The endangered population of Amur tigers (Panthera tigris altaica) in the Russian Far East (RFE) faces an increasing risk of extinction due to infection with canine distemper virus (CDV). Short-lasting CDV infections are unlikely to be maintained in small populations of species with limited connectivity like tigers, where viruses fade out as susceptible hosts are depleted. Multi-host pathogens can persist in more abundant host species that can act as reservoirs of infection for threatened populations. This study combines assessments of host demography, serology and viral phylogeny to establish the relative contribution of domestic dogs and small bodied wild mesocarnivores to the maintenance of CDV, and as sources of infection for tigers. No antibodies were detected among tigers sampled prior to 2000 (n=19), but were measured in 35.7% of tigers in subsequent years (n=56), with at least five discrete transmission events occurring in one well-monitored population. Viral sequences from three tigers and one Far Eastern leopard (P. pardus orientalis) aligned within the Arctic-like clade of CDV, and shared recent common ancestry with viruses from 22 other wild carnivores from the region. Extensive spatial mixing of wild carnivore lineages suggested long chains of transmission consistent with a maintenance population. The exposure of tigers following 2000 coincides with increases in sable (Martes zibellina) numbers and hunting pressure, which could lead to greater pathogen prevalence and potential for spill over from a wild reservoir. The ratio of humans to dogs in rural areas in the RFE are among the lowest in the world (1.73), but the overall number of dogs has been stable during the period of increased CDV exposure in tigers. The only CDV sequence obtained from dogs shared high identity with Asia-4 clade viruses from dogs in Thailand, and was distantly related to wildlife sequences from the RFE. Serum antibodies were detected in dogs in all 26 communities where households were surveyed, but seroprevalence was higher in remote, less densely populated areas, suggesting possible transmission from wildlife. Although the maintenance of CDV in Russian dogs remains unconfirmed, the strong support for a wildlife reservoir limits options for managing the impact of CDV on tiger populations. The high turnover of large and often inaccessible populations of mesocarnivores combines with limitations in vaccine safety, efficacy and delivery, to render the control of CDV in a wildlife reservoir untenable. Managing the impact of CDV on Amur tigers must therefore focus on restoring the size and integrity of remaining tiger populations to withstand future outbreaks. The safety and efficacy of vaccine products for tigers should also be investigated, for use in low coverage vaccination strategies that could enhance the long-term persistence of tiger populations.

The discovery of DNA has been one of the biggest catalysts in genomic research. Sequencing has enabled us to access the wealth of information encoded in DNA and has provided the basis for ground-breaking achievements such as the first complete human genome sequence. Furthermore, it has tremendously advanced our understanding of life-threatening genetic disorders and bacterial and viral infections. With the recent advent of next generation sequencing (NGS) technologies, sequencing became accessible to the majority of researchers and made metagenomic sequencing widely available. However, to realise its true potential, sophisticated and tailor-made bioinformatic programs are essential to translate the collected data into meaningful information. My thesis explored the potential of resolving fine-scale variation in NGS data. The identification and correction of artificial fine-scale variation in the form of biases and errors is imperative in order to draw valid conclusions. Furthermore, resolving natural fine-scale variation in the form of single nucleotide polymorphisms (SNPs) and closely related species or strains is critical for the development of effective treatments and the characterisation of diseases. In recent years, Illumina has emerged as the global market leader in DNA sequencing. However, biases and errors associated with this high-throughput sequencing technology are still poorly understood which has precluded the development of effective noise removal algorithms. In addition, many programs were not designed for Illumina data or metagenomic sequencing. Therefore, a better understanding of the idiosyncrasies encountered in Illumina data is essential and programs must be tested and benchmarked on realistic and reliable in silico data sets to reveal not only their true capacities but also their limitations. I conducted the largest in vivo study of Illumina error profiles in combination with state-of-the-art library preparation methods to date. For the first time, a direct connection between experimental design factors and systematic errors was established, providing detailed insight into the nature of Illumina errors. Further, I tested various error removal techniques and developed a sophisticated Illumina amplicon noise removal algorithm, enabling researchers to choose optimal processing strategies for their particular data sets. In addition, I devised several simulation tools that accurately reflect artificial and natural fine-scale variation. This includes a flexible and efficient read simulation program which is the only program that can directly reflect the impact of experimental design factors. Furthermore, I developed a program simulating the evolution of a virus into a quasi-species. These programs formed the basis for two comprehensive benchmarking studies that revealed the capacities and limitations of viral haplotype reconstruction programs and taxonomic classification programs, respectively. My work furthers our knowledge of Illumina sequencing errors and will facilitate more accurate and effective analyses of sequencing data sets.

Interpretations of osteological remains from mainland Greece during the 1960-1980s led to the suggestion that the most virulent form of malaria, Plasmodium falciparum, was prevalent between the Mesolithic and Late Bronze Age (c. 8700 cal. BC-1100 cal. BC). Although disregarded over the past decade, the theory has regained support in recent years from osteological, epidemiological, environmental and DNA studies. However, the presence of this strain of malaria in prehistoric Greece remains controversial. This thesis evaluates 1) the palaeoclimatic conditions of the Aegean between the Mesolithic and Late Bronze Age and 2) the palaeoenvironmental conditions of three archaeological settlements, with the aim of ascertaining whether the climatic and environmental conditions were as conducive for P. falciparum and the mosquito vectors as the osteological evidence suggested. Equal consideration is given to the so-called ‘lesser strains’ of malaria, P. vivax and P. malariae, the significance of which is considered to have been underestimated in previous studies.