title: The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods.
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.
authors.affiliation: Department of Natural History, Royal Ontario Museum, University of Toronto, Canada. jeanmarcm@gmail.com
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Moncalvo
authors.forename: R Henrik
authors.initials: RH
authors.lastname: Nilsson
authors.forename: Brenda
authors.initials: B
authors.lastname: Koster
authors.forename: Susie M
authors.initials: SM
authors.lastname: Dunham
authors.forename: Torsten
authors.initials: T
authors.lastname: Bernauer
authors.forename: P Brandon
authors.initials: PB
authors.lastname: Matheny
authors.forename: Teresita M
authors.initials: TM
authors.lastname: Porter
authors.forename: Simona
authors.initials: S
authors.lastname: Margaritescu
authors.forename: Michael
authors.initials: M
authors.lastname: Weiss
authors.forename: Sigisfredo
authors.initials: S
authors.lastname: Garnica
authors.forename: Eric
authors.initials: E
authors.lastname: Danell
authors.forename: Gitta
authors.initials: G
authors.lastname: Langer
authors.forename: Ewald
authors.initials: E
authors.lastname: Langer
authors.forename: Ellen
authors.initials: E
authors.lastname: Larsson
authors.forename: Karl-Henrik
authors.initials: KH
authors.lastname: Larsson
authors.forename: Rytas
authors.initials: R
authors.lastname: Vilgalys
mesh_terms: D001487:Basidiomycota / Q000145:classification* / Q000235:genetics / Q000502:physiology; D019295:Computational Biology / Q000379:methods*; D004271:DNA, Fungal / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D012319:RNA Polymerase II / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S; D012339:RNA, Ribosomal, 28S; D012319:RNA Polymerase II