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Lundy, Ian J. "Theoretical population genetics of spatially structured populations /." Title page, contents and summary only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09phl962.pdf.
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Herbots, Hilde Maria Jozefa Dominiek. "Stochastic models in population genetics : genealogy and genetic differentiation in structured populations." Thesis, Queen Mary, University of London, 1994. http://qmro.qmul.ac.uk/xmlui/handle/123456789/1482.
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The theory of probability and stochastic processes is applied to a current issue in population genetics, namely that of genealogy and genetic differentiation in subdivided populations. It is proved that under a reasonable model for reproduction and migration, the ancestral process of a sample from a subdivided population converges weakly, as the subpopulation sizes tend to infinity, to a continuous-time Markov chain called the "structured coalescent". The moment-generating function, the mean and the cond moment of the time since the most recent common ancestor (called the "coalescence time") of a pair of genes are calculated explicitly for a range of models of population structure. The value of Wright's coefficient FST, which serves as a measure of the subpopulation differentiation and which can be related to the coalescence times of pairs of genes sampled within or among subpopulations, is calculated explicitly for various models of population structure. It is shown that the dependence of FST on the mutation rate may be more marked than is generally believed, particularly when gene flow is restricted to an essentially one-dimensional habitat with a large number of subpopulations. Several more general results about genealogy and subpopulation differentiation are proved. Simple relationships are found between moments of within and between population coalescence times. Weighting each subpopulation by its relative size, the asymptotic behaviour of FST at large mutation rates is independent of the details of population structure. Two sets of symmetry conditions on the population structure are found for which the mean coalescence time of a pair of genes from a single subpopulation is independent of the migration rate and equal to that of two individuals from a panmictic population of the same total size. Under graph-theoretic conditions on the population structure, there is a uniform relationship between the FST value of a pair of neighbouring subpopulations, in the limit of zero mutation rate, and the migration rate
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Zenger, Kyall Richard. "Genetic linkage maps and population genetics of macropods." Phd thesis, Australia : Macquarie University, 2002. http://hdl.handle.net/1959.14/47604.
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"November 2001".Thesis (PhD)--Macquarie University, Division of Environmental and Life Sciences, Department of Biological Sciences, 2002.
Bibliography: leaves 136-157.
General introduction -- Molecular markers for comparative and quantitative studies in macropods -- Genetic linkage map construction in the tammar wallaby (M. eugenii) -- Intraspecific variation, sex-biased dispersal and phylogeography of the eastern grey kangaroo (M. giganteus) -- General discussion.
The analysis of DNA using molecular techniques is an important tool for studies of evolutionary relationships, population genetics and genome organisation. The use of molecular markers within marsupials is primarily limited by their availability and success of amplification. Within this study, 77 macropodid type II microsatellite loci and two type I genetic markers were characterised within M. eugenii to evaluate polymorphic levels and cross-species amplification artifacts. Results indicated that 65 microsatellite loci amplified a single locus in M. eugenii with 44 exhibiting high levels of variability. The success of crossspecies amplification of microsatellite loci was inversely proportional to the evolutionary distance between the macropod species. It is revealed that the majority of species within the Macropodidae are capable of using many of the available heterologous microsatellites. When comparing the degree of variability between source-species and M. eugenii, most were significantly higher within source species (P < 0.05). These differences were most likely caused by ascertainment bias in microsatellite selection for both length and purity. -- The production of a marsupial genetic linkage map is perhaps one of the most important objectives in marsupial research. This study used a total of 353 informative meioses and 64 genetic markers to construct a framework genetic linkage map for M. eugenii. Nearly all markers (93.7%) formed a significant linkage (LOD > 3.0) with at least one other marker. More than 70% (828 cM) of the genome had been mapped when compared with chiasmata data. Nine linkage groups were identified, with all but one (LG7; X-linked) allocated to the autosomes. Theses groups ranged in size from 15.7 cM to 176.5 cM, and have an average distance of 16.2 cM between adjacent markers. Of the autosomal linkage groups, LG2 and LG3 were assigned to chromosome 1 and LG4 localised to chromosome 3 based on physical localisation of genes. Significant sex-specific distortions towards reduced female recombination rates were revealed in 22% of comparisons. Positive interference was observed within all the linkage groups analysed. When comparing the X-chromosome data to closely related species it is apparent that it is conserved both in synteny and gene order. -- The investigation of population dynamics of eastern grey kangaroos has been limited to a few ecological studies. The present investigation provides analysis of mtDNA and microsatellite data to infer both historical and contemporary patterns of population structuring and dispersal. The average level of genetic variation across sample locations was exceedingly high (h = 0.95, HE = 0.82), and is one of the highest observed for marsupials. Contrary to ecological studies, both genic and genotypic analyses reveal weak genetic structure of populations where high levels of dispersal may be inferred up to 230 km. The movement of individuals was predominantly male-biased (average N,m = 22.61, average N p = 2.73). However, neither sex showed significant isolation by distance. On a continental scale, there was strong genetic differentiation and phylogeographic distinction between southern (TAS, VIC and NSW) and northern (QLD) Australian populations, indicating a current and / or historical restriction of geneflow. In addition, it is evident that northern populations are historically more recent, and were derived from a small number of southern eastern grey kangaroo founders. Phylogenetic comparisons between M. g. giganteus and M. g. tasmaniensis, indicated that the current taxonomic status of these subspecies should be revised as there was a lack of genetic differentiation between the populations sampled.
Mode of access: World Wide Web.
xv, 182 leaves ill
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Martien, Karen Kay Fear. "Conservation of spatially structured populations : lessons from population genetics /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9979969.
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Montemuiño, Sosa Carlos. "Parallelizing Population Genetics Applications." Doctoral thesis, Universitat Autònoma de Barcelona, 2021. http://hdl.handle.net/10803/673278.
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Amb la creixent disponibilitat de dades a escala de l'genoma per a la investigació genètica, els genetistes de poblacions moleculars han de treballar amb models més complexos, el que no pot fer-se en un temps determinat utilitzant el mètode coalescent estàndard. Aquest escenari va dur a el desenvolupament de diverses aplicacions alternatives de simulació numèrica. Tot i l'accés cada vegada més gran a les agrupacions de computació d'alt rendiment (HPC) a l'acadèmia, no s'està aprofitant en el camp de la genètica de poblacions. L'establiment de paral·lels entre les aplicacions existents és difícil d'aconseguir pels desenvolupadors sense una comprensió completa de la HPC, i les noves aplicacions només aprofiten les capacitats de multiprocessament d'una sola computadora.
En aquesta tesi es proposa una metodologia per establir un paral·lelisme entre les aplicacions coalescents i utilitzar eficaçment tota la potència de processament disponible d'un grup d'HPC. La metodologia introdueix una estratègia per reduir les comunicacions intra-node en el paradigma de pas de missatges. Aquesta solució permet obtenir una millor escalabilitat per a les aplicacions coalescents que requereixen la generació de milions de rèpliques. Com a resultat, els genetistes de poblacions poden utilitzar les eines coalescents estàndard per executar l'anàlisi de Computació Bayesiana Aproximada (ABC) sense dependre d'aplicacions menys precises.
Hem avaluat la nostra estratègia establint un paral·lelisme amb l'aplicació coalescent estàndard de facto i executant experiments a escala de l'genoma en un conglomerat HPC real. Afinant diferents aspectes de la nostra metodologia, hem obtingut importants guanys de rendiment, donant lloc a una velocitat de 4x per sobre de la nostra paral·lelització inicial, que representava una velocitat de 50x per sobre de l'aplicació coalescent de referència.Con la creciente disponibilidad de datos a escala del genoma para la investigación genética, los genetistas de poblaciones moleculares tienen que trabajar con modelos más complejos, lo que no puede hacerse en un tiempo determinado utilizando el método coalescente estándar. Este escenario llevó al desarrollo de varias aplicaciones alternativas de simulación numérica. A pesar del acceso cada vez mayor a las agrupaciones de computación de alto rendimiento (HPC) en la academia, no se está aprovechando en el campo de la genética de poblaciones. El establecimiento de paralelos entre las aplicaciones existentes es difícil de lograr por los desarrolladores sin una comprensión completa de la HPC, y las nuevas aplicaciones sólo aprovechan las capacidades de multiprocesamiento de una sola computadora. En esta tesis se propone una metodología para establecer un paralelismo entre las aplicaciones coalescentes y utilizar eficazmente toda la potencia de procesamiento disponible de un grupo de HPC. La metodología introduce una estrategia para reducir las comunicaciones intra-nodo en el paradigma de paso de mensajes. Esta solución permite obtener una mejor escalabilidad para las aplicaciones coalescentes que requieren la generación de millones de réplicas. Como resultado, los genetistas de poblaciones pueden utilizar las herramientas coalescentes estándar para ejecutar el análisis de Computación Bayesiana Aproximada (ABC) sin depender de aplicaciones menos precisas. Hemos evaluado nuestra estrategia estableciendo un paralelismo con la aplicación coalescente estándar de facto y ejecutando experimentos a escala del genoma en un conglomerado HPC real. Afinando diferentes aspectos de nuestra metodología, hemos obtenido importantes ganancias de rendimiento, cuadruplicando el speedup de nuestra paralelización inicial, la cual representaba una mejora de 50x sobre la aplicación coalescente de referencia.
