Transoceanic dispersal and subsequent diversification on separate continents shaped diversity of the Xanthoparmelia pulla group (Ascomycota)

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

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

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^c FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASCOMYCETES; BIOSYNTHESIS; CONTROLLED STUDY; DNA SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; MOLECULAR EVOLUTION; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; PLESIOMORPHY; POPULATION DISTRIBUTION; SPECIES DIFFERENCE; XANTHOPARMELIA ATROVIRIDIS; XANTHOPARMELIA CALIGINOSA; XANTHOPARMELIA DELISEI; XANTHOPARMELIA FISSURINA; XANTHOPARMELIA GLABRANS; XANTHOPARMELIA IMITATRIX; XANTHOPARMELIA LINEELA; XANTHOPARMELIA LOXODES; XANTHOPARMELIA LUTEONOTATA; XANTHOPARMELIA PERRUGATA; XANTHOPARMELIA POKORNYI; XANTHOPARMELIA PSEUDOGLABRANS; XANTHOPARMELIA PULLA; XANTHOPARMELIA PULLOIDES; XANTHOPARMELIA QUINTARIOIDES; XANTHOPARMELIA RYSSOLEA; XANTHOPARMELIA SQUAMANS; XANTHOPARMELIA SUBHOSSEANA; XANTHOPARMELIA SUBIMITATRIX; XANTHOPARMELIA SUBINCERTA; XANTHOPARMELIA SUBPROLIXA; XANTHOPARMELIA TORULOSA; XANTHOPARMELIA VERISIDIOSA; XANTHOPARMELIA VERRUCELLA; XANTHOPARMELIA VERRUCULIFERA;

ASCOMYCOTA; AUSTRALIA; BIOLOGICAL EVOLUTION; PHYLOGENY; SOUTH AFRICA;

EID: 84862693239     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039683     Document Type: Article

References (88)

