The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
Schoch
Conrad L
CL
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
Sung
Gi-Ho
GH
López-Giráldez
Francesc
F
Townsend
Jeffrey P
JP
Miadlikowska
Jolanta
J
Hofstetter
Valérie
V
Robbertse
Barbara
B
Matheny
P Brandon
PB
Kauff
Frank
F
Wang
Zheng
Z
Gueidan
Cécile
C
Andrie
Rachael M
RM
Trippe
Kristin
K
Ciufetti
Linda M
LM
Wynns
Anja
A
Fraker
Emily
E
Hodkinson
Brendan P
BP
Bonito
Gregory
G
Groenewald
Johannes Z
JZ
Arzanlou
Mahdi
M
de Hoog
G Sybren
GS
Crous
Pedro W
PW
Hewitt
David
D
Pfister
Donald H
DH
Peterson
Kristin
K
Gryzenhout
Marieka
M
Wingfield
Michael J
MJ
Aptroot
André
A
Suh
Sung-Oui
SO
Blackwell
Meredith
M
Hillis
David M
DM
Griffith
Gareth W
GW
Castlebury
Lisa A
LA
Rossman
Amy Y
AY
Lumbsch
H Thorsten
HT
Lücking
Robert
R
Büdel
Burkhard
B
Rauhut
Alexandra
A
Diederich
Paul
P
Ertz
Damien
D
Geiser
David M
DM
Hosaka
Kentaro
K
Inderbitzin
Patrik
P
Kohlmeyer
Jan
J
Volkmann-Kohlmeyer
Brigitte
B
Mostert
Lizel
L
O'Donnell
Kerry
K
Sipman
Harrie
H
Rogers
Jack D
JD
Shoemaker
Robert A
RA
Sugiyama
Junta
J
Summerbell
Richard C
RC
Untereiner
Wendy
W
Johnston
Peter R
PR
Stenroos
Soili
S
Zuccaro
Alga
A
Dyer
Paul S
PS
Crittenden
Peter D
PD
Cole
Mariette S
MS
Hansen
Karen
K
Trappe
James M
JM
Yahr
Rebecca
R
Lutzoni
François
F
Spatafora
Joseph W
JW
D001203:Ascomycota / Q000145:classification / Q000166:cytology / Q000235:genetics*; D017753:Ecosystem; D005800:Genes, Fungal; D010802:Phylogeny; D012098:Reproduction