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Wednesday, February 20, 2008

Is the World of Taxonomy Ready for PLoS Systematics?

Taxonomy has historically been relegated to the back alleys of the publishing world. In-house museum journals, obscure regional or specialty publications and even more obscure foreign language academy reports have hidden many species descriptions, revisions and monographs from the eyes of interested biologists. Not to say this is the only reason for current crisis in taxonomy (see Rodman & Cody 2003), but it certainly contributes. The hard work and insurmountable dedication of the taxonomist to furthering their group of interest should be rewarded and not locked away for the other 5 people in the world working on that genus of organism. Ecologists rely on species descriptions to compare the fauna they find in their studies with the published literature. The imperative nature of correct identifications of species cannot be understated in the medical, infectious disease, and parasitology literature. Without a doubt, quality taxonomic research is invaluable, in high demand and highly underappreciated by funding agencies and other scientists, even those who rely on such work (PEET not withstanding)

The lack of visibility of taxonomic research and the failure to make systematics as a whole relevant to the everyday lives of people has been a burden on the community. Much of the work is tedious yet vital to biodiversity studies, medicine and biotechnology. IrregardlessIrrespective of how one chooses to define a species, the species debate, the issue of perception is pervasive in this field. Many taxonomists are made to feel inferior to their colleagues doing experimental work who bring in much larger grants. The truth of the matter is that taxonomy is not a profitable venture for academic institutions why rely in part on the money they skim off of grants. It is a traditionally an inexpensive field, even with the use of molecular tools to aid in phylogenetic reconstructions. You can easily get by with a microscope, computer and digital camera. DNA extractions are relatively inexpensive and you can send the DNA product off to get analyzed elsewhere affordably, not needing to purchase expensive sequencing equipment.

Taxonomists need to improve the visibility and relevance of the field to ensure a continued, or at the least renewed, interest for the study of species, either from a theoretical, philosophical or practical framework. One way to contribute to increasing the visibility of taxonomic research is to publish in Open Access (OA). Several studies have shown there to be a citation advantage in OA papers (Eysenbach 2006). Zootaxa has taken the initiative in the taxonomy world by offering to publish any peer-reviewed taxonomic work free of charge for subscriber access and $20/page for OA. Other taxonomic "niche" journals exist with various financial differences, but have yet to attain the reputation of Zootaxa to my knowledge. But it is my own feeling that Zootaxa is only known well among other taxonomists, with the majority of other beneficiaries either unable to obtain articles because the bulk of the articles are locked behind the subscriber wall. This also has the effect of making less text available for search engines, such as Google Scholar.

The Public Library of Science (PLoS) may help to alleviate part of the problems of visibility. They have grown to represent the standard in OA publishing and have a successful business model. Their success among scientists can measured by the fact that between all their publications they are PLoS ONE alone is publishing on average 50 high quality papers per week. This is higher than journal, even the weekly big names. It is clear that their model is successful and scientists are actively seeking them out to publish their research. This is a clear argument in favor of wide dissemination (Chapter 3, Recommendation 8A of the Code):
"Authors have a responsibility to ensure that new scientific names, nomenclatural acts, and information likely to affect nomenclature are made widely known. This responsibility is most easily discharged by publication in appropriate scientific journals or well-known monographic series and by ensuring that new names proposed by them are entered into the Zoological Record."
PLoS can make nomenclatural acts widely disseminated by providing them free of charge and out in open for all interested individuals with computer access. The steadily increasing popularity of PLoS ensures taxonomic work reaches a wide audience with a broad range of backgrounds. For instance, if you are working on parasites in humans and are describing a new species of muscle tissue boring pathogenic nematode you can tag the article as "medicine", "Nematoda", "New species", "Systematics", "Pathogen", etc. to reach audiences in non-parasitology fields.

Why would a taxonomist want to reach non-taxonomic areas of science? Citations are low in taxonomy. Species descriptions are read, the names are used in many publications, hopefully with author and year, but somehow the paper describing said species remains out of the list of references. This means indexing services like PubMed and Web of Science miss the uncited species descriptions in the tangled web of cross-reference. For example, Drosophila melanogaster Meigen, 1830, should be the most cited paper in recorded history due to the amount of work on this model organism. So what of biodiversity studies with hundreds of species? This does pose a problem. Nowadays, there is supplementary online material and the citations could be referred there so long as they are properly indexed and the gods who fiddle around with such productivity metrics recognize these citations.

