The hickory shad (Alosa mediocris) is a relatively understudied species of the anadromous fish sub-family Alosinae. This study, the first population genetic analysis of this species, employed 12 neutral microsatellite loci to estimate genetic diversity and population structure in tributaries of lower Chesapeake Bay, Virginia including James River and its tributaries (Appomattox and Chickahominy Rivers), Rappahannock River, and Pamunkey River. Genetic variation was extremely low. Estimates of observed heterozygosity were lower than expected heterozygosity. Significant population structure was detected among the six samples (FST = 0.093, p = 0.01). Effective population sizes were low (Ne ranged from 2 to 134). The lack of genetic diversity, especially compared to that of the American shad, was striking and could be the result of a bottleneck that took place more than thirty years ago which may plausibly account for the low genetic variation observed across all populations.

Microorganisms are an indispensable part of our ecosystem, yet the natural metabolic and ecological diversity of these organisms is poorly understood due to a historical reliance of microbiology on laboratory grown cultures. The awareness that this diversity cannot be studied by laboratory isolation, together with recent advances in low cost scalable sequencing technology, have enabled the foundation of culture-independent microbiology, or metagenomics. The study of environmental microbial samples with metagenomics has led to many advances, but a number of technological and methodological challenges still remain. A potentially diverse set of taxa may be represented in anyone environmental sample. Existing tools for representing the genetic composition of such samples sequenced with short-read data, and tools for identifying variation amongst them, are still in their infancy. This thesis makes the case that a new framework based on a joint-genome graph can constitute a powerful tool for representing and manipulating the joint genomes of population samples. I present the development of a collection of methods, called SCRAPS, to construct these efficient graphs in small communities without the availability or bias of a reference genome. A key novelty is that genetic variation is identified from the data structure using a probabilistic algorithm that can provide a measure of the confidence in each call. SCRAPS is first tested on simulated short read data for accuracy and efficiency. At least 95% of non-repetitive small-scale genetic variation with a minor allele read depth greater than 10x is correctly identified; the number false positives per conserved nucleotide is consistently better than 1 part in 333 x 103. SCRAPS is then applied to artificially pooled experimental datasets. As part of this study, SCRAPS is used to identify genetic variation in an epidemiological 11 sample Neisseria meningitidis dataset collected from the African meningitis belt". In total 14,000 sites of genetic variation are identified from 48 million Illumina/Solexa reads. The results clearly show the genetic differences between two waves of infection that has plagued northern Ghana and Burkina Faso.

New world crocodilians constitute a monophyletic group comprising four species: Crocodylus rhombifer (Cuban crocodile), Crocodylus acutus (American crocodile), Crocodylus intermedius (Orinoco crocodile), and Crocodylus moreletii (Morelet’s crocodile). All of these are in the IUCN Red list of Threatened Species and exhibit geographic distributions covering small to widespread ranges across the Americas and insular Caribbean. With the overarching goal of generating relevant information for the conservation of endangered new world crocodilians, this dissertation integrates genetic and ecological information to provide a context spanning a scale from the species level to specific populations, to analyses of mating systems and breeding strategies in Crocodylus. In addition, my research applies tools of ecological inference to model the influence of environmental factors and natural habitat disturbances in the reproductive success of Crocodylus using a long-term dataset. This work uses C. intermedius and C. acutus as model species to explore four focal questions organized in distinct chapters related to the biology and ecology of crocodilians. In Chapter I, I compare previously reported reproductive traits among C. acutus populations across its geographic range. This comparative analysis reveals a high degree of variability in reproductive traits across C. acutus range and provides potential adaptive explanations for the patterns observed. Crocodylus acutus appears to be one of the most adaptable of crocodilians in terms of nesting requirements, total nests per breeding season, nest mode (hole vs. mound), timing of egg-laying, female minimum reproductive size, clutch size, female nest