Son1e recent con1puter-based developn1ents plant taxonon1y

Transcription

1 Botanical Journal '!f the Linnean Society ( 1991 ), 106: Son1e recent con1puter-based developn1ents plant taxonon1y 1D STEPHEN L. JURY, F.L.S. Botany Department, Plant Science Laboratories, The University of Reading, Whiteknights, Reading RG6 2AS Received January 1991, revised and accepted for publication March 1991 JURY, S. L., 199!. Son1e recent con1puter-based developn1ents in plant taxonon1y. A review is presented of some of the recent computer-based projects in botany, including:!lois (the International Legume Database and Information Service), ESFEDS (European Science Foundation-European Documentation System), Flora Europaea, TDWG (Taxonomic Databases Working Group), Species Plantarum Project, 'Names in Current Use' and BSBI (Botanical Society of the British Isles) database project. ADDITIONAL KEYWORDS:-Databases-!LOIS- Flora Europaea - Species Plantarum Project - systematics. CONTENTS Introduction.!LOIS: International Legume Database and Information Service ESFEDS and Flora Europaea: the Reading contribution TDWG: Taxonomic Databases Working Group SPP: Species Plantarum Project Improving the stability of names: needs and options BSBI Database Conclusions References INTRODUCTION From reading recently published papers, reviews, articles and letters, one could be excused for thinking that plant taxonomy is dying a lingering and painful death. I believe nothing could be further from the truth. It is a fact that little good 'press' has been gained in the world at large by the systematists who have been engaged in a seemingly endless debate on the merits of cladistics, or by those revelling in obscure and ancient literature in pursuit of older names for their nomenclature games. However, a large and growing band of taxonomists have been turning their attention as to how their products can be made more accessible to their customers, that disparate group of people needing systematic information. It is opportune to review some of the recent developments and examine future prospects /91/ $03.00/ The Linnean Society of London

2 122 S. L. JURY ILDIS: INTERNATIONAL LEGUME DATABASE AND INFORMATION SERVICE Frank Bisby must be given much credit for awakening the taxonomic world to the role of information services in taxonomy (Bisby, 1984), and doggedly pursuing his idea of a Vicieae (Leguminosae) database (Adey et al., 1984; Bisby, 1984) to reality and developing it into ILDIS (Bisby, 1986; Bisby & Maxted, in press), now established as a working database at the University of Southampton, using the ALICE software developed by Bob Allkin and Peter Winfield. ILDIS is described as an international project on legume species diversity, directed by an international board of trustees and is a 'not-for-profit organization' registered as a charity under English Law. It aims to provide a source of information for the development of all useful legume crops and products, especially in the arid zones and humid tropics, as well as being a focus for their study and conservation. A variety of publications are planned and already a check-list of African legumes is available (Lock, 1989); extracts of the database with software on discs, e.g. CD-ROM, can be expected as well as an online service (an experimental service is being sponsored by BIOSIS) and an ILDIS enquiry centre. Phase one comprises a species checklist with accepted names, synonyms, authorities and references, and tribe membership. This is being compiled on a regional basis with occurrence by continent, country and province, as well as status and references, all edited by legume taxonomists. Vernacular names, vegetation types, life forms, conservation status and economic importance are included, as are references to descriptions, illustrations and maps. Phase one also provides the 'backbone' that allows the inclusion of data relevant to applied botany. Phase two is under way incorporating data on phytochemical records for secondary chemical compounds (I. Southon, John Buckingham, Jeffrey Harborne and Frank Bisby are progressing on a joint Chapman & Hall/ILDIS venture) as well as nodulation and nitrogen fixation information. Germplasm/seed sources, biotechnology and breeding, economic botany, systematic botany and cytology modules are at the planning stage. When complete, approximately species, i.e. about one-twelfth of the angiosperms, will be included. ESFEDS AND FLORA EUROPAEA: THE READING CONTRIBUTION In the autumn of 1981, a project was started at the University of Reading to create a database of the European flora, Flora Europaea having recently been completed (Tutin et al., ). This project, usually known by the acronym ESFEDS (European Science Foundation-European Documentation System), created a database of the names occurring in Flora Europaea (Heywood et al., 1984; Packer & Kiger, 1989). This included families, genera, species and subspecies, authorities and reference citations to the places ofpublication of these names. The geographical information, endemic status and chromosome data were added. Difficulties were encountered when it came to dealing with the ecological data. Some attempt was made to acquire data to update the Pteridophyta (with the help of Clive Jermy, pteridologist at the Natural History Museum, London), the Caryophyllaceae and the Orchidaceae (with assistance

