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University of Southampton Research Repository Eprints Soton University of Southampton Research Repository ePrints Soton Copyright © and Moral Rights for this thesis are retained by the author and/or other copyright owners. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder/s. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holders. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given e.g. AUTHOR (year of submission) "Full thesis title", University of Southampton, name of the University School or Department, PhD Thesis, pagination http://eprints.soton.ac.uk UNIVERSITY OF SOUTHAMPTON A REVISION OF Vicia SUBGENUS Vicia USING DATABASE TECHNIQUES A Thesis submitted for the Degree of Doctor of Philosophy in the University of Southampton by Nigel Maxted Department of Biology September, 199 0 "What we cannot speak about we must passover in silence" Wittgenstein (1974) "The revolution , if such it is to be, will arise from the application of computers to systematics, both in data-processing and in the more restricted field of production of classifications and keys." Heywood (1974) 11 UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF SCIENCE BIOLOGY Doctor of Philosophy A REVISION OF VICIA SUBGENUS VICIA USING DATABASE TECHNIQUES by Nigel Maxted The thesis investigates the applications of contemporary database technology to enhance the process and production of a taxonomic revision. The current uses of databases and their specific applications to plant taxonomy are discussed. The stages of a revision are outlined and as a result, the revision process is clarified. In order to experiment with the uses of databases during a revision, an exemplar revision of Vicia L. subgenus Vlcia was undertaken. A detailed taxonomic history of the subgenus is provided and the phenetic approach to data analysis is introduced. Phenetic analysis of 1539 specimens, representing the variation within subgenus Vicia, was undertaken for 174 characters, using cluster analysis and ordination techniques. The results of the phenetic analysis are considered in conjunction with data abstracted from the literature and a novel classification of the subgenus is proposed. This comprises nine sections, nine series, thirty eight species and thirty six subspecific taxa. The classification is compared with previous conceptions of taxa relationships. Other revision products are incorporated into a conspectus for the accepted species which includes: a checklist of accepted taxa; comments on type material; synonymised lists; descriptions; phenology; chromosome numbers; geographical distributions; ecological data; taxonomic notes and specimen citations. All data collected during the revision were held in the revision database. The application of database techniques within the exemplar revision were discussed critically. It Is found that use of the techniques facilitated the revision process. This is most apparent in the production of the conspectus, a large proportion of which was produced directly from the revision database. Taxon descriptions were produced directly (via a dBASE program) from the descriptive data for representative specimens of each taxon. After discussing the advantages and disadvantages of applying database techniques to the exemplar revision, a novel conception of the revision paradigm, which incorporates database techniques, is proposed. Comments are made on the need for further developments of taxonomic database management systems to facilitate revisions and broader taxonomic processes in the future. Ill CONTENTS Abstract (iii) Contents (iY) Acknowledgements (viii) VOLUME 1 SECTION ONE - INTRODUCTION CHAPTER ONE GENERAL INTRODUCTION 1.1 Problem Elucidation 1 1.2 What is a Taxonomic Database System ? 3 1.3 Aims 4 1.4 Thesis Plan 5 CHAPTER TWO AN INTRODUCTION TO TAXONOMIC DATABASES 2.1 Introduction to Databases 7 2.2 Taxonomic Databases 19 2.3 Taxonomic Database Management Systems 27 CHAPTER THREE THE TAXONOMIC REVISION 3.1 What is a Taxonomic Revision ? 40 3.2 How to Undertake a Taxonomic Revision 43 3.3 A Clarification of the Revision Paradigm 47 SECTION TWO - EXEMPLAR REVISION CHAPTER FOUR TAXONOMIC INTRODUCTION 4.1 Taxonomic Aims 53 4.2 Delimitation of the Exemplar Taxon 55 4.3 Taxonomic Revision Study Plan 61 CHAPTER FIVE TAXONOMIC HISTORY 5.1 Introduction 64 5.2 Taxonomic History of Subgenus Vicia 67 5.2.1 Vicia Subgenus Vicia Sensu Kupicha (1976) 68 5.2.2 A Concise History of Subgenus Vicia 73 5.3 Summary of Subgenus Vicia Taxonomic History 113 IV CHAPTER SIX METHODS OF DATA GATHERING AND ANALYSIS 6 . 1 Introduction 117 6.2 Operational Taxonomic Units 118 6.2.1 Theoretical foundation 118 6.2.2 Choice of Operational Taxonomic Units 120 6 .3 Character Selection 121 6.3.1 Theoretical Foundation 121 6.3.2 Reasoned Choice of Characters 127 6,, 4 Phenetic Analysis 130 6.4.1 Theoretical Foundation 130 6.4.2 Reasoned Choice of Phenetic Method 136 (a) SPSS* 137 (b) LINKAGE 138 (c) CLUSTAN 142 CHAPTER SEVEN PHENETIC STUDIES ANALYSIS RESULTS 7. 