Dissertations / Theses: 'Biolog; Variation (Genetics)'

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Larsson, Jobs Karl. "Population Fragmentation and Genetic Variation in Grouse." Doctoral thesis, Uppsala University, Department of Ecology and Evolution, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6006.

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In this thesis the genetic variation of two grouse species, the Chinese grouse (Bonasa sewersowi) and the Black grouse (Tetrao tetrix) was examined with neutral genetic markers: microsatellites. Habitat fragmentation and isolation leads to structuring among and loss of genetic variation within populations.

The Chinese grouse in a small population in Lianhuasan nature reserve was found to have undergone a population bottleneck and as a result of isolation and possible inbreeding showed genetic impoverishment hereof.

The Black grouse populations in Europe face various different conditions from widely distributed areas of suitable habitat in the northern and eastern parts of its range to highly naturally and anthropogenically fragmented habitat landscapes in the west.

Structure among populations was found in Great Britain where Wales, Scotland and England showed characteristics of three different genetic entities, indicating very little or no geneflow between these populations.

The Dutch population showed signs of loss of genetic variation as to be expected from a population that has historically decreased in population size from several thousands to tens of individuals in a matter of decades. However the possibility to spot signs of a bottleneck was impaired due to the short time-window in which this can be observed in a population with such a low effective population size (N_E).

The sampled populations in Europe clustered into five different groups of genetic identities. The different clusters were: Great Britain-, the Netherlands-, Fenno-Scandian-, Alpine- and lowland German-Austrian populations. The level of genetic variation when compared over all these different populations decreased as a sign of isolation and small N_E. However it was not feasible to separate the impact of these two factors.

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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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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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Foulkes, Nicholas F. "Molecular biology of the human G 6-PD gene." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.253009.

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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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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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Hadzihalilovic-Numanovic, Amra. "Genetic Variation and Relatedness of Freshwater Pearl Mussel Margaritifera margaritifera L. populations." Licentiate thesis, Karlstad University, Division for Environmental Sciences, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-2410.

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The two papers presented in this thesis focus on population genetic study on freshwater pearl mussel populations in Sweden, using RAPD method. In paper I, I examine genetic variation within and between 5 populations in a single drainage area in south western Sweden. In paper II, I study the evolutionary relationship, and how genetic variation is related to population size, age structure and geographic isolation in 14 populations of freshwater pearl mussel in south central Sweden. In both papers I and II, I found that genetic variation was larger than found in previous studies using other techniques, and variation was larger between than within populations. I did not found any correlation between geographic and genetic distance, which indicates that mussel populations have been adapted locally to environmental factors in a relatively short time. In paper I, I found that genetic distance between populations was greater than found in other studies, despite small geographic distances. In paper II, I found that populations were highly differentiated indicating little gene flow between them. There was no significant positive relation between genetic variation and population size or age structure but there was a significant positive relation between mean age and population size indicating that many populations have gone through bottlenecks recently.

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Obaid, Jian. "What is known about genetic variation among Baltic Sea blue mussels and the promise of proteomics. A literature review." Thesis, Södertörn University College, School of Life Sciences, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-2701.

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The Baltic Sea is an evolutionary young sea that have developed a low salinity in its water from the fresh water that flows from the north and saltwater that flows from the south of the sea. The low salinity is too low for many marine organisms and too high for many freshwater organisms. Species like the blue mussel, which have adapted to the low salinity, may have developed different protein expression as a result. To study which protein that have been expressed in the organism proteome analysis is often used. 2-dimensional electrophoresis may be the only method that can do this kind of analysis.

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Blackman, Benjamin K. "Evolutionary genetics of flowering time regulation and variation in Helianthus." [Bloomington, Ind.] : Indiana University, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3373495.

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Thesis (Ph.D.)--Indiana University, Dept. of Biology 2009.
Title from home page (viewed on Jul 8, 2010). Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5957. Advisers: Loren H. Rieseberg; Scott D. Michaels.

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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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Borge, Thomas. "Genetics and the Origin of Two Flycatcher Species." Doctoral thesis, Uppsala University, Evolutionary Biology, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3919.

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In this thesis, different genetic tools are used to investigate pre- and postzygotic barriers to gene exchange and their role in speciation in the pied flycatcher (Ficedula hypoleuca) and the collared flycatcher (F. albicollis). This species complex consists of four genetically distinct clades that apparently diverged in allopatry (I). Sequencing of introns from autosomal and Z-linked genes from the two species reveals signs of selection on the Z-chromosome. Sexual selection acting on Z-linked genes might explain this pattern (II). By using large-scale genotyping of single nucleotide polymorphisms (SNPs), introgression is observed at autosomal- but not Z-linked loci, mostly from the pied- to the collared flycatcher. Male plumage characters and genes involved in hybrid fitness are largely mapped to the Z-chromosome (III). By studying mate choice of female hybrids I show that there is a link between female preferences and the Z chromosome (IV). The rate of introgression in island versus clinal hybrid zones is consistent with regional differences in hybrid fertility. Asymmetric gene flow from allopatry on the islands may oppose reinforcement, leading to introgression and a partial breakdown of postzygotic isolation. Adaptive introgression may explain the high rate of introgression observed at one of the genetic markers (V). For late breeding female collared flycatchers it appears to be adaptive to use pied flycatchers as social fathers but conspecific males as genetic fathers. Additionally, females in mixed species pairs may reduce hybridization costs by producing an excess of male hybrid offspring that are more fertile than females (VI).

In conclusion, the Z-chromosome appears to play a major role in flycatcher speciation. Sexual selection and reinforcement are important mechanisms in the divergence of these birds. However, gene flow from allopatry, introgression of adaptive genes and adaptive hetrospecific pairing by late breeding collared flycatcher females may work in the opposite direction.

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Scheper, Reiny W. A. "Studies on the biology and genetic variation of phomopsis on grapevine /." Title page, contents and abstract only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phs325.pdf.

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Desai, Kinjal. "Characterizing the impact of single nucleotide variation in breast cancer." Thesis, Dartmouth College, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10144817.

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Genome sequencing technology has enabled the identification of genetic variants that are linked with cancer phenotypes, whether these are somatically acquired mutations or common inherited single nucleotide polymorphisms (SNPs). Whereas coding variants have been reported to disrupt protein function to promote cancer, most variants map to noncoding regions, with no known function. Recently, much effort has gone into annotating the human noncoding genome, enabling the characterization of the functional basis of noncoding SNPs. As an example of functional impact, breast cancer (BrCa) risk-associated SNPs can alter transcription factor binding at distal enhancers.

