Major clades and phylogenetic relationships between lichenized and non-lichenized lineages in ostropales (Ascomycota: Lecanoromycetes)

Taxon

Volumn 59, Issue 5, 2010, Pages 1483-1494

  Baloch, Elisabeth ^a,c   Lücking, Robert ^b   Lumbsch, H Thorsten ^b   Wedin, Mats ^a  

^a SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

^c JODRELL LABORATORY   (United Kingdom)

Author keywords

Belonia; Morphological characters; Ostropomycetidae; Pachyphiale; Phylogeny; Sagiolechiaceae

Indexed keywords

CLADISTICS; DATA SET; FUNGUS; GENETIC ANALYSIS; LICHEN; MORPHOLOGY; NEW GENUS; PHENOTYPIC PLASTICITY; PHYLOGENY; TAXONOMY;

ASCOMYCOTA; COENOGONIACEAE; FUNGI; GOMPHILLACEAE; GRAPHIDACEAE; GYALECTA; GYALECTACEAE; LECANOROMYCETES; ODONTOTREMATACEAE; OSTROPALES; SAGIOLECHIA;

EID: 78149267818     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.595013     Document Type: Article

References (79)

1. Alstrup, V. & Hansen, E.S. 2001. New lichens and lichenicolous fungi from Greenland. Graphis Scripta 12: 41-50.
2. Aptroot, A. & Lücking, R. 2003. Phenotype-based phylogenetic analysis does not support generic separation of Gyalidea and Solorinella (Ostropales: Asterothyriaceae). Biblioth. Lichenol. 86: 53-78.
3. Baloch, E., Gilenstam, G. & Wedin, M. 2009. Phylogeny and classification of Cryptodiscus, with a taxonomic synopsis of the Swedish species. Fung. Divers. 38: 51-68.
4. Baloch, E. & Grube, M. 2006. Evolution and phylogenetic relationships within Porinaceae (Ostropomycetidae), focusing on foliicolous species. Mycol. Res. 110: 125-136.
5. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molec. Biol. Evol. 17: 540-552.
6. Diederich, P. & Etayo, J. 2000. A synopsis of the genera Skyttea, Llimoniella and Rhymbocarpus (Lichenicolous ascomycota, Leotiales). Lichenologist 32: 423-485.
7. Diederich, P., Zhurbenko, M. & Etayo, J. 2002. The lichenicolous species of Odontotrema (syn. Lethariicola) (Ascomycota, Ostropales). Lichenologist 34: 479-501.
8. Ekman, S., Andersen, H.L. & Wedin, M. 2008. The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota). Syst. Biol. 57: 141-156
9. Eriksson, O.E. 1967. On graminicolous pyrenomycetes from Fennoscandia. Ark. Bot. 2: 381-440.
10. Eriksson, O.E. 1981. The families of bitunicate ascomycetes. Opera Bot. 60: 1-220.
11. Eriksson, O.E. & Hawksworth, D.L. 1988. Outline of the ascomycetes- 1988. Syst. Ascomycetum 7: 119-315.
12. Foucard, T. & Thor, G. 1996. Gyalidea praetermissa, a new lichen from Sweden. Lichenologist 28: 101-104.
13. Friedl, T. 1987. Thallus development and phycobionts of the parasitic lichen Diploschistes muscorum. Lichenologist 19: 183-191.
14. Friedl, T. & Gärtner, G. 1988. Trebouxia (Pleurastrales, Chlorophyta) as a phycobiont in the lichen genus Diploschistes. Arch. Protistenk. 135: 147-158.
15. Frisch, A., Kalb, K. & Grube, M. 2006. Contributions towards a new systematics of the lichen family Thelotremataceae. Biblioth. Lichenol. 92: 1-539.
16. Gilenstam, G. 1969. Studies in the lichen genus Conotrema. Ark. Bot., Ser. 2, 7: 149-179.
17. Grube, M., Baloch, E. & Arup, U. 2004a. A phylogenetic study of the Lecanora rupicola group (Lecanoraceae, Ascomycota). Mycol. Res. 108: 506-514.
18. Grube, M., Baloch, E. & Lumbsch, H.T. 2004b. The phylogeny of Porinaceae (Ostropomycetidae) suggests a neotenic origin of perithecia in Lecanoromycetes. Mycol. Res. 108: 1111-1118.
19. Grube, M. & Hawksworth, D.L. 2007. Trouble with lichen: The reevaluation and re-interpretation of thallus form and fruit body types in the molecularera. Mycol. Res. 111: 1116-1132.
20. Hafellner, J. & Kalb, K. 1995. Studies in Trichotheliales ordo novus. Biblioth. Lichenol. 57: 161-186.
21. Hawksworth, D.L. & Sherwood, M.A. 1982. Two new families in the Ascomycotina. Mycotaxon 16: 262-264.
22. Henssen, A. 1976. Studies in the developmental morphology of lichenized Ascomycetes. Pp. 107-138 in: Brown, D.H., Hawksworth D.L. & Bailey R.H., (ed.), Lichenology: Progress and problems. London: Academic Press.
23. Henssen, A. 1995. Sagiolechia atlantica, eine neue Flechte von den Atlantischen Inseln (Ascomycotina, Ostropales). Biblioth. Lichenol. 58: 123-136.
