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1
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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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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Vetayasuporn, Sopit. "Genetic variation in Pinus kesiya." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301651.
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Wright, Dominic. "Genetic variation in zebrafish behaviour." Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414510.
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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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Yang, Ian Anthony. "Genetic variation in COPD pathogenesis /." [St. Lucia, Qld.], 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16860.pdf.
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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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Zhou, Huitong. "Genetic variation in Dichelobacter nodosus Fimbriae." Lincoln University, 2001. http://hdl.handle.net/10182/2244.
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Footrot is a contagious hoof disease of ruminants. It is endemic in New Zealand and throughout sheep and goat farming regions of the world. The disease results from a mixed bacterial infection, but the essential agent is Dichelobacter nodosus, a Gram-negative, anaerobic bacterium that possesses type-IV fimbriae on its surface. Genetic variation in the fimbriae of D. nodosus was investigated in this study. Using the polymerase chain reaction (PCR), the variable region of the gene encoding the fimbrial subunit (fimA) was amplified from bacterial DNA extracted from footrot lesions. Different fimA amplimers were differentiated by single-strand conformation polymorphism (SSCP) analysis. In conjunction with DNA sequencing, 15 unique sequences of D. nodosus fimA were obtained from 14 footrot samples taken from 6 farming regions throughout New Zealand. When these sequences were compared to fimA of known serogroups, it revealed that there were at least 15 D. nodosus strains, representing 8 serogroups, present on New Zealand farms. The predominant serogroup was B which contained 6 strains, followed by serogroups F, H and G. No strains from serogroups D and I were detected in this investigation. Twelve out of the 15 New Zealand D. nodosus strains had fimbriae different to those previously reported and the presence of multiple strains on a single hoof was common (86% of samples). The fimA sequences from the 12 D. nodosus strains incorporated into the footrot vaccine currently available in New Zealand were determined. A primer set targeting the relatively conserved fimA regions and based on the published sequence of serogroup M Nepalese isolates (designated M-Nep), failed to amplify fimA from the vaccine serotype M strain (designated as M-SPAHL). When the downstream primer was substituted with a primer that was specific for other serogroups of D. nodosus, the fimA gene was successfully amplified. Cloning followed by DNA sequencing, revealed that M-SPAHL fimA was different to M-Nep fimA. The predicted amino acid sequence of M-SPAHL fimA did not show homology to any known serogroups or serotypes. The most similar sequence was from serotype F1, and not M-Nep. The sequence difference between M-SPAHL and M-Nep was larger than that expected within a serogroup. The consequences of serological relatedness and sequence dissimilarity are discussed. Only eight of the 15 New Zealand field strains had fimbriae identical to those of the vaccine strains, while the remaining seven strains possessed different fimbriae. In addition, the vaccine contained two more D. nodosus strains, representing two sera groups, that were not found on the New Zealand farms investigated in this study. This may, to some extent, explain why the current footrot vaccine is at times less efficient in New Zealand. Another 17 footrot samples were screened for new or additional D. nodosus strains. Two PCR amplimers (designated X and Y) derived from footrot samples generated SSCP patterns different to those of previously identified strains. DNA sequencing revealed that these two fragments possessed novel sequences. The upstream of X (nt 1-183) was identical to serotype M1 while its downstream (nt 223-414) was identical to serotype F1; the upstream of Y (nt 1-116) was identical to serotype E1 whereas its downstream (nt 148-423) was identical to serotype F1. A 14-mer sequence consisting of two partially overlapping Chi-like sequences, 5'-GCTGGTGCTGGTGA-3', was also found in these fragments. Two primer sets with the downstream primer specific for serotype Fl and the upstream primer specific for serotype M1 or E1, produced PCR products of the expected sizes from the footrot samples from which fragments X and Y were isolated, respectively. These primer sets did not appear to amplify artificially mixed genomic DNA from serotypes M1 and F1 or E1 and F1. However, when the reactions were re-amplified, PCR recombination artefacts were observed, suggesting that PCR recombination does occur, but at a low frequency. It therefore seems more likely that fragments X and Y reflect genuine fimA sequences of D. nodosus which have resulted from in vivo DNA recombination, than from a PCR recombination artifact. The genetic capability for recombination at the fimbrial subunit locus may therefore endow D. nodosus with the ability to alter its antigenic appearance. D. nodosus strains present in footrot lesions can be genotyped using a PCR-SSCP/sequencing technique. However, this typing technique