Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis

LITERATURE CITED

• Breslow NE, Clayton DG. 1993. Approximate inference in generalized linear mixed models. J Am Stat Assoc 88:9–25.
   Google Scholar
• Breuss O. 1983. Eine neue Placidiopsis-Art (Lichenes, Verrucariaceae) aus Norwegen und den Alpen. Plant Syst Evol 142:247–250.
   Google Scholar
• ———. 1985. On the lichen genera Placocarpus and Placidiopsis (Verrucariaceae). Plant Syst Evol 148:313–315.
   Google Scholar
• ———. 1990. Die Flechtengattung Catapyrenium (Verrucariaceae) in Europa. Stapfia 23:1–153.
   Google Scholar
• ———. 1994. Die flechtengattungen Catapyrenium und Placidiopsis (Verrucariaceae) in Nordafrika. Nova Hedwig 58:229–237.
   Google Scholar
• ———. 1996a. Ein verfeinertes Gliederungskonzept für Catapyrenium (lichenisierte Ascomyceten, Verrucariaceae) mit einem Schlüssel für die bisher bekannten Arten. Ann Naturhist Mus Wien 98:35–50.
   Google Scholar
• ———. 1996b. Revision der Flechtengattung Placidiopsis (Verrucariaceae). Öst Z Pilz 5:65–94.
   Google Scholar
• ———. 2000. A peculiar new Catapyrenium species (lichenized Ascomycetes, Verrucariaceae) from Mexico. Linzer Biol Beitr 32:1053–1055.
   Google Scholar
• ———. 2001. Catapyrenium. In: McCarthy PM, ed. Flora of Australia. Vol. 58A, Lichens 3. Melbourne, Australia: ABRS/CSIRO. p 160–161.
   Google Scholar
• ———. 2002a. Catapyrenium. In: Nash TH III, Ryan BD, Gries C, Bungartz F, eds. Lichen flora of the greater Sonoran Desert region I. Tempe: Lichens Unlimited, Arizona State University. p 125–128.
   Google Scholar
• ———. 2002b. Placidiopsis. In: Nash TH III, Ryan BD, Gries C, Bungartz F, eds. Lichen flora of the greater Sonoran Desert region I. Tempe: Lichens Unlimited, Arizona State University. p 383–384.
   Google Scholar
• ———. 2002c. Placopyrenium. In: Nash TH III, Ryan BD, Gries C, Bungartz F, eds. Lichen flora of the greater Sonoran Desert region I. Tempe: Lichens Unlimited, Arizona State University. p 393–397.
   Google Scholar
• ———. 2009. A synopsis of the lichen genus Placopyrenium (Verrucariaceae), with descriptions of new taxa and key to all species. Bibl Lichenol 99:93–112.
   Google Scholar
• ———, Hansen ES. 1988. The lichen genera Catapyrenium and Placidiopsis in Greenland. Plant Syst Evol 159:95–105.
   Google Scholar
• Cannone JJ, Subramanian S, Schnare MN, Collett JR, D’Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR. 2002. The comparative RNA Website (CRW): an online database of comparative sequence and structure information for ribosomal, intron, and other RNA. BMC Bioinformatics 3:2–15.
   Google Scholar
• Crespo A, Blanco O, Hawksworth DL. 2001. The potential of mitochondrial DNA for establishing generic concepts in the parmeliod lichen. Taxon 50:807–819.
   Google Scholar
• Felsenstein J. 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol J Linn Soc 16:183–196.
   Google Scholar
• ———. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.
   Google Scholar
• Gueidan C, Roux C, Lutzoni F. 2007. Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota). Mycol Res 111:1145–1168.
   Google Scholar
• ———, Savić S, Thüs H, Roux C, Keller C, Tibell L, Prieto M, Heiđmarsson S, Breuss O, Orange A, Fröberg L, Amtoft Wynns A, Navarro-Rosinés P, Krzewicka B, Pykälä J, Grube M, Lutzoni F. 2009. Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: recent progress and remaining challenges. Taxon 58:184–208.
