Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi

Fungal Diversity

Volumn 50, Issue , 2011, Pages 59-72

  Thorsten Lumbsch, H ^a   Leavitt, Steven D ^a  

^a FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Cryptic species; Lichens; Monophyly of species; Phylogeny; Ribosomal D.N.A.rcoding; Species circumscription; Taxonomy

Indexed keywords

ASCOMYCOTA; FUNGI;

EID: 80755189426     PISSN: 15602745     EISSN: 18789129     Source Type: Journal    
DOI: 10.1007/s13225-011-0123-z     Document Type: Review

References (166)

1. Aptroot A (2001) Lichenized and saprobic fungal biodiversity of a single Elaeocarpus tree in Papua New Guinea, with the report of 200 species of ascomycetes associated with one tree. Fungal Divers 6:1-11 (Pubitemid 33721115)
2. Arguello A, Del Prado R, Cubas P, Crespo A (2007) Parmelina quercina (Parmeliaceae, Lecanorales) includes four phylogenetically supported morphospecies. Biol J Linn Soc 91:455-467 (Pubitemid 47037841)
3. Arnold AE, Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541-549 (Pubitemid 46597060)
4. Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F (2009) A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst Biol 58:283-297
5. Articus K, Mattsson JE, Tibell L, Grube M, Wedin M (2002) Ribosomal DNA and beta-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species. Mycol Res 106:412-418 (Pubitemid 34805337)
6. Baloch E, Grube M (2009) Pronounced genetic diversity in tropical epiphyllous lichen fungi. Mol Ecol 18:2185-2197
7. Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148-155 (Pubitemid 46273824)
8. Blackwell M (2011) The fungi: 1, 2, 3... 5.1 million species? Am J Bot 98:426-438
9. Brodo IM (1978) Changing concepts regarding chemical diversity in lichens. Lichenologist 10:1-11
10. Brodo IM (1986) Interpreting chemical variation in lichens for systematic purposes. Bryologist 89:132-138
11. Brodo IM, Hawksworth DL (1977) Alectoria and allied genera in North America. Opera Bot 42:1-164
12. Burns JM, Janzen DH, Hajibabaei M, Hallwachs W, Hebert PDN (2008) DNA barcodes and cryptic species of skipper butterflies in the genus Perichares in Area de Conservacion Guanacaste, Costa Rica. Proc Natl Acad Sci USA 105:6350-6355 (Pubitemid 351758349)
13. Buschbom J, Barker D (2006) Evolutionary history of vegetative reproduction in Porpidia s. l. (lichen-forming Ascomycota). Syst Biol 55:471-484
14. Buschbom J, Mueller GM (2006) Testing "species pair" hypotheses: evolutionary processes in the lichen-forming species complex Porpidia flavocoerulescens and Porpidia melinodes. Mol Biol Evol 23:574-586 (Pubitemid 43278269)
15. Carstens BC, Dewey TA (2010) Species delimitation using a combined coalescent and information-theoretic approach: an example from North American myotis bats. Syst Biol 59:400-414
16. Chang JC, Hsu MML, Barton RC, Jackson CJ (2008) High-frequency intragenomic heterogeneity of the ribosomal DNA intergenic spacer region in Trichophyton violaceum. Eukaryot Cell 7:721-726 (Pubitemid 351959906)
17. Chantangsi C, Lynn DH, Brandl MT, Cole JC, Hetrick N, Ikonomi P (2007) Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena. Int J Syst Evol Microbiol 57:2412-2425 (Pubitemid 350031724)
18. Crawford AJ, Lips KR, Bermingham E (2010) Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama. Proc Natl Acad Sci USA 107:13777-13782
19. Crespo A, Perez-Ortega S (2009) Cryptic species and species pairs in lichens: A discussion on the relationship between molecular phylogenies and morphological characters. Anales del Jardín Botánico de Madrid 66:71-81
20. Crespo A, Lumbsch HT (2010) Cryptic species in lichen-forming fungi. IMA Fungus 1:167-170
21. Crespo A, Ferencova Z, Perez-Ortega S, Elix JA, Divakar PK (2010a) Austroparmelina, a new Australasian lineage in parmelioid lichens (Parmeliaceae, Ascomycota). Syst Biodiv 8:209-221
