Molecular phylogeny and systematics of the Ocellularia clade (Ascomycota: Ostropales: Graphidaceae)

Taxon

Volumn 61, Issue 6, 2012, Pages 1161-1179

  Plata, Eimy Rivas ^a,b   Lücking, Robert ^b   Lumbsch, H Thorsten ^b  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Ancestral; Disparity; Lecanoromycetes; Lichenized fungi; Ostropomycetidae; Ribosomal DNA

Indexed keywords

FUNGUS; MAXIMUM LIKELIHOOD ANALYSIS; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; TAXONOMY;

EID: 84871527482     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.616001     Document Type: Article

References (76)

1. Berger, S.A., Krompaß, D. & Stamatakis, A.2011a. Performance, accuracy and web-server for evolutionary placement of short sequence reads under maximum-likelihood. Syst. Biol. 60: 291-302.
2. Berger, S.A., Stamatakis, A. & Lücking, A. 2011b. Morphology based phylogenetic binning of the lichen generaAllographa andGraphis (Ascomycota: Graphidaceae) using molecular site weight calibration. Taxon 60: 1450-1457.
3. Blanco, O., Crespo, A., Divakar, P.K., Esslinger, T.L., Hawksworth, D.L. & Lumbsch, H.T. 2004a. Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data. Mycol. Res. 108: 873-884.
4. Blanco, O., Crespo, A., Elix, J.A., Hawksworth, D.L. & Lumbsch, H.T. 2004b. A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales). Taxon 53: 959-975.
5. Crespo, A., Ferencova, Z., Perez-Ortega, S., Elix, J.A. & Divakar, P.D. 2010. Austroparmelina, a new Australasian lineage in parmelioid lichens (Parmeliaceae, Ascomycota). Syst. Biodivers. 8: 209-221.
6. Elix, J.A., Wirtz, N. & Lumbsch, H.T. 2007. Studies on the chemistry of some Usnea species of the Neuropogon group (Lecanorales, Ascomycota). Nova Hedwigia 85(3-4): 491-501.
7. Frisch, A., Kalb, K. & Grube, M. 2006. Contributions towards a new systematics of the lichen family Thelotremataceae III. Molecular phylogeny of the Thelotremataceae. Biblioth. Lichenol. 92: 517-539.
8. Gaya, E., Lutzoni, F., Zoller, S. & Navarro-Rosinés, P. 2003. Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming Ascomycota). Amer. J. Bot. 90: 1095-1103.
9. Gueidan, C., Savić, S., Thüs, H., Roux, C., Keller, C., Tibell, L., Prieto, M., Heidmarsson, 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.
10. Hale, M.E. 1974. Studies on the lichen family Thelotremataceae part 2. Phytologia 27: 490-501.
11. Hale, M.E. 1978. Studies on the lichen family Thelotremataceae part 4. Mycotaxon 7: 377-385.
12. Hale, M.E. 1980. Generic delimitation in the lichen family Thelotremataceae. Mycotaxon 11: 130-138.
13. Hale, M.E. 1981. A revision of the lichen family Thelotremataceae in Sri Lanka. Bull. Brit. Mus. (Nat. Hist.), Bot. 8: 227-332.
14. Hall, T.A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41: 95-98.
15. Hibbett, D.S. 2007. After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century. Mycol. Res. 111: 1003-1020.
16. Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M., Lücking, R., Lumbsch, H.T., Lutzoni, F., Matheny, P.B., McLaughlin, D.J., Powell, M.J., Redhead, S., Schoch, C.L., Spatafora, J.W., Stalpers, J.A., Vilgalys, R., Aime, M.C., Aptroot, A., Bauer, R., Begerow, D., Benny, G.L., Castlebury, L.A., Crous, P.W., Dai, Y.C., Gams, W., Geiser, D.M., Griffith, G.W., Gueidan, C., Hawksworth, D.L., Hestmark, G., Hosaka, K., Humber, R.A., Hyde, K.D., Ironside, J.E., Kôljalg, U., Kurtzman, C.P., Larsson, K.H., Lichtwardt, R., Longcore, J., Miadlikowska, J., Miller, A., Moncalvo, J.M., Mozley-Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J.D., Roux, C., Ryvarden, L., Sampaio, J.P., Schüssler, A., Sugiyama, J., Thorn, R.G., Tibell, L., Untereiner, W.A., Walker, C., Wang, Z., Weir, A., Weiss, M., White, M.M., Winka, K., Yao, Y.J. & Zhang, N. 2007. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111: 509-547.
