Cardinal characters on a slippery slope - A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str)

Molecular Phylogenetics and Evolution

Volumn 68, Issue 2, 2013, Pages 185-198

  Otálora, Mónica A G ^a   Aragón, Gregorio ^b   Martínez, Isabel ^b   Wedin, Mats ^a  

^a SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^b UNIVERSIDAD REY JUAN CARLOS   (Spain)

Author keywords

Accelerated evolutionary rates; Ancestral state reconstruction; Collemataceae; Cortex; Habitat; Lichen forming fungi

Indexed keywords

ARTICLE; ASCOMYCETES; BAYES THEOREM; CLASSIFICATION; CYTOLOGY; FUNGAL GENE; FUNGUS SPORE; GENETICS; LICHEN (ORGANISM); MICROBIOLOGICAL EXAMINATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTILOCUS SEQUENCE TYPING; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

ASCOMYCOTA; BAYES THEOREM; EVOLUTION, MOLECULAR; GENES, FUNGAL; LICHENS; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; MYCOLOGICAL TYPING TECHNIQUES; PHYLOGENY; SPORES, FUNGAL;

COLLEMATACEAE; FUNGI;

EID: 84877083269     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.04.004     Document Type: Article

References (95)

1. Allen A., Gillooly J., Savage V., Brown J. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. USA 2006, 103:9130-9135.
2. Aragón G., Otálora M.A.G., Martínez I. New data on the genus Leptogium (lichenized Ascomycetes) in the Iberian Peninsula. Nova Hedwigia 2005, 80:199-226.
3. Barraclough T.G., Savolainen V. Evolutionary rates and species diversity in flowering plants. Evolution 2001, 55:677-683.
4. Bhattacharya D., Lutzoni F., Reeb V., Simon D., Nason J., Fernandez F. Widespread occurrence of spliceosomal introns in the rDNA genes of Ascomycetes. Mol. Biol. Evol. 2000, 17:1971-1984.
5. Blanco O., Crespo A., Ree R.H., Lumbsch H.T. Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity. Mol. Phylogenet. Evol. 2006, 39:52-69.
6. Blum O.B. Water relations. The Lichens 1973, 381-400. Academic Press, New York and London. V. Ahmadjian, M.E. Hale (Eds.).
7. Bollback J.P. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 2006, 7:88.
8. Bollback, J.P., 2009. Simmap 1.5 Documentation Online. http://www.simmap.com/pgs/docs.html.
9. Cardillo M. Latitude and rates of diversification in birds and butterflies. Proc. R. Soc. Lond. B Biol. Sci. 1999, 266:1221-1225.
10. Cornelissen J.H.C., Lang S.I., Soudzilovskaia N.A., During H.J. Comparative cryptogam ecology: a review of bryophyte and lichen traits that drive biogeochemistry. Ann. Bot. 2007, 99:987-1001.
11. Davies T.J., Savolainen V., Chase M.W., Moat J., Barraclough T.G. Environmental energy and evolutionary rates in flowering plants. Proc. R. Soc. Lond. B Biol. Sci. 2004, 271:2195-2200.
12. Degelius G. The lichen genus Collema in Europe: morphology, taxonomy, ecology. Symb. Bot. Upsal. 1954, 13:1-499.
13. Degelius G. The lichen genus Collema with special reference to the extra-European species. Symb. Bot. Upsal. 1974, 20:1-215.
14. DePriest P.T. Early molecular investigations of lichen-forming symbionts, 1986-2001. Ann. Rev. Microbiol. 2004, 58:273-301.
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. Fischer A.G. Latitudinal variations in organic diversity. Evolution 1960, 14:64-81.
17. Galloway D.J. Biogeography and ancestry of lichens and other ascomycetes. Ascomycete Systematics. Problems and Perspectives in the Nineties. NATO Advanced Science Institutes Series 1994, 175-184. Plenum Press, New York. D.L. Hawksworth (Ed.).
18. Galloway D. Flora of New Zealand Lichens. Revised Second Edition Including Lichen-Forming and Lichenicolous Fungi 2007, vols. 1 and 2. Manaaki Whenua Press, Lincoln.