22. Crespo A, Kauff F, Divakar PK, del Prado R, Perez-Ortega S, de Paz GA, Ferencova Z, Blanco O, Roca-Valiente B, Nunez-Zapata J, Cubas P, Arguello A, Elix JA, Esslinger TL, Hawksworth DL, Millanes A, Molina MC, Wedin M, Ahti T, Aptroot A, Barreno E, Bungartz F, Calvelo S, Candan M, Cole M, Ertz D, Goffinet B, Lindblom L, Lucking R, Lutzoni F, Mattsson JE, Messuti MI, Miadlikowska J, Piercey-Normore M, Rico VJ, Sipman HJM, Schmitt I, Spribille T, Thell A, Thor G, Upreti DK, Lumbsch HT (2010b) Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence. Taxon 59:1735-1753
23. Cubero OF, Crespo A, Esslinger TL, Lumbsch HT (2004) Molecular phylogeny of the genus Physconia (Ascomycota, Lecanorales) inferred from a Bayesian analysis of nuclear ITS rDNA sequences. Mycol Res 108:498-505 (Pubitemid 38730062)
24. Culberson WL (1969) The use of chemistry in the systematics of the lichens. Taxon 18:152-166
25. Culberson WL (1970) Chemosystematics and ecology of lichenforming fungi. Ann Rev Ecol Syst 1:153-170
26. Culberson WL (1986) Chemistry and sibling speciation in the lichenforming fungi: ecological and biological considerations. Bryologist 89:123-131
27. Culberson CF, Culberson WL (1976) Chemosyndromic variation in lichens. Syst Bot 1:325-339
28. Culberson WL, Culberson CF, Johnson A (1977) Correlations between secondary-product chemistry and ecogeography in the Ramalina siliquosa group (lichens). Pl Syst Evol 127:191-200
29. Culberson WL, Culberson CF, Johnson A (1993) Speciation in lichens of the Ramalina siliquosa complex (Ascomycotina, Ramalinaceae): gene flow and reproductive isolation. Am J Bot 80:1472-1481 (Pubitemid 2029109)
30. Dayrat B (2005) Towards integrative taxonomy. Biol J Linn Soc 85:407-415 (Pubitemid 40962729)
31. Del-Prado R, Cubas P, Lumbsch HT, Divakar PK, Blanco O, de Paz GA, Molina MC, Crespo A (2010) Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation. Mol Phylogen Evol 56:125-133
32. DePriest PT (2004) Early molecular investigations of lichen-forming symbionts: 1986-2001. Ann Rev Microbiol 58:273-301 (Pubitemid 39551988)
33. de Queiroz K (2005) Different species problems and their resolution. Bioessays 27:1263-1269 (Pubitemid 43076169)
34. de Queiroz K (2007) Species concepts and species delimitation. Syst Biol 879-886:879-886 (Pubitemid 350129638)
35. de Sa RO, Heyer WR, Camargo A (2005) Are Leptodactylus didymus and L. mystaceus phylogenetically sibling species (Amphibia, Anura, Leptodactylidae) ? Russ J Herpetol 12:90-92
36. Divakar PK, Blanco O, Hawksworth DL, Crespo A (2005a) Molecular phylogenetic studies on the Parmotrema reticulatum (syn. Rimelia reticulata) complex, including the confirmation of P. pseudoreticulatum as a distinct species. Lichenologist 37:55-65 (Pubitemid 40199107)
37. Divakar PK, Molina MC, Lumbsch HT, Crespo A (2005b) Parmelia barrenoae, a new lichen species related to Parmelia sulcata (Parmeliaceae) based on molecular and morphological data. Lichenologist 37:37-46 (Pubitemid 40199105)
38. Divakar PK, De Paza GA, Del Prado R, Esslinger TL, Crespo A (2007) Upper cortex anatomy corroborates phylogenetic hypothesis in species of Physconia (Ascomycota, Lecanoromycetes). Mycol Res 111:1311-1320 (Pubitemid 350181743)
39. Divakar PK, Figueras G, Hladun NL, Crespo A (2010) Molecular phylogenetic studies reveal an undescribed species within the North American concept of Melanelixia glabra (Parmeliaceae). Fungal Divers 42:47-55
40. Duminil J, Caron H, Scottii I, Cazal S-O, Petit RJ (2006) Blind population genetics survey of tropical rainforest trees. Mol Ecol 15:3505-3513 (Pubitemid 44564264)
41. Egan RS (1986) Correlations and non-correlations of chemical variation patterns with lichen morphology and geography. Bryologist 89:99-110
42. Elix JA (2003) The lichen genus Paraparmelia, a synonym of Xanthoparmelia (Ascomycota, Parmeliaceae). Mycotaxon 87:395-403 (Pubitemid 37181691)
43. Elix JA, Corush J, Lumbsch HT (2009) Triterpene chemosyndromes and subtle morphological characters characterise lineages in the Physcia aipolia group in Australia (Ascomycota). Syst Biodivers 7:479-487
44. Feau N, Decourcelle T, Husson C, Desprez-Loustau ML, Dutech C (2011) Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi. Plos One 6.