With the increasing availability of genome-scale data for genetic research, molecular population geneticists need to work with more complex models, which cannot be done in a time-fashion using the standard coalescent methods. This scenario led to the development of several alternative numerical simulation applications. Despite the ever-increasing access to High Performance Computing (HPC) clusters in the academy, it is not being leveraged in the field of population genetics. Parallelizing existing applications is hard to achieve by developers without a comprehensive understanding of the HPC, and new applications only take advantage of multiprocessing capabilities from a single computer. This thesis proposes a technique to parallelize coalescent applications and effectively use all the available processing power from an HPC cluster. We use a strategy to reduce the intra- node communications in the message-passing paradigm. This solution allows for getting better scalability for coalescent applications that require generating millions of replicas. As a result, population geneticists can use the standard coalescent tools for running Approximate Bayesian Computation (ABC) analysis without relying on less accurate applications. We have evaluated our strategy parallelizing the de facto standard coalescent application and run experiments at genome-scale in a real HPC cluster. We have obtained significant performance gains in tuning different aspects of our approach, leading to a 4x speedup over our initial parallelization, which accounted for a 50x speedup over the reference coalescent application.
Universitat Autònoma de Barcelona. Programa de Doctorat en Informàtica
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Mäki-Petäys, H. (Hannaleena). "Conservation and management of populations in a fragmented forest landscape:behavioural ecology meets population genetics." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514283482.
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The effects of habitat loss and fragmentation on the genetic structure and vulnerability of populations strongly depend on the behaviour of a particular species. In this thesis, I examined the effects of forest fragmentation on genetic population structure with the aim of identifying and evaluating the different genetic and behavioural factors important for species conservation and management on different geographical scales. The species studied were the mound building red wood ants Formica lugubris and F. aquilonia, and a lekking bird, the capercaillie, Tetrao urogallus.
Habitat loss and fragmentation affected the genetic structure in both wood ants and capercaillie. In general, the effects were related to the time since fragmentation and to the level of habitat loss and isolation from the other existing populations. The loss of genetic diversity due to population fragmentation was less observable than the differences in population structure. The response to habitat fragmentation was further dependent on species characteristics such as dispersal and mating behaviour. Sociality affected the genetic vulnerability of wood ant populations by decreasing gene diversity, increasing inbreeding depression and restricting gene flow between subpopulations. The results on the capercaillie in turn suggested that lekking behaviour restricts dispersal of both sexes, thus elevating the occurrence of inbreeding between individuals.
The present study provided important information on species conservation and management in terms of better understanding species' biology and behaviour, as well as increased knowledge concerning the genetic issues that should be taken into account when planning conservation actions. By examining the genetic structure of the species it was possible to clarify the conservation status including the effective population size, the question of origin, and the genetic vulnerability (genetic diversity, inbreeding and inbreeding depression) of the populations and/or species. Overall, the results emphasised the importance of preserving the effective population size and the connectivity of habitat patches when planning species specific management strategies. There were great differences in conservation needs among the species, which should be taken into account especially in local management actions.
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Grillenberger, Bernd K. "Biogeography, population genetics and mating systems of natural Nasonia populations." [S.l. : Groningen : s.n. ; University Library Groningen] [Host], 2009. http://irs.ub.rug.nl/ppn/317.
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Sjödin, Per. "Effects of Selection and Demography on DNA Polymorphism in Black Mustard (Brassica nigra)." Doctoral thesis, Uppsala universitet, Evolutionär funktionsgenomik, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6633.
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The evolution of three genes from the CONSTANS-LIKE gene family is studied in Brassica nigra. We use a combination of population genetic and phylogenetic techniques in order to assess the relative importance of selection and demography on the pattern of DNA variation. The analysis is complicated by the fact that they are recent duplicates of each other and hence there is a potential redundancy factor that has to be considered. The relationship between two of the genes, COa and COb, is however much closer than between any relationship to the third gene, COL1. The three genes are all suspected to play a part in the natural variation of flowering time of B. nigra. The thesis consists of four papers. The first paper is a technical paper concerning when and if the existence of an effective population size can be assumed. More specifically, the impact of population structure and a fluctuating (census) population size on the standard coalescent is studied. The second paper is a population genetic study of B. nigra using micro-satellites and RFLP. The resulting population genetic structure is argued to reflect the early spread of agriculture in Europe. In the third paper the general evolution of the three genes is studied. We find that not all aspects of the data could be accounted for by demography or redundancy effects, but that selection most likely played a part in the evolution of these genes. The fourth paper concerns the functional status of COb, whether it is a pseudogene or not. The most likely scenario is that COb recently became non-functional due to the fixation of a deleterious mutation during a recent bottleneck.
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Gagnon, Nicolas. "Mesure et analyse de l'effet fondateur dans les populations de Charlevoix et du Bas-Saint-Laurent." Thèse, Chicoutimi : Université du Québec à Chicoutimi, 1998. http://theses.uqac.ca.
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Røyrvik, Ellen C. "The peoples of Britain: population genetics, archaeology and linguistics : population genetics, archaeology and linguistics." Thesis, University of Oxford, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.669909.
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The history of peoples has always evoked a great deal of both academic and popular interest, and the peoples of Britain, with its island position and semi-mythic serial invasions, have evoked as much as any. As most of the period during which Britain has been inhabited by modern humans lies in prehistory, archaeology has long been the best method for elucidating the past. In recent years, however, genetics has come to complement the reconstruction of peoples' pasts, with its ability to trace lineal human biology instead of transferable human culture. The purpose of this thesis is to assess population genetics systems of Britain against the backdrop of archaeologically determined history, informed for later periods by linguistics, and attempt to ascertain any marked congruities or incongruities between this history and modern genetic data. The genetic datasets included in this work are the People of the British Isles Project collection, and some ancillary cohorts from surrounding countries. The genetic systems assessed include mitochondrial DNA, classical marker genes, lactase, pigmentation genes and some phenotypes, and finally a suite of candidate genes for determining normal facial variation. In a self-contained section, the principle of relating population genetic data to population histories is illustrated by a study focusing on Central Asia (a larger area), but using fewer genetic markers. The chosen markers systems overall reveal modest amounts of genetic differentiation among different groups in Britain, but consistently highlight Wales and Orkney especially as relatively distanced from the rest of Britain. This is in keeping with the historically quite isolated state of the former, and the comparatively recent heavy influx of Norse Vikings in the latter. Further details are observable from subsets of this study: all are discussed in the context of archaeological and linguistic evidence. These findings provide support and foundation for a forthcoming study from the People of the British Isles Project, using a genome-wide SNP approach rather than selected markers, which will likely increase the nuance of this initial picture and contribute further to answering specific questions regarding Britain's past.
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Asher, Allison Marie. "CONSERVATION GENETICS OF PADDLEFISH: GENETIC EFFECTIVE POPULATION SIZE AND RANGEWIDE GENETIC STRUCTURE." OpenSIUC, 2019. https://opensiuc.lib.siu.edu/dissertations/1693.
