Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota)

Molecular Phylogenetics and Evolution

Volumn 63, Issue 2, 2012, Pages 374-387

  Gaya, Ester ^a   Högnabba, Filip ^b   Holguin, Ángela ^c   Molnar, Katalin ^d   Fernández Brime, Samantha ^e   Stenroos, Soili ^b   Arup, Ulf ^f   Søchting, Ulrik ^g   Boom, Pieter Van den ^h   Lücking, Robert ⁱ   Sipman, Harrie J M ^j   Lutzoni, François ^a  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF HELSINKI   (Finland)

^c UNIVERSIDAD DE LOS ANDES   (Colombia)

^d INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^e UNIVERSITY OF BARCELONA   (Spain)

^f LUND UNIVERSITY   (Sweden)

^g UNIVERSITY OF COPENHAGEN   (Denmark)

^h The Field Museum ^*  (Netherlands)

ⁱ FIELD MUSEUM OF NATURAL HISTORY   (United States)

^j FREIE UNIVERSITÄT BERLIN   (Germany)

more..

Author keywords

Bayesian inference; Caliciales; Lichens; Maximum likelihood; Missing data; Supermatrix; Teloschistales

Indexed keywords

ASCOMYCOTA; BRIGANTIAEACEAE; FUNGI; LECANORALES; LECANORINEAE; LETROUITIACEAE; MEGALOSPORACEAE; PELTIGERALES; PEZIZOMYCOTINA; TELOSCHISTACEAE; TELOSCHISTINEAE;

EID: 84858081642     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.01.012     Document Type: Article

References (128)