1 Introduction 152 7. 2 Subgeneric Analysis of Specimen Data 154 7.2.1 Splitting the Initial Complete Data Set 154 7.2.2 Taxon Location 171 7. 3 Subgeneric Analysis of Taxon Data 191 7. 4 Detailed Study of Closely Related Taxa 207 7.4.1 Analysis Of Section Faba Sensu Kupicha (1976) 207 7.4.2 Analysis Of Section Vicia Sensu Kupicha (1976) 212 7.4.3 Analysis Of Section Hvpechusa Sensu Kupicha (1976) 217 CHAPTER EIGHT LITERATURE-BASED TAXONOMIC EVIDENCE 8.1 Introduction 223 8.2 Phytogeographical Evidence 224 8.3 Cytotaxonomic Evidence 228 8.4 Biosystematic Evidence 239 8.5 Anatomical Evidence 246 8.6 Chemotaxonomic Evidence 249 8.7 Other Non-morphological Evidence 263 8.8 Literature Based Morphological Evidence 264 8.9 Summary of Literature-Based Taxonomic Evidence 2 69 CHAPTER NINE PROPOSED CLASSIFICATIONS AND TAXONOMIC DISCUSSION 9.1 Introduction 273 9.2 Proposed Classifications of Vicia Subgenus Vicia 273 9.3 Discussion of Proposed Classification 276 9.4 The Revision Conspectus 285 9.5 Conclusion of Phytogeographical study 287 9.6 Suggested Future Taxonomic Research 300 SECTION THREE - DATABASE RESULTS AND DISCUSSION CHAPTER TEN APPLICATION OF DATABASE TECHNOLOGY TO THE EXEMPLAR REVISION 10.1 Introduction 303 10.2 Choice Of Proprietary Software 303 10.2.1 Database Management System 304 10.2.2 Computer Aided Taxonomic Product Generation 305 10.3 Exemplar Revision Database Management System 311 10.3.1 Database File Structures 312 A. Curatorial Structure 313 B. Descriptive Structure 316 C. Bibliographic Structure 323 D. Nomenclatural Structure 323 10.3.2 Exemplar Revision Database File Relations 329 10.3.3 Database Software 331 A. Data Capture Program - CELIA 331 B. Specimen To Taxon Data Synthesis 334 Programs - LICEA / CALIE C. Geographic Distribution 341 Program - PHYTOGEOG D. Label Production Programs - LABELS 343 vi 10.3.4 Exemplar Revision Product Generation Using DELTA 345 10.3.5 Exemplar Revision Database System 352 Implementation 10.4 Discussion Of Exemplar Revision Database System Implementation 3 60 CHAPTER ELEVEN PROPOSED TAXONOMIC DATABASE PARADIGM 11.1 Introduction 3 65 11.2 Requirements of The Revision Database Management System 366 11.3 Revision Database Management System Paradigm 373 11.4 Suggested Future Research Priorities 387 11.5 Project Conclusions 389 REFERENCES 39 0 VOLUME 2 APPENDICES Appendix 1. Herbaria Which Loaned Herbarium Specimens 434 Appendix 2. Subgeneric Character Set 436 Appendix 3. Phenetic Analysis Character Set Usage 462 Appendix 4. Example Run Files Used in Phenetic Analysis 468 Appendix 5. Revision Conspectus for Vicia Subgenus Vicia 473 Appendix 6. Distribution of Vicia Subgenus Vicia Taxa 675 Appendix 7. Listing of Database Files Included on Disc 687 Appendix 8. dBASE Program Listings 688 Appendix 9. Directive Files Used for Product Generation 705 Vll ACKNOWLEDGEMENTS I am particularly grateful to the following: Dr. F.A. Bisby, Dr. R.J. White and Dr. R.J. Pankhurst - for supervision, encouragement and stimulating discussion. Dr. R. Allkin - for discussion and advice on the database techniques and numerical methods. Prof. J.T. Williams and Mr. R. Reid - of the International Board for Plant Genetic Resources, who provided advice and financial support for the germplasm collecting trips to Syria, Turkey, Yugoslavia and the Soviet Union. These field trips enabled me to gain a more detailed understanding of Vicia taxa inter-relationships and gave me a chance to obtain germplasm of the rare and novel species included in my study group. Dr. R.M. Polhill, Mr. G. Lewis and Mrs. B. Mackinder - for encouragement, advice and discussion of the project. Mr. R. Crust, Ms. D. Richardson, Mr. J. Williams and Mr. P. Winfield - for help in writing the dBASE II and C programs used during this project. Mr. J. Hepworth, Mr. A. Cotton, Dr. P. Hancock and Ms. F. Baker - for trying to make the CLUSTAN analysis of a large data set work and Dr. J. Henderson of CLUSTAN Ltd. for, at least, partially succeeding. Dr. S. Hollis and Mr. R. Cornick - for assistance in drawing the figures. The Staff of the Department of the Biology, Southampton - for help in numerous ways throughout the project. My thanks are also due to the curators of the Herbaria listed in appendix 1 from whom the specimens used in the project were borrowed. Science and Engineering Research Council - for the earmarked studentship, which provided the core funds for this research project. Finally, I would like to thank Barbara and Rebecca for their love and their healthy disbelief in my intellectual ability. Vlll VOLUME 1 SECTION ONE INTRODUCTION CHAPTER ONE GENERAL INTRODUCTION It is difficult to imagine a world in which humankind does not characterise, describe and order their surroundings, an activity which is as basic to them as the use of language.
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