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1
Pandya, Arpita. "Human Y-chromosomal DNA variation." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298658.
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Bromham, Lindell. "Rate variation in DNA sequence evolution." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339362.
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Adur, Ashwin. "DNA copy number variation in autism." Connect to resource, 2009. http://hdl.handle.net/1811/37275.
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Hill, Catherine E. "Mitochondrial DNA variation in Island Southeast Asia." Thesis, University of Huddersfield, 2005. http://eprints.hud.ac.uk/id/eprint/22331/.
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It is known that Island Southeast Asia was colonised relatively early in the history of modem humans; however, it is still a matter of some debate as to whether the modem inhabitants of Island Southeast Asia are descended from these original inhabitants or are the result of some later migration. Currently, the prevailing theory in both archaeology and linguistics is that the modem inhabitants of Island Southeast Asia are largely descended from an agricultural people who originated in China and Taiwan around 6,000 years ago. From there they are thought to have migrated through the Philippines and into Eastern Island Southeast Asia around 2,500-1,500 B.C. assimilating or replacing the indigenous peoples. However, other researchers have suggested that a model of regional continuity is more suitable for Island Southeast Asia and that the modem inhabitants are the direct descendents of the original Pleistocene inhabitants. Still others have suggested that intermediate models would be more appropriate. This study aimed to use mitochondrial DNA to test the validity of these models. A secondary aim was to look at the mitochondrial DNA of the indigenous Orang AsH groups of the Malay Peninsula in an attempt to reconstruct a picture of the early Pleistocene variation of Southeast Asia. To this end, mitochondrial DNA was obtained and sequenced from 885 individuals from various locations in Island Southeast Asia and also 259 Orang AsHindividuals. This study has demonstrated that the populations of Island Southeast Asia contain a high level of genetic diversity, including a number of novel haplogroups. Significant differences have also been found between Eastern and Western populations suggesting that they have been established long enough to become regionally specific. Most Island Southeast Asian haplogroups date to the Pleistocene or early Holocene which suggests that they are mostly indigenous to the area. Those which could have a connection to Taiwan seem too old to have been part of an 'out of Taiwan' event as it has been traditionally visualised. Only -13% ofmtDNA types (belonging to haplogroups M7clc, D5 and Y2) could be linked to such an event suggesting that if a migration did occur it was demographically minor. xiii A number of novel haplogroups were also found in the Orang Asli which form strong support for the theory that that at least the Semang, if not all Orang Asli groups in part, are descended from the original Pleistocene inhabitants of the Malay Peninsula. These novel haplogroups diverge from the same set of founder types as the haplogroups found across the rest of Eurasia; that they diverge from close to the roots of these founder types suggests they are of considerable antiquity. This, along with expansion dates of -60,000 obtained in this study, suggests that only a single, early 'out of Africa' event took place which led to the peopling of the rest of the world by modem humans.
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Meng, Anming. "DNA fingerprinting and minisatellite variation of swans." Thesis, University of Nottingham, 1990. http://eprints.nottingham.ac.uk/13889/.
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Genetic variation in natural populations of four species of swans (Cygnus bewickii, Cygnus olor, Cygnus buccinator and Cygnus cygnus) has been investigated by examining minisatellite loci using human DNA fingerprinting probes pSPT19.6 and pSPT18.15. It has been found that swan minisatellites are highly variable. However, the degree of variation depends on the population structure and species. Bewick's Swans at Slimbridge have the highest degree of minisatellite variation, Whooper Swans at Caerlaverock come second, and then Mute Swans, and Trumpeter Swans in Montana. Comparative study of DNA fingerprints among populations and among species suggested that swan minisatellites are subject to specific as well as population differentiation, although the function of minisatellites remains an unsolved mystery. Hypervariable minisatellites of swans that are detected by DNA fingerprinting are stably inherited as codominant markers. DNA fingerprinting has been used to study mating behaviour of Mute and Whooper Swans in the wild The results showed that the Whooper swans were almost strictly monogamous and Mute Swans exhibited an adaptable reproductive system. A genomic library from Cygnus olor was constructed and dozens of minisatellites were isolated. Most of the cloned swan minisatellites were variable, some showed specific variation, and one (pcoMS6.1) detected RFLPs in PstI digests of Trumpeter Swans.
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Saunders, Nigel John. "Bacterial phase variation associated with repetitive DNA." Thesis, Open University, 1999. http://oro.open.ac.uk/57999/.
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Phase variation is mechanism of phenotypic switching used by many pathogenic bacterial species. This thesis describes work on three aspects of phase variation. Mathematical models are described which can be used to determine the rate of phase variation and subsequently the influence of variation rate and fitness differences associated with the altered phenotype on population structure. An approach to whole genome analysis has been developed which has been used to identify putative phase variable contingency genes in H. pylori, T. pallidum and N. meningitidis. This has identified many new contingency genes likely to be involved in host - bacterium and bacterium population interactions. Finally, a detailed molecular investigation of the promoter of the phase variable opc gene of N. meningitidis is presented. In this it is shown that the promoter located homopolymeric tract controls transcription by affecting the relative spacing and facing of promoter components, that this determines RNA polymerase binding to the promoter, and that this interaction involves direct contact of the a-subunit of RNA polymerase with the promoter. In addition it is shown that transcription is dependent upon an IHF consensus sequence in the opc promoter.
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Hide, Geoffrey. "Variation in repetitive DNA in African Trypanosomes." Thesis, University of Edinburgh, 1988. http://hdl.handle.net/1842/12083.
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Lundmark, Per Erik. "Genetic and Genomic Analysis of DNA Sequence Variation." Doctoral thesis, Uppsala universitet, Molekylär medicin, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-158486.
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The studies in this thesis describe the application of genotyping and allele specific expression analysis to genetic studies. The role of the gene NPC1 in Triglyceride metabolism was explored in mouse models and in humans on the population level in study I. NPC1 was found to affect hepatic triglyceride metabolism, and to be relevant for controlling serum triglyceride levels in mice and potentially in humans. In study II the utility of the HapMap CEU samples was investigated for tagSNP selection in six European populations. The HapMap CEU was found to be representative for tagSNP selection in all populations while allele frequencies differed significantly in the sample from Kuusamo, Finland. In study III the power of Allele specific expression as a tool for the mapping of cis-regulatory variation was compared to standard eQTL analysis, ASE was found to be the more powerful type of analysis for a similar sample size. Finally ASE mapping was applied to regions reported to harbour long non-coding RNAs and associated SNPs were compared to published trait-associations. This revealed strong cis-regulatory SNPs of long non-coding RNAs with reported trait or disease associations.
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Crompton, Tom. "Mobile DNA and genetic variation in Drosophila melanogaster." Thesis, University of Leicester, 1997. http://hdl.handle.net/2381/30330.
