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Persoonia 22, 2009: 129 –138
www.persoonia.org doi:10.3767/003158509X461486
RESEARCH ARTICLE
INTRODUCTION
The multi-gene sequence datasets generated by the research
consortium ‘Assembling the Fungal Tree of Life’ (AFTOL)
have resulted in several multi-gene phylogenies incorporating
comprehensive taxon sampling across Fungi (Lutzoni et al.
2004, Blackwell et al. 2006, James et al. 2006). AFTOL gener-
ated a data matrix spanning all currently accepted classes in
the Ascomycota, the largest fungal phylum. The phylogenies
produced by AFTOL prompted the proposal of a phylogenetic
classification from phylum to ordinal level in fungi (Hibbett et
al. 2007). Although the Botanical Code does not require the
principle of priority in ranks above family (McNeill et al. 2006),
this principle was nevertheless followed for all taxa. The fol-
lowing ranked taxa were defined: subkingdom, phylum (suffix
-mycota, except for Microsporidia), subphylum (-mycotina),
class (-mycetes), subclass (-mycetidae) and order (-ales). As
in Hibbett et al. (2007), several phylogenetically well-supported
nodes above the rank of order could not be accommodated
in the current hierarchical classification system based on the
International Code of Botanical Nomenclature. To remedy this
deficiency, rankless (or unranked) taxa for unambiguously
resolved nodes with strong statistical support was proposed
(Hibbett & Donoghue 1998). Hybrid classifications that include
both rankless and Linnaean taxa have since been discussed
elsewhere (Jørgensen 2002, Kuntner & Agnarsson 2006), and
applied to diverse organisms from lichens (Stenroos et al. 2002)
and plants (Sennblad & Bremer 2002, Pfeil & Crisp 2005) to
spiders (Kuntner 2006). These studies all attempt to create a
comprehensive code for phylogenetic nomenclature that retains
the current Linnean hierarchical codes.
In keeping with the practice of previous hybrid classifications, we
propose to use names corresponding to clades of higher taxa
that were resolved in this phylogeny as well as preceding studies.
The proposed informal, rankless names for well-supported
clades above the class level in our phylogeny agrees with the
principles of the Phylocode (http://www.ohio.edu/phylocode/).
It is our hope that such names should function as rankless
taxa, facilitating the naming of additional nodes/clades as they
become resolved. Eventual codification will follow the example
of Hibbett et al. (2007) by applying principles of type names
and priority. A number of published manuscripts already provide
background on other supraordinal relationships of Fungi; for
more complete treatments of the various classes, see Blackwell
et al. (2006).
During the AFTOL project a data matrix was generated span-
ning all currently accepted classes in the Ascomycota, the
largest fungal phylum. A multi-gene phylogeny was recently
inferred from these data, demonstrating relevant patterns in
biological and morphological character development as well as
establishing several distinct lineages in Ascomycota (Schoch
et al. 2009). Here we test whether the relationships reported in
Schoch et al. (2009) remain valid by applying both maximum
likelihood (ML) and Bayesian analyses on a more restricted
but denser set of taxa, including expanded sampling in the
Geoglossaceae.
We will therefore address the taxonomic placement of a group
of fungi with earth tongue morphologies that are shown to be
unrelated to other known classes. This morphology is closely
associated with the family Geoglossaceae (Corda 1838). With
typical inoperculate asci and an exposed hymenium, Geoglos-
saceae has long been thought to be a member of Leotiomy-
cetes, though the content of the family itself has experienced
many changes (Nannfeldt 1942, Korf 1973, Spooner 1987,
Platt 2000, Wang et al. 2006a, b). It is currently listed with 48
species and 6 genera in the Dictionary of the Fungi (Kirk et
al. 2008). Several analyses using molecular data supported
a clade including three earth tongue genera, Geoglossum,
Trichoglossum and Sarcoleotia (Fig. 1), and cast doubt upon
their positions in Leotiomycetes (Platt 2000, Gernandt et al.
