The Land Hill and Hidden Hills study areas were the site of the 2006 and 2007 Brigham Young University's archaeological field schools. The two study areas are located in contrasting environments; the Land Hill area is located along the Santa Clara River in southwestern Utah, and the Hidden Hills area was is located on the Shivwits Plateau in northwestern Arizona. The Land Hill study area is located within a well-watered environment which would support a primarily horticultural lifestyle. The Hidden Hills study area is located in an arid environment without permanent streams which would support a more mobile hunting lifestyle. The contrasting environments of these two study areas allowed for a study of the similarities and differences in the use of stone tools. Based on the results of the analysis and comparison of the stone tool and debitage assemblages, from sites in both areas throughout time, suggests that the people in the Land Hills study area actually seemed to be living a lifestyle similar to the people in the Hidden Hills area.

The Alisitos arc segment forms part of the western zone of Jura-Cretaceous Peninsular Ranges batholith of Baja California. It extends south from the ancestral Agua Blanca Fault to the state boundary between Baja Norte and Sur. The study area is located within a fold and thrust belt intruded by a number of plutons that were emplaced during and after the deformational event. The northern end of the Alisitos arc is characterized by subvertical tight to isoclinal folds and high-angle reverse faults that define a northwest trending, southwest vergent fold and thrust belt. The aABF defines the northern limit to the Alisitos arc segment. In this study we present the results of a petrographic study of igneous rocks in order to determine the relative timing and the distribution of deformation within the northern Alisitos arc segment. The study includes samples of the mylonitic shear zone of the aABF, and plutonic samples from intrusions proximal to the aABF emplaced later during regional deformation. These samples were investigated in order to characterize the distribution of the subsolidus strain in grain scale and the sense of shear during later phases of deformation in the northern Alisitos arc. The results are presented and discussed based on the mineralogical and textural observations from the Balbuena pluton, the Piedra Rodada pluton, and volcaniclastics that were deformed within the aABF. The Balbuena pluton, emplaced at ~ 108 Ma after the surrounding country rocks had already been folded, exhibits little if any evidence for subsolidus deformation. In contrast, the Piedra Rodada pluton, emplaced at ~ 105 Ma just to the southwest of the aABF, exhibits a strong magmatic fabric overprinted by a moderate subsolidus fabric to the southwest that grades into a strong subsolidus fabric with proximity to the fault. Kinematics observed from lineation parallel-foliation normal sections exhibit consistent top-to-the southwest sense of shear.

The purpose of this thesis is to underline the importance of developing useful and mutually beneficial relationships between local iwi and museums, and to consider the subsequent implications for museum practice. The thesis assembles a variety of contemporary sources in order to document and construct a chronological narrative of events: minutes and communications; interviews with staff and key participants in the process of acquiring the Partington Collection by the Whanganui Regional Museum; media reports; and a survey of recent literature. The Partington Collection of Whanganui Maori photographs is integral to this examination because of its importance to both Whanganui iwi and the Whanganui Regional Museum. The situation of colonial photography in museums has changed over the century from being viewed as a factual reflection of the cultural imperatives of indigenous peoples, to being viewed as a colonial construct consigning indigenous peoples to their past. Because this Collection is the most comprehensive photographic documentary of Whanganui Maori from the turn of last century it adds immense value to the Museum’s existing collections. However to Whanganui iwi the photographs of their ancestors are taonga tuku iho: far more than just photographic images they are demonstrably and undeniably imbued with the mana of their tupuna. The public auction in 2001 of the Partington Collection created a catalyst for action and an opportunity for Whanganui iwi and the Museum to work together to ensure the return of the photographs to Whanganui, an outcome that was finally achieved in 2002. The thesis concludes that the successful return of the Partington Collection to Whanganui could not have been possible without the long term evolving relationship between iwi and the Museum and in particular the more recent emergence of a bi-cameral governance structure. Furthermore the maintenance of relationships and communication is crucial to the evolution of museum practice. This would suggest a reversal of the traditional perspective that museum practice and procedure is pre-eminent. Instead, this case study demonstrates that relationships are at the heart of museum practice.

