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Introduction and Acknowledgements to the

Catalogue of Diatom Names

 

Elisabeth Fourtanier & J. Patrick Kociolek


Aims of the Catalogue  |   History of Catalogues of Diatom Names  |   The Making of the Catalogue  |   Acknowledgements

Large sections of this introduction are from the Introduction to Part I and Part II of “Catalogue of Diatom Names” (Fourtanier & Kociolek, in prep.) to be published as a “Occasional Paper of the California Academy of Sciences”

 

Aims of the Catalogue

The “Catalogue of Diatom Names” is a compilation of names of diatom genera, species and taxa at infraspecific ranks (62,000) compiled by staff at the California Academy of Sciences (CAS) during the past 12 years. We provide for each name relevant information such as authorship, place and date of publication with page and figure numbers where the taxon was described and illustrated, basionym or replaced synonym when applicable, and nomenclatural status (valid/invalid).  For selected records we include information about the type specimen and type locality.  Whenever possible we provide a link to the Index Nominum Algarum (INA) (see http://ucjeps.berkeley.edu/INA.html), a database of algae names (including at least 40,000 diatom names) compiled by Paul Silva and maintained at the Herbarium of the University of California, Berkeley.

This index does not include names above the rank of genus (e.g. family), and of ranks between genus and species (e.g. subgenus, section). Most of those have been recorded in the Index Nominum Algarum” (INA)

Taxa below the rank of species are treated as trinomials in accordance to Art. 24.1 of the International Code of Botanical Nomenclature (ICBN), which states “The name of an infraspecific taxon is a combination of the name of a species and an infraspecific epithet. A connecting term is used to denote the rank”.

Our aim was for this compilation to be as complete and as accurate as possible. Most of the names in this index have been verified against the publications in which they were originally published. We have made great efforts to include all new names at least up to the year 2000, which represents an addition of 18,000 names to the 44,000 names in VanLandingham’s Catalogue (VLC).  More omissions may be found in the period between 2000 and 2007. In addition to valid names, many invalid names are included. The invalid names are indicated as such with an explanation.  Our assessments of the nomenclatural status (validity) of a name are based on our interpretation of the International Code of Botanical Nomenclature (ICBN).  The ICBN cited here is the St. Louis Code (Greuter et al. 2000). As the ICBN rules are subject to change, these assessments may need to be revised. Current versions of the ICBN (e.g. McNeill et al. 2006) will be used in future versions of the Catalogue.  We also kept all the “sensu” that are listed in the Catalogue of VanLandingham, most of which do not have nomenclatural standing.

We have not expressed taxonomic opinions in this compilation.  In previous catalogues (e.g. Peragallo 1897-1903; Mills 1933-1934; VanLandingham 1967-1978), authors indicated whether they considered a name taxonomically valid, using a different print for the synonym that they believed should be used than for the synonyms they believe should not be used.  In these previous catalogues, a list of synonyms (nomenclatural= homotypic, and taxonomic= heterotypic) was listed with each name.  Taxonomic synonyms are not listed in this catalogue.   This deserves an explanation, since many users of the Catalogue of VanLandingham have become accustomed to having this as part of a “names” catalogue.  Such declarations of taxonomic synonyms are hypotheses of relationships and identity.  As such, they require data to support such hypotheses, including examination of types and other aspects of revisionary studies.  In the past, such data has been scarce or lacking.  Given the scope of this work, we could not offer the types of information and data required to responsibly suggest taxonomic synonymy.  Nomenclatural synonyms, however, for each given name, such as basionyms or replaced synonyms, are given (see under “full record”).

