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.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

“…Highly variable lengths and high evolutionary rates for the nuclear ribosomal cistron in species of Cantharellus, Tulasnella (Cantherellales, Basidiomycota) (61)(62)(63), and some lichens (53) may provide challenges for sequencing and analysis. The upper range of this ITS region variation is likely found in the Glomeromycota, with up to 20% divergence within a single multinucleate spore (64,65).…”

Vascular Streak Dieback of cacao in Southeast Asia and Melanesia: in planta detection of the pathogen and a new taxonomy

“…Clades with bootstrap values of 70 % or greater were considered as significantly supported by the data (Hillis & Bull 1993). For analysis of ITS and LSU sequences, isolates in the genus Botryobasidium were used as outgroup taxa based on the study of Moncalvo et al 2006 that placed Botryobasidium as a sister group to the Clade of Ceratobasidium and Thanatephorus.…”

“…The dataset also contained three sequences of Botryobasidium and one Uthatobasidium. The latter two genera have been shown to be sister to Ceratobasidium and Thanatephorus (Moncalvo et al 2006;Rodriguez-Carres et al 2010) and Botryobasidium botryosum was used as outgroup to root the tree. The dataset contained a total of 823 characters of which 138 ambiguously aligned characters were excluded from analysis.…”

A higher-level phylogenetic classification of the Fungi

“…Equivalent to euagarics clade (Hibbett & Thorn 2001 Equivalent to the cantharelloid clade (Hibbett & Thorn 2001;Moncalvo et al 2007). The Cantharellales as delimited here includes Tulasnella, which is distinguished by unusual basidia with inflated sterigmata, and has been classified in a separate order, Tulasnellales Rea 1922 (e.g.…”