1. Wiens JJ, Penkrot TA, (2002) Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology 51: 69-91.
2. Cracraft J, (1983) Species concepts and speciation analysis. Current Ornithology 1: 159-187.
3. Mayr E, (1963) Animal species and evolution. Cambridge, MA: Harvard University Press.
4. Arguello A, Del Prado R, Cubas P, Crespo A, (2007) Parmelina quercina (Parmeliaceae, Lecanorales) includes four phylogenetically supported morphospecies. Biological Journal of the Linnean Society 91: 455-467.
5. Leavitt SD, Fankhauser JD, Leavitt DH, Porter LD, Johnson LA, et al. (2011) 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). Molecular Phylogenetics and Evolution 59: 587-602.
6. Leavitt SD, Johnson L, St Clair LL, (2011) Species delimitation and evolution in morphologially and chmically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America. American Journal of Botany 98: 175-188.
7. Leavitt SD, Johnson LA, Goward T, St Clair LL, (2011) Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Molecular Phylogenetics and Evolution 60: 317-332.
8. Lumbsch HT, Leavitt SD, (2011) Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi Fungal Diversity 50: 59-72.
9. Elix JA, Corush J, Lumbsch HT, (2009) Triterpene chemosyndromes and subtle morphological characters characterise lineages in the Physcia aipolia group in Australia (Ascomycota). Systematics and Biodiversity 7: 479-487.
10. 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. Mycological Research 112: 472-484.
11. 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. Mycological Research 108: 498-505.
12. 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.
13. Crespo A, Molina MC, Blanco O, Schroeter B, Sancho LG, et al. (2002) rDNA ITS and beta-tubulin gene sequence analyses reveal two monophyletic groups within the cosmopolitan lichen Parmelia saxatilis. Mycological Research 106: 788-795.
14. 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 Diversity 42: 47-55.
15. Hodkinson BP, Lendemer JC, (2011) Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica 106: 108-119.
16. Thell A, Elix JA, Søchting U, (2009) Xanthoparmelia lineola s. l. in Australia and North America. Bibliotheca Lichenologica 99: 393-404.
17. 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.
18. Otálora MAG, Martínez I, Aragón G, Molina MC, (2010) Phylogeography and divergence date estimates of a lichen species complex with a disjunct distribution pattern. American Journal of Botany 97: 216-223.
19. Otalora MAG, Martinez I, Molina MC, Aragon G, Lutzoni F, (2008) Phylogenetic relationships and taxonomy of the Leptogium lichenoides group (Collemataceae, Ascomycota) in Europe. Taxon 57: 907-921.
20. Sérusiaux E, Villarreal A JC, Wheeler T, Goffinet B, (2011) Recent origin, active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia. Journal of Biogeography: no-no.
21. 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.
22. Kroken S, Taylor JW, (2001) A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93: 38-53.
23. Crespo A, Lumbsch HT, (2010) Cryptic species in lichen-forming fungi. IMA Fungus 1: 167-170.
24. Divakar PK, Blanco O, Hawksworth DL, Crespo A, (2005) 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.
25. Baloch E, Grube M, (2009) Pronounced genetic diversity in tropical epiphyllous lichen fungi. Molecular Ecology 18: 2185-2197.
26. Högnabba F, Wedin M, (2003) Molecular phylogeny of the Sphaerophorus globosus species complex. Cladistics 19: 224-232.
27. Fenchel T, Finlay BJ, (2004) The ubiquity of small species: Patterns of local and global diversity. Bioscience 54: 777-784.
28. Finlay BJ, (2002) Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063.
29. Lumbsch HT, Buchanan PK, May TW, Mueller GM, (2008) Phylogeography and biogeography of fungi. Mycological Research 112: 423-424.
30. Crespo A, Lumbsch HT, Mattsson JE, Blanco O, Divakar PK, et al. (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.
31. Hale BW, DePriest PT, (1999) Mason E. Hale's list of epithets in the parmelioid genera. Bryologist 102: 462-544.
32. Crespo A, Kauff F, Divakar PK, Amo G, Arguello A, et al. (2010) Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence. Taxon 59: 1735-1753.
33. Blanco O, Crespo A, Elix JA, Hawksworth DL, Lumbsch HT, (2004) A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales). Taxon 53: 959-975.
34. Del Prado R, Ferencova Z, Armas-Crespo V, De Paz GA, Cubas P, et al. (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.
35. Blanco O, Crespo A, Ree RH, Lumbsch HT, (2006) Major clades of parmeliold lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity. Molecular Phylogenetics and Evolution 39: 52-69.
36. Lumbsch HT, Hipp AL, Divakar PK, Blanco O, Crespo A, (2008) Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota). BMC Evolutionary Biology 8.
37. Esslinger TL, (1978) A new status for the brown Parmeliae. Mycotaxon 7: 45-54.
38. Esslinger TL, (2000) Notes on the brown-colored species of Parmeliaceae (lichenized Ascomycota) in southern Africa. Bryologist 103: 568-591.
39. Elix JA, (2003) The lichen genus Paraparmelia, a synonym of Xanthoparmelia (Ascomycota, Parmeliaceae). Mycotaxon 87: 395-403.
40. 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: 376-386.
41. Amo de Paz G, Lumbsch HT, Cubas P, Elix JA, Crespo A, (2010) The genus Karoowia (Parmeliaceae, Ascomycota) includes unrelated clades nested within Xanthoparmelia. Australian Systematic Botany 23: 173-184.
42. Thell A, Feuerer T, Elix JA, Kärnefelt I, (2006) A contribution to the phylogeny and taxonomy of Xanthoparmelia (Ascomycota, Parmeliaceae). Journal of the Hattori Botanical Laboratory 100: 797-807.
43. Hawksworth DL, Crespo A, (2002) Proposal to conserve the name Xanthoparmelia against Chondropsis nom. cons. (Parmeliaceae). Taxon 51: 807.