   Google Scholar
• Harada H. 1993. A taxonomic study on Dermatocarpon and its allied genera (Lichenes, Verrucariaceae) in Japan. Nat Hist Res 2:113–152.
   Google Scholar
• Harris RC. 1979. The genus Placidiopsis Beltr. (Lichenized Ascomycetes) new to North America as Placidiopsis minor sp. nov. Michigan Bot 18:57–58.
   Google Scholar
• Hasse HE. 1913. Additions to the lichen flora of southern California VIII. Bryologist 16:1–2.
   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 Phylogenet Evol 44:412–426.
   Google Scholar
• Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755.
   Google Scholar
• Ihlen PG, Ekman S. 2002. Outline of phylogeny and character evolution in Rhizocarpon (Rhizocarpaceae, lichenized Ascomycota) based on nuclear ITS and mitochondrial SSU ribosomal DNA sequences. Biol J Linn Soc 77:535–546.
   Google Scholar
• James TY, Kauff F, Schoch C, Matheny B, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsh T, Rauhut A, Reeb V, Arnold A, Amtoft A, Stajich JE, Hosaka K, Sung G, Johnson D, O’Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schueller A, Longcore JE, O’Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lücking R, Budel B, Geiser DM, Aptroot DM, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, Mclaughlin DJ, Spatafora JW, Vilgalys R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822.
   Google Scholar
• Janex-Favre MC, Wagner J. 1986. Recherches ontogéniques et structurales sur les pycnides des Dermatocarpacées (Pyrenolichens). Bull Soc Mycol Fr 102:161–182.
   Google Scholar
• Kauff F, Miadlikowska J, Lutzoni F. 2003. Arc: a program for ambiguous region coding. v 1.5. Durham, North Carolina: Duke University. http://www.lutzonilab.net/downloads
   Google Scholar
• Kjer KM. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from frogs. Mol Phylogenet Evol 4:314–330.
   Google Scholar
• Lawrey JD, Binder M, Diederich P, Molina MC, Sikaroodi M, Ertz D. 2007. Phylogenetic diversity of lichen-associated homobasidiomycetes. Mol Phylogenet Evol 44:778–789.
   Google Scholar
• Littell RC, Milliken GA, Stroup WW, Wolfinger RD. 1996. SAS system for linear models. Cary, North Carolina: SAS Institute Inc.
   Google Scholar
• Lutzoni F, Wagner P, Reeb V, Zoller S. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst Biol 49:628–651.
   Google Scholar
• Maddison WP, Maddison DR. 2003. MacClade: analysis of phylogeny and character evolution. version 4.6. Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• Mason-Gamer RJ, Kellogg EA. 1996. Testing for phylogenetic conflict among molecular datasets in the tribe Triticeae (Gramineae). Syst Biol 49:524–545.
   Google Scholar
• McCullagh P, Nelder JA. 1989. Generalized linear models. London: Chapman & Hall.
   Google Scholar
• Ménard T, Roux C. 1995. Placopyrenium bucekii et remarques sur les Verrucariaceae (Verrucariales, Lichenes). Mycotaxon 53:129–159.
   Google Scholar
• Miadlikowska J, Lutzoni F, Goward T, Zoller S, Posada D. 2003. New approach to an old problem: incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex. Mycologia 95:1181–1203.
   Google Scholar
• Miller AN, Huhndorf SM. 2004. A natural classification of Lasiosphaeria based on nuclear LSU rDNA sequences. Mycol Res 108:26–34.
   Google Scholar
• Naesborg RR, Ekman S, Tibell L. 2007. Molecular phylogeny of the genus Lecania (Ramalinaceae, lichenized Ascomycota). Mycol Res 111:581–91.