requires cloning and screening of D. nodosus fimA sequences, which is both laborious and costly. A rapid molecular typing system for D. nodosus was therefore developed in this study. A close examination of available D. nodosus fimA sequences revealed regions that appear to be specific for serogroups and serotypes. These regions were used to design a panel of sequence-specific oligonucleotide probes (SSOPs), and a rapid and accurate D. nodosus typing system using PCR and reverse dot-blot hybridisation (PCR/oligotyping) was subsequently developed. The variable region of D. nodosus fimA, amplified and labelled with digoxigenin (DIG) in a single multiplex PCR amplification, was hybridised to a panel of group- and type-specific, poly-dT tailed oligonucleotides that were immobilised on a nylon membrane strip. A mixture of positive control poly-dT tailed oligonucleotides was also included on the membrane. After hybridisation the membrane was washed to a defined specificity, and DIG-labelled fragments that had hybridised were detected. The specificity of the oligonucleotides was verified by the lack of cross-reactivity with D. nodosus fimA sequences that had a single base difference. DNA from 14 footrot samples previously genotyped by PCR-SSCP/sequencing, was assayed using the PCR/oligotyping technique. All types of D. nodosus which had been detected previously with a PCR-SSCP/sequencing method were detected by this procedure. However, for three of the 14 footrot samples, PCR/oligotyping detected additional types of D. nodosus. Further PCR amplification using type-specific primers, confirmed that these types were present in the original footrot samples. These results indicate that PCR/oligotyping is a specific, accurate, and useful tool for typing footrot samples. In combination with a rapid DNA extraction protocol, D. nodosus present in a footrot sample can be accurately genotyped in less than two days. Individual animals from the same farm, or the same paddock, were often infected by different strains of D. nodosus. This suggests a host role in mediating footrot infection, or that the interaction between the pathogen and the host is important. In order to better understand the interaction between the bacterium and the host, two polymorphic ovine class II MHC genes DQA1 and DQA2, which have been previously shown to be important in footrot infection, were also investigated in this study. PCR-SSCP/sequencing analysis of the DQA1 locus revealed ten unique ovine DQA1 sequences, with five of them being newly identified. This increases the number of known ovine DQA1 alleles from 8 to 13 (including a null allele), implying a high level of polymorphism at the ovine DQA1 locus. D. nodosus present on 20 footrot infected sheep from the same flock were genotyped, together with the ovine DQA1 and DQA2 genotypes of their hosts. Preliminary results showed that sheep with the same DQA1 and DQA2 genotypes tended to be infected by similar types of D. nodosus. Different types of D. nodosus were generally found on sheep with different genotypes at either the DQA1 or the DQA2 locus. This suggests the diversity in D. nodosus infection may be associated with the heterogeneity in the host MHC. However, as only a small number of animals from the same sire were analysed, further investigation is needed to gain a better understanding of the interaction between D. nodosus and the host MHC.
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Gannett, Lisa Anne. "Genetic variation, difference, deviation, or deviance?" Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape15/PQDD_0023/NQ31121.pdf.
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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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Oballa, Phanuel O. "Genetic variation within Acacia karroo Hayne." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334928.
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Martinson, Jeremy James. "Genetic variation in South Pacific Islanders." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.293422.
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Thakur, Ajay. "Genetic variation of Juglans regia L." Thesis, Bangor University, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.431492.
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Buck, Emily Jane. "Genetic variation of Castanea sativa Mill." Thesis, Bangor University, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428823.
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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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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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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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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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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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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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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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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 (NE).
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 NE. However it was not feasible to separate the impact of these two factors.
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Davies, Robert William. "Factors influencing genetic variation in wild mice." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:ced6a42f-66f5-4001-aaf8-8059d5fcfe27.
