Molecular phylogenetics of the Gloeophyllales and relative ages of clades of Agaricomycotina producing a brown rot

Mycologia

Volumn 103, Issue 3, 2011, Pages 510-524

  Garcia Sandoval, Ricardo ^a   Wang, Zheng ^b   Binder, Manfred ^a   Hibbett, David S ^a  

^a CLARK UNIVERSITY   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Agaricomycotina; Brown rot; Systematics; Taxonomy; Wood decay

Indexed keywords

FRUITING; FUNGAL DISEASE; MORPHOLOGY; MUSHROOM; PATHOGENICITY; PHYLOGENETICS; SAMPLING; SUBSTRATE; TAXONOMY;

APHYLLOPHORALES; BOREOSTEREUM; FUNGI; GLOEOPHYLLUM; HELIOCYBE; NEOLENTINUS; PINACEAE; VELUTICEPS;

FUNGAL DNA; FUNGAL PROTEIN; RIBOSOME DNA;

ARTICLE; BASIDIOMYCETES; CHEMISTRY; CLASSIFICATION; CONIFER; CYTOLOGY; DNA SEQUENCE; GENETICS; METABOLISM; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA GENE; WOOD;

BASE SEQUENCE; BASIDIOMYCOTA; CONIFEROPHYTA; DNA, FUNGAL; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENES, RRNA; MYCOLOGICAL TYPING TECHNIQUES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; WOOD;

EID: 80052390282     PISSN: 00275514     EISSN: 15572536     Source Type: Journal    
DOI: 10.3852/10-209     Document Type: Article

References (92)

