Extended phylogeny and a revised generic classification of the Pannariaceae (Peltigerales, Ascomycota)

Lichenologist

Volumn 46, Issue 5, 2014, Pages 627-656

  Ekman, Stefan ^a   Wedin, Mats ^b   Lindblom, Louise ^c   Jorgensen, Per M ^c  

^a UPPSALA UNIVERSITY   (Sweden)

^b SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^c UNIVERSITY OF BERGEN   (Norway)

Author keywords

Collemataceae; lichen taxonomy; model adequacy; model selection

Indexed keywords

EID: 84905742198     PISSN: 00242829     EISSN: 10961135     Source Type: Journal    
DOI: 10.1017/S002428291400019X     Document Type: Article

References (107)

1. Alfaro, M. E. &Holder, M. T. (2006) The posterior and the prior in Bayesian phylogenetics. Annual Review of Ecology, Evolution, and Systematics 37: 19-42
2. Altekar, G., Dwarkadas, S., Huelsenbeck, J. P. &Ronquist, F. (2004) Parallel Metropolis coupledMarkov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407-415
3. Arvidsson, L. &Galloway, D. J. (1981) Degelia, a new lichen genus in the Pannariaceae. Lichenologist 13: 27-50
4. Belnap, J. (2003) The world at your feet: Desert biological soil crusts. Frontiers in Ecology and the Environment 1: 181-189
5. Blom, H. H. &Lindblom, L. (2009 ['2010']) Degelia cyanoloma (Schaerer) H. H. Blom &L. Lindblom comb. et stat. nov., a distinct species from western Europe. Lichenologist 42: 23-27
6. Bollback, J. P. (2002) Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution 19: 1171-1180
7. Brown, J. M. &Lemmon, A. R. (2007) The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Systematic Biology 56: 643-655
8. Buckley, T. R. (2002) Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Systematic Biology 51: 509-523
9. Cannone, J., Subramanian, S., Schnare, M., Collett, J., D'Souza, L., Du, Y., Feng, B., Lin, N., Madabusi, L., Muller, K., et al. (2002) The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2
10. Clements, F. E. &Shear, C. L. (1931) The Genera of Fungi. New York: H. W. Wilson
11. Cleveland, C. C., Townsend, A. R., Schimel, D. S., Fisher, H., Howarth, R. W., Hedin, L. O., Perakis, S. S., Latty, E. F., Von Fischer, J. C., Elseroad, A. et al. (1999) Global patterns of terrestrial biological nitrogen (N2) fixation in natural ecosystems. Global Biogeochemical Cycles 13: 623-645
12. Culberson, C. F. &Kristinsson, H. (1970) A standardized method for the identification of lichen products. Journal of Chromatography 46: 85-93
13. Darriba, D., Taboada, G. L., Doallo, R. &Posada, D. (2012) jModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9: 772
14. Dodge, C. W. (1948) Lichens and lichen parasites. British-Australian-New Zealand Antarctic Research Expedition 1929-1931, Report Series B, Zoology-Botany 7: 1-276
15. Edwards, S. V., Liu, L. &Pearl, D. K. (2007) Highresolution species trees without concatenation. Proceedings of the National Academy of Sciences of the United States of America 104: 5936-5941
16. Ekman, S. &Blaalid, R. (2011) The devil in the details: Interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae. Systematic Biology 60: 541-561
17. Ekman, S. &Jorgensen, P.M. (2002) Towards a molecular phylogeny for the lichen family Pannariaceae. Canadian Journal of Botany 80: 625-634
18. 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). Systematic Biology 57: 141-156
19. Elvebakk, A., Robertsen, E. H., Park, C. H. &Hong, S. G. (2010) Psorophorus and Xanthopsoroma, two new genera for yellow-green, corticolous and squamulose lichen species, previously in Psoroma. Lichenologist 42: 563-585
20. Galloway, D. J. (1983) New taxa in the New Zealand lichen flora. New Zealand Journal of Botany 21: 191-200
21. Galloway, D. J. &James, P. W. (1985) The lichen genus Psoromidium Stirton. Lichenologist 17: 173-188
22. Galloway, D. J. &Jorgensen, P.M. (1987) Studies in the lichen family Pannariaceae II. The genus Leioderma Nyl. Lichenologist 19: 345-400
23. Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., Wilkinson, A. C., Finn, R. D., Griffiths-Jones, S., Eddy, S. R. et al. (2009) Rfam: Updates to the RNA families database. Nucleic Acids Research 37: D136-140
24. Goldman, N. (1993) Statistical tests of models of DNA substitution. Journal of Molecular Evolution 36: 182-198
