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REVIEW
Naming and outline of Dothideomycetes–2014 including proposals
for the protection or suppression of generic names
Nalin N. Wijayawardene &Pedro W. Crous &Paul M. Kirk &David L. Hawksworth &
Saranyaphat Boonmee &Uwe Braun &Dong-Qin Dai &Melvina J. D’souza &Paul Diederich &
Asha Dissanayake &Mingkhuan Doilom &Singang Hongsanan &E. B. Gareth Jones &
Johannes Z. Groenewald &Ruvishika Jayawardena &James D. Lawrey &Jian-Kui Liu &
Robert Lücking &Hugo Madrid &Dimuthu S. Manamgoda &Lucia Muggia &
Matthew P. Nelsen &Rungtiwa Phookamsak &Satinee Suetrong &Kazuaki Tanaka &
Kasun M. Thambugala &Dhanushka N. Wanasinghe &Saowanee Wikee &Ying Zhang &
André Aptroot &H. A. Ariyawansa &Ali H. Bahkali &D. Jayarama Bhat &Cécile Gueidan &
Putarak Chomnunti &G. Sybren De Hoog &Kerry Knudsen &Wen-Jing Li &
Eric H. C. McKenzie &Andrew N. Miller &Alan J. L. Phillips &Marcin Piątek &
Huzefa A. Raja &Roger S. Shivas &Bernad Slippers &Joanne E. Taylor &Qing Tian &
Yong Wang &Joyce H. C. Woudenberg &Lei Cai &Walter M. Jaklitsch &Kevin D. Hyde
Received: 16 August 2014 /Accepted: 30 September 2014 /Published online: 4 November 2014
#School of Science 2014
Abstract Article 59.1, of the International Code of Nomen-
clature for Algae, Fungi, and Plants (ICN; Melbourne Code),
which addresses the nomenclature of pleomorphic fungi, be-
came effective from 30 July2011. Since thatdate, each fungal
species can have one nomenclaturally correct name in a par-
ticular classification. All other previously used names for this
species will be considered as synonyms. The older generic
epithet takes priority over the younger name. Any widely used
younger names proposed for use, must comply with Art. 57.2
and their usage should be approved by the Nomenclature
Committee for Fungi (NCF). In this paper, we list all genera
currently accepted by us in Dothideomycetes (belonging to 23
In loving memory of Sajith Wijayawardene (09.03.1987-31.05.2014) −
you will always be missed as brother and best friend and I cherish the
memories we had together –N. N. Wijayawardene
Electronic supplementary material The online version of this article
(doi:10.1007/s13225-014-0309-2) contains supplementary material,
which is available to authorized users.
N. N. Wijayawardene ID.-Q. Dai IR. Phookamsak IW. -J . L i I
K. D. Hyde (*)
Key Laboratory for Plant Diversity and Biogeography of East Asia,
Kunming Institute of Botany, Chinese Academy of Science,
Kunming 650201, Yunnan, People’s Republic of China
e-mail: kdhyde3@gmail.com
N. N. Wijayawardene ID.-Q. Dai IR. Phookamsak IK. D. Hyde
World Agroforestry Centre, East and Central Asia,
Kunming 650201, Yunnan, People’s Republic of China
N. N. Wijayawardene IS. Boonmee ID.-Q. Dai IM. J. D'souza I
A. Dissanayake IM. Doilom IS. Hongsanan IR. Jayawardena I
J.-K. Liu ID. S. Manamgoda IR. Phookamsak IK. M. Thambugala I
D. N. Wanasinghe IS. Wikee IH. A. Ariyawansa ID. J. Bhat I
P. Chomnunti IW.-J . L i IQ. Tian IK. D. Hyde
Institute of Excellence in Fungal Research, Chiang Rai 57100,
Thailand
S. Boonmee ID.-Q. Dai IM. J. D'souza IA. Dissanayake IM. Doilom I
S. Hongsanan IR. Jayawardena IJ.-K. Liu ID. S. Manamgoda I
R. Phookamsak IK. M. Thambugala ID. N. Wanasinghe IS. Wikee I
H. A. Ariyawansa ID. J. Bhat IP. Chomnunti IW.- J . L i IQ. Tian
School of Science, Mae Fah Luang University,
Chiang Rai 57100,Thailand
Y. Wa n g
Department of Plant Pathology, Agriculture College,
Guizhou University, Guiyang 550025,
People’sRepublicofChina
P. W. Crous
Forestry and Agricultural Biotechnology Institute (FABI), University
of Pretoria, Pretoria 0002, South Africa
Fungal Diversity (2014) 69:1–55
DOI 10.1007/s13225-014-0309-2
orders and 110 families), including pleomorphic and non-
pleomorphic genera. In the case of pleomorphic genera, we
follow the rulings of the current ICN and propose single
generic names for future usage. The taxonomic placements
of 1261 genera are listed as an outline. Protected names and
suppressed names for 34 pleomorphic genera are listed sepa-
rately. Notes and justifications are provided for possible pro-
posed names after the list of genera. Notes are also provided
on recent advances in our understanding of asexual and sexual
morph linkages in Dothideomycetes. A phylogenetic tree
based on four gene analyses supported 23 orders and 75
families, while 35 families still lack molecular data.
Keywords Article 59.1 .Ascomycota .One name .
Phylogeny .Pleomorphism
Introduction
Dothideomycetes is one of the largest and most significant
classes within Ascomycota (Kirk et al. 2008; Schoch et al.
2009;Hyde et al. 2013). Thousands of species that are
important either as plant pathogens in agriculture and
forestry (Cortinas et al. 2006; Crous et al. 2007;Wikee
et al. 2011,2013a,b;Manamgodaetal.2012), or med-
ical (Siu and Lzumi 2004; da Cunha et al. 2012,2013)
or biotechnological industries (Verkley et al. 2004;
Damm et al. 2008; de Wit et al. 2012; Ohm et al.