Another argument to get your work widely read is that universities aren't appearing to hire people to do basic taxonomy anymore. They need another hook, perhaps molecular evolution or ecology. Even museums are tending to hire individuals with outside specialties. I'm not sure where the future of taxonomy may lie, but larger questions need to be addressed than just what is out there. Taxonomic research helps in many areas of biological science. The more people that know of your work, the more opportunities may be to collaborate on new projects with different directions, making you a more viable applicant. Besides who wants to invest so much into something only to see it hidden away forever?

Are there any barriers to publishing a species description with PLoS? Yes, Chapter 3 of the Code, Article 8.6 states:
"Works produced after 1999 by a method that does not employ printing on paper. For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself."
So species names published in an electronic format are only valid if depositions of the article in question are made at a minimum 5 public institutions. These can be public, university and museum libraries. This barrier is easily overcome if PLoS makes it easy on the authors by forging an agreement 5 institutions to deposit papers in their collections. I would recommend the Smithsonian, the Field Museum and any 3 universities in the U.S. The authors can even archive a paper in their own university's or museum's libraries. Conveniently, PLoS does offer itself in print version for those interested in deforestation.

Another barrier is the high cost of OA publishing. Currently, PLoS ONE charges $1250 for a research article, though they do offer fee waivers to authors who cannot the steep price. For the average working taxonomist, the price would need to drop to at most $600. This is a price I was quoted for a small american journal for a 20 something page description of a new shrimp with COI phylogeny. It was actually twice that, but I can some page charges waived for being a society member. My coauthor and I were shocked when we received the estimate. For almost the same price I could have published OA somewhere else. The costs are especially prohibitive to taxonomists from the developing world. Many of them have done a superb job and picked up the slack after north american taxonomy slipped away because of poor funding. Yet their funds are even less than ours in most cases.

In conclusion, OA publishing offers taxonomists higher visibility, potentially higher citations and a broader readership. The barriers to electronic publishing can be easily overcome with a little initial work. PLoS is the leader in OA publishing and has a strong reputation to maintain among the non-OA or hybrid journals that exist out there, thus the quality of research coming from PLoS journals is high. In particular PLoS ONE, offers several features attractive to taxonomists and idealistic scientists like myself. Their system allows any user to annotate, comment and respond to articles becoming a part of the permanent record of that article. This post-review system allows articles to become a conversation. If another taxonomist were to discover a new character 10 years after the publication of a species name, they could go that article and make an annotation or comment on that article that could then be considered by all other readers. Taxonomists have little to lose and everything to gain by publishing with PLoS and choosing OA.

Eysenbach, G. (2006) Citation Advantage of Open Access Articles. PLoS Biology, 4, e157.

Meigen, J.W. (1830) Systematische Beschreibung der bekannten europäischen zweiflügeligenInsekten, Bd. 6. F.W. Forstmann, Aachen.

Rodman, J. E., and J. H. Cody (2003) The taxonomic impediment overcome: NSF’s Partnerships for Enhancing Expertise in Taxonomy (PEET) as a model. Syst. Biol. 52:428–435.


  1. Great post. I have just circulated its permalink to various pals at the NHM in London who are influential in these matters. P.S. Wearing my grammar police hat, irregardless is not a word. Use either irrespective or regardless instead.

  2. LMAO, Bora and I were having this conversation last night right as I published. I mentioned grammar nazis, he said they would nail for irregardless. It was prophesied! We both agreed we are bloggers and not editors (on our blogs at least).

    Thanks for the circulation! Tell them I'm for hire! lol

  3. *ahem*
    "I came away from it all with a revitalized interest and several ideas of which to improve myself. I will definitely take it more seriously, meaning that I will edit my posts, write more clearly and succinctly, and make better use of online tools and technologies."

  4. Was thinking about this last night, even began half-a-post on it. I am wondering what process or technology the online journals are using to assure that the information will be available ten years from now. I have no ready means of accessing files on 3 1/2" floppies (much less 5 1/4"). Print just seems much more durable and proven compared to bits and bytes. Less accessible true. And sure, there is the option to continually update the data with each new iteration of technology. But that is a process and a cost. And what happens to the servers if PLoS ever goes plop? The books are still on the shelves of moribund journals. But dead servers send no citations. Is anyone redundantly backing up the PLoS databases outside of PLoS?

