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Epitypification_shouldweepitypify_

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Epitypification_shouldweepitypify_

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?

    †1,23Kevin D. HYDE, Ying ZHANG

    1(International Fungal Research and Development Centre, the Research Institute of Resource Insects,

    Chinese Academy of Forestry, Kunming 650224, China) 2(Fungal Research Group, School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai 57100, Thailand) 3(Centre 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

    replacing lost type material or types in poor condition. What can be done if the material that represents a

    If DNA cannot be extracted from types, then we need type species, genus, family or order is lost, is in poor

    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

    GenBank becoming a dustbin for DNA sequences (Hibbett et al., 2007). However, the understanding of

    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

    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

    et al., 2008). This material may not be the type, but no way to repeat the experiment (Shenoy et al.,

    can be collections identified by the same mycologist 2007a).

    who designated the type, or collections by others from

    the same host and location. This DNA data is very

    important to determine the phylogenic status of a HOW TO DECIDE ON AN EPITYPE

    particular fungus, especially for those rarely encoun-

    tered taxa. Furthermore, if it was collected by the According to the definition of an epitype

    original mycologist it is likely to be authentic. As long (Mcneill et al., 2006), the epitype should be identical

    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

    have been unable to locate the type material of this EXAMPLES OF EPITYPIFICATION

    species. Shoemaker and LeClair (1975) systemati-

    cally studied the Massariaceae and examined a By epitypification, a name can be fixed to 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

    (1977) reported this taxon to have asci with 8 asco- Botryosphaeria corticis was made from a commercial

    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

    the central septum. This species therefore needs designating it as the epitype as none of the previous

    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

    (Massariaceae). name of the fungus causing an important disease of

    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-

    tion, and little morphological data could be obtained chilli. However, molecular data could not be obtained

    from the type specimen. The authors therefore ob- from these types. For example, the type specimen of

    Teichospora trabicola Fuckel (G00110113), syntype tained a fresh collection from chilli in Coimbatore in

    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

    Sphaeria michotii Westend.), the holotype specimen ex-epitype living cultures). The phylogenetic status of

    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.

    Even when specimens are in good condition, it is not pathogen and pathogenic genus (Shenoy et al.,

    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,

    and these are characters that might be informative in clarified by designating the epitypes of the type spe-

    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

    (after comparison with the type) and designated as very difficult to locate or obtain. For example, the

    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

    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

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