Xu Jiawu. / "March 2005." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 103-120) / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Ho Hoi Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 107-118). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgments --- p.v / Contents --- p.vii / List of Tables --- p.x / List of Figures --- p.xi / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.5 / Chapter 2.1 --- Introduction to phylogenetic biology --- p.5 / Chapter 2.1.1 --- Definition of phylogenetics --- p.5 / Chapter 2.1.2 --- Why employ molecular genetic markers in phylogenetics? --- p.5 / Chapter 2.2 --- DNA analysis and the contributions to phylogenetics --- p.7 / Chapter 2.2.1 --- Nuclear ribosomal DNA --- p.7 / Chapter 2.2.2 --- Animal mitochondrial DNA (mt DNA) --- p.10 / Chapter 2.3 --- Molecular phylogeny of crustaceans --- p.11 / Chapter 2.3.1 --- Phylogenetic studies of crustaceans using nuclear rRNA --- p.11 / Chapter 2.3.2 --- Population genetic and phylogenetic studies of crustaceans using mtDNA --- p.14 / Chapter 2.4 --- Taxonomy of the genus Eriocheir --- p.23 / Chapter 2.5 --- Distribution of Eriocheir s.l --- p.27 / Chapter 2.6 --- Population genetics of Eriocheir --- p.28 / Chapter 2.6.1 --- Population genetics of Eriocheir japonica --- p.28 / Chapter 2.6.2 --- Population genetics and history of invasion of Eriocheir sinensis --- p.29 / Chapter Chapter 3 --- Materials and Methods --- p.32 / Chapter 3.1 --- Specimens --- p.32 / Chapter 3.1.1 --- Specimens for phylogenetic reconstruction --- p.32 / Chapter 3.1.2 --- Specimens for population genetic study on E. sinensis --- p.33 / Chapter 3.2 --- DNA extraction --- p.33 / Chapter Chapter 3 --- Materials and Methods --- p.32 / Chapter 3.1 --- Specimens --- p.32 / Chapter 3.1.1 --- Specimens for phylogenetic reconstruction --- p.32 / Chapter 3.1.2 --- Specimens for population genetic study on E. sinensis --- p.33 / Chapter 3.2 --- DNA extraction --- p.33 / Chapter 3.3 --- Amplification of genes --- p.36 / Chapter 3.3.1 --- PCR profile --- p.38 / Chapter 3.3.1.1 --- 16S rRNA gene --- p.38 / Chapter 3.3.1.2 --- COI gene --- p.40 / Chapter 3.3.1.3 --- ITS-1 gene --- p.41 / Chapter 3.4 --- DNA sequencing --- p.41 / Chapter 3.4.1 --- Purification of extension products --- p.43 / Chapter 3.4.2 --- Electrophoresis and data collection --- p.44 / Chapter 3.4.3 --- Sequence alignment --- p.44 / Chapter 3.5 --- Phylogenetic construction --- p.45 / Chapter Chapter 4 --- Results --- p.47 / Chapter 4.1 --- Phylogenetic reconstruction of Eriocheir --- p.47 / Chapter 4.1.1 --- PCR products of mitochondrial 16S rRNA and COI gene and nuclear ribosomal ITS-1 gene --- p.47 / Chapter 4.1.2 --- Intraspecific variation --- p.49 / Chapter 4.1.3 --- Genetic variability in mitten crabs based on partial sequences of 16S rRNA gene --- p.49 / Chapter 4.1.4 --- Genetic variability in mitten crabs based on partial sequences of COI gene --- p.53 / Chapter 4.1.5 --- Genetic variability in mitten crabs based on complete sequences of ITS-1 gene --- p.62 / Chapter 4.1.6 --- Phylogenetic analysis --- p.66 / Chapter 4.1.6.1 --- Phylogenetic analysis based on 16S rDNA sequences --- p.66 / Chapter 4.1.6.2 --- Phylogenetic analysis based on COI gene sequences --- p.70 / Chapter 4.1.6.3 --- Phylogenetic analysis based on ITS-1 gene sequences --- p.73 / Chapter 4.2 --- Population genetic study of E. sinensis --- p.77 / Chapter 4.2.1 --- PCR products and intraspecific variation of mitochondrial COI gene for population genetic study of E. sinensis --- p.77 / Chapter 4.2.2 --- Genetic variability in E. sinensis based on partial sequences of COI gene --- p.79 / Chapter 4.2.3 --- Population genetic analysis based on COI gene sequences --- p.86 / Chapter Chapter 5 --- Discussion --- p.93 / Chapter 5.1 --- Phylogeny of Eriocheir --- p.93 / Chapter 5.1.1 --- Phylogenetic relationships --- p.93 / Chapter 5.1.2 --- Taxonomic implications --- p.95 / Chapter 5.1.3 --- Evolutionary history of Eriocheir --- p.97 / Chapter 5.2 --- Population study of E. sinensis --- p.101 / Chapter 5.2.1 --- Genetic variation between Chinese populations --- p.101 / Chapter 5.2.2 --- Genetic variation between native and introduced populations --- p.102 / Chapter Chapter 6 --- Conclusions --- p.104 / Literature Cited --- p.107

