Origin and diversification of major clades in parmelioid lichens (parmeliaceae, ascomycota) during the paleogene inferred by bayesian analysis

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Amo de Paz, Guillermo ^a   Cubas, Paloma ^a   Divakar, Pradeep K ^a   Lumbsch, H Thorsten ^b   Crespo, Ana ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA;

AFRICA; ALECTORIA; ARTICLE; ASCOMYCETES; AUSTRALIA; BAYES THEOREM; BIOGENESIS; BIOGEOGRAPHY; CALIBRATION; CLADISTICS; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; EOCENE; FOSSIL; FUNGAL GENE; GENETIC VARIABILITY; LECANOROMYCETES; MIOCENE; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NEOTROPICS; NONHUMAN; OLIGOCENE; PALEOCLIMATE; PALEOGENE; PALEOTROPICS; PARMELIA; PARMELIACEAE; PLIOCENE; RPB1 GENE; SOUTHERN HEMISPHERE;

ASCOMYCOTA; BAYES THEOREM; GENETIC LOCI; GENETIC VARIATION; LICHENS; PALEONTOLOGY; PHYLOGENY; SPECIES SPECIFICITY; TEMPERATURE; TIME FACTORS;

EID: 82955201613     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028161     Document Type: Article

References (107)

1. Galloway DJ, (1979) Biogeographical elements in the New Zealand lichen flora. In: Bramwell D, editors. Plants and Islands London Academic Press pp. 201-224.
2. Galloway DJ, (1987) Austral lichen genera: some biogeographical problems. Bibl Lichenol 25: 385-399.
3. Galloway DJ, (1988) Plate tectonics and the distribution of cool temperate Southern Hemisphere macrolichens. Bot J Linn Soc 96: 45-55.
4. Galloway DJ, (1991) Phytogeography of Southern hemisphere lichens. In: Nimis PL, CrovelloTJE, editors. Quantitative Approaches to Phytogeography Dordrecht Kluwer Academic Publishers pp. 233-262.
5. Jørgensen PM, Sipman HJM, (2002) The lichen genus Erioderma in the Southeast Asia. Ann Bot Fenn 39: 201-211.
6. Jørgensen PM, van den Boom PPG, Sérusiaux E, (2009) Notes on the lichen genus Erioderma in La Réunion. Cryptogamie, Mycologie 30: 263-268.
7. Crespo A, Gavilán R, Elix JA, Gutiérrez G, (1999) A comparison of morphological, chemical and molecular characters in parmelioid genera. Lichenologist 31: 451-460.
8. Grube M, Kroken S, (2000) Molecular approaches and the concept of species and species complexes in lichenized fungi. Mycol Res 104: 1284-1294.
9. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, et al. (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31: 21-32.
10. Kroken S, Taylor JW, (2001) A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93: 38-53.
11. 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.
12. 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 Jard Bot Madrid 66S1: 71-81.
13. 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.
14. 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.
15. Crespo A, Lumbsch HT, (2010) Cryptic species in lichen-forming fungi. IMA Fungus 1: 167-170.
16. Wirtz N, Printzen C, Lumbsch HT, (2011) Using haplotype networks, estimation of gene flow and phenotypic characters to understand species delimitation in fungi of a predominantly Antarctic Usnea group (Ascomycota, Parmeliaceae). Org Divers Evol in press.
17. Crespo A, Ferencova Z, Pérez-Ortega S, Argüello A, Elix JA, et al. (2010a) Austroparmelina, a new Australasian lineage in parmelioid lichens (Parmeliaceae, Ascomycota): a multigene and morphological approach. Syst Biodivers 8: 201-221.
18. Crespo A, Kauff F, Divakar PK, Amo G, Arguello A, et al. (2010b) Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence. Taxon 59: 1735-1753.
19. Divakar PK, Ferencova Z, Del Prado R, Lumbsch HT, Crespo A, (2010) Remototrachyna, a new tropical lineage in hypotrachynoid lichens (Parmeliaceae, Ascomycota): a multigene and morphological approach. Am J Bot 97: 579-590.
20. Lumbsch HT, Parnmen S, Rangsiruji A, Elix JA, (2010) Phenotypic disparity and adaptive radiation in the genus Cladia (Lecanorales, Ascomycota). Australian Syst Bot 23: 239-247.
21. Parnmen S, Rangsiruji A, Mongkolsuk P, Boonpragob K, Elix JA, et al. (2010) Morphological disparity in Cladoniaceae: The foliose genus Heterodea evolved from fruticose Cladia species (Lecanorales, lichenized Ascomycota). Taxon 59: 841-849.