17. Hibbett, D.S., Pine, E.M., Langer, E., Langer, G. & Donoghue, M.J. 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc. Natl. Acad. Sci. U.S.A. 94: 12002-12006.
18. Hörandl, E. & Stuessy, T.F. 2010. Paraphyletic groups as natural units of biological classification. Taxon 59: 1641-1653.
19. James, T.Y., Kauff, F., Schoch, C.L., Matheny, P.B., Hofstetter, V., Cox, C.J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H.T., Rauhut, A., Reeb, V., Arnold, A.E., Amtoft, A., Stajich, J.E., Hosaka, K., Sung, G.H., Johnson, D., O'Rourke, B., Crockett, M., Binder, M., Curtis, J.M., Slot, J.C., Wang, Z., Wilson, A.W., Schußler, A., Longcore, J.E, O'Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P.M., Powell, M.J., Taylor, J.W., White, M.M., Griffith, G.W., Davies, D.R., Humber, R.A., Morton, J.B., Sugiyama, J., Rossman, A.Y., Rogers, J.D., Pfister, D.H., Hewitt, D, Hansen, K., Hambleton, S., Shoemaker, R.A., Kohlmeyer, J, Volkmann-Kohlmeyer, B., Spotts, R.A., Serdani, M., Crous, P.W., Hughes, K.W., Matsuura, K., Langer, E., Langer, G., Untereiner, W.A., Lucking, R., Budel, B., Geiser, D.M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D.S., Lutzoni, F., McLaughlin, D.J., Spatafora, J.W. & Vilgalys, R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: 818-822.
20. Kalb, K. 2004. New or otherwise interesting lichens II. Biblioth. Lichenol. 88: 301-329.
21. Katoh, K. & Toh, M. 2005. MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucl. Acids Res. 33: 511-518.
22. 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. Molec. Phylogen. Evol. 25: 138-156.
23. Larsson, E. & Larsson, K.H. 2003. Phylogenetic relationships of russuloid basidiomycetes with emphasis on aphyllophoralean taxa. Mycologia 95: 1037-1065.
24. Larsson, K.H., Larsson, E. & Koljalg, U. 2004. High phylogenetic diversity among corticioid homobasidomycetes. Mycol. Res. 108: 983-1002.
25. Liu, Y.J., Whelen, S. & Hall, B.D. 1999. Phylogenetic relationships among ascomycetes: Evidence from the RNA polymerase II su unit. Molec. Biol. Evol. 16: 1799-1808.
26. Lücking, R. 2009. The taxonomy of the genus Graphis sensu Staiger (Ascomycota: Ostropales: Graphidaceae). Lichenologist 41: 319-362.
27. Lücking, R. & Rivas Plata, E. 2008. Clave y guía ilustrada para géneros de Graphidaceae. Glalia 1: 1-41.
28. Lücking, R., Chaves, J.L., Sipman, H.J.M., Umaña, L. & Aptroot, A. 2008. A first assessment of the Ticolichen Biodiversity Inventory in Costa Rica: The genus Graphis; With notes on the genusHemithecium (Ascomycota: Ostropales: Graphidaceae). Fieldiana 46: 1-130.
29. Lumbsch, H.T., Parnmen, S., Rangsiruji, A. & Elix, J.A. 2010. Phenotypic disparity and adaptive radiation in the genus Cladia (Lecanorales, Ascomycota). Austral. Syst. Bot. 23: 239-247.
30. Lutzoni, F., Kauff, F., Cox, C., McLaughlin, D., Celio, G., Dentinger, B., Padamsee, M., Hibbett, D., James, T.Y., Baloch, E., Grube, M., Reeb, V., Hofstetter, V., Schoch, C., Arnold, A.E., Miadlikowska, J., Spatafora, J., Johnson, D., Hambleton, S., Crockett, M., Shoemaker, R., Sung, G.-H., Lücking, R., Lumbsch, H.T., O'Donnell, K., Binder, M., Diederich, P., Ertz, D., Gueidan, C., Hansen, K., Harris, R.C., 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. Amer. J. Bot. 91: 1446-1480.
31. Mangold, A., Martin, M.P., Lücking, R. & Lumbsch, H.T. 2008. Molecular phylogeny suggests synonymy of Thelotremataceae within Graphidaceae (Ascomycota: Ostropales). Taxon 57: 476-486.
32. Mason-Gamer, R.J. & Kellogg, E.A. 1997. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45: 524-545.
33. McCune, B. & Grace, J.B. 2002. Analysis of ecological communities. Gleneden Beach, Oregon: MjM Press.
34. McCune, B. & Mefford, M.J. 1999. PC-ORD: Multivariate analysis of ecological data, version 4.0. Gleneden Beach, Oregon: MjM Software.
35. 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. Int. J. Pl. Sci. 161: 925-968.