1. Alfaro M.E., Zoller S., Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of bayesian markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 2003, 20:255-266.
2. Altekar G., Dwarkadas S., Huelsenbeck J.P., Ronquist F. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 2004, 20:407-415.
3. Ané C., Larget B.R., Baum D.A., Smith S.D., Rokas A. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 2007, 24:412-426.
4. Arup U. A new taxonomy of the Caloplaca citrina group in the Nordic countries, except Iceland. Lichenologist 2006, 38:1-20.
5. Arup U. The Caloplaca holocarpa group in the Nordic countries, except Iceland. Lichenologist 2009, 41:111-130.
6. Arup U., Grube M. Where does Lecanora demissa (Ascomycota, Lecanorales) belong?. Lichenologist 1999, 31:419-430.
7. Bellemère A., Letrouit-Galinou M.A. The lecanoralean ascus: an ultrastructural preliminary study. Ascomycete Systematics 1981, 54-70. Springer, New York, Heidelberg, Berlin. D.R. Reynolds (Ed.).
8. Bellemère A., Letrouit-Galinou M.A. Differentiation of lichen asci including dehiscence and sporogenesis: an ultrastructural survey. Progress and Problems in Lichenology in the Eighties 1987, 137-161. J. Cramer, Stuttgart. E. Peveling (Ed.).
9. Brown J.M., Hedtke S.M., Lemmon A.R., Moriarty Lemmon E. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 2010, 59:145-161.
10. Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Muller K.M., Pande N., Shang Z., Yu N., Gutell R.R. The comparative RNA Website (CRW): an online database of comparative sequence and structure information for ribosomal, intron, and other RNA. BMC Bioinform. 2002, 3:2-15.
11. Carlin B.P., Louis T.A. Bayes and Empirical Bayes Methods for Data Analysis 1996, Chapman and Hall, New York.
12. Castoe T.A., Doan T.M., Parkinson C.L. Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards. Syst. Biol. 2004, 53:448-469.
13. Chang J.T. Full reconstruction of Markov models on evolutionary trees: identifyability and consistency. Math. Biosci. 1996, 137:51-73.
14. Ekman S., Blaalid R. 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. Syst. Biol. 2011, 60. 10.1093/sysbio/syr022.
15. Ekman S., Andersen H.L., Wedin M. The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (Lichenized ascomycota). Syst. Biol. 2008, 57:141-156.
16. Eriksson O.E. Notes on ascomycete systematics. Nos. 3912-4298. Myconet 2005, 11:115-170.
17. Fedorenko N.M., Stenroos S., Thell A., Kärnefelt I., Kondratyuk S.Y. A phylogenetic analysis of xanthorioid lichens (Teloschistaceae, Ascomycota) based on ITS and mtSSU sequences. Bibl. Lichen. 2009, 100:49-84.
18. Frödén P., Lassen P. Typification and emendation of Seirophora Poelt to include species segregated from Teloschistes Norman. Lichenologist 2004, 36:289-298.
19. Gardes M., Bruns T.D. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol. Ecol. 1993, 2:113-118.
20. Gargas A., Taylor J.W. Polymerase chain-reaction (PCR) primers for amplifying and sequencing nuclear 18S rDNA from lichenized fungi. Mycologia 1992, 84:589-592.
21. Gaya E., Lutzoni F., Zoller S., Navarro-Rosinés P. Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming ascomycota). Am. J. Bot. 2003, 90:1095-1103.
22. Gaya E., Navarro-Rosinés P., Llimona X., Hladun N., Lutzoni F. Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes). Mycol. Res. 2008, 112:528-546.
23. Gaya E., Redelings B.D., Navarro-Rosines P., Llimona X., De Caceres M., Lutzoni F. Align, or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study. Mycologia 2011, 103:361-378.
24. Gueidan C., Roux C., Lutzoni F. Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Eurotiomycetes, Ascomycota). Mycol. Res. 2007, 111:1145-1168.
25. Gueidan C., Savic 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., Kristinsson H., Krzewicka B., Pykälä J., Grube M., Lutzoni F. Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: recent progress and remaining challenges. Taxon 2009, 58:184-208.
26. Grube M., Arup U. Molecular and morphological evolution in the Physciaceae (Lecanorales, lichenized Ascomycotina), with special emphasis on the genus Rinodina. Lichenologist 2001, 33:63-72.
27. Hafellner J. Monographie der Flechtengattung Letrouitia (Lecanorales, Teloschistineae). Nova Hedwigia 1983, 35:645-729.
28. Hafellner J. Studien in Richtung einer natürlicheren Gliederung der Sammelfamilien Lecanoraceae und Lecideaceae. Beitrage zur Lichenologie. Festschrift J. Poelt. Beih. Nova Hedwigia 1984, 241-372. J. Cramer, Vaduz. H. Hertel, F. Oberwinkler (Eds.).
29. Hafellner J. A world monograph of Brigantiaea (lichenized Ascomycotina, Lecanorales). Lichen Studies Dedicated to Rolf Santesson. Symbolae Botanicae Upsalienses 1997, 35-74. Acta Universitatis Upsaliensis, Uppsala. L. Tibell, I. Hedberg (Eds.).