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The mouse is a premier model organism for mammalian biological research. They have been instrumental in studies illuminating processes of fundemental importance to genetics including the control of recombination and the process of speciation. However, most of these studies are based on laboratory mice, which are an artificial population with a complex relationship to wild mice. Studies of mammalian biology would benefit from understanding how history has shaped the genome of the present day mouse. In this thesis, I explore factors that contribute to patterns of genetic variation in wild mice, paying particular attention to the process of recombination. I use whole genome sequencing data from three wild populations: 20 French M. m. domesticus; 20 Taiwanese M. m. castaneus; and 10 Indian M. m. castaneus. In addition, I use 13 classical laboratory strains and 6 wild derived inbred strains. These data show that the French and Taiwanese populations have been through recent, severe population bottlenecks, are recipients of considerable migration, and are partially inbred, with about 15-20% of the genome recently homozygous. All of these features are absent from the Indian mice. Signatures of selection reveal that the Prl gene in Indian mice was the result of a full sweep originating from a highly diverged species of mouse. In terms of recombination, the linkage-disequilibrium based rate map of the French and Taiwanese mice is shown to be highly punctuate, while the Indian rate map is comparatively flat, and devoid of population level hotspots. The recombination landscape is shown to dominate nucleotide substitution, notably in the Indian mice, where it reverses a 2:1 strong (C/G) to weak (A/T) mutation bias in favour of a 2:1 weak to strong fixation rate. Dozens of long-extinct, and active, PRDM9 motifs are identified through a comparative genomic approach, which also reveals a highly localized picture of the distribution of GC-biased gene conversion. Separately, a low-coverage reference-panel free read-aware genotype imputation method named STITCH is presented, and shown to accurately impute genotypes in outbred laboratory mice and humans.
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Mizzen, Craig A. "Genetic and epigenetic variation in histone H1." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ58638.pdf.
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Bancroft, David. "Genetic variation and fitness in Soay sheep." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338112.
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Shihab, Hashem Ali. "Predicting the functional effects of genetic variation." Thesis, University of Bristol, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.633144.
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Elucidation of the functional effects of genetic variation within the human genome has the potential to improve our understanding of the molecular mechanisms underlying a plethora of human diseases, as well as leading onto novel diagnostic and therapeutic markers. Technological advances in next-generation sequencing technologies, coupled with the falling costs in whole-genome/ whole-exome sequencing technologies, have led to an explosion of variants being identified for which the functional consequence is unknown. However, characterizing functional variants through lab-based validation has now become time consuming and expensive. Therefore, computational prediction algorithms capable of predicting and/ or prioritizing putative functional variants for further experimentation are assuming ever increasing importance.
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Li, Yinglei. "Genetic Association Testing of Copy Number Variation." UKnowledge, 2014. http://uknowledge.uky.edu/statistics_etds/8.
Full textAbstract:
Copy-number variation (CNV) has been implicated in many complex diseases. It is of great interest to detect and locate such regions through genetic association testings. However, the association testings are complicated by the fact that CNVs usually span multiple markers and thus such markers are correlated to each other. To overcome the difficulty, it is desirable to pool information across the markers. In this thesis, we propose a kernel-based method for aggregation of marker-level tests, in which first we obtain a bunch of p-values through association tests for every marker and then the association test involving CNV is based on the statistic of p-values combinations. In addition, we explore several aspects of its implementation.
Since p-values among markers are correlated, it is complicated to obtain the null distribution of test statistics for kernel-base aggregation of marker-level tests. To solve the problem, we develop two proper methods that are both demonstrated to preserve the family-wise error rate of the test procedure. They are permutation based and correlation base approaches. Many implementation aspects of kernel-based method are compared through the empirical power studies in a number of simulations constructed from real data involving a pharmacogenomic study of gemcitabine. In addition, more performance comparisons are shown between permutation-based and correlation-based approach. We also apply those two approaches to the real data.
The main contribution of the dissertation is the development of marker-level association testing, a comparable and powerful approach to detect phenotype-associated CNVs. Furthermore, the approach is extended to high dimension setting with high efficiency.
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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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Detsika, Maria G. "Genetic variation amongst isolates of Burkholderia cepacia." Thesis, University of Liverpool, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269724.
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Neilson, Tracey C. S. "Genetic characterisation and variation in Gyrodactylus species." Thesis, University of Aberdeen, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421353.