3 COMPUTER-BASED PLANT TAXONOMY 123 from Carlo del Prete, now of Modena). Basically, this database contains the unaltered Flora Europaea data, though large numbers of corrections have been made. At the same time in 1981, John Akeroyd started to work at Reading as a research officer on the revision of volume one of Flora Europaea, some 20 years after its publication. This revision was organized in a rather different way to that in which the original edition was prepared. John Akeroyd was obliged to rely very extensively on published works; there was a limited input from outside botanists, both for the compiling and revision of new accounts, and the checking that had previously been carried out by the 'Regional Advisors'. This was a result of the very limited funding available for the project which was provided solely by the royalties from the sales of Flora Europaea. The Linnean Society, the original sponsors (though not financially), well-managed a trust fund specifically for this purpose, paying John Akeroyd's salary and overheads and a secretary two mornings per week for the last three years, with hindsight insufficient assistance. A manuscript was produced and a copy delivered to Cambridge University Press in January 1989 (Akeroyd, 1988; Akeroyd & Jury, in press). However, the editors were not satisfied that all the errors had been adequately dealt with and Martha Newton, working with John Edmondson at Liverpool Museum, has been checking the text for further inconsistencies. A second version has been presented to the Press, but the go-ahead for publication is not expected until June 1991 with publication in John Akeroyd's work has been very much more substantial than was ever envisaged necessary at the outset: the Flora Europaea editors did not realize the amount of taxonomic work that had gone on in Europe and just how much the Edition One account would need amending. (If they had, I doubt that this project would ever have been started.) It is significant that the species and nomenclature of Flora Europaea have been adopted by the Council of Europe (and are therefore used in legislation) and that volume one, edition two, additions and emendations have not been added to ESFEDS-the revision exists only as a word-processed file. It is planned to publish shortly a synonymic checklist from the data-base produced by ESFEDS, and the data is now being converted from ORACLE to run on both the ALICE software and Advanced Revelation. Such a checklist was one of the original aims of the project. ESFEDS was a project ahead of its time. Computers and programs were not developed to present levels, nor were data standards. Full credit should be given to Professor V. H. Heywood and his staff for the way they overcame the problems, but at a time when technology was advancing at such a rate, their resources proved inadequate. This project has been successful (a checklist will soon be published; data on the Leguminosae have already been transferred to ILDIS by means of transfer formats devised by Tony Sumner of Reading University (and some of these data are now published in Legumes rif Africa: a Checklist, Lock (1989)), and recently a print-out of non-native Italian plants was produced for another research project in Italy. Sadly, funding was not forthcoming to continue active work on ESFEDS after 1985, especially as much new and important data came to light as part of John Akeroyd's work. I believe, in common with many European botanists, that there is a desire for a full revision of Flora Europaea to be undertaken. Professor D. A. Webb and the

