Thesis (Ph. D.)--Stanford University, 2006. / "September 2006." Includes bibliographical references.

博士(政治学) / Doctor of Political Science / 同志社大学 / Doshisha University

This thesis makes several contributions to improve our understanding of Proterozoic-Cambrian evolution of eukaryote life. Chapter 1 provides, for the first time, a quantitative characterization of the evolutionary trends of Proterozoic macroalgae. The analysis reveals that morphological disparity of Paleoproterozoic macroalgae was low but increased in the Mesoproterozoic and Ediacaran, with a plateau in between. There was also a significant increase in thallus surface/volume ratio and maximum canopy height of the Ediacaran macroalgal communities. The prolonged plateau between the Mesoproterozoic and Ediacaran may be related to either nutrient stress or the absence of animal grazing pressure. The Ediacaran increase in surface/volume ratio and morphological complexity may have been driven by decreasing pCO₂ levels and increasing animal grazing pressure. Chapter 2 presents a systematic re-examination of the carbonaceous compression fossils Protoarenicola baiguashanensis Wang, 1982, Pararenicola huaiyuanensis Wang, 1982, and Sinosabellidites huainanensis Zheng, 1980, from the early Neoproterozoic Liulaobei and Jiuliqiao formations in northern Anhui, North China. These fossils were previously interpreted as worm-like metazoans. Our study reveals new morphological features that weaken the metazoan interpretation. Instead, the new data indicate that these fossils can be alternatively interpreted as erect epibenthic organisms, possibly coenocytic algae. Chapter 3 examines two important eukaryote fossils: Horodyskia Yochelson and Fedonkin, 2000, and Palaeopascichnus Palij, 1976, from the upper Ediacaran chert of the Liuchapo Formation in central Guizhou, South China. These exceptionally preserved fossils offer us a unique opportunity to investigate their body constructions and affinities. The morphologies of Horodyskia and Palaeopascichnus support a phylogenetic relationship with agglutinated foraminifers, shedding new light on the divergence of bikont eukaryotes, the rise of rhizarians, and the ecological importance of heterotrophic eukaryotes in Proterozoic ecosystems. Chapter 4 focuses on Cambrian microfossils that represent the primary producers' cyanobacteria and eukaryotic phytoplankton (acritarchs). Careful investigation of the basal Cambrian Yanjiahe Formation in the Yangtze Gorges area and the Yurtus Formation in the Aksu area revealed abundant acanthomorphic acritarchs, clustered coccoidal microfossils, filamentous cyanobacteria, and tubular microfossils. This study confirms previous stratigraphic correlation between the Yanjiahe and Yurtus formations and suggests that animals and phytoplankton radiated in tandem during the Cambrian explosion. / Ph. D.

The Ediacaran, particularly the late Ediacaran-Cambrian (E-") boundary (551-541 Ma), has been noted as a major time of biological and biochemical transition, including: the rise of predators, the emergence of skeletons, the radiation of bioturbators, and large fluctuations in oceanic chemical conditions (e.g. anoxia/euxinia/ferruginia) with emerging data  suggesting that it is not until the late Ediacaran Period (551-542 Ma) when pervasive oxidation of the deep oceans occurred. In addition, the study of Ediacaran paleobiology involves numerous factors, including but not limited to, restricted amount of outcrops, taphonomic biases, metamorphism, enigmatic phylogenetic affinities, non-actualistic atmospheric and oceanic conditions, and unusual taphonomic windows, making it difficult to assign order to the myriad types of fossils (both body and trace) found during this time . It is with these problems in mind that my dissertation focuses on taphonomic questions in the late Ediacaran. We observe fossil through the taphonomic window and thereby colors all aspects of the study of that organism. By understanding how an organism was preserved we can learn about other factors affecting it, such as their taxonomic affinities, paleoecology, and morphology. All of these factors were examined through taphonomic investigations and this can be seen in the analytical path through my chapters. In chapter two I examined the preservation of trace fossils in the late Ediacaran. In chapter three I analyzed the taphonomy of an exceptionally preserved Ediacaran fossil to solve its affinity, tubular trace or tubular soft-bodied fossil. In chapter four, understanding the nature of exceptional preservation, I investigated the taphonomy of an Ediacara fossil in coarse grained sediments. In chapter five, I combined the findings of the previous chapters and applied that knowledge to analyze the in situ three dimensional morphology of an Ediacara fossil. Each of the projects presented pairs new technologic methodologies (SEM, BSE-Z, EDS, Raman, microCT) with traditional paleontological and petrologic investigations (field work, hand sample, and petrographic thin-section analysis). The result of this union of Old and New are findings that expand our understanding of these earliest multicellular organisms, their modes of life, and their biological affinities. / Ph. D.