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Paddlefish (Polyodon spathula) is a commercially and recreationally important species, with a native range that extends over 22 US states. This is a large, long-lived, highly mobile riverine species that has been negatively impacted by habitat fragmentation, historic overharvest, and hatchery supplementation. Dams are the primary cause of habitat fragmentation, blocking migration routes, flooding spawning grounds, and isolating populations. A common management action to mitigate the impacts of habitat fragmentation and maintain harvestable populations is hatchery propagation and stocking. Reduction in stock size, isolation of populations, and stocking can all negatively impact the genetic integrity of Paddlefish. I evaluated the impacts of isolation and hatchery supplementation on the effective population size (Ne) of Paddlefish as well as the range-wide genetic structure of Paddlefish.
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Holmquist, Isabel Rosa. "A population genetics study of transposable elements as genetic drivers." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.516357.
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Lopes, Joao Sollari. "Software development in population genetics." Thesis, University of Reading, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529977.
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Jiang, Hongyu. "Population genetics genealogies under selection." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:141f4e19-d13a-409e-a7c7-aeaabd6b9b88.
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In the presence of selection and mutation, the genealogy of a given sample configuration can be described by two classes of ancestral processes, namely the coalescent-in-a-random-background model of Kaplan et al. (1988) and the dual process with typed lines of Etheridge and Griffiths (2009). These two processes are based on the same forwards population genetics model. However, in the former model, selection is reflected in the ancestral frequencies in the population, while in the latter model, there are branching events that generate virtual ancestral lines. We simulate the dual processes with typed lines and derive the limits of the two ancestral processes under strong selection and under selection-mutation balance to address the question of to what extent the genealogy is distorted. The two ancestral processes generate the same limiting genealogy. In a two-allele population under strong selection, the disfavoured individuals in the sample are instantaneously converted to a random number of favoured individuals, and the limiting genealogy is governed by the usual Kingman’s coalescent. Under selection-mutation balance, all disfavoured individuals in the sample are instantaneously converted to the favoured type, and the limiting genealogy is determined by a time-changed Kingman’s coalescent. The proofs of these limiting processes are based on the convergence result of Mohle (1998, Lemma 1). The studies of selection-mutation balance are then extended to an additive selection model, where each individual is composed of L diallelic loci. In the corresponding dual process with typed lines, the evolution of the virtual lines on a faster timescale can be approximated by a deterministic process, while the evolution of the real lines is independent of the virtual lines. The structure in the limiting genealogy collapses to Kingman’s coalescent. We also let L tend to infinity, and obtain a full description of the limiting genealogy in the background selection model.
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Curtis, Caitlin. "Population Genetics of Antarctic Seals." Scholar Commons, 2009. https://scholarcommons.usf.edu/etd/1918.
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I developed and tested a protocol for determining the sex of individual pinnipeds using the sex-chromosome specific genes ZFX and ZFY. I screened a total of 368 seals (168 crabeater, Lobodon carcinophagus; 159 Weddell, Leptonychotes weddellii; and 41 Ross, Ommatophoca rossii) of known or unknown sex and compared the molecular sex to the sex assigned at the time of collection in the Ross and Amundsen seas, Antarctica. Discrepancies ranged from 0.0% - 6.7% among species. It is unclear, however, if mis-assignment of sex occurred in situ or in the laboratory. It also is possible, however, that the assigned morphological and molecular sex both are correct, owing perhaps to developmental effects of environmental pollution.
I sequenced a portion (ca 475 bp) of the mitochondrial control region of Weddell seals (N = 181); crabeater seals (N = 143); and Ross seals (N = 41). I resolved 251 haplotypes with a haplotype diversity of 0.98 to 0.99. Bayesian estimates of Θ from the program LAMARC ranged from 0.075 for Weddell seals to 0.576 for crabeater seals. I used the values of theta to estimate female effective population sizes (NEF), which were 40,700 to 63,000 for Weddell seals, 44,400 to 97,800 for Ross seals, and 358,500 to 531,900 for crabeater seals. Weddell seals and crabeater seals had significant, unimodal mean pairwise difference mismatch distributions (p = 0.56 and 0.36, respectively), suggesting that their populations expanded suddenly around 731,000 years ago (Weddell seals) and around 1.6 million years ago (crabeater seals). Both of these expansions occurred during times of intensified glaciations and may have been fostered by expanding pack ice habitat.
Autosomal microsatellite based NEs were 147,850 for L. Weddellii, 344,950 for O. rossii, and 939,600 for L. carcinophagus. I screened one X-linked microsatellite (Lw18), which yielded a larger NE estimate for O. rossii than the other two species. Microsatellite NE estimates are compared with previously published mitochondrial NE estimates and this comparison indicates that the Ross seal may have a serially monogamous system of mating. I find no sign of a recent, sustained genetic bottleneck in any of the three species.
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Souleman, Dima. "Genetic consequences of colonization of a metal-polluted environment, population genetics and quantitative genetics approaches." Thesis, Lille 1, 2017. http://www.theses.fr/2017LIL10006/document.
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Les habitats naturels sont de plus en plus détruits et fragmentés par l'expansion urbaine et les activités humaines. La fragmentation des espaces naturels et agricoles par les bâtiments et les nouvelles infrastructures affecte la taille, la connectivité et la qualité des habitats. Les populations d’organismes vivants sur ces territoires anthropisés sont alors plus isolées. Or, la différenciation entre populations d’un même organisme dépend de processus démographiques et génétiques tels que la dérive génétique, le flux génétique, la mutation et la sélection naturelle. La persistance et le développement des populations dans des conditions environnementales modifiées dépendent de mécanismes de tolérance. Dans ce contexte, l'introduction de contaminants tels que des métaux dans l'environnement peut influencer l'évolution des plantes et des animaux en modifiant les forces évolutives et en créant des différences entre populations. Dans ce travail, l’attention a été portée sur les conséquences génétiques de la pollution métallique sur deux espèces, le ver de terre Lumbricus terrestris et une plante modèle Arabidopsis halleri. Deux approches différentes ont été utilisées pour étudier la réponse génétique à la contamination métallique : une approche de génétique des populations chez L. terrestris et une approche de génétique quantitative chez A. halleri. Tout d’abord, il s’est agi d’identifier et de valider de nouveaux marqueurs microsatellites chez L. terrestris. Ensuite, ces marqueurs ont été utilisés afin de caractériser la diversité génétique neutre chez des vers collectés sur des sites agricoles et urbanisés. Parallèlement, l'architecture génétique de la tolérance et de l'hyperaccumulation de Zn chez A. halleri a été explorée à l’aide d’un croisement intraspécifique entre une population métallicole et une population non métallicole. Une densité élevée de marqueurs SNP a été utilisée pour procéder à l'étape de cartographie QTLNatural habitats are more and more destructed and fragmented by urban expansion and human activities. The fragmentation of natural and agricultural areas by buildings and new infrastructures affects the size, connectivity and the quality of habitats. The populations of organisms inhabiting these anthropized territories are then more isolated. However, differentiation between populations of the same organism depends on demographic and genetic processes such as genetic drift, gene flow, mutation and natural selection. Only species that have developed special tolerance mechanisms can persist under changed environmental conditions. The introduction of contaminants such as metals in the environment may influence plants and animals evolution by modifying the evolutionary forces and thus generating differences between populations. In this work, attention was focused on the genetic consequences of metallic pollution on two species, the earthworm Lumbricus terrestris and the plant model Arabidopsis halleri. Two different approaches have been used to study the genetic response to metallic contamination: a population genetic approach was performed in L. terrestris and a quantitative genetic approach was carried on in A. halleri. First, it was a question of identifying and validating new microsatellite markers in L. terrestris. These markers were then used to characterize the neutral genetic diversity in worms collected from agricultural and urban sites. Secondly, genetic architecture of Zn tolerance and Zn hyperaccumulation was conducted investigated for the first time using an intraspecific crossing between metallicolous and non-metallicolous individuals of A. halleri. High density of SNP markers was used to proceed to the QTL mapping step
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Csilléry, Katalin. "Statistical inference in population genetics using microsatellites." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3865.