2001, Lutzoni et al. 2004, Sandnes 2006, Spatafora et al. 2006,
Wang et al. 2006b). Here we present a comprehensive phylum-
wide phylogeny, including data from protein coding genes. We
can confidently place the earth tongue family as separate from
currently accepted classes in Ascomycota.
Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa
above class rank in the Ascomycota Tree of Life
C.L. Schoch
1
, Z. Wang
2
, J.P. Townsend
2
, J.W. Spatafora
3
1
National Center for Biological Information (GenBank), National Library
of Medicine, National Institute of Health, 45 Center Drive, MSC 6510,
Bethesda, Maryland 20892-6510, USA;
corresponding author e-mail: s
choch2@ncbi.nlm.nih.gov
2
Department of Ecology and Evolutionary Biology, Yale University, 165
Prospect Street, New Haven, CT 06520, USA.
3
Department of Botany and Plant Pathology, Oregon State University,
Corvallis, OR 97331, USA.
Key words
Bayesian inference
hybrid classification
maximum likelihood
Abstract Featuring a high level of taxon sampling across Ascomycota, we evaluate a multi-gene phylogeny and
propose a novel order and class in Ascomycota. We describe two new taxa, Geoglossomycetes and Geoglossales,
to host three earth tongue genera: Geoglossum, Trichoglossum and Sarcoleotia as a lineage of ‘Leotiomyceta’.
Correspondingly, we confirm that these genera are not closely related to the genera Neolecta, Mitrula, Cudonia,
Microglossum, Thuemenidum, Spathularia and Bryoglossum, all of which have been previously placed within the
Geoglossaceae. We also propose a non-hierarchical system for naming well-resolved nodes, such as ‘Saccharo-
myceta’, ‘Dothideomyceta’, and ‘Sordariomyceta’ for supraordinal nodes, within the current phylogeny, acting as
rankless taxa. As part of this revision, the continued use of ‘Leotiomyceta’, now as a rankless taxon, is proposed.
Article info Received: 16 April 2009; Accepted: 11 May 2009; Published: 5 June 2009.
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Sarcoleotia globosa 2
Sarcoleotia globosa 3
Geoglossum umbratile
Geoglossum nigritum
Geoglossum glabrum
Microglossum olivaceum
Leotia lubrica
Thuemenidium atropurpureum 1
Microglossum rufum 1
Microglossum rufum 2
Thuemenidium atropurpureum 2
Mitrula elegans
Mitrula brevispora
Lambertella subrenispora
Monilinialaxa
Botryotinia fuckeliana
Cudoniella clavus
Lachnum virgineum
Bryoglossum gracile
Neofabrea malicorticis
Dermea acerina
Cudonia circinans
Spathularia velutipes 1
Spathularia velutipes 2
Neobulgaria pura
Basidiomycota
Taphrinomycotina
Saccharomycotina
Pezizomycetes
Orbiliomycetes
Laboulbeniomycetes
Sordariomycetes
Lichinomycetes
Dothideomycetes
Arthoniomycetes
Eurotiomycetes
Lecanoromycetes
Sarcoleotia globosa 1
‘Sordario-
myceta’
‘Leotio-
myceta’
‘Saccharo-
myceta’
‘Dothideo-
myceta’
Trichoglossum hirsutum 1
Trichoglossum hirsutum 2
Geoglossomycetes
Pezizo-
mycotina
Saccharo-
mycetes
Taphrinomycetes
Neolectomycetes
Schizosaccharomycetes
Leotiomycetes
92
91
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9290
Asco-
mycota
D
C
E
A
B
A
B
C
D
E
Fig. 1 A most likely tree obtained by RAxML for Ascomycota. Subphyla, class and rankless taxa are indicated. Classes containing fungi designated as earth
tongues are indicated in black. The tree was rooted with outgroup Rhizopus oryzae (not shown). Bootstrap values are shown in orange and Bayesian poste-
rior probabilities in blue. Orange, bold branches are supported by more than 80 % bootstrap and 95 % posterior probability, respectively. The full phylogeny,
without collapsed clades, are shown in Fig. 2. The inset figures illustrate morphological ascomal diversity in the earth tongues. The species are as follows:
A. Trichoglossum hirsutum; B. Geoglossum nigritum; C. Microglossum rufum; D. Spathularia velutipes; E. Geoglossum nigritum. Photo credits: A: Zhuliang
Yang; B, D, E: Kentaro Hosaka; C: Dan Luoma.
