@article{matheny2007contributions, abstract = {A phylogeny of the fungal phylum Basidiomycota. is presented based on a survey of 160 taxa and five nuclear genes. Two genes, rpb2, and tef1, are presented in detail. The rpb2 gene is more variable than tef1 and recovers well-supported clades at shallow and deep taxonomic levels. The tef1 gene recovers some deep and ordinal-level relationships but with greater branch support from nucleotides compared to amino acids. Intron placement is dynamic in tef1, often lineage-specific, and diagnostic for many clades. Introns are fewer in rpb2 and tend to be highly conserved by position. When both protein-coding loci are combined with sequences of nuclear ribosomal RNA genes, 18 inclusive clades of Basidiomycota are strongly supported by Bayesian posterior probabilities and 16 by parsimony bootstrapping. These numbers are greater than produced by single genes and combined ribosomal RNA gene regions. Combination of nrDNA with amino acid sequences, or exons with third codon positions removed, produces strong measures of support, particularly for deep internodes of Basidiomycota, which have been difficult to resolve with confidence using nrDNA data alone. This study produces strong boostrap support and significant posterior probabilities for the first time for the following monophyletic groups: (1) Ustilagino-mycetes plus Hymenomycetes, (2) an inclusive cluster of hymenochaetoid, corticioid, polyporoid, Thelephorales, russuloid, athelioid, Boletales, and euagarics clades, (3) Thelephorales plus the polyporoid clade, (4) the polyporoid clade, and (5) the cantharelloid clade. Strong support is also recovered for the basal position of the Dacrymycetales in the Hymenomycetidae and paraphyly of the Exobasidiomycetidae. (C) 2006 Elsevier Inc. All rights reserved.}, author = {Matheny, P. B. and Wang, Z. and Binder, M. and Curtis, J. M. and Lim, Y. W. and Nilsson, R. H. and Hughes, K. W. and Hofstetter, V. and Ammirati, J. F. and Schoch, C. L. and Langer, E. and Langer, G. and McLaughlin, D. J. and Wilson, A. W. and Froslev, T. and Ge, Z. W. and Kerrigan, R. W. and Slot, J. C. and Yang, Z. L. and Baroni, T. J. and Fischer, M. and Hosaka, K. and Matsuura, K. and Seidl, M. T. and Vauras, J. and Hibbett, D. S.}, interhash = {35f4d50a16b2ad89024b75aa402d2bf6}, intrahash = {05a5c0c46e7a0857d1c92fcf0808b17d}, journal = {Molecular Phylogenetics and Evolution}, month = may, number = 2, pages = {430-451}, title = {Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)}, url = {/brokenurl#://000246918800008}, volume = 43, year = 2007 } @article{james2006reconstructing, abstract = {The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia ( unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.}, author = {James, T. Y. and Kauff, F. and Schoch, C. L. and Matheny, P. B. and Hofstetter, V. and Cox, C. J. and Celio, G. and Gueidan, C. and Fraker, E. and Miadlikowska, J. and Lumbsch, H. T. and Rauhut, A. and Reeb, V. and Arnold, A. E. and Amtoft, A. and Stajich, J. E. and Hosaka, K. and Sung, G. H. and Johnson, D. and O'Rourke, B. and Crockett, M. and Binder, M. and Curtis, J. M. and Slot, J. C. and Wang, Z. and Wilson, A. W. and Schussler, A. and Longcore, J. E. and O'Donnell, K. and Mozley-Standridge, S. and Porter, D. and Letcher, P. M. and Powell, M. J. and Taylor, J. W. and White, M. M. and Griffith, G. W. and Davies, D. R. and Humber, R. A. and Morton, J. B. and Sugiyama, J. and Rossman, A. Y. and Rogers, J. D. and Pfister, D. H. and Hewitt, D. and Hansen, K. and Hambleton, S. and Shoemaker, R. A. and Kohlmeyer, J. and Volkmann-Kohlmeyer, B. and Spotts, R. A. and Serdani, M. and Crous, P. W. and Hughes, K. W. and Matsuura, K. and Langer, E. and Langer, G. and Untereiner, W. A. and Lucking, R. and Budel, B. and Geiser, D. M. and Aptroot, A. and Diederich, P. and Schmitt, I. and Schultz, M. and Yahr, R. and Hibbett, D. S. and Lutzoni, F. and McLaughlin, D. J. and Spatafora, J. W. and Vilgalys, R.}, interhash = {acad49f550edb52cd23ec0e0d89506c9}, intrahash = {8a98343dd78dc2ca38c49c732d0b0f34}, journal = {Nature}, month = oct, number = 7113, pages = {818-822}, title = {Reconstructing the early evolution of Fungi using a six-gene phylogeny}, url = {/brokenurl#://000241362700042}, volume = 443, year = 2006 } @article{binder2005phylogenetic, abstract = {Phylogenetic relationships of resupinate Homobasidiomycetes (Corticiaceae s. lat. and others) were studied using ribosomal DNA (rDNA) sequences from a broad sample of resupinate and nonresupinate taxa. Two datasets were analysed using parsimony, a'core'dataset of 142 species, each of which is represented by four rDNA regions (mitochondrial and nuclear large and small subunits), and a 'full' clataset of 656 species, most of which were represented only by nuclear large subunit rDNA sequences. Both datasets were analysed using traditional heuristic methods with bootstrapping, and the full clataset was also analysed with the Parsimony Ratchet, using equal character weights and six-parameter weighted parsimony. Analyses of both datasets supported monophyly of the eight major clades of Homobasicliomycetes recognised by Hibbett and Thorn, as well as independent lineages corresponding to the Gloeophyllum clade, corticioid clade and jaapia argillacea. Analyses of the full clataset resolved two additional groups, the athelioid clade and trechisporoid clade (the latter may be nested in the polyporoid clade). Thus, there are at least 12 independent clades of Homobasicliomycetes. Higher-level relationships among the major clades are not resolved with confidence. Nevertheless, the euagarics clade, bolete clade, athelioid clade and jaapia argillacea are consistently resolved as a monophyletic group, whereas the cantharelloid clade, gomphoid-phalloid clade and hymenochaetoid clade are placed at the base of the Homobasidiomycetes, which is consistent with the preponderance of imperforate parenthesomes in those groups. Resupinate forms occur in each of the major clades of Homobasidiomycetes, some of which are composed mostly or exclusively of resupinate forms (athelioid clade, corticioid clade, trechisporoid clade,jaapia). The largest concentrations of resupinate forms occur in the polyporoid clade, russuloid clade and hymenochaetoid clade. The cantharelloid clade also includes many resupinate forms, including some that have traditionally been regarded as heterobasidiomycetes (Sebacinaceae, Tulasnellates, Ceratobasidiales). The euagarics clade, which is by far the largest clade in the Homobasidiomycetes, has the smallest fraction of resupinate species. Results of the present study are compared with recent phylogenetic analyses, and a table summarising the phylogenetic distribution of resupinate taxa is presented, as well as notes on the ecology of resupinate forms and related Homobasidiomycetes.}, author = {Binder, M. and Hibbett, D. S. and Larsson, K. H. and Larsson, E. and Langer, E. and Langer, G.}, interhash = {35bd7f6066d30b80cb445969c9aa3ae4}, intrahash = {a22933b7525f34cc68071d25347e4519}, journal = {Systematics and Biodiversity}, month = jun, number = 2, pages = {113-157}, title = {The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes)}, url = {/brokenurl#://000231684600001}, volume = 3, year = 2005 }