One of the major functions of a Botanic Garden should be that of research. When a research laboratory was established at Kirstenbosch National Botanic Garden in 1984, it-was decided to start investigating chemical parameters of our indigenous plants, since this is a field that has not received adequate attention in the past. It was hoped to contribute towards the classification of plants by applying chemotaxonomy or chemosystematics, whereby chemical evidence is incorporated with morphological and other information. The genus Protea L. was an obvious choice for the initial material of such research as it is one of the best-known and most prominent genera of our indigenous flora and its taxonomic revision, based mainly on morphological data, was recently completed by Dr. J. P. Rourke (1980) of the National Botanic Gardens, Kirstenbosch. It was hoped that a phytochemical study of Protea species, whereby their free amino acid composition was determined by paper partition chromatography, might be of use in contributing to its taxonomic classification.

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Thesis (Ph. D.)--University of Toledo, 2005. / Typescript. "A dissertation [submitted] as partial fulfillment of the requirements of the Doctor of Philosophy degree in Physics." Includes bibliographical references (leaves 295-304).

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Lei Ho Chee. / Thesis submitted in: December 2006. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 140-153). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.v / Contents --- p.vi / List of Tables --- p.x / List of Figures --- p.xii / Chapter 1 General Introduction --- p.1 / Chapter 2 Literature Review --- p.4 / Chapter 2.1 --- DNA taxonomy --- p.4 / Chapter 2.1.1 --- Definitions --- p.4 / Chapter 2.1.2 --- Significance of DNA taxonomy --- p.5 / Chapter 2.1.3 --- DNA taxonomy in different animals --- p.5 / Chapter 2.1.4 --- Studying DNA taxonomy on Crustacea with different gene markers --- p.6 / Chapter 2.1.4.1 --- Mitochondrial gene makers --- p.6 / Chapter 2.1.4.2 --- Nuclear gene marker --- p.9 / Chapter 2.1.5 --- Phylogenetic construction methods --- p.10 / Chapter 2.2 --- Taxonomy of infraorder Caridea based on morphologies --- p.13 / Chapter 2.3 --- DNA barcodes --- p.29 / Chapter 2.3.1 --- Idea of barcodes --- p.29 / Chapter 2.3.2 --- Significance of DNA barcode --- p.29 / Chapter 2.3.3 --- Mitochondrial COI gene as DNA barcode --- p.30 / Chapter 2.3.3.1 --- Species identification with COI gene --- p.31 / Chapter 2.3.3.2 --- Revealing cryptic species with COI gene --- p.31 / Chapter 2.3.4 --- Limitations of DNA barcodes --- p.32 / Chapter 2.4 --- Species Diagnosis with hybridization methods --- p.34 / Chapter 2.4.1 --- Species diagnosis with mircoarray --- p.35 / Chapter 2.4.2 --- Species diagnosis with dot blot hybridization --- p.35 / Chapter Chapter 3 --- DNA Taxonomy of Infraorder Caridea --- p.39 / Chapter 3.1 --- Introduction --- p.39 / Chapter 3.2 --- Materials and Methods --- p.40 / Chapter 3.2.1 --- Sample collection --- p.40 / Chapter 3.2.2 --- DNA extraction and PCR amplification --- p.41 / Chapter 3.2.3 --- DNA sequencing --- p.48 / Chapter 3.2.4 --- Phylogenetic analysis --- p.49 / Chapter 3.3 --- Results --- p.50 / Chapter 3.3.1 --- Sequence composition --- p.50 / Chapter 3.3.2 --- Comparisons of sequences divergence --- p.52 / Chapter 3.3.3 --- Phylogenetic analysis using the four gene regions --- p.76 / Chapter 3.3.3.1 --- COI --- p.76 / Chapter 3.3.3.2 --- 16S rRNA --- p.95 / Chapter 3.3.3.3 --- 12S rRNA --- p.96 / Chapter 3.3.3.4 --- 18S rRNA --- p.97 / Chapter 3.3.3.5 --- Combined analysis of 16S rRNA and 18S rRNA --- p.98 / Chapter 3.3.3.6 --- Composition vector analysis of 18S rRNA --- p.99 / Chapter 3.3.4 --- Saturation analysis --- p.99 / Chapter 3.4 --- Discussion --- p.105 / Chapter 3.4.1 --- Evaluation of the four DNA markers --- p.105 / Chapter 3.4.1.1 --- COI --- p.105 / Chapter 3.4.1.2 --- 16S rRNA and 12S rRNA --- p.107 / Chapter 3.4.1.3 --- 18SrRNA --- p.109 / Chapter 3.4.2 --- Comparison with morphological classification schemes --- p.111 / Chapter 3.4.2.1 --- Relationships at family level --- p.111 / Chapter 3.4.2.2 --- Relationships at superfamily level --- p.116 / Chapter 3.4.2.3 --- Relationship among superfamilies --- p.121 / Chapter Chapter 4 --- Development of specific probes for caridean family identification --- p.122 / Chapter 4.1 --- Introduction --- p.122 / Chapter 4.2 --- Methods and Materials --- p.123 / Chapter 4.2.1 --- Probe design --- p.123 / Chapter 4.2.2 --- Probe labeling and checking yield --- p.125 / Chapter 4.2.3 --- Preparation of target DNA and dot-blot --- p.126 / Chapter 4.2.4 --- Pre-hybridization and hybridization --- p.128 / Chapter 4.2.5 --- Stripping of membrane --- p.129 / Chapter 4.2.6 --- Preparation of chemicals and reagents --- p.129 / Chapter 4.3 --- Results --- p.131 / Chapter 4.4 --- Discussion --- p.135 / Chapter Chapter 5 --- General Conclusion --- p.138 / Literature cited --- p.140 / Appendices 1. Aligned sequences of mitochondrial COI gene --- p.154 / 2. Aligned sequences of mitochondrial 16S rRNA gene --- p.162 / 3. Aligned sequences of mitochondrial 12S rRNA gene --- p.168 / 4. Aligned sequences of nuclear 18S rRNA gene --- p.172

Ph.d.

Taxonomy has been defined as "the study of classification, including its bases, principles, procedures and rules;" (Simpson 1961). An alternative definition (of systematics) is "the scientific study of the kinds and diversity of organisms and of any and all relationships among them." Taxonomy is therefore, one of the oldest fields of biological science; because in order to classify, even at the most elementary levels, man had to identify organisms. This necessitated observing, and making comparisons, integrating specific data and developing generalizations from these. Since this is the case, one may suggest that taxonomy is an outdated science, as almost everything has been named and 'pigeon-holed' already. It must be borne in mind, however, that early scientists were merely concerned with writing descriptions and giving names, while in modern days taxonomists are interested in more than describing and naming species. Now they attempt to establish relationships and affinities with more accuracy. [...]