25. Guindon, S., Lethiec, F., Duroux, P. &Gascuel, O. (2005) PHYML online -A web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research 33: W557-559
26. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. &Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology 59: 307-321
27. Hamada, M., Sato, K., Kiryu, H., Mituyama, T. &Asai, K. (2009) CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sumof-pairs score. Bioinformatics 25: 3236-3243
28. Henssen, A. (1963) Eine Revision Der Flechtenfamilien Lichinaceae und Ephebaceae. Symbolae Botanicae Upsalienses 18: 1-123
29. Henssen, A. (1965) A review of the genera of the Collemataceae with simple spores (excluding Physma). Lichenologist 3: 29-41
30. Henssen, A. (1979) New species of Homothecium and Ramalodium from S America. Botaniska Notiser 132: 257-282
31. Henssen, A. (1997) Santessoniella, a new cyanophilic genus of lichenized ascomycetes. Symbolae Botanicae Upsalienses 32: 75-93
32. Henssen, A. (1999) New species of Ramalodium and Staurolemma from Australasia (Collemataceae, lichenized ascomycetes). Nova Hedwigia 68: 117-130
33. Henssen, A. (2000) Santessoniella rosettiformis, a new species from South America with notes on S. pulchella (Pannariaceae). Lichenologist 32: 57-65
34. Henssen, A. &Jahns, H. M. (1973 ['1974']) Lichenes. Eine Einführung in Die Flechtenkunde. Stuttgart: Georg Thieme Verlag
35. Henssen, A. &James, P.W. (1980) Parmeliella duplomarginata, a new lichen from New Zealand. Mycotaxon 11: 217-229
36. Henssen, A. &Kantvilas, G. (2000) Santessoniella rugosa (Pannariaceae), a new species from Tasmania. Lichenologist 32: 149-153
37. Holien, H. &Jorgensen, P. M. (2000) A blue-green Psoroma hypnorum found in Trondelag, Central Norway. Graphis Scripta 11: 49-52
38. Huelsenbeck, J. P. &Rannala, B. (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology 53: 904-913
39. James, T. Y., Kauff, F., Schoch, C. L., Matheny, P. B., Hofstetter, V., Cox, C. J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J. et al. (2006) Reconstructing the early evolution of Fungi using a sixgene phylogeny. Nature 443: 818-822
40. Jorgensen, P. M. (1978) The lichen family Pannariaceae in Europe. Opera Botanica 45: 1-123
41. Jorgensen, P. M. (1994) Studies in the lichen family Pannariaceae VI. The taxonomy and phytogeography of Pannaria Del. s. lat. Journal of the Hattori Botanical Laboratory 76: 197-206
42. Jorgensen, P. M. (1998) Studies in the lichen family Pannariaceae VII. On some poorly known Parmeliella-like species from the Southern Hemisphere. Lichenologist 30: 533-541
43. Jorgensen, P. M. (1999) Studies in the lichen family Pannariaceae VIII. Seven new parmelielloid lichens from New Zealand. New Zealand Journal of Botany 37: 257-268
44. Jorgensen, P. M. (2000) New or interesting Parmeliella species from the Andes and Central America. Lichenologist 32: 139-147
45. Jorgensen, P. M. (2001a ['2000']) Survey of the lichen family Pannariaceae on the American continent, north of Mexico. Bryologist 103: 670-704
46. Jorgensen, P.M. (2001b) Studies in the family Pannariaceae X. The lichen genus Protopannaria in the subantarctic islands. Cryptogamie, Mycologie 22: 67-72
47. Jorgensen, P. M. (2002) Kroswia, a new genus in the Pannariaceae. Lichenologist 34: 297-303
48. Jorgensen, P. M. (2003) Conspectus familiae Pannariaceae. Ilicifolia 4: 1-78
49. Jorgensen, P. M. (2004) Further contributions to the Pannariaceae (lichenized Ascomycetes) of the Southern Hemisphere. Bibliotheca Lichenologica 88: 229-253
50. Jorgensen, P. M. (2005a) Additions to the Pannariaceae of North America. Bryologist 108: 255-258
51. Jorgensen, P. M. (2005b) Notes on two subantarctic pannariaceous lichens. Cryptogamie, Mycologie 26: 37-43
52. Jorgensen, P. M. (2007) New discoveries in Asian pannariaceous lichens. Lichenologist 39: 235-243
53. Jorgensen, P. M. (2008) Vahliella, a new lichen genus. Lichenologist 42: 221-225
54. Jorgensen, P. M. (2010) New discoveries in the lichen genus Staurolemma Körb. Nova Hedwigia 90: 153-159
55. Jorgensen, P. M. &Arvidsson, L. (2002) The genus Erioderma (Pannariaceae) in Ecuador and neighbouring countries. Nordic Journal of Botany 22: 87-114
