Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens

LITERATURE CITED

• Aptroot A. 1998. Aspects of the integration of the taxonomy of lichenized and non-lichenized pyrenocarpous ascomycetes. Lichenologist 30:501–514.
   Google Scholar
• ———. 2002. Julella. In: Nash TH III, Ryan BD, Gries C, Bungartz F, eds. Lichen Flora of the Greater Sonoran Desert Region. Vol. I. Tempe, Arizona: Lichens Unlimited, Arizona State University. p 254–256.
   Google Scholar
• ———, van Iperen A. 1998. New ascomycetes and ascomycete records from Papua New Guinea. Nova Hedwigia 67:481–497.
   Google Scholar
• Arx JA von, Müller E. 1975. A re-evaluation of the bitunicate Ascomycetes with keys to families and genera. Stud Mycol 9:1–159.
   Google Scholar
• Barr ME. 1979. A classification of Loculoascomycetes. Mycologia 71:935–957.
   Google Scholar
• ———. 1987. Prodromus to the class Loculoascomycetes. USA: Publ by the author.
   Google Scholar
• Berbee ML. 1996. Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18S rRNA gene sequence data. Mol Biol Evol 13:462–470.
   Google Scholar
• Breuss O. 2002. Thrombium. In: Nash TH III, Ryan BD, Gries C, Bungartz F, eds. Lichen Flora of the Greater Sonoran Desert Region. Vol. I. Tempe, Arizona: Lichens Unlimited, Arizona State University. p 483–484.
   Google Scholar
• Buckley TR, Arensburger P, Simon C, Chambers GK. 2002. Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst Biol 51:4–18.
   Google Scholar
• Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ. 1993. Partitioning and combining data in phylogenetic analysis. Syst Biol 42:384–397.
   Google Scholar
• Clements FE. 1909. The genera of fungi. Minneapolis: HW Wilson Company.
   Google Scholar
• David JC, Hawksworth DL. 1991. Validation of six family names of lichenized ascomycetes. Syst Ascom 10:13–18.
   Google Scholar
• Döring H, Clerc P, Grube M, Wedin M. 2000. Mycobiont-specific PCR primers for the amplification of nuclear ITS and LSU rDNA from lichenized ascomycetes. Lichenologist 32:200–204.
   Google Scholar
• Eriksson O. 1981. The families of bitunicate Ascomycetes. Op Bot 60:1–209.
   Google Scholar
• ———. 1982. Revision of “Outline of the Ascomycetes”. Syst Ascom 1:1–16.
   Google Scholar
• ———, Baral H-O, Currah RS, Hansen K, Kurtzman CP, Rambold G, Laessøe T. 2004. Outline of Ascomycota. Myconet 10:1–99.
   Google Scholar
• Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.
   Google Scholar
• Franck AB. 1877. XI. Klasse. Lichenes. In: Leunis J. Synopsis der Pflanzenkunde. p 1665–1709. Hannover: Hahn’sche.
   Google Scholar
• Fryday AM, Coppins BJ. 2004. A reassessment of the genera Chromatochlamys and Thelenella, and a new species of Strigula from the British Isles. Lichenologist 36:89–95.
   Google Scholar
• Gargas A, Taylor JW. 1995. Phylogeny of Discomycetes and early radiations of the apothecial Ascomycotina inferred from SSU rDNA sequence data. Exp Mycol 19: 7–15.
   Google Scholar
• Grube M, Baloch E, Lumbsch HT. 2004. The phylogeny of Porinaceae (Ostropomycetidae) suggests a neotonic origin of perithecia in Lecanoromycetes. Mycol Res 108: 1111–1118.
   Google Scholar
• Hafellner J. 1984. Studien in Richtung einer natürlicheren Gliederung der Sammelfamilien Lecanoraceae und Lecideaceae. Nova Hedwigia 79:241–37.
   Google Scholar
• Hale ME, Culberson WL. 1966. A third checklist of the lichens of the continental United States and Canada. Bryologist 69:141–182.
   Google Scholar
• ———, ———, 1970. A fourth checklist of the lichens of the continental United States and Canada. Bryologist 73:499–543.
   Google Scholar
• Harris RC. 1973. The corticolous pyrenolichens of the Great Lakes region. Michigan Bot 12:3–68.