2012; Stergiopoulos et al. 2012;Hydeetal.2014)are
included in the Dothideomycetes. A large number of
Dothideomycetes show pleomorphism, that is, they occur
as sexual and asexual states through their life history, but
may be separated in time and space (Kendrick 1979). As
a result dual names have been applied to the same genus
and this has resulted in a great deal of confusion among
scientists interested in Dothideomycetes (Cannon and
Kirk 2000; Wingfield et al. 2012). Furthermore, the dual
names have a direct influence on many allied disciplines,
such as plant quarantine and trade in food and fibre,
human health, industrial mycology, and plant breeding.
Saccardo (1904) promulgated the dual system of fungal
nomenclature (i.e. asexual and sexual morphs with different
P. W. Crous IJ. Z. Groenewald IH. Madrid IG. S. De Hoog I
J. H. C. Woudenberg
CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584
CT Utrecht, The Netherlands
P. M . Ki r k
State Key Laboratory of Mycology, Institute of Microbiology,
Chinese Academy of Sciences, Beijing, 100101,
People_s Republicof China
P. M . Ki r k ID. L. Hawksworth
Mycology Section, Royal Botanic Gardens, Kew, Richmond,
Surrey TW9 3DS, UK
D. L. Hawksworth IC. Gueidan
Department of Life Sciences, The Natural History Museum,
Cromwell Road, London SW7 5BD, UK
D. L. Hawksworth
Departamento de Biología Vegetal II, Facultad de Farmacia,
Universidad Complutense de Madrid, Plaza Ramón y Cajal,
Madrid 28040, Spain
H. Madrid
Center for Genomics and Bioinformatics and Medicine Faculty,
Mayor University, Camino La Pirámide 5750,
Huechuraba Santiago, Chile
U. Braun
Institut Für Biologie, Martin-Luther-Universität, Bereich Geobotanik
Und Botanischer Garten, Herbarium, Neuwerk 21, 06099 Halle
(Saale), Germany
P. Diederich
Musée National d'histoire Naturelle, 25 Rue Munster,
L-2160 Luxembourg, Luxembourg
A. Dissanayake IR. Jayawardena
Institute of Plant and Environment Protection,
Beijing Academy of Agriculture and Forestry Sciences,
Beijing 100097, People’s Republic of China
E. B. G. Jones
Department of Botany and Microbiology, College of Science,
King Saud University, P.O. Box 2455, Riyadh 11451,
Kingdom of Saudi Arabia
J. D. Lawrey
Department of Environmental Science and Policy, George Mason
University, 4400 University Drive, Fairfax, VA 22030-4444, USA
R. Lücking IM. P. Nelsen
Science and Education, Integrative Research (Botany),
The Field Museum, 1400 South Lake Shore Drive, Chicago,
IL 60605-2496, USA
L. Muggia
Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010,
Graz, Austria
L. Muggia
Department of Life Science, University of Trieste,
Via L. Giorgieri 10, Trieste, Italy
M. P. Nelsen
Committee on Evolutionary Biology, University of Chicago,
1025 E. 57th Street, Chicago, IL 60637, USA
S. Suetrong
Fungal Biodiversity Laboratory (BFBD), National Center for
Genetic Engineering and Biotechnology (BIOTEC),
113 Thailand Science Park, Phahonyothin Road, Khlong Nueng,
Khlong Luang, Pathum Thani, Thailand
2 Fungal Diversity (2014) 69:1–55
names) as a solution to the confused situation of asexual and
sexual morphs faced by taxonomists at the time. This was
accepted by the International Botanical Congress (IBC) in
Vienna, Austria (Briquet et al. 1906), and captured in what
became Article 59 in more recent editions of the International
Code of Botanical Nomenclature (ICBN) (Taylor 2011).
The concept of the ‘holomorph’(i.e. the whole life cycle
with sexual and asexual morphs) was first demonstrated by
the Tulasne brothers and Berkeley (1857). Kendrick (1979)
and Sivanesan (1984) are classic mycologists who attempted
to integrate asexual and sexual morphs. Sutton (1980)also
summarized established links between coelomycetous asexual
states and their sexual states, while Seifert et al. (2011) did the
same for hyphomycetous genera. Most of these established
links were based on co-occurrence of both morphs on the
same substrate (Walker and Sutton 1974) or culture-based
methods, particularly the development of asexual morphs
from single ascospore isolates (Leonard and Suggs 1974;
Hyde et al. 1996). However, utilization of PCR and DNA
sequencing in the fungi since the late-1990s (Nilsson et al.
2014), have established and confirmed many sexual and asex-
ual links (e.g. Alternaria-Lewia,Bipolaris-Cochliobolus,
Botryosphaeria-Fusicoccum,Cladosporium-Davidiella,
Mycosphaerella-Ramularia,Teratosphaeria-Kirramyces fide
Crous et al. 2009; Bensch et al. 2012; Manamgoda et al. 2012;
Phillips et al. 2013;Hydeetal.2014), while many other links
have been rejected (e.g. Cercospora-Mycosphaerella,
Paraconiothyrium-Paraphaeosphaeria,Plenodomus-
Leptosphaeria,Pseudocercospora-Mycosphaerella,
Stagonospora-Phaeosphaeria fide Crous et al. 2012;de
Gruyter et al. 2013; Groenewald et al. 2013; Quaedvlieg
et al. 2013,2014; Verkley et al. 2014).