Identifying the targets of risk SNPs remains a challenge. One reason for this is the complex three-dimensional structure of the genome. Local chromatin openness correlates with chromatin activity, and sites of chromatin that are open concurrently across multiple cell types indicates a functional relationship between them. We mapped BrCa risk-associated SNPs to regions of open chromatin to predict the most likely functional risk SNPs. Then, we predicted their targets by identifying the gene promoters whose openness correlated with these risk regions. Further, we validated a gene which is a novel therapeutic target and relevant in breast cancer biology.

In addition to SNPs, noncoding somatic mutations are also predicted to play a role in cancer. In 2012, driver mutations were reported in the telomerase gene promoter, hinting at the relevance of mutations in regulatory elements. This is particularly true when considering oncogenes whose elevated expression in certain cancers is not attributable to coding mutations or copy number amplification. We reveal the enrichment and functional nature of somatic mutations mapping to enhancers that regulate the estrogen receptor gene, which is known to drive over two-thirds of breast cancer.

Attributing function to noncoding SNPs and mutations associated with cancer risk and progression is a growing necessity in this era of whole-genome cancer biology. This thesis demonstrates a methodology to identify the functional consequence and gene targets of significantly mutated or risk variant-bearing enhancer sets to narrow the gap between known and unknown risk factors in BrCa.

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Benovoy, David. "Characterization of transcript isoform variations in human and chimpanzee." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=66918.

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Transcript expression and pre-mRNA processing are emerging as important mechanisms that increase the complexity of eukaryotic transcriptomes. These processes allow a genomic locus to produce a number of mRNAs and proteins with distinct properties that affect function, stability, and sub-cellular localization by controlling the rate of transcript expression, by varying the initiation or termination of transcription and by modulating the inclusion of exons (alternative splicing) in mature mRNAs. Thus, it is crucial to determine the extent of these types of variations to better understand their importance in creating organism diversity. The studies described in this thesis provide the first genome-wide estimations of how single nucleotide polymorphisms (SNPs) affect the regulation of transcript expression and pre-mRNA processing in a human population as well as between humans and chimpanzees using a microarray-based approach. We first demonstrated that transcript expression changes at the isoform level are common between two unrelated individuals and that these changes are heritable and therefore have an underlying genetic component. We then investigated what proportion was under genetic control in a normal human population by conducting a genome-wide association analysis between single nucleotide polymorphisms and transcript isoform variants. We found that 50-55% of transcript expression variation is isoform based. We also extended our comparison of human transcript isoform variation to chimpanzee. We showed that genetic substitutions in regulatory sequences are responsible for some of the isoform variations observed between these two closely related species. We ascertained that in our study these isoform variations are responsible for certain phenotypic differences mostly related to immune responses. These results constitute an important change in the way genetic variations are viewed in humans and chimpa
Le niveau d'expression d'un transcrit et les processus de maturation de celui-ci en ARN messager (ARNm) se révèlent être des mécanismes augmentant la complexité du transcriptome des eucaryotes. Ces processus permettent au même locus génomique de produire plusieurs ARNm et protéines ayant des propriétés distinctes qui affectent leurs fonctions, leur stabilité et leurs localisations intra cellulaire en contrôlant la vitesse de transcription, en variant le site d'initiation ou de terminaison de la transcription et en modulant l'inclusion d'exons (épissage) dans les ARNm matures. Il est donc primordial de déterminer l'ampleur de ces types de variations afin de mieux comprendre leur impact sur la diversite des oraganismes. Les études décrites dans cette thèse fournissent les premières estimations de la façon dont les variations de polymorphism nucléotidique simple (SNP) peuvent affecter la régulation de l'expression d'un transcrit et ses processus de maturation à l'échelle du génome entier. Ces processus sont examinés dans une population humaine et entre humain et chimpanzé en utilisant une méthode basée sur les puces à ADN. Nous démontrons d'abord l'existence d'un nombre important de variations d'isoformes d'ARNm entre deux individus non apparentés et nous démontrons que ces variations sont héritées ce qui leur révèle une composante génétique. Par la suite, nous avons déterminé quelle proportion et quel type de variation au niveau de l'isoform était sous contrôle génétique dans une population humaine. En réalisant une analyse d'association entre l'expression des transcrits du génome entier et les SNPs présents dans cette population, nous avons observé que 50-55% de la variation était à l'échelle de l'isoforme du transcrit. Nous avons aussi étendu cette comparaison au chimpanzé en utilisant les profils d'expression mesurés lors de l'analyse précédente. N

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Lomelin, David. "Using human genetic variation to predict functional elements in non-coding genomic regions." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2010. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3390057.

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Peters, Derek Tilghman. "Isogenic Human Pluripotent Stem Cell Models of Cardiovascular Disease-Associated Genetic Variation." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493401.

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A complex interplay of genetic and environmental factors underlies the development of common human diseases such as cardiovascular disease. Despite widespread use of existing medications, coronary heart disease (CHD), including myocardial infarction (MI), remains a significant cause of morbidity and mortality worldwide. The results of recent human genetic studies have provided unprecedented opportunities to elucidate the genes and molecular pathways that underlie CHD and risk factors like plasma lipid concentrations. Translating these findings into mechanistic insight promises to improve our understanding of disease pathogenesis and aid in the development of novel therapies. Precise functional characterization is required to bridge this gap; yet doing so can be challenging using traditional approaches. The properties of human pluripotent stem cells (hPSCs) make them uniquely suited to address this challenge - they retain a normal human genome in culture, can be genetically modified, and can be differentiated into multiple cell types. The work presented in this thesis demonstrates the use of hPSCs and genome editing technology to generate human disease models in vitro. We developed a genome editing system optimized for hPSCs that can be used to efficiently generate hPSC lines with targeted genetic modifications. Modified and isogenic control hPSCs are then differentiated into a relevant cell type for phenotypic characterization. We applied this approach to investigate the functional effects of human genetic variation underlying plasma lipid concentrations. We used TALEN genome editing to clarify the role of the SORT1 gene as a mediator of cellular metabolic processes. We targeted the ANGPTL3 gene using TALEN and CRISPR/Cas9 genome editing to create an in vitro model of a monogenic disorder, familial combined hypolipidemia, and investigated the putative role of ANGPTL3 in the regulation of low-density lipoprotein cholesterol metabolism. To facilitate the use of hPSC-models to study subtle phenotypes involving human liver, we developed a method for purifying hepatocyte-like cells following hPSC differentiation. Finally, we combined these approaches to model the tissue-specific effects of a common non-coding genetic variant in the chromosome 1p13 locus that is associated with risk of MI. This result demonstrates the feasibility of using hPSCs to characterize disease-associated common genetic variation.
Medical Sciences

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Samocha, Kaitlin E. "Modeling Rare Protein-Coding Variation to Identify Mutation-Intolerant Genes With Application to Disease." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493508.