This study is a multidisciplinary approach to Species Distribution Modelling (SDM) where predictive models have been developed regarding the current distribution and potential spread of two invasive species found in Baltic Sea waters. Invasive species in the Baltic have long been an ecological and economic problem and the two species studied are well known for their adaptability in colonization and detrimental effects on local ecology all over the world. First, the Round Goby (Neogobius Melanostomus) has been steadily colonizing the Swedish Baltic coastline since 2008, the impact of which on local ecosystems is not fully understood. Also, the Chinese Mitten Crab (Eriocheir Sinensis), found in Swedish waters since the 1930’s, has been known to be a robust invader of ecosystems but presence in the Baltic is still not well explained. Four high spatial resolution models have been developed, three respective Round Goby and one for Mitten Crab. Two models are specific to the Blekinge/Hanöbukten region of the Swedish Baltic Sea coast, showing predicted current distribution of Round Goby. Two are predictions of Round Goby and Mitten Crab transferred or projected to other regions, with different approaches in setting model parameters and choosing variables, showing current and potential distribution. This study features: exploratory data analysis and filtering using GIS tools, highly discriminant environmental variable selection and rejection, and several different approaches to modelling in Maxent using custom and default settings. Predictive maps have been developed showing current distribution and potential spread as well as explanatory tabular data outlining direct and indirect drivers of species presence. Maxent has proven to be a powerful predictive tool on a regional basis, and proximity to introduction locations play a major role. Maxent, used in combination with spatial data modelling, exploration and filtering techniques has yielded a valid explanatory model as well. Transferring predictions to other regions is quite sensitive, however, and can depend heavily on species, sampling strategy and similarity of habitat type. Round Goby predictions were successfully created regionally and transferred to Stockholm, but Mitten Crab predictions were not successfully transferred to Blekinge.

Marine and freshwater aquatic invasive species are a huge problem in the United States and its territorial waters with myriad ecological and economic impacts. Current management methods have fallen short. One possible solution is to harvest them for human consumption. This should be done through small scale, carefully regulated, scientifically based programs that are part of a larger overall management strategy. Four case studies (northern snakehead, European green crab, Asian carp, Chinese mitten crab) assessing edibility are included.

The Microsporidia are obligate intracellular parasites that have jettisoned oxidation phosphorylative capabilities during their early evolutionary history and so rely on ATP import from their host and glycolysis for their energy needs. Some species form tight associations with the host’s mitochondria and this is thought to facilitate ATP sequestration by the developing intracellular microsporidian. The human parasite, Enterocytozoon bieneusi has however lost glycolytic capabilities and may rely entirely on ATP import from its host for energy. E. bieneusi belongs to the Enterocytozoonidae microsporidian family and recent rDNA-based phylogenetic studies have suggested it has close evolutionary ties with Enterospora canceri, a crab-infecting intranuclear parasite. Such a close evolutionary relationship implied that glycolysis might also be absent in the intranuclear parasite raising questions as to how this parasite obtains energy from its unusual niche that is physically walled off from the host mitochondria, the main source of ATP in the host cell. In this study, draft genomes of four species of the Enterocytozoonidae namely, Ent. canceri, E. hepatopenaei, Hepatospora eriocheir and Hepatospora eriocheir canceri and one non-Enterocytozoonidae species, Thelohania sp. were assembled and annotated (The genome assembly of Hepatospora eriocheir was provided by Dr. Bryony Williams). Phylogenomics performed with this and publicly available genomic data confirmed the close evolutionary ties between Ent. canceri and E. bieneusi. Comparative genomic analyses also revealed that glycolysis is indeed lost in all members of the Enterocytozoonidae family sequenced in this study, hinting to the relaxation of evolutionary pressures to maintain this pathway at the base of this microsporidian family. Despite this absence, the hexokinase gene was retained in all aglycolytic genomes analysed, and that of Ent. canceri was fused to a PTPA gene. Functional assays and yeast complementation assays suggest that this chimera is able to recognise glucose as a substrate but the heterologously expressed homolog of H. eriocheir cannot. Finally, phylogenomics have been used here to demonstrate that despite the morphological differences between three Hepatospora-like organisms parasitizing different crab hosts, they are the same species. This finding adds more weight to current evidence suggesting that morphology is not an ideal marker for taxonomical classification in the Microsporidia.