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Statistical inference from molecular population genetic data is currently a very active area of research for two main reasons. First, in the past two decades an enormous amount of molecular genetic data have been produced and the amount of data is expected to grow even more in the future. Second, drawing inferences about complex population genetics problems, for example understanding the demographic and genetic factors that shaped modern populations, poses a serious statistical challenge. Amongst the many different kinds of genetic data that have appeared in the past two decades, the highly polymorphic microsatellites have played an important role. Microsatellites revolutionized the population genetics of natural populations, and were the initial tool for linkage mapping in humans and other model organisms. Despite their important role, and extensive use, the evolutionary dynamics of microsatellites are still not fully understood, and their statistical methods are often underdeveloped and do not adequately model microsatellite evolution. In this thesis, I address some aspects of this problem by assessing the performance of existing statistical tools, and developing some new ones. My work encompasses a range of statistical methods from simple hypothesis testing to more recent, complex computational statistical tools. This thesis consists of four main topics. First, I review the statistical methods that have been developed for microsatellites in population genetics applications. I review the different models of the microsatellite mutation process, and ask which models are the most supported by data, and how models were incorporated into statistical methods. I also present estimates of mutation parameters for several species based on published data. Second, I evaluate the performance of estimators of genetic relatedness using real data from five vertebrate populations. I demonstrate that the overall performance of marker-based pairwise relatedness estimators mainly depends on the population relatedness composition and may only be improved by the marker data quality within the limits of the population relatedness composition. Third, I investigate the different null hypotheses that may be used to test for independence between loci. Using simulations I show that testing for statistical independence (i.e. zero linkage disequilibrium, LD) is difficult to interpret in most cases, and instead a null hypothesis should be tested, which accounts for the “background LD” due to finite population size. I investigate the utility of a novel approximate testing procedure to circumvent this problem, and illustrate its use on a real data set from red deer. Fourth, I explore the utility of Approximate Bayesian Computation, inference based on summary statistics, to estimate demographic parameters from admixed populations. Assuming a simple demographic model, I show that the choice of summary statistics greatly influences the quality of the estimation, and that different parameters are better estimated with different summary statistics. Most importantly, I show how the estimation of most admixture parameters can be considerably improved via the use of linkage disequilibrium statistics from microsatellite data.
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Hens, H. (Hilde). "Population genetics and population ecology in management of endangered species." Doctoral thesis, Oulun yliopisto, 2017. http://urn.fi/urn:isbn:9789526215853.
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Abstract Knowledge of the determinants of the viability of populations is essential in order to undertake effective conservation and management of endangered species. In this study, long-term demographic data was combined with genetic data to study the viability of an endangered orchid species, Epipactis atrorubens. The genetic analyses revealed low levels of genetic variation and the presence of population genetic differentiation independent of the spatial scale. Low levels of seed-mediated gene flow, possibly linked to low seedling recruitment, is the likely cause of the low levels of gene flow. Indications of slow post-glacial colonisation rates were found, which together with the low gene flow predict a limited capacity of the species to shift its range to more suitable habitats after environmental change. Low genetic variation as a proxy for low evolutionary potential also suggests that the species has limited capacity to adapt to new environmental conditions. Furthermore, poor seedling recruitment lowers population viability in small populations, as highlighted by the low population growth rates. In addition, we found a strong effect of stochasticity that limits the viability of populations. Both the genetic and demographic analyses indicated low viability of the studied species and that seedling recruitment could be the main determinant for the viabilityTiivistelmä Luonnonsuojelun perusta on populaatioiden elinkykyyn vaikuttavien tekijöiden tuntemus. Tässä väitöskirjatyössä tutkittiin uhanalaisen orkidean, tummaneidonvaipan (Epipactis atrorubens), elinkykyyn vaikuttavia tekijöitä yhdistämällä pitkäaikaisseurannoilla kerätyt demografiset aineistot geneettisin menetelmin kerättyihin aineistoihin. Lajin populaatioiden geneettisen muuntelun määrän havaittiin olevan pieni ja populaatioiden todettiin olevan geneettisesti erilaistuneita maantieteellisestä skaalasta riippumatta. Geneettisen erilaistumisen syy voi olla alhainen geenivirta, joka on seurausta vähäisestä siemendispersaalista ja huonosta taimettumisesta. Populaatioiden evolutiivista historiaa tutkittaessa havaittiin merkkejä hitaasta jääkauden jälkeisestä kolonisaatiosta, mikä yhdessä alhaisen geenivirran kanssa ennustaa, että lajilla on huono kyky siirtyä sille sopivammille alueille, jos ympäristö muuttuu. Huonoa evolutiivista potentiaalia kuvastava vähäinen geneettinen muuntelu ennustaa, että lajilla on huono kyky sopeutua uusiin ympäristöoloihin. Tämän lisäksi huono taimettuminen laskee elinkykyä etenkin pienissä populaatioissa, mikä näkyy muun muassa pienten populaatioiden matalina kasvukertoimina. Stokastinen vaihtelu vaikutti elinkykyä alentavasti, mikä pitäisikin huomioida nykyistä paremmin elinkykyanalyyseissä. Sekä geneettiset että demografiset analyysit osoittivat taimettumisen mahdollisesti olevan määräävä tekijä tummaneidonvaipan populaatioiden elinkyvylle
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Bradshaw-Hajek, Bronwyn. "Reaction-diffusion equations for population genetics." Access electronically, 2004. http://www.library.uow.edu.au/adt-NWU/public/adt-NWU20041221.160902/index.html.
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Funda, Tomas. "Population genetics of conifer seed orchards." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/41805.
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Seed orchards represent the link between breeding and silvicultural activities. They were expected to act as closed, panmictic populations in Hardy-Weinberg equilibrium, meaning that desired genes drafted during previous selection stage would be effectively transmitted from parental to offspring populations; however, extensive research has indicated that this expectation is not met. Scrutinizing seed orchards’ efficiency is of vital importance as it determines the genetic quality of future forest stands.
Population genetics of four tree species’ seed orchards (western larch, Douglas-fir, lodgepole pine, and western redcedar) was studied using microsatellite DNA markers. Partial (family array) and full (bulk seed) pedigree reconstruction of offspring population (seed crops) were conducted using the likelihood-based parentage inference program CERVUS to estimate parental reproductive success, selfing rate, pollen contamination, effective number of parents (Ne), and seedlot genetic worth. Several simplified methods for predicting seed crops’ genetic quality and quantity were evaluated by comparing parental reproductive success with parental fecundities.
In all species, the top 20% of males contributed approximately one half of successful within-orchard pollen, substantially reducing male Ne (45 to 62% of the orchards’ census numbers). Even larger distortion was observed among females (the top 20% of females produced 77% of seed crop in Douglas-fir), reducing female Ne to as little as 13% of the census. Selfing and pollen contamination rates were in the range of previously reported studies, with the exception of high (15.2%) and low (7.3%) selfing rates in Douglas-fir and western redcedar, respectively. Pollen bud production and seed-cone volume were found to be the most reliable proxies to parental reproductive success, genetic worth, and Ne estimates.
An optimization protocol was developed for creating custom seedlots with maximized genetic gain at any Ne while collectively considering parental male and female fecundities, co-ancestry among parents, inbreeding, and variation in seed germination capacity. This protocol can be utilized in any generation’s seed orchard e.g. when seed supply exceeds demand, for mixing surpluses from multiple years, or if a given seed lot fails to meet minimum Ne requirements.
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O'Connell, M. D. "Population genetics of salmon in Wales." Thesis, Swansea University, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.638349.
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Atlantic salmon (Salmo salar L.) were examined using protein electrophoresis and mitochondrial DNA (mtDNA). A total of 614 individuals were examined using allozymes at 19-21 loci. The sites were distributed over five catchments throughout Wales. Significant differences in allele frequencies are observed both within and between rivers. The allele frequencies appear stable over the time period investigated. Multiple enzyme genotypes from 170 individuals were collected at 28 sites from six rivers in Wales. AvaII, DdeI, HaeIII, HinfI and MboI are variable, although DdeI was only assayed in a restricted number of individuals. Sequence divergence appears low in salmon mtDNA. However, small but significant differences are again observed between and within rivers. Preliminary results suggest that mtDNA genotype frequencies remain stable over time. When the data sets are compared, allozymes appear at least as useful as mtDNA in identifying significant differentiation between populations of Welsh salmon. The mtDNA results suggest that future surveys of Atlantic salmon need to sample at least 25 individuals per site, to identify all the genotypes present. Although hatchery samples do not show reduced levels of variability, when compared to natural populations, both data sets reveal the Dee to have the lowest level of within catchment differentiation. The low level of population structuring may be due to the intensive stocking carried out on the river over the last decade. The strict regulation of flow within the catchment may also be responsible for the low value. The monomorphic nature of MDH-3* in Welsh salmon means that variants introduced into the region could be identified. Another potential genetic tag is the MboI B genotype, which is restricted to salmon populations within South-west England and south Wales.
