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1
De, Bustos Cecilia. "Genetic and Epigenetic Variation in the Human Genome : Analysis of Phenotypically Normal Individuals and Patients Affected with Brain Tumors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6629.
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Walker, Tina Kay. "Genetic variation in schistosomes." Thesis, Brunel University, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.278245.
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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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Keightley, Peter D. "Studies of quantitative genetic variation." Thesis, University of Edinburgh, 1988. http://hdl.handle.net/1842/12340.
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Loh, Yong-Hwee Eddie. "Genetic variation in fast-evolving East African cichlid fishes: an evolutionary perspective." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41148.
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Cichlid fishes from the East African Rift lakes Victoria, Tanganyika and Malawi represent a preeminent example of replicated and rapid evolutionary radiation. In this single natural system, numerous morphological (eg. jaw and tooth shape, color patterns, visual sensitivity), behavioral (eg. bower-building) and physiological (eg. development, neural patterning) phenotypes have emerged, much akin to a mutagenic screen. This dissertation encompasses three studies that seek to decipher the underpinnings of such rapid evolutionary diversification, investigated via the genetic variation in East African cichlids.
We generated a valuable cichlid genomic resource of five low-coverage Lake Malawi cichlid genomes, from which the general properties of the genome were characterized. Nucleotide diversity of Malawi cichlids was low at 0.26%, and a sample genotyping study found that biallelic polymorphisms segregate widely throughout the Malawi species flock, making each species a mosaic of ancestrally polymorphic genomes. A second genotyping study expanded our evolutionary analysis to cover the entire East African cichlid radiation, where we found that more than 40% of single nucleotide polymorphisms (SNPs) were ancestral polymorphisms shared across multiple lakes. Bayesian analysis of genetic structure in the data supported the hypothesis that riverine species had contributed significantly to the genomes of Malawi cichlids and that Lake Malawi cichlids are not monophyletic. Both genotyping studies also identified interesting loci involved in important sensory as well as developmental pathways that were well differentiated between species and lineages. We also investigated cichlid genetic variation in relation to the evolution of microRNA regulation, and found that divergent selection on miRNA target sites may have led to differential gene expression, which contributed to the diversification of cichlid species.
Overall, the patterns of cichlid genetic variation seem to be dominated by the phenomena of extensive sharing of ancestral polymorphisms. We thus believe that standing genetic variation in the form of ancestrally inherited polymorphisms, as opposed to variations arising from new mutations, provides much of the genetic diversity on which selection acts, allowing for the rapid and repeated adaptive radiation of East African cichlids.
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Gunn, Melissa Rose School of Biological Earth & Environmental Science UNSW. "The use of microsatellites as a surrogate for quantitative trait variation in conservation." Awarded by:University of New South Wales. School of Biological, Earth and Environmental Science, 2003. http://handle.unsw.edu.au/1959.4/22457.
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Conservation biologists are interested in maintaining genetic variation in small populations, with a view to maintaining fitness and the ability of the species to adapt to changing environmental conditions. The most important type of genetic variation is therefore that which affects fitness and reproduction, and is therefore subject to natural selection. Such fitness traits are often quantitative, i.e. are the result of a suite of loci, and are continuously variable. Microsatellite markers are a popular method of determining the level of variation present in a species??? genome. The assumption is made that microsatellites, which are neutral markers, behave in the same manner as quantitative traits. If this assumption were proved incorrect, then the use of neutral markers in conservation monitoring would have to be re-evaluated. In this study, experiments have been conducted using Drosophila melanogaster to test the assumption that variation in quantitative traits under stabilising selection declines at the same rate as heterozygosity in microsatellite markers, during a population bottleneck. Experimental population bottlenecks were of two effective population sizes (Ne), Ne=2 for one generation and Ne=60 for 35 generations. Based on the effective population size, we expected both types of bottlenecks to lose 25% of neutral genetic variation. Ten replicates of each bottleneck were maintained, along with four large control populations with Ne=320. In each population, heterozygosity (He) for eight microsatellite loci was compared with the heritability and additive genetic variance of two quantitative traits subject to balancing selection: fecundity and sternopleural bristle number. Microsatellite heterozygosity decreased in accordance with neutral predictions, whereas additive genetic variation in quantitative traits altered more than expected in both large and in bottlenecked populations relative to the initial sampling values, indicating that variation in quantitative traits was not being lost at the same rate as predicted by neutral theory. For most traits, the changes in additive genetic variance were congruent in all populations, large or bottlenecked. This congruence suggests that a common process was affecting all populations, such as adaptation. A mite infestation in early generations is a possible source of selective pressure. When bottlenecked populations were compared to the contemporaneous large populations (Ne = 320), the additive genetic variance of most traits was seen to have been lost in accordance with predictions from the loss of microsatellite heterozygosity. Loss of variation in microsatellites can thus be used to predict the loss of variation in quantitative traits due to bottlenecks, but not to predict the potentially much larger changes due to other processes such as adaptation. The effects of concurrent environmental stress and reduced population size were also evaluated. Endangered populations are often subject to environmental stress in addition to reduced population size, but the effect of stress on the additive genetic variance of fitness traits in organisms undergoing population bottlenecks is unknown. If the presence of stress alters the level of additive genetic variance in fitness traits, the viability of such populations could be substantially affected. The loss of microsatellite heterozygosity was not affected by the presence of a stress agent during a bottleneck. I found some significant effects of stress on the additive genetic variance of sternopleural bristles and fecundity; there was also a significant interaction between stress and the response to directional selection in sternopleural bristles. There was also an increase in the coefficient of variation of VA for sternopleural bristles. Stress may therefore affect the manner in which populations respond to selective pressures.
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Roussos, Athanasios. "Morphological variation, population genetics and genetic relatedness in three species of Callopora." Thesis, Swansea University, 2007. https://cronfa.swan.ac.uk/Record/cronfa42590.
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The genus Callopora is typical of a very large number of encrusting neocheilostomate genera and can be used to demonstrate the range of autozooid morphology seen in the group. Morphometric analyses of zooid length (ZL), zooid width (ZW), ovicell length (OL) and ovicell width (OW) were conducted in order to study morphological variation in different populations of Callopora dumerilii, Callopora lineata and CaUopora rylandi and to partition the morphological variation within and between sites and colonies for each species using a nested analysis of variance and a principal component analysis approach. In addition, the genetic structure in populations of these three Callopora species using the mitochondrial DNA COI gene was examined to test hypotheses concerning levels of population differentiation and intrapopulation variation. The relationships of mtDNA lineages within and between species was also investigated to clarify the phylogenetic relationships of the three species and to search for possible phylogenetic subdivisions within species. The morphological characters zooid length and zooid width were significantly different between different sites for Callopora lineata and Callopora dumerilii, but not for Callopora rylandi. However, major differences for these two morphological variables appeared in all three species in between colony within site comparisons. When comparing the ovicell length variable between different sites, noteworthy differences appeared only for Callopora rylandi, whereas considerable differences appeared in all three sites for between colonies within site comparisons. On the other hand, non-significant differences appeared for all three species when comparing ovicell width between different sites whereas highly significant differences appeared for between colony within site comparisons. The results of principal component analysis together with the results from nested ANOVA revealed that for factor 1, which defines aspects of the overall size of the zooid, there were significant differences between sites, as well as between colonies within sites for Callopora rylandi. For Callopora dumerilii and Callopora lineata, it appeared that there were no significant differences between different sites whereas there were notable differences between different colonies within sites. For factor 2, which defines aspects of the shape of the organism, there were significant differences between sites as well as between colonies within sites for both Callopora rylandi and Callopora dumerilii, while for Callopora lineata it emerged that there were no significant differences between sites, but there were important differences between colonies within sites. Analysis of the mitochondrial DNA population structure in these three species based on either haplotype frequencies or sequence divergence showed a large percentage of genetic variation within populations and a much smaller percentage of genetic variation among populations. However, for haplotype frequencies the among populations P values were significant for all species whereas when sequence divergence was taken into account only the P value for Callopora rylandi was significant. Overall nucleotide diversity was similar for Callopora dumerilii and Callopora lineata and higher than that of Callopora rylandi, whereas overall haplotype diversity was similar in all three species. Tajima's D and Fu's Fs test statistic appeared more negative in Callopora rylandi than the other species suggesting greater purifying selection or a recent population expansion. Comparisons based on dn/ds ratio suggested purifying selection as well. Reconstruction of phylogenetic relationships showed three major lineages which are mixed in all three species. Tests of neutrality in these lineages, which do not correspond to species, also suggested the existence of purifying selection.
