@unpublished{douanlameli2006notes, author = {Douanla-Meli, C. and Langer, E.}, interhash = {81fb1639231134e95319e35760f89b14}, intrahash = {ee1216f454067cc3a6328baf059aa7c0}, title = {Notes on clavarioid fungi (Basidiomycota, Aphyllophorales) with interesting species from the Mbalmayo forest reserve, Cameroon}, year = 2006 } @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{moncalvo2006cantharelloid, abstract = {We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that clade. Phylogenetic analyses support monophyly of all genera except Sistotrema, which was highly polyphyletic. Strongly supported monophyletic groups were: (i) Cantharellus-Craterellus, Hydnum, and the Sistotrema confluens group; (ii) Clavulina-Membranomyces and the S. brinkmannii-oblongisporum group, with Multiclavula being possibly sister of that clade; (iii) the Sistotrema eximum-octosporum group; (iv) Sistotrema adnatum and S. coronilla. Positions of Sistotrema raduloides and S. athelioides were unresolved, as were basal relationships. Botryobasidium was well supported as the sister taxon of all the above taxa, while Ceratobasidiaceae was the most basal lineage. The relationship between Tulasnella and members of the cantharelloid clade will require further scrutiny, although there is cumulative evidence that they are probably sister groups. The rates of molecular evolution of both the large and small nuclear ribosomal RNA genes (nuc-rDNA) are much higher in Cantharellus, Craterellus and Tulasnella than in the other cantharelloid taxa, and analyses of nuc-rDNA sequences strongly placed Tulasnella close to Cantharellus-Craterellus. In contrast analyses with RPB2 and mtSSU sequences placed Tulasnella at the base of the cantharelloid clade. Our attempt to reconstruct a "supertree" from tree topologies resulting from separate analyses that avoided phylogenetic reconstruction problems associated with missing data and/or unalignable sequences proved unsuccessful.}, author = {Moncalvo, J. M. and Nilsson, R. H. and Koster, B. and Dunham, S. M. and Bernauer, T. and Matheny, P. B. and Porter, T. M. and Margaritescu, S. and Weiss, M. and Garnica, S. and Danell, E. and Langer, G. and Langer, E. and Larsson, E. and Larsson, K. H. and Vilgalys, R.}, interhash = {f9a3bfd95aa0e748cadbeae6bd364dfa}, intrahash = {8df79eade21e47a9a7d1a68e31ae634f}, journal = {Mycologia}, month = {Nov-Dec}, number = 6, pages = {937-948}, title = {The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods}, url = {/brokenurl#://000245858800011}, volume = 98, year = 2006 } @article{larsson2006hymenochaetales, abstract = {The hymenochaetoid clade is dominated by wood-decaying species previously classified in the artificial families Corticiaceae, Polyporaceae and Stereaceae. The majority of these species cause a white rot. The polypore Bridgeoporus and several corticioid species with inconspicuous basidiomata, live in association with brown-rotted wood, but their nutritional strategy is Dot known. Mycorrhizal habit is reported for Coltricia perennis but needs confirmation. A surprising element in the hymenochaetoid clade is a group of small white to brightly pigmented agarics earlier classified in Omphalina. They form a subclade together with some similarly colored stipitate stereoid and corticioid species. Several are associated with living mosses or one-celled green algae. Hyphoderma pratermissum and some related corticioid species have specialized organs for trapping and killing nematodes as a source of nitrogen. There are no unequivocal morphological synapomorphies known for the hymenochaetoid clade. However almost all species examined ultrastructurally have dolipore septa with continuous parenthesomes while perforate parenthesomes is the normal condition for other homobasidiomycete clades. The agaricoid Hymenochaetales have not been examined. Within Hymenochaetales the Hymenochaetaceae forms a distinct clade but unfortunately all morphological characters supporting Hymenochaetaceae also are found in species outside the clade. Other subclades recovered by the molecular phylogenetic analyses are less uniform, and the overall resolution within the nuclear LSU tree presented here is still unsatisfactory.}, author = {Larsson, K. H. and Parmasto, E. and Fischer, M. and Langer, E. and Nakasone, K. K. and Redhead, S. A.}, interhash = {3054ec8626c9b80dde9de8cfe7ed1776}, intrahash = {88cf489dcf5b1600f55d17eb700aba0c}, journal = {Mycologia}, month = {Nov-Dec}, number = 6, pages = {926-936}, title = {Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade}, url = {/brokenurl#://000245858800010}, volume = 98, year = 2006 }