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A Chemosystematic Study of the Phylogenetic Position of Arabidopsis Thaliana (L.) Heynh

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A Chemosystematic Study of the Phylogenetic Position of Arabidopsis Thaliana (L.) Heynh AN ABSTRACT OF THE THESIS OF Hesh J. Kaplan for the degree of Doctor of Philosophy in Botany and Plant Pathology presented on April 19, 1977 Title: A CHEMOSYSTEMATIC STUDY OF THE PHYLOGENETIC POSITION OF ARABIDOPSIS THALIANA (L.) HEYNH. (BRASSICACEAE) EMPLOYING NUMERICAL METHODS Abstract approved:Redacted for Privacy Kenton L. Chambers The Brassicaceae, Mustard Family, is a well marked natural family, whose tetramerous flowers, tetradynamous stamens, and distinctive bi- carpellary fruits, clearly distinguish it from related families.It is a large family of some 3, 000 recognized species and over 300 genera. Although numerous attempts have been made over the past two centuries to develop a taxonomic system that would organize the family into natural, or at the least convenient, group- ings, no proposal has met with general acceptance. This investigation is a new attempt to understand intergeneric relationships.To scale this effort to a manageable scope, I selected the genus Arabidopsis, in particular the species A. thaliana, as the focus of all investigations. An important aspect of this thesis is that it introduces research techniques that have evolved since the family was last examined. Chemical methods used include protein electrophoresis and thin-layer chromatography of flavonoid and related compounds. A variety of computer-assistednumerical analy- ses were performed on bothchemical and morphological data sets. A total of 54 species were investigated, representing 37 genera. The electrophoresis survey showed that many of the bandsof the enzyme fructose 1, 6- diphosphate aldolase(1.U.B. No. 4.1.2.13) did not represent true isozymes, but were the results ofsecondary inter- actions between the enzymes and phenolic compounds. Theseartifacts were eliminated when a number of precautions wereexercised during the extraction process, notably the washing of the plant extractswith synthetic phenolic-binding compounds (XAD-4 and polyclar-AT). Neither the electrophoresis nor the TLC surveys generateddata sets that produced rational phenograms when clustering strategies were applied.Counter to expectations, each species was characterizedby unique flavonoid idiogram patterns.Similarly, the electrophoretic phenotypes failed to generate reasonable phenograms althoughthey support recognized intrageneric groupings. A correlation was observed between flavonoid distribution and plant habit. A significant quality of the 37 genera analyzed wastheir failure to form consistent groupings. The plants wereshown to be widely scattered in the multidimensional character space, andclusters were markedly influenced by algorithm choice. However, twodistinct groupings did emerge when the several numerical approaches were compared. The groups are separated by differingattitudes of the cotyledons with respect to the seed radicle.This single character difference was reinforced by weak but consistentcorrelations with chemical data.This finding sustains the method devised by de Cando lle and popularized by Schulz, whorelied on cotyledonary position as a primary criterion for delimiting the tribesof the Brassicaceae. As a corollary, my numerical resultsplace Arabidopsis near Sisymbrium and remote from itshistorical allies, Arabis and Cardamine. The limits of the genusArabidopsis and a natural classification system for the Brassicaceae were notresolved by this work. However, the problems inherent inthese tasks were identified. A Chemosystematic Study of the PhylogeneticPosition of Arabidopsis thaliana (L.) Heynh. (Brassicaceae) Employing Numerical Methods by Hesh J. Kaplan A THESIS submitted to Oregon State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Commencement June 1977 APPROVED: Redacted for Privacy Professor of Botany and Plant Pathology in charge of major Redacted for Privacy Chairman of Department of Botany and Plant Pathology Redacted for Privacy Dean of Graduate School Date thesis is presented April 19, 1977 Typed by Mary Jo Stratton forHesh J. Kaplan ACKNOWLEDGEMENTS I wish to thank Dr. Ralph S. Quatrano for his guidance and cont:nued support throughout this research effort. Moreover I am wholly indebted to Dr. Kenton L. Chambers, whose patience, under- standing, and confidence in me has sustained my interest and energies since my arrival at Oregon State University.His counsel and critical comments have been invaluable in completing this work. This project was made possible, in part, by funding from the Herbarium and by grants from the Computer Sciences Department and the Graduate School of Oregon State University. TABLE OF CONTENTS Page I.INTRODUCTION 1 Pivotal Taxonomic Characteristics 4 A History