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Rudd, Danielle Song. "Genomic copy number variation in schizophrenia." Diss., University of Iowa, 2014. https://ir.uiowa.edu/etd/4739.
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Schizophrenia (OMIM 181500) is an incurable and severe psychiatric disorder comprised of three symptom domains (positive symptoms, negative symptoms and cognitive impairments) with a worldwide prevalence of approximately 1%. There is a substantial amount of evidence demonstrating that schizophrenia has a strong a genetic component. Broad-sense heritability estimates range from 64-80% and first-degree relatives of schizophrenia patients have 10-fold increased risk of developing the disorder compared to the general population. It is thought that both single nucleotide polymorphisms and copy number variants (CNVs) contribute to the heritability of schizophrenia. This thesis focuses on the role of CNVs in the etiology of schizophrenia.
We performed a genome-wide CNV analysis of 166 schizophrenia patients and 52 psychiatrically healthy controls. In our overall CNV analysis we did not find any significant differences between cases and controls across a variety of CNV categories, nor did we find significant differences when CNVs were partitioned by size (small, medium or large). However, we were the first group to consider small CNVs (< 100-500 kb) in a multiple-hit model where we observed that a slightly higher proportion of case subjects had two-or-more conservative CNVs. We defined a CNV as conservative if it met any of the following three criteria: 1) a known deleterious CNV, 2) a CNV > 1 Mb that was novel to the Database of Genomic Variants (DGV) or 3) a CNV < 1 Mb that was novel to the DGV and that overlapped the coding region of a gene of interest. Genes of interest included genes with a previous association with a neuropsychiatric disorder, or genes with high or specific brain expression, or an association with any other neurocognitive or neuropsychiatric disorders. Two of our case subjects who harbored the highest amount of conservative CNVs also shared a 15q11.2 breakpoint 1-2 (BP1-2) deletion which is a compelling candidate risk locus for schizophrenia. We also found that a slightly higher proportion of case subjects harbored clinically significant CNVs (conservative CNVs > 1 Mb or clinically recognized as deleterious) when compared to controls. Additionally, we hypothesized that individuals with more severe CNVs would show more neurocognitive deficits and more pronounced abnormalities in brain structure volume, however, we had largely negative results. We also reported a case of childhood-onset schizophrenia who had three large chromosomal abnormalities including a paternally inherited 2.2 Mb deletion of chromosome 3p12.2-p12.1, a de novo 17.6 Mb duplication of chromosome 16q22.3-q24.3 and a de novo 43 Mb deletion of chromosome Xq23-q28.
We were able to confirm previous reports of CNV findings in schizophrenia such as the involvement of large, rare and de novo CNVs. In addition, the work in this thesis leads us to propose a multiple-hit CNV model which requires a shift in the way we currently approach schizophrenia genetics. First, we must identify all CNVs, especially those of smaller size (< 100 kb). Next, we require a more precise understanding of the impact that CNVs have on gene expression, especially in the brain. With all of the right tools in place, we can move towards a disease model for schizophrenia that considers the totality of CNVs in any given individual. We propose that the use of recurrent CNVs such as the 15q11.2 BP1-2 CNV is a good starting point for studying a multiple-hit CNV model.
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Cotsapas, Chris Biotechnology & Biomolecular Sciences Faculty of Science UNSW. "The genetics of variation in gene expression." Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Sciences, 2005. http://handle.unsw.edu.au/1959.4/30204.
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The majority of genetic differences between species and individuals have been hypothesised to impact on the regulation, rather than the structure, of genes. As the details of genetic variation are uncovered by the various genome sequencing projects, understanding the functional effects on gene regulation will be key to uncovering the molecular mechanisms underying the genesis and inheritance of common phenotypes, such as complex human disease and commercially important traits in plants and animals. Unlike coding sequence polymorphisms, genetic variants affecting gene expression will reside in the transcriptional machinery and its regulatory inputs. As these are largely specific to cell- or tissue-types, we would expect that regulatory variants will also affect final mRNA levels in a tissue specific manner. Genetic variation between individuals may therefore be more complex than the sum total of sequence differences between them. Demonstrating this hypothesis is the main focus of this thesis. We use microarrays to measure mRNA levels of approximately 22,000 transcripts in inbred and recombinant inbred strains of mice, and present compelling evidence that the genetic influences on these levels are tissue-specific in at least 85% of cases. We uncover two loci which apparently influence transcript levels of multiple genes in a tissue-specific manner. We also present evidence that failure of microarray data normalisation may cause spurious linkage of expression phenotypes leading to erroneous biological conclusions, and detail a novel, extensible mathematical framework for performing tailored normalisation which can remove such systematic bias. The wider context of these results is then discussed.
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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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Rootsi, Siiri. "Human Y-chromosomal variation in European populations /." Tartu : Tartu University Press, 2004. http://dspace.utlib.ee/dspace/bitstream/10062/1252/5/rootsi.pdf.
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Goropashnaya, Anna. "Phylogeographic Structure and Genetic Variation in Formica Ants." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3803.
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Ehrenreich, Ian Michael. "The Genetics of Phenotypic Variation in Arabidopsis thaliana." NCSU, 2008. http://www.lib.ncsu.edu/theses/available/etd-08062008-162151/.
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All organisms exhibit substantial quantitative trait variation within populations. Such variation is important because it can affect fitness and serve as the substrate for adaptive evolution. Identifying the quantitative trait genes (QTGs) responsible for phenotypic variation is necessary to understand the mechanisms that generate trait variation and to determine the historical action of natural selection on quantitative traits and QTGs. However, in most complex organisms, the genetic mapping of QTGs is difficult and presently not feasible to do systematically at a gene-level resolution. Model organisms that are both tractable in the laboratory and complex developmentally can serve as trial systems for developing broadly applicable methods for QTG mapping. Using the plant genetic model Arabidopsis thaliana, I have attempted to map QTGs for ecologically-significant quantitative traits â shoot branching and flowering time â through a combination of forward and reverse genetic methods. Three main research projects are reported here: i) candidate gene association mapping and linkage mapping of shoot branching; ii) regulatory network-wide candidate gene association mapping of flowering time; and iii) a survey of intra- and interspecific genetic variation at nearly half of the microRNAs (miRNAs) and their binding sites in the genome. These studies have identified strong candidate QTGs for traits that are determinants of A. thaliana fitness in the wild. I synthesize my results with those of other researchers in this area to highlight the achievements, future promise, and looming challenges for statistical genetics in terms of elucidating the genetic basis of trait variation.
