The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010

The contribution of yeast strain background, specifically auxotrophic markers, to stability and fidelity of mtDNA replication was investigated. In summary, the ade2, his3delta200, and hap1 mutations have complex effects on mitochondrial functions, the severity of which appears to depend on other components in the genetic background of the strain. These results are important as many commonly used laboratory strains are related to the respiratory hampered S288c strain and are used for studies of orthologous human mutations associated with various mitochondrial diseases. These observations have added to our understanding of fungal mtDNA replication and have informed the mitochondrial community of problematic strains that need to be considered when using this model organism. The function of the yeast mitochondrial DNA polymerase (Mip1p) carboxyl-terminal extension (CTE) was investigated both in vivo and in vitro by genetically engineering various truncations of the CTE. The respiratory competence of mip1delta175 and mip1delta205 cells, in which Mip1p lacks the C-terminal 175 and 205 residues respectively, are indistinguishable from that of wild-type. In contrast, strains harbouring Mip1pdelta351, Mip1pdelta279, Mip1pdelta241, and Mip1pdelta222 rapidly lose mtDNA. At a low frequency, mip1delta216 cells grow poorly on glycerol. Fluorescence microscopy and Southern blot analysis revealed lower levels of mtDNA in these cells, and rapid loss of mtDNA during fermentative growth. Therefore, only the polymerase-proximal segment of the Mip1p CTE is necessary for mitochondrial function. To determine more precisely the defects associated with polymerase truncation variants, these proteins were overexpressed in yeast and used in a novel non-radioactive mtDNA polymerase assay. The threonine-661 and alanine-661 variants, shown by others to be responsible for the increased mtDNA mutability of various laboratory yeast strains at increased temperature, were examined in combination with CTE-truncations. These experiments suggest that exonuclease function is not effected in the alanine-661 variant at 37 degrees Celsius whereas polymerase activity is, and this higher relative level of exonuclease activity could be a contributing factor to mtDNA instability in S288c-related strains. Lastly, isogenic CTE truncation variants all have less DNA polymerase activity than their parental wild-type. Based on these results, several possible roles for the function of the CTE in mtDNA replication are suggested.

The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010

Thesis (Ph. D.)--University of Hawaii at Manoa, 1994. / Includes bibliographical references (leaves 166-191). / Microfiche. / xiii, 191 leaves, bound ill. 29 cm