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Sequencing exomes—the 1% of the genome that codes for proteins—has increased the rate at which the genetic basis of a patient’s disease is determined. Unfortunately, when a patient does not carry a well-established pathogenic variant, it is extremely challenging to establish which of the tens of thousands of variants identified in that individual is contributing to their disease. In these situations, variants must be prioritized to make further investigation more manageable. In this thesis, we have focused on creating statistical frameworks and models to aid in the interpretation of rare variants and towards establishing gene-level metrics for variant prioritization. We developed a sensitive and specific workflow to detect newly arising (de novo) variants from exome sequencing data of parent-child trios, and created a sequence-context based mutational. This mutational model was the basis of a rigorous statistical framework to evaluate the significance of de novo variant burden not only globally, but also per gene. When we applied this framework to de novo variants identified in patients with an autism spectrum disorder, we found a global excess of de novo loss-of-function variants as well as two genes that harbored significantly more de novo loss-of-function variants than expected. We also used the mutational model to predict the expected number of rare (minor allele frequency < 0.1%) variants in exome sequencing datasets of reference individuals. We found a significant depletion of missense and loss-of-function variants in a subset of genes, indicating that these genes are under strong evolutionary constraint. Specifically, we identified 3,230 genes that are intolerant of loss-of-function variation and that set of genes is enriched for established dominant and haploinsufficient disease genes. Similarly, we searched for regions within genes that were intolerant of missense variation. The most missense depleted 15% of the exome contains 83% of reported pathogenic variants found in haploinsufficient disease genes that cause severe disease. Additionally, both gene-level and region-level constraint metrics highlight a set of de novo variants from patients with a neurodevelopmental disorder that are more likely to be pathogenic, supporting the utility of these metrics when interpreting rare variants within the context of disease.
Medical Sciences

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Coon, Keith Darren. "Genetic variation of maternal and paternal lineages within the Havasupai Indians of northern Arizona." Diss., The University of Arizona, 2002. http://hdl.handle.net/10150/284314.

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The Havasupai Indians are a small (∼600 members), Yuman-speaking population that resides on a reservation in the Grand Canyon region of northern Arizona. Due to their location and cultural practices, they are subjected to extreme geographic and reproductive isolation. Additionally, an influenza epidemic at the turn of the century decreased the reproducing population to 43 females and 42 males. These observations suggest that the Havasupai should contain less genetic diversity than other Native American populations. They are also disproportionately affected by disease, having the third largest incidence of Non Insulin-Dependent Diabetes Mellitus (NIDDM) in the world. An extensive analysis of maternal and paternal variation of the Havasupai was undertaken. Maternal variation was assayed by sequencing the non-coding control region (CR) of mitochondrial DNA (mtDNA), whereas paternal variation was examined using single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) located on the non-recombining portion of the Y-chromosome (NRY). Due to the availability of familial pedigrees dating back to the mid-1800s and spanning eight generations, precise mutation rates were determined for maternal and paternal lineages. The Havasupai thus offer a unique opportunity to explore genetic variation in a small, homogenous Native American population for which extensive genealogical information is readily available. Examination of mtDNA sequences from the complete 1127 by CR of 43 Havasupai individuals along with SNP and STR data from the Y-chromosome of 48 male Havasupai revealed that contrary to our initial prediction, the Havasupai, historically a small population (as evidenced by the limited number of founder haplotypes and low estimates of π), probably maintained a relatively high level of diversity (as evidenced by the number of rare haplotypes, high haplotype diversity, and high estimate of E(ν)), probably a remnant of their association with the larger Pai population from which they are derived. As the level of diversity displayed by the Havasupai seems to have been maintained since the recent population bottleneck, it must have been too small and/or too short to have any detectable effect on the overall diversity of the tribe. Lastly, there appears to be some association between mtDNA mutations and NIDDM in the Havasupai population.

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Cropp, Cheryl D. "Genetic variation in drug transporters in ethnic populations." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3339183.

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Herron, Jon C. "Genetic variation, thermal sensitivity, and thermal acclimation in Volvox aureus and Volvox globator /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/5115.

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Tillquist, Christopher. "Voyages of the Vikings: Human haploid variation in northern Europe." Diss., The University of Arizona, 2002. http://hdl.handle.net/10150/279948.

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Europe is a region characterized by a long history of both settlement and resettlement. This study uses information from the haploid systems of the human genome in order to investigate the presence of population structure in Europe and discuss the mitigating effects of shared population history and the impact of evolutionary forces. By means of two kinds of data from the Y chromosome, the study first establishes patterns of diversity across the entirety of Europe. More in-depth analyses investigate the evolutionary effects of settlement and colonization on overall genetic diversity of populations. Finally, considering data from the entire control region sequence, an effort is made to estimate patterns of mitochondrial diversity and compare their import to that of the Y chromosome.

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Holden, Lindsay Adrian. "Investigating the Role of Genomic Variation in Susceptibility to Environmental Chemicals across Populations." PDXScholar, 2018. https://pdxscholar.library.pdx.edu/open_access_etds/4371.

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No two individuals are identical. This is true at the genetic level and at the phenotypic level. One of the traits that varies between populations is toxicant susceptibility: some individuals are sensitive to the effects of environmental chemical exposure, and others are resistant. This body of work aims to address the impact of genomic copy number variants (CNV)--large (>1 Kb) duplications or deletions across the genome--on the toxicant-susceptibility phenotype. Herein copy number variants were characterized across three commonly used laboratory strains of zebrafish (Danio rerio) and mRNA expression phenotypes were identified in the same strains. It was found that males and females have only a 14% overlap in differentially expressed mRNA transcripts across three common laboratory strains, congruent with the growing body of work identifying sex- and strain-specific phenotypes in zebrafish. Furthermore, identified were two strain-specific response quantitative trait loci (QTL) that explain about a third of the variation in susceptibility to PCB and tested the response QTL using targeted CRISPR-Cas9 editing of the CNV involved. Overall, this body of work defines CNV and mRNA expression variation across zebrafish strains, identifies CNV causal in the PCB-susceptibility phenotype, and confirms the PCB-susceptibility QTL using targeted genomic editing.

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Boettger, Linda M. "Complex Forms of Structural Variation in the Human Genome: Haplotypes, Evolution, and Relationship to Disease." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226090.

