The genus Karoowia (Parmeliaceae, Ascomycota) includes unrelated clades nested within Xanthoparmelia

Australian Systematic Botany

Volumn 23, Issue 3, 2010, Pages 173-184

  Amo De Paz, Guillermo ^a   Lumbsch, H Thorsten ^b   Cubas, Paloma ^a   Elix, John A ^c   Crespo, Ana ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

^c AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; CLADISTICS; CLASSIFICATION; CLUSTER ANALYSIS; DATA SET; FUNCTIONAL MORPHOLOGY; GENETIC ANALYSIS; HYPOTHESIS TESTING; LICHEN; PARSIMONY ANALYSIS; PHENOTYPE; TAXONOMY;

ASCOMYCOTA; FUNGI; KAROOWIA; PARMELIACEAE; XANTHOPARMELIA;

EID: 77954713665     PISSN: 10301887     EISSN: None     Source Type: Journal    
DOI: 10.1071/SB09055     Document Type: Article

References (71)

1. Amo de Paz G, Lumbsch HT, Cubas P, Elix JA, Crespo A (2010) The morphologically deviating genera Omphalodiella and Placoparmelia belong to Xanthoparmelia (Parmeliaceae). The Bryologist 113(2), In press.
2. Armaleo D, Clerc P (1991) Lichen chimeras: DNA analysis suggests that one fungus forms two morphotypes. Experimental Mycology 15, 1-10. doi:10.1016/0147-5975(91)90002-U
3. Arup U, Grube M (1998) Molecular systematics of Lecanora subgenus Placodium. Lichenologist 30, 415-425.doi:10.1017/S0024282992000410
4. Arup U, Grube M (2000) Is Rhizoplaca (Lecanorales, Lichenized Ascomycota) a monophyletic genus? Canadian Journal of Botany 78, 318-327. doi:10.1139/cjb-78-318
5. Blanco O, Crespo A, Divakar PK, Esslinger TL, Hawksworth DL, Lumbsch HT (2004a) Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data. Mycological Research 108, 873-884.doi:10.1017/S0953756204000723 (Pubitemid 39218800)
6. Blanco O, Crespo A, Elix JA, Hawksworth DL, Lumbsch HT (2004b) A molecular phylogeny and a new classification of Parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales).Taxon 53, 959-975. doi:10.2307/4135563
7. Blanco O, Crespo A, Divakar PK, Elix JA, Lumbsch HT (2005) Molecular phylogeny of Parmotremoid Lichens (Ascomycota, Parmeliaceae). Mycologia 97, 150-159. doi:10.3852/mycologia.97.1.150
8. Blanco O, Crespo A, Ree RH, Lumbsch HT (2006) Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity. Molecular Phylogenetics and Evolution 39, 52-69. doi:10.1016/j.ympev.2005.12.015
9. Clauzade G, Roux C (1986, "1985") ?Likenoj de okcidenta Europo. Ilustrita determinlibro.? (Bulletin de la Société Botanique du Centre-Ouest, Nouvelle Serie, Numero Special 7. Royan, France). 893 pp.
10. Common RS (1991) The distribution and taxonomic significance of lichenan and isolichenan in the Parmeliaceae (Lichenized Ascomycotina), as determined by iodine reactions. 1. Introduction and Methods, 2. The Genus Alectoria and associated taxa. Mycotaxon 41, 67-112.
11. Common R, Brodo IM (1995) Bryoria sect. subdivergentes recognized as the new genus Nodobryoria (Lichenized Ascomycotina). The Bryologist 98, 189-206. doi:10.2307/3243304
12. Crespo A, CuberoOF(1998)Amolecular approach to the circumscription and evaluation of some genera segregated from Parmelia s. lat. Lichenologist 30, 369-380.
13. Crespo A, Blanco O, Hawksworth DL (2001) The potential of mitochondrial DNA for establishing phylogeny and stabilising generic concepts in the parmelioid lichens. Taxon 50, 807-819. doi:10.2307/1223708