45. Feige GB, Lumbsch HT, Schmitz KE (1992) The formation of a central cord in the lichen family Roccellaceae (Opegraphales, Ascomycotina)-anatomical studies on Simonyella variegata. Flora 187:159-167
46. Fenchel T, Finlay BJ (2004) The ubiquity of small species: patterns of local and global diversity. Bioscience 54:777-784 (Pubitemid 39073976)
47. Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296:1061-1063 (Pubitemid 34517112)
48. Fontaneto D, Iakovenko N, Eyres I, Kaya M, Wyman M, Barraclough TG (2011) Cryptic diversity in the genus Adineta Hudson & Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach. Hydrobiologia 662:27-33
49. Frohlich J, Hyde KD (1999) Biodiversity of palm fungi in the tropics: are global fungal diversity estimates realistic? Biodivers Conserv 8:977-1004 (Pubitemid 29404848)
50. Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann Rev Ecol Evol Syst 34:397-423 (Pubitemid 38171425)
51. Gargas A, Depriest PT, Grube M, Tehler A (1995) Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268:1492-1495
52. Geiser DM, Pitt JI, Taylor JW (1998) Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc Natl Acad Sci USA 95:388-393 (Pubitemid 28103963)
53. Goffinet B, Miadlikowska J, Goward T (2003) Phylogenetic inferences based on nrDNA sequences support five morphospecies within the Peltigera didactyla complex (lichenized Ascomycota). Bryologist 106:349-364 (Pubitemid 37105863)
54. Gomez A, Wright PJ, Lunt DH, Cancino JM, Carvalho GR, Hughes RN (2007) Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proc Royal Soc B-Biol Sci 274:199-207 (Pubitemid 47055475)
55. Gowan SP (1986) Evolution of secondary natural products in the genus Porpidia (Ascomycota, Porpidiaceae). Am J Bot 73:606
56. Grube M, Kroken S (2000) Molecular approaches and the concept of species and species complexes in lichenized fungi. Mycol Res 104:1284-1294 (Pubitemid 32102790)
57. Grundt HH, Kjolner S, Borgen L, Rieseberg LH, Brochmann C (2006) High biological species diversity in the arctic flora. Proc Natl Acad Sci USA 103:972-975 (Pubitemid 43212206)
58. Gueidan C, Savic S, Thus H, Roux C, Keller C, Tibell L, Prieto M, Heiomarsson S, Breuss O, Orange A, Froberg L, Wynns AA, Navarro-Rosines P, Krzewicka B, Pykala 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
59. Hale ME (1990) A synopsis of the lichen genus Xanthoparmelia (Vainio) Hale (Ascomycotina, Parmeliaceae). Smiths Contrib Bot 74:1-250
60. Hawksworth DL (1976) Lichen chemotaxonomy. In: Brown DH, Hawksworth DL, Bailey RH (eds) Lichenology: progress and problems. Academic, London, pp 139-184
61. Hawksworth DL (1991) The fungal dimension of biodiversity-magnitude, significance, and conservation. Mycol Res 95:641-655
62. Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422-1432 (Pubitemid 34134581)
63. Hawksworth DL, Rossman AY (1997) Where are all the undescribed fungi? Phytopathology 87:888-891 (Pubitemid 27372571)
64. Hodkinson BP, Lendemer JC (2011) Molecular analyses reveal semicryptic species in Xanthoparmelia tasmanica. Biblioth Lichenol 106:108-119
65. Högnabba F, Wedin M (2003) Molecular phylogeny of the Sphaerophorus globosus species complex. Cladistics 19:224-232 (Pubitemid 38069694)
66. Johnson SB, Waren A, Vrijenhoek RC (2008) DNA barcoding of Lepetodrilus limpets reveals cryptic species. J Shellfish Res 27:43-51 (Pubitemid 351544021)
67. Kasuga T, Taylor JW, White TJ (1999) Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling. J Clin Microbiol 37:653-663 (Pubitemid 29091280)
68. Kirk PM, Cannon PF, David JC, Stalpers J (2008) Ainsworth & Bisby's Dictionary of the fungi, 10th edn. CAB International, Wallingford (Oxon)