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Whilst it is commonly accepted that transposable elements can generate genetic variation, the significance of this for the maintenance and dissemination of such elements is controversial. Here long-term laboratory populations of Drosophila melanogaster, maintained at two discrete temperatures, are screened by Southern blotting for the patterns of insertion of several transposable elements (copia, mdg-2, mdg-4 and P). Consistent with a temperature-specific adaptive role for some insertions, several are apparently found at higher frequency in lines at one temperature. Further characterisation of these putatively temperature-selected insertions was attempted. Of three distinct approaches taken towards cloning these insertions, a single-stranded DNA-ligation for PCR-amplification technique, not thought to have been previously exploited for isolating transposable element insertion sites, generated the best results. One copia insertion was successfully sequenced, although single fly PCR experiments suggested that the frequency of this in caged populations was not related to temperature. A major collection of D. melanogaster from the French and Spanish Pyrenees was undertaken along four discrete altitudinal clines, with a view to screening for specific transposable element insertions. A novel strategy was developed for correlation of altitude with mean seasonal temperature of each collection site. Altitudinal variation in the frequency of Thr-Gly length polymorphism at the period locus was found to be consistent with predictions based on known latitudinal clines. This is the first known example of putatively adaptive clinal genetic variation in European populations of Drosophila collected along altitudinal transects. Finally, a fundamental re-examination of the theoretical issues surrounding the possible adaptive significance of transposable elements is developed. It is demonstrated that he extension of ideas on the 'units of selection' to transposable elements has led to confusion. A model of transposable element evolution which presents a coherent alternative to the selfish DNA approach is presented.
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Eng, Ken Khong. "Complete mitochondrial DNA genome variation in Peninsular Malaysia." Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/7872/.
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The peopling of Southeast Asia has been vigorously debated over the past few decades by archaeologists, linguists and anthropologists, as well as evolutionary and population geneticists. Several ethnic minorities in the region, the Orang Asli groups (the Semang, Senoi and Aboriginal Malays) from Peninsular Malaysia, are widely thought of as “relicts” of human diversity in the ancient Sunda continent. However, mitochondrial DNA (mtDNA analysis of these groups has hitherto been restricted to a small number of populations and largely based on the mtDNA control region hypervariable segment I (HVS-I), supplemented by a very small number of whole-mtDNA genomes. In this study, I have both expanded the number of populations examined and analysed 226 lineages at the level of whole-mtDNA genomes from both Orang Asli and modern Malay populations, covering most of the extant mtDNA diversity in Peninsular Malaysia, in the context of Southeast Asian variation more generally, including a total of 2206 complete mtDNA sequences in the phylogeographic analysis. This has confirmed that the Orang Asli populations indeed experienced high genetic drift, likely due to their extremely small group sizes and population subdivision. All three Orang Asli groups have local roots that trace back to ~50 ka, and all have been affected to a greater or lesser extent by subsequent migrations to Peninsular Malaysia. The Semang and Senoi show much less haplogroup diversity than the Aboriginal Malays, although the latter have some indigenous ancestry that is as deep as that of the Semang and Senoi in Peninsular Malaysia. However, this drift, and the loss of lineages that it has entailed, is compensated for by the retention of many related ancient lineages in the extant modern Malay, who therefore provide a more comprehensive view of ancient Malay Peninsula, and more generally ancient Sunda, mtDNA diversity. Indeed, contrary to the model that posits a recent ancestry for Malay in Island Southeast Asia (ISEA), a majority of their maternal lineages appear to have had a local ancestry within Mainland Southeast Asia (MSEA) and the Malay Peninsula. Combining the Orang Asli and Malay data indicates a very deep ancestry for multiple indigenous maternal lineages that date back locally (or regionally) to the late Pleistocene. Many can be traced to the original inhabitants of Southeast Asia, who colonised the Sunda region from South Asia ~50–60 ka. It appears that the spread of the so-called “Coastal Neolithic” foraging groups (who may have engaged in horticulture, but were largely pre-rice agriculture) may have provided the main contribution to the north–south lineage expansions and the spread of Austro-Asiatic languages to the Orang Asli and to the Nicobars may be connected to some of these dispersals. Apart from preserving these ancient lineages, many of which have been lost by drift in the relict populations, the modern Malay also preserve complex maternal influences from further afield at various times stretching back to the Last Glacial Maximum, from ISEA (as far east as the New Guinea region), to a lesser extent from East Asia, and to an even lesser extent South Asia. Climatic change and sea-level rises were likely the most important driving force behind the demographic history of Southeast Asia, mainland as well as insular, as shown by a sharp signal of early Holocene population crash and subsequent re-expansion in both the modern Malay and the Orang Asli. Although there is substantial lineage sharing between modern Malay and their close Sunda neighbours in Sumatra, ISEA lineages amount to little more than a quarter of the maternal variation of Malay, and even if there was a major migration to the Peninsula in the Late Holocene, the majority of their maternal ancestry seems to lie within the bounds of the Sunda continent.
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Ramsfield, Tod. "Variation in the mitochondrial DNA of Chondrostereum purpureum." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq24226.pdf.
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Ulbert, Sebastian. "DNA repair and antigenic variation in Trypanosoma brucei." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2003. http://dare.uva.nl/document/68203.
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Bell, S. R. "Mitochondrial DNA length variation in the mussel Mytilus." Thesis, Swansea University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.636073.
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Three types of mitochondrial DNA length variation in <I>Mytilus</I> were examined. For the purposes of this study, the three variations were termed "macro-length-variation", "micro-length-variation" and "<I>trossulus</I>-length variation". Macro-length-variation was observed at a frequency of 25% at the hybrid <I>M.galloprovincialis/M. edulis</I> population at Mevagissey on the south Cornish coast, southwest England, Mitochondrial DNA (mtDNA) was extracted and digested with a diagnostic enzyme, <I>Eco</I>RI. Positive results with F-genome specific PCR primers and probes indicate that the macro-length-variant is F-genome mtDNA. The normal length for <I>Mytilus </I>mtDNA is approx. 17.4 kb. Macro-length-variants showed mtDNA of lengths between 21.2 and 31.2 kb with an incremental increase of approx. 2.08 kb. Micro-length-variation was observed during polyacrylamide gel electrophoresis of PCR product. Sequence directed bending of the DNA helix is proposed as the cause of the electrophoretic mobility variability. <I>Trossulus</I>-length-variation was studied in five <I>M. trossulus</I> mussels taken from the Gulf of Gdansk in the Baltic Sea. PCR primers flanking the putative control region revealed incremental length increase of approx. 200 bp. PCR product from a normal-length individual and a length-increased individual was cloned and sequenced revealing a single tandem repeat of 190 bp at the extreme 3' end of the putative control region. The repeat junction aligns with a flanking tRNA (tyr) gene. RFLP analysis at a separate PCR locus revealed close similarity between the <I>M. trossulus </I>samples and common <I>M. edulis</I> haplotypes, confirming the findings of previous studies.
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Monckton, Darren G. "DNA sequence variation within and around human minisatellites." Thesis, University of Leicester, 1992. http://hdl.handle.net/2381/34450.