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The main focus of this investigation here involved three of the four most common salmonid Gyrodactylus species (G. salarism G. thymalli, G. derjavini and G. truttae), with particular attention to discriminating between G. salaris and G. thymalli. This was accomplished by characterising uncharacterised areas of the genome, i.e. the intergenic spacer region and 28S subunit of the ribosomal array, and CO1 and ND1 gene regions of the mitochondrial genome. Once characterisation was completed for these species, the more variable regions that would potentially be used for as a more comprehensive molecular diagnostic test, would, only then, be characterised for further chosen Gyrodactylus spp. The result of this investigation has now successfully documented the degree of both intra- and inter-specific variation within the IGS, 28S, ITS, 18S, CO1 and ND1 genomic regions. As a direct result of this study’s information and techniques, the diagnostic facility at the FRS Marine Laboratory is now able to identify each strain and species of all Gyrodactylus species investigated to date. In addition, the two cryptic species of G. salaris and G. thymalli can now be differentiated using three distinct ribosomal regions, namely the IGS, 5’ 28S and 3’ 28S. This project also displays the ability to perform such characterisation on older Gyrodactylus species specimens, specifically those which have been preserved in ethanol for greater than 3 years, which had not been able to be utilised in the past due to the problems of DNA extraction. The strategy of progressive and strategic characterisation (targeting smaller specific areas of the array and progressing in a certain order of profitability variation) of these specimens, sufficiently enabled the poorer quality of the DNA to be productive, and therefore beneficial in this investigation.
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Cesarini, David Alexander. "Essays on genetic variation and economic behavior." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/57897.
Full textAbstract:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Economics, 2010.Cataloged from PDF version of thesis.
Includes bibliographical references.
This thesis is a collection of papers in which behavior genetic methods are used to shed light on individual differences in economic preferences, behaviors and outcomes. Chapter one uses the classical twin design to provide estimates of genetic and environmental influences on experimentally elicited preferences for risk and giving. The paper reports evidence that these preferences are broadly heritable, with estimates suggesting that genetic differences explain approximately twenty percent of individual variation. The results thus point to genes as an important source of individual variation in preferences, a source which has hitherto been largely neglected in the economics literature. The chapter is written with Christopher T. Dawes, Magnus Johannesson, Paul Lichtenstein and Bjorn Wallace. Chapter two shows that these findings also extend to the field. Following a major pension reform in the late 1990s, all Swedish adults had to form a portfolio from a large menu of funds. Matching individual investment decisions to the Swedish Twin Registry, the paper finds that approximately 25% of individual variation in portfolio risk is due to genetic variation. The results, which are complementary to those reported in chapter one, also hold for several other aspects of financial decision-making. The chapter is written with Magnus Johannesson, Paul Lichtenstein, Orjan Sandewall and Bjorn Wallace. Chapter three uses two complementary Swedish datasets to examine the importance of family environment in explaining variation in income, educational attainment, and measures of cognitive and non-cognitive skills. Using seven different sibling types who differ in their degree of genetic relatedness and rearing status, I find moderate family effects on educational attainment, cognitive skills and non-cognitive skills. This contrasts with the effects of family on income, which are low. Additional analyses, based on a sample of identical (MZ) and fraternal (DZ) twins for which more comprehensive income data is available, reveal large and persistent separation of the MZ and DZ correlations over the entire lifecycle, except at very early ages. One interpretation of this finding is that there are strong family effects on the timing of labor market entry. I discuss the relevance of these results for efforts to understand the causes of income inequality.
by David Alexander Cesarini.
Ph.D.
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Noori, Muhammad Yahya. "Genetic variation and virulence of Streptococcus pneumoniae." Thesis, University of Glasgow, 2012. http://theses.gla.ac.uk/4440/.
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Streptococcus pneumoniae or pneumococcus is included among major human pathogens and is responsible for a number of diseases including life-threatening conditions such as pneumonia, meningitis and sepsis. Though pneumococcal vaccines are available, they provide limited coverage against infections as pneumococcus shows extensive variation, which also allows escape from vaccines and antibiotic resistance. It is armed with several virulence factors including capsule, surface proteins, enzymes and toxins, which are variably expressed and altogether determine pneumococcal virulence. The aim of this project was to study pneumococcal genetic variation and its effect on virulence, with a focus on pneumococcal capsule, which is considered the major determinant of virulence and is involved in interaction with host immune system. It is the target for current vaccines and at least 93 pneumococcal serotypes are known, which differ in pathogenicity. To study the effect of capsule on the pneumococcal virulence, capsule-switch mutants were constructed in three genetic backgrounds; TIGR4 (serotype 4, virulent), 403 (serotype 4, avirulent) and D39 (serotype 2, virulent) and were studied for variation in their in vivo and in vitro characteristics. These mutants were compared with their parent strains and other mutants for effects of capsule switching on their growth, formation of capsular polysaccharide, capsular thickness, chain formation and virulence in murine models of infection using MF1 mice. Significant differences were observed in behaviour of parent and mutant strains. To develop a broader insight into pneumococcal virulence, avirulent derivative of strain TIGR4, 403 was genome sequenced and compared with TIGR4 for genetic mutations. To study differences in gene expression both the strains were also compared using microarrays. Genome analysis revealed only few mutations in strain 403 but microarray experiments showed 288 genes to be expressed differently in strain 403. Strain 403 was also tested as live attenuated vaccine to see if it could provide protection against the same and different serotypes, as it can be used as a vehicle for delivery of different polysaccharides to the host body along with the whole set of pneumococcal antigenome. Vaccine trials of 403 were not very fruitful as it failed to provide any protection through intranasal route though partial protection was observed in mice vaccinated intraperitoneally with significant differences in levels of bacteraemia, survival, weight and temperature losses on challenging with homologous strain.
