842 Hyde et al.

/ J Zhejiang Univ Sci B 2008 9(10):842-846

Journal of Zhejiang University SCIENCE B

ISSN 1673-1581 (Print); ISSN 1862-1783 (Online)
www.zju.edu.cn/jzus; www.springerlink.com
E-mail: jzus@zju.edu.cn

Commentary:
Epitypification: should we epitypify?

Kevin D. HYDE†1,2, Ying ZHANG3

(1International Fungal Research and Development Centre, the Research Institute of Resource Insects,
Chinese Academy of Forestry, Kunming 650224, China)
(2Fungal Research Group, School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai 57100, Thailand)
(3Centre for Research in Fungal Diversity, School of Biological Sciences, University of Hong Kong, Hong Kong, China)
†
E-mail: kdhyde1@gmail.com
Received July 31, 2008; revision accepted Aug. 30, 2008

Abstract: Epitypification can solve many taxonomic problems and stabilize the understanding of species, genera, families or
orders. The aim of this paper is to illustrate how to epitypify. A few examples where taxa have been epitypified are considered and
the benefits and disadvantages of epitypification are discussed. We also outline some examples of taxa which need to be epitypi-
fied with reasons.

Key words: Colletotrichum, GenBank, Molecular phylogeny, Taxonomy, Typification

doi:10.1631/jzus.B0860004 Document code: A CLC number: Q939

INTRODUCTION reviews the options that can be used to address the

above problems. Epitypification is the best option for
What can be done if the material that represents a replacing lost type material or types in poor condition.
type species, genus, family or order is lost, is in poor If DNA cannot be extracted from types, then we need
condition, cannot be used to extract DNA, or mo- to designate epitypes that are identical to the exam-
lecular data cannot be obtained? How do we form ined types. When fresh collections are sequenced and
concepts of species, genera, families and orders in those sequences are deposited in GenBank, dried
these cases? Recent publications from the Assem- herbarium material and cultures should also be de-
bling the Fungal Tree of Life (AFTOL) project have posited in accessible herbaria culture collections. If
named exemplar genera to conceptualize orders these rules are followed then we will be able to avoid
(Hibbett et al., 2007). However, the understanding of GenBank becoming a dustbin for DNA sequences
the genera is included, and thus the understanding of whose names cannot be verified by morphology.
the order, may be interpreted differently by various
mycologists, and therefore this approach cannot be
recommended. In the case of genera, species descrip- WHAT IS EPITYPIFICATION?
tions, but not types, have often been used to represent
genera (Kodsueb et al., 2006). Stylized drawings and Article 9.7 of the International Code of Botani-
wrongly identified collections, however, might mean cal Nomenclature (Vienna Code) (Mcneill et al., 2006)
that the generic concept is understood differently by states that “An epitype is a specimen or illustration
various mycologists. Fresh isolates are also generally selected to serve as an interpretative type when the
used to obtain DNA data, but one person’s under- holotype, lectotype, or previously designated neotype,
standing of a species may differ from another’s; thus or all original material associated with a validly pub-
the sequences in GenBank and other public databases lished name, is demonstrably ambiguous and cannot
are surely unreliable (Nilsson et al., 2006). This paper be critically identified for purposes of the precise
 Hyde et al. / J Zhejiang Univ Sci B 2008 9(10):842-846 843

