Cortbase version 2.02

A nomenclatural database of corticioid fungi (Hymenomycetes)

Erast Parmasto1*, Henrik Nilsson2, and Karl-Henrik Larsson2

1 Tartu University, Natural History Museum, 21 Vanemuise St., 51014 Tartu, Estonia
2 Göteborg University, Department of Plant and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden
* to whom correspondence should be addressed


Abstract and Update

Cortbase is a nomenclatural database of corticioid fungi (Corticiaceae s.l. and related hymenomycetes) with basionyms, synonyms, taxonomically correct names, data on name usage, literature references, and evaluation of nomenclatural status. The first version of Cortbase was compiled for the nomenclature and taxonomy of 7333 corticioid names as a stand-alone database for MS-DOS systems and was released as zipped files on a 3.5 inch floppy disk (Parmasto, 1997). The Internet-based Version 2 released in 2004 introduced many new search options and ways of compiling and combining information (Parmasto et al., 2004). The present Version 2.02 of the database includes 8292 species names; several mistakes found in the Version 2.01 have been corrected.

During more than ten years, Cortbase - originally based on a large card index compiled by E. Parmasto - has been a widely used tool to stabilise the nomenclature of an important group of Basidiomycetes. New and inclusive fungal databases such as Index Fungorum and MycoBank have been launched by British and Dutch mycologists (in co-operation with other European mycologists), and a modern, molecular-driven classification system of the fungi - including the polyphyletic corticioids - will be released in the near future (see the AFTOL classification project). We welcome this development, and we will investigate the potential to merge our data with theirs (or otherwise share resources). In the meanwhile we expect to maintain Cortbase and the data it holds, and we'll try to update it as necessary.

We are as always very thankful to all our colleagues and friends for their kind and longstanding support in compiling, maintaining, and correcting the data in Cortbase. Please drop us an email if you would like to made additions or corrections to the data in Cortbase.


Coverage

As traditionally perceived, corticioid fungi (Corticiaceae s.l.) form a group of higher fungi (Basidiomycota, Hymenomycetes) characterized by resupinate fruitbodies with smooth, slightly colliculose, warted, or folded hymenophore. The delimitation of the group has since long been a matter of debate, and it has gradually become clear that Corticiaceae is not only not monophyletic, but polyphyletic to an extent rarely seen before in any organism group. Today, the notion of corticioid fungi should be taken to refer to little more than a convenient label for an assemblage of similar life forms.

The limits of this artificial group are somewhat arbitrary. In addition to the genera and species usually included in Corticiaceae s.l, some related but traditionally distinguished groups (Coniophoraceae, Dichostereaceae, Steccherinaceae, Stereaceae, stipitate stereoid fungi, Thelephoraceae s.str., Tulasnellales, and some groups of polyporoid fungi) are included by some mycologists and excluded by others. In this database, the species of these groups are mainly included when they have homo- or heterotypic synonyms under the genus names of the "true" corticioid fungi.


What are names in current use?

To avoid inadvisable name changes, and to help biologists inexperienced in taxonomy to use correct names, an international project Names in Current Use (NCU) has been initiated and widely supported (cf. Hawksworth, 1991). As one of the main results, a list of generic names in current use of plants and fungi was published some years ago (Greuter et al., 1993). One of the questions to be solved before compiling a NCU list of species names is to define the limits of the term "current". The Special Committee on NCU defined the names as "legitimate names adopted in most recent revision (if any) of the corresponding group, or in a recent flora within whose limits a given taxon occurs..." (Greuter et al., 1993: xvii).

In some groups of fungi, "most recent revisions" are lacking. There are several "good" species described in the beginning of this century in tropical or other regions not visited by collectors afterwards, and not mentioned for decades. There are groups on which no taxonomist is currently actively working. Obviously, for any large group of organisms, the time limit for NCU must be different. In Cortbase, four periods of use of a name have been indicated: 1890-1924, 1925-1954, 1955-1969, and 1970 and later. The names used after 1954 are said to be the names in current use in this database. Nevertheless, several names not used after this date may represent "good" species that have not been included in recent monographs or key works.


Taxonomically correct names

Cortbase is a nomenclatural rather than a taxonomic database. Nevertheless, lest the database be of little use to a wider mycological audience, it was unavoidable for the senior compiler not to give for every species one taxonomically correct name when possible. In most cases, the "correct names" are taken to be those used in the newest surveys of corticioid fungi by Hjortstam (1987), Ginns and Lefebvre (1993) and Hjortstam and Larsson (1995) and subsequent works by the same and other authors.