of Brassicaceae Taxonomy 11 Linnaeus 11 de Candolle 12 Bentham and Hooker 17 Prantl 20 von Hayek 22 Schulz 25 Janchen 29 Abrams 30 Chemical and Numerical Methods 35 Scope of the Study 37 II. MATERIALS AND METHODS 38 Plant Materials 38 Electrophoresis Procedures 45 Standard Procedure 46 Revised Procedure 48 Related Procedures 48 Thin-layer Chromatography 50 Extraction 50 Plate Preparation 51 Chromatography 52 Numerical Methods 53 Computer Programs 54 Similarity Coefficients 56 Clustering Algorithms 60 Wagner Networks 66 Prim Network 67 Principal Component Analysis 67 Additional Computations 67 Description of Characters Included in Numerical Analyses 69 Morphological Data 70 Special Characters 70 Chemical Data 71 Characters Omitted from This Study 74 Page III. RESULTS OF EXPERIMENTS 78 FDP Aldo lase Electrophoresis 78 Optimization of Extraction Protocol 79 Electrophoresis Results 84 Thin-layer Chromatography 97 Numerical Analysis 99 Clustering 100 Supporting Numerical Analyses 112 IV. DISCUSSION OF FINDINGS 123 Enzyme Electrophoresis 123 Flavonoid Idiograms 128 Flavonoids in Brassicaceae Phylogeny 131 Efficacy of Numerical Techniques 136 Brassicaceae Classification 138 The Phylogenetic Position of A.rabidopsis 142 V. CONCLUDING REMARKS 146 BIBLIOGRAPHY 150 APPENDICES Appendix L Electrophoretic Phenotypes 162 Appendix II. TLC Idiograms 183 Appendix III.Supplementary Results of Numerical Analyses 199 LIST OF TABLES Table Page 1 A partial listing of the species of A rabidopsis and their synonyms. 5 2 Listing of plants studied. 39 3 Composition of mineral media. 44 4 List of *MINT programs. 56 5 Spectrophotometric comparison of alternative extraction procedures. 80 6 Similarity coefficients for genera using simple matching coefficients. 101 7 Results of centroid clustering (k = 4). 120 8 Results of centroid clustering (k = 6). 121 9 Genera separated into subsets (ball clusters) by the method of Sale (1971). 122 10 Similarity coefficients for species using simple matching coefficients. 200 11 Correlation coefficients of combined morphological and chemical characteristics. 205 LIST OF FIGURES Figare page 1 Representative fruit types. 8 2 Cotyledon positions. 9 3 The system of Cruciferae according to de Candolle. 14 4 The system of Cruciferae according to Gray. 16 5 The system of Cruciferae according to Bentham and Hooker. 18 6 The system of Cruciferae according to Prantl. 21 7 The system of Cruciferae according to von Hayek. 24 8 The system of Cruciferae according to Schulz. 27 9 The system of Cruciferae according to Janchen. 31 10 The system of Brassicaceae according to Abrams. 34 11 Illustration of a reversal by centroid clustering. 63 12 Matrix for coding chromatogram Rf values. 73 13 Diagrammatic representation of nectary form and position. 76 14 Comparison of absorption spectra of whole plant extracts of Arabidopsis. 82 15 Electrophoretic phenotype of Arabidopsis thaliana (F-995). 85 16 Electrophoretic phenotype of Cardamine oligosperma. 86 Figure Page 17 Illustration of technique for representing electrophoretic phenotypes; banding of Hylandra suecica is shown. 89 18 Densitometer recordings of electrophoretic bands of FDP aldolase of extracts from whole plants of Arabidopsis thaliana. 90 19 The effects upon electrophoretic banding of mixing purified aldolase with heat killed plant extracts. 92 20 FDP aldolase activity assay in Arabidopsis thaliana. 93 21 Electrophoretic phenotypes of Arabidopsis and related species. 95 22 Electrophoretic phenotypes of races of Arabidopsis thaliana. 96 23 TLC idiograms of Iberis, Arabidopsis, Cardaminopsis, and Sisymbrium. 98 24 Phenogram, morphological data, flexible coupling, a = 0.625. 105 25 Phenogram, flavonoid data, Jaccard coefficient, flexible coupling, a = 0.625. 106 26 Phenogram, electrophoresis data, simple matching coefficient, flexible coupling, a = 0.625. 107 27 Phenogram, morphological data, flexible coupling, a = 0.625, genera only. 109 28 Phenogram, morphological data, flexible coupling, a = 0.500, genera only. 110 29 Phenogram, morphological data, flexible coupling, a = 0.700, genera only. 111 30 Shortest connection network. 113 Figure Page 31 Wagner tree (Stanleya ancestral). 115 32 Wagner tree (Arabidopsis ancestral). 116 33 Principal components analysis (morphological data); the first two principal axes. 118 34 Principal components analysis (morphological data); the first and third principal axes. 119 35 Electrophoretic phenotype of Arabis breweri. 163 36 Electrophoretic phenotype of Cardaminopsis arenosa. 164 37 Electrophoretic phenotype of Cardaria draba. 165 38 Electrophoretic phenotype of Iberis sempervirens. 166 39 Electrophoretic phenotype of Idahoa scapigera. 167 40 Electrophoretic phenotype of Lunaria annua. 168 41 Electrophoretic phenotype of Raphanus sativus. 169 42 Electrophoretic phenotype of Thysanocarpus curvipes. 170 43 Electrophoretic
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