An interspecies hybridization is usually viewed from two sides - either as mistakes in a reproduction resulting in decrease of a hybrids fitness (e. g. loss or decrease of viability and fertility) or as a mechanism helping animals adaptively respond to environmental changes resulting in higher fitness. Fitness is usually represented as a set of correlates. One of the correlates is an organism performance which is represented by a set of maximal values from measured physical activities. This thesis focuses on the evaluation of the endurance and the bite force for gecko species E. macularius and E. angramayniu, their interspecies hybrids and intraspecies hybrids to determine their performance. The results show differences in the bite force among each of the tested groups. E. macularius has the lowest bite force, while the highest bite force was measured in E. angramayniu. The bite force of interspecies hybrids is intermediate in comparison to the parent species. Nevertheless, intraspecies hybrids of large form and white form of E. macularius exceeds their parents in measured bite force. The variability in bite force suggests a positive effect of hybridization on fitness. The bite force differences between the large form and the white form of E. macularius support the hypothesis that there exist more...

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DNA microarrays are a potentially disruptive technology in the medical field, but their use in such settings is limited by poor reliability. Microarrays work on the principle of hybridization and can only be as reliable as this process is robust, yet little is known at the molecular level about how the surface affects the hybridization process. This work uses advanced molecular simulation techniques and an experimentally-parameterized coarse-grain model to determine the mechanism by which hybridization occurs on surfaces and to identify key factors that influence the accuracy of DNA microarrays. Comparing behavior in the bulk and on the surface showed, contrary to previous assumptions, that hybridization on surfaces is more energetically favorable than in the bulk. The results also show that hybridization proceeds through a mechanism where the untethered (target) strand often flips orientation. For evenly-lengthed strands, the surface stabilizes hybridization (compared to the bulk system) by reducing the barriers involved in the flipping event. Additional factors were also investigated, including the effects of stretching or compressing the probe strand as a model system to test the hypothesis that improving surface hybridization will improve microarray performance. The results in this regard indicate that selectivity can be increased by reducing overall sensitivity by a small degree. Another factor that was investigated was the effect of unevenly-lengthed strands. It was found that, when unevenly-lengthed strands were hybridized on a surface, the surface may destabilize hybridization compared to the bulk, but the degree of destabilization is dependent on the location of the matching sequence. Taken as a whole, the results offer an unprecedented view into the hybridization process on surfaces and provide some insights as to the poor reproducibility exhibited by microarrays. Namely, the prediction methods that are currently used to design microarrays based on duplex stability in the bulk do a poor job of estimating the stability of those duplexes in a microarray environment.

Because of the greatly increased supply of genetic variation which it provides, introgression is of great importance in determining both the rate and the direction of evolution. Hybridization between the genera Cowania and Purshia provides an excellent model for demonstrating the various products which might be expected from introgression. The present study is an attempt to further investigate phylogenetic relationships of Cowania mexicana and Purshia tridentata by use of cytological and biochemical techniques.

In the past twenty years many workers have made contributions to a better understanding of hybridization and introgression through studies of members of the grass family. The present study is an attempt to increase the understanding of the importance and amount of hybridization and introgression in members of the Tribe Hordeae. This study is concerned with a hybrid complex involving Agropyron subsecundum (Link) Hitchc. (bearded wheatgrass), Agropyron trachycaulum (Link) Malte (slender wheatgrass) and Elymus glaucus Buckl. (blue wild rye).

Hybrid vehicles are an important technology for reducing oil use and transportation-related emissions. It is well-known that hybrid and electric vehicles are often designed and tested using standard cycles such as the Highway Fuel Economy Test (HWY), Urban Dynamometer Driving Schedule (UDDS), and the US06 Supplementary Federal Test Procedure (US06). However, this begs the questions: How does real world driving compare to these cycles? Can a vehicle be designed using real world driving data which saves fuel in the real world compared to a vehicle designed using standard cycles? This thesis investigates this issue using a set of 5000km of real world driving data by light-duty pickup trucks, with the goal to optimize the fuel savings of a mild hybrid truck. The challenge with using a model-based design approach on thousands of kilometers of real driving data is the long model run-time required to iterate through plant and control parameters. Thus, this work develops a novel script which reduces optimization time by 78%. The key is to run the full model of the non-hybrid truck one time on the full driving data set, and then use the resulting vehicle speed, engine efficiency, engine torque, and engine speed, as inputs to the faster script. The script is then used to quickly iterate through the driving data set many times to find optimal control and plant parameters. In this work, exhaustive search is used; however, evolutionary optimization algorithms could also be used and would benefit from the fast script iteration on real world driving cycles. Overall, the use of the real world driving set for design of the mild hybrid truck resulted in a 7.10% decrease in fuel consumption compared to the non-hybrid truck, while the use of standard driving cycles for design resulted in a 5.45% fuel consumption decrease compared to the non-hybrid truck. / Thesis / Master of Applied Science (MASc)