30. Hafellner J., Bellemère A. Elektronenoptische Untersuchungen an Arten der Flechtengattung Bombyliospora und die taxonomischen Konsequenzen. Nova Hedwigia 1981, 35:207-235.
31. Hafellner J., Bellemère A. Elektronenoptische Untersuchungen an Arten der Flechtengattung Brigantiaea. Nova Hedwigia 1981, 35:237-261.
32. Hafellner J., Bellemère A. Elektronenoptische Untersuchungen an Arten der Flechtengattung Letrouitia gen. nov. Nova Hedwigia 1981, 35:263-312.
33. Helms G., Friedl T., Rambold G. Phylogenetic relationships of the Physciaceae inferred from rDNA sequence data and selected phenotypic characters. Mycologia 2003, 95:1078-1099.
34. Henssen A., Jahns H.M. Lichenes-Eine Einführung in die Flechtenkunde 1974, Georg Thieme Verlag, Stuttgart.
35. 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. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 2007, 111:509-547.
36. Hofstetter V., Miadlikowska J., Kauff F., Lutzoni F. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Mol. Phylogenet. Evol. 2007, 44:412-426.
37. Honegger R. The ascus apex in lichenized fungi I. The Lecanora-, Peltigera- and Teloschistes-types. Lichenologist 1978, 10:47-67.
38. Huelsenbeck J.P., Larget B., Miller R.E., Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 2002, 51:673-688.
39. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
40. James T.Y., Kauff F., Schoch C., Matheny B., Hofstetter V., Cox C.J., Celio G., Guiedan C., Fraker E., Miadlikowska J., Lumbsh T., Rauhut A., Reeb V., Arnold A., Amtoft A., Stajich J.E., Hosaka K., Sung G., Johnson D., O'Rourke B., Crockett M., Binder M., Curtis J.M., Slot J.C., Wang Z., Wilson A.W., Schueller 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 D.M., Diederich P., Schmitt I., Schultz M., Yahr R., Hibbett D.S., Lutzoni F., Mclaughlin D.J., Spatafora J.W., Vilgalys R. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 2006, 443:818-822.
41. Kalb K., Archer A.W., Sutjaritturakan J., Boonpragob K. New or otherwise interesting lichens V. Bibl. Lichen. 2009, 99:225-246.
42. Kärnefelt I. Morphology and phylogeny in the Teloschistales. Cryptogam. Bot. 1989, 1:147-203.
43. Kasalicky T., Döring H., Rambold G., Wedin M. A comparison of ITS and LSU nrDNA phylogenies of Fulgensia (Teloschistaceae, Lecanorales), a genus of lichenised ascomycetes. Can. J. Bot. 2000, 78:1580-1589.
44. Kashiwadani H., Inoue M., Moon K.H., Sasaki K. Lichens of Ozegahara Moor and its adjacent areas, central Japan. Memoir. Natl. Sci. Mus. 2002, 38:71-93.
45. Kauff F., Lutzoni F. Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol. Phylogenet. Evol. 2002, 25:138-156.
46. Kirk M.P., Cannon P.F., Minter D.W., Stalpers J.A. Ainsworth & Bisby's Dictionary of the Fungi 2008, CABI, Wallingford, Oxon, UK.
47. Kjer K.M. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from frogs. Mol. Phylogenet. Evol. 1995, 4:314-330.
48. Kondratyuk S.Y., Kärnefelt I. Revision of three natural groups of xanthorioid lichens (Teloschistaceae, Ascomycota). Ukr. Bot. J. 2003, 60:427-437.
49. Larget B.R., Kotha S.K., Dewey C.N., Ané C. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 2010, 26:2910-2911.
50. Lemmon A.R., Brown J.M., Stanger-Hall K., Moriarty Lemmon E. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 2009, 58:130-145.
51. Lewis P.O., Holder M.T., Holsinger K.E. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 2005, 54:241-253.
52. Lindblom L., Søchting U. Taxonomic revision of Xanthomendoza borealis and Xanthoria mawsonii (Lecanoromycetes, Ascomycota). Lichenologist 2008, 40:399-409.
53. Liu Y.J.J., Whelen S., Benjamin D.H. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol. Biol. Evol. 1999, 16:1799-1808.
54. Outline of ascomycota - 2007. Myconet 2007, 13:1-58.
55. Lumbsch H.T., Huhndorf S.M. Myconet Volume 14. Part One. Outline of Ascomycota - 2009. Part Two. Notes on Ascomycete systematics. Nos. 4751-5113. Fieldiana: Life Earth Sci. 2010, 1:1-64.
56. Lumbsch H.T., Schmitt I., Palice Z., Wiklund E., Ekman S., Wedin M. Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences. Mol. Phylogenet. Evol. 2004, 31:822-832.
57. Lutzoni F., Kauff F., Cox C.J., 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., Hambleton S., Crockett M., Shoemaker R., Sung G.H., Lücking R., Lumbsch 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. Assembling the fungal tree of life: progress, classification and evolution of subcellular traits. Am. J. Bot. 2004, 91:1446-1480.
58. Lutzoni F., Wagner P., Reeb V., Zoller S. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst. Biol. 2000, 49:628-651.
59. Maddison W.P., Maddison D.R. MacClade: Analysis of Phylogeny and Character Evolution 2005, Sinauer Associates, Sunderland, MA.
60. Marbach B. Corticole und lignicole Arten der Flechtengattung Buellia sensu lato in den Subtropen und Tropen. Bibl. Lichen. 2000, 74:1-384.