MATERIALS AND METHODS
Data were extracted from the complete data matrix obtained
from the WASABI database (www.aftol.org), incorporating
representatives for all currently accepted classes, and maxi-
mizing the number of orders and available data. Following the
approach of James et al. (2006) we performed a combined
analysis, with both DNA and amino acid data, while allowing
for missing data. This data was supplemented with additional
ribosomal sequences from earth tongue genera obtained and
deposited in GenBank from two previous studies (Wang et al.
2006a, b). To further minimise poorly aligned areas, 219 ad-
ditional columns, which proved variable when viewed in BioEdit
with a 40 % shade threshold, were excluded from the original
AFTOL inclusion set. The refined dataset consisted of 161 taxa
(including outgroups) and 4 429 characters for six different
loci: the nuclear small and large ribosomal subunits (nSSU,
nLSU), the mitochondrial small ribosomal subunit (mSSU) and
fragments from three proteins: transcription elongation factor
1 alpha (TEF1) and the largest and second largest subunits of
131
C.L. Schoch et al.: Geoglossomycetes
RNA polymerase II (RPB1, RPB2). A complete table with the
published GenBank numbers is listed in Table 1.
The phylogenetic analysis was run in RAxML v7.0.0 (Stama-
takis 2006), partitioning by gene (six partitions) and estimating
unique model parameters for each gene, as in Schoch et al.
(2009). Models of evolution were evaluated as in Schoch et al.
(2009) with the same models selected. For DNA sequences,
this resulted in a general time reversible model (GTR) with a
discrete gamma distribution composed of four rate classes
plus an estimation of the proportion of invariable sites. The
amino acid sequences were analysed with a RTREV model
with similar accommodation of rate heterogeneity across sites
and proportions of invariant sites. In addition, protein models for
TEF1 and RPB2 incorporated a parameter to estimate amino
acid frequencies. The tree shown in Fig. 1 was obtained by
using an option in RAxML running a rapid bootstrap analysis
and search for the best-scoring ML tree in one single run. This
meant the GTRCAT model approximation was used, which does
not produce likelihood values comparable to other programs.
The full tree is shown here as Fig. 2 and was deposited in
TreeBASE (www.treebase.org). We also ran 100 repetitions
of RAxML under a gamma rate distribution option. The best
scoring tree was included in TreeBASE.
A second analysis was run using Bayesian inference of maxi-
mum likelihood in MrBayes v3.1.2 (Huelsenbeck & Ronquist
2001, Altekar et al. 2004) using models and parameters that
were comparable to the maximum likelihood run. Data were
similarly partitioned and amino acids were analysed, so that
a mixture of models with fixed rate matrices for amino acid
sequences could be evaluated. In all cases rate heterogeneity
parameters were used by a discrete gamma distribution plus
an estimation of the proportion of invariable sites. A metropolis
coupled Markov Chain Monte Carlo analysis was run for 9
million generations sampling every 200th cycle, starting from
a random tree and using 4 chains (three heated and one cold)
under default settings. Two separate runs were confirmed to
converge using Tracer v1.4.1 (http://tree.bio.ed.ac.uk/software/
tracer/). The first 10 000 sampled trees (2 million generations)
were removed as burn in each run. A 50 % majority rule con
-
sensus tree of 70 000 Bayesian likelihood trees from the two
combined runs was subsequently constructed, and average
branch lengths and posterior probabilities determined. The
numbers of nodes shared with the most likely tree in Fig. 1 was
determined and plotted on the branches. This tree was depos-
ited in TreeBASE, along with the inclusive character set.
