The serpentine endemic, Mimulus nudatus, lives sympatrically on the serpentine soils of Lake County, California, with its probable progenitor, the bodenvag species M. guttatus. This thesis examined the mechanisms which enable M nudatus and M guttatus to coexist in sympatry. In addition, it sought to determine the genetic basis of the postzygotic reproductive isolating barrier between M nudatus and M guttatus, in order to distinguish between the classical allopatric and the ecotypic models of speciation. The postzygotic barrier achieving reproductive isolation between the species was at the seed provisioning stage and was strong for both local and distant populations of M guttatus. In addition, there was some evidence for premating pollinator isolation, since honey bees preferentially visited M guttatus and Dialictus preferred M. nudatus. In spite of the majority of pollinator visits being intra-specific, M nudatus still suffered a reduction in fertility caused by interspecific crossing, although M guttatus experienced no such reduction. To avoid M nudatus being outcompeted into extinction, the two species must thus be sufficiently ecologically different. In the field and in the greenhouse, whilst M guttatus experienced a reduction in fitness as calcium levels decreased, the fitness of M nudatus was independent of calcium levels. Therefore one hypothesis suggested for the ecological differentiation of the two species, was that M nudatus had evolved greater tolerance to calcium deficient soils. The genetic basis of the postzygotic reproductive isolating barrier between M nudatus and M guttatus was investigated by using crosses to a third species, M cupriphilus, which was used since it gave fertile hybrids with both species. It was not possible to determine the genetic basis of the postzygotic reproductive isolating barrier between M nudatus and M guttatus since the results in the crossing program were contradictory. Some results supported the simple two gene complementary interaction system previously found for populations of M guttatus, but others did not. Hence no distinction could be made between the allopatric and ecotypic models of speciation.

The concept of inclusive fitness plays a key role in much of sociobiology. Yet most theoretical studies concerning the evolution of social behavior circumvent inclusive fitness by mobilizing the concept of frequency dependent individual fitness. Given certain assumptions, it is shown that models based on these two different concepts are dynamically equivalent. The models do differ, however, in bookkeeping methods which are advantageous under different circumstances. A knowledge of these circumstances should prove of value to students of social behavior. It is then shown that evolution acts according to an adaptive landscape based on Hamilton's inclusive fitness in the absence of strong selection and inbreeding. This yields an inclusive fitness analogue to much of traditional population genetics. For example, heterozygote superiority in inclusive fitness yields stable polymorphisms, while intermediate dominance results in fixation of one of the alleles. When individuals do not affect one another's fitnesses, the inclusive fitness topography collapses to one based on individual fitness. A general rule for the evolution of social behavior under intermediate dominance is shown to yield Hamilton's Rule as a special case. Next, a general model for examining the evolution of social behavior is developed which, unlike inclusive fitness models, does not require that benefits received be linear functions of the number of social donors encountered. The subsocial route for the evolution of eusociality in haplodiploid organisms is then examined within the context of this model. Nonlinearities render conditions for frequency independent fixation or loss of sister-helping alleles more stringent than expected from models based on the assumption of linear benefits. In particular, both stable polymorphisms and frequency dependent selective thresholds for sister-helping behavior may commonly obtain.

In the past, conifers have been the primary focus of population and conservation genetic studies in Pacific Northwest (PNW) trees. These studies have provided tremendous insight as to how genetic diversity varies across species ranges for these wind-pollinated and mostly wind-dispersed species. With this study of Pacific dogwood (Cornus nuttallii), a broadleaved, PNW species, which utilizes biological vectors for pollen and seed dispersal, we hope to broaden our understanding of tree evolutionary dynamics. Marker development for C. nuttallii found few useful polymorphisms. Of eight microsatellite markers (SSRs) developed from a closely related species, three were monomorphic, while the other five averaged only 4.4 alleles/locus. Furthermore, only a single base pair substitution was found in the rpl16 region of the chloroplast genome after sequencing 2,262 non-coding base pairs in 100 individuals. This lack of diversity, which was found to be ubiquitous throughout the range of C. nuttallii, suggests this species may have endured a prolonged bottleneck in a single glacial refugium prior to recolonization. The cpDNA phylogeographic pattern and a significant decline in both SSR allelic richness (r² = 0.42, p<0.01), and expected heterozygosity (r² = 0.51, p<0.01) support this theory. Low levels of population structure, documented in both chloroplast (D = 0.153) and nuclear genomes (FST = 0.071, RST = 0.036) may suggest high levels of contemporary gene flow between populations are also influencing current patterns of diversity. Despite variation being the precursor for adaptation, a comparison of QST (0.088 for first-year height and 0.113 for bud burst timing) with a refined FST estimate (0.053), indicated that C. nuttallii had either retained or recovered significant phenotypic variation for differential selection to act. Such uniformly low diversity raises the issue of how genetic conservation efforts should proceed with this and other species sharing a similar degree of genetic depauperateness. So that signs of decline may be detected, we suggest population monitoring, especially for those populations occurring at high elevations. Furthermore, we advocate the transfer of seeds from the nearest southern source, in the event that restorative efforts are required to assist this species to cope with the rapidly changing climate.