69. Knowles LL, Carstens BC (2007) Delimiting species without monophyletic gene trees. Syst Biol 56:887-895 (Pubitemid 350129639)
70. Koufopanou V, Burt A, Szaro T, Taylor JW (2001) Gene genealogies, cryptic species, and molecular evolution in the human pathogen Coccidioides immitis and relatives (Ascomycota, Onygenales). Mol Biol Evol 18:1246-1258 (Pubitemid 32660670)
71. Kroken S, Taylor JW (2001) A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93:38-53 (Pubitemid 34290149)
72. LaGreca S (1999) A phylogenetic evaluation of the Ramalina americana chemotype complex (Lichenized Ascomycota, Ramalinaceae) based on rDNA ITS sequence data. Bryologist 102:602-618 (Pubitemid 30042067)
73. Landvik S, Eriksson OE, Berbee ML (2001) Neolecta-a fungal dinosaur? Evidence from beta-tubulin amino acid sequences. Mycologia 93:1151-1163
74. Lange OL, Redon J (1983) Epiphytic lichens in the region of a Chilean fog oasis (Fray Jorge). 2. Ecophysiological characterization of CO2 exchange and water relations. Flora 174:245-284
75. Lange OL, Green TGA, Melzer B, Meyer A, Zellner H (2006) Water relations and CO2 exchange of the terrestrial lichen Teloschistes capensis in the Namib fog desert: measurements during two seasons in the field and under controlled conditions. Flora 201:268-280 (Pubitemid 43766528)
76. Lange OL, Green TGA, Meyer A, Zellner H (2007) Water relations and carbon dioxide exchange of epiphytic lichens in the Namib fog desert. Flora 202:479-487 (Pubitemid 47126754)
77. Lawrey JD, Diederich P (2003) Lichenicolous fungi: interactions, evolution, and biodiversity. Bryologist 106:80-120
78. Leavitt SD, Johnson L, St Clair LL (2011a) Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America. Am J Bot 98:175-188
79. Leavitt SD, Johnson LA, Goward T, St. Clair LL (2011b) Species delimitation in taxonomically difficult lichen-forming fungi: an example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Mol Phylogen Evol 98:175-188
80. Leavitt SD, Fankhauser JD, Leavitt DH, Porter LD, Johnson LA, St Clair LL (2011c) Complex patterns of speciation in cosmopolitan "rock posy" lichens-Discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Mol Phylogen Evol 59:587-602
81. Lefebure T, Douady CJ, Gouy M, Trontelj P, Briolay J, Gibert J (2006) Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments. Mol Ecol 15:1797-1806 (Pubitemid 43725667)
82. Le Gall L, Saunders GW (2010) DNA barcoding is a powerful tool to uncover algal diversity: a case study of the Phyllophoraceae (Gigartinales, Rhodophyta) in the Canadian flora. J Phycol 46:374-389
83. Leuckert C (1985) Probleme der Flechten-Chemotaxonomie-Stoffkombinationen und ihre taxonomische Wertung. Ber Deutsch Bot Gesell 98:401-408
84. Lohtander K, Kallersjo M, Tehler A (1998a) Dispersal strategies in Roccellina capensis (arthoniales). Lichenologist 30:341-350 (Pubitemid 28478401)
85. Lohtander K, Myllys L, Sundin R, Kallersjo M, Tehler A (1998b) The species pair concept in the lichen Dendrographa leucophaea (Arthoniales): analyses based on ITS sequences. Bryologist 101:404-411 (Pubitemid 28460973)
86. Lücking R, del Prado R, Lumbsch HT, Will-Wolf S, Aptroot A, Sipman HJM, Umana L, Chaves JL (2008) Phytogenetic patterns of morphological and chemical characters and reproductive mode in the Heterodermia obscurata group in Costa Rica (Ascomycota, Physciaceae). Syst Biodivers 6:31-41 (Pubitemid 351281008)
87. Lumbsch HT (1994) Die Lecanora subfusca-Gruppe in Australasien. J Hattori Bot Lab 77:1-175