RESULTS
The phylogeny presented in Fig. 1 supports 15 classes (11 in
Pezizomycotina, 1 in Saccharomycotina, 3 in Taphrinomycotina)
with good statistical support (both ML bootstrap and Bayesian
posterior probability) for 14. Phylogenies with all lineages in the
analysed data matrix are included in Fig. 2. A run with 100 repeti-
tions of RAxML under a gamma rate distribution option resulted
in a best scoring tree with a log likelihood of -111983. This tree
shared the same supported nodes with the one presented in
Fig. 1 but had changes in poorly supported nodes regarding
placement of the Eurotiomycetes and Dothideomycetes. The
two Bayesian runs produced trees with harmonic means of
likelihood values of -112094 and -112076, respectively, with
similar topological differences in poorly supported nodes.
As can be seen in Fig. 1, we continue to find low bootstrap and
posterior probability support for Leotiomycetes as a mono-
phyletic clade using a combined analysis of protein and nucleic
acids. In our analysis, this includes Neobulgaria pura as the
earliest diverging lineage. The node internal from this lineage
is found in all ML bootstrap trees, suggesting that this taxon is
unstable in our analyses. No conflicts were detected in Neob-
ulgaria genes under a previous study and missing data did not
affect important nodes (Schoch et al. 2009). A repeat run under
maximum likelihood was done with Neobulgaria pura removed
under the same settings but with only 100 bootstrap repetitions.
This trimmed dataset yielded a congruent phylogeny with in
-
creased bootstrap for Leotiomycetes (78 %; data not shown).
The instability of the placement of Neobulgaria pura does not
compromise any of the conclusions we present here and may
be due to various reasons. Improved taxon sampling will likely
help to resolve its placement in future analyses.
We find support for numerous backbone nodes in Ascomycota,
as did Schoch et al. (2009). Our phylum-wide sampling of
Ascomycota
classes in this study, combined with the results
of a previous study (Schoch et al. 2009), facilitated addressing
the placement of the previously problematic and unsampled
lineages such as the Geoglossaceae in relation to all currently
accepted Ascomycota classes.
Taxonomy
Given their unique ascomatal development, ultrastructure of
ascus apical apparatus, mossy habitat, and our multilocus gene
phylogeny, Geoglossomycetes cl. & ord. nov. is justified here as
incertae sedis in Pezizomycotina and ‘Leotiomyceta’.
Geoglossomycetes, Geoglossales Zheng Wang, C.L. Schoch
& Spatafora, cl. & ord. nov. — MycoBank MB513351,
MB513352
Ascomata solitaria vel gregaria, capitata, stipitata; stipe cylindricus, atrum,
glabrum vel furfuraceus. Regio hymeniali capitata, clavata vel pileata, in-
distinctum ex stipite; hymenium atrum, continuatcum stipite ad praematuro
incrementi grado. Asci clavati, inoperculati, octospori, poro parvo in iodo
caerulescentes. Ascosporae elongatae, fuscae, pullae vel hyalinae, multi-
septatae. Paraphyses filiformes, pullae vel hyalinae. Distributio generalis,
terrestris, habitaile locus fere uliginoso et muscoso.
Type genus. Geoglossum Pers., Neues Mag. Bot. 1: 116. 1794; Geoglos-
saceae.
Ascomata scattered to gregarious, capitate, stipitate; stipe cylin-
drical, black, smooth to furfuraceous. Ascigerous portion capitate,
club-shaped to pileate, indistinguishable from stipe. Hymenium
surface black, continues with stipe at early development stage.