The issue of South China Sea is one of the hottest international disputes in South East Asia due its location amid the connection between Southeast Asia to Northeast Asia and the rich resources. The undecided maritime delimitation makes the situation more complicated. Because each one of the ASEAN Claims has her own consideration of the interest, their claims and policies confront from each other's, and no consensus has been reached. However, encountering the fact that China proclaimed the entire region of South China Sea, ASEAN Claims attempt to unit themselves to deal with the threat, to negotiate the issue of South China Sea with China as a whole, and attempt to internationalize the issue. Thus, this paper is aimed to realize under what circumstance, ASEAN Claims will tend to unite in the issue of South China Sea, or vise versa, in what circumstance makes ASEAN Claims tend to collapse. According to the "Balance of Threat," China's threat to South China Sea affairs leads the changing of the unity of ASEAN Claims directly, and influences the consistency of South China Sea's policy. Besides the United States, the other side of the balance of the two counter powers, the treat brought by China in South China Sea affairs is the key to influence the South China Sea policy consistency of ASEAN Claims. "South China Sea Core interest" is one of match instance.

The newly recognized ammonia-oxidizing archaea (AOA) makes re-evaluation of the contribution to ammonia oxidization by both AOA and ammonia-oxidizing bacteria (AOB) necessary and meaningful. The growing population and increasing anthropogenic activities around coastlines have affected wetland and coastal marine ecosystems through discharging polluted water containing large amounts of reactive inorganic nitrogen. The objectives of this study were to detect the phylogenetic diversity and abundance of ammonia oxidizers including AOA and AOB on different scales and to elucidate the distribution patterns along an anthropogenic pollution gradient from the coastal wetland of the Mai Po Nature Reserve in Hong Kong to the South China Sea (SCS). Generally, besides lineages shared by similar environments, various endemic lineages were also observed in the polluted mangrove sediments of Hong Kong, and in the coastal, and deep-sea surface and subsurface sediments from the SCS indicating their geographical distance should be responsible for these phylogenetic distinctions. The community structures of AOA and AOB observed were proposed to be associated with environmental parameters including metals and total phosphorus (TP) separately in the sediments while their abundance was correlated with the pH value and temperature. On the other hand, along a profile of surface sediments with stable salinity from the coastal margin to the slope in the SCS, a clear community structure transition was detected for both AOA and AOB, showing major differences in each of their responses. Although the abundance of AOA was lower than that of AOB in the subsurface sediment samples from the SCS, the statistical support for relationships between AOA and nitrite concentration shed new light on the active contributor to the subsurface nitrogen cycle in the oxygen minimum zone from the deep-sea sediments. On a large scale, along the anthropogenic pollution gradient from the Pearl River Delta to the coastal margin and then the SCS, the dominant genus transition from Nitrosomonas to Nitrosospira was detected in response to the salinity and anthropogenic influences. Among a wide spectrum of environmental conditions in the western Pacific, a suite of statistical analyses clearly delineated the shallow and deep-sea sediments clusters suggesting that the depth and other contributing environmental factors involved shape the current distribution pattern of AOA. On a global scale, our understanding about the systematics and evolution of AOA was advanced through phylogenetic analyses. Salinity, lifestyle and temperature were proposed to be responsible for the global distribution patterns of AOA. On the basis of studies in the anthropogenic influence areas, the methods to detect specific responses of ammonia oxidizers to known anthropogenic pollution were concluded. Highlights of this study advance not only our understandings about phylogenetic diversity of ammonia oxidizers and the driving forces shaping their community structure and distribution patterns, but also a revised comprehensive view about them on the larger scale. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Baroclinic tides result from the interaction of barotropic tides with topography in stratified oceans. They play an important role in driving deep ocean mixing. In this research, investigations of the dynamics of baroclinic tides and internal solitary waves (ISWs) in the northern South China Sea (SCS) are conducted, mainly by means of the Massachusetts Institute of Technology general circulation model (MITgcm). Firstly, simulations of internal wave generation at the Luzon Strait (LS) are carried out. By conducting three-dimensional (3D), high-resolution experiments, it was found that the generated wave field features a multi-modal structure: large, pronounced ISWs of first mode (amplitude ~120 m) and second mode (amplitude ~120 m) were reproduced. The two north-south aligned ridges in the LS contribute together to the generation of the second mode ISWs, whereas the easternmost ridge of the two is responsible for the first mode ISWs. It was found that multiple generation mechanisms of internal waves could occur in this region, and overall it belongs to a mixed lee wave regime. A specific type of short internal waves arose during the 3D simulation. These ride on a second mode ISW with similar phase speed, trailing a first mode ISW. The short waves possess wavelengths of ~1.5 km and amplitudes of ~20 m, and only show up in the upper layer up to a depth of ~500 m. Scrutiny of the generation process showed that these short waves appear in two distinct regions and are produced due to two mechanisms, namely, the disintegration of an inclined baroclinic bore near the LS, and the overtaking of a second mode ISW in the deep water by a faster first mode ISW. Robust evidence has been sought from satellite imagery and by solving the theoretical Taylor-Goldstein Equation to verify their existence. The effects of superposition of multiple tidal harmonics (diurnal and semidiurnal) on the resultant ISW generation were investigated. It was first found that, by analyzing historical observational data, the occurrence of ISWs in the far-field always follow strong semidiurnal barotropic tidal peaks in the LS, regardless of whether it is the maximum for the diurnal or total tidal strength. However, modelling results of MITgcm and a linear internal tide generation model demonstrate that the diurnal tidal harmonics modulate the arrival time and amplitude of the propagating ISWs. Specifically, it leads to the emergence of the so-called A and B type ISWs and an alternation and transition between the two. Secondly, the shoaling process of ISWs in the northern SCS slope-shelf area is investigated. A series of two-dimensional (2D) experiments are set up to study the shoaling of a large-amplitude second mode concave ISW over a linear slope that resembles the SCS slope. Modelling results show that a strong transformation of the wave profile starts to take place when the wave is approaching the shelf break. A convex type wave is born at the trailing edge of the incident wave and gradually disintegrates into a group of ISWs due to the steepening of the rear wave profile. The frontal face of the wave gets flatter when travelling on the slope, but forms a steep structure right above the shelf break. However, this steep structure shows no tendency to evolve into an ISW: instead, it gets increasingly flat again while evolving on the shelf. The trailing convex wave packet travels faster and merges with the frontal concave wave. Finally, a wave packet with rank-ordered convex ISWs moves forward steadily on the shelf. Energy transfer to the ambient modes is evident, as both first mode and higher modes are clearly seen during and after the shoaling process. First mode ISW evolution is studied too by performing 3D, high-resolution experiments over the wide northern SCS slope and shelf area. It was found that the wave profiles change drastically near the shelf break and the Dongsha Atoll. In agreement with satellite imagery, the wavefront of the leading ISW becomes more spatially oblique with respect to its original orientation as it progresses westward due to the inclination of the slope in the topography. Wave disintegration is prominent in the shallow water zone, and wave polarity reverses near the turning point (at the 130 m isobath), which is consistent with the predictions of weakly nonlinear theory. A series of 2D experiments were set up to inspect the effects of rotation on the shoaling ISW. The results indicate that under the rotation, upon reaching the continental shelf, one shoaling ISW could disintegrate into one ISW packet and one secondary solibore that contains a number of rank-ordered waves with much shorter wavelength than an ISW. The secondary solibore is very pronounced in the northern portion of the northern SCS slope and shelf, but could hardly be discerned in the southern portion, which is consistent with the outcome of 3D simulations.