defence behavior, and female parental care. Besides regional comparisons, this chapter focuses on the largest nesting population of C. acutus located in southeastern Cuba, where the species still occurs at its natural population numbers. In Chapter II, I use molecular tools to elucidate the mating system of the Orinoco crocodile in a reintroduced population in the Llanos of Venezuela. Analyzing 17 polymorphic microsatellite loci from 20 clutches I found multiple paternity in C. intermedius, with half of the clutches fathered by two or three males. Sixteen mothers and 14 fathers were inferred by reconstruction of multilocus parental genotypes. Results showed skewed paternal contributions to multiple-sired clutches in four of the clutches (40%), leading to an overall unequal contribution of offspring among fathers with six of the 14 inferred males fathering 90% of the total offspring, and three of those six males fathering more than 70% of the total offspring. Results of this chapter provide the first evidence of multiple paternity occurring in the Orinoco crocodile and confirm the success of reintroduction efforts of this critically endangered species in Venezuela. In Chapter III, I apply generalized linear mixed models to infer the effect of tropical cyclones and environmental variability on the nesting success of C. acutus in the largest nesting population of the species in southeastern Cuba for a period of 21 years. Results of this chapter report the highest-density nesting for the species documented to date, and one of the highest densities of nesting in relation to other crocodilian species, with an average of 164 nests per year and a density of 17 nests per hectare. Two of the five analyzed nesting sites had consistently higher nests and higher nesting success for the whole 21-year period. Much of the temporal variation in nesting success could be explained by the occurrence of tropical cyclones. I found that occurrence of tropical cyclones within a nesting season negatively affected nesting success, whereas the occurrence of tropical cyclones one or two years before the nesting season positively affected nesting success. Additionally, results of this chapter suggest that higher ambient temperature negatively affected nesting success. Higher-intensity tropical cyclones are expected to strike the coasts of Cuba due to climate change, potentially devastating C. acutus nests if they occur during the nesting season. As the recruitment of C. acutus populations in Cuba heavily rely on nesting success, we propose incorporating information on crocodilian’s nesting success and density, as well as the impact of tropical cyclones on the latter, as key components of coastal resilience when designing plans for coastal adaptation in the context of climate change. In the last chapter, I employed data on mitochondrial DNA (mtDNA) control region and 12 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus between and among localities in South America, North America, Central America and the Greater Antilles. All analyses for both mtDNA and nuclear markers show evidence of strong population genetic structure in the American crocodile, with unique populations in each of the sampling localities. My research results reinforce previous findings showing the greatest degree of genetic differentiation between the continental C. acutus and the Greater Antillean C. acutus. Three new haplotypes unique to Venezuela were reported. These were considerably less distant from Central and North American haplotypes than Greater Antillean haplotypes. Overall evidence of this chapter suggests that Cuban and Jamaican C. acutus share a mtDNA haplotype but currently represent at least two different genetic populations when using nuclear, faster evolving, microsatellite markers. Findings of this chapter offer the first evidence of genetic differentiation among the populations of Greater Antillean C. acutus, the first ever reported haplotypes for the species in Venezuela, and provide important information for the regional planning and in-situ conservation of the species. In conclusion, research findings of my dissertation are the product of combining ecological data collected in the field, genetic data generated in the lab, and the use of a suite of classic and inference-based methodological approaches to gain a better understanding of the behavior and evolution of crocodilians. The dissertation presents the first genetic research on C. intermedius, shows the importance of coastal mangrove conservation for the persistence of C. acutus in Cuba, and depicts phylogeographic linkages among distinct C. acutus populations across the Americas and Greater Antilles. The outcomes of this research provide science-based information to influence decision-making processes for the conservation of threatened crocodilians and their habitats across the study areas.