Asci clavate, inoperculate, thin-walled, J+, usually 8-spored.
Ascospores elongate, dark-brown, blackish to hyaline, septate
when mature. Paraphyses filiform, blackish to hyaline. Global
distribution, terrestrial, habitat usually boggy and mossy.
DISCUSSION
In keeping with the phylogeny presented in Fig. 1, we endorse
use of the -myceta suffix in order to circumscribe well-sup-
ported clades above class. The numbers of these clades are
limited, and the use of such taxa will continue to become more
practical as our biological knowledge base broadens. Use of
this suffix will also allow for the continued use of Leotiomyceta,
a taxon that has already been defined with a Latin diagnosis
provided as a ranked superclass (Eriksson & Winka 1997) and
remains in use (Lumbsch et al. 2005, Wang et al. 2006a). We
propose its continued use, but as a rankless taxon together
with the newly proposed rankless taxa, ‘Saccharomyceta’,
‘Dothideomyceta’ and ‘Sordariomyceta’. Since these taxa are
not currently accepted under the Code (McNeill et al. 2006),
we will refrain from formal designations. The relevant clades
are discussed below with the informal designations indicated
in single quotations.
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Pleospora herbarum
Cochliobolus heterostrophus
Allewia eureka
Pyrenophora phaeocomes
Leptosphaeria maculans
Phoma herbarum
Ascochyta pisi
Sporormiella minima
Westerdykella cylindrica
Pleomassaria siparia
Lepidosphaeria nicotiae
Ulospora bilgramii
Verruculina enalia
Delitschia winteri
Gloniopsis smilacis
Hysterographium mori
Hysterium angustatum
Mytilinidion australe
Mytilinidion rhenanum
Lophium mytilinum
Botryosphaeria tsugae
Botryosphaeria dothidea
Guignardia gaultheriae
Guignardia bidwellii
Tubeufia paludosa
Helicomyces roseus
Mycosphaerella punctiformis
Mycosphaerella graminicola
Mycosphaerella fijiensis
Capnodium coffeae
Scorias spongiosa
Cladosporium cladosporioides
Davidiella tassiana
Dothiora cannabinae
Dothidea sambuci
Sydowia polyspora
Myriangium duriaei
Elsinoë veneta
Schismatomma decolorans
Roccella fuciformis
Roccellographa cretacea
Lobaria scrobiculata
Lobariella pallida
Peltigera degenii
Nephroma parile
Coccocarpia erythroxyli
Lecidea fuscoatra
Hypogymnia physodes
Canoparmelia caroliniana
Pyxine subcinerea
Heterodermia vulgaris
Teloschistes exilis
Diploschistes ocellatus
Glomerobolus gelineus
Trapelia placodioides
Icmadophila ericetorum
Pertusaria dactylina
Ceramothyrium carniolicum
Cyphellophora laciniata
Exophiala salmonis
Staurothele frustulenta
Agonimia sp.