There has been considerable research interest in the molec-
ular phylogeny of the Dothideomycetes in the last four years
with studies based on single and multi-gene rDNA sequence
data (Hyde et al. 2013). These phylogenetic advances have
helped taxonomists to link species or generic names, enabling
us to now propose or select one name for a single species, or
genus. Decisions taken at the XVIII
th
International Botanical
Congress, in Melbourne, Australia in 2011 (Hawksworth
2012) ruled that separate nomenclatural status for naming of
asexual and sexual names morphs of the same species was no
K. Tanaka
Faculty of Agriculture and Life Science, Hirosaki University,
3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
Y. Z h a n g
Institute of Microbiology, Beijing Forestry University, P.O. Box 61,
Beijing 100083, People’s Republic of China
A. Aptroot
ABL Herbarium, G.v.d.Veenstraat 107, NL-3762 XK Soest,
The Netherlands
A. H. Bahkali
College of Science, Botany and Microbiology Department,
King Saud University, Riyadh 1145, Saudi Arabia
D. J. Bhat
No. 128/1-J,AzadHousing Society, Curca, Goa Velha 403108, India
K. Knudsen
Department of Ecology, Faculty of Environmental Sciences,
Czech University of Life Sciences, Prague, Kamýcká 129,
Praha 6—Suchdol CZ–165 21, Czech Republic
E. H. C. McKenzie
ManaakiWhenua Landcare Research, Private Bag 92170, Auckland,
New Zealand
A. N. Miller
Illinois Natural History Survey, University of Illinois,
1816 South Oak Street, Champaign, IL 61820, USA
A. J. L. Phillips
Centro de Recursos Microbiológicos, Departamento de Ciências da
Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de
Lisboa, 2829-516, Caparica Lisbon, Portugal
H. A. Raja
Department of Chemistry and Biochemistry, 457 Sullivan Science
Building, University of North Carolina, Greensboro,
NC 27402-6170, USA
J. E. Taylor
Royal Botanic Garden Edinburgh, 20A Inverleith Row,
Edinburgh EH3 5LR, UK
M. Piątek
Department of Mycology, W. Szafer Institute of Botany, Polish
Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland
B. Slippers
Department of Genetics, Forestry and Agricultural Biotechnology
Institute, University of Pretoria, Pretoria 0002, South Africa
R. S. Shivas
Plant Pathology Herbarium, Department of Agriculture, Fisheries
and Forestry, Dutton Park 4102, Queensland, Australia
L. Cai
State Key Laboratory of Mycology, Institute of Microbiology,
Chinese Academy of Sciences, Beijing 100190,
People’sRepublicofChina
W. M. Jaklitsch
Department of Botany and Biodiversity Research,
Faculty of Life Sciences, University of Vienna,
Rennweg 14, 1030 Wien, Austria
W. M. Jaklitsch
Institute of Forest Entomology, Forest Pathology and Forest
Protection, Department of Forest- and Soil Sciences,
Hasenauerstrasse 38, A-1180 Wien, University of Natural
Resources and Life Sciences, Vienna, Austria
Fungal Diversity (2014) 69:1–55 3
longer permitted; this became effective from 30 July 2011
(Hawksworth 2012; Wingfield et al. 2012). Based on this
ruling, mycologists now have the task to clear up the historical
confusion that has resulted from the practice of dual nomencla-
ture, and in this paper we deal with the largest group of asco-
mycetes, Dothideomycetes. We therefore propose a single name
for pleomorphic dothideomycete genera to be added to the list of
“accepted/protected names”, while other names (sexual/asexual)
will be included in a list of “suppressed names”(Table 1). At the
same time, we incorporate all asexual genera into natural clas-
sification system where molecular data are available. Currently
Tabl e 1 Index to adopted names
of pleomorphic genera Protected names Suppressed names
Alternaria Nees Lewia M.E. Barr & E.G. Simmons
Antennulariella Woron . Antennariella Bat. & Cif., Capnodendron S. Hughes
Anthracostroma Petr. Camarosporula Petr.
Bipolaris Shoemaker Cochliobolus Drechsler
Blasdalea Sacc. & P. Syd. Chrysogloeum Petr.
Botryohypoxylon Samuels & J.D. Rogers Iledon Samuels & J.D. Rogers
Botryosphaeria Ces. & De Not. Fusicoccum Corda
Brooksia Hansf. Hiospira R.T. Moore
Capnodium Mont. Polychaeton (Pers.) Lév.
Cladosporium Link Davidiella Crous & U. Braun
Comminutispora A.W. Ramaley Hyphospora A.W. Ramaley
Curvularia Boedijn Pseudocochliobolus Tsuda et al.
Cyclopeltis Petr. Cyclopeltella Petr.
Elsinoë Racib. Sphaceloma de Bary
Excipulariopsis P.M. Kirk & Spooner Kentingia Sivan. & W.H. Hsieh
Exosporiella P. Ka rst. Anomalemma Sivan.
Exserohilum K.J. Leonard & Suggs Setosphaeria K.J. Leonard & Suggs
Farlowiella Sacc. Acrogenospora M.B. Ellis
Kellermania Ellis & Everh. Planistromella A.W. Ramaley
Kirschsteiniothelia D. Hawksw. Dendryphiopsis S. Hughes
Lecanosticta Syd. Eruptio M.E. Barr
Macrodiplodiopsis Petr. Misturatosphaeria Mugambi & Huhndorf,
Floricola Kohlm. & Volkm.-Kohlm.
Phaeosphaeria I. Miyake Phaeoseptoria Speg.
Phragmocapnias Theiss. & Syd. Conidiocarpus Woron.
Phyllosticta Pers. Guignardia Viala & Ravaz
Polythrincium Kunze Cymadothea F.A. Wol f
Prillieuxina G. Arnaud Leprieurina G. Arnaud
Prosthemium Kunze Pleomassaria Speg.
Pseudodidymella C.Z. Wei et al. Pycnopleiospora C.Z. Wei et al.
Pyrenophora Fr. Drechslera S. Ito
Ramularia Unger
Sphaeropsis Sacc.
Mycosphaerella Johanson
Phaeobotryosphaeria Speg.
Stemphylium Wall r Pleospora Rabenh. ex Ces. & De Not.
Tera t o s pha e r i a Syd. & P. Syd. Colletogloeopsis Crous & M.J. Wingf., Kirramyces J. Walker et al.
Tetraploa Berk. & Broome Tetraplosphaeria Kaz. Tanaka & K. Hiray.
Fig. 1 The best scoring RAxML Dothideomycetes tree from 415 taxa
based on a combined dataset of LSU, SSU, TEF1 and RPB2 sequences
with all lineages collapsed to family level where possible. The tree is the
same as Fig. 1. Bootstrap support values for maximum likelihood (ML,
red) and maximum parsimony (MP,black) greater than 50% are given
above the nodes; Bayesian posterior probabilities (BYPP,green)above
0.90 are given below the nodes. The original strain numbers are given
after the species names. Type and ex-type strains are emphasized in bold.