88. Lumbsch HT (1998a) Taxonomic use of metabolic data in lichenforming fungi. In: Frisvad JC, Bridge PD, Arora DK (eds) Chemical fungal taxonomy. Marcel Dekker, Inc., New York, pp 345-387
89. Lumbsch HT (1998b) The use of metabolic data in lichenology at the species and subspecific levels. Lichenologist 30:357-367 (Pubitemid 28482173)
90. Lumbsch HT (2006) Recent trends in phylogeny and classification of lichen-forming ascomycetes. In: Ganguli BN, Deshmukh SK (eds) Fungi. Multifaceted microbes. Anamaya Publishers, New Delhi, pp 153-168
91. Lumbsch HT, Huhndorf SM (2007) Whatever happened to the pyrenomycetes and loculoascomycetes? Mycol Res 111:1064-1074 (Pubitemid 350103820)
92. Lumbsch HT, Huhndorf SM (2010) Myconet volume 14 outline of ascomycota-2009 notes on ascomycete systematics. Nos. 4751-5113. Fieldiana-Life Earth Sci 1:1-64
93. Lumbsch HT, Mangold A, Martin MP, Elix JA (2008) Species recognition and phylogeny of Thelotrema species in Australia (Ostropales, Ascomycota). Aust Syst Bot 21:217-227
94. Lumbsch HT, Ahti T, Altermann S, Amo de Paz G, Aptroot A, Arup U, Barcenas Peña A, Bawingan PA, Benatti MN, Betancourt L, Björk CR, Boonpragob K, Brand M, Bungartz F, Caceres MES, Candan M, Chaves JL, Clerc P, Common R, Coppins BJ, Crespo A, Dal Forno M, Divakar PK, Duya MV, Elix JA, Elvebakk A, Fankhauser J, Farkas E, Ferraro LI, Fischer E, Galloway DJ, Gaya E, Giralt M, Goward T, Grube M, Hafellner J, Hernandez JE, Herrera Campos MA, Kalb K, Kärnefelt I, Kantvilas G, Killmann D, Kirika P, Knudesn K, Komposch H, Kondratyuk S, Lawrey JD, Mangold A, Marcelli MP, McCune B, Michlig A, Miranda Gonzalez R, Moncada B, Naikatini A, Nelsen MP, Øvstedal DO, Palice Z, Papong K, Parnmen S, Pérez-Ortega S, Printzen C, Rico VJ, Rivas Plata E, Robayo J, Rosabal D, Ruprecht U, Salazar Allen N, Sancho L, Santos de Jesus L, Santos Vieira T, Schultz M, Seaward MRD, Sérusiaux E, Schmitt I, Sipman HJM, Sohrabi M, Søchting U, Søgaard MZ, Sparrius LB, Spielmann A, Spribille T, Sutjaritturakan J, Thammathaworn A, Thell A, Thor G, Thüs H, Timdal E, Truong C, Türk R, Umaña Tenorio L, Upreti DK, van den Boom P, Vivas Rebuelta M, Wedin M, Will-Wolf S, Wirth V, Wirtz N, Yahr R, Yeshitela K, Ziemmeck F, Wheeler T, Lücking R (2011) One hundred new species of lichenized fungi: a signature of undiscovered global diversity. Phytotaxa 18:1-127
95. Lutzoni F, Pagel M, Reeb V (2001) Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411:937-940 (Pubitemid 32601487)
96. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung GH, Lucking R, Lumbsch T, O'Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim YW, 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. Am J Bot 91:1446-1480 (Pubitemid 43193713)
97. Mattsson JE, Lumbsch HT (1989) The use of the species pair concept in lichen taxonomy. Taxon 38:238-241
98. Mayr E (1942) Systematics and the origin of species: From the viewpoint of a zoologist. Columbia University Press, New York
99. Mayr E (1963) Animal species and evolution. Harvard University Press, Cambridge
100. McCune B, Schoch C (2009) Hypogymnia minilobata (Parmeliaceae), a new lichen from coastal California. Bryologist 112:94-100
101. McDonald T, Miadlikowska J, Lutzoni F (2003) The lichen genus Sticta in the Great Smoky Mountains: a phylogenetic study of morphological, chemical, and molecular data. Bryologist 106:61-79 (Pubitemid 36391904)
102. Miralles A, Vasconcelos R, Perera A, Harris DJ, Carranza S (2011) An integrative taxonomic revision of the Cape Verdean skinks (Squamata, Scincidae). Zoolog Scripta 40:16-44