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Groves-Kirkby, Nick. "Genetic analysis of variation in complex traits." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:4541c4e4-4538-4348-bb4b-0df6673344d2.
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Variation is a universal property of life, and much of contemporary genetics research is directed towards understanding the causes of variation in traits. Here I present the results of my investigations into the genetic and other causes of trait variation in humans and mice. I address these questions in the context of two distinct research projects, which use pre-existing data to investigate the causes of trait variation, through a range of analytic techniques. I first extract trait data from historic breeding records from the incipient Collaborative Cross (a genetic reference population of recombinant inbred mice) and use them to map genetic factors affecting litter size and other reproductive traits. Mapping reveals significant quantitative trait loci associated with litter size and time between litters, as well as a number of suggestive loci. I characterise the genetic effects at these loci and investigate candidate genes. The most robust finding, a litter size locus on chromosome 5, explains around 3% of observed variation and 24% of the variation attributable to genetics. Using data obtained from the Netherlands Twin Registry - a longitudinal database of Dutch twins - I investigate the prevalence of parent of origin effects on gene expression traits in peripheral blood in humans. I first phase individuals' genotypes by parental origin and use these genotypes to calculate the heritability of over 44,000 gene expression traits partitioned into that attributable to matching and nonmatching parent of origin. I replicate prior genomewide heritability estimates for many traits, but I find little evidence of widespread parent-of-origin effects on human gene expression in blood. On further examination, the small sample size severely limits the power to detect such effects. Nonetheless, I identify approximately 200 genes enriched for immune system processes that show evidence of parent-of-origin-specific effects on heritability.
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Johnson, Paul Christopher Duncan. "Genetic variation in the aphid Pemphigus spyrothecae." Thesis, University of Cambridge, 2000. https://www.repository.cam.ac.uk/handle/1810/269526.
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This project used genetic variation to investigate dispersal, inbreeding and social behaviour in the aphid Pemphigus spyrothecac. P. spyrothecae is cyclically parthenogenetic, reproducing sexually on the bark of its primary host, Populus nigra, and asexually within galls on the leaf petioles. Within the gall, a soldier caste defends and cleans the gall, potentially reducing its own fitness. P. spyrothecae collected across the UK from 1997 to 1999 and from mainland Europe and America in 1999 were genotyped using seven variable microsatellite markers that I developed in collaboration with William Amos and Kate Llewellyn. Using population genetic analysis, I showed that P. spyrothecae populations were temporally stable over three years, and spatially structured. Populations from trees 5 to 1700 km apart were significantly differentiated, and loosely followed an isolation-by-distance model. There was slight evidence of differentiation between neighbouring trees (5 to 500 m apart), but not between samples taken from within trees (less than 5 m apart). By contrast, P. bursarius, a closely related species that, unlike P. spyrothecae, has a secondary host, showed no differentiation between populations 150 km apart, suggesting that population isolation in P. spyrothecae may be a consequence of losing its secondary host. Populations within trees were highly inbred, probably due to selfing between sexuales from the same clone. This finding corresponds with the theory that female-biased sex ratios in P. spyrothecae evolved through local mate competition. There was no evidence for a correlation between inbreeding and population density. Genetic variation was also found within galls. Of 633 aphids in one gall, 619 shared one genotype, while the remaining 14 were immigrants from at least nine other clones. One immigrant was found among 49 aphids from four other galls. Such a low level of clonal mixing probably favoured the evolution of soldiers, and may represent an investment in dispersal by the clone as an insurance against its death.
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Tavera, Gloria. "Helicobacter pylori Genetic Variation and Gastric Disease." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1565176211647636.
