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The overall aim of this study was to employ a biomolecular technique - ancient DNA (aDNA) - to study two ancient diseases that were endemic in Europe (and therefore Britain) during the medieval period: tuberculosis and leprosy. In humans, the diseases are caused by M. tuberculosis and M. leprae, respectively - both of which are members of the M. tuberculosis complex (MTBC). Skeletal manifestations of both diseases may develop in bone remains, which can be recognized using osteological analysis. In some cases, however, the skeletal changes are ambiguous. Ancient DNA methods are used for case confirmation and to answer historical questions such as the spread, origin and evolution of disease. The first objective of this thesis was to determine whether the MTBC aDNA detection frequency is high enough to plan a larger study to test hypotheses such as possible strain differences in urban and rural areas, as it has been suggested that urbanization assists the spread of tuberculosis, enhancing its virulence. To meet this objective, 60 skeletal remains from 16 different locations in Yorkshire, England were studied. All samples were screened for MTBC aDNA presence and 8 samples were selected for next-generation sequencing (NGS). In the PCR assay screening, only 1 sample produced a positive MTBC amplification. However, when subjected to NGS, this sample together with the other 7 samples did not produce enough sequence reads to allow genome comparisons. An attempt to compare metagenomic content between urban and rural sites was also performed. There was no specific difference in metagenomic content between urban and rural samples. Based on the PCR analysis, the sample St Andrew Fishergate 6, dated to the early 14th century AD, showed evidence of possible tuberculosis infection. NGS analysis further revealed a possible M. tuberculosis and M. leprae mixed infection, albeit with insufficient read coverage to determine genome sequence polymorphism. The second objective was to use NGS to determine the genotype of the M. leprae strains present in skeletons from two mediaeval sites, at Chichester and Raund Furnells, both in England. This study served as a continuation for the previous confirmation by PCR of leprosy in these skeletons. The samples were further subjected to whole M. leprae genome target enrichment before subsequent high-throughput sequencing. For all 3 historical M. leprae isolates, at least 70% genome sequence coverage was obtained, with a mean read depth of 4-10x. The near-complete genome sequences that were obtained allowed subtype identification for each of the ancient M. leprae isolates. Two mediaeval samples from Chichester belonged to the 3I subtype, which is typical of ancient Northern European and contemporary North American isolates. Meanwhile, an M. leprae isolate from Raunds was identified as belonging to the 3K subtype - the first example of this subtype identified in Britain. Transmission of the M. leprae 3K subtype to Britain is suggested to have been associated with the travels of crusaders and pilgrims to the Holy Land during the mediaeval period. The overall conclusion of the work is that although M. leprae aDNA is well preserved in skeletal remains showing osteological signs of leprosy, the same is not true for MTBC preservation in skeletons showing indications of tuberculosis. To test hypotheses such as the effect of urbanisation on tuberculosis, a high frequency of MTBC detection must be achieved, but this is complicated by the very nature of ancient DNA itself - highly fragmented, low endogenous DNA copy, presence of environmental contaminants - and by the possibility of low bacterial load in skeletons at the time of death. In projects where the testing of a high number of samples is required, more stringent selection criteria must be imposed to minimize the impact of destructive analysis.