22. Magallon S, Sanderson MJ, (2001) Absolute diversification rates in angiosperm clades. Evolution 55: 1762-1780.
23. Bell CD, Soltis DE, Soltis PS, (2005) The age of the angiosperms: A molecular timescale without a clock. Evolution 59: 1245-1258.
24. Magallon SA, Sanderson MJ, (2005) Angiosperm divergence times: The effect of genes, codon positions, and time constraints. Evolution 59: 1653-1670.
25. Magallon S, Castillo A, (2009) Angiosperm diversification through time. Am J Bot 96: 349-365.
26. Lücking R, Huhndorf S, Pfister DH, Plata ER, Lumbsch HT, (2009) Fungi evolved right on track. Mycologia 101: 810-822.
27. Berbee ML, Taylor JW, (1993) Dating the evolutionary radiations of the true fungi. Can J Bot 71: 1114-1127.
28. Berbee ML, Taylor JW, (2001) Fungal molecular evolution: gene trees and geologic time. The Mycota. Vol. VII. Part B. Systematics and Evolution In: Mclaughlin DJ, Mclaughlin EG, Lemkeand PAE, editors. Berlin, Heidelberg, New York Springer-Verlag pp. 229-245.
29. Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos N, et al. (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293: 1129-1133.
30. Padovan ACB, Sanson GFO, Brunstein A, Briones MRS, (2005) Fungi evolution revisited: Application of the penalized likelihood method to a Bayesian fungal phylogeny provides a new perspective on phylogenetic relationships and divergence dates of Ascomycota groups. J Mol Evol 60: 726-735.
31. Taylor JW, Berbee ML, (2006) Dating divergences in the Fungal Tree of Life: review and new analyses. Mycologia 98: 838-849.
32. Berbee ML, Taylor JW, (2010) Dating the molecular clock in fungi- how close are we? Fungal Biol Rev 24: 1-16.
33. Elix JA, (1993) Progress in the generic delimitation of Parmelia sensu lato lichens (Ascomycotina: Parmeliaceae) and a synoptic key to the Parmeliaceae. Bryologist 96: 359-383.
34. Wedin M, Döring H, Mattsson JE, (1999) A multi-gene study of the phylogenetic relationships of the Parmeliaceae. Mycol Res 103: 1185-1192.
35. 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. Mol Phylogenet Evol 44: 812-824.
36. Hawksworth DL, Blanco O, Divakar PK, Ahti T, Crespo A, (2008) A first checklist of parmelioid and similar lichens in Europe and adjacent territories, adopting revised generic circumscriptions and with indications of species distribution. Lichenologist 40: 1-21.
37. Persoh D, Rambold G, (2002) Phacopsis- a lichenicolous genus of the family Parmeliaceae. Mycol Prog 1: 43-55.
38. DePriest PT, (1999) Development of Mason E. Hale's list of epithets in the parmelioid genera (lichen-forming ascomycotina): A bibliographic review. Bryologist 102: 442-461.
39. Hale BW, DePriest PT, (1999) Mason E. Hale's list of epithets in the parmelioid genera. Bryologist 102: 462-544.
40. Mattsson J-E, Wedin M, (1999) A re-assessment of the family Alectoriaceae. Lichenologist 31: 431-440.
41. Blanco O, Crespo A, Divakar PK, Esslinger TL, Hawksworth DL, et al. (2004a) Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data. Mycol Res 108: 873-884.
42. 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.
43. 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. Mycol Prog 3: 297-314.
44. Blanco O, Crespo A, Divakar PK, Elix JA, Lumbsch HT, (2005) Molecular phylogeny of parmotremoid lichens (Ascomycota, Parmeliaceae). Mycologia 97: 150-159.
45. 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. Mol Phylogenet Evol 39: 52-69.
46. Arup U, Ekman S, Grube M, Mattsson JE, Wedin M, (2007) The sister group relation of Parmeliaceae (Lecanorales, Ascomycota). Mycologia 99: 42-49.
47. Divakar PK, Crespo A, Blanco O, Lumbsch HT, (2006) Phylogenetic significance of morphological characters in the tropical Hypotrachyna clade of parmelioid lichens (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 40: 448-458.
48. Lumbsch HT, Hipp AL, Divakar PK, Blanco O, Crespo A, (2008) Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota). BMC Evol Biol 8: 257 doi:10.1186/1471-2148-8-257.