   Google Scholar
• ———. 1975. A taxonomic revision of the genus Arthopyrenia Massal. s.lat. (Ascomycetes) in North America. [Dissertation.] Michigan State University.
   Google Scholar
• ———. 1989. A sketch of the family Pyrenulaceae (Melanommatales) in eastern North America. Memoirs of the New York Botanical Garden 49:74–107.
   Google Scholar
• ———. 1995. More Florida Lichens. Including the 10¢ Tour of the Pyrenolichens. Bronx, New York: Publ by the Author.
   Google Scholar
• Henssen A, Jahns HM. 1973. Lichenes. Stuttgart: Georg Thieme Verlag.
   Google Scholar
• Höhnel F von. 1907. Fragmente zur Mykologie III. Mitt., Nr. 92–155. Sitzungsber Kaiserl Akad Wiss Wien, Math-Naturw Kl, Abt. 1 , 116:615–647.
   Google Scholar
• Holmgren PK, Holmgren NH, Barnett LC. 1990. “Index Herbariorum I.” 8th Ed. New York: The New York Botanical Garden.
   Google Scholar
• Huelsenbeck JP, Rannala B, Masly JP. 2000. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288:2349–2350.
   Google Scholar
• ———, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755.
   Google Scholar
• Karplus K, Barrett C, Hughey R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14:846–856.
   Google Scholar
• Kauff F, Lutzoni F. 2002. Phylogeny of 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
• Koerber GW. 1855. Systema Lichenum Germaniae (I–XXXIV). Die Flechten Deutschlands mikroscopisch geprüft, kritisch gesichtet, charakteristisch beschrieben und systematisch geordnet. Breslau: Trewendt & Granier.
   Google Scholar
• Kopačevskaja EG, Makarevič MF, Oxner AN. 1977. Handbook of the lichens of the U.S.S.R. 4. Verrucariaceae—Pilocarpaceae. Leningrad: Nauka.
   Google Scholar
• Larget B, Simon DL. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750–759.
   Google Scholar
• Lindemuth R, Wirtz N, Lumbsch HT. 2001. Phylogenetic analysis of nuclear and mitochondrial rDNA sequences supports the view that loculoascomycetes (Ascomycota) are not monophyletic. Mycol Res 105:1176–1181.
   Google Scholar
• Lockhart PJ, Steel M, Hendy MD, Penny D. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11:605–612.
   Google Scholar
• Lönnroth KJ. 1858. Descriptiones generum specierumque lichenum, quas nova invenit vel limitibus novis determinavit. Flora 41:627–653.
   Google Scholar
• Lücking R. 1997. Additions and Corrections to the Knowledge of the Foliicolous Lichen Flora of Costa Rica. The Family Gomphillaceae. Bibl Lich 65:1–109.
   Google Scholar
• ———, Stuart BL, 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, Schmitt I, Palice Z, Wiklund E, Ekman S, Wedin M. 2004. Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences. Mol Phylogenet Evol 31:822–832.
   Google Scholar
• Luttrell ES. 1951. Taxonomy of pyrenomycetes. Univ Missouri Stud 24:1–120.
   Google Scholar
• ———. 1955. The ascostromatic Ascomycetes. Mycologia 47:511–532.
   Google Scholar
• Lutzoni F, Pagel M, Reeb V. 2001. Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411: 937–940.
   Google Scholar
• Mayrhofer H. 1987a. Monographie der Flechtengattung Thelenella. Bibl Lich 26:1–106.
   Google Scholar
• ———. 1987b. Ergänzende Studien zur Taxonomie der Gattung Protothelenella. Herzogia 7:313–342.
   Google Scholar
• ———. 2002a. Protothelenella. In: Nash TH III, Ryan BD, Gries C, Bungartz F, eds. Lichen Flora of the Greater Sonoran Desert Region. Vol. I. Tempe, Arizona: Lichens Unlimited, Arizona State University. p 408–409.
   Google Scholar
• ———. 2002b. Thelenella. In: Nash TH III, Ryan BD, Gries C, Bungartz F, eds. Lichen Flora of the Greater Sonoran Desert Region. Vol. I. Tempe, Arizona: Lichens Unlimited, Arizona State University. p 479–481.