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Hypervariable minisatellites have found increasing use in a wide range of applications including linkage analysis, relationship testing and forensic medicine. Conventional length analysis via restriction digestion, agarose gel electrophoresis and Southern blot hybridization produces at best, less than 100 resolvable alleles and involves inherently error prone length estimations. Forensic analyses based on such a system have recently been heavily criticised and the population assumptions used to calculate match frequencies questioned. However, allele length is not the only criterion by which minisatellite variability may be assessed. All well characterised hypervariable human minisatellites also show variation in the dispersion patterns of minisatellite variant repeats. At the most well characterised human minisatellite MS32, MVR variation has been assayed by both restriction analyses and a more direct MVR-PCR approach. Both procedures have shown that allele length analysis seriously underestimates the true variability at minisatellite loci. Many individuals incorrectly typed as homozygous by length analysis have been demonstrated to be heterozygous by internal MVR mapping. MVR allelic analysis has been used to directly show the existence of many hundreds of different alleles, each one absolutely defined, from which we can infer the existence of many thousands of alleles. With a theoretical capacity to define many millions of alleles MVR analysis adds a new dimension to the study of variation in human DNA. The high observed allelic variability is directly reflected in the very high individual specificity obtained when MVR-PCR is applied to total genomic DNA to obtain a diploid code of the two superimposed alleles. MVR diploid code analysis produces a highly portable digital output which provides unambiguous match criteria. Diploid code analysis may be used to obtain highly discriminatory information from mixed DNA samples and, via the use of allele specific flanking primers in knockout MVR-PCR, from admixtures far lower than currently approachable. MVR analysis of allelic variation has revealed the existence of a terminal mutation hotspot which has been confirmed in studies of de novo mutation events in pedigrees. This work has revealed the complex nature of minisatellite mutation, with, for the first time, strong evidence for a role for unequal interallelic exchange and preliminary evidence for a size increase bias.
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Rehner, Stephen Austin. "Systematics, mating compatibility, and ribosomal DNA variation in Agrocybe section Pediadeae /." Thesis, Connect to this title online; UW restricted, 1989. http://hdl.handle.net/1773/5122.
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Watson, Michael Robert. "Heritable epigenetic variation of DNA methylation targets in plants." Thesis, University of Leeds, 2013. http://etheses.whiterose.ac.uk/5898/.
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DNA methylation marks regulate gene expression and genome structure. Stability and dynamics of DNA methylation patterns are influenced by four major factors including de novo methylation, maintenance methylation, passive loss of methylation and active demethylation. Maintenance methylation functions are still well conserved among plants and animals, which separated more than 1.5 billion years ago. In contrast, demethylation mechanisms differ considerably among plants and mammals. Interfering with DNA methylation and demethylation systems could be a source of heritable epigenetic variation if DNA methylation changes are introduced that transcend into stable heritable gene expression changes. The high tolerance of plants to DNA methylation changes makes them an ideal experimental system to exploit DNA methylation and demethylation systems. In this study, four strategies have been developed and tested for their capacity to induce heritable epigenetic variation by interfering with DNA methylation and demethylation systems. These strategies included a chemical treatment with a DNA methylation inhibitor, genetic demethylation using a mutant deficient in the maintenance methyltransferase MET1 and transgenic approaches to over-express MET1 and to express the human TET3 demethylase. While chemical demethylation only generated non-heritable changes, inactivating MET1 induced stable DNA methylation and expression changes at specific loci. Expression of the human TET3 protein also induced locus-specific loss of methylation but the efficiency of demethylation varied in individual transformants independent of TET3 level, which suggests that demethylation is locus-specific but stochastic.
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Whittaker, S. L. "Genetics of P. infestans - variation in DNA content and ploidy." Thesis, Bangor University, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.280024.
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Jones, Catherine S. "Mitochondrial DNA variation in British house mice (Mus domesticus, Rutty)." Thesis, University College London (University of London), 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.426183.
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Morphometric, karyological and historical evidence indicates that Caithness and Orkney House mice (Mus.domesticus Rutty) are genetically distinct from other British mice, suggesting they are descended from introductions. Mitochondrial DNA is a small, rapidly evolving, maternally inherited molecule; hence each mtDNA molecule carries in its sequence the history of its lineage uncomplicated by recombination. Thus, mtDNA RFLPs can be used for analysing possible patterns of colonisation and gene flow in these populations. Highly purified mtDNA was isolated from each mouse and mapped, using the high resolution restriction method, with respect to the published sequence of mouse mtDNA. This allowed the types and incidence of mutational change by which mtDNA evolves in the House mouse to be evaluated. A total of 23 mtDNA composite genotypes, assayed using 14 restriction enzymes, were recognised among the British mice examined and a genetic "break" observed between individuals from the north of Britain (Orkney, Ireland and N.E. Scotland; N.W lineage) and those from the south (British mainland, south of Caithness and Sutherland; S.E lineage)~ The approximate location of this "break" corresponds with the Great Glen fault, which marks a boundary between inhospitable moorland, occupied by Apode7ltus. Geographic orientation of mtDNA variability is concordant with data from other sources, including the paternal Y-chromosome DNA. The House mouse is unlikely to have survived the 1ast glaciation, dating the earliest possible British colonisation to about 10,000 B.P. An integrated approach, using evidence from anthropological, palaeontological, genetical and historical sources, permits the progression of the house mouse to be followed through Europe. These data indicate that Mus domesticus probably reached North-West Europe and Britain in the Iron
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Akhtar, Mahmood. "The role of DNA methylation in genetic variation of Listeria." Thesis, University of Nottingham, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267155.
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O'Sullivan, Helen Mary. "DNA transactions involved in pilin variation in Neisseria meningitidis C311." Thesis, University of Liverpool, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333670.
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Gomaa, R. "Analysis of mitochondrial DNA variation in the Egyptian population and its implications for forensic DNA analysis." Thesis, Nottingham Trent University, 2010. http://irep.ntu.ac.uk/id/eprint/357/.