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Russell, Joanne Ritchie. "Molecular variation in Theobroma species." Thesis, University of Reading, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386981.
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Mathieson, Iain. "Genes in space : selection, association and variation in spatially structured populations." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:85f051b6-2121-49cf-9468-3ca7ba77cc4a.
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Spatial structure in a population creates distinctive patterns in genetic data. There are two reasons to model this process. First, since the genetic structure of a population is induced by its historical spatial structure, it can be used to make inference about history and demography. Second, these models provide corrections to other analyses that are confounded by spatial structure. Since is it is now common to collect genome-wide data on many thousands of samples, a major challenge is to develop fast, scalable, approximate algorithms that can analyse these datasets. A practical approach is to focus on subsets of the data that are most informative, for example rare variants. First we look at the problem of estimating selection coefficients in spatially structured populations. We demonstrate this approach using classical datasets of moth colour morph frequencies, and then use it in a model incorporating both ancient and modern DNA to estimate the selective advantage of one of the best known examples of local adaptation in humans, lactase persistence in Europeans. Next, we turn to the problem of association studies in spatially structured populations. We demonstrate that rare variants are more confounded by non-genetic risk than common variants. Excess confounding is a consequence of the fact that rare variants are highly in- formative about recent ancestry and therefore, in a spatially explicit model, about location. Finally, we use this insight into rare variants to develop methods for inference about population history using rare variant and haplotype sharing as simple summary statistics. These approaches are extremely fast and can be applied to genome-wide data on thousands of samples, yet they provide an accurate description of the history of a population, both identifying recent ancestry and estimating migration rates between subpopulations.
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Gresham, David J. "Genetic variation and disease in the Roma (Gypsies)." Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2001. https://ro.ecu.edu.au/theses/1516.
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The Roma (Gypsies) are a European people composed of a mosaic of culturally heterogeneous populations. Linguistic analyses point to their origins in the Indian subcontinent. Cultural diversity in extant Romani populations suggests that they are descended from a mixture of Indian populations. Previous population genetic studies of the Roma have supported this claim by demonstrating the genetic heterogeneity of Romani populations. More recently, medical genetic research has detected identical founder mutations in separated Romani populations, which provides evidence of their relatedness. In this thesis, the genetic heritage of the Roma and its significance for genetic disease and research is investigated. Male and female lineages were analysed in eight traditionally endogamous Romani populations. Asian specific Y chromosome haplogroup VI-68 and mitochondrial DNA (mtDNA) haplogroup M were detected in all populations and accounted for 39% and 25% of all lineages respectively. Diversity within haplogroups was assessed by genotyping Y chromosome short tandem repeats (YSTRs) and sequencing the mtDNA hypervariable segment 1 (HVSl). Lineages within haplogroups VI-68 and M were found to be closely related suggesting that Romani populations are predominantly descended from a single Indian ethnic population. The differing historical legacies of Romani populations and adherence to endogamous practices have resulted in genetic substructure and limited diversity within populations. Thus, the Roma are shown to comprise a conglomerate of related admixed population isolates. The unique genetic heritage of the Roma provides a powerful tool for the positional cloning of monogenic disease genes. This is demonstrated through the reduction of the critical chromosomal region for a novel genetic disorder, hereditary motor and sensory neuropathy type Lom (HMSNL). In the initial report, the HMSNL disease locus was defined as a 3cM region on chromosome 8q24. In this study, refined genetic mapping utilising historical and parental recombinations observed in Romani individuals from different populations reduced the HMSNL critical interval to 202kb. Sequence analysis of two genes contained within this genomic interval found all affected individuals to be homozygous for a CT mutation in codon 148 of N-myc downstream regulated gene 1 (NDRGJ), resulting in a truncating Rl48X mutation. Investigation of the population distribution of the R148X disease allele shows that it occurs in six of eight separated Romani populations. Another founder mutation, C283Y in the y-sarcoglycan gene (SGCG), which causes limb girdle muscular dystrophy type 2C (LGMD2C), was found in two of eight Romani populations. Profound founder effects are apparent within Romani populations with a carrier frequency of 19.5% determined for the R148X mutation in the Lom population, and 6.25% for the C283Y allele in the Turgovzi population. High carrier frequencies for autosomal recessive diseases can be expected to pose a significant health risk for these communities. Thus, community-wide carrier testing represents a potential means of addressing this health problem. A pilot community based carrier-testing program was implemented in a Romani community of north eastern Bulgaria and relevant attitudes assessed by means of a questionnaire. Community-based carrier screening was demonstrated to be an appropriate approach to improving health amongst the Roma.
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Archer, Jason Allan. "Genetic variation in the efficiency of feed utilisation by animals." Title page, table of contents and abstract only, 1996. http://web4.library.adelaide.edu.au/theses/09PH/09pha6711.pdf.
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Bibliography: leaves 186-200. Analyses feed intake and growth data from cattle, which indicates that genetic variation exists in post-weaning effiency and growth. Concludes with a consideration of how post-weaning feed intake information can be used in genetic improvement programs.
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Rogell, Björn. "Genetic variation and local adaptation in peripheral populations of toads." Uppsala : Acta Universitatis Upsaliensis, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-107395.
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Murtagh, Gareth James. "Sex and variation in lichen-forming fungi." Thesis, University of Nottingham, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285566.
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Stewart, John E. B. (John Edward Bakos). "Genetic Variation in a Population of the Plains Woodrat Neotoma micropus." Thesis, University of North Texas, 1988. https://digital.library.unt.edu/ark:/67531/metadc500709/.
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Neotoma micropus from Jack County, Texas, were studied over a 9-month period. Loci from blood and saliva were used to determine genetic variation within the population. Deviations from Hardy-Weinberg equilibrium were found at one locus. The average temporal F over all seven loci was 0.040. Genetic structuring was subtle, fluctuated on a seasonal basis, and was due to differential migration or predation on genotypes. Heterozygotes tended to move more than homozygotes, and a greater proportion of heterozygotes were lost from the population during each season. Genetic variation was maintained in the population by immigrant individuals. This differential in dispersal of genotypes fits current models of reorganization within the genome of populations.
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Elis, Mabon. "Evolutionary genetics of flower colour variation in Antirrhinum." Thesis, University of East Anglia, 2018. https://ueaeprints.uea.ac.uk/69572/.
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Phenotypic differences between species and populations can reveal much about how they have adapted and responded to a complex set of environmental cues. Studies have shown that genetic control of some traits is centralised to single genomic regions, while others are regulated at many unlinked loci dispersed throughout the genome. One trait that shows an enormous degree of variation between plant species is flower colour, and its tractability makes it an ideal trait for studying genetic differences underlying species differentiation. Antirrhinum majus has long been used as a model for studying floral traits, including colour. The 20-30 wild Antirrhinum species use diverse patterns on their flowers, formed by producing and accumulating magenta anthocyanins and yellow aurones in different tissues, to attract pollinators. In this project, I sought to genetically map flower colour phenotypes to the Antirrhinum genome. Several Antirrhinum species were crossed to A. majus to generate segregating populations. I used a combination of bulked segregant analysis, individual genotyping of segregating populations and analysis of genome sequences from wild accessions to test whether genes governing each colour trait were concentrated at particular loci or dispersed across many chromosomes. I found that variation in magenta not previously characterised maps to the known ROSEA-ELUTA (ROS-EL) locus where transcription factors regulating anthocyanin production are encoded. Yellow phenotypes from three species mapped to chromosome 2, where there is reduced recombination between A. majus and many wild species, and where an aurone biosynthetic enzyme is encoded. However, there appear to be some additional modifiers of flower colour in these species, not linked to the ROS-EL and chromosome 2 loci. These results fit neither the central- nor dispersed-control models of genetic control, but rather an intermediate hypothesis - that flower colour can be changed by selection acting on a modest number of loci spread throughout the genome.