Coccidioides immitis
Ajellomyces capsulatum
Aspergillus protuberus
Eupenicillium limosum
Caliciopsis orientalis
Peltula umbilicata
Peltula auriculata
Lichinella iodopulchra
Epichloë typhina
Claviceps purpurea
Elaphocordyceps capitata
Elaphocordyceps ophioglossoides
Cordyceps cardinalis
Nectria cinnabarina
Hypocrea lutea
Bionectria cf. aureofulva
Melanospora tiffanyae
Bertia moriformis
Gondwanamyces capensis
Ceratocystis fimbriata
Halosphaeria appendiculata
Corollospora maritima
Glomerella cingulata
Verticillium dahliae
Cryptosporella hypodermia
Gnomonia gnomon
Endothia gyrosa
Diaporthe eres
Calosphaeria pulchella
Magnaporthe grisea
Gaeumannomyces medullaris
Ophiostoma stenoceras
Sordaria fimicola
Neurospora crassa
Xylaria hypoxylon
Lindra thalassiae
Lulworthia grandispora
Stigmatomyces protrudens
Hesperomyces virescens
Pyxidiophora avernensis
Botryotinia fuckeliana
Monilinia laxa
Lambertella subrenispora
Mitrula brevispora
Mitrula elegans
Bryoglossum gracile
Lachnum virgineum
Cudoniella cf. clavus
Dermea acerina
Neofabraea malicorticis
Microglossum rufum 2
Microglossum rufum 1
Thueminidium atropurpureum 1
Thueminidium atropurpureum 2
Leotia lubrica
Microglossum olivaceum
Spathularia velutipes 1
Spathularia velutipes 2
Cudonia circinans
Neobulgaria pura
Geoglossum glabrum
Geoglossum nigritum
Geoglossum umbratile
Trichoglossum hirsutum 1
Trichoglossum hirsutum 2
Sarcoleotia globosa 2
Sarcoleotia globosa 3
Sarcoleotia globosa 1
Arthrobotrys elegans
Orbilia vinosa
Aleuria aurantia
Scutellinia scutellata
Pyronema domesticum
Eleutherascus lectardii
Sarcosoma latahense
Gyromitra californica
Verpa conica
Caloscypha fulgens
Ascobolus carbonarius
Saccobolus dilutellus
Peziza vesiculosa
Sarcosphaera crassa
Saccharomyces cerevisiae
Candida glabrata
Eremothecium gossypii
Candida tropicalis
Debaryomyces hansenii
Taphrina wiesneri
Taphrina deformans
Saitoella complicata
Schizosaccharomyces pombe
Neolecta vitellina
Neolecta irregularis
Fomitopsis pinicola
Grifola frondosa
Calostoma cinnabarinum
Calocera cornea
Cryptococcus neoformans
Basidio-
myco
ta
Sordariomycetes
Dothideomycetes
Lecanoromycetes
Eurotiomycetes
L
aboulbenio-
myce
tes
Orbiliomycetes
Orbiliales
Pezizomycetes
Pezizales
Geoglossomycetes, cl. nov.
Geoglossales, ord. nov.
Leotiomycetes
Helotiales
Rhytismatales
Pyxidiophorales
Laboulbeniales
Lulworthiales
Xylariales
Sordariales
Ophiostomatales
Magnaporthales
Calosphaeriales
Diaporthales
Microascales
Hypocreales
Coronophorales
Melanosporales
Pleosporales
Mytilinidiales
Hysteriales
Botryosphaeriales
Capnodiales
Dothideales
Myriangiales
Pertusariales
Peltigerales
Lecanorales
Teloschistales
Ostropales
Agyriales
Eurotiales
Onygenales
Chaeto-
thyriales
Verrucariales
Coryneliales
Arthoniomycetes
Arthoniales
Lichinomycetes
Lichinales
Schizosaccharomycetes,
Schizosaccharomycetales
Asco-
myco
ta
Outgroup
Rhizopus oryzae
(not shown)
‘Saccharo-
myce
t
a’
‘Dothideo-
myce
t
a’
‘Leotio-
myce
t
a’
‘Sordario-
myce
t
a’
Pezizo-
mycotina
Saccharo-
mycotina
Taphrino-
mycotina
Neolectomycetes
Neolectales
Saccharomycetes
Saccharomycetales
Taphrinomycetes
Taphrinales
l l
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Fig. 2 A most likely tree obtained by RAxML for Ascomycota (as in Fig. 1). Phyla, subphyla, class, order and rankless taxa are indicated. Taxa designated as
earth tongues are indicated in orange. The tree is displayed as two subtrees – orange arrows indicate where the subtrees were joined. The tree was rooted
with outgroup Rhizopus oryzae (not shown). Bootstrap values are shown in orange above nodes and Bayesian posterior probabilities in blue below. Numbers
were removed for nodes with 100 % bootstrap and 100 % posterior probability.
