Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

Abstract

Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

A higher-level phylogenetic classification of the Fungi

“…Anamorphs variable, including phialidic and arthroconidial forms. This name was employed by Lutzoni et al (2004) and Geiser et al (2007), in the same sense as the present classification, but without a formal diagnosis.…”

“…The members of this order were formerly classified within the Lecanorales, but Reeb et al (2004) and Lutzoni et al (2004) demonstrated that the Acarosporaceae diverged earlier than the Lecanoromycetidae and Ostropomycetidae. This early divergence within the Lecanoromycetes was confirmed by Wedin et al (2005) Ascomycetes lichenisati algas virides vel cyanobacteria thallo continentes.…”

“…This subclass includes the bulk of lichenized discomycetes and corresponds to the phylogenetic circumscription of this subclass by Reeb et al (2004), Lutzoni et al (2004) Order: Lecanorales Nannf., Nova Acta R. Soc. Scient.…”

“…1) LSU 6 MPBS ¼ 53 Ré blová (2006, fig. 1 The circumscription of this class and the classification within the Eurotiomycetes presented here are derived from the phylogenetic re-delimitation of this class by Ekman & Tønsberg (2002), Lutzoni et al (2004) and Geiser et al (2007), reflecting the inference of shared ancestry between Eurotiomycetes, comprising Coryneliales, Onygenales and Eurotiales and Chaetothyriomycetes. Three subclasses, Chaetothyriomycetidae, Eurotiomycetidae, and Mycocaliciomycetidae, are defined to represent the major lineages within Eurotiomycetes.…”

Wood production, wood technology, and biotechnological impacts

“…morphological, ultrastructural and biochemical) characters is available to the scientific community which will be continuously updated as the understanding of phylogenetic relationships improves and additional annotations become available (Lutzoni et al 2004, http://ocid.nacse.org/research/aftol/). The major advantage of this database is that its datasets are provided and verified by experts of fungal systematics and the type specimens for each taxa are carefully selected.…”