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Rowell, Jennie Lynn. "GENETIC VARIATION IN THE DOMESTICATED DOG AS A MODEL OF HUMAN DISEASE." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338237356.
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SUSCA, Roberta Rosa. "Patterns of genetic and linguistic variation. A study of uniparental markers." Doctoral thesis, Università degli studi di Ferrara, 2017. http://hdl.handle.net/11392/2488149.
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This dissertation is divided in three sections and focuses on two of the projects I worked on during my three-years PhD, funded by a European Research Council (ERC) grant LanGeLin.
Both the projects share the uniparental markers as tool used for the investigation of the human evolutionary history, but each of them addresses different scientific questions by means of a different combination of molecular and statistical methods.
Part I is a technical summary on current knowledge about uniparental markers features and on the pros and cons of their usage for addressing questions stemming from the fields of linguistics and archaeology.
Part II summarizes the results of one of the ERC-founded LanGeLin works; here I describe the comparison of patterns of genetic and liguistic diversity in 36 Eurasian populations. The ERC-founded LanGeLin project aims to improve our understanding about the coevolution of language and genes. R. Sokal and L.L. Cavalli-Sforza in 1988 showed that a correlation between genetic and linguistic variation within major language families is actually present, but due to imperfect methods to quantify linguistic variation, it has been difficult to compare populations belonging to distant linguistic groups. Thanks to the newly PCM linguistic method, a new way to compare languages is now available, based on stable linguistic syntax features. It is now possible to test the correlation between genetic and linguistic data in a broad geo-linguistic scale, as this thesis will do, and to interpret in evolutionary terms both the rule and the exceptions. It is also possible to study maternal and paternal lineages separately, to inquire their migrational histories. Two different migrational histories emerged, with women dispersing at a higher rate than men. When comparing genetic and linguistic features a neither obvious nor simple pattern is detectable: correlations between languages and DNA variants depend on the geographical area and the genetic markers considered.
Part III addresses questions related with the analysis of complete mitochondrial sequences from Mesolithic (Ms) times, which allowed us to address questions regarding Neolithic (Ne) and pre-Neolithic (pN) peopling of Sardinia. We investigated the role of two Ms Sardinian mtDNA sequences in the European context. Little is known about the genetic prehistory of Sardinia because of the scarcity of pN human remains. Modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Ne farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here I present the first and oldest complete mtDNA sequences from Sardinia, dated back to 10,000 yBP. These two individuals belong to rare mtDNA lineages never been found before in Ms samples and that are currently present at low frequencies also in the whole Europe. When compared with other European pN data, the Ms Sardinian sequences appeared already well differentiated, and in general more similar to pre-Last Glacial Maximum populations, than to coeval sequences. As a side project, I was also involved in the study of the differences in twinning rate (tr) among human populations of Africa (where the tr is maximum), Europe and Asia (where the tr is minimum). The contact point between these projects was represented by the common bioinformatics and biostatistical tools needed for analysis of large genomic. Although I considered that, for the sake of consistency, this thesis will mostly focus on the ERC-funded project, I am enclosing, in the final Manuscripts section, both papers produced during my doctoral years.Questa tesi riassume l’attività di ricerca da me svolta durante i tre anni di dottorato, sovvenzionato dal progetto ERC LanGeLin, il cui scopo principale è di migliorare le conoscenze sulla co-evoluzione di lingue e geni. I progetti descritti condividono l’uso di marcatori uniparentali usati per gli studi di evoluzione umana, ma differiscono per la combinazione di metodi molecolari e statistici. La Parte I descrive lo stato dell’arte dei marcatori uniparentali e i pro e contro del loro utilizzo in ambito linguistico e archeologico. La Parte II riassume i risultati delle ricerche condotte nell’ambito del progetto LanGeLin che descrive la diversità dei pattern genetici e linguistici in 36 popolazioni Euroasiatiche. Il progetto LanGeLin (Language and Gene Lineages), finanziato dal “European Research Council” ha lo scopo di testare l’ipotesi di Darwin presentata in “Origine delle specie”. Darwin intuì che l’albero filogenetico delle diverse sottospecie umane, potesse sovrapporsi a quello ottenuto a partire dalle diverse lingue, offrendo di fatto la possibilità di studiare la genealogia delle lingue e allo stesso tempo capire come le differenze tra queste avrebbero permesso di far luce sugli aspetti elusivi della storia demografica umana. R. Sokal e L.L. Cavalli-Sforza nel 1988 hanno elucidato come la comparazione dei vocaboli rifletta la correlazione fra variabilità genetica e linguistica nelle maggiori famiglie linguistiche ma, a causa di metodi linguistici, risulta difficile comparare popolazioni derivanti da gruppi linguistici distanti. Il nuovo metodo linguistico PCM si basa sulle caratteristiche linguistiche più stabili della sintassi. È stato dunque possibile, anche in questa tesi, testare su larga scala geo-linguistica la correlazione tra dati genetici e linguistici. Lo studio delle discendenze materne e paterne è stato condotto separatamente per indagarne le relative storie di migrazione: due differenti storie sono emerse dall’analisi del Ychr (discendenza patrilineare) e del mtDNA (discendenza matrilineare). Non ovvie considerazioni sono scaturite dalla comparazione delle caratteristiche genetiche e linguistiche, che ha portato a definire come la correlazione tra lingue e sequenza genetica sia dipendente dall’area geografica e dai marcatori genetici considerati. La Parte III descrive l’analisi di sequenze di mtDNA del Mesolitico (Ms) che ci ha permesso di indagare sul popolamento della Sardegna in periodo Neolitico (Ne) e pre-Neolitico (pN). Lo studio è stato incentrato su due sequenze mitocondriali sarde Ms in relazione al contesto europeo. C’è ancora molta incertezza sulla variabilità genetica della Sardegna preistorica, a causa della scarsità di resti umani Ne. Dal punto di vista genetico, i sardi moderni possono considerarsi un gruppo a se stante rispetto al resto dell’Europa continentale, mostrando alti livelli di diversità interna e una forte vicinanza con i primi coltivatori europei del Ne. Questa tesi riporta le due prime sequenze mtDNA complete sarde, datate circa 10000 anni fa. I due individui confermano un’occupazione mesolitica dell’isola e rappresentano un aplotipo mai trovato prima in Sardegna mesolitica e con basse frequenze nell’intera Europa. Le due sequenze risultano ben differenziate se comparate con altri dati europei pN, e più simili a popolazioni dell’era pre-glaciale che a popolazioni coeve. Analisi di inferenza Bayesiana hanno mostrato come i primi abitanti dell’isola abbiano contribuito poco al popolamento attuale dell’isola, la cui diversità genetica deriva da migrazioni dal continente in tempi neolitici. Un progetto portato avanti parallelamente, ha riguardato lo studio di frequenze alleliche in gemelli dizigotici provenienti da popolazioni umane africane, europee ed asiatiche. Le tecniche bioinformatiche e biostatistiche usate per le analisi genomiche su larga scala, fanno da collante con i precedenti progetti descritti.