1. Abascal F, Posada D, Zardoya R. 2007. MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol 24:1-5.
2. Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
3. Baldauf S, Palmer J. 1993. Animals and fungi are each other's closest relatives-congruent evidence from multiple proteins. Proc Natl Acad Sci USA 90: 11558-11562.
4. Baldrian P, Valásková V. 2008. Degradation of cellulose by basidiomycetous fungi. FEMS Microbiol Rev 32:501-521.
5. Bell CD, Soltis DE, Soltis PS. 2005. The age of the angiosperms: a molecular timescale without a clock. Evolution 59:1245-1258.
6. Berbee ML, Taylor JW. 1993. Dating the evolutionary radiations of the true fungi. Can J Bot 71:1114-1127.
7. Binder M, Hibbett DS. 2002.Higher level phylogenetic relationships of Homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions. Mol Phylogenet Evol 22:76-90.
8. Binder M, Hibbett DS, Larsson K-H, Larsson E, Langer E, Langer G. 2005. The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes). Syst Biodivers 3:113-157.
9. Burgoyne P, van Wyk A, Anderson J, Schrire B. 2005. Phanerozoic evolution of plants on the African plate. J African Earth Sci 43:13-52.
10. Chamuris GP. 1988. The non-stipitate stereoid fungi in the northeastern United States and adjacent Canada. Berlin: J. Cramer. 247 p.
11. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88.
12. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
13. Esteban L, de Palacios P. 2009. Comparative wood anatomy in Abietoideae (Pinaceae). Bot J Linn Soc 160:184-196.
14. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:738-791.
15. Felsenstein J. 1989. PHYLIP-phylogeny inference package. Version 3.2. Cladistics 5:164-166.
16. Gardes M, Bruns T. 1993. ITS primers with enhanced specificity of basidiomycetes: application to the identification of mycorrhizae and rust. Mol Ecol 2(2):113-118.
17. Gernandt D, Magallón S, López G, Flores O, Willyard A, Liston A. 2008. Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. Int J Plant Sci 169(8):1086-1099.
18. Gilbertson RL. 1980. Wood-rotting fungi of North America. Mycologia 72(1):1-49.
19. Gilbertson RL, Ryvarden L. 1986. North American polypores. Oslo: Fungiflora. 885 p.
20. Ginns JH. 1984. Griseoporia, a new genus for Hexagonia carbonaria. Mycotaxon 20(2):559-565.
21. Hibbett DS. 1996. Phylogenetic evidence for horizontal transmission of Group 1 introns in the nuclear ribosomal DNA of mushroom-forming fungi. Mol Biol Evol 13(7):903-917.
22. Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Ericksson OE, Huhndrorf S, James T, Kirk PM, Lücking R, Lumbsch HT, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Kõljalg U, Kurtzman CP, Larsson KH, Litchward R, Longore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüßler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao Y-J, Zhang N. 2007. A higher level phylogenetic classification of the Fungi. Mycol Res 111(5):509-547.
23. Hibbett DS, Donoghue MJ. 1995. Progress toward a phylogenetic classification of the Polyporaceae through parsimony analyses of ribosomal sequences. Can J Bot 73(S1):S853-S861.
24. Hibbett DS, Donoghue MJ. 2001. Analysis of character correlations among wood decay mechanisms, mating systems and substrate ranges in homobasidiomycetes. Syst Biol 50(2):215-242.
25. Hibbett DS, Grimaldi D, Donoghue MJ. 1997. Fossil mushrooms from Miocene and Cretaceous ambers and the evolution of homobasidiomycetes. Am J Bot 84(7):981-991.
26. Hibbett DS, Matheny PB. 2009. The relative ages of ectomycorrhizal mushrooms and their plant host estimated using Bayesian relaxed molecular clock analyses. BMC Biology 7(1):13.
27. Hibbett DS, Vilgalys R. 1993. Phylogenetic relationships of Lentinus (Basidiomycotina) inferred from molecular and morphological characters. Syst Bot 18:409-433.
28. Hjortstam K, Tellería MT. 1990. Columnocystis, a synonym of Veluticeps. Mycotaxon 37:53-56.
29. Jensen KA Jr, Houtman CJ, Ryan ZC, Hammel KE. 2001. Pathways for extracellular Fenton chemistry in the brown-rot basidiomycetes Gloeophyllum trabeum. Appl Environ Microbiol 67:2705-2711.
30. Kim SY, Jung HS. 2000. Phylogenetic relationships of the Aphyllophorales inferred from sequence analysis of nuclear small subunit ribosomal DNA. J Microbiol 38(3):122-131.
31. Kim SY, Jung HS 2001. Phylogenetic relationships of the Polyporaceae based on gene sequences of nuclear small subunit ribosomal RNAs. Mycobiology 29:73-79.
