digital tocDigital diversity: publication of new names is now completely electronic

Commentary by P. David Polly

Article number: 16.2.1E
https://doi.org/10.26879/131
Copyright Palaeontologia Electronica, May 2013

Author biography
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Final citation: Polly, P. David, 2013. Digital diversity: publication of new names is now completely electronic. Palaeontologia Electronica Vol. 16, Issue 2; 1E:11p. https://doi.org/10.26879/131
palaeo-electronica.org/content/2013/441-commentary-digital-diversity

Nearly thirteen years ago, Palaeontologia Electronica became the first digital journal to publish new taxonomic names (Gee, 2000). Three new species of foraminifera were named by Takayanagi in a paper by Scott et al. (2000): Eggerella matsunoi, Haplophragmoides hatai, and Haplophragmoides nishikizawensis (Figure 1). Those names, whose validity was made possible by changes in the 4th Edition of the International Code of Zoological Nomenclature (ICZN, 1999), were heralds of the changing landscape of scientific publishing.

digital fig1FIGURE 1. Type specimens of the first species names published in Palaeontologia Electronica by Takayanagi in 2000, the foraminifera Eggerella matsunoi (1), Haplophragmoides hatai (2), and Haplophragmoides nishikizawensis (3).Rules of taxonomic nomenclature exist to provide an objective, fair, and stable means of applying names to species, genera, and family-level taxa. Those rules govern only names and say nothing about what biological principles should be used to define a taxon or what methods should be used to recognize one. The Principle of Priority states that when different names have been applied to the same taxon, the name that was first published takes priority over later ones. The Principle is invoked when a scientist revises a group using whatever tools and conventions are currently available and finds that two or more name-bearing holotype specimens are lumped together. The newly reconstituted group assumes the name of whichever type was first established. Perhaps the most famous application of the Principle of Priority was the synonymy of the widely known name Brontosaurus Marsh 1879 with the earlier name Apatosaurus Marsh 1877. Despite early recognition that the two belonged to the same genus, the junior name Brontosaurus was popularized in the 20th Century by skeletons exhibited with that name in the galleries of Yale's Peabody Museum and New York's American Museum of Natural History.

Who published which name first is therefore an important and sometimes contentious issue. Most taxonomic names are proposed with little fanfare, but in some cases authors compete for the right to name new species. O. C. Marsh, the author of Brontosaurus and Apatosaurus, and E. D. Cope were famously rivals in their 19th Century efforts to name new fossil taxa from the American west, sometimes dictating short papers by telegraph in effort to establish priority for their new names. For names to be correctly applied, it is important that the scientific community have access to the appropriate details: who named it, when was it named, what differentiates it from others, and where can the type material can be examined? The rules of nomenclature stipulate what constitutes a valid publication so that these questions can be objectively answered. Most important, a valid publication must be distributed widely in the scientific community in such a way that the who, when, what, and where cannot be falsified by an author to gain priority. If rivals like Cope and Marsh had been able to publish taxonomic names by nailing broadsheets to church doors in Laramie, they would have been able to get them out instantly but the scientific community would likely have no record of them. Likewise if rivals were able to back-date publications in order to attain priority, a tit-for-tat response could escalate until the dates on the papers were older than the fossils themselves. The surest way to prevent such behavior is to require that papers that name new species be published in a durable, widely distributed format. If everyone has a copy of the description, nobody can falsify the details.

Electronic publication has been a challenge for the rules of nomenclature, not because of its digital nature per se, but because of the client-server model. Most digital publishing is done over the World Wide Web. The original files are stored on the publishers server and readers use client software, such as an Internet browser with a PDF reader plug-in, to access the files. The publisher has the technical capability of altering the original files at any time, thus jeopardizing the very principle that the rules of nomenclature exist to protect. If rivals like Cope and Marsh were electronic publishers, one can easily imagine rampant revisionism. Until 2012, therefore, both the ICZN and the International Code of Botanical Nomenclature (ICBN, which was recently renamed the International Code of Nomenclature for Algae, Fungi, and Plants) insisted that durable copies be made widely available to ensure that fraud could be detected.

digital fig2FIGURE 2. Type specimen of Rhabdophyllites diapros, the first plant species name published in Palaeontologia Electronica by Danehy et al. in 2007.The 4th edition of the ICZN in 2000 made allowances for electronic publishing, so long as durable, simultaneously produced versions of the work were widely distributed. PE served as a valid publisher for Takayanagi's names because we started pressing CD-ROMs of our issues that we archived in several libraries around the world and sold at cost to subscribers. Unsurprisingly, the CDs were in low demand since our pages also appeared open-access in HTML and PDF format on the Internet, but the principles enshrined in the Code to prevent fraud were met. The publication of the "Vienna Code", as the 2005 edition of the ICBN is known, similarly recognized electronic publication for botanical names so long as durable, simultaneously produced versions of the work were distributed in printed format. PE converted its archival format from CD-ROM to print (at great increase in cost) and was then able to validly publish plant, algal, and fungal names. We also made the print volumes available at cost through the print-on-demand services of Lulu.com. The nightmare vision expressed by former PE Executive Editor Norman Macleod that, "I would be severely depressed if in ten years I walk into an office and find a series of bound volumes of PE printouts" (Gee, 2000) had nearly come true since we still publishing the print volumes in 2010 thanks to the Vienna Code. Nevertheless, we were able to publish our first plant name, Rhabdophyllites diapros, a name given by Danehy et al. in 2007 to a dicot plant from the Eocene of Mississippi (Figure 2).

