The Challenges of Taxonomy

commentary Challenges for taxonomy The discipline will have to reinvent itself if it is to survive and flourish. One reason is that taxonomists lack clearly H. Charles J. Godfray achievable goals that are both realistic and rel- Taxonomy, the classification of living evant. Of course it would be great to describe things, has its origins in ancient Greece and every species of organism on Earth, but we are in its modern form dates back nearly still monumentally uncertain as to how many 250 years, to when Linnaeus introduced the species there are (probably somewhere binomial classification still used today. Lin- between 4 million and 10 million); this goal is naeus, of course, hugely underestimated the just not realistic at present. There are various number of plants and animals on Earth. As projects aimed at listing, for example, all the subsequent workers began to describe more valid described species of animal in Europe, and more species, often in ignorance of each or butterflies on Earth (see Box 1, overleaf). others’ work, the resulting confusion and These aims are eminently achievable and very chaos threatened to destroy the whole enter- worthwhile, but the results are like raw, un- prise while still in its infancy. In today’s annotated DNA sequences: unexciting and of jargon, we might call this the first bioinfor- relatively little value in themselves to non- matics crisis. Using the tools then available, specialists. Taxonomists need to agree on nineteenth-century taxonomists solved this deliverable projects that will receive wide sup- crisis in a brilliant way that has served the port across the biological and environmental subject well since then. They invented a sciences, and attract public interest. complex set of rules that determine how a A second problem is part of the legacy of species should be named and associated more than 200 years of systematics. Many with a type specimen; how generic and high- taxonomists spend most of their career try- er taxonomic categories should be handled; ing to interpret the work of nineteenth- and how conflicts over the application of century systematicists: deconstructing names should be resolved. All these rules their often inadequate published descrip- From paper to screen: is it time for taxonomy to revolved around publications in books and tions, or scouring the world’s museums for break with tradition and unify on the Internet? scientific journals, and their descendants type material that is often in very poor con- form the current codes of zoological and dition. A depressing fraction of published being a scientist at this particular time in biological nomenclature. systematic research concerns these issues. history is the vast amount of information But today much of taxonomy is perceived In some taxonomic groups the past acts as a that is available, essentially free, via one’s to be facing a new crisis — a lack of prestige dead weight on the subject, the complex desktop computer. I can download the and resources that is crippling the continu- synonymy and scattered type material sequences of millions of genes, the positions ing cataloguing of biodiversity. In the United deterring anyone from attempting a of countless stars. Yet, with a few wonderful Kingdom, a Parliamentary Select Commit- modern revision. As Frank-Thorsten Krell exceptions, the quantity of taxonomic infor- tee is currently conducting an enquiry into pointed out in Correspondence (Nature mation available on the web is pitiful, and MUSEUM, LONDON HISTORY NATURAL the health of the subject for the second time 415, 957; 2002), “original descriptions have what is present (typically simple lists) is of in 10 years, and similar concerns are being to be referred to for ever, independent of the little use to non-taxonomists. But surely tax- expressed around the world. In this article paper’s quality”. onomy is made for the web: it is an informa- I shall first explore why descriptive taxono- The problems do not always lie in the past. tion-rich subject, often requiring copious my is in such straits (in contrast, its sister Even today, many species are being described illustrations. At present, the output of much subject, phylogenetic taxonomy, is flourish- poorly in isolated publications, with no taxonomy is expensive printed mono- ing). Then, after this essentially negative attempt to relate a new taxon to existing graphs, or papers in low-circulation jour- exercise, I will argue that taxonomy can species and classifications. Many of these nals available only in specialized libraries. prosper again, but only if it reinvents itself as ‘new’ species will have been described before, These are not attractive ‘deliverables’ for a twenty-first-century information science. so sorting out the mess will be the headache of major research funders. It needs to adopt some of the solutions that the next generation of taxonomists. It is not molecular biologists have developed to cope surprising if funding bodies view much of Two models of taxonomy with the second bioinformatics crisis: the what taxonomists do as poor value for money. The taxonomy of a group of organisms does huge explosion of sequence, genomic, pro- One of the astonishing things about not reside in a single publication or a single teomic and other molecular data. institution, but instead is an ill-defined integral of the accumulated literature on that The problem group. The literature is bound together and Why can’t descriptive taxonomy attract his discipline is cross-references itself using the venerable large-scale funds in the same way as other big made for the web: rules of taxonomy encapsulated in the codes. programmes like the Human Genome Pro- T But this is not the only way to organize a tax- ject or the Sloan Digital Sky Survey? All three it is information-rich onomy. The taxonomy of a particular group projects are enabling science: not in them- could reside in one place and be adminis- selves generating new ideas or testing and often requires tered by a single organization. It could be hypotheses, but allowing many new areas of self-contained and require reference to no research to be opened up. copious illustrations. other sources. NATURE | VOL 417 | 2 MAY 2002 | www.nature.com © 2002 Macmillan Magazines Ltd 17 commentary My main argument is that to address the shall sketch one possible way a unitary tax- type material that underpin distributed tax- problems outlined above, and for taxonomy onomy might be achieved. I am not a profes- onomies do require administration, which is to flourish now and in the future, it has to sional taxonomist and am under no illusion currently undertaken by our great museums move from the first to the second model: that what follows will be the best or even a and herbaria. Nearly all these organizations from having a distributed to a unitary orga- viable model, but I hope it will bring out the are enthusiastically embracing modern web nization. Such a massive task could only be issues involved. technologies. Hosting web revisions is some- accomplished group by group, as resources thing I see as a logical extension of their moves became available. I believe a number of A unitary taxonomy towards becoming, in part, modern informa- things would then follow. First, the only Introduce as a formal taxonomic procedure tion storehouses. It is absolutely clear, how- logical way to organize a unitary taxonomy the ‘first web revision’. This would be a revi- ever, that they need more money in order to and to make it widely available is on the web. sion of a major group of organisms to a stan- do this. They might also undertake the intel- The web is currently used, if used at all, as an dard decided on by the International Com- lectual administration of the web revision — adjunct to the distributed, printed taxono- mission on Zoological Nomenclature, or the the refereeing and editing — although they my, but I think it should replace it. Second, International Botanical Congress, or equiva- would probably devolve this to committees the core of taxonomy is a description of each lent body (let’s just call it the international drawn from a wider constituency (the equiva- species and a means of distinguishing committee). The revision would include a lent of a journal’s editorial board). among them; to this core has been added the traditional description of each taxon and the However it worked, standards would exercise of resolving their evolutionary rela- location of type material. It might also need to be set and monitored by the interna- tionships. I believe that taxonomy needs to include material not currently required in a tional committee, who would also deter- expand to include other aspects of the formal description, for example keys and, for mine which institute houses which taxono- species’ biology, to become an information many groups, photographs or other illustra- my, and would prevent duplication of effort. science that curates our accumulated knowl- tions. For some organisms a gene sequence edge of that species in the way a gene annota- might be required. It would also include a Advantages tion in a genome database organizes our treatment of existing known synonyms to I believe that what I have described is evolu- knowledge of a particular protein. Third, I preserve contact with the older literature. tionary rather than revolutionary in that it think it is essential that the unitary taxono- This draft first web revision would be placed preserves the hard-won successes of current my of different groups evolves from the on the web for comments from the commu- taxonomy while dispensing with the histori- present taxonomy. We must preserve the nity, then after changes have been made in cal baggage.

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