There are many examples worldwide of cultural conflict between visitors and hosts at popular tourist destinations (Robinson & Boniface, 1999). This study investigated the culturally inappropriate behaviour of climbing Uluru (Ayers Rock) in Central Australia. In an effort to better understand the effects of culture and personal schemata on visitor behaviour, the study examined the potential for a number of antecedent variables to predict climbing behaviour. Variables representing the measurable elements of subjective culture (Betancourt & Lopez, 1997) were assessed to have the most relevance in the context of the study, and became the focus of investigations. They included visitor attitudes, beliefs, values and social norms. The Theory of Reasoned Action (TRA) (Fishbein & Ajzen, 1975) was adopted as a methodological framework to guide analysis. The study sample was selected systematically and comprised visitors to Uluiy - Kata Tjuta National Park. Data was collected in two stages. Initially, an elicitation survey was conducted to establish the behavioural outcome and social influence beliefs that visitors associated with the action of climbing Uluru. The resulting belief scales were incorporated into a main study survey. This second stage included self-administered pre-visit and post-visit questionnaires that were completed by 433 respondents. The research instruments measured climbing behaviour, climbing intention and a range of variables assumed to be determinants of climbing behaviour. These included visitor attitude towards the climb, perception of social pressure to climb (subjective norm), climbing outcome beliefs, beliefs about the influence of salient social referents, values visitors' associated with their trip, prior behaviour and prior knowledge. Sociodemographic characteristics of the sample were also measured. The compiled data was screened and statistically analysed using a number of procedures within the SPSS data analysis program including factor, regression, cluster and discriminant analyses. All of the hypothesised relationships proposed in the TRA framework were found to be significant. Visitors' climbing intention predicted actual climbing behaviour and both attitude and subjective norm contributed to the prediction of intention. Composite climbing and social influence beliefs also respectively predicted attitude and subjective norm, thereby confirming the salience of these particular beliefs in relation to climbing Ulupi. All of the visitor beliefs were summarised intO meaningfhl categories using factor analysis. Three climbing belief dimensions ('benefit beliefs,' 'fear beliefs,' 'impact beliefs') and two social influence belief dimensions ('external referents,' 'credible referents') emerged from the analysis and these factors were found to vary for different visitor segments. The greatest contrasts were evident between groups that climbed Uluru and those that did not climb. Relative to non-climbers, tourists who made the climb approached it with a positive attitude and believed that the activity would produce beneficial outcomes, would not be culturally or physically detrimental, and that people they associated with the climb, and in particular representatives of the tourism industry, were supportive of the behaviour. When composite belief dimensions were incorporated into a modified Theory of Reasoned Action model, the predictive capacity of the model was enhanced. Also, the climbing fear component was found to make no contribution to the prediction of overall climbing attitude. When visitor trip values were also added to the extended TRA model as a fourth level of predictor variables, they were found to collectively predict visitor attitudes about the benefits of climbing Uluru and social influence to climb. The value of challenge in a visitor's trip was the dominant predictor in all instances. The study concluded that visitors to Uluru - Kata Tjuta National Park were heterogeneous with regard to the beliefs they held about climbing Uluru and that when all beliefs were considered together, visitor sub-groups could be meaningfblly differentiated according to their comprehensive belief profiles about the climb. Tourists were categorised into a three-level typology representing a continuum from 'consonant' through 'self-determined' to 'dissonant' visitors. The 'consonant' segment was the largest group and members were in a state of belief affirmation about climbing Uluru. They mostly climbed Ulupi and comprised younger males seeking challenge experiences. A number of implications for theory and practice were discussed. These focused on better understanding visitors at cultural tourism sites and more appropriately managing their behaviours to achieve compatible outcomes for hosts and guests. Recommendations for further research were also suggested.

One of the most debated topics in forensic anthropology and archaeology is the estimation of the time elapsed since death and the biological age of the body from skeletonised bodies, or fragments of them. Usually, standard analytical and morphological approaches tend to suffer from weaknesses, highly relying on the expertise of the forensic scientists and on their subjective interpretation of the macroscopic and microscopic bone features to draw conclusions. In order to improve the accuracy and the objectivity of these estimations, biomolecular approaches seem to be the most promising way to address the problem. Between all the biomolecules available to conduct this type of studies, proteins are the ones able to survive longest in biological tissues through the decomposition process. Furthermore, they also convey several modifications which can be related with ageing phenomena both in vivo and post-mortem, with protein deamidation being the most commonly occurring in forensic and in archaeological contexts. All these features make proteins an interesting target for new applications in forensic sciences, with the potential to become new biomarkers for biological and geological age estimations. The research presented here applied proteomic methods to experimental forensic and archaeological bones and teeth to investigate how the decomposition process and the environmental conditions impact the proteins degradation and modification, and evaluated also the effects that the decomposition of a body may have on the surrounding burial environment using a metagenomic approach to evaluate changes within the soil microbial community. Results showed that proteomic analyses on bones can provide interesting information about the ageing phenomena in forensic and archaeological scenarios; in particular, the new potential biomarkers proposed here may become in future a molecular support to the estimation of post-mortem interval and age-at-death, improving the ability of scientists to find the truth behind complicated forensic contexts.