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Winney, Bruce Joseph. "Cormorant population genetics and Turaco phylogenetics." Thesis, University of Nottingham, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285767.
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Haubold, Bernhard. "The population genetics of fluorescent pseudomonas." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390493.
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Nicol, Elizabeth. "Long-term effects of oestrogenic effluent exposure on wild fish populations." Thesis, Brunel University, 2014. http://bura.brunel.ac.uk/handle/2438/10826.
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Freshwater streams in the developed world are becoming increasingly dominated by treated wastewater. Continually discharged into most surface waters, these effluents contain a suite of bioactive man-made chemicals, including steroid and non-steroid oestrogens, which have been found to feminise male fish, skew sex ratios, and cause reproductive failure. However, the consequences of reproductive disruption remain poorly explored at the population level. This thesis was initiated to evaluate how oestrogenic contaminants might influence the population ecology of a common cyprinid, the roach (Rutilus rutilus). An investigation encompassing population structure, multigenerational exposure and the role of additional drivers of fish population dynamics was undertaken to contextualise the effects of oestrogenic effluents on wild fish populations. Population genetic analysis of UK roach found they exhibit moderately high levels of genetic diversity and significant intra-river genetic structure. Genetically differentiated local subpopulations indicate little interbreeding and limited gene flow, consistent with a typical metapopulation that has not been homogenised by restocking. Similarly, my thesis demonstrates no significant relationship between effluent exposure and Ne (effective population size) or genetic diversity of roach populations, albeit a 65% reduction in Ne is possible at highly polluted sites. River stretches contaminated with high levels of effluent can support breeding populations, which recruit successfully with minimal immigration from less contaminated sites. Multigenerational effects of effluent exposure on roach were also evaluated experimentally using reproductive success from breeding adults over three generations. Lifelong exposure to 100% treated effluent resulted in feminised phenotypes (ovarian cavities and intersex condition) in males but no observable effect on females. Additionally, despite gonadal disruption in males and effluent exposure of their mothers, I found no detrimental effect on their ability to compete with control fish. Instead, reproductive success was primarily determined by body size. A novel approach considering additional fish population drivers suggests that genetic diversity and species diversity decline in parallel with an increasing presence of disturbed land, when combined with geographical isolation. In conclusion, group assemblage and genetic structure of fish populations appears multi-causal and cannot be disaggregated, such that a single environmental characteristic can be shown to drive patterns of population success.
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Howell, Bruce F. "The Use of Genetic Polymorphisms and Discriminant Analysis in Evaluating Genetic Polymorphisms as a Predictor of Population." Thesis, University of North Texas, 2002. https://digital.library.unt.edu/ark:/67531/metadc3138/.
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Discriminant analysis is a procedure for identifying the relationships between qualitative criterion variables and quantitative predictor variables. Data bases of genetic polymorphisms are currently available that group such polymorphisms by ethnic origin or nationality. Such information could be useful to entities that base financial determinations upon predictions of disease or to medical researchers who wish to target prevention and treatment to population groups. While the use of genetic information to make such determinations is unlawful in states and confidentiality and privacy concerns abound, methods for human “redlining” may occur. Thus, it is necessary to investigate the efficacy of the relationship of certain genetic information to ethnicity to determine if a statistical analysis can provide information concerning such relationship. The use of the statistical technique of discriminant analysis provides a tool for examining such relationship.
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Vemula, Satya Ravikanth. "Population genetics of Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) differentiation and quantification of overwintering and spring migratory populations in northern Mississippi /." Diss., Mississippi State : Mississippi State University, 2009. http://library.msstate.edu/etd/show.asp?etd=etd-03242009-153844.
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Klaoudatos, D. "Reproductive ecology, population genetics and population dynamics of selected Decapod crustaceans." Thesis, Swansea University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.637807.
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The reproductive ecology of three species of Decapod crabs, the shore crab (Carcinus maenas), the velvet crab (Necora puber) and the edible crab (Cancer pagurus), were studied in Swansea Bay and South Gower. Spawning occurs over winter and spring (shore crab), winter (edible crab), and summer (velvet crab). Berried females occur in spring and summer (shore crab), winter spring and summer (edible crab), summer and autumn (velvet crab). Eggs hatch in spring and summer (shore crab, edible crab), summer and winter (velvet crab). Copulation occurs in summer and autumn (shore crab), summer, autumn and winter (edible crab, velvet crab). Shore crabs from Swansea Queen’s Dock have a different reproductive cycle compared to the shore crabs from Tawe Barrage Impoundment and Mumbles Pier. More than one spawning periods or an extended spawning period was indicated for the shore crabs in the Docks. The genetic makeup of the shore crab populations present in Swansea Queen’s Dock and Mumbles Pier was compared using SSCP and cloning analysis of the 16S rRNA. Four different haplotypes were identified all of which were present in the Docks and one in the Pier, with low level of genetic divergence, and close relationship of the identified haplotypes with published shore crab haplotypes. AMOVA showed no significant difference between the study populations and published shore crab haplotypes. However, all identified haplotypes were different from published shore crab haplotypes, indicating a degree of reproductive isolation of the Swansea shore crab populations. Analysis of the permit return data for 1980-2002 of the edible and velvet crab fishery for the South Wales Sea Fisheries Committee District indicated that a combination of factors including overfishing, environmental conditions, and the “Sea Empress” oil spill in 1996 have contributed to a decline in landings that continues to date with limited signs of recovery.
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Bycroft, Clare. "Genomic data analyses for population history and population health." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:c8a76d94-ded6-4a16-b5af-09bbad6292a2.
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Many of the patterns of genetic variation we observe today have arisen via the complex dynamics of interactions and isolation of historic human populations. In this thesis, we focus on two important features of the genetics of populations that can be used to learn about human history: population structure and admixture. The Iberian peninsula has a complex demographic history, as well as rich linguistic and cultural diversity. However, previous studies using small genomic regions (such as Y-chromosome and mtDNA) as well as genome-wide data have so far detected limited genetic structure in Iberia. Larger datasets and powerful new statistical methods that exploit information in the correlation structure of nearby genetic markers have made it possible to detect and characterise genetic differentiation at fine geographic scales. We performed the largest and most comprehensive study of Spanish population structure to date by analysing genotyping array data for ~1,400 Spanish individuals genotyped at ~700,000 polymorphic loci. We show that at broad scales, the major axis of genetic differentiation in Spain runs from west to east, while there is remarkable genetic similarity in the north-south direction. Our analysis also reveals striking patterns of geographically-localised and subtle population structure within Spain at scales down to tens of kilometres. We developed and applied new approaches to show how this structure has arisen from a complex and regionally-varying mix of genetic isolation and recent gene-flow within and from outside of Iberia. To further explore the genetic impact of historical migrations and invasions of Iberia, we assembled a data set of 2,920 individuals (~300,000 markers) from Iberia and the surrounding regions of north Africa, Europe, and sub-Saharan Africa. Our admixture analysis implies that north African-like DNA in Iberia was mainly introduced in the earlier half (860 - 1120 CE) of the period of Muslim rule in Iberia, and we estimate that the closest modern-day equivalents to the initial migrants are located in Western Sahara. We also find that north African-like DNA in Iberia shows striking regional variation, with near-zero contributions in the Basque regions, low amounts (~3%) in the north east of Iberia, and as high as (~11%) in Galicia and Portugal. The UK Biobank project is a large prospective cohort study of ~500,000 individuals from across the United Kingdom, aged between 40-69 at recruitment. A rich variety of phenotypic and health-related information is available on each participant, making the resource unprecedented in its size and scope. Understanding the role that genetics plays in phenotypic variation, and its potential interactions with other factors, provides a critical route to a better understanding of human biology and population health. As such, a key component of the UK Biobank resource has been the collection of genome-wide genetic data (~805,000 markers) on every participant using purpose-designed genotyping arrays. These data are the focus of the second part of this thesis. In particular, we designed and implemented a quality control (QC) pipeline on behalf of the current and future use of this multi-purpose resource. Genotype data on this scale offers novel opportunities for assessing quality issues, although the wide range of ancestral backgrounds in the cohort also creates particular challenges. We also conducted a set of analyses that reveal properties of the genetic data, including population structure and familial relatedness, that can be important for downstream analyses. We find that cryptic relatedness is common among UK Biobank participants (~30% have at least one first cousin relative or closer), and a full range of human population structure is present in this cohort: from world-wide ancestral diversity to subtle population structure at sub-national geographic scales. Finally, we performed a genome-wide association scan on a well-studied and highly polygenic phenotype: standing height. This provided a further test of the effectiveness of our QC, as well as highlighting the potential of the resource to uncover novel regions of association.