No description available.

Identifying single nucleotide polymorphisms (SNPs) that are involved in common and complex diseases, such as cancer, is a major challenge in current molecular epidemiology. Knowledge of such SNPs is expected to enable timely diagnosis, effective treatment, and, ultimately, prevention of human disease. However, the tremendous number of SNPs on the human genome, which is estimated at more than eleven million, poses challenges to obtain and analyze the information of all the SNPs. In this thesis we address the problem of selecting representative SNP markers for supporting effective disease-gene association studies. Our goal is to facilitate the genotyping and analysis procedure, associated with such studies, by providing effective prioritization methods for SNP markers based on both their allele information and functional significance. However, the problem of SNP selection has been proven to be NP-hard in general, and current selection methods impose certain restrictions and use heuristics for reducing the complexity of the problem. We thus aim to develop new heuristic algorithms and systems to advance the state-of-the-art, while relaxing the restrictions. To address this challenge, we formulate several SNP selection problems and present novel algorithms and a database system based on the two major SNP selection approaches: tag SNP selection and functional SNP selection. Furthermore, we describe an innovative approach to combine both tag SNP selection and functional SNP selection into one unified selection process. We demonstrate the improved performance of all the proposed methods using comparative studies. / Thesis (Ph.D, Computing) -- Queen's University, 2009-06-22 15:26:14.061

No description available.

In the past, conifers have been the primary focus of population and conservation genetic studies in Pacific Northwest (PNW) trees. These studies have provided tremendous insight as to how genetic diversity varies across species ranges for these wind-pollinated and mostly wind-dispersed species. With this study of Pacific dogwood (Cornus nuttallii), a broadleaved, PNW species, which utilizes biological vectors for pollen and seed dispersal, we hope to broaden our understanding of tree evolutionary dynamics. Marker development for C. nuttallii found few useful polymorphisms. Of eight microsatellite markers (SSRs) developed from a closely related species, three were monomorphic, while the other five averaged only 4.4 alleles/locus. Furthermore, only a single base pair substitution was found in the rpl16 region of the chloroplast genome after sequencing 2,262 non-coding base pairs in 100 individuals. This lack of diversity, which was found to be ubiquitous throughout the range of C. nuttallii, suggests this species may have endured a prolonged bottleneck in a single glacial refugium prior to recolonization. The cpDNA phylogeographic pattern and a significant decline in both SSR allelic richness (r² = 0.42, p<0.01), and expected heterozygosity (r² = 0.51, p<0.01) support this theory. Low levels of population structure, documented in both chloroplast (D = 0.153) and nuclear genomes (FST = 0.071, RST = 0.036) may suggest high levels of contemporary gene flow between populations are also influencing current patterns of diversity. Despite variation being the precursor for adaptation, a comparison of QST (0.088 for first-year height and 0.113 for bud burst timing) with a refined FST estimate (0.053), indicated that C. nuttallii had either retained or recovered significant phenotypic variation for differential selection to act. Such uniformly low diversity raises the issue of how genetic conservation efforts should proceed with this and other species sharing a similar degree of genetic depauperateness. So that signs of decline may be detected, we suggest population monitoring, especially for those populations occurring at high elevations. Furthermore, we advocate the transfer of seeds from the nearest southern source, in the event that restorative efforts are required to assist this species to cope with the rapidly changing climate.

Errata is pasted onto front end-paper. / Bibliography: leaves 166-171. / ix, 171 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis considers the question of fixation probabilities and mean absorption times for alleles when a population is divided into a number of subpopulations with asymmetric migration between the subpopulations. The emphasis of the thesis is on small populations and conservation genetics. Results have important implications for management of remnant subpopulations in order to maintain genetic diversity when migration between the remnant subpopulations is not symmetric. / Thesis (Ph.D.)--University of Adelaide, Dept. of Applied Mathematics, 1999?

Thesis (Ph. D.)--University of Adelaide, Dept. of Crop Protection, 1997. / Includes bibliographical references (leaves 180).

Thesis (Ph.D.) - James Cook University, 2005. / Typescript (photocopy) Bibliography: leaves 148-167.