4 124 S. L. JURY late Professors Tutin and Valentine have been replaced on the Flora Europaea Editorial Committee by Drs J. R. Akeroyd, F. A. Bisby, J. R. Edmondson and S. L. Jury to provide a committee prepared to act. Any further revision should now be undertaken on a European scale, not just by a group of botanists or editors in the United Kingdom. There is now a great deal of excellent taxonomic work being undertaken in Europe, particularly Spain and these botanists need to be much more involved at all levels. This will not only be necessary to obtain funding for the project, but also to obtain the same international recognition as the first edition received. It is also clear that any revisionary process must involve the use of a database and modern data-handling technology. It has been agreed that ESFEDS with the ALICE software will be used. Frank Bisby and Benito Valdes of Sevilla were asked by the Editorial Committee of Flora Europaea to organize a meeting to prepare a plan for the next phase of the Flora Europaea project. Flora Europaea can claim two great successes: the bringing together of Europe's botanists to communicate and collaborate with each other to a far, far greater extent than previously, and the stimulation of a large amount of taxonomic research to fill the gaps. It is particularly heartening that the Flora Iberica project is now on a sure footing with two of ten volumes now published; the second and final volume of the Mountain Flora if Greece is just published, and Flora Hellenica, Flora Nordica and a Flora if Austria project are all now underway. Future Flora Europaea Editors must collaborate in a new way with these and other projects, as well as with the numerous individual botanists on the continent of Europe to ensure that a consensus taxonomy emerges. A meeting to develop a so-called 'consensus taxonomy' was requested under an initiative taken by the Council of the Linnean Society of London. This international meeting was held in London on 25 February with a considerable amount of agreement and enough enthusiasm to hold a second meeting, also in London, in June. TDWG: TAXONOMIC DATABASES WORKING GROUP Recently, the above group organized a Symposium in Delphi, Greece, ll-16 October 1990 with the title 'Designs for a Global Plant Species Information System' (GPSIS). Ninety-seven delegates attended this meeting, including taxonomists, computer programmers, system designers, system managers and the users and consumers of plant taxonomic data. The participants considered the needs of the users and consumers, examined models of information systems used in other disciplines and debated relationships amongst the various existing plant information systems and projects. They decided that there was a common need for a system with a central list or taxonomic backbone to enable clear and accurate communication of information to consumers and allow databases of other relevant plant information to be linked via this central backbone. It was agreed that the taxonomic backbone should contain: a list of plant names (genus, species and infraspecific taxa with authorities and reference to place of publication), indications of important synonymy, family (and lower levels if available), geographical distribution (floristic region and countries of occurrence) and bibliographic references to recent monographs or floristic treatments (including indications of the quality of the works available on the species). All these should follow TDWG standards.

5 COMPUTER-BASED PLANT TAXONOMY!25 Some 'users' threatened to undertake the work themselves if the botanical community did not deliver the goods in a reasonable time. This meeting was therefore highly successful and delegates demanded a 'hidden agenda' from the organizers. As no such agenda had been planned, an 'Action Group' was set up. SPP: SPECIES PLANTARUM PROJECT A complication in the GPSIS debate was the existence of plans for a Species Plantarum Project proposed by a consortium of seven major botanical institutions (Royal Botanic Gardens, Kew, UK; Missouri Botanical Garden, St Louis, Missouri, USA; New York Botanical Garden, USA; Museum National d'histoire Naturelle, Paris, France; Rijksherbarium, Leiden, Netherlands; Smithsonian Institution, Washington, USA; Conservatoire et Jardin botaniques de Ia Ville de Geneve, Switzerland) (Davies, 1990). The new Species Plantarum was outlined by Dick Brummitt in Delphi as being in the style of Flora Europaea, (i.e. with keys, short descriptions and indications of geographical occurrence, etc.) and was to be prepared as acceptable monographic works became available and completed in 50 years. Such a project would be computer-based, using modern data-handling technology. A meeting of the GPSIS Action Group met under the chairmanship of Sir John Burnett. The conclusions of this group were accepted by the planners of the Species Plantarum Project at a meeting on Sunday 11 November 1990, before the two-day launch of the project on 12 and 13 November at the Royal Botanic Gardens, Kew (Gee, 1990). A large and distinguished international audience in the Jodrell Laboratories' lecture theatre heard Peter Raven, Director of the Missouri Botanical Garden, elaborate the plans. The meeting agreed that a rapidly produced checklist was the priority, rather than a steady long-term production of the Flora-type accounts. The SPP organizers had clearly accepted much of the feeling from the Delphi meeting. A council was set up to consist of some 25 members, some 15 being nominated at the meeting. This Council was expected to meet in February A further Editorial Committee was also planned, but not appointed. The secretariat of the project will be based at the Royal Botanic Gardens, Kew under the charge of Professor G. Ll. Lucas, the Deputy Director. Nancy Morin of the Missouri Botanical Garden was also elected onto the Council. IMPROVING THE STABILITY OF NAMES: NEEDS AND OPTIONS Another international conference with 120 distinguished botanists from 20 countries met 20th-23rd February 1991 at Kew to consider the needs for stability in plant nomenclature and ways in which the International Code of Botanical Nomenclature (Greuter et al., 1988) could be amended to achieve this (Stace, 1991). Considerable debate was generated by the proposals for the drawing up of a list of names in current use. Some delegates (e.g. W. Greuter (Berlin), R. K. Brumitt (Kew) and D. L. Hawksworth (Kew)) wished to develop this list and give those taxa included special 'protected status'. Others (e.g. C. jeffrey (Kew)) wished to obtain protection through increased use of the existing articles in the code. C. J. Humphries (London) argued that the progressive and dynamic discipline of biology that considers the history of life