19. Gillooly J.F., Allen A.P., West G.B., Brown J.H. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc. Natl. Acad. Sci. USA 2005, 102:140-145.
20. Grube M., Hawksworth D.L. Trouble with lichen: the re-evaluation and re-interpretation of thallus form and fruit body types in the molecular era. Mycol. Res. 2007, 111:1116-1132.
21. Gueidan C., Roux C., Lutzoni F. Using a multigene analysis to assess generic delineation and character evolution in the Verrucariaceae (Verrucariales, Ascomycota). Mycol. Res. 2007, 111:1145-1168.
22. Hawksworth D.L. Co-evolution and detection of ancestry in lichens. J. Hattori Bot. Lab. 1982, 52:323-329.
23. Henssen A. A review of the genera of the Collemataceae with simple spores (excluding Physma). Lichenologist 1965, 3:29-41.
24. Henssen A. The lecanoralean centrum. Ascomycetes Systematics 1981, 139-234. Springer Verlag, New York. D.R. Reynolds (Ed.).
25. 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., Bergerow 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-Standrige S., Oberwinkler F., Parmasto E., Reeb V., Rogers J.D., Roux C., Ryvarden L., Sampaio J.P., Schüssler 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.
26. 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.
27. Jonsson A.V., Moen J., Palmqvist K. Predicting lichen hydration using biophysical models. Oecologia 2008, 156:259-273.
28. Jørgensen P.M. On some Leptogium species with short Mallotium hairs. Svensk Bot. Tids. 1973, 67:53-58.
29. Jørgensen P.M. Contributions to a monograph of the Mallotium-hairy Leptogium species. Herzogia 1975, 3:433-460.
30. Jørgensen P.M. Further notes on European taxa of the lichen genus Leptogium, with emphasis on the small species. Lichenologist 1994, 26:1-29.
31. Jørgensen P.M. Further notes on hairy Leptogium species. Symb. Bot. Upsal. 1997, 32:113-130.
32. Jørgensen P.M. Collemataceae. Nordic Lichen Flora 2007, 3:14-42.
33. Jørgensen P.M., James P.W. Studies on some Leptogium species of Western Europe. Lichenologist 1983, 15:109-125.
34. Jørgensen P.M., Nash T.H. Leptogium. Lichens Unlimited 2004, vol. 2:330-350. Arizona State University, Tempe, Arizona. T.H. Nash, B.D. Ryan, P. Diederich, C. Gries, F. Bungartz (Eds.).
35. Katoh K., Toh H. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 2008, 9:212.
36. Lancaster L.T. Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages. BMC Evol. Biol. 2010, 10:162.
37. Lanfear R., Ho S.Y.W., Love D., Bromham L. Mutation rate is linked to diversification in birds. Proc. Natl. Acad. Sci. USA 2010, 107:20423-20428.
38. Lange O.L., Belnap J., Reichenberger H. Photosynthesis of the cyanobacterial soil-crust lichen Collema tenax from arid lands in southern Utah, USA: role of water content on light and temperature responses of CO2 exchange. Funct. Ecol. 1998, 12:195-202.
39. Lücking R. Predicting species richness in tropical lichenized fungi with 'modular' combinations of character states. Biodivers. Conserv. 2012, 21:2341-2360.
40. Lücking R., Rivas E., Chaves J.L., Umaña L., Sipman H. How many tropical lichens are there really?. Bibl. Lichenologica 2009, 100:399-418.
41. Lumbsch H.T., Hipp A.L., Divakar P.K., Blanco O., Crespo A. Accelerated evolutionary rates in tropical and oceanic Parmelioid lichens (Ascomycota). BMC Evol. Biol. 2008, 8:257.
42. Lutzoni F., Pagel M. Accelerated evolution as a consequence of transitions to mutualism. Proc. Natl. Acad. Sci. USA 1997, 94:11422-11427.
43. Lutzoni F., Kauff F., Cox J.C., 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., Sung G.H., Lücking R., Lumbsch H.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.
44. Maddison, W., Maddison, D., 2001. MacClade: Analysis of Phylogeny and Character Evolution, Version 4.01. Massachusetts, Sinauer, Sunderland.