24. Henssen, A. & Jahns, H.M. 1974. Lichenes: Eine Einführung in die Flechtenkunde. Stuttgart: Thieme.
25. Henssen, A. & Lücking, R. 2002. Morphology, anatomy, and ontogeny in the Asterothyriaceae (Ascomycota: Ostropales), a misunderstood group of lichenized fungi. Ann. Bot. Fenn. 39: 273-299.
26. 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., Koljalg, 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., Schussler, 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.
27. Hillis, D.M. & Bull, J.J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42: 182-192.
28. Huelsenbeck, J.P. & Bollback, J.P. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50: 351-366.
29. Huelsenbeck, J.P. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
30. Katoh, K., Kuma, K., Toh, H. & Miyata, T. 2005. MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
31. 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 Res. 30: 3059-3066.
32. Katoh, K. & Toh, H. 2008a. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFTbased framework. BMC Bioinformatics 9: 212.
33. Katoh, K. & Toh, H. 2008b. Recent developments in the MAFFT multiple sequence alignment program. Briefings Bioinformatics 9: 286-298.
34. Kauff, F. & Büdel, B. 2005. Ascoma ontogeny and apothecial anatomy in the Gyalectaceae (Ostropales, Ascomycota) support the re-establishment of the Coenogoniaceae. Bryologist 108: 272-281.
35. 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. Molec. Phylog. Evol. 25: 138-156.
36. Kirk, P.M., Cannon, P.F., David, J.C. & Stalpers, J.A. (eds.). 2009. Ainsworth & Bisby's Dictionary of the Fungi, 10th ed. Wallingford: CAB International.
37. Liu, Y.J., Whelen, S. & Hall, B.D. 1999. Phylogenetic relationships among ascomycetes: Evidence from an RNA polymerase II subunit. Molec. Biol. Evol. 16: 1799-1808.
38. Lücking, R., Serusiaux, E.L. & Vezda, A. 2005. Phylogeny and systematics of the lichen family Gomphillaceae (Ostropales) inferred from cladistic analysis of phenotype data. Lichenologist 37: 123-169.
39. Lücking, R., Stuart, B.L. & Lumbsch, H.T. 2004. Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: Evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences. Mycologia 96: 283-294.
40. Lumbsch, H.T. & Huhndorf, S. 2007. Outline of Ascomycota-2007. Myconet 13: 1-58.
41. Lumbsch, H.T., Lücking, R. & Tibell, L. 2009. Molecular data place Tylophoron as an additional calicioid genus in Arthoniales (Ascomycota). Biblioth. Lichenol. 99: 285-296.
42. Lumbsch, H.T., Mangold, A., Lücking, R., García, M.A. & Martín, M.P. 2004a. Phylogenetic position of the genera Nadvornikia and Pyrgillus (Ascomycota) based on molecular data. Symb. Bot. Upsal. 34(1): 9-17.
43. Lumbsch, H.T., Schmitt, I., Lücking, R., Wiklund, E. & Wedin, M. 2007a. The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited. Mycol. Res. 111: 508-508.
44. Lumbsch, H.T., Schmitt, I., Mangold, A. & Wedin, M. 2007b. Ascus types are phylogenetically misleading in Trapeliaceae and Agyriaceae (Ostropomycetidae, Ascomycota). Mycol. Res. 111: 1133-1141.
45. Lumbsch, H.T., Schmitt, I., Palice, Z., Wiklund, E., Ekman, S. & Wedin, M. 2004b. Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences. Molec. Phylog. Evol. 31: 822-832.
46. 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.
47. Lutzoni, F., Pagel, M. & Reeb, V. 2001. Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411: 937-940.
48. 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.
49. 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., Budel, B., Scheidegger, C., Timdal, E., Stenroos, S., Brodo, I., Perlmutter, G.B., Ertz, D., Diederich, P., Lendemer, J.C., May, P., Schoch, C.L., Arnold, A.E., Gueidan, C., Tripp, E., Yahr, R., Robertson, C. & Lutzoni, F. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two proteincoding genes. Mycologia 98: 1088-1103.
50. Nannfeldt, J.A. 1932. Studien über die Morphologie und Systematik der nicht-lichenisierten inoperculaten Discomyceten. Nova Acta Regiae Soc. Sci. Upsal., Ser. IV, 8: 1-368.
51. Nylander, J.A.A., Ronquist, F., Huelsenbeck, J.P. & Nieves-Aldrey, J.L. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53: 47-67.