14. Crespo A, Lumbsch HT, Mattsson JE, Blanco O, Divakar PK, Articus K, Wiklund E, Bawingan PA, Wedin M (2007) Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear rpb1 gene. Molecular Phylogenetics and Evolution 44, 812-824. doi:10.1016/j.ympev.2006.11.029 (Pubitemid 47053993)
15. Crespo A, Ferencova Z, Pérez-Ortega S, Argüello A, Elix JA, Divakar PK (2010) Austroparmelina, a new Australasian lineage in parmelioid lichens (Parmeliaceae, Ascomycota): a multigene and morphological approach. Systematics and Biodiversity 8, 209-221.
16. Culberson CF (1972) Improved conditions and new data for the identification of lichen products by a standardized thin-layer chromatographic method. Journal of Chromatography. A 72, 113-125. doi:10.1016/0021-9673(72) 80013-X
17. Culberson CF, Johnson A (1982) Substitution of methyl tert.-butyl ether for diethyl ether in standardized thin-layer chromatographic method for lichen products. Journal of Chromatography. A 238, 483-487. doi:10.1016/S0021-9673(00) 81336-9
18. Culberson CF, Culberson WL, Johnson A (1981) A standardized TLC analysis of b-orcinol depsidones. The Bryologist 84, 16-29. doi:10.2307/3242974
19. Del Prado R, Ferencova Z, Armas-Crespo V, Amo de Paz G, Cubas P, Crespo A (2007) The arachiform vacuolar body: an overlooked shared character in the ascospores of a large monophyletic group within Parmeliaceae (Xanthoparmelia Clade, Lecanorales). Mycological Research 111, 685-692. doi:10.1016/j.mycres. 2007.04.002 (Pubitemid 47077630)
20. Divakar PK, Crespo A, Blanco O, Lumbsch HT (2006) Phylogenetic significance of morphological characters in the tropical Hypotrachyna clade of parmelioid lichens (Parmeliaceae, Ascomycota). Molecular Phylogenetics and Evolution 40, 448-458. doi:10.1016/j.ympev.2006.03.024 (Pubitemid 44038597)
21. Divakar PK, Lumbsch HT, Ferencova Z, Del Prado R, Crespo A (2010) Remototrachyna, a newly recognized tropical lineage of lichens in the hypotrachynoid clade (Parmeliaceae, Ascomycota), originated in the Indian subcontinent. American Journal of Botany 97, 579-590.doi:10.3732/ajb.0900140
22. Edgar RC (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792-1797. doi:10.1093/nar/ gkh340 (Pubitemid 38832724)
23. Elix JA (1993) Progress in the generic delimitation of Parmelia sensu lato lichens (Ascomycotina: Parmeliaceae) and a synoptic key to the Parmeliaceae. The Bryologist 96, 359-383. doi:10.2307/3243867
24. Elix JA (1994) Xanthoparmelia. In ?Flora of Australia. Volume55 Lichens-Lecanorales 2, Parmeliaceae? (Ed. C Grgurinovic) pp. 201-308.(Australian Biological Resouces Study: Canberra)
25. Elix JA (1997) New species and new combinations in the lichen family Parmeliaceae (Ascomycotina) from South Africa. Mycotaxon 63, 335-343.
26. Elix JA (1999) Further new species and new reports in the lichen family Parmeliaceae (Ascomycotina) fromSouthAfrica.Mycotaxon70, 103-110.
27. Elix JA (2000) A new species of Karoowia from Australia. Australasian Lichenology 46, 18-20.
28. Elix JA (2001)ARevision of the lichen genus Paraparmelia ElixJ. Johnst. Bibliotheca Lichenologica 80, 1-224.
29. Elix JA (2003) The lichen genus Paraparmelia, a synonym of Xanthoparmelia (Ascomycota, Parmeliaceae). Mycotaxon 87, 395-403.
30. Eriksson O, Hawksworth DL (1986) Notes on Ascomycete systematics. nos. 1-224. Systema Ascomycetum 5, 113-174.
31. Esslinger TL (1977) A chemosystematic revision of the brown Parmeliae. The Journal of the Hattori Botanical Laboratory 42, 1-211.
