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.

@article{moncalvo2006cantharelloid, 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.}, title = {The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods}, journal = {Mycologia}, year = {2006}, volume = {98}, number = {6}, pages = {937-948}, url = {/brokenurl#<Go to ISI>://000245858800011}, keywords = {DNA-sequences, accuracy, basidiomycota, data, difference, evolution, fungi, length, missing, mitochondrial, mtssu, mushroom-forming, nlsu, nssu, nuclear, phylogeny, rdna, ribosomal, rpb2, sequences, test}, 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.} }

%0 = article %A = 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. %D = 2006 %T = The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods %U = /brokenurl#<Go to ISI>://000245858800011

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.

@article{binder2005phylogenetic, author = {Binder, M. and Hibbett, D. S. and Larsson, K. H. and Larsson, E. and Langer, E. and Langer, G.}, title = {The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes)}, journal = {Systematics and Biodiversity}, year = {2005}, volume = {3}, number = {2}, pages = {113-157}, url = {/brokenurl#<Go to ISI>://000231684600001}, keywords = {DNA-sequences, community, corticiaceae, corticioid, ectomycorrhizal, fungi, heterobasidiomycetes, large, mycobionts, nuclear, parsimony, piriformospora-indica, polyporaceae, ratchet, rdna, ribosomal, sebacinoid, septal, sequences, significance, status, structure, subunit, systematics, taxonomic, taxonomy, tylospora-fibrillosa, ultrastructure}, 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.} }

%0 = article %A = Binder, M. and Hibbett, D. S. and Larsson, K. H. and Larsson, E. and Langer, E. and Langer, G. %D = 2005 %T = The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes) %U = /brokenurl#<Go to ISI>://000231684600001

Homobasidiomycete fungi display many complex fruiting body morphologies, Including mushrooms and puffballs, but their anatomical simplicity has confounded efforts to understand the evolution of these forms, Wt performed a comprehensive phylogenetic analysis of homobasidiomycetes, using sequences from nuclear and mitochondrial ribosomal DNA, with an emphasis on understanding evolutionary relationships of gilled mushrooms and puffballs. Parsimony-based optimization of character states on our phylogenetic trees suggested that strikingly similar gilled mushrooms evolved at least six times, from morphologically diverse precursors, Approximately 87% of gilled mushrooms are in a single lineage, which we call the ''euagarics.'' Recently discovered 90 million-year-old fossil mushrooms are probably euagarics, suggesting that (i) the origin of this clade must have occurred no later than the mid-Cretaceous and (ii) the gilled mushroom morphology has been maintained in certain lineages for tens of millions of Sears, Puffballs and other forms with enclosed spore-bearing structures (Gasteromycetes) evolved at least four times, Derivation of Gasteromycetes from Forms with exposed spore-bearing structures (Hymenomycetes) is correlated with repeated loss of forcible spore discharge (ballistospory). Diverse fruiting body forms and spore dispersal mechanisms have evolved among Gasteromycetes, Nevertheless, it appears that Hymenomycetes have never been secondarily derived from Gasteromycetes, which suggests that the loss of ballistospory has constrained evolution in these lineages.

@article{hibbett1997evolution, author = {Hibbett, D. S. and Pine, E. M. and Langer, E. and Langer, G. and Donoghue, M. J.}, title = {Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {1997}, volume = {94}, number = {22}, pages = {12002-12006}, url = {/brokenurl#<Go to ISI>://A1997YD50600047}, keywords = {basidiomycotina, fungi, nuclear, phylogenetic-relationships, taxa}, abstract = {Homobasidiomycete fungi display many complex fruiting body morphologies, Including mushrooms and puffballs, but their anatomical simplicity has confounded efforts to understand the evolution of these forms, Wt performed a comprehensive phylogenetic analysis of homobasidiomycetes, using sequences from nuclear and mitochondrial ribosomal DNA, with an emphasis on understanding evolutionary relationships of gilled mushrooms and puffballs. Parsimony-based optimization of character states on our phylogenetic trees suggested that strikingly similar gilled mushrooms evolved at least six times, from morphologically diverse precursors, Approximately 87% of gilled mushrooms are in a single lineage, which we call the ''euagarics.'' Recently discovered 90 million-year-old fossil mushrooms are probably euagarics, suggesting that (i) the origin of this clade must have occurred no later than the mid-Cretaceous and (ii) the gilled mushroom morphology has been maintained in certain lineages for tens of millions of Sears, Puffballs and other forms with enclosed spore-bearing structures (Gasteromycetes) evolved at least four times, Derivation of Gasteromycetes from Forms with exposed spore-bearing structures (Hymenomycetes) is correlated with repeated loss of forcible spore discharge (ballistospory). Diverse fruiting body forms and spore dispersal mechanisms have evolved among Gasteromycetes, Nevertheless, it appears that Hymenomycetes have never been secondarily derived from Gasteromycetes, which suggests that the loss of ballistospory has constrained evolution in these lineages.} }

%0 = article %A = Hibbett, D. S. and Pine, E. M. and Langer, E. and Langer, G. and Donoghue, M. J. %D = 1997 %T = Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences %U = /brokenurl#<Go to ISI>://A1997YD50600047