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Dubé, Marie-Pierre. "New approaches in human genetic analysis." Thesis, McGill University, 1999. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=36581.
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The present thesis covers two aspects of statistical analysis applied to the genetics of human diseases. First, the significance of LOD-score results for the confirmation of linkage is addressed, with special emphasis on small pedigrees. A new analytical approach is presented for the linkage analysis of heterogenetic traits, using hereditary spastic paraplegia as a model, a disease well suited for the analyses. The critical significance values for confirmation of linkage are evaluated using Bayesian statistics, and empirical P-values for LOD score results are calculated using computer simulation methods. The presented analytical approach resulted in conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity.The second part addresses linkage-disequilibrium based fine mapping in the French Canadian population. The performance of five linkage-disequilibrium based fine-mapping methods is evaluated using French Canadian chromosomes with one of three diseases found in this population: oculopharyngeal muscular dystrophy (OPMD), hidrotic ectodermal dysplasia (HED), and sensorimotor polyneuropathy with or without agenesis of the corpus callosum (ACCPN). The gene for OPMD was recently mapped and cloned, allowing us to evaluate the performance of the methods with the OPMD results, and to make predictions about the ACCPN and HED putative gene positions. In addition, a new approach to linkage-disequilibrium based fine mapping is presented using FrenchCanadian ascending genealogies. The method involves two steps. First, the likely founding couple of a mutation-bearing chromosome is identified using a computerised randomisation statistic. Then, using a delete-d jackknife resampling scheme, the distribution of gene mapping estimates is calculated from the count of ancestral recombinants and ancestral meioses joining the identified founding couple to the disease gene carriers. Gene mapping estimates are calculated from each marker individually, and confidence intervals of the estimates are derived from the jackknife distributions. The method, when applied to French Canadian families with OPMD, successfully confirmed the localisation of PABP2 responsible for OPMD and performed better than other linkage disequilibrium-based mapping models.
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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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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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Sotheran, Wendy. "Genetic predisposition to breast cancer in selected individuals in Guernsey." Thesis, University of Southampton, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264721.
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Auton, Adam. "The estimation of recombination rates from population genetic data." Thesis, University of Oxford, 2007. http://ora.ox.ac.uk/objects/uuid:dc38045b-725d-4afc-8c76-94769db3534d.
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Genetic recombination is an important process that generates new combinations of genes on which natural selection can operate. As such, an understanding of recombination in the human genome will provide insight into the evolutionary processes that have shaped our genetic history. The aim of this thesis is to use samples of population genetic data to explore the patterns of variation in the rate of recombination in the human genome. To do this I introduce a novel means of estimating recombination rates from population genetic data. The new, computationally efficient method incorporates a model of recombination hotspots that was absent in existing methods. I use samples from the International HapMap Project to obtain recombination rate estimates for the autosomal portion of the genome. Using these estimates, I demonstrate that recombination has a number of interesting relationships with other genome features such as genes, DNA repeats, and sequence motifs. Furthermore, I show that genes of differing function have significantly different rates of recombination. I explore the relationship between recombination and specific sequence motifs and argue that while sequence motifs are an important factor in determining the location of recombination hotspots, the factor that controls motif activity is unknown. The observation of many relationships between recombination and other genome features motivates an attempt to quantify the contributions to the recombination rate from specific features. I employ a wavelet analysis to investigate scale-specific patterns of recombination. In doing so, I reveal a number of highly significant correlations between recombination and other features of the genome at both the fine and broad scales, but find that relatively little of the variation in recombination rates can be explained. I conclude with a discussion of the results contained in the body of the thesis, and suggest a number of areas for future research.
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Corcoran, Pádraic. "Neurospora tetrasperma from Natural Populations : Toward the Population Genomics of a Model Fungus." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-208791.
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The study of DNA sequence variation is a powerful approach to study genome evolution, and to reconstruct evolutionary histories of species. In this thesis, I have studied genetic variation in the fungus Neurospora tetrasperma and other closely related Neurospora species. I have focused on N. tetrasperma in my research because it has large regions of suppressed recombination on its mating-type chromosomes, had undergone a recent change in reproductive mode and is composed of multiple reproductively isolated lineages. Using DNA sequence data from a large sample set representing multiple species of Neurospora I estimated that N. tetrasperma evolved ~1 million years ago and that it is composed of at least 10 lineages. My analysis of the type of asexual spores produced using newly described N. tetrasperma populations in Britain revealed that lineages differ considerably in life history characteristics that may have consequences for their evolution. A comparative genomic analysis using three genomes of N. tetrasperma and the genome of N. crassa revealed that the mat a chromosomes in the lineages examine have been introgressed from other Neurospora species and that this introgression has reduced levels of molecular degeneration on the mating-type chromosomes. Finally, I generated a population genomic dataset composed of 92 N. tetrasperma genomes and two genomes of other Neurospora species. Analysis of these genomes revealed that all strains of N. tetrasperma have large regions of suppressed recombination on their mating-type chromosomes ranging from 69-84% of the chromosome and that the extent of divergence between mating-type chromosomes within lineages varies greatly (from 1.3 to 3.2%). I concluded that the source of this great divergence mating-type chromosome is large-scale introgression from other Neurospora species, and that these introgressed tracts have become fixed within N. tetrasperma lineages. I also discovered that genes within non-recombining introgressed regions of the mating-type chromosome have severely reduced levels of genetic variation as compared to the autosomes, and exhibit signatures of reduced molecular degeneration. My analysis of variation in coding regions revealed that positive selection on the introgressed regions has resulted in the removal of deleterious mutations and is responsible for the reductions in molecular degeneration observed.
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Hoitzing, Hanne. "Controlling mitochondrial dynamics : population genetics and networks." Thesis, Imperial College London, 2017. http://hdl.handle.net/10044/1/58020.
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Mitochondria form an essential component of nearly all eukaryotic cells, are implicated in numerous diseases and may play important roles in ageing. Mitochondrial populations are dynamic, controlled and heterogeneous, with different types -- both mutant and wildtype -- potentially coexisting in single cells. This thesis will study the dynamics of both mitochondria and their genetic material (mtDNA) to improve our understanding of the role of these dynamics in pathology and ageing. This study suggests, as well as critically evaluates, reasons for the existence of complex continuous mitochondrial networks using coarse-grained mathematical models, underlining a nonlinear relation between functionality and network structure. Understanding the link between morphology and function is important as disruption of the former is directly implicated in cellular dysfunction. We perform experiments in which we measure the influence of mitochondrial fusion and division events on integrated mitochondrial membrane potential, an indicator of functionality, and find evidence for its conservation. The cellular homeostatic control acting on a mitochondrial population is poorly understood; to address this, we study the influence of general feedback control strategies on mutant and wildtype mtDNA dynamics. We introduce a simple linear control mechanism that captures a wide variety of biologically observed dynamics, and study optimal parameterisations through the construction of an energy-based mitochondrial cost function. Not only cellular control, but also gene-therapeutic control of mtDNA is studied, allowing us to investigate optimal treatment strategies to reduce mutant loads. The cellular proportion of mutant mtDNA molecules, known as heteroplasmy, is crucial in mitochondrial disease and we study the influence of cellular mtDNA exchange on heteroplasmy dynamics and mutant expansion during ageing. We find that this exchange of genetic material can induce preferential mutant expansion during ageing (even in the face of selection against mutants) through a stochastically driven increase in cellular mean heteroplasmy levels.
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Urbach, Ena. "Evolution and population genetics of Prochlorococcus marinus." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/37755.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1995, and Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1995.Includes bibliographical references.
by Ena Urbach.
Ph.D.
