@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{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 }