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Genomic mutations arise in many forms, varying from single base pair substitutions to complicated sets of overlapping copy number variants (CNVs). While each type of variation contributes to phenotype, complex structural variation, which contains multiple mutations, is difficult to type across many individuals and is largely omitted from genomic studies. This thesis presents methods to type complex structural variation, understand how it evolves, and integrate these complex variants into association studies to phenotypes. We focused on four structurally complex regions in the human genome. The 17q21.31 region contains an inversion, previously uncharacterized overlapping copy number variants, and SNPs that associate to the female meiotic recombination rate and female fertility1. The haptoglobin (HP) gene at chromosome 16q22.2 contains a 1.7 kb tandem duplication2, previously uncharacterized paralogous gene conversion, and nearby SNPs that associate to cholesterol levels3. The haptoglobin related gene (HPR) at chromosome 16q22.2, segregates as a multi-allelic copy number variant (mCNV) specifically in African populations. Lastly, complement component 4 (C4) at chromosome 6p21.3, contains a length polymorphism, paralogous sequence variation, and copy number variation segregating in humans and non-human primates4. We developed methods to characterize the complex structural variation in each of these four regions, type the variation at the population level and integrate it into association studies. Briefly, we determined the breakpoints of each individual structural variant, typed each variant in a population cohort, and learned which variants segregate together through trio inheritance patterns. Once these structural haplotypes were defined, we phased them with surrounding SNP haplotypes and used this data as a reference panel for imputation into disease cohorts, and to better understand their evolutionary history. We found that two overlapping duplications in the 17q21.31 region rose rapidly and independently to high frequency within European populations, and may account for the regional association to female fertility and the female meiotic recombination rate. We also found that a recurrent deletion in the HP gene associates to total cholesterol and LDL cholesterol levels. The methods developed in this thesis enable the integration of structurally complex variation into future association studies so that we can begin to understand their effects on phenotypes.

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Castro, Júnior Francisco Pires de. "Ciclos de vidas comparados e variabilidade genética de Aedes aegypti (DIPTERA: CULICIDAE) do semi-árido paraibano." Universidade Estadual da Paraíba, 2010. http://tede.bc.uepb.edu.br/tede/jspui/handle/tede/1659.

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Made available in DSpace on 2015-09-25T12:18:15Z (GMT). No. of bitstreams: 1 Francisco Pires de Castro Junior.pdf: 1073998 bytes, checksum: 0a983b393aefcf1ab9cbbfd9564a9389 (MD5) Previous issue date: 2010-02-04
The efficiency of a program to control Aedes aegypti depends on the knowledge about the biological and genetic variations that occur between their populations. The present study addressed to compare the life cycles patterns and genetic variability among populations of A. aegypti collected in different regions of Paraiba semi-arid. Life cycles were studied at environmental temperature (26 ± 2ºC, relative humidity of 60 ± 10% and photophase of 12 hours), the period of development and viability of egg phases, larva and pupa, sex ratio, longevity, fecundity and size of adults were evaluated daily. Beyond these variables grouping analysis (Cluster Analysis), using a matrix of Euclidean distance by the method of unweighted average was used. The Analysis of gene structure of populations was carried out by total DNA extractions and RAPD-PCR analysis. Phase s durations of egg, larva and pupa varied from 3.79 to 4.79 days, 9.15 to 10.89 days and 2.18 to 2.59 days, respectively. Adults longevity of A. aegypti means variation from 37.82 to 58.29 days for males and from 40.03 to 73.07 days for females. Populations of A. aegypti from Serra Branca and Cuité cities presented major similarity in relation to the formed groupings. Genetic variability indexes showed highest diversity in Barra de Santana population (P = 93.33%, H = 0.373), however, it was lowest in Cuité population (P = 60.00%, H o o = 0.171). According to the results it was verified that there is a distinct pattern of development among populations of A. aegypti from different municipalities of Paraíba semi-arid. Genetic diversity heterozygosity H and polymorphisms indexes suggest a high intrapopulation genetic variation and low interpopulation variability. Such fact may indicate constant migration of the vectors to these locations with high number of individuals.
A eficiência de um programa de controle do Aedes aegypti depende do conhecimento sobre as variações biológicas e genéticas que ocorrem entre as suas populações. A presente pesquisa teve por objetivo comparar os padrões dos ciclos de vida e variabilidade genética entre populações de A. aegypti coletadas em diferentes regiões do semi-árido paraibano. Os ciclos de vida foram estudados a temperatura ambiente de 26 ± 2º C, umidade relativa de 60 + 10% e fotofase de 12 horas. Diariamente avaliou-se o período de desenvolvimento e a viabilidade das fases de ovo, larva e pupa, razão sexual e longevidade, fecundidade e comprimento de asas dos adultos. Alèm destas variáveis foi realizada, uma análise de agrupamento ( Cluster analyses ), utilizando-se uma matriz de distância euclidiana através do método da média nãoponderada. A análise da estrutura gênica das populações foi realizada através das Extrações de DNAs totais e análise por RAPD-PCR. As durações das fases de ovo, larva e pupa, variaram de 3,79 a 4,79 dias, 9,15 a 10,89 dias e de 2,18 a 2,59 dias, respectivamente. A longevidade dos adultos de A. aegypti apresentou uma variação de 37,82 a 58,29 dias para os machos e 40,03 a 73,07 dias para as fêmeas. As populações de A. aegypti de Serra Branca e Cuité apresentam maior similaridade, em relação aos agrupamentos formados. Os índices de variabilidade genética apresentaram maior diversidade na população de Barra de Santana (P = 93,33 %; H o = 0,373) e o menor na população de Cuité (P = 60,00%; H = 0,171). Em função dos resultados verificou-se que há um padrão diferenciado de desenvolvimento entre as populações de A. aegypti procedentes de diferentes municípios do semi-árido paraibano. Os índices de diversidade genética heterozigosidade H o o e polimorfismos sugerem elevada variação genética intrapopulacional e baixa variabilidade interpopulacional. Tal fato pode indicar constantes migrações de vetores para essas localidades com elevado número de indivíduos.

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Li, Xiang. "STRESS-INDUCED GENETIC CHANGE IN FLAX REVEALS GENOME VARIATION MECHANISM." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1565964370435691.

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26

Dankwa, Selasi. "Sialic acid variation as a determinant of Plasmodium invasion of erythrocytes in malaria infection." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467188.

