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

• Other Authors: Ho, Ka Chai.
• Format: Others
• Language: English; Chinese
• Published: 2007
• Subjects: Nephropidae > Phylogeny > Molecular aspects; Mitochondrial DNA > Analysis
• Online Access: http://library.cuhk.edu.hk/record=b5893097; http://repository.lib.cuhk.edu.hk/en/item/cuhk-325846

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