133
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Subphylum Taphrinomycotina
As in recent studies using large multi-gene datasets (Spatafora
et al. 2006, Sugiyama et al. 2006, Liu et al. 2009, Schoch et al.
2009), we find ML bootstrap support here for the monophyly of
the Taphrinomycotina. The addition of sequences from protein
coding genes has been vital to the establishment of statistical
support for this grouping. Recent work has shown that the short
generation times characteristic of species in this group make
phylogenetic analyses particularly susceptible to long branch
attraction artefacts (Liu et al. 2009). The placement of Neolecta
in this subclade is also confirmed here. The club-shaped apoth-
ecia of the members of Neolecta share superficial similarity with
those of the Geoglossaceae. Neolecta was long thought to be
included in the Geoglossaceae until molecular work proved oth-
erwise (Landvik 1996). In support of its placement in this early
diverging group, Neolecta has several presumably ancestral
features, such as simplified non-poricidal asci without croziers
and the absence of paraphyses (Redhead 1979, Landvik et al.
2003). With additional sampling of both taxa and genes we find
here moderate support for the monophyly of Taphrinomycotina,
and thus demonstrate that the earliest diverging clade of the
Ascomycota was dimorphic, with both filamentous and yeast
growth forms. Nevertheless, it remains apparent that this part
of the Ascomycota tree remains under sampled. This lack of
adequate sampling is supported by the recent description of a
clade labelled ‘Soil Clone Group I’ (SCGI). SCGI is ubiquitous
in soil and is only known from environmental sequence data
(Porter et al. 2008). It appears possible that they form a novel
early diverging lineage outside of Taphrinomycotina. Very little
remains known about their ecology, morphology and general
biology.
Rankless taxon ‘Saccharomyceta’
‘Saccharomyceta’ includes the two remaining subphyla of
Ascomycota, Saccharomycotina and Pezizomycotina. Saccha-
romycotina comprises the ‘true yeasts’ (e.g., Saccharomyces
cerevisiae), although hyphal growth has been documented in
some taxa (e.g., Eremothecium). The Pezizomycotina consists
of the majority of filamentous, ascoma producing species, but
numerous species are additionally capable of yeast and yeast-
like growth phases. Thousands of species are only known
to reproduce asexually. These two subphyla form a well-sup-
ported, monophyletic group that has been recovered in a large
number of studies across a diversity of character and taxon
sets. The recognition of ‘Saccharomyceta’ highlights the shared
common ancestry of these two taxa and the inaccurate charac-
terisation of Saccharomycotina as a primitive or basal lineage
of the Ascomycota. Rather, its small genome size (Dujon et al.
2004) and dominant yeast growth phase can be characterized
as derived traits for this subphylum.
Rankless taxon ‘Leotiomyceta’
We apply ‘Leotiomyceta’ as a rankless taxon containing the
majority of fungi with a diversity of inoperculate asci (e.g.,
fissitunicate, poricidal, deliquescent). ‘Leotiomyceta’ excludes
the earliest diverging classes of Pezizomycotina, Pezizomy-
cetes and Orbiliomycetes. It was first defined as a superclass
(Eriksson & Winka 1997). This definition has remained in
use (Lumbsch et al. 2005, Spatafora et al. 2006). Included in
this clade are the informal, rankless taxa ‘Dothideomyceta’,
‘Sordariomyceta’, as well as the classes Eurotiomycetes, Le-
canoromycetes, Lichinomycetes, and a newly proposed class,
Geoglossomycetes.