O gênero Partamona compreende 33 espécies, distribuídas do sul do México ao sul do Brasil. O gênero tem sido amplamente estudado em diferentes níveis: citogenético, etológico e morfológico. O presente trabalho teve como objetivo contribuir com dados moleculares para o conhecimento do grupo, realizando estudos populacionais por meio da caracterização do DNA mitocondrial por PCR+RFLP e da análise de regiões de microssatélites do DNA genômico de duas espécies: P. mulata de distribuição restrita ao sul de Mato Grosso e norte do Mato Grosso do Sul, e P. helleri de distribuição mais ampla, do sul da Bahia até Santa Catarina. Foram detectados apenas dois haplótipos em P. mulata, os quais diferiram entre si por apenas um sítio de restrição. As análises estatísticas demonstraram não haver estruturação entre as populações sugerindo que esta espécie possa ter passado por recente afunilamento populacional. Em P. helleri foram observados dez haplótipos sendo alguns exclusivos e outros compartilhados. Análises estatísticas apontaram alta estruturação entre as populações e a distribuição filogeográfica observada sugere um possível isolamento por fragmentação da Mata Atlântica durante o Pleistoceno. A análise dos locos microssatélites mostrou baixa variabilidade genética em ambas espécies e discreta estruturação entre as populações, não relacionada com a distribuição geográfica das mesmas. Isto pode ser conseqüência de migração de machos entre populações visto que as rainhas são filopátricas ou, fragmentação dos habitats pela rápida degradação do cerrado e da Mata Atlântica, ou por alelos nulos causados pelo uso de primers heteroespecíficos. A análise de parentesco entre abelhas de um mesmo ninho apontou a existência de apenas uma patrilínea em P. mulata sugerindo monoandria para esta espécie. Foram encontradas duas patrilíneas em algumas colônias de P. helleri, o que pode ser resultante de fecundação por mais de um macho ou substituição recente da rainha. A caracterização parcial do DNAmt de duas espécies de Partamona poderá contribuir em estudos filogenéticos tanto do gênero quanto de outras espécies de Meliponini. A análise populacional mostrou o status da variabilidade genética das espécies, suas possíveis histórias evolutivas e a possível relação desta com degradação dos ambientes onde estas estão distribuídas. / The Partamona genus comprises 33 species distributed from south Mexico to south Brazil. This genus has been studied at different levels: cytogenetical, ethological and morphological. This work aimed at to contribute with molecular data for the knowledge about the group performing a population study employing the PCR+RFLP of mtDNA, and analysis of microsatellite loci from nuclear DNA of two species, P. mulata which is distributed in south Mato Grosso and north Mato Grosso do Sul, and P. helleri which geographic distribution is wider, from Santa Catarina to southern Bahia. It was detected two haplotypes in 58 colonies of P. mulata, each one differing by one single restriction site. The statistical analyses indicated no differentiation among populations suggesting that the species could have passed through a recent populational bottleneck. It was observed ten haplotypes in 47 colonies of P. helleri, some exclusive and others shared among populations. Statistical analysis pointed high population differentiation and the observed phylogeography distribution suggested a possible recent isolation probably by Atlantic Forest fragmentation during the Pleistocene. The microsatellite analysis showed low genetic variability in both species and discrete population structuring, not related to the geographic distribution. This might be consequence of migration of males, since the queens are highly phylopatric, or habitat fragmentation by degradation of savanna and Atlantic forest areas, or null alleles caused by the use of heterospecific primers. The relatedness investigation revealed only one patriline in nest mates of P. mulata that suggests monoandry for this species. It was found two patrilines in P. helleri that can be resulted from more than one mating or recent queen replacement. The partial characterization of the mtDNA of two Partamona species can contribute to further phylogenetic studies among bees of this genus or among other Meliponini species. The populational analysis showed the genetic variability status of the species, their putative evolutionary histories and the possible relation between the results and the environmental degradation in their distribution areas.

Much of modern population genetics revolves around neutral genetic differences among individuals, populations, and species. In this dissertation, I study how sex-specific life history traits affects neutral diversity levels within populations (polymorphism) and between species (divergence) on autosomes and sex chromosomes. In chapter 1, I consider the effects of sex specific life histories, and particularly generation times, on substitution rates along the great ape phylogeny. Using a model that approximates features of the mutational process in most mammals, and fitting the model on data from pedigree-studies in humans, I predict the effects of life history traits on specific great ape lineages. As I show, my model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among great ape lineages. The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant apes, given sex-specific life histories. In so doing, it largely bridges the gap reported traditional fossil-based estimates of mutation rates, and recent pedigree-based estimates. In chapter 2, I consider the effects of sex- and age- dependent mortalities, fecundities, reproductive variances and mutation rates on polymorphism levels in humans. Using a coalescence framework, I provide closed formulas for the expected polymorphism rate, accounting for life history effects. These formulas generalize and simplify previous models. Applying the model to humans, my results suggest that the effects of life history – and of sex differences in generation times in particular – attenuate how changes in historical population sizes affect X to autosome polymorphism ratios. Applying these results to observations across human populations, I find that life history effects and demographic histories can largely explain the reduction in X to autosome polymorphism ratios outside Africa. More generally, my work elucidates the major role of sex-specific life history traits – and male and female generation times in particular – in shaping patterns of neutral genetic diversity within and between species.

