Phylogeny of the Lobariaceae (lichenized Ascomycota: Peltigerales), with a reappraisal of the genus Lobariella

Lichenologist

Volumn 45, Issue 2, 2013, Pages 203-263

  Moncada, Bibiana ^a   Lücking, Robert ^b   Betancourt Macuase, Luisa ^a  

^a UNIVERSIDAD DISTRITAL FRANCISCO JOSÉ DE CALDAS   (Colombia)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Colombia; Costa Rica; Ecuador; faveolate; foveolate; isidia; Key words Brazil; lichen; phyllidia; scrobiculate; taxonomy

Indexed keywords

EID: 84874455756     PISSN: 00242829     EISSN: 10961135     Source Type: Journal    
DOI: 10.1017/S0024282912000825     Document Type: Article

References (88)

1. Acharius, E. (1803) Methodus qua omnes detectos lichens secundum organa carpomorpha ad genera, species et varietates redigere atque observationibus illustrare tentavit Erik Acharius (Methodus Lichenum). Cum tab. aen. Stockholm: Ulrich.
2. Acharius, E. (1810) Lichenographia Universalis. Cum tab. aen. color. Go? ttingen: Danckwerts.
3. Argu? ello, A., Del Prado, R., Cubas, P. & Crespo, A. (2007) Parmelia quercina (Parmeliaceae, Lecanorales) includes four phylogenetically supported morphospecies. Biological Journal of the Linnean Society 91: 455-467. (Pubitemid 47037841)
4. Awasthi, D. D. (2007) A Compendium of the Macrolichens from India, Nepal and Sri Lanka. Dehra-Dun, India: Bishen Singh Mahendra Pal Singh.
5. Cannon, P. F. & Kirk, P. M. (2007) Fungal Families of the World.Wallingford: CAB International.
6. Chen, J.-B. (1993) Chemical notes on three species of Sticta from China. Lichenologist 25: 455-458.
7. Chen, J., Wang, Z. &Wang, L. (1994) The lichen genus Sticta from Yunnan of China. Acta Mycologica Sinica 13: 29-33.
8. Clements, F. E. (1909) The Genera of Fungi. Minneapolis: H. W. Wilson.
9. Cornejo, C. & Scheidegger, C. (2010) Lobaria macaronesica sp. nov., and the phylogeny of Lobaria sect. Lobaria (Lobariaceae) in Macaronesia. Bryologist 113: 590-604.
10. Crespo, A. & Lumbsch, H. T. (2010) Cryptic species in lichen-forming fungi. IMA Fungus 1: 167-170.
11. Crespo, A. & Pérez-Ortega, S. (2009) Cryptic species and species pairs in lichens: a discussion on the relationship between molecular phylogenetics and morphological characters. Anales del Jardín Botánico de Madrid 66S1: 71-81.
12. Crespo, A., Molina, M. C., Blanco, O., Schroeter, B., Sancho, L. G. & Hawksworth, D. L. (2002) rDNA ITS and -tubulin gene sequence analyses reveal two monophyletic groups within the cosmopolitan lichen Parmelia saxatilis. Mycological Research 106: 788-795. (Pubitemid 35197637)
13. Culberson, C. F., Culberson, W. L. & Johnson, A. (1977) Second Supplement to 'Chemical and Botanical Guide to Lichen Products'. Missouri Botanical Garden, St. Louis: American Bryological and Lichenological Society.
14. Delise, D. (1822) Histoire de Lichens. Genre Sticta. Caen: Chalopin.
15. Divakar, P. K., Blanco, O., Hawksworth, D. L. & Crespo, A. (2005) Molecular phylogenetic studies on the Parmotrema reticulatum (syn. Rimelia reticulata) complex, including the confirmation of P. pseudoreticulatum. Lichenologist 37: 55-65. (Pubitemid 40199107)
16. Drummond, A. J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
17. Elix, J. A. & Tønsberg, T. (2006) Notes on the chemistry of Scandinavian Lobaria species. Graphis Scripta 18: 27-28.
18. Galloway, D. J. (1988) Studies in Pseudocyphellaria (lichens) I. The New Zealand species. Bulletin of the British Museum (Natural History), Botany Series 17: 1-267.
19. Galloway, D. J. (1992) Studies in Pseudocyphellaria (lichens) III. The South American species. Bibliotheca Lichenologica 46: 1-275.
20. Galloway, D. J. (1994) Studies in Pseudocyphellaria (lichens) IV. Palaeotropical species (excluding Australia). Bulletin of the Natural History Museum, London 24: 115-159.
21. Galloway, D. J. (1995) The extra-European lichen collections of Archibald Menzies MD, FLS (1754- 1842). Edinburgh Journal of Botany 52: 95-139.