6 126 S. L. JURY would be severely constrained by the proposals of the conference and that as the quality of nomenclature is always dependent on taxonomy it should denounce rather than pursue stabilization. D. J. Mabberley (Oxford) represented those botanists discovering older names in obscure literature who considered that once these name changes had been made, a greater nomenclative stability would ensue. However, it became clear that if any lists of 'Names in current use' were to be compiled (and some already are, e.g. fungi and fossil plant species) then they need to be related to the much-needed GPSIS 'backbone': the projects should be linked. BSBI DATABASE Recently the Botanical Society of the British Isles has entered the scene, proposing to establish a database on the British flora, at an estimated cost to the society in excess of spread over several years. At the time of writing, Clive Stace (Leicester) has produced a word-processed camera-ready copy manuscript for a new Flora of the British Isles. This has been carried out in conjunction with Mr D. H. Kent who has been working on a new checklist of the British flora to replace the out-of-date one by the latej. E. Dandy (1958). It is planned that the data necessary to produce a new edition of Dandy's book be input as soon as practicable and that copy be produced directly from this database for publication. English Names of Wild Flowers (Dony, Jury & Perring, 1986), another BSBI publication, will soon be out-of-print and it is envisaged that English names will be added to the database to produce an enlarged third edition of this work. Two other major projects are currently being sponsored by the BSBI. These are a census catalogue giving details of all vice-county occurrences of species in the British Isles. The distribution of plants and animals in Great Britain and Ireland has long been studied and recorded on a county basis. (Watson ( ) gave a series of 112 vice-counties for Great Britain, and Praeger (1901) 40 for Ireland. Large counties are divided and very small ones amalgamated. The divisions of Watson and Praeger are still used and, as a result of boundary changes, do not now correspond to present administrative counties.) This should help stimulate hunting for new county records by the production and publication of county checklists. An investigation into the cytology of British plants is underway by R. J. Cornall at the University of Leicester, based on the earlier records and work of the late D. H. Valentine. This information is also held on computer and it is hoped this will also become part of the BSBI British Flora Database. Eventually, it is hoped, all the references given by Simpson (I 969) can be included in the database and these updated to include those given by Kent in BSBI Abstracts (Kent, ), as well as the records of the Lousley Card Index belonging to the BSBI and currently housed at the Natural History Museum, London. This will then give a useful database on British and Irish botany which could eventually be available for consultation by all, on-line, through a computer network and the taxonomic backbone as envisaged by GPSIS, though no doubt at a price. Such systems are already well-established by libraries which are now able to undertake literature searches at modest cost. A similar network has already been established by the microbiologists and is

7 COMPUTER-BASED PLANT TAXONOMY 127 known as MINE, the Microbial Information Network Europe, part of the European Laboratory Without Walls (ELWW) created and sponsored by the Biotechnology Action Programme of the Commission of the European Communities (Aguilar, 1990). The computer networks set up by groups of Universities' libraries show that there are no problems with computer technologies, system design or management. Most of the technology is already available and experts exist who can put this into practice. It is exciting that taxonomists and other botanists are now working to get their act together at the planetary level to set up a system. Other databases could be mentioned, such as that of the Botanic Gardens Conservation Secretariat based at Kew for rare and threatened plants in cultivation in Botanic Gardens. The work undertaken by this secretariat is proving most valuable, not least the development of the International Transfer Format for Botanic Garden Plant Records (Synge, 1987, approved by the third meeting of the Taxonomic Databases Working Group in Edinburgh in 1987). Several other important Databases are also being developed, e.g. at the Missouri Botanical Garden for both the Flora of North America and Flora of China Projects (Morin, 1989); others exist for the Flora of South Africa and Flora of Australia and reference should be made to Morin et al. ( 1989). CONCLUSIONS Much work is actively going on, and it is likely that we shall see excitmg developments in this decade. The House of Lords Select Committee on Science and Technology has set up a Sub-Committee II-Systematic Biology Research under the Chairmanship of Lord Dainton to consider systematic biology research in the United Kingdom. (It has invited oral and written evidence from the Linne an Society of London, amongst others.) Vern on Heywood reports that he has already participated in two major reviews of the state of taxonomy (and there have been others), e.g. Royal Society, 1963; NERC, 1976; ESRC, 1977; Smith, 1979) and that he is to be involved in another for NERC (Natural Environment Research Council): let us hope it will be third time lucky. There is an awakening to the need for systematics. Perhaps we can hope for a modest increase in funding. It seems that provision has been made for the development of equipment and techniques-blue skies research, but not for the later continued routine use to survey and document such findings throughout the great diversity of organisms. If we are not careful the great schemes mentioned will not develop, but will sit on the shelf unusable. Man will become the poorer by the gradual loss of plant diversity. Who will be able to use the existing Floras and taxonomic literature to identify species, let alone write them for those vast areas of the world as yet unrecorded? But perhaps we have woken up at the eleventh hour! REFERENCES ADEY, M. E., ALLKIN, R., BISBY, F. A. & WHITE, R. J., The Vicieae aatabase: an experimental taxonomic monograph. In R. Allkin & F. A. Bisby (Eds) Databases in Systematics: London: Academic Press. AGUILAR, A., MI.NE, The Microbial Information.Network Europe. Brussels: Pamphlet, D.G. XII, Directorate Biology, Division Biotechnology, European Laboratory Without Walls, European Community.