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Sialic acids are acidic sugars that terminate glycan chains on proteins or lipids on vertebrate cell surfaces. They vary greatly in structure, presentation and amount, all of which are important physiologically, but can also impact the tissue and host tropism of diverse pathogens. Parasites of the genus Plasmodium cause malaria, a disease characterized by a cyclical process of parasite invasion of host erythrocytes, growth and replication and fresh invasion of new erythrocytes. During erythrocyte invasion – an event central to malaria pathogenesis – proteins on the surface of the parasite, known as invasion ligands, bind to specific erythrocyte receptors, many of which are sialylated. In this dissertation, we determined how sialic acid variation impacts erythrocyte invasion by the zoonotic parasite, Plasmodium knowlesi and the most virulent human parasite, Plasmodium falciparum. For studies on P. knowlesi, we determined if Neu5Gc, a sialic acid that is absent in humans but present in most other primates, is a major determinant of parasite tropism. We used the recently described ex vivo erythrocyte culture system to transgenically express the CMAH enzyme, responsible for production of Neu5Gc. P. knowlesi showed significantly increased invasion of Neu5Gc-expressing human erythrocytes, providing evidence that loss of Neu5Gc in humans restricts P. knowlesi invasion of human erythrocytes. We then biochemically characterized two P. knowlesi invasion ligands of the EBL family and found they specifically bind Neu5Gc. These ligands potentially mediate Neu5Gc-dependent invasion of human and macaque erythrocytes. We finally showed that in natural human infections, P. knowlesi can adapt to infect erythrocytes independently of sialic acid. We also studied the use of sialic acid-containing erythrocyte receptors by P. falciparum using the ex vivo erythrocyte culture system. We determined the importance in invasion of glycophorin B (GPB), receptor for P. falciparum invasion ligand, EBL-1, and one of the highly sialylated receptors on the erythrocyte surface. We specifically knocked down gene expression of GPB as well as two well characterized receptors involved in P. falciparum invasion – GPA, the largest contributor to erythrocyte sialic acid and GPC, another sialylated receptor. Invasion assays using P. falciparum laboratory strains and field isolates revealed that GPB is a dominant receptor in P. falciparum invasion, of comparable importance to GPA.
Biological Sciences in Public Health

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Latta, IV Leigh C. "Plastic and Genetic Determination of Population, Community, and Ecosystem Properties in Freshwater Environments." DigitalCommons@USU, 2010. https://digitalcommons.usu.edu/etd/618.

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The hierarchy of biological organization, from molecules to ecosystems, describes the relationships among various biological systems. Of particular interest is assessing how the factors that primarily determine the nature of one hierarchical level also have transcendent qualities that affect the ecology and evolution of higher hierarchical levels. The goal of this dissertation was to use a bottom-up approach to examine the transcendent effects of two factors that strongly determine the nature of their associated level of biological organization. The first, phenotypic plasticity, is a primary factor that determines the phenotype of an individual. The second factor, genetic diversity, largely determines the phenotypic distributions associated with populations. Controlled laboratory experiments on taxa from a freshwater tri-trophic food web were employed to examine the transcendent effects of phenotypic plasticity and genetic diversity on the biological hierarchy because relationships between individuals and populations from different trophic levels are well documented for numerous freshwater species. The results show that phenotypic plasticity can induce changes in population means and variances that promote population persistence and evolvability, and that plasticity provides a mechanistic explanation of community stability in response to changing environments. Similarly, genetic diversity may act as a signal that induces phenotypic plasticity in individuals, modulates community richness and ecosystem properties, and suggests a potential mechanism for the changes in biodiversity. Thus, results from this dissertation show that plasticity and genetic variation can shape the attributes of other biological groups higher in the biological hierarchy, and, in some cases, may also provide a mechanistic explanation for variability observed in higher levels of the biological hierarchy. These results highlight the importance of integrating traditionally disparate biological disciplines and may help to unify biology as a field.

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Ross, Michelle. "Genetic variation in the French Canadian populations of the Saguenay-Lac St. Jean and Charlevoix Regions." Thesis, McGill University, 1991. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=59994.

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The Saguenay-Lac St. Jean and Charlevoix regions of Quebec are characterized by high incidences of hereditary diseases such as vitamin D-dependent rickets type I (VDD1), cystic fibrosis, and tyrosinemia. This phenomenon may be due to founder effect or genetic drift. Therefore, one may also detect differences in allele frequencies of neutral polymorphisms between these populations and the general population. An assessment of genetic variation was performed utilizing genetic markers spanning chromosome 12q14. Allele frequencies for the genetic markers in the sample populations did not differ significantly from those published for other Caucasian populations. One haplotype, observed in strong linkage disequilibrium with the VDD1 mutation, was found to be infrequent on normal chromosomes. This suggests that all of the VDD1 mutant alleles could be identical by descent, in keeping with a founder effect for VDD1 in northeastern Quebec.

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29

Jordan, Daniel Michael. "Predicting the Effects of Missense Variation on Protein Structure, Function, and Evolution." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17464216.

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Estimating the effects of missense mutations is a problem with many important applications in a variety of fields, including medical genetics, evolutionary theory, population genetics, and protein structure and design. Many popular methods exist to solve this problem, the most widely used of which are PolyPhen-2 and SIFT. These methods, along with most other popular methods, rely on multiple sequence alignments of orthologous protein sequences. Based on the amino acids observed in each column of the alignment, they produce a profile describing how tolerated each amino acid is at each position. They then compare the wild-type and variant amino acids to this profile to produce a prediction. In practice, these methods are fast, robust, and relatively reliable. However, from a theoretical perspective, they have at least three significant shortcomings: 1. They use effects on selection as a proxy for effects on phenotype and protein structure and function. 2. They treat each position as independent, ruling out most forms of interactions between sites. 3. They do not explicitly model the process of evolution, instead assuming that sequences we observe more or less represent an equilibrium state. With the recent explosion of sequencing technology, as well as the steady increase of computational power, we are now beginning to have enough data to investigate these simplifications and see how much they really affect the performance of these methods. In this dissertation, I present three such investigations. First, I describe a modified predictor designed to predict risk for a specific disease, hypertrophic cardiomyopathy (HCM), rather than general seletive effect. This method achieves significantly higher accuracy than methods without such specific domain knowledge. Next, I describe a model of pairwise interactions between sites, demonstrating both statistically and with in vivo evidence that approximately 7-12% of disease-causing variants may be mispredicted by these methods due to such interactions. Finally, I describe a hybrid method that uses an alignment-based estimator to inform a parametric model of evolution, resulting in a small but significant improvement in accuracy.
Biophysics

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Al-Sulaimani, Maha Saleh. "Genetic variation in the FMO2 gene : evolution & functional consequences." Thesis, Queen Mary, University of London, 2011. http://qmro.qmul.ac.uk/xmlui/handle/123456789/2324.

