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