36. Miadlikowska, J., Kauff, F., Hofstetter, V., Fraker, E., Grube, M., Hafellner, J., Reeb, V., Hodkinson, B.P., Kukwa, M., Lücking, R., Hestmark, G., Otalora, M.G., Rauhut, A., Büdel, B., Scheidegger, C., Timdal, E., Stenroos, S., Brodo,I., Perlmutter, G.B., Ertz, D., Diederich, P., Lendemer, J.C., Tripp,E., Yahr, R., May, P., Gueidan, C., Arnold, A.E., Robertson, C. & Lutzoni, F. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetical analyses of three ribosomal RNA and two protein-coding genes. Mycologia 98: 1088-1103.
37. Moncalvo, J.M., Vilgalys, R., Redhead, S.A., Johnson, J.E., James, T.Y., Aime, M.C., Hofstetter, V., Verduin, S.J.W., Larsson,E., Baroni, T.J., Thorn, R.G., Jacobsson, S., Clemencon, H. & Miller, O.K., Jr. 2002. One hundred and seventeen clades of euagarics. Molec. Phylogen. Evol. 23: 357-400.
38. Mugambi, G.K. & Huhndorf, S.M. 2009. Parallel evolution of hysterothecial ascomata in ascolocularous fungi (Ascomycota, Fungi). Syst. Biodivers. 7: 453-464.
39. Müller, J. 1885. Lichenologische Beiträge 22. Flora 68: 499-502, 503-518, 528-533.
40. Müller, J. 1887. Graphideae Féeanae inclus. trib. affinibus nec non Graphideae exoticae Acharii, El. Friesii et Zenkeri e novo studio speciminum originalium expositae et in novam dispositionem ordinatae. Mém. Soc. Phys. Genève 29(8): 1-80.
41. Müller, J. 1888. Lichenologische Beiträge 27. Flora 71: 17-25, 44-48.
42. Müller, J. 1890. Lichenes epiphylli novi. Basel.
43. Nelsen, M.P., Lücking, R., Grube, M., Mbatchou, J.S., Muggia, L., Rivas Plata, E. & Lumbsch, H.T. 2009. Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta. Stud. Mycol. 64: 135-144.
44. Parnmen, S., Rangsiruji, A., Mongulsuk, P., Boonpragob, K., Elix, J.A. & Lumbsch, H.T. 2010. Morphological disparity in Cladoniaceae: The foliose genus Heterodea evolved from fruticose Cladia species (Lecanorales, Ascomycota). Taxon 59: 841-849.
45. Penn, O., Privman, E., Ashkenazy, H., Landan, G., Graur, D. & Pupko, T. 2010a. GUIDANCE: A web server for assessing alignment confidence scores. Nucl. Acids Res. 38 (Web Server issue): W23-W28.
46. Penn, O., Privman, E., Landan, G., Graur, D. & Pupko, T. 2010b. An alignment confidence score capturing robustness to guide-tree uncertainty. Molec. Biol. Evol. 27: 1759-1767.
47. Podani, J. 2010. Monophyly and paraphyly: A discourse without end? Taxon 59: 1011-1015.
48. Posada, D. 2008. jModelTest: Phylogenetic model averaging. Molec. Biol. Evol. 25: 1253-1256.
49. Rivas Plata, E. & Lücking, R. 2012. High diversity of Graphidaceae (lichenized Ascomycota: Ostropales) in Amazonian Perú. Fungal Diversity, DOI 10.1007/s13225-012-0172-y.
50. Rivas Plata, E. & Lumbsch, H.T. 2011. Parallel evolution and phenotypic disparity in lichenized fungi: A case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales). Molec. Phylogen. Evol. 61: 45-63.
51. Rivas Plata, E., Hernández, J.E., Lücking, R., Staiger, B., Kalb, K. & Cáceres, M.E.S. 2011. Graphis is two genera-A remark-able case of parallel evolution in lichenized Ascomycota. Taxon 60: 99-107.
52. Rivas Plata, E., Lücking, R. & Lumbsch, H.T. 2008. When family matters: An analysis of Thelotremataceae (lichenized Ascomycota: Ostropales) as bioindicators of ecological continuity in tropical forests. Biodivers. & Conservation 17: 1319-1351.
53. Rivas Plata, E., Lücking, R., Sipman, H.J.M., Mangold, A., Kalb, K. & Lumbsch, H.T. 2010. A world-wide key to the thelotremoid Graphidaceae, excuding the Ocellularia-Myriotrema-Stegobolus clade. Lichenologist 42: 187-189.
54. Rivas Plata, E., Lumbsch, H.T. & Lücking, R. 2012. A new classification for the lichen family Graphidaceae s.lat. (Ascomycota: Lecanoromycetes: Ostropales). Fungal Diversity 52: 107-121.
55. Salisbury, G. 1971. The Thelotremata of Angola and Mocambique. Revista Biol. (Lisbon) 7: 271-280.
56. Salisbury, G. 1978. Thelotrema Achariana et Feeana. Nova Hedwigia 29: 405-427.
