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. / Forestry, Faculty of / Graduate

The study was divided into three main sections. In the first section, temporal stability of genetic structure of red imported fire ant populations and effective population sizes were assessed with the help of microsatellites. The second part of the study was focused on the development of new microsatellite markers for the population genetics study of fire ants. The third part of the study was aimed at describing the association of phenotypic and genotypic characters of polygyne hybrid (Solenopsis invicta x richteri) fire ant in a colony and identifying the origin of polygyny in hybrid imported fire ant colony. Meridian, Yazoo City and Crystal Springs in Mississippi and Mobile, Alabama were selected for conducting the study. The overall FST estimates and the pairwise FST estimates between the populations of study, indicated little genetic differentiation and low spatial variation in the nuclear genetic structure of red imported fire ant. Gene flow estimates indicated that there is extensive movement between these populations. From 2006 to 2008 the FST estimates decreased and gene flow estimates increased, indicating that there is no equilibrium between genetic drift and migration in the populations studied. Effective population sizes ranged from 10 -17 in these populations.We have isolated and characterized an additional 11 polymorphic microsatellite loci in the invasive ant S. invicta from a population in Lauderdale County, Mississippi. The observed and effective number of alleles ranged from two to six (average 3.1818 ± S. E. 0.0486). Probability tests indicated significant deviations from the Hardy-Weinberg equilibrium at three loci. The polymorphism information content of the microsatellites ranged from 0.1482 to 0.6208.Identifying multiple inseminated queens in a colony and sequencing the critical region of Gp-9 locus (1600 base pairs) in individuals with the polygyne allele strongly indicate the association of phenotypic and genotypic characters of polygyny in a hybrid imported fire ant colony. A 100% match of Gp-9B and Gp-9b alleles and concordance in the critical amino acid substitutions of the Gp-9 locus in the hybrid fire ant with S. invicta Buren provides the evidence that polygyny in the hybrid imported fire ant colony is derived from S. invicta.

Mémoire de maîtrise (M.Med.Exp.)--Université du Québec à Chicoutimi, 1998. / Document électronique également accessible en format PDF. CaQCU

Thesis (Ph. D.)--University of Michigan, 1971. / Includes bibliographical references (leaves 106-110).

published_or_final_version / Biological Sciences / Master / Master of Philosophy

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The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.

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