22. Galloway, D. J. (1997) Studies on the lichen genus Sticta (Schreber) Ach. IV. New Zealand species. Lichenologist 29: 105-168. (Pubitemid 27158832)
23. Galloway, D. J. (2007) Flora of New Zealand Lichens. Revised Second Edition Including Lichen-Forming and Lichenicolous Fungi. Volumes 1 and 2. Lincoln, New Zealand: Manaaki Whenua Press.
24. Galloway, D. J. & Arvidsson, L. (1990) Studies in Pseudocyphellaria (lichens) II. Ecuadorean species. Lichenologist 22: 103-135.
25. Galloway, D. J. & Laundon, J. R. (1988) Proposal to conserve Pseudocyphellaria against several names (Ascomycotina, Lobariaceae). Taxon 37: 480-482.
26. Galloway, D. J., James, P. W. & Wilkins, A. L. (1983) Further nomenclatural and chemical notes on Pseudocyphellaria in New Zealand. Lichenologist 15: 135- 145.
27. Gardes, M. & Bruns, T. D. (1993) ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rust. Molecular Ecology 2: 113-118.
28. Goffinet, B. & Goward, T. (1998) Is Nephroma silvaeveteris the cyanomorph of Lobaria oregana? Insights from molecular, chemical and morphological characters. In Lichenographia Thomsoniana: North American Lichenology in Honor of John W. Thomson (M.G. Glenn, R. C. Harris, R. Dirig & M. S. Cole, eds): 41-52. Ithaca, New York: Mycotaxon Ltd.
29. Goward, T., McCune, B. & Meidinger, D. (1994) The Lichens of British Columbia. Illustrated Keys. Part 1 - Foliose and Squamulose Species. Special Report Series, 8, Research Program, B.C. Ministry of Forests. Victoria, Canada: Crown Publications.
30. Gyelnik, V. (1935) De familia Heppiacearum, II. Feddes Repertorium Specierum Novarum Regni Vegetabilis 38: 307-313.
31. Hall, T. A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
32. Harris, R. A. (1979) A glossary of surface sculpturing. California Department of Food and Agriculture, Bureau of Entomology 28: 1-31.
33. Ho?gnabba, F., Stenroos, S. & Thell, A. (2009) Phylogenetic relationship and evolution of photobiont associations in the Lobariaceae (Peltigerales, Lecanoromycetes, Ascomycota). Bibliotheca Lichenologica 100: 157-187.
34. Jørgensen, P. M. & Galloway, D. J. (2011) Proposal to conserve Pseudocyphellaria, nom. cons (Lobariaceae: Ascomycota) with a conserved type. Taxon 60: 1770-1771.
35. Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066. (Pubitemid 34851225)
36. Katoh, K., Asimenos, G. & Toh, H. (2009) Multiple alignment ofDNA sequences withMAFFT. Methods in Molecular Biology 537: 39-64.
37. 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. Molecular Phylogeny and Evolution 25: 138-156. (Pubitemid 35169398)
38. Kirk, P. M., Cannon, P. F., Minter, D. W. & Stalpers, J. A. (2008) Dictionary of the Fungi. 10th edn. Wallingford: CAB International.
39. Kondratyuk, S. Y. & Galloway, D. J. (1995) Lichenicolous fungi and chemical patterns in Pseudocyphellaria. Bibliotheca Lichenologica 57: 327-345.
40. Link, H. F. (1833) Handbuch zur Erkennung der Nutzbarsten und am Ha?ufigsten Vorkommenden Gewa?chse. Berlin: Haude und Spener.
41. Lu? cking, R., Rivas Plata, E., Chaves, J. L., Uman? a, L. & Sipman, H. J. M. (2009). How many tropical lichens are there. . . really? Bibliotheca Lichenologica 100: 399-418.
42. Lu? cking, R., Hodkinson, B. P., Stamatakis, A. & Cartwright, R. A. (2011) PICS-Ord: unlimited coding of ambiguous regions by Pairwise Identity and Cost Scores Ordination. BMC Bioinformatics 12: 10.
43. Lumbsch, H. T. (2002). Analysis of phenolic products in lichens for identification and taxonomy. In Protocols in Lichenology. Culturing, Biochemistry, Ecophysiology and Use in Biomonitoring (I. Kranner, R. P. Beckett & A. K. Varma, eds): 281-295. Berlin: Springer.
44. Lumbsch, H. T., Ahti, T., Altermann, S., Amo De Paz, G., Aptroot, A., Arup, U., Ba'rcenas Pen? a, A., Bawingan, P. A., Benatti, M. N., Betancourt, L. et al. (2011) One hundred new species of lichenized fungi: a signature of undiscovered global diversity. Phytotaxa 18: 1-127.