The tree was rooted with Schismatomma dirinellum (S-F206034) and
S. decolorans (DUKE 47570)
4 Fungal Diversity (2014) 69:1–55
Fungal Diversity (2014) 69:1–55 5
Dothideomycetes comprises of 23 orders, 110 families and 1261
genera. However, 23 orders and 76 families are supported by
molecular data, while 36 families lack molecular data.
The draft of this manuscript with 71 initial authors from
all disciplines interested in Dothideomycetes was first
prepared and placed online on the International Commission
on the Taxonomy of Fungi (ICTF) webpage (http://www.
fungaltaxonomy.org/) on 20 February 2014. Comments were
then invited from interested parties who were also invited
to co-author the paper. A draft version was discussed at
Fig. 1 (continued)
6 Fungal Diversity (2014) 69:1–55
the “Genomes and Genera”symposium in Amsterdam on
the 24–25 April 2014 and some of the more contentious
cases in the Nomenclature Sessions during the 10
th
Inter-
national Mycological Congress (IMC10) in Bangkok,
Thailand, on 3–8 August 2014.
Materials and methods
The proposed names are based on Kirk et al. (2008,
2013), Lumbsch and Huhndorf (2010) and Hyde et al.
(2013). The links between asexual and sexual morphs take
Fig. 1 (continued)
Fungal Diversity (2014) 69:1–55 7
into account the important publications of Kendrick
(1979), Sivanesan (1984), Sutton (1980), Seifert et al.
(2011), Hyde et al. (2011), Wijayawardene et al. (2012)
and other recent research based on culture and molecular
phylogeny (e.g. Crous et al. 2009,2013; de Gruyter et al.
2013; Boonmee et al. 2012,2014b; Chomnunti et al. 2011;
Fig. 1 (continued)
8 Fungal Diversity (2014) 69:1–55
Liu et al. 2011; Manamgoda et al. 2012; Phillips et al. 2013;
Wijayawardene et al. 2014a,b,c).
Proposed names are selected depending on the following
criteria:
1. The evidence for established links
a. Culture-based (e.g. single-spore) methods
b. Molecular methods
2. Number of epithets in Index Fungorum and MycoBank
3. The oldest generic name
4. Other significant aspects, such as pathogenic importance
and industrial applications
5. Usage of the name in literature and databases
The oldest name is accepted where it conforms best
with current practice, while usage of a widely used
name is proposed when this is more significant. Pro-
posed names (protected names) are listed in the first
column (Table 1) of the table and second column com-
prises suppressed names. The suppressed name could be
a sexual, asexual or a synasexual morph. Asterisk marks
(*) are added for genera which we provide notes on
recent changes and naming. Genera marked with (
#
)
refer to changes made via articles in the same journal
volume and annotated under the family or order (i.e.
Ariyawansa et al. 2014c; Boonmee et al. 2014b;
Hongsanan et al. 2014c; Thambugala et al. 2014c;
Fig. 1 (continued)
Fungal Diversity (2014) 69:1–55 9
Phookamsak et al. 2014). In the present outline, we
have added (C) = coelomycetous and (H) = hyphomy-
cetous asexual genera against entries where known.
In giving preference here to the earliest validly pub-
lished generic name regardless of the morph represented
by the type specimen of the type species of the genus,
we are aware that Art. 57.2 of the current Code (McNeill
et al. 2012) requires that in cases where a well-
established asexually typified name is preferred, there
should first be a formal proposal made to the Nomencla-
ture Committee for Fungi (NCF). We regard this is an
unnecessarily time-consuming process, and proposals to
delete this provision were strongly supported in the No-
menclature Sessions at IMC10 and will be made to the
next International Botanical Congress in 2017. Inclusion
in Lists of Accepted Names which are approved in due
course by the NCF is a preferable way to handle such
cases, and for Dothideomycetes, this article will be the
basis of the eventual list for this class.
Phylogenetic analyses
Sequences (Table 1) were obtained from GenBank following
Hyde et al. (2013) and other recent publications (eg. Crous
et al. 2013; Phillips et al. 2013; Quaedvlieg et al. 2013,2014;
Slippers et al. 2013; Wijayawardene et al. 2013,2014a,b,c;
Pérez-Ortega et al. 2014). DNA sequences for each gene
region (small subunits ribosomal RNA (SSU), large subunits
ribosomal RNA (LSU), the translation elongation factor-1
alpha (TEF1) and the second largest subunit of RNA poly-
merase II (RPB2) were initially aligned using Bioedit (Hall
2004) and ClustalW v. 1.6 (Thompson et al. 1997).
Alignments were manually checked and optimized wher-
ever necessary. The dataset was refined visually in
BioEdit v. 7.0.1 (Hall 2004). All absent genes were coded as
missing data.
The phylogenetic analyses of the combined LSU,
SSU, TEF1 and RPB2 data were performed using max-
imum likelihood, Bayesian and maximum parsimony
algorithms.
Maximum likelihood (ML) analysis was performed at the
RAxML 7.2.8 as part of the “RAxML-HPC2 on TG”tool
(Stamatakis 2006) implemented in raxmlGUI v.0.9b2
(Silvestro and Michalak 2010). A general time reversible
model (GTR) was applied with a discrete gamma distri-
bution and four rate classes. Hundred thorough maxi-
mum likelihood (ML) tree searches were done in
RAxML v. 7.2.7 under the same model. Maximum like-
lihood bootstrap values (MLBP) equal or greater than 50
% are given above each node (Fig. 1).