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Hamilton, Katherine Elaine. "Structural and regulatory gene variation in Salmonid fishes." Thesis, Queen's University Belfast, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356872.
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De, Winter Gunnar. "The ecology and evolution of individual behavioural variation." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/44995/.
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Central to this thesis is the investigation of how several factors (e.g. morphology, ecology, and social conditions) co-vary with consistent individual behavioural variation. Additionally, conceptual work explores the reach of consistent inter-individual behavioural variation in several novel contexts. In doing so, the aim is to contribute novel findings to the quickly growing compendium of knowledge concerning 'animal personality' in various settings. In summary, during this PhD the following research has been performed: • Through the use of lab-reared juvenile three-spined stickleback (Gasterosteus aculeatus) whose parents came from different habitats, I investigated the relative contribution of plasticity and (epi)genetic mechanisms on three behaviours (boldness, activity, and sociality). While these behaviours did not differ between juveniles from both populations, correlations of body length with specific behaviours did. (Chapter 2) • During fieldwork on the Scottish island of North Uist, seven populations of wild three-spined stickleback were surveyed for boldness, exploratory behaviour, and activity. Furthermore, the defensive morphology of these fish was quantified following an armour-staining protocol. Bold fish were found to be less armoured, directly contradicting the phenotypic compensation hypothesis, while more active fish were more armoured, which contradicts the idea that armour is energetically costly. (Chapter 3) • Spurred on by the findings on morphology-behaviour correlations, the ecology of the studied populations was assessed with a focus on parasitism by three common macro-parasites of three-spined stickleback, predation by trout, competition with the nine-spined stickleback, and the availability of resources. I found that all these factors, to some extent, influence individual behavioural variation. Importantly, this study provides the first observational evidence that less-explored factors, such as resource availability and interspecific competition, can be highly relevant influences on individual behaviour. (Chapter 4) • Next, a study on the effect of group behavioural composition on group foraging behaviour was done. With the help of a research visit to Aarhus University, similar experiments were performed on stickleback and social spiders (Stegodyphus dumicola). Group behavioural composition had a strong effect in both study systems, but experience was a more relevant influence on group foraging behaviour in stickleback. By using two different study organisms from quite disparate animal taxa, this allows me to develop hypotheses concerning the evolutionary origin and maintenance of individual behavioural variation and its tentative link with sociality. (Chapter 5) • Lastly, the phenomenon of consistent individual variation in behaviour is explored in novel contexts through conceptual essays (Chapter 6). o Do bacteria offer a suitable system to study ‘personality’? o How can animal personality be leveraged to improve animal welfare? o Are non-antagonistic interspecific interactions an overlooked yet important factor in the study of animal personality?
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Fredman, David. "Computational exploration of human genome variation /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-025-7/.
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Kvernes, Macpherson Carina. "Studying genetics of leaf shape variation in Arabidopsis lyrata." Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-160116.
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The relationship between leaf and its environment has resulted in a tremendous diversification of leaf shape within and between plants species, which is important to cope with the differing environmental conditions. Arabidopsis lyrata is a prime model plant that shows leaf shape variation within species and between related species. In Cardamine and Capsella, the RCO genes (homeodomain leucine zipper family transcription factors) are involved in shaping leaves, yielding more complex shaped leaves (leaflets). In A. thaliana, over the course of evolution, the RCO-A and RCO-B paralogous genes have been deleted that led to the loss of lobes (leaf simplification). Based on previous quantitative trait locus (QTL) mapping results, these gene family members are thought to control leaf shape variation also in A. lyrata. Since the paralog involved in leaf shape variation is unknown, both copies of the RCO genes (AL6G13350 and AL6G13360) were sequenced. The study aimed to identify whether DNA sequence variation exists in the two paralogous RCO genes, which could explain the phenotype variation both within population and between A. lyrata populations, along with related species A. arenosa. The results showed limited variation in the coding regions in the form of indels, single nucleotide polymorphisms (SNPs) and amino acid substitutions resulting in no significant difference in phenotype between genotype (p>0.139). The most variants were rare and increasing the number of individuals within the populations, to cover the full phenotypic spectrum, may lead to different results. Not being able to obtain the nucleotide sequence of the promotor region, further analysis is required since it is an important region for gene expression, which could explain phenotype variation for leaf shape in Arabidopsis lyrata.
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Marcar, Nico Emile. "Genotypic variation for manganese efficiency in cereals /." Title page, abstract and contents only, 1986. http://web4.library.adelaide.edu.au/theses/09PH/09phm313.pdf.
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Scheet, Paul A. "A flexible and computationally tractable model for patterns of population genetic variation/." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/8932.
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Patel, Tulsi. "Investigating genetic variation in Alzheimer's disease." Thesis, University of Nottingham, 2018. http://eprints.nottingham.ac.uk/52447/.
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Alzheimer's disease (AD) is the most common form of dementia, now the leading cause of death in the UK, which affects more than 35 million people worldwide. Genome-wide association studies identified 20 genetic loci associated with disease susceptibility, however these only exerted small effects on risk. Next-generation sequencing is now being employed to identify more of the missing heritability. This project utilised whole-exome sequencing to explore genetic variation using the Brains for Dementia Research (BDR) resource, a well-characterised cohort of neuropathologically confirmed samples. Exome-wide and candidate gene approaches were employed to assess coding variants for association with AD, using single-variant and burden tests. Coding variants in other neurodegenerative disease genes were also analysed as potential susceptibility factors for AD. Furthermore, polygenic risk scores (PRS) were generated to explore the ability to classify case and control individuals based on their genetic profiles. A synonymous variant in PILRA (rs2405442) was nominally associated with 3-fold increased risk of AD, also contributing strongly to PILRA burden. It was previously linked to AD through risk gene ZCWPW1; however, it has not been directly associated until now. Additional variants in GWAS gene ABCA7 (rs3764645, rs3752234, rs3752237, rs4147915) and rare variants in CLU were also implicated, further supporting their roles in AD susceptibility. A variant in PD gene LRRK2 (rs35303786) inferred protection against AD, implicating potential pleiotropy across the two diseases. PRS could distinguish AD cases from controls with 85.3% accuracy and also identified controls with high PRS but no cognitive impairments. This could be useful for identifying individuals at risk of developing AD in the future. We have uncovered tentative associations both in established and newly identified loci; highlighting several interesting candidates for further investigation. Although there remains a large amount of missing heritability, we hope that as the BDR resource grows, we will achieve increased power to detect significant associations with AD.
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Young, J. R. "The molecular genetics of antigenic variation in Trypanosoma brucei." Thesis, University of Cambridge, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372285.
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Forsberg, Lena. "Genetic variation and regulation of oxidative stress related genes /." Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4241-2/.
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Sharkey, Andrew M. "Genetic variation in the rodent malaria parasite Plasmodium chabaudi." Thesis, University of Edinburgh, 1989. http://hdl.handle.net/1842/14391.