45. Magnusson, A. H. (1940) Studies in species of Pseudocyphellaria - the crocata group. Acta Horti Gothoburgensis 14: 1-36.
46. Mangold, A., Marti'n, M. A., Lu? cking, R. & Lumbsch, H. T. (2008). Molecular phylogeny suggests synonymy of Thelotremataceae within Graphidaceae (Ascomycota: Ostropales). Taxon 57: 476-486. (Pubitemid 351929780)
47. Mason-Gamer, R. J. & Kellogg, E. A. (1997) Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Systematic Biology 45: 524-545.
48. Miadlikowska, J. & Lutzoni, F. (2000) Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical and large subunit nuclear ribosomal DNA data. International Journal of Plant Science 161: 925-968.
49. Miadlikowska, J. & Lutzoni, F. (2004) Phylogenetic classification of Peltigeralean fungi (Peltigerales, Ascomycota). American Journal of Botany 91: 449- 464.
50. Miadlikowska, J., McCune, B. & Lutzoni, F. (2002) Pseudocyphellaria perpetua, a new lichen from western North America. Bryologist 105: 1-10. (Pubitemid 34271309)
51. Moncada, B. (2012) Diversity, ecogeography, and systematics of the lichen genus Sticta in Colombia. In Abstracts of the 7th IAL Symposium, 9-13 January 2012, Bangkok, Thailand, p. 127.
52. Moncada, B. & Lu? cking, R. (2012) Ten new species of Sticta and counting: Colombia as a hot spot for unrecognized diversification in a conspicuous macrolichen genus. Phytotaxa 74: 1-29.
53. Moncada, B., Betancourt, L. & Lu? cking, R. (2012a) Diversity and phylogeny of the genus Lobariella (Lobariaceae). In Abstracts of the 7th IAL Symposium, 9- 13 January 2012, Bangkok, Thailand, p. 160.
54. Moncada, B., Lu? cking, R., Parmnen, S. & Lumbsch, H. T. (2012b) Sticta fuliginosa (Lobariaceae): species or morphotype? In Abstracts of the 7th IAL Symposium, 9-13 January 2012, Bangkok, Thailand, p. 159.
55. Nylander, W. (1860) Synopsis Methodica Lichenum Omnium Hucusque Cognitorum Praemissa Introductione Lingua Gallica Tractata. Paris: Martinet.
56. Nylander, W. (1875) Addenda nova ad Lichenographiam Europaeam. Continuatio secunda et vicesima.Flora 58: 358-365.
57. Orange, A., James, P. W. & White, F. J. (2001) Microchemical Methods for the Identification of Lichens. London: British Lichen Society.
58. Penn, O., Privman, E., Ashkenazy, H., Landan, G., Graur, D. & Pupko, T. (2010a) GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Research 38: W23-W28.
59. Penn, O., Privman, E., Landan, G., Graur, D. & Pupko, T. (2010b) An alignment confidence score capturing robustness to guide-tree uncertainty. Molecular Biology and Evolution 27: 1759-1767.
60. Remane, R. & Holzinger, W. (1995) Zygina hypermaculata nov. spec., eine neue Zwergzikade aus demOstalpenraum (Homoptera, Auchenorrhyncha: Cicadellidae). Carinthia II 185/105: 713-721.
61. Ryan, B. D. & Galloway, D. J. (2002) Pseudocyphellaria. In Lichen Flora of the Greater Sonoran Desert Region, Volume I (T. H. Nash III, B. D. Ryan, C. Gries & F. Bungartz, eds): 413-415. Tempe, Arizona: Lichens Unlimited, Arizona State University.
62. Sato, H., Kawakami, H., Hara, H., Komine, M., Takahashi, Y., Yamamoto, Y. & Yoshimura, I. (2011) Materials for the study of distributions of lichenized fungi (27). Lobaria sachalinensis. Lichenology 10: 67- 70.
63. Schumm, F. (2003) Die Flechtengattung Lobaria auf Madeira. Herzogia 16: 91-112.
64. Spielmann, A. A. (2009) Estudos Taxonômicos em Parmotrema s. l. (Parmeliaceae, Ascomycota Liquenizados) comA ́ cido Salazínico. Sa?o Paulo: Instituto de Botânica da Secretaria de Estado do Meio Ambiente.
65. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690. (Pubitemid 44642609)
66. Stamatakis, A., Hoover, P. & Rougemont, J. (2008) A fast bootstrapping algorithm for the RAxML web- Servers. Systematic Biology 57: 758-771.
67. Stenroos, S., Stocker-Wo?rgo? tter, E., Yoshimura, I., Myllys, L., Thell, A. & Hyvo?nen, J. (2003) Culture experiments and DNA sequence data confirm the identity of Lobaria photomorphs. Canadian Journal of Botany 81: 232-247. (Pubitemid 36704407)