52. Orange, A. 2009. A new species of Petractis (Ostropales s.lat., lichenized Ascomycota) from Wales. Lichenologist 41: 213-221.
53. Posada, D. 2008. jModelTest: Phylogenetic model averaging. Molec. Biol. Evol. 25: 1253-1256.
54. Rehner, S.A. & Samuels, G.J. 1994. Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNAsequences. Mycol. Res. 98: 625-634.
55. Ronquist, F. & Huelsenbeck, J.P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
56. Schmitt, I., del Prado, R., Grube, M. & Lumbsch, H.T. 2009. Repeated evolution of closed fruiting bodies is linked to ascoma development in the largest group of lichenized fungi (Lecanoromycetes, Ascomycota). Molec. Phylog. Evol. 52: 34-44.
57. 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. 2009. 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.
58. Sherwood, M.A. 1977a. The ostropalean fungi. Mycotaxon 5: 1-277.
59. Sherwood, M.A. 1977b. The ostropalean fungi II: Schizoxylon, with notes on Stictis, Acarosporina, Coccopeziza, and Carestiella. Mycotaxon 6: 215-260.
60. Sherwood, M.A. 1981. Convergent evolution in discomycetes from bark and wood. Bot. J. Linn. Soc. 82: 15-34.
61. Sherwood-Pike, M.A. 1987. The ostropalean fungi III: The Odontotremataceae. Mycotaxon 28: 137-177.
62. Spatafora, J.W., Sung, G.H., Johnson, D., Hesse, C., O'Rourke, B., Serdani, M., Spotts, R., Lutzoni, F., Hofstetter, V., Miadlikowska, J., Reeb, V., Gueidan, C., Fraker, E., Lumbsch, T., Lücking, R., Schmitt, I., Hosaka, K., Aptroot, A., Roux, C., Miller, A.N., Geiser, D.M., Hafellner, J., Hestmark, G., Arnold, A.E., Budel, B., Rauhut, A., Hewitt, D., Untereiner, W.A., Cole, M.S., Scheidegger, C., Schultz, M., Sipman, H. & Schoch, C.L. 2006. A five-gene phylogeny of Pezizomycotina. Mycologia 98: 1018-1028.
63. Staiger, B., Kalb, K. & Grube, M. 2006. Phylogeny and phenotypic variation in the lichen family Graphidaceae (Ostropomycetidae, Ascomycota). Mycol. Res. 110: 765-772.
64. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
65. Stamatakis, A., Hoover, P. & Rougemont, J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57: 758-771.
66. Swofford, D.L. 2004. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b.10. Sunderland, Massachusetts: Sinauer.
67. Talavera, G. & Castresana, J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56: 564-577.
68. Vězda, A. 1966. Flechtensystematische Studien III. Die Gattungen Ramonia Stiz. und Gloeolecta Lett. Folia Geobot. Phytotax. 1: 154-175.
69. Vězda, A. 1967. Flechtensystematische Studien VI. Die Gattung Sagiolechia Massal. Folia Geobot. Phytotax. 2: 383-396.
70. Vězda, A. & Poelt, J. 1990. Solorinellaceae, eine neue Familie der lichenisierten Ascomyceten. Phyton (Horn) 30: 47-55.
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. 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.
73. Wedin, M., Döring, H. & Gilenstam, G. 2004. Saprotrophy and lichenization as options for the same fungal species on different substrata: Environmental plasticity and fungal lifestyles in the Stictis-Conotrema complex. New Phytol. 164: 459-465.
74. Wedin, M., Döring, H. & Gilenstam, G. 2006. Stictis s.lat. (Ostropales, Ascomycota) in northern Scandinavia, with a key and notes on morphological variation in relation to lifestyle. Mycol. Res. 110: 773-789.
75. Wedin, M., Döring, H., Könberg, K. & Gilenstam, G. 2005a. Generic delimitations in the family Stictidaceae (Ostropales, Ascomycota): The Stictis-Conotrema problem. Lichenologist 37: 67-75.
76. Wedin, M., Wiklund, E., Crewe, A., Döring, H., Ekman, S., Nyberg, A., Schmitt, I. & Lumbsch, H.T. 2005b. Phylogenetic relationships of Lecanoromycetes (Ascomycota) as revealed by analyses of mtSSU and nLSU rDNA sequence data. Mycol. Res. 109: 159-172.
77. Wedin, M., Wiklund, E., Jørgensen, P.M. & Ekman, S. 2009. Slippery when wet: Phylogeny and character evolution in the gelatinous cyanobacterial lichens (Peltigerales, Ascomycetes). Molec. Phylog. Evol. 53: 862-871.
78. Winka, K., Ahlberg, C. & Eriksson, O.E. 1998. Are there lichenized Ostropales? Lichenologist 30: 455-462.
79. 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.