The senior compiler of Cortbase has different opinion in several areas on the classification of corticioid fungi, but it would be inappropriate to make any taxonomic rearrangements in this database. For a taxonomist who does not agree with the arrangements used by the corticiologists indicated above, the option "Data on a species" presents all available names for selection. In following Ginns and Lefebvre, Hjortstam, and Larsson, a low number of cases where nomenclaturally unacceptable names have been indicated as correct ones were revealed, including the species of the genus Phlebiella P. Karst. According to the Art. 42.1 of the International Code of Botanical Nomenclature (Greuter and al., 1994), this genus is not validly published (Donk, 1963: 163). It has not been described in Latin after 1934, or in any other language before this date. Nevertheless, the senior compiler of the database retained this taxonomically "good" but invalid genus to have its species retrievable. There are also some other species names in current use in spite of their nomenclatural invalidity, and some names published ad int. have been used due to the unavailability of valid names.

There are hundreds of species described in or named under the "corticioid" genera Merulius Boehm. non Fr.: Fr., Irpex Fr.: Fr., and Hypochnus Fr., species which really belong to the unrelated groups Agaricales, Cantharellales, polypores, pyrenomycetes, etc. The senior compiler has not yet been able to find nomenclaturally correct names for all these species, and possibly there are several mistakes in the present dataset. It will be several years before the most enigmatic names will be deciphered - if they ever will be.


Data on species (validation, sanctioning, and periods of use)

When compiling the database, the question of valid publication of names had, in many cases, to be solved arbitrarily. According to the article 32.4 of the International Code of Botanical Nomenclature (Greuter and al., 1994), when coining a new combination, a direct or (before 1953) indirect reference to its basionym must be given. It may be simply its author's name (Art 32.5); however, in the Examples 5-8 of this article, more information than only name is given. When Kuntze combined more than 300 species of corticioid fungi in the genus Terana Adans. in 1892, the only "indirect reference" was the basionym's author's name abbreviation, sometimes misprinted at that. If similarly proposed new combinations are to be considered invalid, many names in current use must be replaced by new ones, including the names combined by Patouillard, Bondartsev and Singer and others. To avoid these name changes, we have to be extremely tolerant towards new combinations based on indirect references in the older litterature.

Many basionyms of corticioid fungi have been sanctioned by Fries. In such cases, a reference to their author and place of valid publication has been given in two different ways. Most authors have indicated the citation published in one of the Fries' validating books (e.g., Merulius tremellosus Schrad. : Fr., Syst. mycol. 1: 327, 1821). For the senior compiler of this database, when a name of a species described earlier was sanctioned, a special status to an already existing name has been assigned by Fries. Accordingly, not the place of sanctioning but the place of valid description of a species is the most important information to be given in a citation. In the database, this is given (e.g.: Merulius tremellosus Schrad. : Fr. (1794) in Spic. fl. Germ. 139. - Sanctioned by Fries in Syst. mycol. 1, 1821.) In this, we have followed the suggestions given by Gams and Kuyper (1995: 28-29). In the database, the period of use of a name is indicated independently of its taxonomic status; it is not an evaluation of the nomenclatural status but an item of information to be used with some caution. The nomenclatural status is indicated using the words legitimate, validly published but illegitimate, not validly published, and rejected in this genus. When a species was published under a misapplied generic name, its status is only mentioned when not validly published.


Implementation

The new version of Cortbase features eight possible search options. In common for all options is an extensive interlinking to facilitate rapid information retrieval of nested matches; for example, when listing accepted and rejected species in a genus, all species names are linked to the "Check a name" function, the result of which in turn is linked to "Data on a species". Where applicable, each search run is provided with a dynamically generated link to the Aphyllophorales database at CBS for retrieval of the corresponding information in that database. For a discussion of the terms relevant to interpretation of nomenclatural and taxonomical information (such as sanctioning, periods of name usage, and taxonomically correct names), the user is referred to Parmasto (1997).

  1. Check a name. This function returns data on a species name, including its author and the corresponding citation. The basionym and the taxonomically correct names are specified where known.
  2. Data on a species. This function returns full data on a species. In addition to providing information on basionym and taxonomically correct name, it also lists all homotypic and heterotypic synonyms, including data on type, sanctioning, time periods for name usage, and nomenclatural status (validly published or not, legitimate or not). In cases where a species has been synonymized with another, the mycologist proposing the synonymization is specified.
  3. List accepted and rejected species in a genus. For any given genus, this function lists, in turn, all accepted species, all rejected species, and all species that at some point have been assigned to the genus but which presently are of unknown systematic affiliation or status.
  4. Check herbarium for type specimens. This function lists the types kept in any of the 146 herbaria and collections covered by Cortbase.
  5. Names by an author. This function lists all names authored by a specified author. Obedience to internationally accepted author abbreviations (Brummit and Powell, 1992) is expected.
  6. List all genera in the database. This function lists all genera in the database.
  7. List all species with types marked "In need of restudy". This function lists all type specimens that are in need of restudy.
  8. List all valid basionyms with no data on type. This function lists all valid basionyms with no data on type. It is hoped that this function together with the previous one will serve to attract attention to areas of corticioid mycology where even small efforts will be of great value.