61. Marshall D.C. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 2010, 59:108-117.
62. Marshall D.C., Simon C., Buckley T.R. Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors. Syst. Biol. 2006, 55:993-1003.
63. Mason-Gamer R.J., Kellogg E.A. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 1996, 45:524-545.
64. Matzer M., Mayrhofer H. Saxicolous species of the genus Rinodina (lichenized Ascomycetes, Physciaceae) in southern Africa. Bothalia 1996, 26:11-30.
65. Mayrhofer H. Ascosporen und die Evolution der Flechtenfamilie Physciaceae. J. Hattori Bot. Lab. 1982, 52:313-321.
66. Mayrhofer H. Die saxicolen Arten der Flechtengattung Rinodina und Rinodinella in der Alten Welt. J. Hattori Bot. Lab. 1984, 55:327-493.
67. McGuire J.A., Witt C.C., Altshuler D.L., Remsen J.V. Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Syst. Biol. 2007, 56:837-856.
68. McKillen Burgess J. The North and Middle American Species of the Lichen Genera Bombyliospora and Lopadium with Anthraquinone Pigments 1963, Department of Botany and Plant Pathology, Michigan State University, East Lansing.
69. 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., May P., Schoch C.L., Arnold A.E., Gueidan C., Tripp E., Yahr R., Robertson C., Lutzoni F. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 2006, 98:1088-1103.
70. Miadlikowska J., Lutzoni F. Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical, and large subunit nuclear ribosomal DNA data. Int. J. Plant Sci. 2000, 161:925-958.
71. Miadlikowska J., Lutzoni F. Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits. Am. J. Bot. 2004, 91:449-464.
72. Muggia L., Grube M., Tretiach M. A combined molecular and morphological approach to species delimitation in black-fruited, endolithic Caloplaca: high genetic and low morphological diversity. Mycol. Res. 2008, 112:36-49.
73. Nordin A. Taxonomy and phylogeny of Buellia species with pluriseptate spores (Lecanorales, Ascomycotina). Acta Univ. Ups. Symb. Bot. Ups. 2000, 33:1-117.
74. Nordin A., Mattsson J.E. Phylogenetic reconstruction of character development in Physciaceae. Lichenologist 2001, 33:3-23.
75. Nylander J.A.A. MrModeltest v2. Program Distributed by the Author 2004, Evolutionary Biology Centre, Uppsala University.
76. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
77. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
78. Persoh D., Beck A., Rambold G. The distribution of ascus types and photobiontal selection in Lecanoromycetes (Ascomycota) against the background of a revised SSU nrDNA phylogeny. Mycol. Prog. 2004, 3:103-121.
79. Poelt J. Classification. Appendix A. The Lichens 1973, 599-632. Academic Press, New York, London. V. Ahmadjian, M.E. Hale (Eds.).
80. Poelt J. Ioplaca gen. nov. Teloschistacearum (Flechten des Himalaya 16). Khumbu Himal - Ergebnisse Forschungsunternehmens Nepal Himalaya 1977, 6:443-446.
81. Poelt J., Hafellner J. Apatoplaca - genus novum Teloschistacearum (Lichenes). Mitt. Bot. Staatssamml. München 1980, 16:503-528.
82. Poelt J., Mayrhofer H. Studien uber Ascosporen-Typen der Flechtengattung Rinodina. Beih. Sydowia 1979, 8:312-331.
83. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. http://www.beast.bio.ed.ac.uk/Tracer.
84. Rambold G., Mayrhofer H., Matzer M. On the ascus types in the Physciaceae (Lecanorales). Plant Syst. Evol. 1994, 192:31-40.
85. Rannala B. Identifiability of parameters in MCMC Bayesian inference of phylogeny. Syst. Biol. 2002, 51:754-760.
86. Reeb V., Lutzoni F., Roux C. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol. Phylogenet. Evol. 2004, 32:1036-1060.
87. Reese Næsborg R., Ekman S., Tibell L. Molecular phylogeny of the genus Lecania (Ramalinaceae, lichenized Ascomycota). Mycol. Res. 2007, 111:581-591.
88. Rehner S.A., Samuels G.J. Taxonomy and phylogeny of Gliocladium analyzed from nuclear large subunit ribosomal DNA-sequences. Mycol. Res. 1994, 98:625-634.
89. Rodriguez F., Oliver J.L., Marin A., Medina J.R. The general stochastic-model of nucleotide substitution. J. Theor. Biol. 1990, 142:485-501.
90. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
91. Santesson J. Anthraquinones in Caloplaca. Phytochemistry 1970, 9:2149-2166.
92. Santesson R. Foliicolous lichens I. A revision of the taxonomy of the obligately foliicolous lichenized fungi. Acta Univ. Ups. Symb. Bot. Ups. 1952, 12:1-590.
93. Scheidegger C., Mayrhofer H., Moberg R., Tehler A. Evolutionary trends in the Physciaceae. Lichenologist 2001, 33:25-45.
94. 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., Büdel 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. The ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst. Biol. 2009, 58:224-239.
95. Sipman H. A monograph of the lichen family Megalosporaceae. Bibl. Lichen. 1983, 18:1-241.
