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DNA taxonomy of infraorder Caridea (Crustacea: Decapoda).

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

Identiferoai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_325862
Date January 2007
ContributorsLei, Ho Chee., Chinese University of Hong Kong Graduate School. Division of Biology.
Source SetsThe Chinese University of Hong Kong
LanguageEnglish, Chinese
Detected LanguageEnglish
TypeText, bibliography
Formatprint, xiv, 191 leaves : ill. ; 30 cm.
RightsUse of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

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