Archaeologically excavated historic cemeteries are a unique and largely untapped dataset for answering questions about past populations using empirical methods. One such question centers around the assumptions that infant mortality was high in societies without modern fertility control and that infant remains are more likely to be poorly preserved and recovered from archaeological contexts than adult bones. To assess this, excavated osteological populations of European descent from historic cemeteries (1600-1950 AD) were studied for their age composition as compared to historical records and Model life tables. These datasets were then considered in their taphonomic contexts to determine which factors most affect preservation and recovery. The resulting calculation of the mortality and preservation of each population were compared statistically with traditional high mortality estimates, and appliedexperimentally to cemetery populations with an unknown number of infants and children. Osteologically derived infant mortality was found to range most commonly from 10-35%, with a 10-15% loss between burial and recovery. These figures were found to be useful in assessing early life mortality in more ancient populations. The most unexpected result was the finding that loss of data, and the resulting inability to study osteological questions with excavated historic cemeteries in general, correlated with substandard archaeological methods in some historic cemetery excavations rather than natural forces. A revival of basic, traditional archaeological methodology is necessary to maintain professional ethics; the modernization of cultural resource law in America is needed to facilitate this.

It is acknowledged that some microbes have interrupted distributions, yet these distributions have rarely been correlated with environmental variables. The wild biogeography of the fermenting yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus are explored in this study, considering multiple environmental variables as potential effectors of each species' geographical distributions. I demonstrate that summer temperatures predict maximum species distribution limits for both S. paradoxus and S. cerevisiae on oak bark, and that S. paradoxus is more likely to be isolated from larger, older trees. Modelling these data predicts a generally denser southern European population of S. paradoxus, with S. cerevisiae being scarce on oak bark throughout Europe. It was not possible to recover ancient Saccharomyces DNA sequences from samples of sub-fossilized oaks, from Greco-Roman and North African amphora residues, or from North African 6th-14th Century pottery residues, which may be a consequence of the low concentration of these species in comparable modern environmental samples. Even from air dried breads and recent wines, Saccharomyces aDNA was not recovered as part of this study, although ancient DNA sequences from plants and other yeasts were identified in other samples via the same methods. Any future recovery of ancient Saccharomyces sequences may therefore be challenging. Novel plant sequences possibly belonging to the Musaceae family and Pinus genus were identified from 6th-14th century AD North African pottery; as well as a Vicia-like DNA sequence from a 13th-12th century BC North African amphora.

Tuberculosis (TB) has killed millions of people throughout history and still isone of the leading causes of death. Since the early 1990s, ancient DNA(aDNA) research has made considerable contributions to the study of thisinfectious disease in the past. While early studies used polymerase chainreactions (PCRs) solely to identify the TB-causing organisms, namely theMycobacterium tuberculosis complex (MTBC), later approaches extended thefocus to assign the actual disease-causing species or strains of the MTBCbut were either directed at single or few individuals or only provided few data. This research project has screened a large set of European skeletaland dental samples from individuals of the 1st–19th centuries AD for IS6110,an insertion sequence believed to be specific to the MTBC, and has identifieda number of individuals that may indeed have suffered from TB. Reports ofIS6110-like elements in other mycobacteria, however, challenge thesuitability of IS6110 for detecting MTBC. Two sequences similar but notidentical to IS6110 were revealed from several of the samples analysed,supporting the proposal that IS6110 should not serve as the sole target foridentifying MTBC from archaeological material. It cannot be establishedwhere these sequences derive from, but application of a MycobacteriumspecificPCR and targeting of genomic regions of the MTBC that containsingle nucleotide polymorphism (SNPs) indicate that at least some of thesamples contain a range of unknown, most likely environmental, bacterialand/or mycobacterial species. Yet, screening for IS6110 together with thedetection of large sequence polymorphisms (LSPs) and SNPs in othergenomic regions has identified eight individuals to unambiguously containMycobacterium tuberculosis aDNA. Apart from one individual which wasrecovered from Northern France, these skeletons derived from Britisharchaeological excavation sites. The SNP and LSP results enabled theallocation of infecting MTBC strains into various classification systemsreported in clinical literature and revealed that M. tuberculosis strains variedthroughout different time periods, thereby mainly confirming evolutionarypathways suggested in previous studies. Additionally, it was found thatdistinct strains co-existed temporally, and maybe even spatially, in Britainand that at least one individual harboured two different MTBC strains,suggesting a mixed infection. Application of next generation sequencingenabled one of the 19th century strains from Britain to be characterised ineven more detail, revealing closest similarity to a M. tuberculosis strainisolated at the beginning of the 20th century in North America.