application of the name of a taxon. When an epitype is to previous type material. Hence before epitypifying a
designated, the holotype, lectotype, or neotype that species, the type material should be located, loaned
the epitype supports must be explicitly cited.” It has and carefully studied. This should include detailed
become relatively common to epitypify fungi (Alves examination of morphological characters and other
et al., 2008; Crous et al., 2007; Phillips et al., 2006; data such as host, location, or anamorphic relation-
2007; Shenoy et al., 2007b; Than et al., 2008) and this ship. The next step is to obtain a fresh specimen. The
paper will examine whether it is a good idea to epitype specimen should undoubtedly have all of the
epitypify fungi and will also point out some of the characters exhibited in the type and if possible be
associated problems. obtained from the same location and host. Of course
There are many reasons to epitypify. Often the this is not always possible. We have recently searched
type material has been lost or is in poor condition. The for a fresh collection of Colletotrichum circinans
genus may be relatively well known, e.g., Massaria (Berk.) Vogl., the cause of smudge in onion (Walker,
inquinans (Tode) De Not.; however, unless there is a 1925); however, the original site is now a housing
type that can serve to represent the genus, it is possi- estate. We have also searched for the type of Colle-
ble that each individual mycologist may have a dif- totrichum falcatum Went which was described from a
ferent understanding of the taxon representing this small village in central Java (Went, 1893). Amazingly
genus. More recently with the advent of molecular the sugarcane plantation is in its original location
phylogenetics, living material is needed for se- (although part has been destroyed for housing) and
quencing as in most cases the ancient herbarium during a recent trip we were able to obtain a fresh
specimens cannot be successfully sequenced. There- collection.
fore, even if the type material is in relatively good DNA data obtained from different strains iso-
condition, one could argue that the taxon needs lated from different locations or environments are
epitypifying, so that living material is available for often identical. For example, the internal transcribed
gene research. This is evident in the paper by Hibbett spacer (ITS) sequences of two isolates of Botryos-
et al.(2007). In that paper, each order was represented phaeria cortices (Demaree & M.S. Wilcox) Arx & E.
by 1~6 exemplar genera. The understanding of each Müll. from North Carolina showed no significant
genus, however, may differ. Many mycologists may difference from those isolated from New Jersey from
not have seen good type material and their under- the same host (Phillips et al., 2006). The rDNA (28S,
standing of a taxon/genus/family may be based on 18S) and RNA polymerase II (RPB2) sequences of
literature or stylized drawings of the type or repre- Trematosphaeria pertusa Fuckel on a dead stump of
sentative (possibly misidentified) collections. The Fraxinus excelsior L. from Deux Sèvres, France,
individual understanding of an order may, therefore, were almost the same with those of the one from
be questionable. The AFTOL project has sequenced Haute Garonne (France) occurring on submerged
numerous taxa and derived a framework for modern wood of Platanus (Zhang et al., 2008). Thus as long
taxonomy (Aime et al., 2006; Binder and Hibbett, as the collections are morphologically identical to the
2006; Celio et al., 2006; Geiser et al., 2006), yet few type, a fresh collection from a different location could
of the fungi sequenced were types. This could lead to feasibly be designated as an epitype.
erroneous data being generated and since strains may It has recently proven possible to extract DNA
not have been deposited in culture collections and and obtain the DNA sequences from old herbarium
herbarium material is scarcely available, thus there is material with kits (Fredricks et al., 2005; O′Gorman
no way to repeat the experiment (Shenoy et al., et al., 2008). This material may not be the type, but
2007a). can be collections identified by the same mycologist
who designated the type, or collections by others from
the same host and location. This DNA data is very
HOW TO DECIDE ON AN EPITYPE important to determine the phylogenic status of a
particular fungus, especially for those rarely encoun-
According to the definition of an epitype tered taxa. Furthermore, if it was collected by the
(Mcneill et al., 2006), the epitype should be identical original mycologist it is likely to be authentic. As long
844 Hyde et al. / J Zhejiang Univ Sci B 2008 9(10):842-846

as enough DNA data can be obtained from this old Sometimes, the traditional concept for a species
material which should be identical to the type, it could differs from that observed in the type protologue and
also be designated as an epitype. early descriptions. This is the case with Massaria
inquinans (Tode) De Not., the type species of Mas-
saria, which represents the family Massariaceae. We
EXAMPLES OF EPITYPIFICATION have been unable to locate the type material of this
species. Shoemaker and LeClair (1975) systemati-
By epitypification, a name can be fixed to a cally studied the Massariaceae and examined a
specimen or a culture, which is very important for specimen of Massaria inquinans (CLXXX) lodged at
phylogenetic study of this taxon. A fresh collection of University of Uppsala (UPS). Shoemaker and Kokko
Botryosphaeria corticis was made from a commercial (1977) reported this taxon to have asci with 8 asco-
field of Vaccinium corymbosum L. in the USA and a spores with no-constriction at each septum. We have
culture was obtained. Epitypification of Botryos- examined the specimen of UPS CLXXX and found it
phaeria corticis with this specimen was carried out by to have asci with 4 ascospores that are constricted at
designating it as the epitype as none of the previous the central septum. This species therefore needs
cultures was connected with the type specimen (BPI epitypification so that all mycologists have the same
598729) (Phillips et al., 2006). Because of this, the basic understanding of this taxon, genus and family
name of the fungus causing an important disease of (Massariaceae).
blueberry (cane canker) has been stabilized. Collec- We are studying the type specimens of genera of
totrichum capsici (Syd.) Butler & Bisby is an eco- the order Pleosporales and have found that about
nomically important taxon that causes anthracnose in 20%~30% of herbarium specimens are in bad condi-
chilli. However, molecular data could not be obtained tion, and little morphological data could be obtained
from the type specimen. The authors therefore ob- from these types. For example, the type specimen of
tained a fresh collection from chilli in Coimbatore in Teichospora trabicola Fuckel (G00110113), syntype
India and designated this as the epitype of C. capsici. of Metacoleroa dickiei (Berk. & Br.) Petr. (K(M)
More importantly they obtained living cultures and 143928), the type specimen of Leptosphaeria mi-
deposited these in public culture collections (as chotii (Westend.) Sacc. (Belgium, 89509-75) (as
ex-epitype living cultures). The phylogenetic status of Sphaeria michotii Westend.), the holotype specimen
this taxon has thus been stabilized and cultures are of Pleospora scirpicola (DC.) P. Karst. (as Sphaeria
freely available for future work in this important scirpicola DC.) (G00110110) are all in poor condition.
pathogen and pathogenic genus (Shenoy et al., Even when specimens are in good condition, it is not
2007b). Similarly, the phylogenetic characters of always possible to evaluate some valuable characters,
Mycosphaerella and Teratosphaeria have also been such as ascospore sheaths, type of ascus dehiscence,
clarified by designating the epitypes of the type spe- and these are characters that might be informative in
cies of these two genera (Verkley et al., 2004; Crous classification (Eriksson, 1982; Hawksworth, 1994).
et al., 2007). Therefore fresh material should be located and de-
Some specimens, especially old types, can be tailed descriptions of these taxa should be published
very difficult to locate or obtain. For example, the (after comparison with the type) and designated as
neo-type specimen of Trematosphaeria pertusa (type epitypes which should include living material for
species of Trematosphaeria) is kept in Persoon’s future study.
exsiccata in the University of Leiden (L). According
to the rule of the herbarium, this specimen could only
be studied in the herbarium, and it is very difficult to POSSIBLE PROBLEMS ASSOCIATED WITH
obtain funding for such. Thus this has been poorly EPITYPIFICATION
studied (Boise, 1985), and limited morphological
characters for this taxon can be found in the It is very important that an epitype is identical to
protologue. With such a situation, designation of an the original type; however, since the type may be lost,
epitype would be beneficial. or in poor condition, it is not always possible to verify
 Hyde et al. / J Zhejiang Univ Sci B 2008 9(10):842-846 845