 

History of Catalogues of Diatom Names

The study of diatoms emerged in the early 1800’s (e.g. Agardh’s 1830-1832 “Conspectus Criticus Diatomacearum”;  Bory 1822-1831 in “Dictionnaire Classique  d’Histoire Naturelle”). In 1832 there were about 500 published diatom names.  From that time the description of new diatoms and the proliferation of new names accelerated, thanks to progress in microscopy, and to the remarkable contributions of authors such as Ehrenberg and Kützing. About 4,000 diatom names were published in the 20 year span between 1833 and 1854 (inclusive).  Important contributors in the second half of the 19th century include Gregory, W. Smith, Greville, Grunow, Ralfs, Rabenhorst, Cleve, A. Schmidt, Van Heurck, Pantocsek, Rattray, the Peragallo brothers, De Toni, and Kunze.  By the end of 1903, about 25,000 names had been published.   Some large monographs/compilations also appeared during that period: Ralfs in Pritchard’s “An History of Infusoria, including the Desmidaceae and Diatomaceae” (1861), is a very exhaustive compilation of the state of knowledge on the diatoms at the time.  Similarly, De Toni’s “Sylloge Algarum” (1891-1894) is a remarkably complete taxonomic treatment of diatoms and other algae.  Other major contributions were more narrow in scope, such as Pantocsek’s “Beiträge zur Kenntnis der Fossilen Bacillarien Ungarns” (1886-1905), H. & M. Peragallo’s “Diatomées Marines de France” (1897-1908), and Van Heurck’s “Synopsis des Diatomées de Belgique”  (1880-1885).  In the monumental “Atlas der diatomaceen-Kunde” (1874-1959) initiated by A. Schmidt, an estimated 10,000 diatom taxa are illustrated, including ca. 2,000 new to science.

The first catalogues that were intended mainly as indices of diatom names, not as monographs or taxonomic revisions, were published at the end of the 19th century.  These include Habirshaw’s “Catalogue of the Diatomaceae with Reference to the various published Descriptions and Figures”, published in New York in 1877 (265 pp., handwritten, reproduced with the Edison Electric Pen process).  This first edition was followed by several others, published in very small numbers; all are quite rare. A second edition (1881), with xxii + 58 pp. printed pages, was published and edited by R. Hitchcock; it is incomplete covering only the first part (to Bacillaria). Another edition (1885), with 343 +11 hand-written pages, was published by H.H. Chase. According to VanLandingham (1969, vol. 3, p. 1689) Chase published a fourth edition (351pp.) in 1887 and a fifth edition (501 pp.) in 1894. Both VanLandingham (1969) and De Toni (1891) suggest a unique typed copy had been made for Julien Deby. This copy is often cited by De Toni (1891, 1894) (“Habirsh.-Chase Cat. 1888”, “exemplar Debyanum”). Chase also published another edition in 1907 (662 pp., “done on the type-writer”). This copy, present in the CAS library, is not mentioned by VanLandingham or Stafleu & Cowan (1979). According to Stafleu & Cowan there is also a French edition, (“edition française revue et augmentée par J. Pelletan, Paris 1879”). About 6,500 names are listed in Habirshaw 1885. The catalogues of Habirshaw consist of an alphabetized list of diatom names, followed by authorship and a bibliographic reference in abbreviated form. Other citations of the names are also included, and some synonyms are listed.  There is no interpretation on whether a listed name is “accepted” or not.

The “Catalogue Général des Diatomées” was published by Maurice Peragallo in 16 handwritten lithographed fascicles (32 pages in 4to. printed on one side), according to a partial copy at CAS. Another complete copy at CAS is bounded in 2 volumes dated 1897 and 1903 respectively.  Peragallo remarked in his introduction on the number of synonyms that were cluttering the nomenclature, and the number of “uncertain” names for species described by older authors without adequate description, illustration, and ambiguous types.  He wrote: “maintenant que l’étude des Diatomées se répend l’établissement d’un Catalogue et la révision de la nomenclature des Diatomées est absolument indispensable; c’est là le but que je me suis proposé, heureux si je puis ainsi être utile à ceux qui s’occupent de Diatomées”.   Peragallo used Habirshaw’s catalogue as a starting point, adding as many names as possible.  Unlike Habirshaw, Peragallo made interpretations. He listed synonyms, and offered his opinion as to which names should be retained (“conservés”)  (round characters) and which should not be used, at least for now (“espèces...clairement synonymes ou dont les documents existant à leur sujet n’ont pas permis une définition suffisante”) (italic characters).  The data includes, name of the taxon, authorship, place and date of publication (in abbreviated form), synonyms, other citations of the name, and, indicated by the type of print, an opinion regarding the value of a name (round characters: to keep, italics: to drop).  The “Catalogue Général des Diatomées” lists about 17, 000 names.