The distinction between the durable and the on-line copies of papers created new areas of uncertainty for nomenclature. According to the rules, priority stemmed from the durable, distributed copy of the publication, not the on-line version. So long as the durable version was produced at the same time as the on-line version went live, there was no problem. However, the growth of "early on-line" editions of print journals often put new names into public view before the printed version established the formal date for priority. Names in the early on-line edition were formally nomen nudums without priority according to the nomenclature rules until the print edition was distributed. In some cases this led to an electronic age rivalry for taxonomic priority. For example, Gündüz and colleagues named Spermophilus taurensis, a new ground squirrel from Turkey, in the journal Molecular Phylogenetics and Evolution (Gündüz et al., 2007a). After the early on-line edition of the paper was published in February 2007, Özkurt and colleagues submitted a manuscript to the journal Zootaxa applying the name Spermophilus torosensis to the same species. The latter was published 19 July (Özkurt et al. 2007), only weeks after the former came out in print in June. Spermophilus taurensis retained priority, but only narrowly (Gündüz et al., 2007b).

Starting last year, truly electronic, online publications are recognized by both codes. The botanists were first, recognizing PDFs as valid publications in the new Code (ICN, 2012). The principle on which this change was based is that PDFs are easily downloaded and saved by readers, archived by libraries, and harvested by on-line repositories. Thus, even though PDFs are not physically durable, they are so widely distributed that it would be difficult for a publisher to alter all copies after the original publication, regardless of the fact that they retain control over the original server files. The ICZN followed suite in September, 2012 by amending the 4th Edition of the Code to allow purely electronic publications to be considered valid from 2011 onward with the stipulation that names be registered in the digital name repository ZooBank (zoobank.org) and that evidence of the registration be published in the work (ICZN, 2012). Upon registration, ZooBank issues an LSID (Life Science Identifier), which is a unique identification number presented in uniform resource name (URN) format, that serves as a "watermark" for the new name in the digital publication and which can be used to retrieve it from the ZooBank archive. Ironically for PE's first electronic taxonomic names, publication by CD-ROM is no longer recognized as valid under the amended ICZN.

Starting in 2013, we register all new taxonomic names in ZooBank and publish the LSID to comply with the new rules. We now ask our authors to provide us with the details necessary to register names at the time they submit their manuscripts. We have also registered in ZooBank all 95 zoological names that we published since 2000, including Takayangi's first three (Table 1). To further comply with the new rules, PE will be digitally archived with the CLOCKSS, a non-profit archiving venture between publishers and libraries that provide access to electronic periodicals in perpetuity (clockss.org/), through a partnership with the Indiana University ScholarWorks initiative (scholarworks.iu.edu/). Finally MacLeod's vision of a truly paper-less electronic paleontology journal has been realized.

REFERENCES

Danehy, D. R., Wilf, P. and Little, S. A. 2007. Early Eocene Macroflora from the Red Hot Truck Stop Locality (Meridian, Mississippi, USA). Palaeontologia Electronica 10.3.17A: 1-31.

Gee, H. 2000. Online naming of species opens digital age for taxonomy. Nature, 408: 278.

Gündüz, ?., Jaarola, M., Tez, C., Yeniyurt, C., Polly, P. D. and Searle, J. B. 2007a. Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Anatolia, with a description of a new species. Molecular Phylogenetics and Evolution 43: 916-935.

Gündüz, ?., Jaarola, M., Tez, C., Yeniyurt, C., Polly, P. D. and Searle, J. B. 2007b. Spermophilus taurensis Günduz et al. 2007 and S. torosensis Özkurt et al., 2007 (Scuiridae, Rodentia) are synonyms for the same species of Ground squirrel from the Taurus Mountains of southern Turkey. Zootaxa, 1663: 67-68.

ICN 2012. International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code). (Regnum Vegetabile 154). Koeltz Scientific Books: Koenigstein, Germany.

ICZN 1999. International Code of Zoological Nomenclature, 4th Edition. International Trust for Zoological Nomenclature: London.

ICZN, 2012. Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication. ZooTaxa, 3450: 1-7.

Özkurt, ?.Ö., Sözen, M., Yi?it, N., Kandemir, I., Çolak, R., Gharkheloo, M.M. and Çolak, E. 2007. Taxonomic status of the genus Spermophilus (Mammalia, Rodentia) in Turkey and Iran with description of a new species. Zootaxa, 1529, 1-15.

Scott, D. B., Takayanagi, Y., Hasegawa, S. and Saito, T. 2000. Illustration and reevaluation of affinities of Neogene Foraminifera described From Japan. Palaeontologia Electronica 3.2.8A: 1-41.