The assemblage of ca. 6–4 Ma volcanic rocks exposed at the Sagehen Research station in the Truckee-Tahoe region of the northern Sierra Nevada, United States, is interpreted to be, within the Ancestral Cascades volcanic arc, a Lassen-type stratovolcano complex. Sagehen is of particular importance because it is one of the few Tertiary arc volcanic centres in California which has not been heavily glaciated during the Pleistocene. The volcanic rocks are variably porphyritic or aphanitic, including abundant plagioclase with clinopyroxene and amphibole. The rocks range from basalt to basaltic-andesite to andesite in composition. Basalts are olivineand clinopyroxene-bearing with minor phenocrysts of plagioclase. The basaltic-andesites are primarily pyroxene bearing while the andesites contain pyroxene-, plagioclase- and hornblende porphyritic phases. Sagehen arc lavas are calc-alkaline and enriched in the large ion lithophile elements and depleted in High Field Strength Elements. The basalts are depleted in Zr and Hf while the andesites are enriched with Zr and Hf relative to the middle rare earth elements. Compared to previously studied Ancestral Cascade arc samples, Sagehen region basalts have lower 143Nd/144Nd isotopic values that do not correspond to proposed mantle-lithosphere mixing lines, while the andesite samples appear to represent the interplay of these two components on a 87Sr/86Sr vs. 143Nd/144Nd. The trace element data and isotopic plots suggest that the melts that produced the basalts are from subduction modified mantle wedge peridotites that ponded near the base of the lithosphere similar to the generation of other subduction related calc-alkaline lavas along convergent continental margins. The andesitic samples appear to be the result of further modification through crustal assimilation as seen in the higher isotopic Sr contents in the andesites and Ce/Smpmn vs. Tb/Ybpmn plots. Finally, the proposed map units from Sylvester & Raines (2007) were found to contain various geochemical facies based on the samples collected indicating that some map units may have to be redefined or sub-divided.

The field of molecular evolution has benefited greatly from the use of ancestral sequence reconstruction as a methodology to better understand the molecular mechanisms associated with functional divergence. The method of ancestral sequence reconstruction has never been experimentally validated despite the method being exploited to generate high profile publications and gaining wider use in many laboratories. The failure to validate such a method is a consequence of 1) our inability to travel back in time to document evolutionary transitions and 2) the slow pace of natural evolutionary processes that prevent biologists from ‘witnessing’ evolution in action (pace viruses). In this thesis research, we have generated an experimentally known phylogeny of fluorescent proteins in order to benchmark ancestral sequence reconstruction methods. The tips/leaves of the fluorescent protein experimental phylogeny are used to determine the performances of various ASR methods. This is the first example of combining experimental phylogenetics and ancestral sequence reconstruction.

The genealogy of a random sample of a population of organisms can be represented as a rooted binary tree. Population dynamics determine a distribution over sample genealogies. For large populations of constant size and in the absence of selection effects, the coalescent process of Kingman determines a suitable distribution. Neuhauser and Krone gave a stochastic model generalising the Kingman coalescent in a natural way to include the effects of selection. The model of Neuhauser and Krone determines a distribution over a class of graphs of randomly variable vertex number, known as ancestral selection graphs. Because vertices have associated scalar ages, realisations of the ancestral selection graph process have randomly variable dimensions. A Markov chain Monte Carlo method is used to simulate the posterior distribution for population parameters of interest. The state of the Markov chain Monte Carlo is a random graph, with random dimension and equilibrium distribution equal to the posterior distribution. The aim of the project is to determine if the data is informative of the selection parameter by fitting the model to synthetic data. / Foundation for Research Science and Technology Top Achiever Doctoral Scolarship

