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<p>This dissertation discusses molecular analyses of dental and skeletal material from victims of the Black Death with the goal of both identifying and describing the evolutionary history of the causative agent of the pandemic. Through this work, <em>Yersinia pestis</em> DNA was successfully identified in skeletal material from a well-documented Black Death burial ground, the East Smithfield cemetery of London, England (1348 -1350). The thesis presents two major methodological advancements in the field of ancient pathogen research: 1) it describes a protocol to confirm the authenticity of ancient pathogen DNA, thus circumventing tenuous issues relating to modern contaminants, and 2) it demonstrates the applicability of DNA capture methods to isolate ancient pathogen DNA from its complex metagenomic background common to ancient DNA extracts. The dissertation is comprised of three publications. The first, submitted to the journal BMC Systems Biology, describes a computational software program for oligo design that has applications to PCR, and capture techniques such as primer extension capture (PEC) and array-based capture. The second manuscript, published in the Proceedings of the National Academy of Sciences, presents a novel capture technique for retrieval of the <em>pestis</em>-specific pPCP (9.6kb) plasmid which can be used as a simple screening tool for the presence of <em>Y. pestis</em> DNA in ancient remains, and describes a method for authenticating ancient pathogen DNA. The third paper, published in the journal Nature, presents a draft genome of <em>Yersinia pestis </em>isolated from the individuals of the East Smithfield collection, thus presenting the first ancient pathogen genome in published literature. Evolutionary changes as they relate to phylogenetic placement and the evolution of virulence are discussed within an anthropological framework.</p> / Doctor of Philosophy (PhD)

<p>This thesis uses stable isotopic analysis to identify diet, geographic origins and long-term residency in a sub-sample of the Smith’s Knoll skeletal collection, soldiers who died during the June 6^th 1813 Battle of Stoney Creek. The major objectives of this study have been to differentiate between two major modes of dietary consumption, one wheat-based, the other maize-based, in an attempt to decipher British colonial from American soldiers. These objectives were paired with stable oxygen and strontium isotopes, two isotopic elements presently used to identify migration and regional origins. Oxygen isotopic results from teeth suggest that, as children, 5 individuals may have originated in North America. Nine individuals have isotopic signatures indicative of both a North American or United Kingdom origins. The isotopic composition from bone collagen and phosphate suggest similar geographic origins, with diets composed of both wheat- and maize-based foods. Bone phosphate values indicate that 2 individuals possibly resided in North America. The remaining 20 individuals have bone values indicative of long-term residency in both geographic regions with a significant amount of dietary mixing. These results suggest that other military participants, soldiers from the King’s 8^th Regiment and Canadian militiamen, may also be represented in this study. Prior investigations have omitted this crucial information, focusing their historic research primarily on the British 49^th Regiment. The data presented in this thesis offers a broader geographic, pan-nationalistic perspective on the possible infantrymen and militiamen who fought during the battle, including select Canadian militiamen from the Niagara region and the King’s 8^th Regiment from Britain.</p> / Master of Arts (MA)