44. Esslinger TL, (1977) A chemosystematic revision of the brown Parmeliae. Jour Hattori Bot Lab 42: 1-211.
45. 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.
46. Culberson CF, Culberson WL, Esslinger TL, (1977) Chemosyndromic variation in the Parmelia pulla group. Bryologist 80: 125-135.
47. Elix JA, (2002) Chemical variations of the lichen Neofuscelia pulla (Ascomycotina: Parmeliaceae) sensu Esslinger. Australasian Lichenology 51: 7-9.
48. Elix JA, Corush J, Lumbsch HT, (2009) Triterpene chemosyndromes and subtle morphological characters characterise lineages in the Physcia aipolia group in Australia (Ascomycota). Systematics and Biodiversity 7: 479-487.
49. Richardson JE, Weitz FM, Fay MF, Cronk QCB, Linder HP, et al. (2001) Rapid and recent origin of species richness in the Cape flora of South Africa. Nature 412: 181-183.
50. Lumbsch HT, Schmitt I, Barker D, Pagel M, (2006) Evolution of micromorphological and chemical characters in the lichen-forming fungal family Pertusariaceae. Biological Journal of the Linnean Society 89: 615-626.
51. Schmitt I, Lumbsch HT, (2004) Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes. Molecular Phylogenetics and Evolution 33: 43-55.
52. Lumbsch HT, Schmitt I, (2002) Molecular data shake the Pertusariaceae tree into order. Lichenology 1: 37-43.
53. Sanmartin I, Ronquist F, (2004) Southern Hemisphere biogeography inferred by event-based models: Plant versus animal patterns. Systematic Biology 53: 216-243.
54. Sanmartin I, Wanntorp L, Winkworth RC, (2007) West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting. Journal of Biogeography 34: 398-416.
55. Leavitt SD, Johnson L, St Clair LL, (2011) Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America. American Journal of Botany 98: 175-188.
56. Leavitt SD, Johnson LA, Goward T, St. Clair LL, (2011) Species delimitation in taxonomically difficult lichen-forming fungi: an example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Molecular Phylogenetics and Evolution in press: xx-xx.
57. Wirtz N, Printzen C, Lumbsch HT, (2012) Using haplotype networks, estimation of gene flow and phenotypic characters to understand species delimitation in fungi of a predominantly Antarctic Usnea group (Ascomycota, Parmeliaceae). Organisms Diversity & Evolution 12: 17-37.
58. Rivas Plata E, Lumbsch HT, (2011) Parallel evolution and phenotypic divergence in lichenized fungi: a case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales). Molecular Phylogenetics and Evolution 61: 45-63.
59. Elix JA, (1999) New species of Neofuscelia (Lichenized Ascomycotina, Parmeliaceae) from the Southern Hemisphere. Mycotaxon 71: 431-456.
60. Elix JA, (1994) Neofuscelia. Flora of Australia 55: 68-85.
61. Culberson CF, (1972) Improved conditions and new data for the identification of lichen products by a standardized thin-layer chromatographic method. Journal of Chromatography 72: 113-125.
62. Culberson CF, Culberson WL, Johnson A, (1981) A standardized TLC analysis of ß-orcinol depsidones. Bryologist 84: 16-29.
63. 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 238: 438-487.
64. Orange A, James PW, White FJ, (2001) Microchemical Methods for the Identification of Lichens: British Lichen Society. 101 p.
65. Feige GB, Lumbsch HT, Huneck S, Elix JA, (1993) Identification of lichen substance by a standardized high-performance liquid-chromatographic method. Journal of Chromatography 646: 417-427.
66. 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.
67. 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.
68. Lohtander K, Myllys L, Sundin R, Kallersjo M, Tehler A, (1998) The species pair concept in the lichen Dendrographa leucophaea (Arthoniales): Analyses based on ITS sequences. Bryologist 101: 404-411.
69. 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.
70. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
71. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
72. Posada D, (2008) jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
73. Zwickl DJ, (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Austin: The University of Texas at Austin.
74. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
75. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL, (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology 53: 47-67.
76. 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.
77. Page RDM, (1996) Treeview: an application to display phylogenetic trees on personal computers. Computer Applied Biosciences 12: 357-358.
78. Amo de Paz G, Cubas P, Divakar PK, Lumbsch HT, Crespo A, (2011) Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota) during the Paleogene inferred by Bayesian analysis. Plos One 6.
79. Pybus OG, Harvey PH, (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society of London Series B-Biological Sciences 267: 2267-2272.
80. Drummond AJ, Rambaut A, (2007) Beast: Bayesian evoluionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
81. Rambaut A, (2007) TreeEdit v.1.0a10. http://tree.bio.ed.ac.uk/software/treeedit/.
82. Poinar GO Jr, Peterson EB, Platt JL, (2000) Fossil Parmelia in new world amber. Lichenologist 32: 263-269.
83. Rambaut A, Drummond AJ, (2007) Tracer v1.4, Available from http://beast.bio.ed.ac.uk/Tracer.
84. Rambaut A, (2009) FigTree 1.2.2. http://tree.bio.ed.ac.uk/software/figtree/.
85. Huelsenbeck JP, Bollback JP, (2001) Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology 50: 351-366.
86. Bollback JP, (2006) SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7.
87. Lopez-Vaamonde C, Wikstrom N, Kjer KM, Weiblen GD, Rasplus JY, et al. (2009) Molecular dating and biogeography of fig-pollinating wasps. Molecular Phylogenetics and Evolution 52: 715-726.
88. Ree RH, Smith SA, (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 4-14.