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The genetic sequence of human mitochondrial DNA (mtDNA) is of particular interest to forensic investigations involving human identification, as well as population genetics. The current mtDNA database is lacking sufficient representatives of African mitochondrial DNA sequences compared to European and Asian sequences. The present study was concerned with the analysis of mtDNA in the Egyptian population. FTA cards were used for blood sample collection, storage, and shipment and DNA extraction. An optimised laboratory protocol for rapid PCR amplification of the mitochondrial hypervariable regions was developed. A database of 261 mitochondrial hypervariable region I (HVI) sequences and 78 hypervariable region II (HVII) sequences was established from 261 adult Egyptians. A total of 113 polymorphic sites were reported in the HVI region (nt16024-16365) which identified a total of 187 different haplotypes, of which 151 were unique to single individuals. The most commonly observed HVI haplotype was identical to the Cambridge Reference Sequence (CRS). Analysis of 78 HVII sequences (nt73-340) revealed a total of 42 polymorphic sites that identified 62 different haplotypes, of which 51 were unique to single individuals. Sites that showed the highest variability in the HVI and HVII regions agreed with the previously reported mutational hotspots. Combination of the HVI and HVII data resulted in identification of 207 different mitochondrial haplotypes, of which 183 (~88%) were unique to single individuals. Such a large number of unique mitochondrial haplotypes indicates a high diversity of mtDNA in the Egyptian population, which has a direct impact on forensic applications, since the significance of a match between an evidence sample and a reference sample depends on the population frequency of a profile. The random match probabilities in the HVI and HVII datasets were 2.34% and 3.22%, respectively. Combination of the two datasets reduced the random match probability to 1.28%. The genetic diversities in the HVI and HVII sequences were estimated to be 0.9804 and 0.9803, respectively, whereas, the genetic diversity in the combined dataset was 0.9911. A new strategy was developed to facilitate Restriction Fragment Length Polymorphism (RFLP) analysis of the whole mitochondrial genome for the purpose of haplogroup assignment. All the Egyptian individuals were assigned to well known mitochondrial haplogroups and the frequency distribution of different lineages was estimated. A mixed maternal ancestry of the Egyptian population was reported via detection of a mixture of mitochondrial DNA lineages with varying racial backgrounds. The most frequently reported mitochondrial lineages were haplogroup T (13.8%) followed by haplogroups L3 (12.6%), H (12.3%), U (~10%) and M (8.4%). The genetic relationship between Egypt and its neighbours was revealed, and it was found that present day Egyptians were the closest African population to the Middle East and Europe, with an overall 62.5% European, 25% African, and 12.5% Asian mitochondrial lineages. The data presented here will enrich the limited Egyptian mitochondrial DNA reference data currently available for forensic applications.
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MacDonald, Catherine. "Intraspecific and interspecific molecular variation in the Coelopidae." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367108.
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Coleman-Hulbert, Anna Luella. "Mitochondrial Inheritance and Natural Phenotypic Variation among Caenorhabditis briggsae Populations." PDXScholar, 2010. https://pdxscholar.library.pdx.edu/open_access_etds/340.
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Mutations affecting the mitochondrial electron transport chain cause numerous neurodegenerative disorders in humans and affect longevity in other organisms. A natural model system to study the relationship between mitochondrial function and aging within an evolutionary or population genetic context has been lacking. Natural populations of Caenorhabditis briggsae nematodes were recently found to harbor mitochondrial genetic variation with likely functional consequences for aging. Specifically, C. briggsae isolates containing high frequencies of a deletion mutation affecting the mitochondrial NADH dehydrogenase 5 (ND5) gene were found to have reduced reproductive fitness and lifespan and elevated levels of mutagenic superoxide. Here, rates of growth and aging and aerobic respiratory capacity were evaluated in several isolates spanning the range of mitochondrial genetic variation in this species. There is considerable variation among isolates for all measured traits, although the observed relationships between isolate-specific trait means and ND5 deletion frequency did not always conform to my expectations. In an effort to determine whether the among-isolate phenotypic variation is due to mitochondrial rather than to nuclear genetic variation, inter-population hybrids of C. briggsae were created and compared to the progenitor isolates. Surprisingly, evidence for paternal mitochondrial inheritance was detected in many of these hybrid lines. Where mitochondrial genomes were maternally inherited as expected, intergenomic epistasis appears to contribute to fitness, longevity, and aging in this species.
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Adrian, Andrew B. "Fine scale recombination variation in Drosophila melanogaster." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/2175.
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The study of natural variation is a principle component of biology. One process that affects levels of natural variation is meiotic recombination—the process by which homologous chromosomes break and interchange genetic information with one another during the formation of gametes. Surprisingly, this factor that shapes levels of natural variation across the genome itself presents with a great deal of variation. That variation manifests itself at many levels: within genomes, between individual organisms, across populations, and among species. The factors and mechanisms responsible for the non-random patterning of recombination events across the genome remain particularly elusive in most cases. Herein, I utilize a combination of bioinformatic and molecular genetic approaches to better explain recombination patterning. I explore several factors that are now known to contribute to the distribution of recombination events across genomes. In particular, I demonstrate that transcriptional activity during meiosis is associated with, and partially predictive of crossing over events in Drosophila melanogaster. Additionally, I present a model which is capable of accounting for approximately 40% of the variation in crossover rates in Drosophila based on the localization of several previously identified DNA motifs. Lastly, I present preliminary data describing how recombination patterns are altered under naturally stressful conditions, a key insight that is necessary for uniting our findings at one level of variation with the many others. These findings support a multifactorial model for crossover distribution that includes both genetic and epigenetic factors and will further progress the field in developing a comprehensive understanding of recombination localization.
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Dunlop, Gordon. "Linking germination traits of oilseed rape (Brassica napus L.) to DNA markers." Thesis, Abertay University, 2000. https://rke.abertay.ac.uk/en/studentTheses/22973d1e-546d-4238-9ed8-32a4403f3a52.
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Oilseed rape has become an important weed in arable rotations and a feral plant of field margins, soil dumps and roadsides. Seed persistence in the soil following induced secondary dormancy is thought to perpetuate these weed and feral populations. Potential variation between cultivars has been suggested in previous work in the extent of secondary dormancy and other germination traits, and in underlying genetic heterogeneity. The aim of this work was to quantify in more detail inter- and intra- cultivar variation in germination traits for six oilseed rape cultivars, to confirm that variation was consistent in laboratory and field, and to ascertain whether there is a genetic base to this variation. The cultivars are Askari, Bristol, Gazelle, Libravo, Martina and Rocket, selected on the basis of their suspected heterogeneity. Laboratory germination tests were conducted at 4°C, 10°C and 19°C on a thermal plate and confirmed substantial inter-cultivar variation in germination rate, induction of secondary dormancy and the temperature stimuli required for dormancy break. The phenotypic traits were quantified by mathematical parameters and cultivars ranked in order of decreasing heterogeneity. DNA analysis was made on leaf tissue of early, middle and late germinating phenotypes using two simple sequence repeat primers. There was heterogeneity and phenotypic variability generally, but a direct association between phenotype and genotype was found only in the cultivar Martina. Field emergence trials revealed non-linearity in emergence and a strong similarity between laboratory germination and field emergence curves. Cultivar heterogeneity was found to be similar for emergence rate and post-winter emergence. Again there was evidence of an association between heterogeneity in emergence and genetic heterogeneity in the DNA markers. The results suggest that standard seed testing should be carried out at low temperatures to detect any hidden variability in germination. Plant breeders should be cautious about introducing variability into new breeding lines as this might increase the potential persistence of feral populations and the risk of gene transfer to later.
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Smith, Melvin N. E. "Variation among native and alien populations of hoary mustard, Hirschfeldia incana (L.) Lagreze-Fossat, and the application of DNA melting analysis to investigate microsatellite (SSR) variation." Thesis, Swansea University, 2010. https://cronfa.swan.ac.uk/Record/cronfa42609.