Maximum-parsimony analyses were performed by
PAUP v. 4.0b10 (Swofford 2002) using the heuristic
search option with 1,000 random taxa addition and tree
bisection and reconnection (TBR) as the branch swap-
ping algorithm. All characters were unordered and of
equal weight and gaps were treated as missing data. The
Tree Length (TL), Consistency Indices (CI), Retention
Indices (RI), Rescaled Consistency Indices (RC) and
Homoplasy Index (HI) were calculated for each tree
generated. Maxtrees were unlimited, branches of zero
length were collapsed and all multiple, equally parsimo-
nious trees were saved. Clade stability was assessed
using a bootstrap (BT) analysis with 1,000 replicates,
each with 10 replicates of random stepwise addition of taxa
(Hillis and Bull 1993). Maximum parsimony bootstrap values
(MPBP) equal or greater than 50 % are given above each node
(Fig. 1).
The model of evolution was estimated by using
MrModeltest 2.2 (Nylander 2004). Independent Bayes-
ian phylogenetic analyses were performed in MrBayes
v. 3.1.2 (Huelsenbeck and Ronquist 2001) using a uni-
form [GTR+I+G] model, lsetnst=6 rates=invgamma;
prsetstatefreqpr =dirichlet (1,1,1,1). Posterior probabili-
ties (PP) (Rannala and Yang 1996; Zhaxybayeva and
Gogarten 2002) were determined by Markov Chain
Monte Carlo sampling (BMCMC) in MrBayes v. 3.0b4
(Huelsenbeck and Ronquist 2001). Six simultaneous
Markov chains were run for 10,000,000 generations and trees
were sampled every 100th generation (resulting in 10,000
total trees).
Phylogenetic trees were visualized with Treeview v. 1.6.6
(Page 1996) and MEGA 5 (Tamura et al. 2011).
Results
Phylogenetic analyses
The combined LSU, SSU, TEF1 and RPB2 data set consists
of 415 taxa, with Schismatomma dirinellum (S-F206034)
and S. decolorans (DUKE 47570) which representing the
outgroup taxa. The dataset consists of 4,302 characters after
alignment, 1,496 characters are conserved, and 2,228 char-
acters are parsimony informative, while 2,767 are variable
characters. A heuristic search with random addition of taxa
(1,000 replicates) and treating gaps as missing characters
generated six equally parsimonious trees. The best scoring
RAxML trees are shown in Fig. 1. Bootstrap support (BS)
values of MP and ML (equal to or above 50 %) and
Bayesian Posterior Probabilities (BYPP) with those equal
or greater than 0.90 given below each node are shown on
the upper branches.
Twenty-three orders (Abrothallales,Acrospermales,
Asterinales,Botryosphaeriales,Dothideales,Dyfrolomycetales,
Capnodiales,Hysteriales,Jahnulales,Lichenoconiales,
10 Fungal Diversity (2014) 69:1–55
Lichenotheliales,Microthyriales,Monoblastiales,
Mytilinidiales,Myriangiales,Natipusillales,Patellariales,
Phaeotrichales,Pleosporales,Strigulales,Trypetheliales,
Tubeufiales and Venturiales) are recognized. This agrees with
Hyde et al. (2013) and Pérez-Ortega et al. (2014), the latter who
introduced Abrothallales. In their analyses, Pérez-Ortega et al.
(2014)showedAbrothallales grouped with Patellariales
however, in our analyses Abrothallales groups with
Asterinales and Lichenoconiales. Recently introduced fami-
lies by Slippers et al. (2013)viz. Aplosporellaceae Slippers
et al., Melanopsaceae Phillips et al. and Saccharataceae
Slippers et al. clustered within Botryosphaeriales with high
bootstrap values. Aureobasidiaceae Thambugala & K.D.
Hyde grouped as a distinct clade in Dothideales
(Thambugala et al. 2014a). New clades appeared for
Camarosporium sensu stricto (Camarosporiaceae fide
Wijayawardene et al. in prep.) and Homortomyces with low
and high bootstrap values respectively. Wiesneriomycetaceae
grouped as a sister clade to Tubeufiaceae and this agrees with
Suetrong et al. (2014). Extremaceae and Neodevriesiaceae
appeared as new distinct clades in Capnodiales as shown by
Quaedvlieg et al. (2014). However, Teratosphaeriaceae sep-
arated into two distinct clades (Fig. 1) which does not agree
with Quaedvlieg et al. (2014).
Outline of the Dothideomycetes
Class Dothideomycetes sensu O.E. Erikss. & Winka
Subclass Dothideomycetidae P.M. Kirk et al. ex C.L.
Schoch et al.
Asterinales M.E. Barr ex D. Hawksw. & O.E. Erikss.*
Asterinaceae Hansf. (=Lembosiaceae Hosag.)*
Asterina Lév.*
Asterinella Theiss.
#
Asterotexis Arx
#
Batistinula Arx
#
Cirsosia G. Arnaud
#
Echidnodella Theiss. & Syd.
#
Halbania Racib.
#
Lembosia Lév.*
Meliolaster Höhn.
#
Parasterinopsis Bat.
#
Platypeltella Petr.*
Prillieuxina G. Arnaud* (see in Table 1)
Schenckiella Henn.*
Trichasterina G. Arnaud
#
Trichopeltos pora Bat. & Cif.*
Uleothyrium Petr.
#
Vize l l opsis Bat. et al.*
#
for notes see under Asterinaceae
Capnodiales Woro n.
Antennulariellaceae Woron.
Achaetobotrys Bat. & Cif.*
Antennulariella Woron.* (see Table 1)
Capnofrasera S. Hughes
Capnodiaceae (Sacc.) Höhn. ex Theiss.
Capnodium Mont.* (see in Table 1)
Leptoxyphium Speg.
Phragmocapnias Theiss. & Syd.* (see in Table 1)
?Plurispermiopsis Pereira-Carv. et al.*
Scoriadopsis J.M. Mend.
Scorias Fr.
Cladosporiaceae Nann.