103. Molina MD, Crespo A, Blanco O, Hladun N, Hawksworth DL (2002) Molecular phylogeny and status of Diploicia and Diplotomma, with observations on Diploicia subcanescens and Diplotomma rivas-martinezii. Lichenologist 34:509-519 (Pubitemid 38231494)
104. Molina MD, Crespo A, Blanco O, Lumbsch HT, Hawksworth DL (2004) Phylogenetic relationships and species concepts in Parmelia s.str. (Parmeliaceae) inferred from nuclear ITS rDNA and beta-tubulin sequences. Lichenologist 36:37-54 (Pubitemid 38610640)
105. Monaghan MT, Wild R, Elliot M, Fujisawa T, Balke M, Inward DJ, Lees DC, Ranaivosolo R, Eggleton P, Barraclough TG, Vogler AP (2009) Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Syst Biol 58:298-311
106. Moura CJ, Harris DJ, Cunha MR, Rogers AD (2008) DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments. Zoolog Scripta 37:93-108
107. Muggia L, Grube M, Tretiach M (2008) A combined molecular and morphological approach to species delimitation in black-fruited, endolithic Caloplaca: high genetic and low morphological diversity. Mycol Res 112:36-49
108. Myllys L, Lohtander K, Kallersjo M, Tehler A (1999) Sequence insertions and ITS data provide congruent information on Roccella canariensis and R. tuberculata (Arthoniales, Euascomycetes) phylogeny. Mol Phylogen Evol 12:295-309 (Pubitemid 129499309)
109. Myllys L, Lohtander K, Tehler A (2001) Beta-tubulin, ITS and group I intron sequences challenge the species pair concept in Physcia aipolia and P. caesia. Mycologia 93:335-343
110. Nash TH (2008) Lichen biology, 2nd edn. Cambridge University Press, Cambridge
111. Nelsen MP, Gargas A (2009) Assessing clonality and chemotype monophyly in Thamnolia (Icmadophilaceae). Bryologist 112:42-53
112. Nevo E (2001) Evolution of genome-phenome diversity under environmental stress. Proc Natl Acad Sci USA 98:6233-6240 (Pubitemid 32488222)
113. Nylander W (1866a) Circa novum in studio Lichenum criterium chemicum. Flora 49:198-201
114. Nylander W (1866b) Hypochlorite of lime and hydrate of potash. Two new criteria in the study of lichens. Translated and communicated by the Rev. W. A. Leighton. J Linn Soc Bot 9:358-365
115. O'Brien HE, Miadlikowska J, Lutzoni F (2009) Assessing reproductive isolation in highly diverse communities of the lichenforming fungal genus Peltigera. Evolution 63:2076-2086
116. O'Donnell K, Cigelnik E (1997) Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol Phylogen Evol 7:103-116 (Pubitemid 127347168)
117. Opanowicz M, Blaha J, Grube M (2006) Detection of paralogous polyketide synthase genes in Parmeliaceae by specific primers. Lichenologist 38:47-54 (Pubitemid 41816360)
118. Otalora MAG, Martinez I, Aragon G, Molina MC (2010) Phylogeography and divergence date estimates of a lichen species complex with a disjunct distribution pattern. Am J Bot 97:216-223
119. Ott S, Lumbsch HT (2001) Morphology and Phylogeny of ascomycete lichens. In: Hock B (ed) Fungal Associations. A comprehensive treatise on fungi as experimental systems for basic and applied research, vol IX, The Mycota. Springer, Berlin, pp 189-210
120. Ott S, Brinkmann M, Wirtz N, Lumbsch HT (2004) Mitochondrial and nuclear ribosomal DNA data do not support the separation of the Antarctic lichens Umbilicaria kappenii and Umbilicaria antarctica as distinct species. Lichenologist 36:227-234 (Pubitemid 39027110)
121. Papke RT, Ramsing NB, Bateson MM, Ward DM (2003) Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5:650-659 (Pubitemid 36953526)
122. Parnmen S (2011) Molecular evolution and species delimitation of lichens in the genus Cladia (Lecanorales, Ascomycota). Srinakharinwirot University, Bangkok