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Whiteley, Rachel. "Quantitative and molecular genetic variation in Ulmus laevis Pall. /." Uppsala : Dept. of Plant Biology and Forest Genetics, Swedish Univ. of Agricultural Sciences, 2004. http://epsilon.slu.se/s313.pdf.
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Cardno, Alastair George. "The quantitative genetics of clinical variation in psychotic illnesses." Thesis, Cardiff University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394591.
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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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Shringarpure, Suyash. "Statistical Methods for studying Genetic Variation in Populations." Research Showcase @ CMU, 2012. http://repository.cmu.edu/dissertations/117.
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The study of genetic variation in populations is of great interest for the study of the evolutionary history of humans and other species. Improvement in sequencing technology has resulted in the availability of many large datasets of genetic data. Computational methods have therefore become quite important in analyzing these data. Two important problems that have been studied using genetic data are population stratification (modeling individual ancestry with respect to ancestral populations) and genetic association (finding genetic polymorphisms that affect a trait). In this thesis, we develop methods to improve our understanding of these two problems.
For the population stratification problem, we develop hierarchical Bayesian models that incorporate the evolutionary processes that are known to affect genetic variation. By developing mStruct, we show that modeling more evolutionary processes improves the accuracy of the recovered population structure. We demonstrate how nonparametric Bayesian processes can be used to address the question of choosing the optimal number of ancestral populations that describe the genetic diversity of a given sample of individuals. We also examine how sampling bias in genotyping study design can affect results of population structure analysis and propose a probabilistic framework for modeling and correcting sample selection bias.
Genome-wide association studies (GWAS) have vastly improved our understanding of many diseases. However, such studies have failed to uncover much of the variation responsible for a number of common multi-factorial diseases and complex traits. We show how artificial selection experiments on model organisms can be used to better understand the nature of genetic associations. We demonstrate using simulations that using data from artificial selection experiments improves the performance of conventional methods of performing association. We also validate our approach using semi-simulated data from an artificial selection experiment on Drosophila Melanogaster.
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Ochola, Harold Martin Owino. "Using genomics and population genetics to understand genetic variation in Malawi Plasmodium falciparum clinical isolates." Thesis, University of Liverpool, 2013. http://livrepository.liverpool.ac.uk/15753/.
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The natural selection imposed by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum, leading to an ever-changing landscape of genetic variation. We have carried out whole-genome sequencing of 93 P. falciparum clinical isolates from Malawi and used population genetic methods to investigate the genetic diversity and regions under selection. In addition, by computing XP-EHH, PCA and FST we have compared the Malawi isolates to five dispersed others (Kenya, Mali, Burkina Faso, Cambodia and Thailand), and identified genes potentially under positive directional selection. Geographic stratification of genetic diversity in the populations followed continental lines and small population differences were observed within Africa. Positive directional selection signals were identified at or near pfdhps, pfcrt, pfmdr1 and pfgch1 (known drug targets) and in several merozoite invasion ligands (e.g., msp3.8, trap and ama1). We discuss the role of drug selection in promoting fixation of alleles between populations with differing adaptation to local drug pressure. Analysis of copy number variation in Malawi provides a detailed catalogue of new and previously identified gene deletions and duplications with critical roles in cytoadherence, gametocytogenesis, invasion and drug response. This work provides the first genome-wide scan of selection and CNV in Malawi to guide future studies in investigating parasite evolution, changing malaria epidemiology, and monitoring and evaluating impact of malaria interventions as they are deployed.
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Lee, Peter Daniel. "Building a model for mapping genetic variation affecting gene expression." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85931.
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The majority of genetic traits including most common diseases are believed to be multigenic and arise both from variations in coding sequences as well as from regulatory polymorphisms. Genome-wide approaches are needed to develop models for understanding this complexity. This thesis develops approaches for studying genetic variation affecting gene expression on a genome-wide scale. This included development of experimental design principles and analytical methods for microarray data. These principles were then applied to characterize differences between commonly-used A/J and C57BL/6J inbred mouse strains at the molecular level identifying over 2000 genes differentially expressed between these strains across 4 tissues. To further investigate the role of genetic variation in genome-wide expression changes, we analyzed expression profiles of lung tissue obtained from a panel of recombinant congenic strains (RCS) derived from the same inbred strains. An ANOVA was applied using a model to test the association of expression profiles with donor-strain of origin (DSO, inferred from RCS genotyping data), and with genetic background. This model identified over 1500 genes whose expression levels were associated with DSO status (P<0.05) having adjusted for the variability due to predominant strain of background, suggestive of cis-regulatory variation in these genes. We randomly selected 50 positive genes displaying association between DSO and 80 negative genes for validation using allelic imbalance (AI), a method that uses intragenic SNPs for detecting genes with cis-regulatory variation that measures allele-specific transcript levels in cDNA of heterozygous individuals. Of the genes chosen, 54% of positive versus 27% of negative genes contained at least one SNP within ≥ 1 kbp of 3' UTR sequenced (P<0.05 Fisher exact test). Al was found in 63% of positive genes versus 23% of negative genes (P<0.01 Fisher exact test) representing a greater than 10-fo
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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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Yue, Wei. "Characterization of genetic variation in secondary metabolites in Fusarium." Diss., Kansas State University, 2017. http://hdl.handle.net/2097/36235.
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Doctor of PhilosophyGenetics Interdepartmental Program
Christopher Toomajian
Secondary metabolites (SMs), low molecular weight molecules that are not essential for normal organism growth and development, may confer a selective advantage in some environments. Fungal SMs are structurally and functionally diverse and include mycotoxins, plant regulators and pigments, and the genes that work together in SM biosynthetic pathways are physically clustered in the genome. Fusarium, a genus of filamentous fungi, is noted for SM production, especially mycotoxins, which may contribute to plant pathogenesis. Fusarium species exhibit differences in their SM profiles, and comparative genomics studies have found corresponding differences in the SM gene clusters in some Fusarium species. The investigation of differences in the genomes and SM gene clusters between closely related species, such as F. proliferatum and F. fujikuroi, may help explain their phenotypic divergence, including differences in SM profiles. In addition, the study of intra-species SM variation may indicate how SM loci affect a pathogen’s fitness traits. My research includes three main projects that address different aspects of Fusarium SM variability. To carry out my projects, I established a feasible Genotyping-by-Sequencing (GBS) protocol for Fusarium. One project explored the genetic bases underlying phenotypic divergence related to SM profiles and pathogenicity between F. proliferatum and F. fujikuroi using a quantitative genetics approach. Specifically, I 1) constructed the first high density genetic map based on progeny from an interspecific cross between these two species; and 2) detected a novel regulatory locus for gibberellic acid production and identified a region affecting onion virulence that includes the fumonisin gene cluster. The second project characterized the F. proliferatum parent genome from the previous cross and its SM gene clusters using a comparative genomics approach. Specifically, I 1) assembled the F. proliferatum genome into 12 chromosomes with a combined length of ~43 Mb; 2) annotated this assembly and characterized its 50 SM gene clusters; and 3) detected over 100 F. proliferatum specific genes that might play roles in this species’ host specificity and plant pathogenicity. The third project used a population genomics approach to explore how different F. graminearum chemotypes, or isolates classified based on the accumulation of alternate trichothecene toxin types, may differ for fitness traits and whether trichothecene genes are directly responsible for these differences. Specifically, I 1) genotyped over 300 F. graminearum strains from New York and the upper Midwest in the U.S. and from South America using our GBS protocol; 2) detected two major subpopulations that were correlated, though imperfectly, to the predicted 3-acetyl deoxynivalenol (3ADON) and 15-acetyl deoxynivalenol (15ADON) chemotypes in the U.S.; 3) identified a rapid linkage disequilibrium decay over a few tens of kb followed by a slower decay to background levels over a distance of 200 kb to 400 kb in selected subpopulations in the U.S.; and 4) found that neither chemotype has a clear fitness advantage in a small set of isolates from New York, but that isolates belonging to one genetic subpopulation may on average have a fitness advantage over isolates from the other subpopulation.