57. Savic, S., Tibell, L., Gueidan, C. & Lutzoni, F. 2008. Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera. Mycol. Res. 112: 1307-1318.
58. Schoch, C.L., Shoemaker, R.A., Seifert, K.A., Hambleton, S., Spatafora, J.W. & Crous, P.W. 2006.A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98: 1041-1052.
59. Schoch, C.L., Sung, G.H., Lopez-Giraldez, F., Townsend, J.P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P.B., Kauff, F., Wang, Z., Gueidan, C., Andrie, R.M., Trippe,K., Ciufetti, L.M., Wynns, A., Fraker, E., Hodkinson, B.P., Bonito,G., Groenewald, J.Z., Arzanlou, M., de Hoog, G.S., Crous, P.W., Hewitt, D., Pfister, D.H., Peterson, K., Gryzenhout, M., Wingfield, M.J., Aptroot, A., Suh, S.O., Blackwell,M., Hillis, D.M., Griffith, G.W., Castlebury, L.A., Rossman, A.Y., Lumbsch, H.T., Lücking, R., Budel, B., Rauhut, A., Diederich, P., Ertz, D., Geiser, D.M., Hosaka, K., Inderbitzin, P., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Mostert, L., O'Donnell, K., Sipman, H., Rogers, J.D., Shoemaker, R.A., Sugiyama, J., Summerbell, R.C., Untereiner, W., Johnston, P.R., Stenroos, S., Zuccaro, A., Dyer, P.S., Crittenden, P.D., Cole, M.S., Hansen, K., Trappe, J.M., Yahr, R., Lutzoni, F. & Spatafora, J.W. 2009b. The Ascomycota tree of life: A phylum wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst. Biol. 58: 224-239.
60. Schoch, C.L., Wang, Z., Townsend, J.P. & Spatafora, J.W. 2009a. Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life. Persoonia 22: 129-138.
61. Spatafora, J.W., Sung, G.H., Johnson, D., O'Rourke, B., Serdani, M., Spotts, R., Lutzoni, F., Hofstetter, V., Miadlikowska, J., Reeb, V., Gueidan, C., Fraker, E., Lumbsch, H.T., Lücking, R., Schmitt, I., Hosaka, K., Aptroot, A., Roux, C., Miller, A., Geiser, D., Hafellner, J., Hestmark, G., Arnold, A.E., Büdel, B., Rauhut, A., Hewitt, D., Untereiner, W.A., Cole, M.S., Scheidegger, C., Schultz, M., Sipman, H.J.M. & Schoch, C. 2006. A five-gene phylogeny of the Pezizomycotina. Mycologia 98: 1018-1028.
62. Staiger, B. 2002. Die Flechtenfamilie Graphidaceae: Studien in Richtung einer natürlicheren Gliederung. Biblioth. Lichenol. 85: 1-526.
63. Staiger, B. & Kalb, K. 1995. Haematomma-Studien. I. Die Flechtengattung Haematomma. Biblioth. Lichenol. 59: 1-198 pp.
64. Staiger, B., Kalb, K. & Grube, M. 2006. Phylogeny and phenotypic variation in the lichen family Graphidaceae (Ostropomycetidae, Ascomycota). Mycol. Res. 110: 765-772.
65. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum-likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-90.
66. Stamatakis, A., Ludwig, T. & Meier, H. 2005. RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics21: 456-463.
67. Tehler, A. & Irestedt, M. 2007. Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota). Cladistics 23: 432-454.
68. Vainio, E.A. 1890. Étude sur la classification naturelle et la morphol gie des lichens du Brésil, I. Acta Soc. Fauna Fl. Fenn. 7: 1-247.
69. Vainio, E.A. 1921. Lichenes insularum Philippinarum III. Ann. Acad. Sci. Fenn., Ser. A 15(6): 1-368.
70. Vainio, E.A. 1923. Lichenes in Insula Trinidad a Professor R. Thaxter Collecti. Proc. Amer. Acad. Arts 58: 129-147.
71. Vilgalys, R. & Hester, M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172: 4238-4246.
72. Wirth, M. & Hale, M.E., Jr. 1963. The lichen family Graphidaceae in Mexico. Contr. U.S. Natl. Herb. 36(3): 63-119.
73. Wirth, M. & Hale, M.E., Jr. 1978. Morden-Smithsonian Expedition to Dominica: The lichens (Graphidaceae). Smithsonian Contr. Bot. 40: 1-64.
74. Zahlbruckner, A. 1905. Thelotremaceae; Diploschistaceae. Pp. 118-122 in: Engler, A. & Prantl, K. (eds.), Die natürlichen Pflanzen-familien, 1. Teil, Abt. 1. Leipzig: Engelmann.
75. Zahlbruckner, A. 1923. Catalogus lichenum universalis, vol. 2. Leipzig: Gebr. Borntraeger
76. 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