Studying species at the molecular level can provide insights into how ecological and biological processes interrelate resulting in the diversity we see today. This information can be applied to conserve species at risk of extinction, or to better manage genetic diversity in species of economic importance. Species that inhabit freshwater riverine systems commonly exhibit population structures that are related to their relative dispersal capability, contemporary stream structure and/or historical stream structure. This thesis examined the populations genetic structure of wild and cultured stocks of the commercially farmed freshwater crayfish, C. quadricarinatus (von Martens), using genetic markers characterized by different modes of inheritance. C. quadricarinatus is distributed naturally in riverine systems in northern Australia, and southern Paupa New Guinea (PNG) and inhabits a variety of freshwater ecosystems ranging from ephemeral to permanent. Life history characteristics of C. quadricarinatus suggest a high level of genetic structuring among wild stocks might exist. However, seasonal flooding coupled with low topography across its distribution in northern Australia may promote sufficient gene flow among rivers to produce genetic homogeneity. Historical gene flow may also influence modern genetic structure as many distinct riverine catchments that C. quadricarinatus inhabits, were once connected at times of lower sea level. Insight into genetic relationships among C. quadricarinatus populations will allow for better management practices of wild populations in the future. The study investigated phylogenetic relationships among C. quadricarinatus representing 17 discrete natural drainages across the natural range in Australia and PNG, using 16s and COI gene sequences. Sequence analysis of both genes resolved two distinct genealogical lineages in Australia and three in PNG. The two divergent Australian lineages concur with original taxonomic descriptions of Reik (1969) based on external morphological differences. The three C. quadricarinatus populations sampled in PNG were all genetically distinct from each other, with one exhibiting a close association with an Australia lineage. The immense physical barriers (rugged mountain ranges) to gene flow in PNG will almost certainly have reduced dispersal capabilities for C. quadricarinatus. During times of lowered sea levels in the past, Australia and southern PNG were a single landmass with terrestrial and freshwater organisms theoretically able to disperse over associated land and via freshwater connections. The close genetic relationship between PNG and Australian C. quadricarinatus support a recent freshwater connection and hence gene flow between northern Australia and PNG C. quadricarinatus populations. Genetic differentiation among some C. quadricarinatus lineages exhibit as much genetic divergence at 16s RNA sequences as taxonomically recognised sub-species in the Cherax genus. Since C. quadricarinatus was originally described as different species based on external morphological differences (Reik, 1969), it is recommended that the taxonomy of C. quadricarinatus in Australia and PNG be re-evaluated. C. quadricarinatus specific microsatellite markers were developed for this study. Five variable loci were employed to investigate the extent of contemporary gene flow among fourteen C. quadricarinatus wild river populations in northern Australia. High FST and genetic distance estimates observed among pair wise comparisons of C. quadricarinatus populations are consistent with limited or no gene flow occurring among drainages. Speculation that C. quadricarinatus may disperse between adjacent or nearby drainages at times of flood, either across floodplains, or via flood plumes therefore seems highly unlikely among the populations examined in the current study. No significant correlation was observed between geographic distance and genetic distance among C. quadricarinatus populations here. C. quadricarinatus populations most closely resemble an island-like model, where gene flow is independent of geographic distance among populations and where genetic divergence occurs to a greater or lesser extent as a result of genetic drift within otherwise isolated populations. A significant number of C. quadricarinatus populations showed deviations from expected Hardy-Weinberg equilibrium (HWE). Samples sizes may not have been sufficiently large to reflect a true representation of genotypic proportions present in the sampled populations due to the highly variable nature of microsatellite loci. Deviations from HWE equilibrium, however, can also result from null alleles. Null allele estimates suggested a large proportion of null alleles were present in the C. quadricarinatus populations analysed. This may be a result of C. quadricarinatus populations confined to discrete drainages experiencing independent evolution, resulting in mutations in primer binding sites. The growing economic potential of C. quadricarinatus culture, both domestically and internationally, prompted expanding the current study to examine genetic diversity levels in commercial C. quadricarinatus stocks. The study employed five microsatellite markers to quantify genetic diversity in four Australian and three C. quadricarinatus culture stocks from overseas. Many C. quadricarinatus culture stocks also showed deviations from HWE expectations. This was not a surprising result given that the wild populations also deviated and domestication can also influence HWE. Relatively high levels of genetic diversity were observed. This probably results from intentional mixing of discrete river strains for production of the first commercial stock. Genetic differentiation estimates among culture stocks and assignment tests indicated that overseas culture stocks are most likely derived from the first commercial culture stock developed in Australia and then disseminated widely (the Hutchings stock). Robin Hutchings was a known supplier of live C. quadricarinatus to many international culture initiatives. Assignment of culture stocks back to their wild origins indicated that all C. quadricarinatus culture stocks sampled possess alleles that originate from the Flinders River (proportions ranged from 33-94%). Domestication of C. quadricarinatus to date has not resulted in significant reductions in levels of genetic diversity (heterozygosity or alleles richness) when compared to wild populations sampled in this study. Comparing culture stocks to wild populations to gauge their 'genetic health' may not be a suitable scale for evaluating genetic diversity in culture stocks. Wild populations are essentially evolving independently, are subjected to harsh seasonal environmental fluctuations resulting in periodic population crashes (genetic bottlenecks), with little or no recruitment from neighbouring drainages (gene flow). This study does however indicate that there is a large amount of genetic diversity distributed among wild populations that has yet to be exploited in culture. Genetic diversity in wild populations provides a resource for future stock improvement programs for C. quadricarinatus culture and thus requires careful conservation and appropriate management.

Thesis (M. Sc.)--University of Canterbury, 2006. / Typescript (photocopy). Includes bibliographical references (leaves 91-100). Also available via the World Wide Web.

Thesis (M. Sc.)--University of Canterbury, 2006. / Typescript (photocopy). Includes bibliographical references (leaves 79-88). Also avialable via the World Wide Web.

Thesis (Ph. D.)--University of Canterbury, 2007. / Typescript (photocopy). Includes bibliographical references (p. 121-135). Also available via the World Wide Web.

Thesis (M.A.)--State University of New York at Binghamton, Department of Anthropology, 2009. / Includes bibliographical reference (leaves: 181-197).

Thesis (M.Sc.)--York University, 2008. Graduate Programme in Higher Education. / Typescript. Includes bibliographical references (leaves 91-96). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR38784