend. Körber und Epilichen Clements ex Hafellner—zwei nahe verwandte Flechtengattungen. Nov Hedwig 30: 673–695.
   Google Scholar
• ———. 1984. Studien in Richtung einer natürlicheren Gliederung der Sammelfamilien Lecanoraceae und Lecideaceae. Nov Hedwig Beih 79:241–371.
   Google Scholar
• ———. 1988. Principles of classification and main taxonomic groups. In: Galun M, ed. CRC Handbook of Lichenology. Vol. III. Boca Raton, Florida: CRC Press. p 41–52.
   Google Scholar
• ———. 1993. Acarospora and Pleopsidium—zwei lichenisierte Ascomycetengattungen (Lecanorales) mit zahlreichen Konvergenzen. Nov Hedwig 56:281–305.
   Google Scholar
• ———. 1995. Toward a better circumscription of the Acarosporaceae (lichenized Ascomycotina, Lecanorales). Crypt Bot 5:99–104.
   Google Scholar
• ———, Poelt J. 1976. Rhizocarpon schedomyces spec. nov., eine fast delichenisierte parasitische Flechte, und seine Verwandten. Herzogia 4:5–14.
   Google Scholar
• ———, Hertel H, Rambold G, Timdal E. 1993. A new outline of the Lecanorales. Published by the authors. 14 p.
   Google Scholar
• Hakulinen R. 1954. Die Flechtengattung Candelariella Mü ller Argoviensis. Ann Bot Soc Zool-Bot Fenn ‘Vanamo’ 27:1–127.
   Google Scholar
• Helms G, Friedl T, Rambold G. 2003. Phylogenetic relationships of the Physciaceae inferred from rDNA sequence data and selected phenotypic characters. Mycologia 95: 1078–1099.
   Google Scholar
• Henssen A, Jahns HM. 1974. Lichenes. Eine Einführung in die Flechtenkunde. Stuttgart, Germany: G. Thieme Verlag.
   Google Scholar
• ———, Lü cking R. 2002. Morphology, anatomy and ontogeny in the Asterothyriaceae (Ascomycota: Ostropales), a misunderstood group of lichenized fungi. Ann Bot Fenn 39:273–299.
   Google Scholar
• Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F. 2007. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Mol Phyl Evol (In press).
   Google Scholar
• Honegger R. 1980. The ascus apex in lichenized fungi. II. The Rhizocarpon-type. Lichenologist 12:157–172.
   Google Scholar
• Kasalicky T, Döring H, Rambold G, Wedin M. 2000. A comparison of ITS and LSU nrDNA phylogenies of Fulgensia (Teloschistaceae, Lecanorales), a genus of lichenised ascomycetes. Can J Bot 78:1580–1589.
   Google Scholar
• Kauff F, Lutzoni F. 2002. Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol Phyl Evol 25:138–156.
   Google Scholar
• Kirk PM, Cannon PF, David JC, Stalpers JA, eds. 2001. Ainsworth & Bisby’s Dictionary of the Fungi. 9th ed. Wallingford, UK: CAB International: Cambridge: University Press.
   Google Scholar
• Lawrey J. 1986. Biological role of lichen substances. Bryologist 89:111–122.
   Google Scholar
• ———, Diederich P. 2003. Lichenicolous fungi: interactions, evolution, and biodiversity. Bryologist 106:80–120.
   Google Scholar
• Liu YJ, Hall BD. 2004. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc Natl Acad Sci USA 101:4507–4512.
   Google Scholar
• Lücking R, Sérusiaux E, Ve zda A. 2005. Phylogeny and systematics of the lichen family Gomphillaceae (Ostropales) inferred from cladistic analysis of phenotype data. Lichenologist 37:123–170.
   Google Scholar
• ———, Stuart B, Lumbsch HT. 2004. Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences. Mycologia 96:283–294.
   Google Scholar
• Lumbsch HT. 2002. How objective are genera in filamentous ascomycetes? Persp Plant Ecol Evol Syst 5:91–101.
   Google Scholar
• ———, Schmitt I, Döring H, Wedin M. 2001. Molecular systematics supports the recognition of an additional order of Ascomycota: the Agyriales. Mycol Res 105:16–23.
   Google Scholar
• ———, ———, Palice Z, Wiklund E, Ekman S, Wedin M. 2004a. Supraordinal phylogenetic relationships of Lecanoromycetes based on Bayesian analysis of combined nuclear and mitochondrial sequences. Mol Phyl Evol 31:822–832.
   Google Scholar
• ———, Mangold A, Lücking R, García MA, Martín MP. 2004b. Phylogenetic position of the genera Nadvornikia and Pyrgillus (Ascomycota) based on molecular data. Symb Bot Upps 34:9–17.
   Google Scholar
• Luttrell ES. 1955. The ascostromatic Ascomycetes. Mycologia 47:511–532.
   Google Scholar
• Lutzoni F, Brodo IM. 1995. A generic redelimitation of the Ionaspis-Hymenelia complex (lichenized Ascomycotina). Syst Bot 20:224–258.