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King, Rachel, and n/a. "Spatial Structure and Population Genetic Variation in a Eucalypt Species Complex." Griffith University. Australian School of Environmental Studies, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20050113.091713.
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In this study, the relative influences of selection, gene flow, and other evolutionary forces on the spatial structure of genetic variation within a eucalypt species complex (the spotted gums: genus Corymbia, section Politaria) were assessed. The study investigated the spatial genetic structure among four putative species of spotted gum (broad-scale), as well as within a single population (fine-scale)of one species, using both molecular and quantitative markers. The spotted gum complex occurs naturally across a range of 2500 km in eastern Australia. Spatial genetic variation within and between the four putative spotted gum species was examined using both chloroplast and nuclear markers. No significant differentiation was found between the three northern species of the complex, C. citriodora, C. variegata and C. henryi. The southern species, C. maculata, shared no haplotypes with any of the three northern species. These results disagree in part with those reported in a previous allozyme based study in which C. henryi was found to be significantly divergent from C. variegata (with which it is sympatric) and more closely aligned with C. maculata. Re-analysis of the allozyme data provided evidence of selection acting at the PGM2 locus within populations of C. variegata and C. henryi. The exclusion of this locus from the data set led to concordance between the cpDNA and nDNA analyses. Restricted gene flow and evidence of isolation by distance were identified as the dominant processes influencing the contemporary distribution of the cpDNA haplotypes. No geographic structure of haplotypes was found and complex genealogical relationships between haplotypes indicated the combined effects of past fragmentation, range expansion and possible long distance dispersal events. The variation and spatial structure in both neutral molecular markers and quantitative genetic traits were compared to explore the relative influences of dispersal and selection within a single eucalypt population. Both mature trees (n=130) from a natural population of C. variegata and their progeny (n=127) were sampled. A very high outcrossing rate (98%) was estimated for the population based on data from seven microsatellite loci. This suggested regular pollenmediated gene flow into the population, further supported by the observed high levels of genetic diversity and polymorphism. Significant positive spatial structure was found between parent trees occurring up to 150 m apart in the natural forest, although genetic distance between these individuals suggested limited relatedness (i.e. less than half-sib relatedness). The effect of pollen-mediated gene flow appears, therefore, to swamp any effect of nearest neighbour inbreeding which has been reported in other studies of eucalypt populations and has been attributed to limited seed dispersal. Resistance to the fungal disease Sporothrix pitereka (Ramularia Shoot Blight) was measured on progeny from each of the population study trees. Substantial resistance variability was found, along with a high estimate in heritability of resistance (0.44 ± 0.06), indicating significant additive genetic variation within the population. Spatial analysis showed no significant spatial structure with resistant and susceptible genotypes apparently distributed randomly throughout the population. The lack of concordance between the molecular and quantitative markers suggests that there may be a cost to resistance. Temporal variation in the severity of disease outbreaks may have then led to differential selection of seedlings across many generations, maintaining variability in disease resistance and facilitating the apparent random distribution of disease resistant and susceptible genotypes throughout the population. C. variegata is an important commercial forestry species. The identification of strong genetic control in the disease resistance trait, as well as significant adverse genetic and phenotypic correlations between susceptibility and growth traits, will aid future breeding programs. Controlled crosses between resistant genotypes from this population should result in strong genetic gains in both resistance and growth, with little costs associated with inbreeding depression due to the highly outcrossed nature of the population.
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King, Rachel. "Spatial Structure and Population Genetic Variation in a Eucalypt Species Complex." Thesis, Griffith University, 2004. http://hdl.handle.net/10072/365496.
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In this study, the relative influences of selection, gene flow, and other evolutionary forces on the spatial structure of genetic variation within a eucalypt species complex (the spotted gums: genus Corymbia, section Politaria) were assessed. The study investigated the spatial genetic structure among four putative species of spotted gum (broad-scale), as well as within a single population (fine-scale)of one species, using both molecular and quantitative markers. The spotted gum complex occurs naturally across a range of 2500 km in eastern Australia. Spatial genetic variation within and between the four putative spotted gum species was examined using both chloroplast and nuclear markers. No significant differentiation was found between the three northern species of the complex, C. citriodora, C. variegata and C. henryi. The southern species, C. maculata, shared no haplotypes with any of the three northern species. These results disagree in part with those reported in a previous allozyme based study in which C. henryi was found to be significantly divergent from C. variegata (with which it is sympatric) and more closely aligned with C. maculata. Re-analysis of the allozyme data provided evidence of selection acting at the PGM2 locus within populations of C. variegata and C. henryi. The exclusion of this locus from the data set led to concordance between the cpDNA and nDNA analyses. Restricted gene flow and evidence of isolation by distance were identified as the dominant processes influencing the contemporary distribution of the cpDNA haplotypes. No geographic structure of haplotypes was found and complex genealogical relationships between haplotypes indicated the combined effects of past fragmentation, range expansion and possible long distance dispersal events. The variation and spatial structure in both neutral molecular markers and quantitative genetic traits were compared to explore the relative influences of dispersal and selection within a single eucalypt population. Both mature trees (n=130) from a natural population of C. variegata and their progeny (n=127) were sampled. A very high outcrossing rate (98%) was estimated for the population based on data from seven microsatellite loci. This suggested regular pollen–mediated gene flow into the population, further supported by the observed high levels of genetic diversity and polymorphism. Significant positive spatial structure was found between parent trees occurring up to 150 m apart in the natural forest, although genetic distance between these individuals suggested limited relatedness (i.e. less than half-sib relatedness). The effect of pollen-mediated gene flow appears, therefore, to swamp any effect of nearest neighbour inbreeding which has been reported in other studies of eucalypt populations and has been attributed to limited seed dispersal. Resistance to the fungal disease Sporothrix pitereka (Ramularia Shoot Blight) was measured on progeny from each of the population study trees. Substantial resistance variability was found, along with a high estimate in heritability of resistance (0.44 ± 0.06), indicating significant additive genetic variation within the population. Spatial analysis showed no significant spatial structure with resistant and susceptible genotypes apparently distributed randomly throughout the population. The lack of concordance between the molecular and quantitative markers suggests that there may be a cost to resistance. Temporal variation in the severity of disease outbreaks may have then led to differential selection of seedlings across many generations, maintaining variability in disease resistance and facilitating the apparent random distribution of disease resistant and susceptible genotypes throughout the population. C. variegata is an important commercial forestry species. The identification of strong genetic control in the disease resistance trait, as well as significant adverse genetic and phenotypic correlations between susceptibility and growth traits, will aid future breeding programs. Controlled crosses between resistant genotypes from this population should result in strong genetic gains in both resistance and growth, with little costs associated with inbreeding depression due to the highly outcrossed nature of the population.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
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Judson, Olivia P. "Parasites, sex and genetic variation in a model metapopulation." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296922.