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Hall, Emmi. "Population genetics and tolerance in Nereis diversicolor." Thesis, University of East Anglia, 2010. https://ueaeprints.uea.ac.uk/39131/.
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Wedgwood-Oppenheim, Bruce Andrew. "Immunity and the population genetics of malaria." Thesis, University of Edinburgh, 1997. http://hdl.handle.net/1842/13219.
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A theoretical model of malaria populations is constructed in an attempt to reflect the important features of the human-mosquito-malaria system under the key assumption that strain-specific immunity occurs, and is controlled by alleles at a single locus (to be referred to as the immuno-allelic locus) in the parasite genome. The model is more realistic with regard to the nature of malaria than previous models of strain-structured malaria populations, and includes such features as a short period of immune memory and competition between parasites growing in hosts. The model is complex, and is thus designed to be examined through computer simulation. Both the epidemiological and genetic effects of strain structure on malaria populations are studied. For example, the effects of the number alleles at the immuno-allelic locus on the proportion of hosts infected are examined. Also, the degree of genetic heterogeneity of malaria parasites inside hosts compared to the total level of genetic heterogeneity of the parasite population is examined. This is done by calculating the value of the statistic GST for a neutral locus in the parasite genome (referred to as GST(n)). The degree of genetic heterogeneity in a parasite population is of interest as it determines the degree to which sexual recombination will lead to the generation of novel genotypes. The generation of such novel genotypes is important as it may allow evasion of a new vaccine, or the development of resistance to anti-malarial drug. In the simulations examined, GST(n) is found to decrease (the degree of genetic heterogeneity increases) with increasing numbers of alleles at the immuno-allelic locus. It also decreases with increasing levels of transmission in the population. This latter result appears to agree qualitatively with the findings of recent population-genetic field studies. The importance of taking into account the epidemiology of a parasite population when examining its genetics is also highlighted. Finally, the importance of the effects of a strain structure on methods of control of malaria populations are discussed.
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Gifford, Danna R. "Population genetics of rifampicin-resistant Pseudomonas aeruginosa." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:044b9258-4f10-4e77-9ff6-aa4035cec33b.
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Antibiotic resistance is generally associated with a cost in terms of reduced competitive fitness in the absence of antibiotics. Despite this 'cost of resistance', the cessation of antibiotic treatment does not result in significant reductions in the prevalence of resistance. The maintenance of resistance, in spite of the costs, has been attributed to the rarity of reversion mutations, relative to compensatory mutations at other loci in the genome. However, the large size of bacteria populations, and the potential for migration, suggest that reversion mutations should occasionally be introduced to resistant populations. In this thesis, I show that additional mechanisms can prevent fixation of reversion mutations even if they do occur. Using an experimental evolution approach, with rifampicin resistance in Pseudomonas aeruginosa as a model system, I measured the costs of resistance in several environments and followed the adaptive dynamics of resistant populations where a sensitive lineage had invaded by migration. The results suggest that several additional mechanisms contribute to the maintenance of antibiotic resistance. Most rifampicin resistance mutations are not unconditionally costly in all environments, suggesting that migration between environments could maintain a resistant reservoir population. In environments where resistance is initially costly, the fixation of a revertant is not guaranteed, even if introduced through migration. Revertant fixation was impeded or prevented by clonal interference from adaptation in the resistant strain. Revertants that did successfully replace the resistant strain were forced to adapt to do so. Contrary to assumptions in the existing literature, fitness in the resistant strains was not recovered by general compensatory mutations, but instead by adaptive mutations specific to the environment. The data challenge several assumptions about the maintenance of antibiotic resistance: that resistance mutations are always costly, that the rarity of back mutations prevents the reversion of resistance, and that resistant strains recover fitness by compensatory mutations.
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Amenga-Etego, Naam-Kayagre Lucas. "Plasmodium falciparum population genetics in northern Ghana." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:023a6b97-5a30-4a66-bcad-0d85271062fd.
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The main thrust of this thesis was to characterize P.falciparum genetic diversity in northern Ghana. To do this, I used simple techniques to purify P. falciparum DNA from clinical samples across a rural setting for whole-genome sequencing. The goal was to provide a framework for exploring host-parasite genetic interactions. Utilizing Illumina deep sequencing data for 277 isolates I analyzed P. falciparum genetic diversity and described within-host diversity across this area. I observed random mating (ie no population structure) in the local parasite population, and a high genetic diversity indicative of high out-crossing. Moreover, when I aggregated my data with similar published data from Burkina Faso and Mali (sites ≈500km apart), no population structure was evident. In contrast, sites sampled in Cambodia and Thailand (≈ 800km apart) were found to have greater population structure and high potential for inbreeding. This may be driven by differences in transmission intensity between the sites sampled in West Africa and southeast Asia. To demonstrate the utility of deep sequencing data, I focused on the genomic regions of pfdhfr, pfdhps and pfcrt, known to be under antimalarial drug selection. I surveyed the full diversity of point mutations already characterized in these genes and discovered previously unknown variants. However, in order to provide a means to follow up on new variants or interesting candidate regions in large clinical samples with limited parasite DNA, I assessed the Sequenom iPLEX platform for high-throughput genotyping of P. falciparum polymorphisms. This necessitated developing a method appropriate for assigning genotypes in haploid genome mixtures common in natural infections. Finally, I used this method to type host and parasite markers in a case-control sample set from this region for exploring host-parasite genetic interactions. I found that children who have the sickle-cell trait and carry parasites that have pfdhfr resistant alleles lose their protection against severe malaria as compared to children who have normal haemoglobin and are infected with parasites with these resistant alleles.
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Martin, Hilary Chenevix. "Genomic approaches to medical and population genetics." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:44fc9605-a2a8-4b91-9ea9-989fb8203d27.
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Over the last fifteen years, rapid advances in genotyping and DNA sequencing technologies have revolutionised genetic and biomedical research. In this thesis, we present some applications of these technologies in studying rare disease, population genetics and meiotic recombination. We begin by reviewing previous research in these areas in Chapter 1. Then in Chapter 2, we present some case studies of Mendelian neurological disorders that were carried out as part of a large clinical whole-genome sequencing project, WGS500. These led to the discovery of several new genes for a type of severe early-onset epilepsy called Ohtahara Syndrome, and of a particularly interesting mutation that tentatively suggests a role for a glutamate receptor gene, GRIA3, in circadian rhythm control. In Chapter 3, we examine some general lessons learnt from the WGS500 project, including the utility of sequencing family members to reduce the number of candidate pathogenic variants, and the perils of focusing on candidate genes. Chapter 4 describes a population sequencing project on the platypus, in which we sequenced 58 samples from across the whole species range. Our results provide insights into the population structure and history of this fascinating mammal, and also into the ongoing evolution of its remarkable chain of ten sex chromosomes. Finally, in Chapter 5, we describe a study of the effect of maternal age on meiotic recombination, the largest of its kind to date. Our results from multiple cohorts suggest a small but significant positive effect of maternal age on the number of crossovers, but with substantial heterogeneity between cohorts that is likely due to sampling noise, though confounders may also play a role. These studies illustrate the power of genomic approaches for investigating fundamental biological processes at the population, individual and cellular levels.
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Poetter, Karl. "Molecular population and evolutionary genetics of Rickettsiae /." The Ohio State University, 1989. http://rave.ohiolink.edu/etdc/view?acc_num=osu148767034687517.
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Heist, Edward J. "Population genetics of selected species of sharks." W&M ScholarWorks, 1994. https://scholarworks.wm.edu/etd/1539616691.