32. Feige GB, Lumbsch HT, Huneck S, Elix JA (1993) Identification of lichen substances by a standardized high-performance liquid-chromatographic method. Journal of Chromatography. A 646, 417-427. doi:10.1016/0021-9673(93)83356-W (Pubitemid 23266809)
33. Felsenstein J (1985) Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 39, 783-791. doi:10.2307/2408678
34. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for Basidiomycetes - Application to the identification of mycorrhizae and rusts. Molecular Ecology 2, 113-118. doi:10.1111/j.1365-294X.1993.tb00005.x
35. Gaya E, Lutzoni F, Zoller S, Navarro-Rosines P (2003) Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming Ascomycota). American Journal of Botany 90, 1095-1103. doi:10.3732/ajb.90.7.1095
36. Grube M, Arup U (2001) Molecular and morphological evolution in the Physciaceae (Lecanorales, Lichenized Ascomycotina), with special emphasis on the genus Rinodina. Lichenologist 33, 63-72. doi:10.1006/lich.2000.0297 (Pubitemid 32592740)
37. Grube M, Hawksworth DL (2007) Trouble with lichen: the re-evaluation and re-interpretation of thallus form and fruit body types in the Molecular Era. Mycological Research 111, 1116-1132. doi:10.1016/j.mycres.2007.04.008 (Pubitemid 350110393)
38. Hale ME Jr (1984) An historical review of the genus concept in lichenology. Beiheft zur Nova Hedwigia 79, 11-23.
39. Hale ME (1989) A monograph of the lichen genus Karoowia Hale (Ascomycotina: Parmeliaceae). Mycotaxon 35, 177-198.
40. Hale ME (1990) A synopsis of the lichen genus Xanthoparmelia (Vainio) Hale (Ascomycotina, Parmeliaceae). Smithsonian Contributions to Botany 74, 1-250.
41. Hale BW, DePriest PT (1999)
42. Mason E. Hale?s list of epithets in the parmelioid genera. The Bryologist 102, 462-544. doi:10.2307/3244234
43. Hawksworth DL, Crespo A (2002) Proposal to conserve the name Xanthoparmelia against Chondropsis Nom. Cons. (Parmeliaceae). Taxon 51, 807.doi:10.2307/1555046
44. Högnabba F (2006) Molecular phylogeny of the genus Stereocaulon (Stereocaulaceae, Lichenized Ascomycetes). Mycological Research 110, 1080-1092.doi:10.1016/j.mycres.2006.04.013 (Pubitemid 44389953)
45. Huelsenbeck JP, Ronquist F (2001) MrBayes: bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.doi:10.1093/bioinformatics/17.8. 754
46. James PW, HenssenA(1976) The morphological and taxonomic significance of cephalodia. In ?Lichenology: Progress and Problems?. (EdsDHBrown, DL Hawksworth and RH Bailey) pp. 27-77. (Academic Press: London)
47. Llimona X, HladunNL(2001) Checklist of the lichens and lichenicolous fungi of the Iberian Peninsula and Balearic Islands. Bocconea 14, 1-581.
48. Lohtander K, Myllys L, Sundin R, Källersjö M, Tehler A (1998) The species pair concept in the lichen Dendrographa leucophaea (Arthoniales): analyses based on ITS sequences. The Bryologist 101, 404-411.
49. Lumbsch HT, Hipp AL, Divakar PK, Blanco O, CrespoA(2008) Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota). BMC Evolutionary Biology 8, 257. doi:10.1186/1471-2148-8-257
50. 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 G-H, Lücking R, Lumbsch T, O?Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, 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. American Journal of Botany 91, 1446-1480. doi:10.3732/ajb.91.10.1446
51. Myllys L, Lohtander K, Källersjö M, Tehler A (1999) Sequence insertions and ITS data provide congruent information on Roccella canariensis and R. tuberculata (Arthoniales, Euascomycetes) phylogeny. Molecular Phylogenetics and Evolution 12, 295-309. doi:10.1006/mpev.1999.0620 (Pubitemid 129499309)