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Donahoo, Ryan Scott. "Genetic variation in Xanthomonas axonopodis pv. dieffenbachiae." [Gainesville, Fla.] : University of Florida, 2003. http://purl.fcla.edu/fcla/etd/UFE0000676.
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Dastgheib, Alireza. "The role of genetic variation in osteoporosis." Thesis, University of Sheffield, 2015. http://etheses.whiterose.ac.uk/9972/.
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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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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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Olsson, Jenny. "Genetic diversity and hardiness in Scots pine from Scandinavia to Russia." Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-160222.
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The postglacial recolonization of northern Europe supposedly originated from Western Europe and the Russian Plain, however, recent molecular and macrofossil-based investigations suggest that the history may be more complex than previously thought. This study aims to investigate the genetic diversity and population structure of Scots pine from Scandinavia to Russia to re-evaluate its recolonization history, and to examine whether the pattern of spatial genetic diversity has any adaptive significance. Populations ranging from Norway to Russia were sampled and genotyped using genotyping-by-sequencing. The seedlings were freeze tested to provide an average degree of hardiness for every population. Eight hundred and thirty-two seedlings were analyzed, and 6,034 SNPs were recovered in these individuals after stringent filtering. Population structure was investigated using fastStructure and differentiation between populations was estimated with pairwise FST and analysis of molecular variance (AMOVA) to assess the genetic variability. Genetic diversity was measured as observed heterozygosity, H0, in populations, clusters and overall. Two genetic clusters were detected in the samples, one in Norway and Sweden and one in Russia. These clusters are weakly differentiated (FST = 0.01202) with only 0.66 % variation between them. Highest variation was found within populations (98.8 %) and the overall genetic diversity for all populations was high (Ho = 0.2573). The weak differentiation and high diversity are indicative of extensive gene flow between populations in this species. The composition of the clusters across the sampled area suggests a westward recolonization from the Russian Plain into Scandinavia, and a possible local origin of another polymorphism in Norway and Sweden. No clear relationship between cold hardiness and genetic variation was detected. The clinal variation in cold hardiness reflects local adaptation, and the difference between genetic and phenotypic variation is likely due to epigenetic regulation or polygenic inheritance. More extensive genome scan is needed to understand the genetic basis of local adaptation.
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Benavides, Lucille H. "Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae)." Texas A&M University, 2004. http://hdl.handle.net/1969.1/3319.
Full textAbstract:
The eastern subterranean termite, Reticulitermes flavipes, is the most widely dispersed termite in North America. The genus Reticulitermes spp. is responsible for 80% of total termite damage caused to urban structures each year. Little is known about the genetic structure of termites, particularly at the colony level. Evidence for what genetically defines a termite colony is a hotly debated topic in current literature due to the implications such findings would have regarding current lawsuits against pest control operations. Information on termite genetic structure is sparse.
In this study, the genetic variation and gene flow among Texas populations of R. flavipes at the statewide level and city level was examined. A 324-337 base pairs segment of the mtDNA, AT-rich region was a polymerase chain reaction amplified from 104 different termite specimens from 12 Texas cities. The DNA extracts were then subjected to PCR amplification using specific primers and it was then sequenced. Using the sequence data and appropriate statistical measures it was found that, at the statewide level, nucleotide and haplotypic diversity is low. Gene flow was found to be low on a statewide basis. At the city level nucleotide and haplotypic diversity was high. The findings of this study provide insights into termite genetic structure.
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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.
Full textAbstract:
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.
Full textAbstract:
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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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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Lundmark, Per Erik. "Genetic and Genomic Analysis of DNA Sequence Variation." Doctoral thesis, Uppsala universitet, Molekylär medicin, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-158486.
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The studies in this thesis describe the application of genotyping and allele specific expression analysis to genetic studies. The role of the gene NPC1 in Triglyceride metabolism was explored in mouse models and in humans on the population level in study I. NPC1 was found to affect hepatic triglyceride metabolism, and to be relevant for controlling serum triglyceride levels in mice and potentially in humans. In study II the utility of the HapMap CEU samples was investigated for tagSNP selection in six European populations. The HapMap CEU was found to be representative for tagSNP selection in all populations while allele frequencies differed significantly in the sample from Kuusamo, Finland. In study III the power of Allele specific expression as a tool for the mapping of cis-regulatory variation was compared to standard eQTL analysis, ASE was found to be the more powerful type of analysis for a similar sample size. Finally ASE mapping was applied to regions reported to harbour long non-coding RNAs and associated SNPs were compared to published trait-associations. This revealed strong cis-regulatory SNPs of long non-coding RNAs with reported trait or disease associations.