Acknowledgements

Support in part by grants of the Estonias Science Foundation (1993-1995), Open Estonia Foundation (1992, 1994), and by stipends of the Hesler Endowment Fund, Tennessee State University (1988), Swedish Institute (1992), and The Royal Society, London (1994). Botanical Institutes of the Free University of Berlin (1991), Louisiana State University (1994), Göteborg University (1994, 1995), and Uppsala University (1995) have financially or otherwise supported the studies by E. Parmasto in the libraries of these institutions. He is very grateful for the possibility to use personal libraries and databases of his colleagues Drs Kurt Hjortstam (Alingss, Sweden), Seppo Huhtinen (Turku, Finland), Walter Gams (The Netherlands), Karl-Henrik Larsson (Göteborg, Sweden), Ronald H. Petersen (Knoxville, USA), and Leif Ryvarden (Oslo, Norway). We gratefully acknowledge the collaboration and exchange of nomenclatural data with Dr Joost Stalpers (Baarn, The Netherlands). E. Parmasto would like to thank the Directors and Librarians of the libraries of the following institutions: Centraalbureau voor Schimmelcultures (The Netherlands), US National Fungus Collections (Beltsville), Botanical Garden and Botanical Museum of the Free University of Berlin, Botanical Institute of the Helsinki University, International Mycological Institute (Egham, UK), Department of Plant Taxonomy of Göteborg University, Royal Botanical Gardens (Kew), V.L. Komarov Botanical Institute (St. Petersburg, Russia), Main Library of the Russian Academy of Sciences (St. Petersburg), Saltykov Shchedrin Public Library (St. Petersburg), Section of Cryptogamic Botany of the State Museum of Natural History (Stockholm), Estonian Academy of Sciences (Tallinn), Estonian Naturalists' Society (Tartu), Tartu University, Botanical Museum of the Uppsala University, and Carolina Rediviva (Uppsala University Library). After the release of the first (DOS) versions of Cortbase, Drs Werner Greuter (Berlin), Paul Kirk (Egham, UK), Karl-Henrik Larsson (Göteborg), Karen K. Nakasone (Madison) and many other colleagues have sent the senior author numerous corrections, additions, and reprints on various aspects on corticioid taxonomy. Henrik Nilsson particularly wishes to extend his sincere gratefulness to Johan Alfredsson, Bjrn Trnqvist, and Dr. Roger Eriksson for invaluable help and advice on technical matters. Klas Benjaminsson of Bomb Mediaproduktion is acknowledged for the Cortbase logotype. Together with saying cordial thanks for this help, the authors of Cortbase hope that this generous help will continue.

References


Brummit R.K. and Powell C.E. (eds) 1992. Authors of plant names. Royal Botanical Gardens, Kew.
Donk, M.A. 1963. The generic names proposed for Hymenomycetes - XIII. Additions and corrections to parts I-IX, XII (Conclusion). Taxon 12: 153-168.
Gams, W. and Kuyper, T.W. 1995. Elias Fries as sanctioning authority for fungal names. Symb. Bot. Ups. 30 (3): 25-31.
Ginns J. and Lefebvre M.N.L. 1993. Lignicolous corticioid fungi (Basidiomycota) of North America. Mycol. Memoir 19. APS Press, St. Paul.
Greuter, W. and al. 1993. NCU-3. Names in current use for extant plant genera. Regnum Veg. 129. Koeltz Scientific Books, Knigstein.
Greuter, W. and al. 1994. International Code of Botanical Nomenclature (Tokyo Code). Regnum Veg. 131. Koeltz Scientific Books, Knigstein.
Hawksworth, D.L. (ed.) 1991. Improving the stability of names: needs and options. Regnum Veg. 123. Koeltz Scientific Books, Knigstein / Taunus.
Hjortstam K. 1987. A check-list to genera and species of corticioid fungi (Hymenomycetes). Windahlia 17: 55-85.
Hjortstam K. and Larsson K.-H. 1995. Annotated check-list to genera and species of corticioid fungi (Aphyllophorales, Basidiomycota) with
   special regard to tropical and subtropical areas. Windahlia 21: 1-75.
Parmasto E. 1997. CORTBASE - A nomenclatural database of corticioid fungi (Hymenomycetes). Mycotaxon 61: 467-471.
Parmasto E, Nilsson RH, Larsson K-H. 2004. Cortbase version 2 - extensive updates of a nomenclatural database for corticioid fungi (Hymenomycetes).
   Phyloinformatics 1:5. PDF

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