123. Pfenninger M, Schwenk K (2007) Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evol Biol 7.
124. Poelt J (1972) Die taxonomische Behandlung von Artenpaaren bei den Flechten. Bot Not 125:77-81
125. Poelt J (1983) Musterbeispiele analoger Lagerdifferenzierung bei Flechten: Almbornia, Speerschneidera, Seirophora gen. nov. Flora 174:439-445
126. Poelt J (1992) Lichenologie und Lichenologen in Bayern eine Reverenz vor den Amateuren. Hoppea 50:527-536
127. Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP (2006) Sequencebased species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595-609
128. Printzen C (2010) Lichen Systematics: the role of morphological and molecular data to reconstruct phylogenetic relationships. In: Lüttge U (ed) Progress in botany, vol 71. Springer, Berlin, pp 233-275
129. Printzen C, Ekman S (2002) Genetic variability and its geographical distribution in the widely disjunct Cavernularia hultenii. Lichenologist 34:101-111
130. Printzen C, Ekman S, Tonsberg T (2003) Phylogeography of Cavernularia hultenii: evidence of slow genetic drift in a widely disjunct lichen. Mol Ecol 12:1473-1486 (Pubitemid 36708454)
131. Ray J (1686) Historia plantarum, vol 1. Clark, London
132. Rogers RW (1989) Chemical variation and the species concept in lichenized ascomycetes. Bot J Linn Soc 101:229-239
133. Rooney AP, Ward TJ (2005) Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth and death of a concerted evolution paradigm. Proc Natl Acad Sci USA 102:5084-5089
134. Ruiz-Sanchez E, Sosa V (2010) Delimiting species boundaries within the Neotropical bamboo Otatea (Poaceae: Bambusoideae) using molecular, morphological and ecological data. Mol Phylogen Evol 54:344-356
135. Ruprecht U, Lumbsch HT, Brunauer G, Green TGA, Turk R (2010) Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological characters. Ant Sci 22:727-741
136. Saunders GW (2008) A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea-Neodilsea complex and Weeksia. Botany 86:773-789 (Pubitemid 352018907)
137. Schmit JP, Mueller GM (2007) An estimate of the lower limit of global fungal diversity. Biodivers Conserv 16:99-111
138. Schmitt I, Lumbsch HT (2009) Ancient horizontal gene transfer from bacteria enhances biosynthetic capabilities of fungi. Plos One 4.