Acroconidiella J.C. Lindq. & Alippi (H)
Cladosporium Link (H)* (see in Table 1)
Graphiopsis Trail (H)
Hoornsmania Crous (H)
Rachicladosporium Crous et al. (H)
Toxicocladospori um Crous & U. Braun (H)
Verrucocladosporium K. Schub. et al. (H)
Dissoconiaceae Crous & de Hoog*
Dissoconium de Hoog et al. (H)
Pseudoveronaea Crous & Batzer*
Ramichloridium Stahel (H)*
Uwebraunia Crous & M.J. Wingf. (H)*
Metacapnodiaceae S. Hughes & Corlett
Capnobotrys S. Hughes (H)
Capnophialophora S. Hughes (H)
Hyphosoma Syd.
Metacapnodium Speg.*
Extremaceae Quaedvlieg & Crous*
Extremus Quaedvlieg & Crous (H)*
Petrophila de Hoog & Quaedvlieg (H)*
Pseudoramichloridium Cheewangkoon & Crous (H)*
Staninwardia B. Sutton (C)*
Ver m i c on i a Egidi & Onofri (H)*
Mycosphaerellaceae Lindau
Acervuloseptoria Crous & Jol. Roux (C)*
Achorodothis Syd.
Amycosphaerella Quaedvlieg & Crous*
Fungal Diversity (2014) 69:1–55 11
Annellosympodiella Crous & Assefa*
Asperisporium Maubl. (H)
Brunneosphaerella Crous
Bryopelta Döbbeler & Poelt*
Caryophylloseptoria Ver k ley e t al. ( C)*
Cercospora Fresen. (H)*
Cercosporella Sacc. (H)
Colletogloeum Petr. (C)*
Distocercospora N. Pons & B. Sutton (H)
Dothistroma Hulbary (C)
Euryachora Fuckel
Gillotia Sacc. & Trotter
Lecanosticta Syd. (C)* (see in Table 1)
Lembosiopsis Theiss.*
Lophiosphaerella Hara*
Melanodothis R.H. Arnold
Microcyclosporella J. Frank et al. (H)
Mycoporis Clem.*
Neoceratosperma Crous & Cheew. (H)*
Neomycosphaerella Crous*
Neopenidiella Quaedvlieg & Crous (H)*
Neopseudocercospora Crous (H)*
Neoseptoria Quaedvlieg et al. (C)*
Pallidocercospora Crous (H)
Paracercospora Deighton (H)*
Paramycosphaerella Crous & Jol. Roux*
Passalora Fr. (H)
Periconiella Sacc. (H)
Phaeocercospora Crous (H)
Phaeophleospora Rangel (C)*
Phloeospora Wallr. (C)*
Placocrea Syd.
Polyphialoseptoria Quaedvlieg et al. (C)*
Polysporella Woron.
Polythrincium Kunze (H)* (see in Table 1)
Pseudocercospora Speg. (H)*
Pseudocercosporella Deighton (H)
Pseudostigmidium Etayo
Ramularia Unger (H)* (see in Table 1)
Ramulispora Miura (H)
Ruptoseptoria Quaedvlieg et al. (C)*
Scolecostigmina U. Braun
Septoria Sacc. (C)*
Sonderhenia H.J. Swart & J. Walker (C)
Sphaerellothecium Zopf
Sphaerulina Sacc.*
Stigmidium Trevis.
Stromatoseptoria Quaedvlieg et al. (C)*
Trochophora R.T. Moore (H)
?Wernerella Nav.-Ros. et al.
Xenomycosphaerella Quaedvlieg & Crous*
Zasmidium Fr. (H)*
Zymoseptoria Quaedvlieg & Crous (C)*
Neodevriesiaceae Quaedvlieg & Crous*
Neodevriesia Quaedvlieg & Crous (H)*
Piedraiaceae Viégas ex Cif. et al.
Piedraia Fonseca & Leão
Teratosphaeriaceae Crous & U. Braun
Acidomyces B.J. Baker et al. (H)
Apenidiella Quaedvlieg & Crous (H)*
Aulographina Arx & E. Müll.*
Austroafricana Quaedvlieg & Crous*
Batcheloromyces Marasas et al. (H)
Baudoinia J.A. Scott & Unter. (H)
Capnobotryella Sugiy. (H)
Catenulostroma Crous & U. Braun (H)
Constantinomyces Egidi & Onofri (H)*
Devriesia Seifert & N.L. Nick. (H)
Elasticomyces Zucconi & Selbmann (H)
Eupenidiella Quaedvlieg & Crous (H)*
Euteratosphaeria Quaedvlieg & Crous*
Friedmanniomyces Onofri (H)
Hispidoconidioma Tsuneda&Davey(H)
Hortaea Nishim. & Miyaji (H)
Incertomyces Egidi & Zucconi (H)*
Lapidomyces de Hoog & Stielow (H)*
Meristemomyces Isola & Onofri (H)*
Microcyclospora J. Frank et al. (H)
Monticola Selbmann & Egidi (H)*
Mycophycias Kohlm. & Volkm.-Kohlm
Myrtapenidiella Quaedvlieg & Crous (H)*
Neocatenulostroma Quaedvlieg & Crous (H)*
Neophaeothecoidea Quaedvlieg & Crous (H)*
Neotrimmatostroma Quaedvlieg & Crous*
Oleoguttula Selbmann & de Hoog (H)*
Pachysacca Syd.*
Parapenidiella Crous & Summerell (H)
Parateratosphaeria Quaedvlieg & Crous*
Penidiella Crous & U. Braun (H)
Phacellium Bonord. (H)
Phaeothecoidea Crous (H)
Pseudotaeniolina J.L. Crane & Schokn. (H)
Pseudoteratosphaeria Quaedvlieg & Crous*
Queenslandipenidiella Quaedvlieg & Crous (H)*
Ramopenidiella Crous & R.G. Shivas (H)*
Readeriella Syd. & P. Syd. (C)*
Recurvomyces Selbmann & de Hoog (H)
Stenella Syd. (H)
Suberoteratosphaeria Quaedvlieg & Crous*
Teratosphaer ia Syd. & P. Syd.* (see in Table 1)
Teratosphaer icola Quaedvlieg & Crous*
12 Fungal Diversity (2014) 69:1–55
Teratosphaeriopsis Quaedvlieg & Crous*
Xenoconiothyrium Crous & Marinc. (C)
Xenopenidiella Quaedvlieg & Crous (H)*
Xenoteratosphaeria Quaedvlieg & Crous*
Capnodiales,generaincertae sedis
Arthrocatena Egidi & Selbmann*
Catenulomyces Egidi & de Hoog (H)*
Cystocoleus Thwaites*
?Eriosporella Höhn. (C)*
Hyphoconis Egidi & Quaedvlieg (H)*
Mucomycosphaerella Quaedvlieg & Crous*
Neohortaea Quaedvlieg & Crous (H)*
Perusta Egidi & Stielow*
Ramimonilia Stielow & Quaedvlieg (H)*
Dothideales Lindau*
Aureobasidiaceae K.M. Thambugala & K.D. Hyde*
Aureobasidium Viala & G. Boyer (H)
#
Columnosphaeria Munk
#
Kabatiella Bubák (H)
#
Pseudoseptoria Speg.