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H. incana is a native species of the Mediterranean and Middle East. As a neophyte (alien) it has undergone a large range expansion in Northern Europe, the Americas, Asia and Australasia. Casual field observations suggested that within its native range, the dominant life strategy of H.incana was annual, whereas in the British flora it was predominantly perennial. Populations from native and alien ranges were studied in the field and in common garden experiments. Phenotypic differences in morphological and physiological characteristics were compared. Plants derived from neophyte British populations made larger leaf rosettes, flowered later (> 140 days) and exhibited a perennial life cycle. Plants from native. North African and Southern European populations (excepting those from montane Spain) made smaller rosettes, flowered early (< 110 days) and died after flowering once. Neophyte populations from California were similar to native populations. Some native populations (e.g. Cypress) did not survive a British winter. Unlike native populations, initiation of flowering in neophyte British populations was stimulated by a period of vernalisation. These results suggest that life strategy changes have occurred in neophyte populations of H. incana as this species expanded its range northwards, and implies possible genetic differences. Ten microsatellite primers, previously described for related Brassicaceae species, were therefore investigated for potential use in the assessment of H. incana population genetic structure. Five primers successfully amplified a product of expected size, of which 3 were subscequently sequenced to confirm the presence of the SSR. The application of real-time PCR DNA melting analysis to identify SSR variation was investigated using Roche SYBR green and Corbett HRM platforms. SSR variation could be detected using DNA melt analysis, but due to difficulty identifying the composition of heterozygous SSR's the technique could not be sufficiently refined to investigate population diversity. However, preliminary results indicated possible SSR variation between isolated populations.
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Modin, Helena. "Multiple sclerosis : linkage analysis and DNA variation in a complex trait /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-792-4/.
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Fredriksson, Mona. "Using Minisequencing Technology for Analysing Genetic Variation in DNA and RNA." Doctoral thesis, Uppsala University, Department of Medical Sciences, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4789.
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<p>In this thesis, the four-color fluorescence tag-microarray minisequencing system pioneered by our group was further developed and applied for analysing genetic variation in human DNA and RNA. A SNP marker panel representing different chromosomal regions was established and used for identification of informative SNP markers for monitoring chimerism after stem cell transplantation (SCT). The success of SCT was monitored by measuring the allelic ratios of informative SNPs in follow-up samples from nine patients with leukaemia. The results agreed with data obtained using microsatellite markers. Further the same SNP marker panel was used for evaluation of two whole genome amplification methods, primer extension preamplification (PEP) and multiple displacement amplification (MDA) in comparison with genomic DNA with respect to SNP genotyping success and accuracy in tag-array minisequencing. Identical results were obtained from MDA products and genomic DNA.</p><p>The tag-microarray minisequencing system was also established for multiplexed quantification of imbalanced expression of SNP alleles. Two endothelial cell lines and a panel of ten coding SNPs in five genes were used as model system. Six heterozygous SNPs were genotyped in RNA (cDNA) from the cell lines. Comparison of the relative amounts of the SNPs alleles in cDNA to heterozygote SNPs in genomic DNA displayed four SNPs with significant imbalanced expression between the SNP alleles. Finally, the tag-array minisequencing system was modified for detection of splice variants in mRNA from five leukaemia cell lines. A panel of 20 cancer-related genes with 74 alternatively splice variants was screened. Over half of the splice variants were detected in the cell lines, and similar alternative splicing patterns were observed in each cell line. The results were verified by size analysis of the PCR product subjected to the minisequencing primer extension reaction. The data from both methods agreed well, evidencing for a high sensitivity of our system.</p>
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Angleby, Helen. "Analysis of domestic dog mitochondrial DNA sequence variation for forensic investigations." Licentiate thesis, Stockholm, Kungl. tekniska högskolan (KTH), 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-299.
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Bell, Joanna Sharlene. "Mismatch repair in DNA recombination and antigenic variation in Trypanosoma brucei." Thesis, University of Glasgow, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394819.
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Mowforth, Miriam A. G. "Variation in nuclear DNA amounts in flowering plants : an ecological anlaysis." Thesis, University of Sheffield, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326707.
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Smyth, Audra Jayne. "Sequence variation in Leishmania kinetoplast DNA minicircles and diagnosis of leishmaniasis." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386238.
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Hernandez, D. M. G. "Genetic variation and DNA methylation in the context of neurological disease." Thesis, University College London (University of London), 2016. http://discovery.ucl.ac.uk/1485836/.
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Understanding genetic control of biological processes is an important goal in the post-genome era. GWA studies have been successful in identifying loci linked to disease and recently in revealing disease risk alleles. However, pinpointing key genes and their alterations within associated loci remains a central challenge. Described is the completion of a large, international metaanalysis and replication study of existing PD GWA data, confirming 6 previously identified loci and identifying and confirming an additional 5 novel loci; thus, expanding our understanding of the genetic basis of PD. Following this is an effort to annotate the consequences of genetic variation within the context of normal human brain tissue by generating and integrating data to investigate the effects of common genetic variability on DNA methylation in four brain regions of 150 neurologically normal individuals, 600 samples total. Genome-wide SNP data is generated and 27,578 CpG sites assessed in each brain region. Results show methylation patterns differ between brain regions, genotype is correlated with methylation levels and DNA methylation QTL occur more often in sites outside of CpG islands. Next, an expanded map of DNA methylation in human brain assessing 486,428 CpG sites is generated and proximal CpG sites are integrated with known PD loci implicated by GWA studies; thus, gaining potential mechanistic insight into pathogenesis of disease. Significant DNA methylation QTL for 19 of 28 PD risk loci are identified, demonstrating the correlation of risk alleles for neurological disease with a biologically relevant trait in human brain tissue is a manageable goal. Lastly, analyses show CpG sites within normal human brain exhibit significant age-associated increases in methylation with an enrichment of changes at CpG islands of functionally related transcripts; thus, providing a footing for future integration of age-related epigenetic changes into disease models exhibiting age as a primary risk factor.
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Givens, Chandler Brooke. "Genetic Variation Among Geographically Disparate Yellow Perch Broodstock Populations." VCU Scholars Compass, 2006. http://hdl.handle.net/10156/1385.
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Kuhn, Kristen Leigh. "Patterns of Microsatellite and Mitochondrial DNA Variation Among Anadromous and Freshwater Alewife (Alosa pseudoharengus) Populations." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/KuhnKL2004.pdf.
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Mutun, Serap Borst David Wellington. "Intraspecific mitochondrial DNA variation in the lubber grasshopper, Romalea guttata (Orthoptera : Acrididae)." Normal, Ill. Illinois State University, 1999. http://wwwlib.umi.com/cr/ilstu/fullcit?p9942647.
