Wu, Tsz Huen. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 89-106). / Abstracts in English and Chinese. / Chapter Chapter 1 --- General Introduction to thesis --- p.1 / Chapter Chapter 2 --- Literature review --- p.3 / Chapter 2.1 --- Introduction --- p.3 / Chapter 2.1.1 --- General introduction to barnacles --- p.3 / Chapter 2.1.2 --- Classification of barnacles --- p.4 / Chapter 2.1.3 --- Importance of barnacles --- p.4 / Chapter 2.2 --- Molecular phylogenetics of barnacles --- p.6 / Chapter 2.2.1 --- What is phylogenetics --- p.6 / Chapter 2.2.2 --- Phylogenetic studies on barnacles --- p.7 / Chapter 2.2.3 --- Choices on characters for barnacle phylogenetics: Morphological characters vs. molecular characters --- p.11 / Chapter 2.2.4 --- Choices of molecular markers in phylogenetic and population genetic studies on barnacles --- p.14 / Chapter 2.3 --- The use of barnacles as model organism in population genetic studies --- p.21 / Chapter 2.3.1 --- Pleistocene glaciations --- p.22 / Chapter 2.3.2 --- Oceanographic pattern and habitat availability --- p.23 / Chapter Chapter 3 --- Phylogenetic relationship of barnacles in family Chthamalidae --- p.26 / Chapter 3.1 --- Introduction --- p.26 / Chapter 3.2 --- Materials and methods --- p.31 / Chapter 3.2.1 --- "Sample collection, DNA extraction and amplification" --- p.31 / Chapter 3.2.2 --- Phylogenetic analyses --- p.34 / Chapter 3.3 --- Results --- p.35 / Chapter 3.4 --- Discussion --- p.40 / Chapter 3.4.1 --- Subfamily Notochthamalinae --- p.40 / Chapter 3.4.2 --- Subfamily Chthamalinae --- p.42 / Chapter 3.4.3 --- Subfamily Euraphiinae --- p.42 / Chapter 3.4.4 --- Phylogenetic relationship in the family Chthamalidae --- p.43 / Chapter 3.4.5 --- Suggestions on taxonomy of Chthamalidae --- p.45 / Chapter Chapter 4 --- Cryptic Diversity and Genetic Structure of the Acorn Barnacle Chthamalus moro in the Northwest Pacific --- p.47 / Chapter 4.1 --- Introduction --- p.47 / Chapter 4.2 --- Materials and methods --- p.53 / Chapter 4.2.1 --- "Sample collection, DNA extraction and amplification" --- p.53 / Chapter 4.2.2 --- Phylogenetic analysis --- p.55 / Chapter 4.2.3 --- Population genetic analysis --- p.55 / Chapter 4.3 --- Results --- p.57 / Chapter 4.3.1 --- Phylogenetic analysis --- p.57 / Chapter 4.3.2 --- "Population genetics analyses, demographic history and neutrality" --- p.61 / Chapter 4.4 --- Discussion --- p.72 / Chapter 4.4.1 --- Origin and the systematic status of the three lineages --- p.72 / Chapter 4.2.2 --- Demographic history of the three lineages --- p.81 / Chapter 4.3.3 --- Contemporary distribution and genetic connectivity of the three lineages --- p.84 / Chapter Chapter 5 --- Concluding remarks --- p.87 / References --- p.89

Finally, the gene tree of the true crabs, Brachyura, confirms that the basal "Podotremata" is paraphyletic, with the Raninoidea and Cyclodorippoidea more closely related to Eubrachyura than to the other podotremes. Within the monophyletic Eubrachyura, the analysis supports the reciprical monophyly of the two subsections, Heterotremata and Thoracotremata. All of the Old World freshwater crabs cluster together, representing an early diverged lineage in the Heterotremata. / From the inferred phylogeny, we have obtained new insights on the evolution of decapods. First, the spiny lobster from the family Palinuridae is found to be paraphyletic with the polyphyletic Synaxidae nested within it. The Stridentes forms a monophyletic assemblage, indicating that the stridulating sound