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Phylogenetic analysis and molecular identification of clawed lobsters (Nephropidae) based on mitochondrial DNA.

Ho, Ka Chai. / Thesis submitted in: November 2006. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 127-145). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.v / Table of Contents --- p.vi / List of Tables --- p.ix / List of Figures --- p.x / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter 1.1 --- Molecular phylogeny of Metanephrops --- p.1 / Chapter 1.2 --- Identification of Nephropidae using DNA barcodes --- p.3 / Chapter Chapter 2 --- Literature Review --- p.5 / Chapter 2.1 --- Molecular phylogenetic studies of crustaceans --- p.5 / Chapter 2.1.1 --- Molecular phylogeny and reasons of using molecular markers in phylogenetic studies --- p.5 / Chapter 2.1.2 --- Characteristics of animal mitochondrial genome --- p.7 / Chapter 2.1.3 --- Examples of crustacean phylogenetic studies derived from mitochondrial DNA --- p.8 / Chapter 2.2 --- Identification of species based on DNA barcode --- p.17 / Chapter 2.2.1 --- Traditional taxonomy and its current practice --- p.17 / Chapter 2.2.2 --- Needs for DNA barcode --- p.18 / Chapter 2.2.3 --- Molecular identification based on DNA barcodes --- p.21 / Chapter 2.3 --- Taxonomy of Nephropidae --- p.28 / Chapter 2.3.1 --- Classification and phylogenetic relationship of Nephropidae --- p.28 / Chapter 2.3.2 --- Classification and distribution of Metanephrops --- p.31 / Chapter 2.3.3 --- Evolutionary history of Metanephrops --- p.36 / Chapter Chapter 3 --- Molecular Phylogeny of Metanephrops --- p.38 / Chapter 3.1 --- Introduction --- p.38 / Chapter 3.2.1 --- Species studied and sample collection --- p.41 / Chapter 3.2.2 --- DNA extraction --- p.43 / Chapter 3.2.3 --- Amplification of mitochondrial genes --- p.43 / Chapter 3.2.4 --- Nucleotide sequencing --- p.46 / Chapter 3.2.4.1 --- Asymmetric PCR --- p.46 / Chapter 3.2.4.2 --- Purification of asymmetric PCR products --- p.47 / Chapter 3.2.5 --- Sequence alignment --- p.47 / Chapter 3.2.6 --- Phylogenetic analyses --- p.48 / Chapter 3.3 --- Results --- p.50 / Chapter 3.3.1 --- PCR products of 16S rRNA and COI genes --- p.50 / Chapter 3.3.2 --- Nucleotide composition of 16S rRNA gene alignments --- p.52 / Chapter 3.3.3 --- Nucleotide composition of COI gene alignments --- p.54 / Chapter 3.3.4 --- Intraspecific and interspecific genetic variation --- p.56 / Chapter 3.3.5 --- Phylogenetic analysis based on 16S rRNA gene sequences --- p.61 / Chapter 3.3.6 --- Phylogenetic analysis based on COI gene sequences --- p.68 / Chapter 3.3.7 --- Phylogenetic analysis based on combined data set --- p.74 / Chapter 3.4 --- Discussion --- p.80 / Chapter 3.4.1 --- Interspecific genetic divergence --- p.80 / Chapter 3.4.2 --- Monophyly of the four species groups --- p.81 / Chapter 3.4.3 --- Phylogenetic relationship in Metanephrops --- p.84 / Chapter 3.4.4 --- Evolutionary history of Metanephrops --- p.90 / Chapter Chapter 4 --- Molecular Identification of Nephropidae --- p.92 / Chapter 4.1 --- Introduction --- p.92 / Chapter 4.2 --- Materials and methods --- p.93 / Chapter 4.2.1 --- Species studied and sample collection --- p.93 / Chapter 4.2.2 --- DNA extraction --- p.95 / Chapter 4.2.3 --- Amplification of genes --- p.95 / Chapter 4.2.4 --- PCR profiles for mitochondrial genes --- p.97 / Chapter 4.2.5 --- Nucleotide sequencing --- p.97 / Chapter 4.2.6 --- Purification of asymmetric PCR products --- p.97 / Chapter 4.2.7 --- Sequence alignment --- p.97 / Chapter 4.2.8 --- Cluster analysis --- p.97 / Chapter 4.2.9 --- Graphical summary of species similarity --- p.98 / Chapter 4.2.10 --- Testing of molecular identification system in Nephropidae --- p.98 / Chapter 4.3 --- Results --- p.100 / Chapter 4.3.1 --- PCR products and sequence alignments of 16S rRNA and COI genes --- p.100 / Chapter 4.3.2 --- Species identification for clawed lobsters --- p.100 / Chapter 4.3.2.1 --- 16S rRNA profile --- p.100 / Chapter 4.3.2.2 --- COI profile --- p.108 / Chapter 4.4 --- Discussion --- p.116 / General Conclusion --- p.124 / Literature Cited --- p.127 / Appendices --- p.146

Identiferoai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_325846
Date January 2007
ContributorsHo, Ka Chai., Chinese University of Hong Kong Graduate School. Division of Biology.
Source SetsThe Chinese University of Hong Kong
LanguageEnglish, Chinese
Detected LanguageEnglish
TypeText, bibliography
Formatprint, x, 171 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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