by Lee Ka Lun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 153-167). / Abstracts in English and Chinese. / Abstract (in English) --- p.i / Abstract (in Chinese) --- p.iv / Acknowledgements --- p.vi / List of Figures --- p.vii / List of Tables --- p.xv / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- "Seasonal population structure, life cycle and body allometry of the planktonic copepod Calanus sinicus" / Chapter 2.1 --- Literature Review / Chapter 2.1.1 --- Taxonomy of Calanidae --- p.6 / Chapter 2.1.2 --- Geographical and seasonal distribution of Calanus sinicus --- p.7 / Chapter 2.1.3 --- Body length and body weight of Calanus sinicus --- p.11 / Chapter 2.2 --- Introduction --- p.14 / Chapter 2.3 --- Materials and Methods --- p.17 / Chapter 2.3.1 --- Field sampling --- p.17 / Chapter 2 3.2 --- Identification and enumeration of zooplankton --- p.19 / Chapter 3 3.2 --- Body length and weight of Calanus sinicus --- p.19 / Chapter 2.4 --- Results --- p.20 / Chapter 2.4.1 --- Temperature --- p.20 / Chapter 2.4.2 --- Salinity --- p.21 / Chapter 2.4.3 --- Ambient Chlorophyll a concentration --- p.22 / Chapter 2.4.4 --- Seasonal occurrence and distribution of Calanus sinicus in northern Taiwan --- p.23 / Chapter 2.4.5 --- Seasonal occurrence and distribution of Calanus sinicus in Hong Kong --- p.26 / Chapter 2.4.6 --- Life cycle of Calanus sinicus in northern Taiwan --- p.27 / Chapter 2.4.7 --- Life cycle of Calanus sinicus in Hong Kong --- p.28 / Chapter 2.4.8 --- Stage ratio index --- p.28 / Chapter 2.4.9 --- Seasonal changes in biomass of Calanus sinicus --- p.29 / Chapter 2.4.10 --- Seasonal changes in the abundances of other copepods in northern Taiwan --- p.29 / Chapter 2.4.11 --- Seasonal changes in the abundances of other copepods in Hong Kong --- p.30 / Chapter 2.4.12 --- Seasonal changes in biomass of other copepods --- p.31 / Chapter 2.4.13 --- Seasonal variations in body size --- p.31 / Chapter 2.4.14 --- Seasonal changes in sex composition in adults --- p.32 / Chapter 2.5 --- Discussions --- p.32 / Chapter Chapter 3 --- Diel vertical migration and gut pigment rhythm of the planktonic copepod Calanus sinicus / Chapter 3.1 --- Literature review --- p.87 / Chapter 3.1.1 --- Diel vertical migration of Calanus sinicus --- p.87 / Chapter 3.1.2 --- Diel feeding rhythm of Calanus sinicus --- p.91 / Chapter 3.1.3 --- Measurement of grazing rate --- p.93 / Chapter 3.2 --- Introduction --- p.96 / Chapter 3.3 --- Materials and Methods --- p.98 / Chapter 3.3.1 --- Zooplankton sampling and physical parameters --- p.98 / Chapter 3.3.2 --- Identification and enumeration --- p.100 / Chapter 3.3.3 --- Gut pigment fluorescence --- p.100 / Chapter 3.4 --- Results --- p.101 / Chapter 3.4.1 --- Temperature and salinity --- p.101 / Chapter 3.4.2 --- Ambient chlorophyll a concentration --- p.102 / Chapter 3.4.3 --- Diel vertical migration --- p.103 / Chapter 3.4.4 --- Gut pigment content --- p.106 / Chapter 3.5 --- Discussion --- p.107 / Chapter Chapter 4 --- Use of molecular markers in population analysis of Calanus sinicus / Chapter 4.1 --- Literature Review --- p.134 / Chapter 4.2 --- Introduction --- p.138 / Chapter 4.3 --- Materials and Methods --- p.142 / Chapter 4.3.1 --- "Collection, preservation, and identification of Calansn sinicus samples" --- p.142 / Chapter 4.3.2 --- DNA sequence determination for Calanus sinicus --- p.143 / Chapter 4.4 --- Results --- p.144 / Chapter 4.5 --- Discussion --- p.145 / Chapter Chapter 5 --- Conclusion --- p.150

Lam, Yin Ha. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 188-203). / Abstracts in English and Chinese. / ABSTRACT --- p.i / ACKNOWLEDGEMENTS --- p.vi / CONTENTS --- p.viii / LIST OF TABLES --- p.xi / LIST OF FIGURES --- p.xiv / Chapter Chapter 1 --- Literature Review / Chapter 1.1 --- Crisis in world fisheries --- p.1 / Chapter 1.2 --- Marine Protected Areas (MPAs) --- p.3 / Chapter 1.3 --- Connectivity of fish populations --- p.7 / Chapter 1.4 --- The South China Sea --- p.12 / Chapter 1.5 --- Objectives and significance of the study --- p.14 / Chapter 1.6 --- The target species in the present study --- p.14 / Chapter 1.6.1 --- Family Siganidae --- p.14 / Chapter 1.6.2 --- Difficulties in