Mitochondria are intracellular organelles responsible for oxidative phosphorylation. They contain their own DNA which encodes some components involved in oxidative phosphorylation. Mitochondrial DNA is very susceptible to mutations. Mitochondrial abnormalities have been observed in several disorders of muscle and brain. Alzheimer's disease is a form of dementia characterized by the formation of numerous neuritic plaques and neurofibrillary tangles. There is evidence suggesting a possible role for mitochondrial abnormalities in Alzheimer's disease. The goal of this project was to determine if there were quantitative changes in mitochondrial DNA content in large neurons from Alzheimer's disease patients, compared to age-matched control patients. The relative mitochondrial DNA content per unit area was assessed in brain sections from Alzheimer's disease subjects and age-matched control subjects using in situ hybridization to mitochondrial DNA. The results were not conclusive due to technical concerns with the in situ hybridization technique which are discussed. / Thesis / Master of Science (MS)

Michaux's sumac (Rhus michauxii) is a federally endangered rhizomatous shrub endemic to the southeastern United States, with two of the largest populations located at Maneuver Training Center--Fort Pickett, VA (Fort Pickett), and a nearby property, Deepwater. Michaux's sumac requires soil disturbance and fire to maintain healthy populations. Before being added to the endangered species list, 47% of populations were extirpated due to habitat loss, fire suppression, and hybridization with smooth sumac (Rhus glabra). Concerns with hybridization include hybrid swamping if hybrids are fertile, or outbreeding depression if hybrids display reduced fitness. I used genotyping-by-sequencing to estimate the extent of hybridization at Fort Pickett and Deepwater, and to assess how such hybridization may impact survival of Michaux's sumac as a distinct species at each of these locations. Additionally, population structure was examined using DAPC (discriminant analysis of principal components) and Admixture analyses to determine whether the colonies at Fort Pickett and Deepwater make up separate populations, meta-populations, or one large population. Analysis of 107,344 SNPs (single nucleotide polymorphisms) using Introgress and Admixture software suggested widespread hybridization at both Fort Pickett and Deepwater, with hybrids present in most of the sampled colonies. Population structure analyses revealed differentiation between the Fort Pickett and Deepwater populations, but little evidence of separate populations among the colonies sampled at Fort Pickett. These results are important for conservation planning to ensure the long-term survival of Michaux's sumac at Fort Pickett and Deepwater and can be used to help inform future management decisions. / Master of Science / Michaux's sumac (Rhus michauxii) is a small, federally endangered shrub endemic to the southeastern United States, with populations remaining in North Carolina, Virginia, and Georgia. To date, the largest known colonies of Michaux's sumac are in Virginia at Maneuver Training Center--Fort Pickett, VA (Fort Pickett), and at a nearby privately owned property called Deepwater. Michaux's sumac requires soil disturbance and fire to reduce competition and maintain healthy populations. It currently faces threats from habitat loss due to agricultural land use and fire suppression, and hybridization with a closely related species, smooth sumac (Rhus glabra). Hybridization is a threat to Michaux's sumac at Fort Pickett and Deepwater because it co-occurs with smooth sumac throughout the area. This study determined how much smooth sumac and Michaux's sumac are hybridizing in these locations and assessed whether hybridization is a threat to the long-term survival of the populations at each site. A secondary goal of the study was to gain a better understanding of how genetically similar the colonies within and between locations are to one another. Understanding the level of hybridization and the population structure of Michaux's sumac is important for making management decisions to protect the species. I found widespread hybridization between Michaux's and smooth sumac, with hybrid individuals at nearly all the colonies sampled. Additionally, there is evidence that Fort Pickett and Deepwater comprise two distinct populations, but the colonies inside each area are likely not separate populations. These results will inform future conservation management decisions for the species.

The genus Populus consists of many ecologically and economically important forest tree species. Their rapid growth makes them one of the most productive hardwoods growing in temperate latitudes. Populus spp. frequently hybridize where their ranges overlap, and poplar hybrids are the most frequently planted genotypes for fiber production. To better understand the genomics of hybridization in Populus, we sampled and sequenced the genome of 574 poplar trees from six east-west transects across the hybrid zone between Populus trichocarpa and Populus balsamifera in western North America. I used these data to characterize population structure within and between transects, and hybridization between the species. There was a consistent transition from greater P. balsamifera ancestry in the north and east to greater P. trichocarpa ancestry in the south and west. Hybridization between the species was common across each of the six transects, though more common in colder climates. The results also showed that both latitude and longitude affect the genetic structure of this species complex, and that subtle introgression from P. balsamifera may facilitate adaptation of P. trichocarpa to colder climates. / Master of Science / The genus Populus has many ecologically and economically important forest tree species. Balsam poplar (Populus balsamifera) and black cottonwood (Populus trichocarpa) are two such species, both for fiber production and models for understanding tree biology and adaptation. Whereas black cottonwood is distributed close to the west coast of North America from California through Alaska, balsam poplar mostly occurs across the interior of Canada from Newfoundland through Alberta. Where their ranges overlap, the species often hybridize. In this study, we used genome sequencing of trees collected across six east-west transects from Washington state through British Columbia, Canada, and Alaska to understand genetic variation and the geography of hybridization. I found evidence of widespread hybridization across all transects. While the influence of P. balsamifera was extensive in northern populations, a large number of pure P. trichocarpa were found in southern populations. The transition from P. trichocarpa to P. balsamifera was also steeper in the south than the north, with a narrower hybrid zone in the south. Additionally, I found that gene flow among some populations was limited by temperature and geographical barriers. Taken together, my results suggest genetic structure and hybridization within and between these species is driven by climate variation, and that P. balsamifera ancestry may help northern P. trichocarpa populations adapt to their local environments.

Master of Science