   Google Scholar
• ———, Poelt J. 1985. Die Flechtengattung Microglaena sensu Zahlbruckner in Europa. Herzogia 7:13–79.
   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
• Morgan-Jones G, Swinscow TDV. 1965. On the genus Microglaena Körb. Lichenologist 3:42–54.
   Google Scholar
• Nannfeldt JA. 1932. Studien über die Morphologie und Systematik der nicht-lichenisierten inoperculaten Discomyceten. Nov Act Reg Soc Sci Upsal 8:1–368.
   Google Scholar
• Nylander W. 1855. Essai d’une nouvelle classification des lichens (second mémoire). Mém Soc Sci Nat Cherbourg 3:161–202.
   Google Scholar
• Pabst G. 1876. Cryptogamen-Flora. Die Flechten und Pilze. Gera: Griesbach.
   Google Scholar
• Page RDM. 1996. Treeview: an application to display phylogenetic trees on personal computers. Comp Appl Biosci 12:357–358.
   Google Scholar
• Poelt J. 1973. Classification. In: Ahmadjan V, Hale ME, eds. The Lichens. New York: Academic Press.
   Google Scholar
• ———, Vězda A. 1981. Bestimmungsschlüssel europäischer Flechten. Ergänzungsheft II. Bibl Lich 16:1–390.
   Google Scholar
• Rabenhorst L. 1870. Kryptogamen-Flora von Sachsen, der Oberlausitz, Thüringen und Nordböhmen mit Berücksichtigung der benachbarten Länder. 2. Abt. Die Flechten. Leipzig: Kummer.
   Google Scholar
• Rannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43:304–311.
   Google Scholar
• Reynolds DR. 1971. Wall structure of a bitunicate ascus. Planta 98:244–257.
   Google Scholar
• ———. 1981. Ascomycete Systematics. The Luttrellian Concept. New York, Heidelberg, Berlin: Springer Verlag.
   Google Scholar
• ———. 1989. The bitunicate ascus paradigm. Bot Review 55:1–52.
   Google Scholar
• Rodriguez F, Oliver JF, Martín A, Medina JR. 1990. The general stochastic model of nucleotide substitution. J Theor Biol 142:485–501.
   Google Scholar
• Swinscow TDV. 1964. Pyrenocarpous lichens: 6. Lichenologist 2:276–283.
   Google Scholar
• Swofford DL. 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• Vězda A. 1968. Taxonomische Revision der Gattung Thelopsis Nyl. (Lichenisierte Fungi). Folia Geobot Phytotax 3:363–406.
   Google Scholar
• Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246.
   Google Scholar
• Watson W. 1929. The classification of lichens. New Phytologist 28:1–16.
   Google Scholar
• Wedin M, Tehler A, Gargas A. 1998. Phylogenetic relationships of Sphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences. Pl Syst Evol 209:75–83.
   Google Scholar
• Xia XH, Xie Z, Kjer KM. 2003. 18S ribosomal RNA and tetrapod phylogeny. Syst Biol 52:283–295.
   Google Scholar
• Zahlbruckner A. 1907. Lichenes (Flechten). B. Spezieller Teil. In: Engler A, Prantl K. Die natürlichen Pflanzenfamilien. 1. Teil pp 49–249. Leipzig: W. Engelmann.
   Google Scholar
• ———. 1926. Lichenes (Flechten). B. Spezieller Teil. In: Engler A, Prantl K. Die natürlichen Pflanzenfamilien. 2. Auflage Band 8 pp 61–270. Leipzig: W. Engelmann.
   Google Scholar
• Zhou S, Stanosz GR. 2001. Primers for amplification of mtSSU rDNA, and a phylogenetic study of Botryosphaeria and associated anamorphic fungi. Mycol Res 105: 1033–1044.
   Google Scholar
• Zoller S, Scheidegger C, Sperisen C. 1999. PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. Lichenologist 31:511–516.
   Google Scholar
• Zschacke H. 1934. Epigloeaceae, Verrucariaceae und Dermatocarpaceae. In: Rabenhorst’s Kryptogamenflora von Deutschland, Österreich und der Schweiz. Band 9, 1. Abteilung, 1. Teil. Leipzig. pp 44–695.
   Google Scholar