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Goulson, David. "Maintenance of phenotypic variation in the butterfly, Maniola jurtina." Thesis, Oxford Brookes University, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.293305.
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Smith, Thomas C. A. "Within genome variation of germ-line and somatic mutation." Thesis, University of Sussex, 2017. http://sro.sussex.ac.uk/id/eprint/68212/.
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Variation in the mutation rate along the human genome, if not properly understood and accounted for, has the potential to confound evolutionary studies, produce spurious driver candidates in cancer studies, and hinder the diagnostics aimed at understanding the etiologies of genetic diseases. In this thesis I consider mutation rate variation in both the germ-line and somatic tissues, at varying scales. In the germ-line, the major advance of this thesis over previous works is use of direct methods to analyse the magnitude, scale and determinants of mutation rate variation. This has enabled us to tease apart the evolutionary and mutational forces, whilst directly quantifying the variation in the human mutation rate at different scales; at large scales the variation appears to be quite modest, however at the single nucleotide scale there is potentially huge cryptic variation in the mutation rate. I envisage that within the near future, the increase in de novo mutations coming from pedigree studies will allow for even greater understanding. I extend this work into somatic tissues, however due to the quality of data and heterogeneity of samples and cell types, the primary findings lean towards highlighting areas of improvement for next genereation sequencing (NGS) pipelines - I show ~4% of all single nucleotide variants from cancers appear to be errors - and develop methods with which future studies could provide more insight. With these methods and the ever increasing flow of somatic single nucleotide variants, coupled with the continual improvements in NGS technology, it should soon be possible to provide accurate answers to the questions posed of somatic mutation rate variation in this thesis.
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SSEKIMPI, PUPULIO SSEMOMBWE NKUNA ABBY. "CHROMOSOME VARIATION IN DROSOPHILA SPECIES OF THE MULLERI COMPLEX." Diss., The University of Arizona, 1986. http://hdl.handle.net/10150/183809.
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Drosophila species in mulleri complex show five rod-shaped and one pair of dot-shaped chromosome. The sex-chromosomes represent the largest pair in the female, but are heteromorphic in the male, the Y-chromosome being shorter than the X-chromosome. The purpose of the research presented here is to determine whether chromosomes in the mulleri cluster species are longer than in the mojavensis cluster. The length of X-, Y-chromosomes and the rod-like autosomes were compared among the ten species studied. All the rod-like chromosomes were measured in 30 or more brain cells in each of the ten species. The length of the X-chromosomes were measured in hybrid female larvae. Also the metaphase chromosomes were stained for heterochromatin. The results of this study do not support the division of the mulleri complex into the two clusters. This study shows that the X-chromosome in mulleri complex can be divided into three categories; the long X-chromosome found in D.sp.A, D.aldrichi and D.wheeleri; the intermediate or medium X-chromosome found in D.mojavensis, D.mulleri, D.sp.S, and D.sp.S-5; and the short X-chromosome found in D.arizonensis, D.mayaguana, and D.sp.N. The intermediate and the short X-chromosome groups represent species from the two clusters. The Y-chromosome appears to be most variable of all. Based on overall chromosome lengths the ten species can be placed into three groups; (1) D.sp.A, D.aldrichi, D.wheeleri, D.sp.S, and D.sp.S-5 in the long chromosome group, (2) D.mojavensis and D.mulleri in the medium chromosome group and (3) D.arizonensis, D.sp.N and D.mayaguana in the short chromosome group. The differences in chromosome length seem to be due to heterochromatin. The results seem to suggest that the ancestral species had the mulleri-mojavensis chromosome length (i.e. medium) and the mulleri gene arrangement. The chromosomes of the species in the long chromosome group are a result of addition of heterochromatin. However the amount of heterochromatin gained varies from chromosome to chromosome within species and also from species to species among corresponding chromosomes. The sex chromosomes in the short chromosome group seem to have become shorter due to loss of heterochromatin while the autosomes generally remained unchanged. Heterochromatin seems to play a significant role in crosscompatibility among these species.
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Barrera, Luis A. "Towards a Systematic Approach for Characterizing Regulatory Variation." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:26718710.
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A growing body of evidence suggests that genetic variants that alter gene expression are responsible for many phenotypic differences across individuals, particularly for the risk of developing common diseases. However, the molecular mechanisms that underlie the vast majority of associations between genetic variants and their phenotypes remain unknown. An important limiting factor is that genetic variants remain difficult to interpret, particularly in noncoding sequences. Developing truly systematic approaches for characterizing regulatory variants will require: (a) improved annotations for the genomic sequences that control gene expression, (b) a more complete understanding of the molecular mechanisms through which genetic variants, both coding and noncoding, can affect gene expression, and (c) better experimental tools for testing hypotheses about regulatory variants.
In this dissertation, I present conceptual and methodological advances that directly contribute to each of these goals. A recurring theme in all of these developments is the statistical modeling of protein-DNA interactions and its integration with other data types. First, I describe enhancer-FACS-Seq, a high-throughput experimental approach for screening candidate enhancer sequences to test for in vivo, tissue-specific activity. Second, I present an integrative computational analysis of the in vivo binding of NF-kappaB, a key regulator of the immune system, yielding new insights into how genetic variants can affect NF-kappaB binding. Next, I describe the first comprehensive survey of coding variation in human transcription factors and what it reveals about additional sources of genetic variation that can affect gene expression. Finally, I present SIFTED, a statistical framework and web tool for the optimal design of TAL effectors, which have been used successfully in genome editing and can thus be used to test hypotheses about regulatory variants. Together, these developments help fulfill key needs in the quest to understand the molecular basis of human phenotypic variation.Biophysics
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Sawyer, Sarah Lynn. "Using SNPs to study complex genetic disease : a population and evolutionary genetics perspective /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-967-6/.
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Johansson, Åsa. "Genome Variation in Human Populations : Exploring the Effects of Demographic History and the Potential for Mapping of Complex Traits." Doctoral thesis, Uppsala University, Department of Genetics and Pathology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7293.
Full textAbstract:
A major challenge in human genetics is to understand the genetic variation underlying common diseases. In this thesis, I focus on forces creating differences between individuals and genomic regions, methods for characterizing genomic variation, and the association between genomic and phenotypic variation. Genetic markers are widely used to locate genes associated with different phenotypes. In my first paper, I describe novel algorithms for automatic genotype determination of microsatellite markers, a procedure which is currently both time-consuming and error prone.
The co-segregation of genetic markers in a population leads to non-random association of alleles at different loci - linkage disequilibrium (LD). LD varies throughout the genome and differs between populations due to factors such as their demographic history. In my second paper, I discuss the increased power, for mapping of human traits, that results from studying a population with appreciable levels of LD such as is found in the Swedish Sami population.
Lately, large-scale analyses of single nucleotide polymorphisms (SNPs) have become available and efforts have been made to identify a set of SNPs, which captures most of the genome variation in a population (tagSNPs). In my third paper, I describe the limitations of this approach when applied to data from an independent population sample of randomly ascertained SNPs. The transferability of tagSNPs between populations is poor, presumably due to variation in allele frequencies and the bias towards common SNPs used in most studies.
The level of genomic variation is influenced by population structure, recombination and mutation rate, as well as natural selection. During the exodus from Africa, humans have adapted to new environmental conditions. In my fourth paper, I describe a new method for identifying genomic regions carrying signatures of recent positive selection and apply this to an available dataset of millions of SNPs.