56. Jorgensen, P.M. &Galloway, D. J. (1989) Studies in the lichen family Pannariaceae III. The genus Fuscoderma, with additional notes and a revised key to Leioderma. Lichenologist 21: 295-301
57. Jorgensen, P.M. &Galloway, D. J. (1992) Pannariaceae. Flora of Australia 54: 246-293
58. Jorgensen, P. M. &Gjerde, I. (2012) Notes on some pannariaceous lichens from New Caledonia. Cryptogamie, Mycologie 33: 3-9
59. Jorgensen, P. M. &James, P. W. (1990) Studies in the lichen family Pannariaceae IV. The genus Degelia. Bibliotheca Lichenologica 38: 253-276
60. Jorgensen, P.M. &Palice, Z. (2010) Additions to the lichen family Pannariaceae in Ecuador. Nordic Journal of Botany 28: 623-628
61. Jorgensen, P. M., Ekman, S. &Wedin, M. (2013) (2143) Proposal to conserve the name Fuscopanna-ria against Moelleropsis (lichenized Ascomycota). Taxon 62: 629
62. Katoh, K. &Toh, H. (2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9: 212
63. 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. Molecular Phylogenetics and Evolution 25: 138-156
64. Keuck, G. (1977) Ontogenetische-systematische Studie über Erioderma in Vergleich mit anderen cyanophilen Flechtengattungen. Bibliotheca Lichenologica 6: 1-175
65. Kirk, P. M., Cannon, P. F., Minter, D. W. &Stalpers, J. A. (eds) (2008) Ainsworth &Bisby's Dictionary of the Fungi.Wallingford, Oxon: CAB International
66. Kiryu, H., Tabei, Y., Kin, T. &Asai, K. (2007) Murlet: A practical multiple alignment tool for structural RNA sequences. Bioinformatics 23: 1588-1598
67. Kolaczkowski, B. &Thornton, J. W. (2007) Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Molecular Biology and Evolution 24: 2108-2118
68. Kubatko, L. S. &Degnan, J. H. (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56: 17-24
69. Lanfear, R., Calcott, B., Ho, S. Y. W. &Guindon, S. (2012) PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 1695-1701
70. Lartillot, N. &Philippe, H. (2004) A Bayesian mixture model for across-site heterogeneities in the aminoacid replacement process. Molecular Biology and Evolution 21: 1095-1109
71. Lartillot, N., Brinkmann, H. &Philippe, H. (2007) Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evolutionary Biology 7: S4
72. Lartillot, N., Lepage, T. &Blanquart, S. (2009) Phylo-Bayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 2286-2288
73. Lemmon, A. R. &Moriarty, E. C. (2004) The importance of proper model assumption in Bayesian phylogenetics. Systematic Biology 53: 265-277
74. Lindblom, L. &Ekman, S. (2005) Molecular evidence supports the distinction between Xanthoria parietina and X. aureola (Teloschistaceae, lichenized Ascomycota). Mycological Research 109: 187-199
75. Lumbsch, H. T. &Huhndorf, S. M. (2010) Myconet Volume 14. Part One. Outline of Ascomycota -2009. Part Two. Notes on Ascomycete Systematics. Nos. 4751-5113. Fieldiana, Life and Earth Sciences 1: 1-64
76. Misof, B. &Misof, K. (2009) A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: A more objective means of data exclusion. Systematic Biology 58: 21-34
77. Muggia, L., Nelson, P., Wheeler, T., Yakovchenko, L. S., Tonsberg, T. &Spribille, T. (2011) Convergent evolution of a symbiotic duet: The case of the lichen genus Polychidium (Peltigerales, Ascomycota). American Journal of Botany 98: 1647-1656
78. Newton, M. A. &Raftery, A. E. (1994) Approximate Bayesian inference with the weighted likelihood bootstrap. Journal of the Royal Statistical Society Series B Methodological 56: 3-48
79. Notredame, C. &Abergel, C. (2003) Using multiple alignment methods to assess the quality of genomic data analysis. In Bioinformatics and Genomes: Current Perspectives (M. A. Andrade, ed.): 30-55. Wymondham: Horizon Scientific Press
80. Notredame, C., Higgins, D. G. &Heringa, J. (2000) TCoffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302: 205-217
81. Nylander, J. A. A. (2004) MrAIC.pl. Version 1.4.4. Distributed by the author. URL: Www.abc.se/~nylander/.
82. Ota'lora,M. A. G.,Arago'n, G.,Molina,M. C.,Marti'nez, I. &Lutzoni, F. (2010) Disentangling the Collema-Leptogium complex through amolecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota). Mycologia 102: 279-290
83. Ota'lora, M. A. G., Salvador, C., Marti'nez, I. &Arago'n, G. (2013) Does the reproductive strategy affect the transmission and genetic diversity of bionts in cyanolichens? A case study using two closely related species. Microbial Ecology 65: 517-530