this. Therefore subjective judgement has to be used to poorly characterised and is unavailable to researchers
decide on a specimen that can be designated as an unless the high costs of buying these cultures from
epitype. Thus, although there may be a chance of American Type Culture Collection (ATCC) are paid.
error, designating an epitype is a better approach to The ex-epitype is well characterised, is freely avail-
move forward, than having many interpretations of able (in six public culture collections) and has been
what characters of the type species of a genus, family sequenced using several genes. We would therefore
or order may comprise. There is a chance that the type recommend that the epitype is used to represent this
may be newly located at a later date; however, this is species as it was derived from the same host in the
unlikely. If this did happen, the original type (if in same area and has identical morphology to the type.
good condition, freely available and DNA can be Others may disagree and thus attempt by Than et
extracted and sequenced) should represent the species. al.(2008) to stabilize the species may not have
It is very unlikely, however, that an isolate of the type worked.
could be located at a later date. Interestingly, the story does not stop here! Col-
Colletotrichum acutatum Simmonds is an im- letotrichum acutatum isolates cluster into groups
portant pathogen that was introduced by Simmonds based on restriction fragment length polymorphism
(1965) without a type, and validated in 1968 with a (RFLP) of mitochondrial DNA (mtDNA), RFLPs of
broad concept. This was demonstrated by the selec- the 900-bp glutamine synthase (GS) intron and se-
tion of several type specimens from a range of hosts quence analysis of the glutaraldehyde-3-phosphate
(Simmonds, 1968). Than et al.(2008) considered that dehydrogenase (G3PD) intron 2, and the GS intron 2
Simmonds (1965; 1968)’s broad concept of C. acu- gene (Guerber et al., 2003; MacKenzie et al., 2008;
tatum has created uncertainties in the species concept. Peres et al., 2008). These groups might represent
No viable ex-type cultures of C. acutatum were lo- phylogenetically distinct species of C. acutatum
cated and further there were no viable cultures of this sensu lato (Guerber et al., 2003). It will be interesting
taxon on Papaya from the type locality. Than et al. to establish which group(s) the ex-paratype with pink
(2008) therefore designated a specimen of living cultures and the epitype with orange to grey cultures
culture stored at Queensland Department of Primary cluster in. There will no doubt be more written on this
Industries and Fisheries, Plant Pathology Herbarium, subject.
Indooroopilly, Australia (BRIP 28519), as an epitype
from Papaya (same host as type) from Yandina
ACKNOWLEDGEMENT
(nearby location). Subsequent to this publication, it
has been discovered that a culture of C. acutatum had
Dr. Roger Shivas (Queensland Plant Pathology
been sent by Simmonds to Dingley in New Zealand
Herbarium) and Dr. Peter Johnson (Landcare New
(and then to ATCC 56816) (Guerber and Correll,
Zealand) are thanked for bringing to the attention of
2001). This culture, however, was not derived
Dr. Hyde the problems associated with the C. acu-
ex-holotype. The culture Simmonds sent to Dingley is
tatum epitype.
given as culture No. 16633D [p.225 in (Guerber and
Correll, 2001)]. This culture was also sent by Sim-
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