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Thesis (Ph. D.)--Illinois State University, 1999.<br>Title from title page screen, viewed July 24, 2006. Dissertation Committee: David W. Borst (chair), Angelo P. Capparella, Sabine S. Loew, Edward L. Mockford, Carleton J. Phillips, Douglas W. Whitman. Includes bibliographical references (leaves 77-89) and abstract. Also available in print.
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Niemi, A. K. (Anna-Kaisa). "Mitochondrial DNA variation in extremely selected traits: longevity and elite athletic performance." Doctoral thesis, University of Oulu, 2005. http://urn.fi/urn:isbn:951427699X.
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Abstract
Mitochondria contain a maternally inherited 16,568bp genome (mtDNA) that encodes for 13 out of more than 70 subunits of complexes of the respiratory chain that produce ATP by oxidative phosphorylation (OXPHOS). As a byproduct of OXPHOS, reactive oxygen species (ROS) are formed, which may play a role in ageing. MtDNA has accumulated numerous polymorphisms during evolution, leading to haplogroups characterized by ancient polymorphisms and defined by letters. MtDNA polymorphisms are thought to be neutral, but some may be slightly deleterious or even advantageous and may influence phenotypes of complex traits. Interestingly, several complex traits such as longevity and maximal aerobic power show maternal inheritance. Associations between mtDNA polymorphisms and longevity have been reported, but no systematic study has been made of the role of mtDNA in longevity. In addition, there are no previous reports on mtDNA haplogroups in elite athletic performance.
Associations are demonstrated here between mtDNA haplogroups J, K and U and longevity in Finns. Interestingly, subhaplogroup J2 and haplogroup K, which were found in increased frequency among the 225 very old subjects studied, were not found among the 52 endurance athletes but were present in 11% of the 89 sprint athletes Uncoupling of OXPHOS reduces ATP and ROS production. Thus, a mitochondrial genome with a higher level of uncoupling may promote longevity but may not be favourable in situations that require a high level of ATP production, such as elite endurance performance. A more detailed analysis also showed an association between a combination of three common mtDNA polymorphisms and longevity in both the Finns and the Japanese, providing the first epidemiological support for the assumption that the nature of a mutation is determined by interactions with other mutations in mtDNA. In addition, a systematic approach was applied to study the role of mtDNA in longevity. Association analyses of mtDNA allele combinations in longevity revealed that the mtDNA control region, the tRNA and rRNA genes and the nucleotide repeats in mtDNA may play a role in longevity, since the alleles and allele combinations that showed the strongest associations with longevity, either negative or positive, were among these genes. Differences in overall variation in mtDNA between the very old and their controls were also studied, revealing more differences at synonymous (silent) sites than at non-synonymous (amino acid altering) sites.
The findings support previous data suggesting that certain mtDNA haplogroups are associated with longevity. In addition, those haplogroups that increased in frequency among the very old Finns were not found among Finnish endurance athletes. Also, a novel systematic approach was applied to study mtDNA alleles, allele combinations and overall sequence variation in longevity, suggesting that there are interactions between various mtDNA positions and that the tRNA and rRNA genes and short tandem repeats in mtDNA may play a role in longevity.
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Mastana, Sarabjit Singh. "Genetic variation and structure in selected human populations : serogenetic and DNA studies." Thesis, University of Newcastle Upon Tyne, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.261150.
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Plaster, C. A. "Variation in Y chromosome, mitochondrial DNA and labels of identity on Ethiopia." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1331901/.
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There is a paucity of genetic studies of Ethiopia. This thesis aims to establish the extent and distribution of variation in NRY and mtDNA genetic markers as well as ethnic and linguistic labels of identity 45 ethnic groups. A wide range of NRY and mtDNA haplogroups were observed, including both those typically observed in Africa and those more frequently observed outside Africa. Significant correlations were revealed between NRY and mtDNA diversity. Nearly all ethnic groups were significantly differentiated from each other, although the pattern of similarities indicates some recent gene flow between northern ethnic groups and some groups to the south. Significant correlations were observed between almost all measures of linguistic and ethnic similarity and measures of NRY and mtDNA genetic distance. A wide range of values for diversity of sample donors' ethnic and linguistic identity was observed across groups. There was no evidence that the language of the sample donor is more likely to be inherited from parents of one sex rather than the other. There was a general decrease in the proportion of sample donors speaking the traditional language of their ethnic groups compared with the donor's parents and grandparents, with a corresponding increase in the proportion of sample donors speaking Amhara as a first language. Restricting analysis to samples from donors with ethnic identity in common with their parents and grandparents had significant effects on the degree of genetic distinctiveness of ethnic groups. Increasing the level of resolution of NRY and mtDNA haplotypes did not substantially alter the patterns of diversity and distance observed in and amongst ethnic groups. This thesis makes an important contribution to understanding the distribution of genetic diversity in Ethiopia.
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Cosner, Mary Elizabeth. "Phylogenetic and molecular evolutionary studies of chloroplast DNA variation in the campanulaceae /." The Ohio State University, 1993. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487847761306203.
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Elguzouli, Amna Eltayeb. "MITOCHONDRIAL DNA SEQUENCE VARIATION IN THE AFRICAN ARMYWORM SPODOPTERA EXEMPTA (LEPIDOPTERA: NOCTUIDAE)." OpenSIUC, 2013. https://opensiuc.lib.siu.edu/theses/1346.