68. Sua'rez, A. & Lu? cking, R. (2013) Sticta viviana (lichenized Ascomycota: Peltigerales: Lobariaceae), a new species from Colombian paramos. Lichenologist 45 (in press).
69. Takahashi, K., Wang, L.-S., Tsubota, H. & Deguchi, H. (2006) Photosymbiodemes Sticta wrightii and Dendriscocaulon sp. (lichenized Ascomycota) from Yunnan, China. Journal of the Hattori Botanical Laboratory 100: 783-796. (Pubitemid 44884642)
70. Thomas, M. A., Ryan, D. J., Farnden, K. J. F. & Galloway, D. J. (2002) Observations on phylogenetic relationships within Lobariaceae Chevall. (Lecanorales, Ascomycota) in New Zealand, based on ITS-5.8s molecular sequence data. Bibliotheca Lichenologica 82: 123-138.
71. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680. (Pubitemid 24354800)
72. Tønsberg, T. & Goward, T. (2001) Sticta oroborealis sp. nov. and other Pacific North American lichens forming dendriscocauloid cyanotypes. Bryologist 104: 12-23. (Pubitemid 32398681)
73. Vainio, E. A. (1890) Etude sur la classification et la morphologie des lichens du Brésil, I. Acta Societatis pro Fauna et Flora Fennica 7: V-XXIX, 1-247.
74. Vilgalys, R. & Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238-4246. (Pubitemid 20236711)
75. White, T. J., Bruns, T. D., Lee, S. & Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols (M. A. Innis, D. H. Gelfand, J. J. Sninsky & T. J. White, eds): 315-322. San Diego: Academic Press.
76. Wiklund, E. &Wedin, M. (2003) The phylogenetic relationships of the cyanobacterial lichens in the Lecanorales suborder Peltigerineae. Cladistics 19: 419- 431. (Pubitemid 37316982)
77. Wilkins, A. L. (1993) The distribution, biosynthetic and possible evolutionary inter-relationship of triterpenoids in New Zealand Pseudocyphellaria species. Bibliotheca Lichenologica 53: 277-288.
78. Yamamoto, Y., Hara, K., Komine, M. & Yoshimura, I. (2005) Materials for the study of distributions of lichenized fungi (12). Lobaria kurokawae, Lobaria isidiosa and Lobaria retigera. Lichenology 4: 105-111.
79. Yoshimura, I. (1969) Taxonomy of Lobaria subdissecta and its allies. Journal of the Hattori Botanical Laboratory 32: 57-66.
80. Yoshimura, I. (1971) The genus Lobaria of eastern Asia. Journal of the Hattori Botanical Laboratory 34: 231- 364.
81. Yoshimura, I. (1984) Taxonomic studies on Lobaria crenulata and its allies. Journal of the Hattori Botanical Laboratory 57: 97-126.
82. Yoshimura, I. (1998a) Vainio and Lobaria, old and modern concepts. In Recollecting Edvard August Vainio (M. P. Marcelli & T. Ahti, eds): 85-94. Sa?o Paulo, Brazil: CETESB - Companhia de Tecnologia
83. Yoshimura, I. (1998b) Lobaria in Latin America: taxonomic, geographic and evolutionary aspects. In Lichenology in Latin America: History, Current Knowledge and Applications (M. P. Marcelli & M. R. D. Seaward, eds): 129-134. Sa?o Paulo, Brazil: CETESB - Companhia de Tecnologia de Saneamento Ambiental.
84. Yoshimura, I. (2002) Lobariella. In Lichen Flora of the Greater Sonoran Desert Region, Volume 1 (T. H. Nash III, B. D. Ryan, C. Gries & F. Bungartz, eds): 270-272. Tempe, Arizona: Lichens Unlimited, Arizona State University.
85. Yoshimura, I. (2004) Lobaria. In Lichen Flora of the Greater Sonoran Desert Region, Volume 2 (T. H. Nash III, B. D. Ryan, C. Gries & F. Bungartz, eds): 351-352. Tempe, Arizona: Lichens Unlimited, Arizona State University.
86. Yoshimura, I. & Arvidsson, L. (1994) Taxonomy and chemistry of the Lobaria crenulata group in Ecuador. Acta Botanica Fennica 150: 223-333.
87. Zhou, S. & Stanosz, G. R. (2001) Primers for amplification of mt SSU rDNA, and a phylogenetic study of Botryosphaeria and associated anamorphic fungi. Mycological Research 105: 1033-1044. (Pubitemid 32974186)
88. 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. (Pubitemid 29532221)