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Flavin-containing monooxygenase 2 (FMO2) is involved in the metabolism of xenobiotics, including therapeutic drugs. FMO2 exists in two forms: a functional and a non-functional form. The functional allele is found only in Africa and individuals of recent African origin. The aims of the project were to determine the frequency of functional FMO2 in Africa and obtain insights into the evolutionary history of the FMO2 gene. Six hundred and eighty nine samples from nine African population groups were genotyped for six high-frequency SNPs, and the genetic diversity within FMO2 was characterized by sequencing 3.44 kb of genomic DNA, encompassing the entire coding sequence and some flanking intronic sequences in 48 African individuals. Haplotypes were inferred using Phase and the relationship between mutations was revealed using reduced-median and median-joining Network. Test statistics were used to determine whether the genetic variation is compatible with neutral evolution. Genotyping indicated that deleterious SNPs occur mostly on a non-functional allele and that the frequencies of three were significantly different (P<0.05) among populations. Resequencing identified 32 variants. Genetree was used to estimate the time to the most recent common ancestral sequence (~0.928 million years) and the ages of some of the mutations. Results indicate that the frequency of full-length 23238C alleles is relatively uniform across sub-Saharan Africa. Interestingly, this is not the case for the inferred potentially functional 23238C alleles, which frequency differed significantly (P<0.05) across sub-Saharan Africa. iv The results also provide evidence that the frequency of functional FMO2 in east and west-Africa is high (≥0.54), which has important implications for therapy with drugs that are substrates for FMO2. A Ka/Ks > 1, and low nucleotide sequence diversity of intronic regions of 23238C alleles indicate a possible selective sweep.

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Trotter, Meridith V., and n/a. "Frequency-dependent selection and the maintenance of genetic variation." University of Otago. Department of Zoology, 2008. http://adt.otago.ac.nz./public/adt-NZDU20081114.120926.

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Frequency-dependent selection has long been a popular heuristic explanation for the maintenance of genetic diversity in natural populations. Indeed, a large body of theoretical and empirical work has already gone into elucidating the causes and consequences of frequency-dependent selection. Most theoretical work, to date, has focused either on the diallelic case, or dealt with only very specific forms of frequency-dependence. A general model of the maintenance of multiallelic genetic diversity has been lacking. Here we extend a flexible general model of frequency-dependent selection, the pairwise interaction model, to the case of multiple alleles. First, we investigate the potential for genetic variation under the pairwise interaction model using a parameter-space approach. This approach involves taking a large random sample of all possible fitness sets and initial allele-frequency vectors of the model, iterating each to equilibrium from each set of random initial conditions, and measuring how often variation is maintained, and by which parameter combinations. We find that frequency- dependent selection maintains full polymorphism more often than classic constant-selection models and produces more skewed equilibrium allele frequencies. Fitness sets with some degree of rare advantage maintained full polymorphism most often, but a variety of non-obvious fitness patterns were also found to have positive potential for polymorphism. Second, we further investigate some unusual dynamics uncovered by the parameter-space approach above. Long-period allele-frequency cycles and a small number of aperiodic trajectories were detected. We measured the number, length and domains of attraction of the various attractors produced by the model. The genetic cycles produced by the model did not have periods short enough to be observable on an ecological time scale. In a real world system, allele-frequency cycling is likely to be indistinguishable from stable equilibrium when observed over short time scales. Third, we use a construction approach to model frequency-dependent selection with mutation under the pairwise interaction model. This approach involves the construction of an allelic polymorphism by bombarding an initial monomorphism with mutant alleles over many generations. We find that frequency-dependent selection is able to generate large numbers of alleles at a single locus. The construction process generates a wide range of allele- frequency distributions and genotypic fitness relationships. We find that constructed polymorphisms remain permanently invasible to new mutants. Analysis of constructed fitness sets may even reveal a signature of positive frequency dependence. Finally, we examine the numbers and distributions of fitnesses and alleles produced by construction under the pairwise interaction model with mutation from existing alleles, using several different methods of generating mutant fitnesses. We find that, relative to more general construction models, generating mutants from existing alleles lowers the average number of alleles maintained by frequency-dependent selection. Nevertheless, while the overall numbers of alleles are lower, the polymorphisms produced are more stable, with more natural allele-frequency distributions. Overall, frequency-dependent selection remains a powerful mechanism for the maintenance of genetic variation, although it does not always work in intuitively obvious ways.

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Dannewitz, Johan. "Genetic and Ecological Consequences of Fish Releases : With Focus on Supportive Breeding of Brown Trout Salmo trutta and Translocation of European Eel Anguilla anguilla." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3764.

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33

Liu, Yang. "Data mining methods for single nucleotide polymorphisms analysis in computational biology." HKBU Institutional Repository, 2011. http://repository.hkbu.edu.hk/etd_ra/1287.

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34

Mamdani, Firoza. "Genetic variation and lithium response in bipolar disorder." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82285.

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The importance of genes in the etiology of bipolar disorder (BD) has been substantiated through family, twin and adoption studies. The search for susceptibility genes, however, has proved to be an arduous task with disease complexity leading to the non-replication of published results. We have used lithium treatment response as a classification variable, thus providing a phenotypically more homogeneous sample to work with. With this sample we carried out pharmacogenetic studies to identify genes involved in the etiology of BD and/or in the response to Li. The phosphoinositide and cAMP pathway have been shown to be involved in Li's mode of action. Thus, a gene responsible for regulating inositol metabolism (prolyl endopeptidase, PREP) and three cAMP responsive element binding proteins (CREB1-3) were investigated. We have found an association indicating a possible role of CREB1 and 2 in the etiology of BD and Li response. Further studies in larger, independent samples and the analysis of additional markers should be undertaken to confirm these findings.

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35

Shi, Niu 1963. "Demographic changes and genetic variation of an alfalfa (Medicago sativa L.) population." Thesis, The University of Arizona, 1991. http://hdl.handle.net/10150/277907.

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The objectives of this study were to describe demographic change in an alfalfa population and determine whether genetic changes were associated with stand loss in an alfalfa field during the year of establishment. A nondormant composite population (AZ-88NDC) was sown at 1944 seeds per square meter in Oct. 1988 at Tucson, AZ. Only 29% of the seeds sown germinated and emerged. Survivorship curve of the emerged seedling population had some characteristics of Deevey type III. Two heavy mortality periods were observed. Low temperatures might be the major cause of the first heavy stand loss. The second significant stand loss could be explained by increased density stress. Isozyme profiles were produced from 60 day survivors dug from the field, unselected greenhouse-grown AZ-88NDC (='Unsel') and 300-d progenies produced by intermating plants surviving 300 days. Significant differences were observed in overall level of population heterozygosity of 60-d and unselected populations based on fixation indices of six isozyme loci. This suggests that genetic changes may be associated with establishment of an alfalfa stand.