45. Maddison, W., Maddison, D. 2007. Mesquite 2.01. http://mesquiteproject.org/mesquite/mesquite.html.
46. Magain N., Sérusiaux E. A further new species in the lichen genus Arctomia: A. borbonica from Reunion (Mascarene archipelago). MycoKeys 2012, 4:9-21.
47. 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.
48. 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.
49. Miadlikowska J., Kauff F., Hofstetter V., Fraker E., Grube M., Hafellner J., Reeb V., Hodkinson B.P., Kukwa M., Lücking R., Hestmark G., Otálora M.A.G., Rauhut A., Büdel B., Scheidegger C., Timdal E., Stenroos S., Brodo I., Perlmutter G., Ertz D., Diederich P., Lendemer J.C., Schoch C., Tripp E., Yahr R., May P., Gueidan C., Arnold A.E., 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, 98:1089-1102.
50. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, pp. 1-8.
51. Mittelbach G.G., Schemske D.W., Cornell H.V., Allen A.P., Brown J.M., Bush M.B., Harrison S.P., Hurlbert A.H., Knowlton N., Lessios H.A., McCain C.M., McCune A.R., McDade L.A., McPeek M.A., Near T.J., Price T.D., Ricklefs R.E., Roy K., Sax D.F., Schluter D., Sobel J.M., Turelli M. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 2007, 10:315-331.
52. Muggia L., Nelson P., Wheeler T., Yakovchenko L.S., Tønsberg T., Spribille T. Convergent evolution of a symbiotic duet: the case of the lichen genus Polychidium (Peltigerales, Ascomycota). Am. J. Bot. 2011, 98:1647-1656.
53. Müller J. Lichenologische Beiträge 22. Flora 1885, 68:503-518.
54. Myllys L., Tehler A., Lohtander K. Beta-tubulin, ITS and group I intron sequences challenge the species pair concept in Physcia aipolia and P. caesia. Mycologia 2001, 93:335-343.
55. Nash T.H. Nitrogen, its metabolism and potential contribution to ecosystems. Lichen Biology 2008, 216-233. Cambridge University Press, Cambridge. second ed. T.H. Nash (Ed.).
56. Otálora M.A.G., Wedin M. Collema fasciculare belongs in Arctomiaceae. Lichenologist 2013, 45:295-304.
57. Otálora M.A.G., Martínez I., Molina M.C., Aragón G., Lutzoni F. Phylogenetic relationships and taxonomy of the Leptogium lichenoides group (Collemataceae) in Europe. Taxon 2008, 57:907-921.
58. Otálora M.A.G., Aragón G., Molina M.C., Martínez I., Lutzoni F. Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota). Mycologia 2010, 102:279-290.
59. Pagel M., Venditti C., Meade A. Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 2006, 314:119-121.
60. Penn O., Privman E., Ashkenazy H., Landan G., Graur D., Pupko T. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 2010, 38:W23-W28.
61. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
62. Qiu B.S., Gao K.S. Photosynthetic characteristics of the terrestrial blue-green alga, Nostoc flagelliforme. Eur. J. Phycol. 2001, 36:147-156.
63. Rambaut, A., 2009. FigTree 1.3.1. http://tree.bio.ed.ac.uk/software/figtree.
64. Rambaut, A., Drummond, A.J., 2007. Tracer 1.5. http://beast.bio.ed.ac.uk/Main_Page.
65. Rivas-Plata E., Lumbsch H.T. Parallel evolution and phenotypic disparity in lichenized fungi: a case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales). Mol. Phylogenet. Evol. 2011, 61:45-63.
66. Ronquist F., Teslenko M., van der Mark P., Ayres D., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2011, 61:539-542.
67. Rundel P.W. The role of morphology in the water relations of desert lichens. J. Hattori Bot. Lab. 1982, 53:315-320.
68. Schemske D.W. Biotic interactions and speciation in the tropics. Speciation and Patterns of Diversity 2009, 219-239. Cambridge University Press, Cambridge. R.K. Butlin, J.R. Bridle, D. Schluter (Eds.).