With further developments in diatom studies in the early part of the 20th century, the need for a new catalogue was filled by Mills, who published “An Index to the Genera and Species of the Diatomaceae and their Synonyms” between 1932 and 1935. There are an estimated 26,000 entries in Mills’ Index.  Mills explains in his introduction that his “Index” was originally compiled as a references for his own use, originally based on the Catalogue of Habirshaw, however it was discontinued for a time on the issue of Peragallo’s Catalogue. During the following 30 years he had indexed all the new species, noted the alterations in nomenclature rendered necessary in Peragallo’s work.  He published the work at the urging of his friends.  The format is very similar to that of Peragallo’s; an opinion is given whether a species is “recognized” (capital letters) or synonym (small type).  Entries include some synonyms and citations.

With the aim of continuing the compilation of Mills, and keeping the list of diatom names current, two unpublished card files, the “New Species File” and the “Bibliography file”, were created around 1930 under the direction of Ruth Patrick, at the Diatom Herbarium of the Philadelphia Academy of Natural Sciences (ANSP). For many years, the files were maintained by Diatom Herbarium staff, particularly Margaret “Peg” Henderson and Su-Ing Yong, supervised by Charles Reimer; since 2003, the files have been maintained by staff in the Patrick Center’s Phycology and Project Support Sections in consultation with Drs Patrick and Reimer (See Keller et al. 2005).  Starting in 2004 new additions are computerized.  The Files are unpublished but are available for consultation by visitors at ANSP.  Information recorded in the “New Species File” includes, as in Mills, the scientific name with authorship, place and year of publication, pages, and comments on the nomenclatural status.  Copies of the original illustrations and descriptions are also recorded.

VanLandingham’s “Catalogue of the Fossil and Recent Genera and Species of Diatoms and their Synonyms” (VLC) was published in 8 volumes between 1969 and 1979, and covers diatom names published up to the year 1964. Intended as a revision of Mills’ Index, VLC contains 44,000 entries (18,000 more than Mills), including 4,000 entries of names published before 1935, which were omitted from Mills’ Index.  VanLandingham corrected some of the errors in Mills (some traceable to earlier catalogues), but not all. He consulted the New Species File at ANSP but also used other sources, and added names published post 1930 that do not appear in the ANSP “New species File” (ca. 3,500 entries).  A departure from Mills in the format is the dropping of the use of abbreviations: authorships are spelled out, and full references are to be found at the end of each volume. This adds clarity, despite the fact that no system is provided to distinguish between several references published by an author in the same year.  VanLandingham also provides taxonomic interpretations, following in many cases the opinions of Hustedt: “In most cases, the opinions and interpretations of P.T. Cleve will be continued in the present work as they were in the Mills Index (except in cases of conflict with Hustedt)”.  Besides this statement in the introduction of his first volume (1967, p. vii), VanLandingham does not indicate the origin of the taxonomic interpretations.  Although these interpretations are subjective, the list of synonyms is of value to anyone interested in a particular taxon.  Like Mills, VanLandingham uses upper case letters for “valid taxonomic entries: the continued use of which is recommended”, and lower case letters for “invalid, poorly described, or doubtful taxonomic entries, the use of which is not recommended. Synonyms of taxonomic units in upper case letters are presented in lower case letters”. VanLandingham reminds the readers in the Introduction to his last volume (1979) “those entries presented in lower case letter (uncapitalized) do not imply that there is anything invalid or wrong with that taxon; many of these “synonyms” are simply a matter of convenience for the author of this catalogue. We are all reminded that taxonomy is always subject to debate, and that there is no such thing as a taxonomic truth”.