96. Søchting U. Two major anthraquinone chemosyndromes in Teloschistaceae. Bibl. Lichen. 1997, 68:135-144.
97. Søchting U. Chemosyndromes with chlorinated anthraquinones in the lichen genus Caloplaca. Bibl. Lichen. 2001, 78:395-404.
98. Søchting U., Frödén P. Chemosyndromes in the lichen genus Teloschistes (Teloschistaceae, Lecanorales). Mycol. Prog. 2002, 1:257-266.
99. Søchting U., Lutzoni F. Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae). Mycol. Res. 2003, 107:1266-1276.
100. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
101. Steel M. Should phylogenetic models be trying to 'fit an elephant?'. Trends Genet. 2005, 21:307-309.
102. Stiller J.W., Hall B.D. The origin of red algae: implications for plasmid evolution. Proc. Natl. Acad. Sci. USA 1997, 94:4520-4525.
103. Strugnell J., Norman M., Jackson J., Drummond A.J., Cooper A. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol. Phylogenet. Evol. 2005, 37:426-441.
104. * and Other Methods) 2002, Sinauer Associates, Sunderland, Mass.
105. Tibell L. Tholurna dissimilis and generic delimitations in Caliciaceae inferred from nuclear ITS and LSU rDNA phylogenies (Lecanorales, lichenized ascomycetes). Mycol. Res. 2003, 107:1403-1418.
106. Vězda A. Foliicole Flechten aus der Republik Guinea (W. Africa) II. Acta Musei Silesiae 1974, 23:173-190.
107. Vilgalys R., Hester M. Rapid identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 1990, 172:4238-4246.
108. Vobis G. Bau und Entwicklung der Flechten-Pycnidien und ihrer Conidien. Bibl. Lichen. 1980, 14:1-141.
109. Vondrák J., Říha P., Arup U., Søchting U. The taxonomy of the Caloplaca citrina group (Teloschistaceae) in the Black Sea region; with contributions to the cryptic species concept in lichenology. Lichenologist 2009, 41:571-604.
110. Vondrák J., Šoun J., Hrouzek P., Říha P., Kubasek J., Palice Z., Søchting U. Caloplaca subalpina and C. thracopontica, two new saxicolous species from the Caloplaca cerina group (Teloschistales). Lichenologist 2008, 40:375-386.
111. Wedin M., Baloch E., Grube M. Parsimony analyses of mtSSU and nrITS sequences reveal the natural relationships of the lichen families Physciaceae and Caliciaceae. Taxon 2002, 51:655-660.
112. Wedin M., Döring H., Ekman S. Molecular phylogeny of the lichen families Cladoniaceae, Sphaerophoraceae, and Stereocaulaceae (Lecanorales, Ascomycotina). Lichenologist 2000, 32:171-187.
113. Wedin M., Döring H., Nordin A., Tibell L. Small subunit rDNA phylogeny shows the lichen families Caliciaceae and Physciaceae (Lecanorales, Ascomycotina) to form a monophyletic group. Can. J. Bot. 2000, 78:246-254.
114. Wedin M., Grube M. Proposal to conserve the name Physciaceae against Caliciaceae (Lecanorales, Ascomycota). Taxon 2002, 51:802.
115. Wedin M., Wiklund E., Crewe A., Döring H., Ekman S., Nyberg å., Schmitt I., Lumbsch H.T. Phylogenetic relationships of Lecanoromycetes (Ascomycota) as revealed by analyses of mtSSU and nLSU rDNA sequence data. Mycol. Res. 2005, 109:159-172.
116. White T.J., Bruns T.D., Lee S.B., Taylor J.W. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols. A Guide to Methods and Applications 1990, 315-322. Academic Press, New York. M.A. Innis, D.H. Gelfand, J.J. Sninsky, T.J. White (Eds.).
117. Wiens J.J. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 2003, 52:528-538.
118. Wiens J.J. Missing data and the design of phylogenetic analyses. J. Biomed. Inform. 2006, 39:34-42.
119. Wiens J.J., Morrill M.C. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst. Biol. 2010, 60:719-731.
120. Wiklund E., Wedin M. The phylogenetic relationships of the cyanobacterial lichens in the Lecanorales suborder Peltigerineae. Cladistics 2003, 19:419-431.
121. Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: A System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. http://www.ceb.csit.fsu.edu/awty.
122. Zahlbruckner, A., 1898. Lichenes (Flechten). B. Spezieller Teil. In: Engler, A. (Ed.), Syllabus der Pflanzenfamilien, Berlin, p. 46.
123. Zahlbruckner, A., 1907. Lichenes (Flechten). B. Spezieller Teil. In: Engler, A., Prantl, K. (Eds.), Die natürlichen Pflanzenfamilien, Leipzig, pp. 193-249.
124. Zahlbruckner, A., 1926a. Catalogus Lichenum Universalis. Borntraeger, Leipzig.
125. Zahlbruckner A. Lichenes (Flechten). B. Spezieller Teil. Die natürlichen Pflanzenfamilien 1926, 61-270. Verlag von Wilhelm Engelmann, Leipzig. A. Engler, K. Prantl (Eds.).
126. Zharkikh A. Estimation of evolutionary distances between nucleotide-sequences. J. Mol. Evol. 1994, 39:315-329.
127. Zolan M.E., Pukkila P.J. Inheritance of DNA methylation in Coprinus cinereus. Mol. Cell. Biol. 1986, 6:195-200.
128. Zoller S., Lutzoni F., Scheidegger C. Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation. Mol. Ecol. 1999, 8:2049-2059.