69. Schmitt I., Mueller G., Lumbsch H.T. Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens. Mycologia 2005, 97:362-374.
70. Schmitt I., del Prado R., Grube M., Lumbsch H.T. Repeated evolution of closed fruiting bodies is linked to ascoma development in the largest group of lichenized fungi (Lecanoromycetes, Ascomycota). Mol. Phylogenet. Evol. 2009, 52:34-44.
71. Schmitt I., Crespo A., Divakar P.K., Frankhauser J.D., Herman-Sackett E., Kalb K., Nelsen M.P., Rivas-Plata E., Shimp A.D., Widhelm T., Lumbsch H.T. New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 2009, 23:35-40.
72. Sierk H.A. The genus Leptogium in North America and North of Mexico. Bryologist 1964, 67:245-317.
73. Simon D.M., Hummel C.L., Sheeley S.L., Bhattacharya D. Heterogeneity of intron presence or absence in rDNA genes of the lichen species Physcia aipolia and P. stellaris. Curr. Genet. 2005, 47:389-399.
74. Sipman H.J.M., Aptroot A. Where are the missing lichens?. Mycol. Res. 2001, 105:1433-1439.
75. Smith S.A., Donoghue M.J. Rates of molecular evolution are linked to life history in flowering plants. Science 2008, 322:86-89.
76. Souza-Egipsy V., Valladares F., Ascaso C. Water distribution in foliose lichen species: interactions between method of hydration, lichen substances and thallus anatomy. Ann. Bot. 2000, 86:595-601.
77. Spribille T., Muggia L. Expanded taxon sampling disentangles evolutionary relationships and reveals a new family in Peltigerales (Lecanoromycetidae, Ascomycota). Fungal Divers. 2012, 59. 10.1007/s13225-012-0206-5.
78. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
79. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
80. Trevisan V. Caratteri di tre nuovi generi di Collemacee 1853, Padova.
81. Trevisan V. Sulle Garovaglinee, nuovo tribu di Collemacee. Rendiconti del R. Ist. Lomb. di Sc. e Lett. Ser. 1880, 2(13):65-77.
82. Verdon D. Leptogium. Flora Aust. 1992, 54:173-192.
83. Vilgalys R., Hester M. Rapid identification and mapping of enzymatically amplified ribosomal DNA from several Crytococcus species. J. Bacteriol. 1990, 172:4238-4246.
84. Wallace A.R. Tropical Nature and Other Essays 1878, Macmillan, New York.
85. Webster A., Payne R., Pagel M. Molecular phylogenies link rates of evolution and speciation. Science 2003, 301:478.
86. Wedin M., Wiklund E. The phylogenetic relationships of Lecanorales suborder Peltigerineae revisited. Symb. Bot. Upsal. 2004, 34:469-475.
87. Wedin M., Döring H., Gilenstam G. Saprotrophy and lichenization as options for the same fungal species on different substrata: environmental plasticity and fungal lifestyles in the Stictis-Conotrema complex. New Phytol. 2004, 164:459-465.
88. 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.
89. Wedin M., Wiklund E., Jørgensen P.M., Ekman S. Slippery when wet: phylogeny and character evolution in the gelatinous cyanobacterial lichens (Peltigerales, Ascomycetes). Mol. Phylogenet. Evol. 2009, 53:862-871.
90. Wiens J.J. Combining data sets with different phylogenetic histories. Syst. Biol. 1998, 47:568-581.
91. Wiklund E., Wedin M. The phylogenetic relationships of cyanobacterial lichens in the Lecanorales suborder Peltigerineae. Cladistics 2003, 19:419-431.
92. Wright S.D., Gray R.D., Gardner R.C. Energy and the rate of evolution: inferences from plant rDNA substitution rates in the western Pacific. Evolution 2003, 57:2893-2898.
93. Yang Z. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.
94. Zahlbruckner A. Catalogus Lichenum Universalis 1924, vol. 3. Borntraeger, Leipzig.
95. Zoller S., Scheidegger C., Sperisen C. PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. Lichenologist 1999, 31:511-516.