The “Index Nominum Algarum” (INA) contains ca. 200,000 cards of algal names (including an estimated 40,000 diatom cards) and is housed at the Herbarium of the University of California, Berkeley. The INA has been compiled by Paul Silva since 1949 and contains nomenclatural information (including type information) directly derived from examination of original publications.  It is accompanied by a card file containing bibliographic references, the “Bibliographia Phycologica Universalis” (BPU). Entries made after 1986 are computerized.   The INA is available online at http://ucjeps.berkeley.edu/INA.html.  The INA is largely not computerized, but the cards have been scanned and can be easily viewed as image files on the Herbarium website. All of the diatom cards have been indexed and are easy to find.  Despite some omissions (the INA is missing ca. 20,000 diatom names, about 15,000 of which are valid), it is a very valuable resource. The data has been very competently and carefully entered, and the occurrence of errors is extremely rare.  The INA entries also include statements on the nomenclatural status (valid, unless otherwise indicated), and cite types, and original localities.

The Ellis & Messina Catalogues (Micropaleontology press) first launched by Brooks Ellis  (assisted by Angelina Messina) were the Foraminifera Catalogue (1934), and the Ostracoda (1952).  The first volume of the “Diatom Catalogue” was published in 1982. There are currently 7,500 entries in the Diatom Catalogue. The catalogue, that focuses on fossil taxa, reproduces the complete type descriptions for genus- and species-level taxa, including full-size reproduction of original figures and charts. Diagnoses in western European languages are given verbatim, while those in Russian, Chinese, and other non-western languages are translated by professional micropaleontologists. The stratigraphic level, locality and depository of the type material are given for each taxon, and bibliographic references and taxonomic terms are expanded and verified against the Ellis and Messina database. Between 200 and 300 taxa are added yearly to each catalogue.  The catalogues are available online to subscribers (http://micropress.org/e_m.html).

 

This catalogue

In the 30 years following the publication of the Catalogue of VanLandingham, thanks to progress in diatom research, and microscopy (SEM), many new diatom taxa were described and there is today an urgent need for an updated catalogue. In the process of preparing this catalogue, we discovered that 10,000 new names were published between 1965 and 2001.  In addition there are over 6,000 names published in or before 1964 that were not included in VanLandingham’s catalogue.

Because of the availability of computers, a different approach was taken to develop this catalogue.  Our data is organized in a database (currently FileMakerPro version 8.0v2). This allows for many options to search, sort and export the data.

This catalogue attempts to be as complete and accurate as possible.  We have verified the information against original publications for 50% of the entries.  Authors are cited in full (not abbreviated), a publication number is attached to each entry to remove any ambiguity in the case of several publications by the same author in a same year.

Our most significant deviation from the format of the catalogue of VanLandingham is that we do not offer taxonomic opinions.  As discussed previously, we do not list taxonomic synonyms, and usually do not offer references to citations and other taxonomic treatment of a particular taxon.  Besides the subjective nature of taxonomic opinions, the task of properly and professionally collecting, sorting and evaluating such opinions seemed unrealistic given our resources. Similarly unrealistic would be to attempt to establish, for each taxon, a complete list of suggested synonyms, or a complete list of citations. The synonymies suggested by VanLandingham, however, have been entered in the database, and could be retraced through a fairly simple search. Another significant difference with the catalogue of VanLandingham is that we have interpreted the nomenclatural status (valid/invalid) of most names.

 

The Making of the Catalogue

This project was initially funded by a NSF Grant to Patrick Kociolek (DEB-9505269).

The data is organized in a relational database (FileMakerPro) comprising 3 main tables: a “publication” table, a “genus” table, and a “species” table for names of diatoms at species and infraspecific ranks.

We started with building the publication table from a compilation of our own holdings, and the references listed at the end of each volume of VanLandingham’s catalogue. This publication database continues to be updated (12,654 records in July 2007).

In the years 1997-1998, a table of verified names of diatom genera was built, and resulted in the publication of the “Catalogue of diatom genus names” (Fourtanier & Kociolek 1999).