morphological differentiation in Siganidae --- p.17 / Chapter 1.6.3 --- Systematic studies of Siganidae by molecular method --- p.20 / Chapter 1.6.4 --- Population genetic studies of Siganidae using molecular Marker --- p.24 / Chapter 1.7 --- Structure of the Thesis --- p.26 / Chapter Chapter 2 --- Population structure of Siganus canaliculatus/S. fuscescens species complex in the South China Sea based on mirochondrial DNA control region / Chapter 2.1 --- Introduction --- p.29 / Chapter 2.2 --- Materials and methods --- p.36 / Chapter 2.2.1 --- Collection of specimens --- p.36 / Chapter 2.2.2 --- "DNA extraction, PCR amplification and sequencing" --- p.37 / Chapter 2.2.3 --- Sequence analysis --- p.39 / Chapter 2.3 --- Results --- p.42 / Chapter 2.3.1 --- Genetic diversity --- p.42 / Chapter 2.3.2 --- Phylogenetic analysis and population genetic structure --- p.42 / Chapter 2.3.3 --- Historical demography --- p.46 / Chapter 2.4 --- Discussion --- p.47 / Chapter 2.4.1 --- Genetic diversity and demographic history --- p.47 / Chapter 2.4.2 --- Phylogeographical patterns --- p.51 / Chapter 2.4.3 --- Phylogeographical patterns and present day oceanic currents --- p.56 / Chapter 2.4.4 --- Population structure: Indian Ocean vs. Pacific Ocean --- p.61 / Chapter 2.4.5 --- Population structures in the South China Sea --- p.64 / Chapter 2.4.6 --- Implication for fisheries management --- p.72 / Chapter Chapter 3 --- Morphological differentiation in Siganus canaliculatus/S. fuscescens species complex / Chapter 3.1 --- Introduction --- p.92 / Chapter 3.2 --- Materials and methods --- p.94 / Chapter 3.2.1 --- Collection of specimen --- p.95 / Chapter 3.2.2 --- Morphometric measurements --- p.95 / Chapter 3.2.3 --- Spots counts --- p.96 / Chapter 3.2.4 --- Statistical analysis of data。 --- p.98 / Chapter 3.3 --- Results --- p.100 / Chapter 3.3.1 --- Univariate analysis --- p.100 / Chapter 3.3.2 --- Multivariate analysis --- p.103 / Chapter 3.4 --- Discussion --- p.106 / Chapter 3.4.1 --- Meristic characters --- p.106 / Chapter 3.4.2 --- Morphometric measurements --- p.107 / Chapter 3.4.2.1 --- Comparison with the previous works --- p.107 / Chapter 3.4.2.2 --- Comparison of morphometric indices among groups and populations --- p.112 / Chapter 3.5 --- Summary --- p.117 / Chapter Chapter 4 --- "The Siganus canaliculatus and S, fuscescens species complex- An evaluation" / Chapter 4.1 --- Introduction --- p.149 / Chapter 4.2 --- Materials and methods --- p.154 / Chapter 4.3 --- Results and discussion --- p.155 / Chapter 4.3.1 --- Meristic and morphometries --- p.156 / Chapter 4.3.2 --- Spots counts --- p.160 / Chapter 4.3.3 --- Cryptic species --- p.165 / Chapter Chapter 5 --- General Conclusions --- p.183 / References --- p.188

This dissertation evaluates the applicability and effectiveness of the 1982 United Nations Convention on the Law of the Sea (UNCLOS) as a settlement mechanism for addressing the South China Sea (SCS) dispute, the most complex and challenging ocean-related regional conflict in East Asia. This dissertation answers these broad questions: Does UNCLOS create a constitution for the ocean? Is UNCLOS successful in preventing or managing conflicts pertaining to marine resources? Hoes does the SCS dispute settlement bridge the gap of International Relations (IR) and International Law (IL)? Since 1980s, the regime concept came to be used as one vehicle to cross the disciplinary divide between IL and IR. This dissertation seeks to foster dialogue between political scientists and international lawyers by viewing UNCLOS as an international regime and exploring its internal coherence and its external relationship with other international regimes and institutions in this region. I argue that there can be little doubt about the centrality of UNCLOS in the legal framework for ocean management, albeit it may be perceived to have certain shortcomings. The most pervasive threats to the SCS stability and obstacles to solve the dispute are caused by the lack of political will to implement the dispute settlement mechanism of UNCLOS. This paper proposes a pragmatic settlement regime of five dimensions to solve the SCS dispute and accelerate ocean governance in this region.