In order to gain a greater understanding of the genetic makeup of the Maltese population, mitochondrial DNA HVR1 and HVR2, and Y-chromosomal and autosomal STRs were amplified in a representative sample of the Maltese population. The results showed that the Maltese have close genetic ties with Sicily and mainland Italy both from a matrilineal and a patrilineal perspective, whilst no conclusive evidence was found for a Phoenician link between the Maltese and the Lebanese population. In order to try and gain an insight into the Maltese population throughout time, a study was conducted on three Maltese archaeological burial places dating from the Neolithic to the Roman period. The study extracted and amplified ancient DNA sequences from these three sites and compared the resulting mtDNA sequences with the modern Maltese population. The results showed that aDNA survives in the Maltese archaeological record, and that some haplotypes found during the Roman period in Malta are also found in the modern day population, whilst other haplotypes present in the archaeological samples are not visible in the modern Maltese population.

Maize (Zea mays ssp. mays), a crop of great importance worldwide, is characterised by its great adaptability and its extraordinary variability both at the molecular and the phenotypic level. Behind these remarkable features lies a complex evolutionary history. The main aim of this research is to contribute to a better understanding of it by answering questions about the origin, phylogenetic relationships, and initial dispersion of maize, using South America as a case study. To achieve this aim, archaeological specimens and primitive landraces were genotyped at 20 microsatellite loci. Sequences of Adh2-UM, a locus informative of the routes of initial dispersion of maize in South America, were also obtained. The data gathered were analysed using tree-building and network methods, and a Bayesian model-based clustering approach to infer population structure. Our results are consistent with a model of initial dispersion by which after its introduction, maize spread along the Andes and through eastern Bolivia and northwest Argentina towards the east of the continent to the area of Paraguay and southern Brazil, and gave rise to the maize distributed to the east of the Andean mountains. Analysis of population structure indicate that variation among the races analysed is more phenotypic than genetic, and that considerable amounts of gene flow has been occurring at a macro-regional level. We believe that cultural practices and cultural contacts played a fundamental role in making maize on these areas more genetically similar, while at the same time keeping maize phenotypically different. Further studies of ancient DNA, coupled with archaeological and ethnographical knowledge of cultural trajectories, have the huge potential of contributing to a better understanding of how and since when these macro-regional areas of gene flow have been in place.

Sainfoin (Onobrychis viciifolia), is a traditional forage legume whose agricultural use has been in constant decrease in Western Europe since the 1960's. However, growing evidence suggests that it may be of great interest in the context of sustainable agriculture, thanks to numerous beneficial properties (nutritional, environmental and anthelmintic). In the frame of a large project network, an extensive O. viciifolia (and other Onobrychis species) germplasm has been gathered and several accessions were grown in small plots on an experimental field at NIAB, Cambridge. Measurements of morphological and agronomical traits were performed on these plots. Cytological and molecular genetics studies were also carried on the germplasm.Accessions were found to be highly variable in their agronomical traits, with differences in productivity. It was observed that O. viciifolia was relatively resistant to diseases, but that persistence was the main difficulty to overcome. O. viciifolia accessions were also found to be variable in their morphological traits. Statistical analyses on both morphological and agronomical traits showed strong links with accessions' geographic origins. The most important trend observed is a general distinction between Western European accessions and accessions from the rest of the world.It was found that most O. viciifolia were tetraploids, suggesting that agricultural domestication led to polyploidy. Other Onobrychis species were found to be either diploid or tetraploid with varying basic chromosome numbers, which tends to confirm the assumption that an aneuploidy event occurred in Onobrychis genetic history.AFLP and SSR fingerprinting were attempted to investigate O. viciifolia genetic diversity. The potential of these techniques was shown, but the latest improvements needed to obtain solid data were not achieved during this study. Still, it was shown that molecular marker assisted breeding programmes can be elaborated for O. viciifolia.Phylogenetic analyses were performed through sequencing of different DNA regions. Substantial genetic diversity was observed among O. viciifolia accessions, with again a general distinction between Western European accessions and accessions from the rest of the world. A clarification of the Onobrychis genus is suggested, as it appeared that many species must be synonyms, and that many taxonomic sections are weakly supported.Overall, it appeared that O. viciifolia potential has probably not been fully exploited, and that there is an important potential for improvement in the gemplasm studied here. Due to its superiority in animal husbandry and agroecologic impact, O. viciifolia improvement can be suggested as a valuable alternative to extensively used forage legumes.