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36

Carrara, Susan. "Genetic variation among cultivated selections of mamey sapote (Pouteria spp. [Sapotaceae])." FIU Digital Commons, 2004. http://digitalcommons.fiu.edu/etd/2054.

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Mamey sapote [Pouteria spp., Sapotaceae] is a tree fruit of economic and cultural importance in Central America, Mexico, and the Caribbean islands. It contributes greatly to local economies, habitats, and human nutrition. This study is among the first to analyze genetic variability among cultivated selections of mamey sapote. The Amplified Fragment Length Polymorphism (AFLP) molecular technique was used to estimate levels of genetic diversity and similarity between individual specimens in the germplasm collections of Fairchild Tropical Botanic Garden and University of Florida. The study found overall low levels of genetic diversity within these collections. However, higher relative levels of genetic diversity were found in a group of selections from northern Costa Rica and Nicaragua. It is anticipated that future plant collection in that region will capture greater genetic diversity among cultivated types. In addition, 'Pantin' selections were used to investigate the level of variation within supposedly identical selections. This baseline information can be applied to the management and expansion of the germplasm collections by identifying duplicate selections and homonyms and by locating geographical areas for future collection.

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37

Barker, Carl. "Ecological, genetic and metabolic variation in populations of Tilia cordata." Thesis, Edge Hill University, 2017. http://repository.edgehill.ac.uk/10392/.

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Predicting the responses of tree species to rapid environmental change requires an understanding of their ecology, reproductive strategy, population connectivity and levels of adaptive variation. This project examines these aspects for an understudied UK native tree genus Tilia L. Comparison of edaphic and physiographic variables indicated that Tilia cordata Mill. is more generalist than T. platyphyllos Scop., as well as preferring locations with higher potential incident solar radiation and greater levels of organic carbon content. Examination of fine-scale spatial genetic structure indicates that T. cordata has a mixed reproductive system with approximately half of all individuals within sampled populations being of clonal origin. The incidence of clonality was weakly negatively correlated to historic summer temperatures and positively so to the proportion of canopy trees within samples, suggesting both fertility limitations and time since disturbance affect vegetative growth in the species. Clonal reproduction is not expected to impact future outcrossing success due to the fine scale of its effects on spatial genetic structure, being much smaller than typical pollen movements associated with outcrossing. T. cordata populations exhibited weak clinal spatial genetic structure at coarser scales (tens of kilometres) across two locations, which likely reflect historic dispersal limitations across a contiguous landscape and effective pollen movement at scales less than two kilometres. Fragmentation has not yet eroded genetic variation except in the demes with the smallest size (not necessarily the most isolated), suggesting that larger fragments may ultimately suffer the same fate. Finally, low metabolic variation between UK populations of T. cordata despite contrasting environmental conditions during sampling indicates high levels of phenotypic plasticity, while variation in a functional trait and a group of unidentified metabolite concentrations suggest avenues for examining local adaptation in the future.

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Strittmatter, Laura Anne. "Linking Human Genetic Variation to Mitochondrial Metabolism." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11428.

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Genetic variation has a powerful impact on human metabolism and disease. Traditionally, this relationship has either been studied at a high level using top-down descriptive studies of patients with genetically defined inborn errors of metabolism, or else from the bottom up, with molecular biology and biochemical studies of single proteins. Recent advances in genetic sequencing, metabolic profiling technology, and structural biology are rapidly enabling the integration of these approaches towards a more complete description of human metabolism.

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39

Bos, Antoine. "Natural variation in cold adaptation and freezing tolerance in Arabidopsis thaliana." Doctoral thesis, Umeå : Department of Ecology and Environmental Science, Umeå University, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1947.

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40

Frankenstein, Nicoletta Vasiliki. "Variation of Small rDNA in Tylosema esculentum." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1301602376.

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41

Hu, Xianghong. "Statistical methods for Mendelian randomization using GWAS summary data." HKBU Institutional Repository, 2019. https://repository.hkbu.edu.hk/etd_oa/639.

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Mendelian Randomization (MR) is a powerful tool for accessing causality of exposure on an outcome using genetic variants as the instrumental variables. Much of the recent developments is propelled by the increasing availability of GWAS summary data. However, the accuracy of the MR causal effect estimates could be challenged in case of the MR assumptions are violated. The source of biases could attribute to the weak effects arising because of polygenicity, the presentence of horizontal pleiotropy and other biases, e.g., selection bias. In this thesis, we proposed two works, expecting to deal with these issues.In the first part, we proposed a method named 'Bayesian Weighted Mendelian Randomization (BMWR)' for causal inference using summary statistics from GWAS. In BWMR, we not only take into account the uncertainty of weak effects owning to polygenicity of human genomics but also models the weak horizontal pleiotropic effects. Moreover, BWMR adopts a Bayesian reweighting strategy for detection of large pleiotropic outliers. An efficient algorithm based on variational inference was developed to make BWMR computationally efficient and stable. Considering the underestimated variance provided by variational inference, we further derived a closed form variance estimator inspired by a linear response method. We conducted several simulations to evaluate the performance of BWMR, demonstrating the advantage of BWMR over other methods. Then, we applied BWMR to access causality between 126 metabolites and 90 complex traits, revealing novel causal relationships. In the second part, we further developed BWMR-C: Statistical correction of selection bias for Mendelian Randomization based on a Bayesian weighted method. Based on the framework of BWMR, the probability model in BWMR-C is built conditional on the IV selection criteria. In such way, BWMR-C delicated to reduce the influence of the selection process on the causal effect estimates and also preserve the good properties of BWMR. To make the causal inference computationally stable and efficient, we developed a variational EM algorithm. We conducted several comprehensive simulations to evaluate the performance of BWMR-C for correction of selection bias. Then, we applied BWMR-C on seven body fat distribution related traits and 140 UK Biobank traits. Our results show that BWMR-C achieves satisfactory performance for correcting selection bias. Keywords: Mendelian Randomization, polygenicity, horizontal pleiotropy, selection bias, variation inference.

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Chiucchi, James Ernest Jr. "Genetic Diversity, Inbreeding and Diet Variation in an Endangered Rattlesnake, the Eastern Massasauga (Sistrurus c. catenatus)." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1316110529.