84. Ovstedal, D. O. &Fryday, A. M. (2011) A new species of Protopannaria (Pannariaceae, Ascomycota) from the southern New Zealand shelf islands, and additional records of Protopannaria from South America. Australasian Lichenology 68: 12-15
85. Passo, A., Stenroos, S. &Calvelo, S. (2008) Joergensenia, a new genus to accommodate Psoroma cephalodinum (lichenized Ascomycota). Mycological Research 112: 1465-1474
86. Pupko, T., Huchon, D., Cao, Y., Okada, N. &Hasegawa, M. (2002) Combining multiple data sets in a likelihood analysis: Which models are the best? Molecular Biology and Evolution 19: 2294-2307
87. Rambaut, A. &Drummond, A. J. (2009) Tracer, Version 1.5. University of Edinburgh. URL: Http://tree. bio.ed.ac.uk/software/tracer/.
88. Richardson, D. H. S., Anderson, F., Cameron, R. &Seaward, M. R. D. (2010) World distribution and ecology of Degelia plumbea s. l. British Lichen Society Bulletin 107: 52-62
89. Ronquist, F. &Huelsenbeck, J. P. (2003) MrBayes 3: Bayesian phylogenetic inference undermixedmodels. Bioinformatics 19: 1572-1574
90. Ronquist, F., Teslenko, M., van Der Mark, P., Ayres, D., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A. &Huelsenbeck, J. P. (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542
91. Schoch, C. L., Sung, G.-H., Lo'pez-Gira'ldez, F., Townsend, J. P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P. B., Kauff, F., Wang, Z. et al. (2009) The Ascomycota tree of life: A phylumwide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology 58: 224-239
92. Smith, S. A. &Dunn, C. W. (2008) Phyutility: A phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715-716
93. Spribille, T. &Muggia, L. (2013) Expanded taxon sampling disentangles evolutionary relationships and reveals a new family in Peltigerales (Lecanoromycetidae, Ascomycota). Fungal Diversity 58: 171-184
94. Spribille, T., Jorgensen, P. M., Schulz, M. &Houde, I. (2007) Santessoniella saximontana, a new lichen species from British Columbia. Bibliotheca Lichenologica 96: 287-297
95. Spribille, T., Pe'rez-Ortega, S., Tonsberg, T. &Schirokauer, D. (2010) Lichens and lichenicolous fungi of the Klondike Gold Rush National Historic Park, Alaska, in a global biodiversity context. Bryologist 113: 439-515
96. Suchard, M. A., Kitchen, C. M. R., Sinsheimer, J. S. &Weiss, R. E. (2003) Hierarchical phylogenetic models for analyzing multipartite sequence data. Systematic Biology 52: 649-664
97. Swinscow, T. D. V. &Krog, H. (1988) Macrolichens of East Africa. London: British Museum (Natural History).
98. Tavares, C. N. (1950) Liquenes da Serra do Gereš. Portugalia Acta Biologica, Serie B 3: 1-188
99. Tuckerman, E. (1872) Genera Lichenum: An Arrangement of North American Lichens. Amherst: Edwin Nelson
100. Vainio, E. (1890) Etude sur la classification naturelle et la morphologie des lichens du Bre'sil. Pars I. Acta Societatis pro Fauna et Flora Fennica 7: 1-256
101. Venditti, C., Meade, A. &Pagel, M. (2010) Phylogenies reveal new interpretation of speciation and the Red Queen. Nature 463: 349-352
102. Wedin, M. &Wiklund, E. (2004) The phylogenetic relationships of Lecanorales suborder Peltigerineae revisited. Symbolae Botanicae Upsalienses. 34: 469-475
103. Wedin, M., Jorgensen, P. M. &Wiklund, E. (2007) Massalongiaceae fam. nov., an overlooked monophyletic group among the cyanobacterial lichens (Peltigerales, Lecanoromycetes, Ascomycota). Lichenologist 39: 61-67
104. Wedin, M., Wiklund, E., Jorgensen, P. M. &Ekman, S. (2009) Slippery when wet: Phylogeny and character evolution in the gelatinous cyanobacterial lichens (Peltigerales, Ascomycetes). Molecular Phylogenetics and Evolution 53: 862-871
105. Wedin, M., Jorgensen, P. M. &Ekman, S. (2011) Vahliellaceae, a new family of cyanobacterial lichens (Peltigerales, Ascomycetes). Lichenologist 43: 67-72
106. Yang, Z. (2006) Computational Molecular Evolution. Oxford: Oxford University Press
107. Zahlbruckner, A. (1926) B. Spezieller Teil. In Die Natu &̈rlichen Pflanzenfamilien nebst ihren Gattungen und wichtigeren Arten insbesondere den Nutzpflanzen. Band 8. Flechten (Lichenes). 2nd ed. (A. Engler &K. Prantl, eds): 61-263. Leipzig: Wilhelm Engelmann