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In the Saccharomyces cerevisiae genome the regions adjacent to the 32 chromosome ends, the subtelomeres, are tethered at the nuclear periphery during vegetative / somatic growth and during sporulation / gametogenesis. This is in contrast to the rest of the genome, the interstitial regions, which are located throughout the nucleus. There is evidence that recombination between different subtelomeres is the exceptionally frequent, but that subtelomeres and interstitial regions do not recombine. These features of recombination involving subtelomeres may result from a structure that interacts with the subtelomeres, partitioning them from interstitial regions. Our aim was to characterise which part of the subtelomeres this recombination barrier interacts with. As a tool for estimating the rate and efficiency of recombination between different regions, a set of insertions into the S. cerevisiae genome was engineered. This set included 11 insertions at regular intervals along the terminal 10% of one chromosome arm, marking an interstitial region and the subtelomere. In addition, insertions were also made into a sample of other subtelomeres and interstitial regions. Both recombination during vegetative growth (mitotic recombination) and during sporulation (meiotic recombination) were assayed, between numerous combinations of these insertions. In agreement with previous studies, our results indicate that recombination between interstitial regions and subtelomeres is less efficient than recombination between different interstitial regions. Moreover, this is true of both mitotic and meiotic recombination. However, our efficiency data indicate this may result from tethering of subtelomeres at the nuclear periphery, rather than a partition in the nucleus. Tethering may suppress recombination between subtelomeres and most interstitial regions, simply by maintaining a large relative distance between these two regions. In contrast, the efficiency of mitotic and meiotic recombination between subtelomeres appear to be very different. Mitotic recombination between different subtelomeres appears to be exceptionally efficient, while meiotic recombination between different subtelomeres appears to be inefficient.

This thesis addresses gaps that exist in the theory and knowledge of ancient DNA (aDNA). Much of the underlying basis of the field has been neglected in the excitement that followed the first aDNA studies. Therefore the results of many studies have been based on untested assumptions about the nature of post mortem DNA damage, sample preservation, contamination, and the efficacy of sample decontamination techniques. The validity of such results is questionable if the assumptions prove false. Hydrolytic post mortem DNA damage may modify recovered aDNA sequences. This thesis reports new insights into the biochemical basis of, predisposition of certain sequences and nucleotide positions towards, and subsequent effects of, such damage. Parallels of post mortem damage with in vivo mutation also enable insights into DNA sequence evolution. The long-term survival of DNA, and contamination of samples with exogenous DNA are two related problems characteristic to aDNA. The survival of endogenous DNA within bone, teeth and hair samples, the susceptibility of such samples to contamination, and the efficacy of decontamination techniques used to remedy such problems are investigated. The results highlight serious flaws in using bone and teeth as a DNA source. In contrast, the results demonstrate that hair may present a valuable DNA source for future studies. Numerous studies have reported the retrieval of ancient pathogen DNA from human samples. Analyses of the DNA content within teeth extracted from putative victims of the 2^nd plague argue that such studies are at great risk from DNA degradation, and contamination arising due to environmental microorganisms. An extrapolation of these results using basic physical and chemical theory is used to evaluate the potential survival of aDNA in ancient Egyptian remains. This suggests that positive results from such samples are unlikely.