49. Mägdefrau K, (1957) Flechten und Moose in baltischen Bernstein. Ber Deut Bot Ges 70: 433-435.
50. Poinar GO, Peterson EB Jr, Platt JL, (2000) Fossil Parmelia in new world amber. Lichenologist 32: 263-269.
51. Rikkinen J, Poinar GO, (2002) Fossilised Anzia (Lecanorales, lichen-forming Ascomycota) from European Tertiary amber. Mycol Res 106: 984-990.
52. 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.
53. Lutzoni F, Pagel M, Reeb V, (2001) Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411: 937-940.
54. Wedin M, Wiklund E, Crewe A, Döring H, Ekman S, et al. (2005) Phylogenetic relationships of Lecanoromycetes (Ascomycota) as revealed by analyses of mtSSU and nLSU rDNA sequence data. Mycol Res 109: 159-172.
55. Thell A, Stenroos S, Feuerer T, Kärnefelt I, Myllys L, et al. (2002) Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and ß-tubulin sequences, morphology, anatomy and secondary chemistry. Mycological Progress 1: 335-354.
56. Thell A, Högnabba F, Elix JA, Feuerer T, Kärnefelt I, et al. (2009b) Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers. Lichenologist 41: 489-511.
57. Takamatsu S, Matsuda A, (2004) Estimation of molecular clocks for ITS and 28S rDNA in Erysiphales. Mycoscience 45: 340-344.
58. 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.
59. Sérusiaux E, Villarreal JC, Wheeler T, Goffinet B, (2011) Recent origin, active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia. J Biogeogr 38: 1138-1151.
60. Divakar PK, Upreti DK, (2005) A new species in Melanohalea (Parmeliaceae, Ascomycotina) and new lichen records from India. Lichenologist 37: 511-517.
61. Thell A, Elix JA, Søchting U, (2009a) Xanthoparmelia lineola s. l. in Australia and North America. Bibl Lichenol 99: 393-404.
62. Amo De Paz G, Lumbsch HT, Cubas P, Elix JA, Crespo A, (2010a) The genus Karoowia (Parmeliaceae, Ascomycota) includes unrelated clades nested within Xanthoparmelia. Aust Syst Bot 23: 173-184.
63. Amo De Paz G, Lumbsch HT, Cubas P, Elix JA, Crespo A, (2010b) The morphologically deviating genera Omphalodiella and Placoparmelia belong to Xanthoparmelia (Parmeliaceae). Bryologist 113: 376-386.
64. Hodkinson BP, Lendemer JC, (2011) Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica 106: 108-119.
65. Leavitt SD, Johnson L, Clair LL St, (2011) 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.
66. Galloway DJ, Quilhot W, (1998) Checklist of Chilean lichen-forming and lichenicolous fungi. Gayana Botánica (Chile) 55: 111-185.
67. Givnish TJ, Renner SS, (2004) Tropical intercontinental disjunctions: Gondwana breakup, immigration from the boreotropics, and transoceanic dispersal. Int J Plant Sci (Chicago) 165: S1-S6.
68. Cook LG, Crisp MD, (2005) Not so ancient: the extant crown group of Nothofagus represents a post-Gondwanan radiation. Proc R Soc B 272: 2535-2544.
69. Knapp M, Stäckler K, Havell D, Delsuc FDR, Sebastiani F, et al. (2005) Relaxed Molecular Clock Provides Evidence for Long-Distance Dispersal of Nothofagus (Southern Beech). PLoS Biol 3: e14.
70. Heinrichs J, Lindner M, Groth H, Hentschel J, Feldberg K, et al. (2006) Goodbye or welcome Gondwana? insights into the phylogenetic biogeography of the leafy liverwort Plagiochila with a description of Proskauera gen. nov (Plagiochilaceae, Jungermanniales). Plant Sys Evol 258: 227-250.
71. Meudt HM, Simpson BB, (2006) The biogeography of the austral, subalpine genus Ourisia (Plantaginaceae) based on molecular phylogenetic evidence: South American origin and dispersal to New Zealand and Tasmania. Biol J Linn Soc 87: 479-513.
72. Perrie L, Brownsey P, (2007) Molecular evidence for long-distance dispersal in the New Zealand pteridophyte flora. J Biogeogr 34: 2028-2038.
73. Hosaka K, Castellano MA, Spatafora JW, (2008) Biogeography of Hysterangiales (Phallomycetidae, Basidiomycota). Mycol Res 112: 448-462.
74. Moncalvo JM, Buchanan PK, (2008) Molecular evidence for long distance dispersal across the Southern Hemisphere in the Ganoderma applanatum-australe species complex (Basidiomycota). Mycol Res 112: 425-436.