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AN ABSTRACT OF THE THESIS OF AMNA E. ELGUZOULI, for the Master of Science degree in ZOOLOGY, presented on May 8, 2012, at Southern Illinois University TITLE: Mitochondrial DNA sequence variation in the African Armyworm Spodoptera exempta (Lepidoptera: Noctuidae) MAJOR PROFESSOR: Kamal M. Ibrahim The African Armyworm remains problematic as a serious pest of cereals in sub-Sahara Africa. The population genetic structure of African armyworms was investigated to better understand the species' population dynamics and the extent to which the two major outbreak areas in East Africa and Southern Africa are linked by gene flow. Specifically, I characterized the genetic variation of armyworm samples from Tanzania and South Africa and assessed whether the periodic swarming of armyworms homogenizes populations throughout the species range. The variability of a range of mitochondrial genes was screened. A 413 base pair long fragment of the Cytochrome Oxidase I gene (COI), located within positions 1688 to 2175 of the reference locust mitochondrial genome was found to be an ideal marker. This sequence is part of the Folmer region of the COI gene that is used as a 'barcode' for all animal taxa. Haplotype diversity was found to be comparable to reports in the Spruce Budworm (Choristoneuru fumiferana), which, like the African armyworm, undergoes sporadic population buildup. The sequences were A+T rich particularly at the first codon position confirming previous findings in other insect species. ii A population genetic analysis of the sequence variation revealed that African armyworm populations are genetically structured and do not form a single panmictic population. Despite the limited sampling in this study, a clear picture of significant genetic separation between Tanzanian and South African armyworm populations has been confirmed. This leads to the conclusion that the extent of mixing resulting from the well documented tracking of the Inter Tropical Convergence Zone by outbreak populations does not connect Tanzanian and South Africa armyworm populations. Many rare haplotypes that are one mutation step from one of two common haplotypes were observed; a parsimony based haplotype network supports the hypothesis that these rare haplotype may have arisen during the regional population expansions. However, because the southern and northern regions that were sampled share the same two common haplotypes, neither the phylogenetic trees nor the haplotype networks yielded geographic signal that show where the rare haplotypes may have evolved. The presence of many unique singleton haplotypes, coupled with the pattern of their mismatch distribution, suggests exponential growth of localized armyworm populations. Outbreak populations arise separately in different locations across the species geographic distribution; it appears that the sizes of these populations become large enough for new mutations to produce new variants in each location. The fact that the two commonest haplotypes were present both in South Africa and in Tanzania indicates that some exchange of migrants does take place between the two regions. Alternatively, since the haplotypes that are unique to each region are derived from, and a single mutation step away from, these two common haplotypes, this could indicate that the two common haplotypes were shared in the ancestral populations and that no current gene flow takes iii place. In either case, it is apparent that the periodic swarming of armyworms does not homogenize the entire species range. What are the implications of these findings to the control of armyworm infestations? Armyworm population dynamics in the species' northern range appears to be decoupled from its population dynamics in the south. This implies that this pest's control strategies need to be region specific. However, this study had only two sampling points. It is plausible that a stepping-stone type of link exists in between and that I have sampled the extreme northern and southern ends of the link. A finer scale, multipoint sampling throughout the species geographic range, preferably during multiple years, is required in order to answer this question unambiguously. This would assist in developing an outbreak early warning system and in determining if multi-region control strategy is warranted. I also draw attention to another caveat to the above conclusions: a significant proportion of the divergence between the two sampling localities is attributable to two rare but highly divergent haplotypes. The possibility of these two haplotypes belonging to another, as yet unknown moth species, has been discussed. In addition to the above insights, this study has assessed the utility of the large number of universal mtDNA primers in the study of armyworm population genetics.
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Elrod, Diana Adams. "Mitochondrial DNA Sequence Variation in Populations of the Nine-Banded Armadillo (Dasypus novemcinctus)." Thesis, University of North Texas, 2000. https://digital.library.unt.edu/ark:/67531/metadc2577/.
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Four populations of nine-banded armadillos, Dasypus novemcinctus, were investigated in the south-central United States in order to assess genetic variation in an isolated population (Electric Island, Lake Hamilton, Garland County, Arkansas); a semi-isolated population (Arkansas Post, Arkansas County, Arkansas), and two free ranging populations (southern Arkansas and central Texas). A 233 basepair sequence of the D-loop region of mitochondrial DNA was sequenced in individuals from each population. Individuals and populations were compared to assess relatedness among populations and individuals. Higher sequence diversity was detected in the semi-isolated population, while lower sequence diversity was observed in the isolated and free ranging populations. Overall, all populations exhibited low genetic variation when compared to genetic variation for other mammals. The results support the hypothesis that rapid range expansion combined with the organism's unique reproductive strategies have promulgated low genetic variation in the North American populations of nine-banded armadillos.
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Lindstedt, Elenor. "Genetic variation between and within populations of Leucorrhinia dubia in Sweden, Finland and Norway." Thesis, Högskolan i Halmstad, Akademin för ekonomi, teknik och naturvetenskap, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:hh:diva-30990.
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Genom att extrahera, amplifiera och sekvensera DNA från ben av trollsländeartenLeucorrhinia dubia ämnar jag få en inblick i hur arter invandrat till Skandinavien sedan densenaste istiden och en mindre inblick i den genetiska variationen av arten i Skandinavien. Fördetta valdes en mitokondrisk gen (cytochrome c oxidase subunit I, COI) och en nukleär (28sribosomal RNA subunit D7). Totalt blev det 112 sekvenser (55 av COI genen och 57 för D7genen) från 10 olika populationer i Sverige, Norge och Finland som delade upp sig i tvåseparata klader med lite variation mellan individerna i de fylogenetiska träden. Utseendet påträden skulle kunna tyda på att L. dubia invandrat till Skandinavien flera gånger och kansketill och med från flera refuger, en i söder i Centraleuropa och en i öster i närheten avKaukasus. Trädens utseende tyder även på att arten egentligen är flera, kanske kryptiska arter.
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Labuschagne, Jeanine. "Molecular methods for genotyping selected detoxification and DNA repair enzymes / J. Labuschagne." Thesis, North-West University, 2010. http://hdl.handle.net/10394/4599.
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The emerging field of personalized medicine and the prediction of side effects experienced due to pharmaceutical drugs is being studied intensively in the post genomic era. The molecular basis of inheritance and disease susceptibility is being unravelled, especially through the use of rapidly evolving new technologies. This in turn facilitates analyses of individual variations in the whole genome of both single subjects and large groups of subjects.
Genetic variation is a common occurrence and although most genetic variations do not have any apparent effect on the gene product some do exhibit effects, such as an altered ability to detoxify xenobiotics.
The human body has a highly effective detoxification system that detoxifies and excretes endogenous as well as exogenous toxins. Numerous studies have proved that specific genetic variations have an influence on the efficacy of the metabolism of pharmaceutical drugs and consequently the dosage administered.
The primary aim of this project was the local implementation and assessment of two different genotyping approaches namely: the Applied Biosystems SNaPshot technique and Affymetrix DMET microarray. A secondary aim was to investigate if links could be found between the genetic data and the biochemical detoxification profile of participants. I investigated the approaches and gained insight into which method would be better for specific local applications, taking into consideration the robustness and ease of implementation as well as cost effectiveness in terms of data generated.
The final study cohort comprised of 18 participants whose detoxification profiles were known. Genotyping was performed using the DMET microarray and SNaPshot techniques. The SNaPshot technique was used to genotype 11 SNPs relating to DNA repair and detoxification and was performed locally. Each DMET microarray delivers significantly more data in that it genotypes 1931 genetic markers relating to drug metabolism and transport. Due to the absence of a local service supplier, the DMET - microarrays were outsourced to DNALink in South Korea. DNALink generated raw data which was analysed locally.
I experienced many problems with the implementation of the SNaPshot technique. Numerous avenues of troubleshooting were explored with varying degrees of success. I concluded that SNaPshot technology is not the best suited approach for genotyping. Data obtained from the DMET microarray was fed into the DMET console software to obtain genotypes and subsequently analysed with the help of the NWU statistical consultation services. Two approaches were followed: firstly, clustering the data and, secondly, a targeted gene approach. Neither of the two methods was able to establish a relationship between the DMET genotyping data and the detoxification profiling.
For future studies to successfully correlate SNPs or SNP groups and a specific detoxification profile, two key issues should be addressed: i) The procedure for determining the detoxification profile following substrate loading should be further refined by more frequent sampling after substrate loading. ii) The number of participants should be increased to provide statistical power that will enable a true representation of the particular genetic markers in the specific population. The statistical analyses, such as latent class analyses to cluster the participants will also be of much more use for data analyses and interpretation if the study is not underpowered.<br>Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.