   Google Scholar
• ———, Pagel M, Reeb V. 2001. Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411: 937–940.
   Google Scholar
• ———, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung G-H, Lücking R, Lumbsch T, O’Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim Y-W, Matheny 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
• Marbach B. 2000. Corticole und lignicole Arten der Flechtengattung Buellia sensu lato in den Subtropen und Tropen. Bibl Lichen 74:1–384.
   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
• Peršoh D, Beck A, Rambold G. 2004. The distribution of ascus types and photobiontal selection in Lecanoromycetes (Ascomycota) against the background of a revised SSU nrDNA phylogeny. Mycol Progress 3:103–121.
   Google Scholar
• Poelt J. 1974. Classification. In: Ahmadjian V, Hale ME, eds. The lichens. New York: Academic Press. p 599–632.
   Google Scholar
• Pöykkö H, Hyvärinen M, Backorb M. 2005. Removal of lichen secondary metabolites affects food choice and survival of lichenivorous moth larvae. Ecology 86:2623–2632.
   Google Scholar
• Rambold G, Triebel D. 1992. The inter-lecanoralean associations. Bibl Lichen 48:1–201.
   Google Scholar
• ———, Friedl T, Beck A. 1998. Photobionts in lichens: possible indicators of phylogenetic relationships? Bryologist 101:392–397.
   Google Scholar
• Reeb V, Lutzoni F, Roux C. 2004. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol Phyl Evol 32:1036–1060.
   Google Scholar
• Reynolds DR, ed. 1981. Ascomycete systematics. The Luttrellian Concept. New York, Heidelberg, Berlin: Springer Verlag. 242 p.
   Google Scholar
• ———. 1989. The bitunicate ascus paradigm. Bot Rev 55:1–52.
   Google Scholar
• Rikkinen J. 1995. What’s behind the pretty colours? A study on the photobiology of lichens. Bryobrothera 4:1–239.
   Google Scholar
• Rundel PW. 1978. The ecological role of secondary lichen substances. Biochem Syst Ecol 6:157–170.
   Google Scholar
• Santesson R, Moberg R, Nordin A, Tønsberg T, Vitikainen O. 2004. Lichen-forming and lichenicolous fungi of Fennoscandia. Museum of Evolution, Uppsala University, Uppsala, Sweden: Majornas CopyPrint AB, Göteborg.
   Google Scholar
• Scheidegger C, Mayrhofer H, Moberg R, Tehler A. 2001. Evolutionary trends in Physciaceae. Lichenologist 33: 25–45.
   Google Scholar
• Schmitt I, Lumbsch HT. 2004. Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes. Mol Phyl Evol 33:43–55.
   Google Scholar
• ———, Mueller G, Lumbsch HT. 2005. Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens. Mycologia 97:362–374.
   Google Scholar
• Sherwood MA. 1977. The Ostropalean fungi. Mycotaxon 5: 1–277.
   Google Scholar
• Solhaug KA, Gauslaa Y. 1996. Parietin, a photoprotective secondary product of the lichen Xanthoria parietina. Oecologia 108:412–418.
   Google Scholar
• Søchting U, Lutzoni F. 2003. Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae). Mycol Res 107:1266–1276.
   Google Scholar
• Staiger B, Kalb K. 1995. Haematomma-Studien. I. Die Flechtengattung Haematomma. Bibl Lichen 59:1–198.
   Google Scholar
• Stenroos S, DePriest P. 1998. SSU rDNA phylogeny of cladoniiform lichens. Am J Bot 85:1548–1559.
   Google Scholar
• Thell A, Feuerer T, Kärnefelt I, Myllys L, Stenroos S. 2004. Monophyletic groups within the Parmeliaceae identified by ITS rDNA, β-tubulin and GAPDH sequences. Mycol Prog 3:297–314.
   Google Scholar
• Tibell L. 1984. A reappraisal of the taxonomy of Caliciales. Nov Hedwig Beih 79:597–713.
   Google Scholar
• Timdal E. 1991. A monograph of the genus Toninia (Lecideaceae, Ascomycetes). Opera Bot 110:1–137.
   Google Scholar
• Tschermak-Woess E. 1988. The algal partner. In: Galun M, ed. CRC Handbook of Lichenology. Vol. I. Boca Raton, Florida: CRC Press. p 39–92.
   Google Scholar
• Wedin M, Baloch E, Grube M. 2002. Parsimony analyses of mtSSU and nITS rDNA sequences reveal the natural relationships of the lichen families Physciaceae and Caliciaceae. Taxon 51:655–660.
   Google Scholar
• ———, Wiklund E, Crewe A, Döring H, Ekman S, Nyberg Å, Schmitt I, Lumbsch HT. 2005. Phylogenetic relationships of Lecanoromycetes (Ascomycota) as revealed by analyses of mtSSU and nLSU rDNA sequence data. Mycol Res 109:159–172.
   Google Scholar
• Wiens JJ. 2006. Missing data and the design of phylogenetic analyses. J Biomed Informat 39:34–42.
   Google Scholar