The effect of human activity on the natural world is increasingly shaping the evolution of species. The capacity of evolution to occur in individuals of a species, via natural selection acting on the genotypes of local populations through successive generations, is known as local adaptation. In southwest England, historical mining activity has resulted in a patchwork of highly metal-contaminated rivers across the region. Where the ecological diversity in many of these rivers has been decimated, metal-tolerant brown trout (Salmo trutta L.) populations seem to thrive. What are the mechanisms underlying this apparent metal-tolerance? And can it be attributed to processes of local adaptation? This thesis takes a multi-faceted approach in assessing this, by exploring the patterns and processes involved in metal-tolerance in brown trout populations in southwest England. A series of investigations were undertaken, including the use of neutral genetic markers (microsatellites), reduced representation genome sequencing (RAD-seq), common-garden exposure experiments, and genome-wide analysis of hepatic gene expression (RNA-seq). The microsatellite analysis illustrated that metal-tolerant trout have a different genetic architecture compared to fish in clean rivers and, using Bayesian analysis, these demographic differences were correlated with key periods of mining history. We then developed an approach to facilitate robust screening of genome-wide polymorphic loci through a method of parameter optimisation for RAD-seq. This approach formed the basis for identifying loci for investigating the genomic processes of local adaptation in metal-tolerant trout. We present genome-wide (RAD-seq) data highly indicative that neighbouring trout populations, differently impacted by unique ‘cocktails’ of metal pollutants have evolved both parallel and convergent mechanisms of metal tolerance. Through a common garden experiment, exposing metal-tolerant and metal-naïve fish to a mixture of metals, we were able to hone in on the physiological mechanisms underlying metal-tolerance. Finally, through RNA-seq, we observed that metal-tolerant fish showed little to no changes in hepatic gene expression when exposed to metals, pointing to innate mechanisms of metal handling. Together, the marriage of these various investigations showcases the remarkable ability of local adaptation in conferring metal-tolerance to brown trout populations in southwest England, and, importantly, the resilience of species’ in the face of human-altered environments.

Pearl oysters of the genus Pinctada include some economically important species. The taxonomy of some of the species is problematic. Phylogenetic relationship of the species in the genus is also poorly studied. In the present study, phylogenetic relationships of P. chemnitzi, P. fucata, P. margaritifera, P. maxima, P. nigra, P. radiata (from China), P. fucata martensii (from Japan), P. albina and P. imbricata (from Australia) were studied with Pteria penguin as an outgroup, and genetic variation of Chinese P. fucata, Japanese P. fucata martensii and Australian P. imbricata populations were investigated (1) to address the taxonomic confusion and phylogeny of pearl oysters, (2) to understand the genetic connections between the Chinese P. fucata, Japanese P. fucata martensii and Australian P. imbricata in west Pacific and (3) to provide information for the genetic improvement program initiated in China. / Since P. fucata, P. fucata martensii and P. imbricata are synonymous, to study the genetic differentiation and genetic variation of such widely distributed populations is helpful in understanding their genetic connections. For this purpose, five populations, three from China (Daya Bay, Sanya Bay and Beibu Bay), one from Japan (Mie Prefecture) and one from Australia (Port Stephens) were studied using AFLP technique. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise GST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese. Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and GST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow. / The above three wild Chinese populations in southern China were compared with the three adjacent cultured populations using AFLP markers. Three pairs of primers generated 184 loci among 179 individuals in populations from Beibu Bay, Daya Bay and Sanya Bay. A high level of genetic diversity, ranging from 0.363 in a wild population in Sanya Bay to 0.388 in a wild population in Beibu Bay, was observed within both wild and cultured populations, indicating an absence of strong bottleneck effects in the history of cultured P. fucata populations. Yet cultured populations in Sanya Bay and Beibu Bay had more fixed loci than the corresponding wild populations. Genetic differentiation in most pairwise comparisons of populations was significant. AMOVA indicated that genetic variation among populations were very low (1.77%) though significant, while more than 98% variation resided among individuals within population. These findings provide no evidence to show that hatchery practice of pearl oyster in China to date has significantly affected the genetic diversity of the cultured populations, and suggest that all populations are competent for selection. Yet the significant genetic differentiation among populations implies that any translocation of individuals for genetic improvement program should be managed with caution for the preservation of genetic diversity in natural populations. / The internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were compared among the above nine taxa, based on