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McGlashan, Dugald James. "Consequences of Dispersal, Stream Structure and Earth History on Patterns of Allozyme and Mitochondrial DNA Variation of Three Species of Australian Freshwater Fish." Thesis, Griffith University, 2000. http://hdl.handle.net/10072/366647.
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Freshwater systems offer important opportunities to investigate the consequences of intrinsic biological and extrinsic environmental factors on the distribution of genetic variation, and hence population genetic structure. Drainages serve to isolate populations and so preserve historical imprints of population processes. Nevertheless, dispersal between and within drainages is important if the biology of the species confers a good dispersal capability. Knowledge of the population genetic structure or phylogeographic patterns of Australia's freshwater fish fauna is generally depauperate, and the present study aimed to increase this knowledge by investigating patterns of genetic diversity in three Australian species of freshwater fish. I was interested in the relative importance of dispersal capability, the hierarchical nature of stream structure and the consequences of earth history events on patterns of genetic diversity among populations. I examined three species from three families of Australian freshwater fish, Pseudomugil signifer (Pseudomugilidae), Craterocephalus stercusmuscarum (Atherinidae) and Hypseleotris compressa (Gobiidae). These species are abundant, have wide overlapping distributions and qualitatively different dispersal capabilities. I was interested in attempting to unravel how the biological, environmental and historical factors had served to influence the patterns and extent of genetic diversity within each species, thereby inferring some of the important evolutionary processes which have affected Australia's freshwater fauna. I used allozyme and 500-650bp sequences from the ATPase6 mitochondrial DNA (mtDNA) gene to quantify the patterns of genetic variation at several hierarchical levels: within populations, among populations within drainages and among drainages. I collected fish at several spatial scales, from species wide to multiple samples within drainages; samples were collected from the Northern Territory, Queensland and New South Wales. The species with the highest potential for dispersal, H. compressa, exhibited the lowest levels of genetic differentiation as measured at several allozyme loci (H. compressa: FST=0.014; P. signifer FST=0.58; C. stercusmuscarum FST=0.74). Populations of H. compressa also had low levels of mtDNA differentiation, with many recently derived haplotypes which were widespread along the coast of Queensland. This suggested either considerable gene flow occurs or recent demographic change in the populations sampled. As there was no relationship between geographic distance and genetic differentiation, the populations appeared to be out of genetic drift - gene flow equilibrium, assuming the two-dimensional stepping stone model of gene flow. Estimating contemporary gene flow was thus difficult. It was apparent that there has been a recent population expansion and / or contraction of H. compressa populations. It was concluded that there has been considerably more connectivity among populations of H. compressa in the recent past than either of the other study species. Populations of P. signifer showed considerable genetic subdivision at different hierarchical levels throughout the sampled range, indicating gene flow was restricted, especially between separate drainages. Two widely divergent regional groups which had high ATPase6 sequence divergence and approximately concordant patterns at allozyme loci were identified. Interestingly, the groups mirrored previous taxonomic designations. There was also significant subdivision among drainages within regional groups. For example, the adjacent Mulgrave-Russell and Johnstone drainages had individuals with haplotypes that were reciprocally monophyletic and had large allozyme frequency differences. This allowed me to examine the patterns of genetic differentiation among populations within drainages of two essentially independent, but geographically close systems. There was as much allozyme differentiation among populations within subcatchments as there was between subcatchments within drainages, and significant isolation by distance among all populations sampled within a drainage. This suggested that the estuarine confluence between subcatchments was not a barrier to P. signifer, but that distance was an important component in the determination of the distribution of genetic diversity within drainages in P. signifer. There were three main areas of investigation for C. stercusmuscarum: comparing upland and lowland streams of the drainages in north Queensland, investigating the consequences of eustasy on coastal margin populations and examining the intriguing distribution of the two putative sub species, C. s. stercusmuscarum and C. s. fulvus in south east Queensland. First, as populations in upland areas of east coast flowing rivers are above large discontinuities in the river profile, their occurrence is presumably the result of gene flow to and / or from lowland areas, or the result of invasions via the diversion of western flowing rivers. Concordant patterns at both genetic markers revealed that the latter possibility was the most likely, with fixed allozyme differences between upland and lowland populations, and large mtDNA sequence divergence. Indeed, it appeared that there may have been two independent invasions into the upland areas of rivers in North Queensland. Second, lowland east coast populations also had large, although not as pronounced, levels of population subdivision. Lack of isolation by distance, but with a concomitant high level of genetic differentiation among many comparisons, was consistent with a scenario of many small, isolated subpopulations over the range. Interestingly, widespread populations in central Queensland coastal populations (drainages which receive the lowest rainfall) were relatively genetically similar. This was consistent with the widest part of the continental shelf which at periods of lower sea level apparently formed a large interconnected drainage, illustrating the effect of eustatic changes on populations inhabiting a continental margin. Third, putative C. s. fulvus in lowland coastal Queensland drainages were genetically more similar to a population of C. s. fulvus collected from a tributary of the Murray-Darling (western flowing) than they were to adjacent putative C. s. stercusmuscarum. This implied that populations in south east Queensland, north to approximately the Burnett River, appeared to be derived from western flowing streams, and not via dispersal from other lowland east coast populations. Determining the relative importance of intrinsic and extrinsic factors to the development of population genetic structure is a difficult task. The present study demonstrated that the species with the highest dispersal potential had the lowest levels of genetic differentiation, waterfalls can limit gene flow, eustasy acts to join and separate populations leading to complex genetic patterns and that drainage rearrangements are important in determining the distribution of genetic diversity of populations now inhabiting isolated drainages. A difficulty with generalising about population genetic structure in obligate freshwater animals is the unique history of not only each drainage, but also the streams within that drainage and the idiosyncratic biological dynamics of the populations inhabiting those drainages.<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>Australian School of Environmental Studies<br>Full Text
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Peterson, Russ. "An examination of Crassostrea virginica nuclear DNA variation along the North Carolina coast /." Electronic version (PDF), 2006. http://dl.uncw.edu/etd/2006/petersonr/russpeterson.pdf.
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Siemann, Liese Anne 1966. "Mitochondrial DNA sequence variation in North Atlantic long-finned pilot whales, Globicephala melas." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/11943.
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Bofkin, Lee Nathan Marc. "The causes and consequences of variation in evolutionary processes acting on DNA sequences." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613925.
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Beech, Robin Nicholas. "Insertion-deletion variation in the DNA of three natural populations of Drosophila melanogaster." Thesis, University of Edinburgh, 1987. http://hdl.handle.net/1842/10772.
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Henson, Brian Junior. "Evolution, Variation, and Excision of Developmentally Regulated DNA Elements in the Heterocystous Cyanobacteria." Miami University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=miami1132247140.
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