The type genus of Geoglossaceae, Geoglossum was initially
proposed by Persoon (1794). Persoon described it as club-
shaped, with unitunicate, inoperculate asci, with the type
species given as Geoglossum glabrum Pers. Trichoglossum
have historically been classified in Geoglossaceae, and Sar-
coleotia has historically been classified in the Helotiaceae
(Leotiomycetes). These inoperculate Discomycetes produce
terrestrial, stipitate, clavate ascomata, commonly referred to as
earth tongues, which include Leotia, Microglossum, Cudonia,
and Spathularia. In terms of ascomatal development, species
of Geoglossum, Trichoglossum, and Sarcoleotia possess a
hymenium that freely develops towards the base, while other
earth tongue fungi feature a distinct ridge to their hymenium,
implying a developmental stage during which the hymenium is
enclosed (Schumacher & Sivertsen 1987, Spooner 1987, Wang
et al. 2006b). An enclosed hymenium has been observed as
well in several other lineages, such as Cyttaria, Erysiphales
and Rhytismatales in the Leotiomycetes (Korf 1983, Gargas
et al. 1995, Johnston 2001). Although the name earth tongue
implies these fungi are terrestrial and have no direct associa-
tion found with other organisms, Trichoglossum, Geoglossum
and Sarcoleotia globosa have often been recorded in boggy
habitats abundant with bryophytes (Seaver 1951, Dennis 1968,
Schumacher & Sivertsen 1987, Spooner 1987, Jumpponen et
al. 1997, Zhuang 1998). Ascus apical morphology is one of
the major features in distinguishing higher ascomycetes, and
operculate ascomycetes as members of Pezizales have an
apical or subapical operculum which is thrown back at spore
discharge while a definite plug is present in the thickened
‘inoperculate’ ascus apex as in species of the Helotiales (Korf
1973). Ultrastructure of the ascus apical apparatus suggested
no close relationship between Leotia lubrica and species of
Geoglossum and Trichoglossum. A structure known as a tractus
connects the uppermost spore to the apical wall and the spores
to each other in Trichoglossum hirsutum, but is never found in
other species of the Helotiales and is possibly homologous to
structures in Sordariomycetes and Pezizomycetes (Verkley
1994). Recent molecular phylogenetic analyses (Sandnes
2006, Wang et al. 2006a, b) confirmed that the earth tongue
fungi are not monophyletic. At least two origins occurred in
Leotiomycetes: in Leotia and allies in Helotiales, and in Cudo-
nia and allies in Rhytismatales. Geoglossum, Trichoglossum.
Sarcoleotia (Geoglossomycetes as we define it) represent a
third, independent lineage of earth tongues, which we confirmed
does not belong within the Leotiomycetes.
DNA-only and combined model analyses produced conflicting
placements of Geoglossaceae within Pezizomycotina. Previ-
ous analyses applying nucleotide sequences only placed the
order as a sister group to the Lichinomycetes (Lutzoni et al.
2004, Spatafora et al. 2006), which includes a small number
of lichenised species mainly associated with cyanobacteria
(Reeb et al. 2004). Our sampling of Lichinomycetes includes
two genera, Peltula and Lichinella that encompass at least
some of the ascal diversity, i.e., rostrate and deliquescent,
present in the class. In contrast, our combined amino acid and
nucleotide model analyses resolved Geoglossaceae as an
isolated, unique lineage of ‘Leotiomyceta’ with no supported
sister relationship, in agreement with Schoch et al. (2009). Dif-
ferent levels of missing data underlie these two conflicting
topologies, and several phenomena can potentially explain this
conflict, ranging from model misspecification to long-branch
attraction. Regardless of these concerns, our conclusion that
the Geoglossaceae is a monophyletic lineage, unallied with
members of the Leotiomycetes and any of the other large fungal
classes remains strongly supported.
Eurotiomycetes and Lecanoromycetes are the two remaining
classes in ‘Leotiomyceta’. Eurotiomycetes is arguably the most
ecologically diverse class within Ascomycota including lichen-
ised species, saprobes and pathogens of animals and plants.
As currently defined, this class incorporates several distinct
orders and three subclasses spanning virtually all known fun-
