@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#<Go to ISI>://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#<Go to ISI>://000241362700042},
  volume = 443,
  year = 2006
}