producing organ evolved only once in the spiny lobsters. Moreover, the spiny lobsters originated in the shallower water rocky reefs of the Southern Hemisphere and then invaded deep sea habitats and diversified. / In sum, I demonstrate the utility of the nuclear protein-coding gene markers in decapod phylogeny and they are informative across a wide range of taxonomic levels. I propose that nuclear protein-coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics. / Second, we show that hermit crabs have a single origin, but surprisingly, that almost all other major clades and body forms within the Anomura, are derived from within the hermit crabs. The crab-like form and squat lobster form have each evolved at least twice from separate symmetrical hermit crab ancestors. These remarkable cases of multiple parallelism suggest considerable phenotypic flexibility within the hermit crab ground plan, with a general tendency towards carcinization. Rather than having a separate origin from other major clades, hermit crabs have given rise to most other major anomuran body types. / The high diversity of decapods has attracted the interest of carcinologists but there is no consensus on decapod phylogeny in spite of the endeavors using both morphological and molecular approaches. New sources of information are necessary to elucidate the phylogenetic relationships among decapods. In the present study, I attempted to develop and apply the nuclear protein-coding gene markers on decapod phylogeny. Using only two protein-coding genes, we have successfully resolved most of the infraordinal relationships with good statistical support, indicating the superior efficiency of these markers compared to nuclear ribosomal RNA and mitochondrial genes commonly used in phylogenetic reconstruction of decapods. Apparently these two types of markers suffer from the problems of alignment ambiguities and rapid saturation, respectively. Subsequently, I tried to apply the nuclear protein-coding genes in revealing interfamilial and intergeneric evolutionary history in three selected decapod groups, the spiny lobster (family Palinuridae), the infraorder Anomura and the true crabs of the infraorder Brachyura to further evaluate the utility of these markers and reconstruct the evolutionary history the groups. Trees with robust support can be obtained using sequences of three to five genes for the infraorders and families tested including the most speciose Brachyura. The genes are shown to be informative in elucidating interspecific phylogeny as well. / Tsang, Ling Ming. / Adviser: Ka Hou Chu. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 127-153). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Li, Chi Pang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 127-141). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.v / Contents --- p.vi / List of Tables --- p.ix / List of Figures --- p.x / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.3 / Chapter 2.1 --- Caridean phylogeny --- p.3 / Chapter 2.1.1 --- Informative morphological characters in Caridean shrimps --- p.3 / Chapter 2.1.2 --- Brief history of Caridean classifications --- p.4 / Chapter 2.1.3 --- Natantia/Reptantia scheme vs. Dendrobranchiata/Pleocyemata scheme --- p.8 / Chapter 2.2 --- Phylogney of the family Hippolytidae --- p.10 / Chapter 2.3 --- Molecular approach to phylogeny --- p.11 / Chapter 2.3.1 --- Use of molecular data --- p.11 / Chapter 2.3.2 --- Use of mitochondrial gene markers in crustaceans --- p.12 / Chapter 2.3.3 --- Use of nuclear gene markers in crustaceans --- p.14 / Chapter Chapter 3 --- Phylogeny of the Infraorder Caridea Based on five Nuclear Genes --- p.27 / Chapter 3.1 --- Introduction --- p.27 / Chapter 3.2 --- Materials and Methods --- p.28 / Chapter 3.2.1 --- Sample Collection --- p.28 / Chapter 3.2.2 --- DNA extraction and PCR amplification --- p.28 / Chapter 3.2.3 --- DNA sequencing --- p.29 / Chapter 3.2.4 --- Phylogenetic analysis --- p.30 / Chapter 3.3 --- Results --- p.34 / Chapter 3.3.1 --- Enolase --- p.34 / Chapter 3.3.2 --- NaK --- p.35 / Chapter 3.3.3 --- PEPCK --- p.37 / Chapter 3.3.4 --- Histone --- p.38 / Chapter 3.3.5 --- 18S rRNA --- p.39 / Chapter 3.3.6 --- Combined dataset --- p.41 / Chapter 3.3.7 --- Substitution saturation analysis --- p.43 / Chapter 3.4 --- Discussion --- p.44 / Chapter 3.4.1 --- Evaluation of the five nuclear gene markers --- p.44 / Chapter 3.4.1.1 --- Nuclear protein coding genes --- p.44 / Chapter 3.4.1.2 --- 18S rRNA --- p.81 / Chapter 3.4.2 --- Superfamilies and families --- p.82 / Chapter 3.4.2.1 --- Superfamilies --- p.82 / Chapter 3.4.2.2 --- Families --- p.86 / Chapter 3.4.3 --- Basal groups --- p.86 / Chapter 3.4.4 --- Procarididae --- p.88 / Chapter Chapter 4 --- Phylogeny of the family Hippolytidae --- p.90 / Chapter 4.1 --- Introduction --- p.90 / Chapter 4.2 --- Materials and Methods --- p.91 / Chapter 4.2.1 --- Sample Collection --- p.91 / Chapter 4.2.2 --- DNA extraction and PCR amplification --- p.91 / Chapter 4.2.3 --- DNA sequencing --- p.95 / Chapter 4.2.4 --- Phylogenetic analysis --- p.95 / Chapter 4.3 --- Results --- p.95 / Chapter 4.3.1 --- Enolase --- p.95 / Chapter 4.3.2 --- NaK --- p.98 / Chapter 4.3.3 --- 16S rRNA --- p.99 / Chapter 4.3.4 --- Combined dataset --- p.100 / Chapter 4.4 --- Discussion --- p.118 / Chapter 4.4.1 --- "Resurrection of family Lysmatidae Dana,1852" --- p.118 / Chapter 4.4.2 --- Other hippolytid clades --- p.120 / Chapter 4.4.2.1 --- """Hippolytidae""" --- p.120 / Chapter 4.4.2.2 --- Bythocarididae --- p.121 / Chapter 4.4.3 --- Superfamily Alpheoidea --- p.122 / Chapter Chapter 5 --- General Conclusion --- p.125 / References --- p.127

Ma, Ka Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 88-103). / Abstracts in English and Chinese. / ABSTRACT --- p.i / ACKNOWLEDGEMENTS --- p.vii / CONTENTS --- p.ix / LIST OF TABLES --- p.xi / LIST OF FIGURES --- p.xii / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Molecular phylogenetics --- p.1 / Chapter 1.2 --- Phylogeny of the penaeoid shrimps --- p.2 / Chapter 1.2.1 --- Interfamilial relationships of Penaeoidea --- p.3 / Chapter 1.2.2 --- Ingergeneric relationships of Penaeidae --- p.8 / Chapter 1.2.3 --- Interspecific relationships of Penaeus s.l --- p.11 / Chapter 1.3 --- Molecular markers for decapods phylogenetics studies --- p.14 / Chapter 1.3.1 --- Mitochondrial markers --- p.14 / Chapter 1.3.2 --- Nuclear markers --- p.16 / Chapter Chapter 2 --- Molecular phylogeny of superfamily Penaeoidea / Chapter 2.1 --- Introduction --- p.19 / Chapter 2.2 --- Materials and methods --- p.21 / Chapter 2.3 --- Results --- p.28 / Chapter 2.4 --- Discussion --- p.40 / Chapter 2.5 --- Conclusions --- p.48 / Chapter Chapter 3 --- Molecular phylogeny of genus Penaeus sensu lato / Chapter 3.1 --- Introduction --- p.50 / Chapter 3.2 --- Materials and methods --- p.50 / Chapter 3.3 --- Results --- p.56 / Chapter 3.4 --- Discussion --- p.74 / Chapter 3.5 --- Conclusions --- p.84 / Chapter Chapter 4 --- General conclusions --- p.85 / References --- p.88