sequences determined by the present study and those available from Genl3ank. The phylogenetic analysis indicates that the pearl oysters studied constitute three clades: clade I with the small oysters P. fucata, P. fucata martensii and P. imbricata, clade II with P. albina, P. nigra, P. chemnitzi and P. radiata, and clade III and clade III with the big pearl oysters P. margaritifera and P. maxima forming the basal clade. Clade II is made up two subclades: clade IIA consisting of P. albina and P. nigra and clade IIB consisting of P. chemnitzi and P. radiata. The topology of the phylogenetic tree and substitution pattern of ITS sequences suggest that P. margaritifera and P. maxima are primitive species and P. chemnitzi is a recent species. The genetic divergences between clades ranged from 28% to 76.5%, and between subclades, 8.7-10.2%. In clade I, the interspecific genetic divergences ranged from 0.6% to 1.4%, and overlapped with interspecific divergences (0.6-1.1%), indicating that P. fucata, P. fucata martensii and P. imbricata may be conspecific. Based on amplified fragment length polymorphism (AFLP) markers and ITS sequences from more individuals, analyses of the populations of these three taxa also support the conclusion that Chinese P. fucata, Japanese P. fucata martensii and Australian P. imbricata are the same species, with P. fucata being the correct name. The genetic divergence between P. albina and P. nigra was also very low (1.2%), suggesting that they may represent two subspecies that can only be distinguished by shell color. The genetic divergences between P. maxima and P. margaritifera, and between clade IIA and clade IIB ranged from 8.3% to 10.2%, suggesting that they are closely related, respectively. The ITS1 sequence of P. radiata from GenBank is almost identical to that of P. chemnitzi determined in the present study, suggesting that the specimen used for the P. radiata sequence was possibly misidentified. / Yu Dahui. / "August 2005." / Adviser: Ka Hou Chu. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6125. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 100-124). / 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, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Tsoi Kwok Ho. / "September 2006." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (p. 139-169). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via 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

Background: There are approximately 12 million statin users in the United Kingdom. Reports of statin intolerance occurs between 7 and 29% of users, manifesting as muscle ache, fatigue or more seriously, muscle breakdown leading to myopathy. Creatine phosphokinase (CK) levels are used as a biomarker of statin-induced muscle damage. Non-adherence or discontinuation of therapy is a common result of intolerance and can result in negative cardiovascular disease-related outcomes. Aim: This thesis attempts to identify trends in record-linked medical data in a Scottish Caucasian cohort (GoDARTS) that best represent statin intolerance in order to study associated genetic factors. Methods: Prescribing trends such as switching or discontinuation of statin therapy were examined, and thresholds created to select true cases of intolerance. Information on CK levels was gathered from medical records and appropriate test results were utilized. Genotypic data was gathered for the variants and genetic regions of interest using a variety of methods including chip-based genotyping followed by imputation, TAQMAN genotyping, and exome sequencing. Subsequently hypothesis-based association analyses were conducted, including linear and logistic regressions, followed by meta-analyses, regional GWAS followed by a regional meta –analysis. Results: The phenotypes of statin intolerance were validated both internally and externally. Previously reported missense variants in LILRB5 (Asp247Gly) and CKM (Glu83Gly) were replicated and shown to be associated with CK levels irrespective of statin usage in the GoDARTS cohort and the clinical trial setting (JUPITER). Further, the CKM variant was also associated with inducibility of CK at times of tissue injury. The Asp247 genotype in LILRB5 was associated with increased risk of statin intolerance, and was replicated in associations with non-compliance to statin therapy and the development of myalgia in the JUPITER trial. The association with myalgia showed a stratified effect based on therapy (statin or placebo), with those on placebo showing the genotype effect. Further, the variant was also associated with increased risk of statin-induced myositis, cases of which had been clinically adjudicated and exome sequenced for the PREDICTION-ADR consortium. Further exploration of the LILR gene region showed an association with variants in LILRB2 (His20Arg and Val235Met) which were in strong LD with each other but were not in linkage with the variant in LILRB5. Stratified analysis revealed that the risk for carriers of the LILRB2 variants was increased depending on the genotype carried at the LILRB5 variant. Conclusions: This study characterises novel genetic factors associated with statin intolerance impacting adherence. The findings point to the immunomodulatory effects of statins. The results suggest that true statin-induced myalgia and non-specific myalgia are distinct, with a possible role for the immune system in their development. The findings encourage further investigation into the immune-physiology of statin-induced muscle damage and identifies genetically susceptible groups who are more likely to be statin intolerant.