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Fast-evolving RNA viruses are a leading cause of morbidity and mortality among human and animal populations, contributing significantly to both global health and economic burden. The advent and revolution of high-throughput sequencing has empowered phylogenetic analyses with increasing amounts of temporally and spatially sampled viral data. Moreover, the parallel advancement in molecular evolution and phylogenetic methods has provided investigators with a unique opportunity to gain detailed insight into the evolutionary and epidemiological dynamics of emerging viral pathogens. Using state-of-the-art statistical approaches, this thesis addresses some of the important but controversial questions in viral emergence. Chapter 2 introduces a new framework to quantify and investigate reassortment events in influenza A viruses. By developing a computationally efficient algorithm to calculate the largest common subtree for a pair of tree sets, which are estimated from diffe rent parts of the genome for the same taxa set, the level of phylogenetic incongruency due to reassortment can be appropriately ascertained. Chapters 3, 4 and 5 investigate the evolutionary origins of three diff erent viruses: the novel emergence and cross-species transmission of SARSCoV, the genesis and dissemination of the unique HCV circulating recombinant form, and the ancient divergence of all influenza viruses, respectively. Moreover, Chapter 4 presents an improved statistical framework, which provides more precise evolutionary estimates, by utilizing the hierarchical bayes approach to investigate recombination events in emerging RNA viruses. The last empirical study, presented in Chapter 6, applies the recently developed Bayesian phylogeography models to a large viral sequence dataset sampled from southern Viet Nam to examine the fine-scale spatiotemporal dynamics of endemic dengue in Southeast Asia. The work presented here reflects both the advancements made in sequencing technology and statistical phylogenetics, along with some of the challenges that remain in studying the emergence of fast-evolving RNA viruses. This thesis proposes new and improved solutions to these evolutionary problems, such as incorporating non-vertical evolution (i.e. homologous recombination and reassortment) into the phylodynamic framework, with the aim of facilitating future investigations of emerging viral diseases.

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Purpose: The purpose of this study was to investigate the relationship between anthropometric measurements, proximal and distal lower extremity muscle performance, core muscle endurance, lower extremity flexibility, and neuromuscular control with the incidence of injury in recreational runners over one season. Also, when a relationship was established, we sought to evaluate the predictive validity for any of the variables being investigated for risk of injury in this population. Study Design: Prospective cohort Methods: Anthropometric measurements, proximal and distal isometric lower extremity muscle performance, isometric core muscle endurance, lower extremity flexibility and neuromuscular control were measured in 75 recreational runners prior to the start of a graded marathon training program. Incidence of injury was tracked over the course of 18 weeks, May 2014 – October 2014. Data was analyzed comparing the differences between injured and non-injured groups. Results: There were 33 repetitive stress injuries yielding a gross injury rate of 46% (male n=13, female n=20). Of all the variables analyzed, 5 variables emerged as possible a predictors including age, dominant limb rear foot posture, non dominant limb ankle DF ROM (extended), limb difference of Y balance scale composite scores and limb difference in the 6 M hop test. These variables were entered into a binary logistic regression analysis. Results of the regression indicated only the composite Y balance score difference variable as yielding a significant contribution (p = 0.01), with and predictive validity, (OR = 1.46, 95% CI =1.127 – 1.892). The model predicted 69.2% of the injuries with a specificity of 82% and sensitivity of 54.5%. A cutoff point of 3.6% was determined using a receiver operating characteristic curve. Runners were 3 times more likely to get injured with an asymmetry ≥ 3.6%. Conclusions: An asymmetry of lower extremity neuromuscular control ≥ 3.6% measured by the Y balance scale has been identified as a potential risk factor for injury in recreational runners. Clinical Relevance: This test can be performed as part of a pre-training screening or physical and may be helpful in identifying recreational runners at risk for injury.

Lead is a highly toxic metal that has been used by humans for over 2000 years. Over this time it has become increasingly apparent that despite its usefulness, lead is one of the most highly toxic substances known to man. Current research into lead exposure of humans focuses on low-level chronic exposure and its effects on learning and behaviour. However, investigations into lead exposure of wildlife are still focussed on mortalities, particularly of waterfowl and raptors, with little known about low-level exposures or the effects on other species. This study examines the exposure of free-ranging kea (Nestor notabilis) from the Aoraki/ Mt Cook village and national park, takahe (Porphyrio hochstetteri) from Tiritiri Matangi, Kapiti and Mana Islands, and the lead associated syndrome of clenched-claw paralysis and leg paresis in harriers (Circus approximans) in New Zealand. Thirty-eight kea had detectable blood lead with concentrations ranging from 0.028 mg/L to 3.43 mg/L (mean = 0.428 mg/L ± 0.581). Analysis of tissue samples found that seven of 15 birds died with elevated tissue lead. Lead exposure may be an important contributing factor in kea mortality. As a result of these findings, lead abatement in areas frequented by kea is being considered. Eighteen of 45 takahe had detectable blood lead concentrations ranging from 0.015 mg/L to 0.148 mg/L (mean = 0.028 mg/L ± 0.042). Analysis of tissue samples from offshore island and Murchison Mountains birds found that all had detectable lead. Despite levels of lead exposure in the population being low and unlikely to result in overt clinical signs, it is widespread and there may be significant exposure of birds living around old buildings. An investigation into the clinical signs, pathology and response to treatment of clenched-claw paralysis and leg paresis in wild harriers was carried out. Harriers with clenched feet had significantly higher blood lead concentrations than those without. In conclusion, lead is a major factor in the expression of this clinical syndrome but other factors not yet identified are playing a role. This study demonstrates that lead is widespread in the New Zealand environment exposing a diverse range of avifauna, and has made some progress towards exploring some of its effects on health and survival.