#
Pseudosydowia K.M. Thambugala & K.D. Hyde*
Saccothecium Fr.
#
Selenophoma Maire (C)*
#
for notes see under Aureobasidiaceae
Dothideaceae Chevall.*
Coleophoma Höhn. (C)
#
Cylindroseptoria Quaedvlieg et al. (C)
#
Delphinella (Sacc.) Kuntze
#
Dictyodothis Theiss. & Syd.
#
Dothidea Fr.
#
Dothiora Fr.
#
Endoconidioma Tsuneda e t a l.
#
Endodothiora Petr.
#
Hormonema Lagerb. & Melin (H)*
Kabatina R. Schneid. & Arx (H)
#
Neocylindroseptoria K.M. Thambugala & K.D.
Hyde*
Phaeocryptopus Naumov
#
Plowrightia Sacc.
#
?Pringsheimia Schulzer*
Stylodothis Arx & E. Müll.
#
?Sydowia Bres.*
#
for notes see under Dothideaceae
Dothideales,generaincertae sedis
Celosporium Tsuneda & M.L. Davey*
Lichenoconiales Diederich et al.
Lichenoconiaceae Diederich & Lawrey
Lichenoconium Petr. & Syd. (C)
Lichenotheliales K. Knudsen et al.
Lichenotheliaceae Henssen
Karschia Körb.*
Lichenostigma Hafellner
Lichenothelia D. Hawksw.
Myriangiales Starbäck
Elsinoaceae Höhn. ex Sacc. & Trotter*
Elsinoë Racib.* (see in Table 1)
Molleriella G. Winter*
Myriangiaceae Nyl.*
Anhellia Racib.*
Ascostratum Syd. & P. Syd.*
Butleria Sacc.*
Dictyocyclus Sivan. et al.*
Diplotheca C.C. Gordon & C.G. Shaw*
Eurytheca De Seynes*
Hemimyriangium J. Reid & Piroz*
Micularia Boedijn*
Myriangium Mont. & Berk.*
Zukaliopsis Henn.*
Subclass Pleosporomycetidae C.L. Schoch et al.
Pleosporales Luttrell ex M.E. Barr
Aigialaceae Suetrong et al.
Aigialus S. Schatz & Kohlm.
Ascocratera Kohlm.
Fissuroma J.K. Liu et al.
Neoastrosphaeriella J.K. Liu et al.
Rimora Kohlm. et al.
Amniculicolaceae Yin. Zhang et al.
?Amniculicola Y. Zhang & K.D. Hyde*
?Anguillospora Ingold (H)*
Murispora Y. Zhang bis et al.
Neomassariosphaeria Y. Zhang bis et al.
Anteagloniaceae K.D. Hyde et al.
Anteaglonium Mugambi & Huhndorf
Fungal Diversity (2014) 69:1–55 13
Bambusicolaceae D.Q. Dai & K.D. Hyde
Bambusicola D.Q. Dai & K.D. Hyde
Biatriosporaceae K.D. Hyde
Biatriospora K.D. Hyde & Borse
Coniothyriaceae W.B. Cooke
Coniothyrium Corda (C)*
Camarosporaceae Wijayawardene & K.D. Hyde*
Camarosporium Schulzer (C)*
Corynesporascaceae Sivan.
Corynespora Güssow (H)*
Corynesporasca Sivan.
Cucurbitariaceae G. Winter
Cucurbidothis Petr.*
Cucurbitaria Gray*
Curreya Sacc.
Pyrenochaeta De Not. (C)*
Pyrenochaetopsis Gruyter et al. (C)
Rhytidiella Zalasky
Syncarpella Theiss. & Syd.*
Delitschiaceae M.E. Barr
Delitschia Auersw.
Ohleriella Earle
Semidelitschia Cain & LuckAllen
Diademaceae Shoemaker & C.E. Babc.
Comoclathris Clem.
Diadema Shoemaker & C.E. Babc.
Diademosa Shoemaker & C.E. Babc.
Didymellaceae Gruyter et al.
Ascochyta Lib. (C)*
Boeremia Aveskamp et al. (C)
Chaetasbolisia Speg. (C)
Dactuliochaeta G.L. Hartm. & J.B. Sinclair (C)
Didymella Sacc.*
Epicoccum Link (H)
Leptosphaerulina McAlpine*
Macroventuria Aa
Microsphaeropsis Höhn. (C)
Mixtura O.E. Erikss. & J.Z. Yue*
Monascostroma Höhn.
Phoma Sacc. (C)*
Piggotia Berk. & Broome (C)
Pithomyces Berk. & Broome (H)*
Didymosphaeriaceae Munk (=Montagnulaceae)*
Alloconiothyrium Verkle y & S tie l ow (C)
#
Barria Z.Q. Yuan*
Bimuria D. Hawksw. et al.
#
Deniquelata Ariyawansa & K.D. Hyde
#
Didymocrea Kowalski
#
Didymosphaeria Fuckel
#
Julella Fabre*
Kalmusia Niessl
#
Karstenula Speg.
#
Letendraea Sacc.*
Montagnula Berl.