139. Schmitt I, Mueller G, Lumbsch HT (2005) Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens. Mycologia 97:362-374 (Pubitemid 40938806)
140. Schmitt I, del Prado R, Grube M, Lumbsch HT (2009) Repeated evolution of closed fruiting bodies is linked to ascoma development in the largest group of lichenized fungi (Lecanoromycetes, Ascomycota). Mol Phylogen Evol 52:34-44
141. Schoch CL, Sung GH, Lopez-Giraldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou M, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lucking R, Budel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW (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
142. Schröngge K, Barr B, Wardlaw JC, Napper E, Gardner MG, Breen J, Elmes GW, Thomas JA (2002) When rare species become endangered: cryptic speciation in myrmecophilous hoverflies. Biol J Linn Soc 75:291-300
143. Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Resour 9:83-89
144. Seifert KA, Samson RA, Dewaard JR, Houbraken J, Levesque CA, Moncalvo JM, Louis-Seize G, Hebert PDN (2007) Prospects for fungus identification using C01 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci USA 104:3901-3906 (Pubitemid 47181551)
145. Seymour FA, Crittenden PD, Wirtz N, Ovstedal DO, Dyer PS, Lumbsch HT (2007) Phylogenetic and morphological analysis of Antarctic lichenforming Usnea species in the group Neuropogon. Ant Sci 19:71-82 (Pubitemid 46662193)
146. Simon UK, Weiss M (2008) Intragenomic variation of fungal ribosomal genes is higher than previously thought. Mol Biol Evol 25:2251-2254
147. Simon DM, Hummel CL, Sheeley SL, Bhattacharya D (2005) Heterogeneity of intron presence or absence in rDNA genes of the lichen species Physcia aipolia and P. stellaris. Curr Genet 47:389-399 (Pubitemid 40909177)
148. Sipman HJM, Aptroot A (2001) Where are the missing lichens? Mycol Res 105:1433-1439 (Pubitemid 34137588)
149. Sites J, Marshall J (2004) Operational criteria for delimiting species. Annu Rev Ecol Evol Syst 35:199-227 (Pubitemid 40059719)
150. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21-32 (Pubitemid 32066164)
151. Tehler A (1982) The species pair concept in lichenology. Taxon 31:708-714
152. Tehler A, Kallersjo M (2001) Parmeliopsis ambigua and P. hyperopta (Parmeliaceae): species or chemotypes? Lichenologist 33:403-408 (Pubitemid 32996881)
153. Templeton AR (2001) Using phylogeographic analyses of gene trees to test species status and processes. Mol Ecol 10:779-791 (Pubitemid 32406360)
154. Thell A, Elix JA, Sochting U (2009) Xanthoparmelia lineola s.l. in Australia and North America. Biblioth Lichenol 99:393-404
155. Velmala S, Myllys L, Halonen P, Goward T, Ahti T (2009) Molecular data show that Bryoria fremontii and B. tortuosa (Parmeliaceae) are conspecific. Lichenologist 41:231-242
156. Vieites DR, Wollenberg KC, Andreone F, Köhler J, Glaw F, Vences M (2009) Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory. Proc Natl Acad Sci USA 106:8267-8272
157. Vondrak J, Riha P, Arup U, Sochting U (2009) The taxonomy of the Caloplaca citrina group (Teloschistaceae) in the Black Sea region; with contributions to the cryptic species concept in lichenology. Lichenologist 41:571-604
158. Vrijenhoek RC (2009) Cryptic species, phenotypic plasticity, and complex life histories: Assessing deep-sea faunal diversity with molecular markers. Deep-Sea Res Part Ii-Top Stud Oceanogr 56:1713-1723
159. Vrijenhoek RC, Schutz SJ, Gustafson RG, Lutz RA (1994) Cryptic species of deep-sea clams (Mollusca, Bivalvia, Vesicomyidae) from hydrothermal vent and cold-water seep environments. Deep-Sea Res Part I-Oceanogr Res Pap 41:1171-1189
160. Wang HY, Lumbsch HT, Guo SY, Huang MR, Wei JC (2010) Ascomycetes have faster evolutionary rates and larger species diversity than basidiomycetes.
161. Wedin M, Westberg M, Crewe AT, Tehler A, Purvis OW (2009) Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (Ascomycota, Fungi) complex. Cladistics 25:161-172
162. Weisse T (2006) Biodiversity of freshwater microorganisms-Achievements, problems, and perspectives. Pol J Ecol 54:633-652 (Pubitemid 46219321)
163. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976-978 (Pubitemid 36994812)
164. Wirtz N, Printzen C, Lumbsch HT (2008) The delimitation of Antarctic and bipolar species of neuropogonoid Usnea (Ascomycota, Lecanorales): a cohesion approach of species recognition for the Usnea perpusilla complex. Mycol Res 112:472-484
165. Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci USA 107:9264-9269
166. Zemlak TS, Ward RD, Connell AD, Holmes BH, Hebert PDN (2009) DNA barcoding reveals overlooked marine fishes. Mol Ecol Res 9:237-242