   Google Scholar
• Navarro-Rosinés P, Roux C, Gueidan C. 2007. La Genroj Verrucula kaj Verruculopsis (Verrucariaceae, Verrucariales). Bull Soc Linn Provence 58:133–180.
   Google Scholar
• Nimis PL, Martellos S. 2004. Keys to the lichens of Italy I. Terricolous species. Trieste: Edizioni Goliardiche. 341 p.
   Google Scholar
• Nylander JA. 2004. MrModeltest version 2. Program distributed by the author. Uppsala University Evolutionary Biology Centre.
   Google Scholar
• Nylander W. 1853a. Collectanea lichenologica in Gallia meridionali et Pyrenaeis. Bot Not 10–11:151–165.
   Google Scholar
• ———. 1853b. Lichenes Algerienses novi. Annal Sci Nat Bot 20(3):315–320.
   Google Scholar
• Orange A. 2004. The Verrucaria fuscella group in Great Britain and Ireland. Lichenologist 36:173–182.
   Google Scholar
• Otálora MAG, Aragón G, Molina MC, Martínez I, Lutzoni F. 2010. Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota). Mycologia 102:279–290.
   Google Scholar
• Prieto M, Aragón G, Martínez I, Breuss O. 2008. A new species of Anthracocarpon (Verrucariaceae) from Argentina. Bryologist 111:128–132.
   Google Scholar
• Reeb V, Lutzoni F, Roux C. 2004. Contribution of RPB2 to multilocus phylogenetic studies of the Pezizomycotina (Euascomycetes, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of poly-spory. Mol Phylogenet Evol 32:1036–1060.
   Google Scholar
• Rehner SA, Samuels GJ. 1994. Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequenes. Mycol Res 98:625–634.
   Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574.
   Google Scholar
• Roux C. 2005. Likenoj de Okcidenta Eŭropo. Suplemento 4a: eltiräĵoj (extraits). Bull Inform Assoc Fr Lichénol 30:5–14.
   Google Scholar
• Savić S, Tibell L. 2009. Taxonomy and species delimitation in Sporodictyon (Verrucariaceae, Verrucariales) in northern Europe and the adjacent Arctic—reconciling molecular and morphological data. Taxon 58:585–605.
   Google Scholar
• ———, ———, Gueidan C, Lutzoni F. 2008. Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera. Mycol Res 112:1307–1318.
   Google Scholar
• Staiger B. 2002. Die Flechtenfamilie Graphidaceae. Studien in Richtung einer natürlicheren Gliederung. Bibl Lichenol 85:1–526.
   Google Scholar
• Stamatakis A, Ludwig T, Meier H. 2005. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690.
   Google Scholar
• Swofford D. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sunder-land, Massachusetts: Sinauer Associates.
   Google Scholar
• Thomson JW. 1987. The lichen genera Catapyrenium and Placidiopsis in North America. Bryologist 90:27–39.
   Google Scholar
• Thüs H. 2002. Taxonomie, Verbreitung und Ökologie silicoler Süßwasserflechten im außeralpinen Mitteleuropa. Bibl Lichenol 83:1–214.
   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
• Wheeler WC. 1990. Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure. Cladistics 6: 269–275.
   Google Scholar
• White TJ, Bruns T, Lee S, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. 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.
   Google Scholar
• Zahlbruckner A. 1921–1922. Catalogus Lichenum Universalis Band 1. Leipzig: Gebrüder Borntraeger.
   Google Scholar
• Zehetleitner G. 1978. Über einige parasitische Arten der Flechtengattung Verrucaria. Nova Hedwig 29:683–734.
   Google Scholar
• Zschacke H. 1933–1934. Epigloeaceae, Verrucariaceae und Dermatocarpaceae. In: Zahlbruckner A, ed. Dr L. Rabenhorst’s Kryptogamen-Flora von Deutschland, Österreich und der Schweiz, 2. Aufl., Bd. 9, Abt. 1, Teil 1. Leipzig: Akademische Verlagsanstalt. p 44–695.
   Google Scholar