52. Nash TH III, Elix JA (2004) Xanthoparmelia. In ?Lichen Flora of the Greater Sonoran Desert Region, Vol. 2?. (EdsTHIII Nash,BDRyan, P Diederich, C Gries, F Bungartz) pp. 566-604. (Lichens Unlimited, Arizona State University: Arizona)
53. Nash TH III, Hafellner J, Common RS (1990) Omphalora, a new genus in the Parmeliaceae. Lichenologist 22, 355-365. doi:10.1017/S002428299000041X
54. Nash TH III, Gries C, Elix JA (1995) A revision of the lichen genus Xanthoparmelia in South America. Bibliotheca Lichenologica 56, 1-158.
55. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology 53, 47-67. doi:10.1080/10635150490264699 (Pubitemid 38370420)
56. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL (2007) AWTY (Are We There Yet?): a system for graphical exploration of mcmc convergence in bayesian phylogenetics. Bioinformatics 24, 581-583. doi:10.1093/bioinformatics/btm388
57. Page RDM (1996) Treeview: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12, 357-358.
58. Parnmen S, Rangsiruji A, Mongkolsuk P, Boonpragob K, Elix JA, Lumbsch HT (2010) Morphological plasticity in Cladoniaceae: the foliose genus Heterodea evolved from fruticose Cladia species (Lecanorales, Ascomycota). Taxon 59, 841-849. Poelt J, Vêzda A (1981) Bestimmungsschl?ssel europäischer Flechten. Ergänzungsheft II. Bibliotheca Lichenologica 16, 1?390
59. Samson RA, Stalpers JA, Verkerke W (1979) A simplified technique to prepare fungal specimens for scanning electron microscopy. Cytobios 24, 7-11.
60. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504. doi:10.1093/bioinformatics/18.3.502
61. Shimodaira H, Hasegawa M (2001) Consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247. doi:10.1093/ bioinformatics/17.12.1246
62. Søchting U, Lutzoni F (2003) Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae). Mycological Research 107, 1266-1276. doi:10.1017/S0953756203008529 (Pubitemid 38231116)
63. Strimmer K, Rambaut A (2002) Inferring confidence sets of possibly misspecified gene trees. Proceedings of the Royal Society of London. Series B. Biological Sciences 269, 137-142. doi:10.1098/rspb.2001.1862 (Pubitemid 34107156)
64. Swofford DL (2002) PAUP*: Phylogenetic Analysis Using Parsimony (and other methods) 4.0 Beta. (Sinauer Associates: Sunderland, MA)
65. Tehler A, Irestedt M (2007) Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota). Cladistics 23, 432-454. doi:10.1111/j.1096-0031.2007.00156.x (Pubitemid 47512277)
66. Thell A, Feuerer T, Kärnefelt I, Myllys L, Stenroos S (2004) Monophyletic groups within the parmeliaceae identified by ITS rDNA, b-tubulin and GAPDH sequences. Mycological Progress 3, 297-314. doi:10.1007/s11557-006- 0100-1
67. Thell A, Feuerer T, Elix JA, Kärnefelt I (2006)Acontribution to the phylogeny and taxonomy of Xanthoparmelia (Ascomycota, Parmeliaceae). The Journal of the Hattori Botanical Laboratory 100, 797-807.
68. Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172, 4238-4246.
69. White TJ, Bruns TD, Lee SB, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In ?PCR Protocols?. (Eds MA Innis, DH Gelfand, JJ Sninsky, TJ White) pp. 315-322. (Academic Press: San Diego, CA)
70. 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.
71. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. The University of Texas, Austin.