Around the same time we started the construction of the “species table”.  Staff at CAS entered data from VanLandingham’s Catalogue (44,000 entries).  The information was split between various fields.  Additional fields were added later as we improved the database.  Once the data were entered, we divided the database into 2 sections: Names published after 1930 (i.e. post Mills), and names published up to 1930.  The names published after 1930 were then sent to ANSP (13,500 diatom names), where the Diatom Herbarium staff under the supervision of Charles Reimer compared the VLC entries against the New Species File (NSF) (22,000 NSF cards post Mills). Based on this comparison, diatom staff at ANSP noted when discrepancies occurred between NSF and VLC data (2,500 discrepancies), and added 12,000 names, as well as their corresponding bibliographic references to the publication table.

Meanwhile the Diatom staff at CAS started verifying VLC data for those names published on or before 1930 (30,500 diatom names) against the original references, and correcting inaccuracies such as page, authors citations, original reference. We also took note of the nomenclatural status of names (valid/invalid).

During this process we added a few names as we came across publications that had not been previously processed (ca. 1,000 names including 100 published before 1964)

In 2003-2004 we compared the database at CAS with the Index Nominum Algarum (INA).  Paul Silva & Richard Moe generously provided us with an electronic copy of the card files, which facilitated the process.  We added 4,600 names from the INA that were missing from our compilation (including 3,400 names pre-1930), and noted discrepancies between the INA cards with our data (12,000 discrepancies noted). In this process we added the corresponding references from the BPU to our species table (1,060 references).

The nature of the discrepancies with ANSP or INA, concerned generally the year of publication, the page or figure citation, the spelling of the name, the citation of the authorship, and sometimes the place of valid publication.

In the years 2004-2005, we dealt with the discrepancies within the group of names in the “Abas-Bruniopsis” part. We found most convenient (time saving) to work through the diatom names by author, and by publication within each author. The database was then sorted by alphabetic order of genus and species, and examined, for homonyms, redundant new combinations, and for final editing.

Our current tasks consist of continuing to address the discrepancies in the data, and keeping up with the literature by adding newly published names.

 

Acknowledgements

We are very much indebted to the many people who have contributed to this project.

The database structure had been initially set by Al Mahood and Pat Kociolek. We gratefully acknowledge Bill Eschmeyer for many discussions on the design of his inspiring work on fish nomenclature and catalogue, Liz Bogan for numerous improvements, modifications and fine programming in the tables, Jean DeMouthe for her help in maintaining the database, as well as Stan Blum, Jon Fong, and the computer staff at CAS. We are particularly grateful to Jon Fong for the design of these web pages.

The laborious task of data entry was very competently performed at CAS by Cynthia Strathmann, Lisa David, Alicia Cordero, Kristen Nutile, Elizabeth Ruck. CAS staff Molli McDonald verified many records against original publications and Linda Novitski matched and compared INA cards with our existing records. Each of them brought a wonderful spirit, high intellect, and common sense to a project that required all of these attributes.

Staff at ANSP, including Margaret Henderson, and Su-Ying, under the supervision of Charles Reimer, very skillfully compared ANSP cards with our records, and entered names missing from our compilation.

We are very grateful to Paul Silva (Jepson Herbarium, UC Berkeley) for his encouragements and guidance during this project, and for his patience in explaining points nomenclatural difficulty. The quality and completeness of this catalogue has been greatly improved thanks to his generosity in sharing with us the INA cards. We also wish to acknowledge Dick Moe (Jepson Herbarium, UC Berkeley) who facilitated exchanges of data between CAS and UCB.

Many of the references consulted in this work were not at CAS. We gratefully recognize the library staff at CAS, in particular Larry Currie and Patti Shea-Dinner, who arranged for numerous interlibrary loans. Other references were found at the Libraries of the UC Berkeley and we wish to thank the librarians who assisted us.

Other persons who aided by providing other advice or literature include: Drs John Barron, David Williams, Nina Strelnikova, Galina Khursevich, Marina Potapova, Sam VanLandingham, Sarah Spaulding, Robert Edgar, Gene Stoermer and Ditmar Metzeltin.

We also wish to thank our families for all of their help, support and tolerance during the development of this sometimes all-encompassing project.