32. Kim SY, Park SY, Ko KS, Jung HS. 2003. Phylogenetic analysis of Antrodia and related taxa based on partial mitochondrial SSU rDNA sequences. Antonie van Leeuwenhoek 83:81-88.
33. Kirk PM, Cannon PF, Minter DW, Stalpers JA. 2008. Ainsworth & Bisby's dictionary of the Fungi. 10th ed. Wallingford, UK: CAB International. 771 p.
34. Kretzer AM, Bruns TD. 1999. Use of atp6 in fungal phylogenetics: an example from Boletales. Mol Phylogenet Evol 13(3):483-492.
35. Larsson KH. 2007. Rethinking the classification of corticioid fungi. Mycol Res 111(9):1040-1063.
36. LePage B, Basinger J. 1995. Evolutionary history of the genus Pseudolarix Gordon (Pinaceae). Int J Plant Sci 156(6):910-950.
37. Lim YW. 2001. Systematic study of corticioid fungi based on molecular sequence analyses [doctoral dissertation]. Seoul: Seoul National University. 228 p.
38. Lindner D, BanikMT. 2008.Molecular phylogeny of Laetiporus and other brown-rot polypore genera in North America. Mycologia 100(3):417-430.
39. Liu YJ, Hall BD. 2004. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc Natl Acad Sci USA 101(13):4507-4512.
40. Liu YJ, Whelen S, Hall BD. 1999. Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16(2):1799-1808.
41. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Gail C, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Maidlikowska 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, 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(10):1446-1480.
42. Maddison DR, Maddison WP. 2000. MacClade 4: analysis of phylogeny and character evolution. Version 4.02. Sunderland, Massachusetts: Sinauer Associates.
43. Magallón SA. 2004. Dating lineages: molecular and paleontological approaches to the temporal framework of clades. Int J Plant Sci 4:S7-S21.
44. Magallón SA, Sanderson MJ. 2005. Angiosperm divergence times: the effect of genes, codon positions and time constrains. Evolution 59(8):1653-1670.
45. Maheshwari H. 2007. Deciphering angiosperm origins. Curr Sci 92(5):606-611.
46. Martin JK, Gilbertson RL. 1973. The mating system and some other cultural aspects of Veluticeps berkeleyi. Mycologia 65(3):548-557.
47. Martinez D, Challacombe J, Morgenstern I, Hibbett DS, Schmoll M, Kubicek C, Ferreira P, Ruiz-Duenas F, Martinez A, Kersten P, Hammel K, Wymelemberg A, Gaskell J, Lindquist E, Sabat G, BonDurant S, Larrondo L, Canessai P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro A, Lavin J, Oguiza J, Master E, Henrissat B, Coutinho P, Harris P, Magnuson J, Baker S, Bruno K, Kenealy W, Hoegger P, Kües U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee C, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev I, Brettin T, Rokhsar D, Berka R, Cullen D. 2009. Genome, transcriptome and secretome analysis of wood decay fungus Postia placenta supports unique mechanism of lignocellulose conversion. Proc Natl Acad Sci USA 106:1954-1959.
48. Matheny PB. 2005. Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). Mol Phylogenet Evol 35:1-20.
49. Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo J-M, Ge Z-W, Yang Z, Slot JC, Ammirati JF, Baroni TJ, Bougher N, Hughes KW, Lodge DJ, Kerrigan RW, Seidl MT, Aanen D, DeNitis M, Daniele G, Desjardin D, Kropp B, Norvell L, Parker A, Vellinga E, Vilgalys R, Hibbett DS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982-995.
50. Matheny PB, Wang Z, Binder M, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Hofstetter V, Ammirati JF, Schoch CL, Langer E, Langer G, Kerrigan RW, Slot JC, Yang Z, Baroni TJ, Fisher M, Hosaka K, Matsuura K, Seidl MT, Vauras J, Hibbett DS. 2007. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phylogenet Evol 43:430-451.
51. Miller C. 1976. Early evolution in the Pinaceae. Rev Paleobot Palynol 21(1):101-117.
52. Moncalvo JM, Lutzoni FM, Rehner SA, Johnson J, Vilgalys R. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst Biol 49:278-305.
53. Morgenstern I, Klopman S, Hibbett DS. 2008. Molecular evolution and diversity of lignin degrading heme peroxidases in the Agaricomycetes. J Mol Evol 66: 243-257.
54. Nakasone KK. 1990a. Cultural studies and identification of wood-inhabiting Corticiaceae and selected Hymenomycetes from North America. Berlin: J. Cramer. 412 p.
55. Nakasone KK. 1990b. Taxonomic study of Veluticeps (Aphyllophorales). Mycologia 82:622-641.
56. Nakasone KK. 2004. Morphological studies in Veluticeps, Pileodon and related taxa. Sydowia 56:38-60.
57. O'Donnell K, Lutzoni FM, Ward TJ, Benny GL. 2001. Evolutionary relationships among mucoralean fungi (Zygomycota): evidence for family polyphyly on a large scale. Mycologia 93:286-296.