#
Neokalmusia Kaz. Tanaka et al.*
Paracamarosporium Wijayawardene & K.D. Hyde (C)*
Paraconiothyrium Verkl e y (C)*
Paraphaeosphaeria O.E. Erikss.*
Phaeodothis Syd. & P. Syd.
#
Pseudocamarosporium Wijayawardene & K.D. Hyde (C)*
Pseudotrichia Kirschst.*
Tremateia Kohlm. et al.
#
#
for notes see under Didymosphaeriaceae
Dothidotthiaceae Crous & A.J.L. Phillips
Dothidotthia Höhn.
Muellerites L. Holm*
Thyrostroma Höhn. (H)*
Halojulellaceae Suetrong et al.
Halojulella Suetrong et al.
Halotthiaceae Ying Zhang et al.
Halotthia Kohlm.
Mauritiana Poonyth et al.
Phaeoseptum Ying Zhang et al.
Pontoporeia Kohlm.
Hypsostromataceae Huhndorf
Hypsostroma Huhndorf
Lentitheciaceae Y. Zhang ter et al.
Katumotoa Kaz. Tanaka & Y. Harada
14 Fungal Diversity (2014) 69:1–55
Lentithecium K.D. Hyde et al.
Setoseptoria Quaedvlieg et al. (C)
Tingoldiago K. Hiray. & Kaz. Tanaka
Leptosphaeriaceae M.E. Barr
Acicuseptoria W. Quaedvlieg et al. (C)*
Alternariaster E.G. Simmons*
Chaetoplea (Sacc.) Clem.*
Heterospora (Boerema et al.) Gruyter et al.*
Leptosphaeria Ces. & De Not.*
Neophaeosphaeria M.P.S. Câmara
Paraleptosphaeria Gruyter et al.
Plenodomus Preuss (C)*
Subplenodomus Gruyter et al. (C)*
Lindgomycetaceae K. Hiray. et al.
Clohesyomyces K.D. Hyde
Hongkongmyces Tsang et al.*
Lindgomyces K. Hiray. et al.
Lolia Abdel-Aziz & Abdel-Whab (C)
Lophiostomataceae Sacc.
Dimorphiopsis Crous (C)*
Lophiostoma Ces. & De Not.
Macrodiplodiopsis Petr.* (see in Table 1)
Tumularia Descals & Marvanová (H)
Lophiotremataceae K. Hiray. & Kaz.
Lophiotrema Sacc.
Massariaceae Nitschke
Massaria De Not.
Massarinaceae Munk
Massarina Sacc.
Stagonospora (Sacc.) Sacc. (C)*
Melanommataceae G. Winter
Aposphaeria Sacc. (C)*
Asymmetricospora J. Fröhl. & K.D. Hyde
Bertiella (Sacc.) Sacc. & P. Syd.
Beverwykella Tubaki (H)
Bicrouania Kohlm. & Volkm.-Kohlm.
Byssosphaeria Cooke
Calyptronectria Speg.
Caryosporella Kohlm.
Exosporiella P. Karst. (H)* (see in Table 1)
Herpotrichia Fuckel
Mamillisphaeria K.D. Hyde et al.
Melanomma Nitschke ex Fuckel
Mycopappus Redhead & G.P. White (H)*
Navicella Fabre*
Nigrolentilocus R.F. Castañeda & Heredia
Ohleria Fuckel
Sporidesmiella P.M. Ki r k ( H)
Xenostigmina Crous (H)*
Morosphaeriaceae Suetrong et al.
Helicascus Kohlm.
Morosphaeria Suetrong et al.
Phaeosphaeriaceae M.E. Barr*
Amarenographium O.E. Erikss. (C)
#
Amarenomyces O.E. Erikss.
#
Ampelomyces Ces. ex Schltdl. (C)
#
Bricookea M.E. Barr
#
Chaetosphaeronema Moesz (C)
#
Dematiopleospora Wanasinghe et al.*
Dothideopsella Höhn.*
Entodesmium Riess
#
Eudarluca Speg.
#
Loratospora Kohlm. & Volkm.-Kohlm.
#
Neosetophoma Gruyter et al. (C)
#
Neostagonospora Quaedvlieg et al. (C)
#
Nodulosphaeria Rabenh
#
Ophiobolus Riess
#
Ophiosphaerella Speg.*
Paraphoma Morgan-Jones & J.F. White (C)
#
Parastagonospora Quaedvlieg et al. (C)
#
Phaeosphaeria I. Miyake* (see in Table 1)
Phaeosphaeriopsis M.P.S. Câmara et al.
#
Phaeostagonospora A.W. Ramaley (C)
#
Sclerostagonospora Höhn. (C)
#
Scolecosporiella Petr. (C)
#
?Scolicosporium Lib. ex Roum. (C)*
?Septoriella Oudem. (C)
#
Setomelanomma M. Morelet
#
Setophoma Gruyter et al. (C)
#
Tiarospora Sacc. & Marchal (C)
#
Vrys t a atia Quaedvlieg et al. (C)
#
Wojnowicia Sacc. (C)*
Xenoseptoria Quaedvlieg et al. (C)
#
#
for notes see under Pahaeosphaeriaceae
Platystomaceae J. Schröt.
Ostropella (Sacc.) Höhn.
Fungal Diversity (2014) 69:1–55 15
Platystomum Trevis.
Xenolophium Syd.
Pleomassariaceae M.E. Barr
Lichenopyrenis Calat. et al.
Peridiothelia D. Hawksw.
Prosthemium Kunze (C)* (see in Table 1)
Splanchnonema Corda
Pleosporaceae Nitschke
Alternaria Nees (H)* (see in Table 1)
Bipolaris Shoemaker (H)* (see in Table 1)
Clathrospora Rabenh.
Curvularia Boedijn (H)* (see in Table 1)
Decorospora Inderb. et al.
Dendryphion Wall r. (H)
Edenia M.C. González et al. (H)
Exserohilum K.J. Leonard & Suggs (H)* (see in Table 1)
Extrawettsteinina M.E. Barr
Marielliottia Shoemaker (