8 128 S. L. JURY AKEROYD,J. R., The revision of Flora Europaea, vol. I. Lagascalia, 15 (Extra): AKEROYD,J. R. &JURY, S. L., in press. The revision of Flora Europaea. Botanika Chronika (Patras). BISBY, F. A., /LDIS: International Legume Database & Information Service, Project Plan, Version 3. Unpublished Research Group Report. Southampton: ILDIS. BISBY, F. A., The Vicieae Database Project: products and services. Webbia, 38: BISBY, F. A., Information services in taxonomy. In R. Allkin & F. A. Bisby (Eds), Databases in Systematics: London: Academic Press. BISBY, F. A. & MAXTED, N., in press. ILDIS: International Legume Database and Information Service. Botanika Chronika ( Patras). DANDY, J. E., List of British Vascular Plants. London: British Museum (Natural History). DAVIES, R., Species plantarum project. Taxon, 39: GEE, H., Database for plant species. Nature, 348: 275. ESRC, Taxono"!)l in Europe. ESRC Review no. 13. Committee of European Science Research Councils. Strasbourg: European Science Foundation. GREUTER, W. et al., International Code of Botanical Nomenclature. Konigstein: Koeltz Scientific Books. HEYWOOD, V. H., MOORE, D. M., DERRICK, L. N., MITCHELL, K. A. & SCHEEPEN,J. VAN, The European Taxonomic Floristic and Biosystematic Documentation System. In R. Allkin & F. A. Bisby (Eds), Databases in Systematics: London: Academic Press. KENT, D. H., BSBI Abstracts, London: BSBI. LOCK, J. M., Legumes of Africa: a Checklist. Kew: Royal Botanic Gardens. MORIN, N., Flora of North America Project. In N. R. Morin, R. D. Whetstone, D. Wilken & K. L. Tomlinson (Eds), Floristics for the 21st Century: St Louis: Missouri Botanical Garden. MORIN, N. R., WHETSTONE, R. D., WILKEN, D. & TOMLINSON, K. L. (Eds), Floristics for the 21st Century. St Louis: Missouri Botanical Garden. NERC, The Role of Taxonomy in Ecological Research. NERC publications, series B, 14. London: Natural Environment Research Council. PACKER,]. G. & KIGER, R. W., Flora Europaea and the European Documentation System. InN. R. Morin, R. D. Whetstone, D. Wilken & K. L. Tomlinson (Eds), Floristics for the 21st Century: StLouis: Missouri Botanical Garden. PRAEGER, R. L., Irish Topographical Bota'!)l. Dublin: The Royal Irish Academy. ROYAL SOCIETY, Taxonomy: Report of a Committee by the Council of the Royal Sociery. London: The Royal Society. SIMPSON, N. D., A Bibliographical Index of the British Flora. Bournemouth. SMITH, E., Taxonomy in Britain. London: HMSO. STACE, C. A., Naming names in botany. Nature, 350: 466. SYNGE, H. (Ed.), The International Tranifer Format for Botanic Garden Plant Records. Pittsburgh: Hunt Institute for Botanical Documentation. TUTIN, T. G. et al. (Eds), Flora Europaea, 5 vols. Cambridge: Cambridge University Press. WATSON, H. C., Cybele Britannica, 4 vols. London: Longman & Co.