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Miller, S. Shea. "Oat beta-glucan: Biochemistry, structure and genetic variation." Thesis, University of Ottawa (Canada), 1992. http://hdl.handle.net/10393/7507.
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An enzymatic assay designed for measurement of $\beta$-glucan in barley was modified to allow measurement of total $\beta$-glucan content in oats by manipulating the grinding and incubation protocol. Using the modified enzymatic assay, the range of genetic and environmental variation of $\beta$-glucan content in Canadian domestic and breeder's lines of oats was assessed using several cultivars grown in 5 locations in eastern Canada in 3 growing seasons. Analysis of variance indicated that the predominant source of variation was genetic. A second assay using Flow Injection Analysis (FIA) to measure $\beta$-glucan was also evaluated. Although a high correlation was observed for the results of the two methods (r = 0.90), the results obtained using FIA tended to be somewhat lower than those obtained using the modified enzymatic assay: the enzymatic assay was judged to be more accurate for estimation of total $\beta$-glucan in oats. Nevertheless, because of its greater speed and simplicity, FIA would be a valuable screening tool for routine-applications. Using the enzymatic assay, $\beta$-glucan content was also measured in 18 primitive species of Avena to evaluate possible sources of germplasm for expanding the range of $\beta$-glucan content currently available in domestic cultivars. A comparison of $\beta$-glucan content with protein content, oil content and thousand kernel weight in domestic oats showed that these quality parameters are independent of $\beta$-glucan concentration in oats. Scanning microspectrofluorometry was used to map $\beta$-glucan distribution in single kernels of oats: differences were observed within single kernels, and also among kernels from different cultivars of oats. Microscopic examination suggests that the different distribution patterns are due to differences in cell wall thickness adjacent to the germ and around the periphery of the kernel, and also to differences in cell size and shape in the central endosperm. A high $\beta$-glucan (Marion) and a low $\beta$-glucan oat cultivar (OA516-2) were selected for isolation and preliminary characterization of the endosperm cell walls, which are the major source of $\beta$-glucan in the oat kernel. It was concluded that the differences in $\beta$-glucan content that were observed in whole groats were not due to differences in the composition of isolated endosperm cell walls, but to variation in cell size and cell wall thickness in different areas of the groats. (Abstract shortened by UMI.)
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Crompton, Tom. "Mobile DNA and genetic variation in Drosophila melanogaster." Thesis, University of Leicester, 1997. http://hdl.handle.net/2381/30330.
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Whilst it is commonly accepted that transposable elements can generate genetic variation, the significance of this for the maintenance and dissemination of such elements is controversial. Here long-term laboratory populations of Drosophila melanogaster, maintained at two discrete temperatures, are screened by Southern blotting for the patterns of insertion of several transposable elements (copia, mdg-2, mdg-4 and P). Consistent with a temperature-specific adaptive role for some insertions, several are apparently found at higher frequency in lines at one temperature. Further characterisation of these putatively temperature-selected insertions was attempted. Of three distinct approaches taken towards cloning these insertions, a single-stranded DNA-ligation for PCR-amplification technique, not thought to have been previously exploited for isolating transposable element insertion sites, generated the best results. One copia insertion was successfully sequenced, although single fly PCR experiments suggested that the frequency of this in caged populations was not related to temperature. A major collection of D. melanogaster from the French and Spanish Pyrenees was undertaken along four discrete altitudinal clines, with a view to screening for specific transposable element insertions. A novel strategy was developed for correlation of altitude with mean seasonal temperature of each collection site. Altitudinal variation in the frequency of Thr-Gly length polymorphism at the period locus was found to be consistent with predictions based on known latitudinal clines. This is the first known example of putatively adaptive clinal genetic variation in European populations of Drosophila collected along altitudinal transects. Finally, a fundamental re-examination of the theoretical issues surrounding the possible adaptive significance of transposable elements is developed. It is demonstrated that he extension of ideas on the 'units of selection' to transposable elements has led to confusion. A model of transposable element evolution which presents a coherent alternative to the selfish DNA approach is presented.
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Derero, Abayneh. "Genetic variation in Cordia africana Lam. in Ethiopia." Göttingen Cuvillier, 2007. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=016247698&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
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