title: 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 Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708-0338 USA;
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
authors.forename: Frank
authors.initials: F
authors.lastname: Kauff
authors.forename: Cymon J
authors.initials: CJ
authors.lastname: Cox
authors.forename: David
authors.initials: D
authors.lastname: McLaughlin
authors.forename: Gail
authors.initials: G
authors.lastname: Celio
authors.forename: Bryn
authors.initials: B
authors.lastname: Dentinger
authors.forename: Mahajabeen
authors.initials: M
authors.lastname: Padamsee
authors.forename: David
authors.initials: D
authors.lastname: Hibbett
authors.forename: Timothy Y
authors.initials: TY
authors.lastname: James
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Baloch
authors.forename: Martin
authors.initials: M
authors.lastname: Grube
authors.forename: Valérie
authors.initials: V
authors.lastname: Reeb
authors.forename: Valérie
authors.initials: V
authors.lastname: Hofstetter
authors.forename: Conrad
authors.initials: C
authors.lastname: Schoch
authors.forename: A Elizabeth
authors.initials: AE
authors.lastname: Arnold
authors.forename: Jolanta
authors.initials: J
authors.lastname: Miadlikowska
authors.forename: Joseph
authors.initials: J
authors.lastname: Spatafora
authors.forename: Desiree
authors.initials: D
authors.lastname: Johnson
authors.forename: Sarah
authors.initials: S
authors.lastname: Hambleton
authors.forename: Michael
authors.initials: M
authors.lastname: Crockett
authors.forename: Robert
authors.initials: R
authors.lastname: Shoemaker
authors.forename: Gi-Ho
authors.initials: GH
authors.lastname: Sung
authors.forename: Robert
authors.initials: R
authors.lastname: Lücking
authors.forename: Thorsten
authors.initials: T
authors.lastname: Lumbsch
authors.forename: Kerry
authors.initials: K
authors.lastname: O'Donnell
authors.forename: Manfred
authors.initials: M
authors.lastname: Binder
authors.forename: Paul
authors.initials: P
authors.lastname: Diederich
authors.forename: Damien
authors.initials: D
authors.lastname: Ertz
authors.forename: Cécile
authors.initials: C
authors.lastname: Gueidan
authors.forename: Karen
authors.initials: K
authors.lastname: Hansen
authors.forename: Richard C
authors.initials: RC
authors.lastname: Harris
authors.forename: Kentaro
authors.initials: K
authors.lastname: Hosaka
authors.forename: Young-Woon
authors.initials: YW
authors.lastname: Lim
authors.forename: Brandon
authors.initials: B
authors.lastname: Matheny
authors.forename: Hiromi
authors.initials: H
authors.lastname: Nishida
authors.forename: Don
authors.initials: D
authors.lastname: Pfister
authors.forename: Jack
authors.initials: J
authors.lastname: Rogers
authors.forename: Amy
authors.initials: A
authors.lastname: Rossman
authors.forename: Imke
authors.initials: I
authors.lastname: Schmitt
authors.forename: Harrie
authors.initials: H
authors.lastname: Sipman
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Stone
authors.forename: Junta
authors.initials: J
authors.lastname: Sugiyama
authors.forename: Rebecca
authors.initials: R
authors.lastname: Yahr
authors.forename: Rytas
authors.initials: R
authors.lastname: Vilgalys