  5. This comment has been removed by the author.

  6. Yeah, but, why would you want to keep citing the original description of Drosophila every time you write a paper about it unless it is a taxonomic revision. When I write a non-taxonomic paper on the biology, say, the mating behavior, of a particular snail species, I don't see a reason for citing the description & all the subsequent revisions of that species unless the mating behavior ties in with a specific taxonomic issue.

  7. In addition to the problem of current taxonomic works being available is the problem of really old (classic) taxonomic works being readily available. The Assembling the Tree of Life: Decapoda group has done some really great work compiling lists of classic references and making many of them available as PDFs. the main page is here:

  8. The ICZN's rule here is just a specific example, illustrating a much more general problem, of the difficulty of traditional media in keeping pace with the rapid evolution of publishing technology and methods. Personally, I'm not seriously worried about these journals going belly up with their content evaporating into the ether. I think we're past all that.

  9. I'm all for it, Kevin. Any new online journal can archive, maintain, and distribute itself as well or better than any print journal from the last half century. That's a moot point.

    Zootaxa is an excellent example of a successful taxonomic journal with a promising future. The most important thing is to maintain and support peer-review.

  10. Jason - all PLoS papers are automatically saved on 4 servers in 4 cities on 2 continents. That should suffice, unless the entire human civilization loses electrical power, in which case PLoS papers are our least concern.

  11. Aydin, I feel that a species encompasses alot of information all bundled into one name. It is an author's hypothesis of that organism based on morphological and sometimes molecular characters. It may be argued that it is also an implicit hypothesis of that organism's evolution. When you use an organism's name you are acknowledging all that authors work that went into the identification and description. All the counting of morphological traits, histological sectioning, perhaps some enzymes assays, behavioral observations/experiments or phylogenetic reconstructions are implicit in that name. Why should this work, like any work, go unacknowledged? It is no different than something like "The Theory of Island Biogeography MacArthur & Wilson, 1967,...." without citing it in the bibliography of the paper.

    I agree that revisions are not necessary unless they bear on an important taxonomic issue, but the recognized author of a name should be cited when it is used.

  12. A, many of the tree of life groups have a done an excellent job putting up papers past copyright. As have some labs. And we should support the work of the Biodiversity Heritage Library. They do have 21 titles under Crustacea starting from 1829.


    I have some old works that I've scanned in muyself as well. I will make these available someday soon.

  13. Emmett, I'm not worried either and Bora's comment above is comforting as well. There has been a lot of buzz on the taxonomy listserves in the past about working this into the Code. I really hope the Zoological Congress and version of the Code incorporates this, perhaps looking to journals like Zootaxa and PLoS as examples to base the relevant parts of a new Code on.

    Peter, Biology has been slow to pick up on online and open access journals relative to other fields. Taxonomy is still working in the early 1900s, sometimes, in that respect. I'm hoping that younger or more technicalogically aware people out there are going to push for a new taxonomy that keeps pace with the rest of the world. Also, one that contributes to increasing access to the developing world

  14. Thanks for the clarification Bora!

  15. Nice advocacy essay, Kevin! Am I the only non-scientist commenting? As a "civilian" with a keen interest in current biological research, I think PLoS is a wonderful resource.

  16. This is an important aspect of the "crisis in taxonomy". Zootaxais currently the best example of an open access taxonomy journal. PLoS, however, does not seem to be an option. A look through the subject listings of PLoS One reveals neither "taxonomy" nor "sustematics" nor anything else related to taxonomy. Looking through their recent articles, I doubt that anything taxonomic would be welcomed by their editors.

  17. In a recent article, Dubois (2008,A partial but radical solution to the problem of nomenclatural taxonomix inflation and synonymy load. Biological Journal of the Linnean Society 93: 857-863) discussed the problem of an increasing number of taxonomic names and the load of synonymies. Dubious recognized three reasons for an increasing number of species description – one should be unwarranted descriptions in an effort to increase citations. We discuss this aspect in a comment on Dubois (same paper, in press), arguing that although new names may increase the prestige of the taxonomist, few journals actually put authors of taxonomic names in the reference lists and hence it does not affect citation figures. This practice in fact instead deflates the importance of taxonomic work in a world with increasing bibliometric evaluations of research output.


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