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43

Lindroos, Katarina. "Accessing Genetic Variation by Microarray Technology." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2002. http://publications.uu.se/theses/91-554-5251-5/.

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44

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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45

Larsson, Lena C. "Disentangling small genetic differences in large Atlantic herring populations: comparing genetic markers and statistical power." Doctoral thesis, Stockholms universitet, Zoologiska institutionen, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-8338.

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Genes are the foundation of evolution and biodiversity. The genetic structure of natural populations needs to be understood to maintain exploited resources rationally. This thesis focuses on genetic variability and methods to determine spatial and temporal genetic heterogeneities. Intense human exploitation generates particular challenges to conserve genetic diversity of fishes since it has genetic effects. My research concerns one of our most valuable fish species: the Atlantic herring (Clupea harengus). I analyzed Atlantic herring samples from the North and Baltic Seas. The objectives were to determine: 1) spatial genetic structure, 2) whether allozymes and microsatellites provide similar descriptions of the differentiation pattern, or 3) if they are influenced by selection, 4) factors affecting statistical power when testing for genetic differentiation, and 5) the temporal stability of the genetic structure. The results show: 1) very low levels of spatial genetic differentiation in Atlantic herring; a major component is a difference between the Baltic and North Seas, 2) a concordant pattern with allozymes and microsatellites, 3) that selection influences a microsatellite locus, which can be a low salinity adaptation, 4) that statistical power is substantial for frequently used sample sizes and markers; the difference in power between organelle and nuclear loci is partly dependent on the populations’ stage of divergence, and 5) no changes in amount of genetic variation or spatial genetic structure over a 24-year period; the selection pattern in one microsatellite locus remained. The notion that the large population sizes make herring unlikely to lose genetic diversity may be disputed. I found small local effective population sizes, and the evidence of selection hints of a distinct evolutionary lineage in the Baltic. When Atlantic herring is managed as very large units, there can be detrimental genetic effects if certain population segments are excessively harvested.

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46

McCracken, Carrie L. "Genetic Relationships Between Two Rare Plant Species, Aliciella caespitosa and A. tenuis, and Their Putative Progenitor, A. subnuda." DigitalCommons@USU, 2001. https://digitalcommons.usu.edu/etd/7333.

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Isolated populations have potential to become new species that should have less genetic variation than their ancestors. Small populations are more likely to lose genetic variation, which is, thus, expected to be greater in ancestors. Aliciella caespitosa and A. tenuis, two endemic species, may be derived from small populations of A. subnuda, a widespread species. Chloroplast DNA sequences were used to test this hypothesis. Allozyme data were used to compare genetic variation and numbers of alleles. Chloroplast data do not support the proposed relationships between A. subnuda and the other two species. Allozyme data were not more variable in A. subnuda. The data suggest that A. tenuis is derived from A. caespitosa, although the former did not show lower allozyme diversity. I detected fewer alleles in A. tenuis. These data suggest that the original population of A. tenuis was not small enough to lose genetic variation relative to its progenitor.

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Parsley, Meghan. "Adaptive Variation in Tiger Salamander Populations." TopSCHOLAR®, 2017. https://digitalcommons.wku.edu/theses/2056.

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Amphibians face an unknown future in a time of rapid environmental change due to global climate perturbations. Since amphibians are perceived to be indicators of ecosystem health, understanding the causes of their declines can improve our perception of threats to other species. Molecular techniques have allowed us to explore how environmental change affects genetic variation and to predict evolutionary adaptive potential of amphibian populations. The identification of populations with the greatest potential to respond to changing environmental variables may be an important conservation strategy to aid in future management efforts. I utilized targeted exon capture sequencing to identify adaptive variation in California tiger salamanders (CTS; Ambystoma californiense), a species threatened by land use change and hybridization with barred tiger salamanders (A. mavortium). I identified 17 and 26 outlier loci for balancing selection in historic and recent samples of CTS respectively. The outlier loci corresponded to genes of various functions, though none of the outliers associated significantly with the change in several tested environmental variables. Despite the lack of environmental correlations detected, it must also be considered that the outlier loci could be involved in epistatic interactions where many genes with small effects influence a single phenotype with fitness benefits. Additional hypotheses to explain the observed changes in allele frequencies and outliers may be the effects of UV-B radiation, pesticide use, or indirect effects of climate change.

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Morgan, Kendall Kennedy. "Context-dependency of mutation and the maintenance of genetic variation for life-history traits in natural populations of Daphnia pulicaria /." view abstract or download file of text, 2001. http://wwwlib.umi.com/cr/uoregon/fullcit?p3018384.

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Thesis (Ph. D.)--University of Oregon, 2001.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 93-104). Also available for download via the World Wide Web; free to University of Oregon users.

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Keele, John Wiliam. "Estimation of (co)variance components by weighted and unweighted symmetric differences squared, and selected MIVQUE's : relationships between methods and relative efficiencies /." The Ohio State University, 1986. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487266011223482.

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Husby, Arild. "Ecological genetics of populations experiencing changing environmental conditions." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/5672.

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A major goal in evolutionary biology is to understand how ecological factors shape the phenotypic and genetic variation that we observe in natural populations and in this thesis I examine how rapid changes in temperature have influenced phenotypic and genetic variation in morphological and life history traits in long-term studies of great tits. In Chapter 1 I review what is known about the effects of environmental change on natural populations, and outline the quantitative genetic framework that is available to study genetic variation in natural populations. Much focus on the effects of climate change has concerned species’ phenology, far less attention has been given to other traits. In Chapter 2 I examine the effects changing environmental conditions have had on the proportion of females that produce second broods. Temperature operates mainly through indirect effects (such as food abundance) but may also have more direct effects. In Chapter 3 I show that over a 36 year period body size have declined in line with predictions from Bergmann’s rule and I explore the genetic basis of this decline and the environmental factors involved. Although we can learn much from population level responses, there is a great deal of additional information to be gained by studying between-individual responses. In Chapter 4 I therefore compare the multivariate pattern of between-individual variation in phenotypic plasticity and its genetic basis for laying date and clutch size, in two great tit populations. Environmental changes may also directly affect the expression of genetic variance as well as the strength of selection acting on a trait, and in Chapter 5 I show that, for laying date, the environment induces a positive covariance between strength of selection and the expression of additive genetic variance, something that may enhance the rate of adaptation. Finally, in Chapter 6 I discuss and summarise the wider implications of the findings from this thesis.

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Dissertations / Theses on the topic 'Biolog; Variation (Genetics)'

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