58. Pegler DN. 1983. The genus Lentinus. Kew Bull Add Ser X, 1-281.
59. Peterson K, Lyons J, Nowak K, Takacs C, Wargo M, McPeek M. 2004. Estimating metazoan divergence times with a molecular clock. Proc Natl Acad Sci USA 101:6536-6541.
60. Phillippe M, Bamford M, McLoughlin S, Alves L, Falcon-Lang H, Gnaedinger S, Ottone E, Pole M, Rajanikanth A, Shoemaker R, Torres T, Zamuner A. 2004. Biogeographic analysis of Jurassic-Early Cretaceous wood assemblages from Gondwana. Rev Paleobot Palynol 129:141-173.
61. Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808.
62. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
63. Rambaut A. 2008. FigTree. Edinburgh: Institute of Evolutionary Biology, Univ Edinburgh.
64. Redhead SA, Ginns JH. 1985. A re-appraisal of agaric genera associated with brown rots of wood. Trans Mycol Soc Japan 26:349-381.
65. Reeb V, Lutzoni F, Roux C. 2004. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol Phylogenet Evol 32: 1036-1060.
66. Rehner S, Buckley E. 2005. A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97:84-98.
67. Ridout B. 1999. Timber decay in buildings: the conservation approach to treatment. New York: Routledge. 252 p.
68. Robison MM, Chiang B, Horgen PA. 2001. A phylogeny of the genus Agaricus based on mitochondrial atp6 sequences. Mycologia 93:30-37.
69. Roger AJ, Sandbloom O, Doolittle WF, Philippe H. 1999. An evaluation of elongation factor 1α as a phylogenetic marker for eukaryotes. Mol Biol Evol 16:218-233.
70. Rokas A, Carroll SB. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 22: 1337-1344.
71. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
72. Rune F. 1994. Neolentinus-a well founded genus in Pleurotaceae that includes Heliocybe. Mycol Res 98: 542-544.
73. Sanderson M. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol 19:101-109.
74. Sanderson M. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19: 301-302.
75. Simon L, Bousquet J, Levesque R, Lalonde M. 1993. Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants. Nature 363(6424):67-69.
76. Singer R. 1944. Notes on taxonomy and nomenclature of the polypores. Mycologia 36:65-69.
77. Smith S, Currah R, Stockey R. 2004. Cretaceous and Eocene poroid hymenophores from Vancouver Island, British Columbia. Mycologia 96:180-186.
78. Soltis DE, Moore MJ, Burleigh JG, Soltis PS. 2009. Molecular markers and concepts of plant evolutionary relationships: progress, promise and future prospects. Critic Rev Plant Sci 28(1, 2):1-15.
79. Stamatakis A. 2006. RAxML_IV_HPC: maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
80. Swofford DL. 2001. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sunderland, Massachusetts: Sinauer Associates.
81. Taylor JW, Berbee ML. 2006. Dating divergences in the fungal tree of life: review and new analyses. Mycologia 98:838-849.
82. Taylor TN, Hass H, Kerp H, Krings M, Hanlin R. 2005. Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism. Mycologia 97:269-285.
83. Thorn RG, Moncalvo J-M, Reddy CA, Vilgalys R. 2000. Phylogenetic analyses and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoid-lentinoid fungi. Mycologia 92: 241-252.
84. Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified DNA from several Cryptococcus species. J Bacteriol 172:4238-4246.
85. Vlasák J, Kout J, Dvorák D. 2010. Taxonomical position of polypore Dichomitus albidofuscus: Donkioporia albidofusca comb. nov. Mycol Prog 9:147-150.
86. Wang Z. 2006. Multilocus phylogenetic analyses of the Polyporales (Homobasidiomycetes, Basidiomycota) and the Helotiales (Leotiomycetes, Ascomycota) [doctoral dissertation]. Worcester, Massachusetts: Clark Univ. Press. 185 p.
87. Wang Z, Binder M, Dai Y-C, Hibbett DS. 2004. Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequences. Mycologia 96:1015-1029.
88. White TJ, Bruns T, Lee S, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols. New York: Academic Press. p 315-322.
89. Wikström N, Savolainen V, Chase MW. 2001. Evolution of the angiosperms: calibrating the family tree. Proc R Soc London B 268(1482):2211-2220.
90. Yoon SI, Kim SY, Lim YW, Jung HS. 2003. Phylogenetic evaluation of stereoid fungi. J Microbiol Biotechnol 13: 406-414.
91. Zavada M. 2007. The identification of fossil angiosperm pollen and its bearing on the time and place of the origin of angiosperms. Plant Syst Evol 263:117-134.
92. Zhang N, Blackwell M. 2002. Molecular phylogeny of Melanospora and similar pyrenomycetous fungi. Mycol Res 106:148-155.