75. Michalak I, Zhang LB, Renner SS, (2010) Trans-Atlantic, trans-Pacific and trans-Indian Ocean dispersal in the small Gondwanan Laurales family Hernandiaceae. J Biogeogr 37: 1214-1226.
76. Renner SS, Strijk JS, Strasberg D, Thebaud C, (2010) Biogeography of the Monimiaceae (Laurales): a role for East Gondwana and long-distance dispersal, but not West Gondwana. J Biogeogr 37: 1227-1238.
77. Nash TH III, Elix JA, (2002) Myelochroa. In: Nash TH, Ryan BD, Gries C, Bungartz F, editors. Lichen Flora of the greater Sonoran Desert Region. Tempe, vol 1 Arizona Arizona State University pp. 288-289.
78. Wolfe JA, (1985) Distribution of major vegetational types during the Tertiary. In: Sundquist ET, Broecker WS, editors. The carbon cycle and atmospheric CO2: Natural variations archean to present WashingtonDC American Geophysical Union pp. 357-375.
79. Utescher T, Mosbrugger V, (2007) Eocene vegetation patterns reconstructed from plant diversity- A global perspective. Palaeogeogr Palaeocl 247: 243-271.
80. Zachos JC, Dickens GR, Zeebe RE, (2008) An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451: 279-283.
81. Rea DK, Zachos JC, Owen RM, Gingerich PD, (1990) Global change at the Paleocene-Eocene boundary: climatic and evolutionary consequences of tectonic events. Palaeogeogr Palaeocl 79: 117-128.
82. Sloan LC, Barron EJ, (1992) Paleogene climatic evolution: a climate model investigation of the influence of continental elevation and sea-surface temperature upon continental climate. In: Prothero DR, Berggren WA, editors. Eocene-Oligocene climate and biotic evolution New York Princeton University Press pp. 202-217.
83. Lumbsch HT, Schmitt I, Lücking R, Wiklund E, Wedin M, (2007a) The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited. Mycol Res 111: 257-267.
84. Lumbsch HT, Schmitt I, Mangold A, Wedin M, (2007b) Ascus types are phylogenetically misleading in Trapeliaceae and Agyriaceae (Ostropomycetidae, Ascomycota). Mycol Res 111: 1133-1141.
85. Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, et al. (2006) New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98: 1088-1103.
86. Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111: 509-547.
87. Pybus OG, Harvey PH, (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proc R Soc B Biol Sci 267: 2267-2272.
88. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
89. Castresana J, (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540-552.
90. Talavera G, Castresana J, (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564-577.
91. Posada D, (2008) jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256.
92. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
93. Drummond AJ, Rambaut A, (2007) Beast: Bayesian evoluionary analysis by sampling trees. BMC Evol Biol 7: 214.
94. Zwickl DJ, (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation. The University of Texas at Austin, Austin.
95. Huelsenbeck JP, Ronquist F, (2001) Mrbayes: Bayesian Inference of Phylogenetic Trees. Bioinformatics 17: 754-755.
96. Kurokawa S, (1994): Japanese species of Parmelia Ach. (sens. str.), Parmeliaceae (2).- J Jpn Bot 69: 121-126.
97. Rambaut A, (2007) TreeEdit v.1.0a10.http://tree.bio.ed.ac.uk/software/treeedit/.
98. Schoch CL, Sung GH, Lopez-Giraldez F, Townsend JP, Miadlikowska J, et al. (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.
99. Shimodaira H, Hasegawa M, (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247.
100. Strimmer K, Rambaut A, (2002) Inferring confidence sets of possibly misspecified gene trees. Proc R Soc B Biol Sci 269: 137-142.
101. 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.
102. Ho SYW, Phillips MJ, (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol 58: 367-380.
103. Rambaut A, Drummond AJ, (2007) Tracer v.1.4.1. In,http://tree.bio.ed.ac.uk/software/tracer/.
104. Rambaut A, (2009) FigTree 1.2.2.http://tree.bio.ed.ac.uk/software/figtree/.
105. Nimis PL, (1993) The Lichens of Italy. An annotated catalogue. Monografie XII Torino Museo Regionale di Scienze Naturali.
106. Sanmartín I, Ronquist F, (2004) Southern Hemisphere biogeography inferred by event-based models: plant versus animal patterns. Syst Biol 53: 216-243.
107. Zachos J, Pagani M, Sloan L, Thomas E, Billups K, (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292: 686-693.