The genealogy of a random sample of a population of organisms can be represented as a rooted binary tree. Population dynamics determine a distribution over sample genealogies. For large populations of constant size and in the absence of selection effects, the coalescent process of Kingman determines a suitable distribution. Neuhauser and Krone gave a stochastic model generalising the Kingman coalescent in a natural way to include the effects of selection. The model of Neuhauser and Krone determines a distribution over a class of graphs of randomly variable vertex number, known as ancestral selection graphs. Because vertices have associated scalar ages, realisations of the ancestral selection graph process have randomly variable dimensions. A Markov chain Monte Carlo method is used to simulate the posterior distribution for population parameters of interest. The state of the Markov chain Monte Carlo is a random graph, with random dimension and equilibrium distribution equal to the posterior distribution. The aim of the project is to determine if the data is informative of the selection parameter by fitting the model to synthetic data. / Foundation for Research Science and Technology Top Achiever Doctoral Scolarship

The genealogy of a random sample of a population of organisms can be represented as a rooted binary tree. Population dynamics determine a distribution over sample genealogies. For large populations of constant size and in the absence of selection effects, the coalescent process of Kingman determines a suitable distribution. Neuhauser and Krone gave a stochastic model generalising the Kingman coalescent in a natural way to include the effects of selection. The model of Neuhauser and Krone determines a distribution over a class of graphs of randomly variable vertex number, known as ancestral selection graphs. Because vertices have associated scalar ages, realisations of the ancestral selection graph process have randomly variable dimensions. A Markov chain Monte Carlo method is used to simulate the posterior distribution for population parameters of interest. The state of the Markov chain Monte Carlo is a random graph, with random dimension and equilibrium distribution equal to the posterior distribution. The aim of the project is to determine if the data is informative of the selection parameter by fitting the model to synthetic data. / Foundation for Research Science and Technology Top Achiever Doctoral Scolarship

The genealogy of a random sample of a population of organisms can be represented as a rooted binary tree. Population dynamics determine a distribution over sample genealogies. For large populations of constant size and in the absence of selection effects, the coalescent process of Kingman determines a suitable distribution. Neuhauser and Krone gave a stochastic model generalising the Kingman coalescent in a natural way to include the effects of selection. The model of Neuhauser and Krone determines a distribution over a class of graphs of randomly variable vertex number, known as ancestral selection graphs. Because vertices have associated scalar ages, realisations of the ancestral selection graph process have randomly variable dimensions. A Markov chain Monte Carlo method is used to simulate the posterior distribution for population parameters of interest. The state of the Markov chain Monte Carlo is a random graph, with random dimension and equilibrium distribution equal to the posterior distribution. The aim of the project is to determine if the data is informative of the selection parameter by fitting the model to synthetic data. / Foundation for Research Science and Technology Top Achiever Doctoral Scolarship

Les années 2000 ont vu l'apparition des technologies de séquençage haut-débit permettant de faire chuter le coût en temps et argent du séquençage du génome complet et ouvrant la perspective à des analyses de la phylogénie des espèces à l'échelle de génome entiers. Dans cette optique des méthodes pour l'inférence de l'histoire évolutive de l'ordre de marqueurs génomiques le long d'un phylogénie ont été développées. Cependant, les assemblages d'une majorité des grands génomes d'eucaryotes demeurent incomplètement résolues et ne permettent donc pas, en tant que tel, leur exploitation pour la reconstruction de l'histoire évolutive de l'ordre des gènes de ces espèces. C'est dans ce contexte que nous avons développé l'algorithme adseq qui permet de conjointement reconstruire l'histoire évolutive de l'ordre de gènes en considérant la fragmentation des génomes actuels et améliorant l'assemblage de ceux-ci par génomique comparative / The early 2000s saw the emergence of high-throughput sequencing technologies that would bring down the time and cost of sequencing the entire genome and opening the perspective to whole genome-scale species phylogeny. In this perspective, methods for the inference of evolutionary history of the order of genomic markers along a phylogeny have been developed. However, assemblies of a majority of the large eukaryotic genomes remain incompletely resolved and therefore do not, as such, allow their exploitation for the reconstruction of evolutionary history of the order of the genes of these species. It is in this context that we have developed the algorithm ADseq which allows to jointly reconstruct the evolutionary history of the order of genes by considering the fragmentation of the extant genomes and improve the assembly of these by comparative genomics