Cette méta-analyse révise et accroit le corpus de données d’analyses de la teneur isotopique du collagène osseux (δ 13C et δ 15N) et du carbonate des os et de l’émail dentaire (δ 13C et δ 18O) mesuré sur quatre collections ostéologiques canadiennes, afin d’étudier l’identité culturelle et l’adaptation alimentaire dans la vallée du Saint-Laurent, du XVIIe au XIXe siècle. Ces sites correspondent aux trois gouvernements de la colonie du Canada : le Vieux Cimetière de Trois-Rivières (1650-1865) et le cimetière de la première église paroissiale de Notre-Dame à Montréal (1691-1796), ouverts durant la période de la Nouvelle-France, et le cimetière Saint-Matthew à la ville de Québec (1771-1860) apparu au début du Régime Britannique. Le site de Sainte-Marie-de-Beauce (1748-1878) ajoute un comparatif, en contexte rural, à ces sites urbains. Dans un premier temps, la compilation des données démontre une incompatibilité entre les chercheurs en ce qui concerne les δ 15N du collagène et les δ 13C du carbonate osseux mesurés. Pour explorer la variation en δ 15N, l’effet de l’utilisation d’un agent acidifiant (acide chlorhydrique, HCl) a été testé, de même que la reproductibilité des résultats. Un enrichissement en 15N a été observé chez les échantillons traités avec du HCl à 2 % et 5 %. La variabilité des mesures entre les séquences d’analyses, malgré la constance de la mesure de l’étalon interne, n’a pu être expliquée. Dans un deuxième temps, la diversité culturelle des sites a été explorée. Par l’analyse des comportements migratoires et alimentaires à l’enfance (δ 18O et δ 13C de l’émail dentaire, respectivement), des « identités culturelles » ont été suggérées, soit : possiblement Autochtone, Inuit, Canadien Français ou Anglais, Nord-Américain (Acadien, Louisianais ou Terre-Neuvien), prisonniers de la Nouvelle-Angleterre, individu de descendance Africaine et Européen. L’hypothèse de la mise en esclavage de certains de ces individus, basée sur trois caractéristiques, le lieu d’origine, le décès avant l’âge de 17 ans et un changement drastique d’alimentation, a permis de considérer cet aspect de l’histoire canadienne. Dans un troisième temps et finalement, l’étude du carbonate des os (δ 13Ccarb) de même que du collagène osseux (δ 13Ccoll et δ 15N) a permis d’aborder l’adaptation alimentaire au Québec ancien. Globalement, les quatre sites suggèrent une rétention des traditions alimentaires Européennes (alimentation de type C3), tendance similaire à ce qui a été observé pour des sites coloniaux nord-américains, situés en contexte continental (tels que la Louisiane et l’Ontario). Les Canadiens français de Montréal semblent consommer plus de ressources C4 (telles que le maïs, la canne à sucre ou le rhum) que les migrants intracontinentaux (de l’Amérique du Nord tels que les Acadiens et Louisianais). Inversement, à Québec, les immigrants des Îles Britanniques ont consommé plus de ressources C4 que les individus nés localement. Comme les ressources marines étaient consommées par des individus à Montréal, une explication a été proposée en relation avec les restrictions alimentaires du calendrier liturgique Catholique. / This meta-analysis reviews and expands the dataset and analysis of bone collagen (δ 13C and δ 15N) and carbonate content of bone and tooth enamel (δ 13C and δ 18O) measured on four key sites, to study dietary adaptation in the St. Lawrence Valley from the 17th to the 19th centuries. These sites correspond to the three governments of the colony of Canada: The Old Cemetery of Trois-Rivières (1650-1865) and the cemetery of the first parish church of Notre-Dame in Montreal (1691-1796), both opened during the New France era, while the Saint-Matthew cemetery in Quebec City (1771-1860), belongs to the British Regime. The Sainte-Marie-de-Beauce cemetery (1748-1878) adds a rural comparison to these urban sites. Firstly, a compilation of the data demonstrated incompatibilities between some researchers concerning the bone collagen δ 15N and the bone carbonate δ 13C measured. The effect of various concentrations of an acidifying agent (hydrochloric acid, HCl) on δ 15N was tested, as was the reproducibility of the results. Enrichment in 15N was observed in samples treated with 2 % and 5 % HCl. The variability of measurements between analytical sequences, despite the consistency of the internal standard measurement, could not be explained. Secondly, the population diversity of the sites was explored. Based on the analysis of migratory and dietary behaviors at childhood (from tooth enamel δ 18O and δ 13C, respectively), the following "cultural identities" were suggested: Indigenous, Inuit, French or Anglo-Canadians, North American (as Acadians, Louisianians or Newfoundlanders), prisoners from New England, individual of African descent and European immigrants. The hypothesis of enslavement for some of these individuals was based on the following conditions: origin, death before the age of 17 years and a major shift in diet. This allowed for a deeper comprehension of this aspect of Canadian history. Thirdly and finally, bone carbonate (δ 13Ccarb), and bone collagen (δ 13Ccoll and δ 15N) were used to address the central theme of the thesis, which is the dietary adaptation. Overall, the four sites suggest a retention of European dietary traditions (C3-type diet), a trend similar to what has been perceived at other North American colonial sites located in continental settings (such as Louisiana and Ontario). The French Canadians in Montreal would have consumed more C4 resources (as maize, sugar cane or rum) than the intracontinental migrants (from North America as Acadians or Louisianians). Conversely, the British Isles immigrants consumed more C4 resources that the locally born individuals in Quebec City. Finally, as marine resources were consumed by some individuals in Montreal, an explanation was proposed in relation to Catholic food restrictions.

In anthropology, elemental analysis of bone and teeth can provide significant details about an individual’s life history, such as diet, toxicity exposure, residency, and migration patterns. Intra-individual comparisons can help to gather information about a single individual’s life, while inter-individual comparisons can help illustrate a community’s life history during these periods. However, current methods of elemental analysis commonly involve the destruction of skeletal samples, which can damage a collection’s integrity and be perceived as disrespectful by descendant communities. Preliminary research has validated handheld x-ray fluorescence spectrometry (HHXRF) as an accurate and reliable method of analysis appropriate for determining the elemental composition of archaeological bone and teeth. In this study, teeth from 16 individuals (N=16) from the pre-conquest Classic Period (AD 625-1100) Maya site of Altun Ha, Belize, were analyzed using HHXRF to identify trace elements to gain a better understanding of the lives of the individuals and community. This study expands upon preliminary research by increasing the sample size and utilizes a filter to increase sensitivity to elements of interest. Diet and mobility were assessed using calcium (Ca), strontium (Sr), and bromine (Br) ratios. Net photon counts per element of interest were extracted and converted into ratios. An inter- and intra-individual comparison model was used. Results of calculated Sr/Ca ratios show a general increased reliance on marine subsistence sources within the sample. Shifts that do not align with this trend are present in several individuals, indicating social complexity of Altun Ha. Results of Br/Ca ratios are less clear in regard to diet and warrant further investigation.

Because it signified the violent transition from the Plantagenet to Tudor dynasty, the death of King Richard III at the Battle of Bosworth’s Field was a monumental event. After five centuries, his skeleton was rediscovered by an archaeological team at a site, formerly the location of the Greyfriars Priory Church. The presentation uses the forensic evidence to examine the extent to which the perceived image of Richard III is the result of Tudor propaganda.