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Molecular genetic techniques were used to elucidate genetic population structure in three species of sharks, the coastal sandbar shark (Carcharhinus plumbeus) and Atlantic sharpnose shark (Rhizoprionodon terraenovae), and the pelagic shortfin mako (Isurus oxyrinchus). Allozyme analysis and analysis of restriction fragment length polymorphisms (RFLP) of mitochondrial DNA (mtDNA) were used to test the null hypothesis that the mid-Atlantic Bight and the Gulf of Mexico sandbar sharks consist of a single gene pool. RFLP analysis of mtDNA was used to determine the pattern and level of genetic divergence in the sandbar shark between the western North Atlantic and the Eastern Indian Ocean, and within the entire species range of the cosmopolitan shortfin mako and the Atlantic sharpnose shark. No significant genetic divergence was detected in the sandbar shark between the mid-Atlantic Bight and Gulf of Mexico. Genetic variation was extremely low but homogeneously distributed. A significant degree of genetic divergence was detected between North Atlantic and Australian sandbar sharks. All Australian sandbar shark mtDNAs were fixed for alleles other than those detected in the North Atlantic. The hypothesis that the shortfin mako comprises a single panmictic population was rejected. The overall probability of drawing samples with such disparate allele frequencies from a single gene pool was &<&0.001. The only barrier to gene flow detected appeared to be the equatorial Atlantic. Samples from Brazil, Australia, and California were not significantly different from each other, however all three were significantly different from the North Atlantic sample. The shortfin mako exhibited a considerably higher level of genetic variation than the sandbar shark. The Atlantic sharpnose shark did not exhibit significant differences in allele frequency throughout its range. The level of genetic variation detected in mtDNA was intermediate to that of the sandbar shark and the shortfin mako.
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Van, der Merwe Aletta Elizabeth. "Population genetic structure and demographical history of South African abalone, Haliotis midae, in a conservation context." Thesis, Stellenbosch : University of Stellenbosch, 2009. http://hdl.handle.net/10019.1/3974.
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Thesis (PhD (Genetics))--University of Stellenbosch, 2009.ENGLISH ABSTRACT: South African abalone, Haliotis midae, has been the subject of major concern regarding its survival and conservation over the last decade or more. Being the only one of five endemic species with commercial value, there is considerable interest and urgency in genetic management and improvement of this species. Limited genetic information and the increasing conservation concern of this species are considered the key motivations for generating information on the micro- and macro-evolutionary processes of H. midae, the overall objective of this study. This study reported the first microsatellite and Single Nucleotide Polymorphism (SNP) markers developed specifically for Haliotis midae. Both these marker types were applied to elucidate the degree of gene flow in nine natural abalone populations whilst testing for two contrasting hypotheses; panmixia versus restricted gene flow. Data was analysed using a series of methodological approaches ranging from traditional summary statistics to more advanced MCMC based Bayesian clustering methods with and without including spatial information. Using only microsatellite data, the historical demography of the species was also examined in terms of effective population size and population size fluctuations. Finally, the evolutionary positioning and origin of Haliotis midae with regards to other Haliotis species was investigated based on mitochondrial and nuclear sequence data. Both microsatellite and SNP data gave evidence for subtle differentiation between West and East coast populations that correlates with a hydrogeographic barrier in the vicinity of Cape Agulhas. Population substructure was supported by AMOVA, FCA and Bayesian clustering analysis. Clustering utilizing spatial information further indicated clinal variation on both sides of the proposed barrier with a region in the middle coinciding with a secondary contact zone, indicating possible historical isolation during glacial periods. Overall, the similar degree of substructure observed with both microsatellites and SNPs supported the existence of contemporary and/or historical factors with genome-wide effect on gene flow. The population expansion measured with the microsatellites was inconsistent with the known recent decline but taking the species’ life cycle and large effective population size into account, a shrinkage in population size will probably only be apparent in a few generations time. On a macro-evolutionary scale, this study presents the first classification of South African abalone as a monophyletic group within the Haliotidae family. The topology based on the combined mitochondrial and nuclear dataset is highly suggestive of a relatively recent radiation of the SA species from the Indo-Pacific basin. The study concludes by describing the most likely factors that could have affected overall population structure and makes suggestions on how the given genetic information should be incorporated into strategies aimed towards the effective management and conservation of Haliotis midae.
AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is oor die laaste dekade of meer die onderwerp van groot bekommernis betreffende die spesie se oorlewing en bewaring. Aangesien dit die enigste van vyf endemiese SA spesies is met kommersiёle waarde, is daar besonderse belang en erns in die genetiese beheer en verbetering van die spesie. Beperkte genetiese inligting en ‘n toenemende behoefte om die spesie te bewaar is die hoof motivering agter die generering van informasie rakende mikro- en makro-evolusionêre prosesse in Haliotis midae en is die oorhoofse doel van hierdie studie. Hierdie studie beskryf die eerste mikrosatelliete en enkel basispaar polimorfismes wat ontwikkel is spesifiek vir Haliotis midae. Beide tipe merkers is aangewend om die mate van gene vloei in nege wilde perlemoen populasies te ondersoek terwyl twee hipoteses ondersoek is; panmiksie versus beperkte gene vloei. Data is geanaliseer deur gebruik te maak van ‘n reeks metodieke benaderings wat wissel van tradisionele opsommings statistieke tot meer gevorderde MCMC gebasseerde groeperings metodes met of sonder die gebruik van geografiese data. Mikrosatelliet data is ook aangewend om die historiese demografie van die spesie te bepaal in terme van effektiewe populasie grootte asook veranderinge in populasie groottes. Laastens is die evolusionêre posisionering en oorsprong van Haliotis midae teenoor ander Haliotis spesies ondersoek deur gebruik te maak van mitokondriale en nukleêre DNA volgorde data. Beide mikrosatelliet en enkel basispaar polimorfisme data lewer bewys van ‘n subtiele genetiese verskil tussen wes en ooskus populasies wat verband hou met ‘n hidrografiese skeiding in die omgewing van Kaap Agulhas. Populasie struktuur is ondersteun deur die analise van molekulêre variansie (AMOVA), faktoriale komponente analise asook Bayesiese groeperings analise. Groeperings analise wat geografiese informasie insluit dui klinale genetiese variasie aan beide kante van die skeiding aan met ‘n area in die middel wat ooreenstem met ‘n sekondêre kontak gebied. In totaal, ondersteun die soortgelyke mate van struktuur verkry met beide die mikrosatelliete en enkel basispaar polimorfismes die bestaan van hedendaagse en/of historiese faktore met genoom wye invloed op gene vloei. Die toename in populasie grootte vasgestel deur die mikrosatelliet data stem nie ooreen met die onlangse afname waargeneem in die spesie nie, maar met inagneming van Haliotis midae se lewenssiklus en groot effektiewe populasie grootte, sal die afname in populasie grootte moontlik eers oor ‘n paar generasies na vore kom. Op ‘n makro-evolusionêre skaal lewer hierdie studie die eerste klassifikasie van Suid-Afrikaanse perlemoen as ‘n monofiletiese groep binne die Haliotidae familie. Die topologie gebaseer op ‘n gesamentlike mitkondriale en nukleêre datastel is hoogs aanduidend van ‘n relatiewe onlangse verspreiding van die Suid-Afrikaanse spesies uit die Stille-Indiese Oseaan. Die studie sluit af deur die mees algemene faktore te bespreek wat populasie struktuur kon beïnvloed het en maak voorstelle op watter wyse hierdie genetiese inligting aangewend kan word vir die effekiewe beheer en bewaring van Haliotis midae.
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Agustin, Liza Q. "Effects of population bottlenecks of levels of genetic diversity and patterns of differentiation in feral populations of Oreochromis mossambicus." Thesis, Queensland University of Technology, 1999.
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Moodley, Yoshan. "Population structuring in Southern Africa zebras." Doctoral thesis, University of Cape Town, 2002. http://hdl.handle.net/11427/3174.
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Crous, Ilse. "Craniosynostosis in a South Africa population." Master's thesis, Faculty of Health Sciences, 2021. http://hdl.handle.net/11427/33611.
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Background: Craniosynostosis refers to the premature fusion of calvarial bones which lead to restricted growth potential. Compensatory growth occurs in the dimensions not restricted by fusion and causes progressive distortion in the skull shape. The majority of craniosynostosis cases occur in isolation and are so called non-syndromic craniosynostosis. In about 30 % of all cases, anomalies are noted along with the craniosynostosis, often defining a described and recognised syndrome. The aim is to delineate the phenotype observed in a South African population. Methods: In this descriptive study, hospital records for the preceding five years were retrospectively reviewed to describe the profile of patients with craniosynostosis seen at the Red Cross War Memorial Children's Hospital in Cape Town. In addition to the retrospective review, a sub cohort of patients were prospectively phenotyped. The patients were subdivided into three groups namely: non-syndromic craniosynostosis, syndromic craniosynostosis and craniosynostosis with additional features. The last group included patients who had additional malformations or clinical findings without a syndromic diagnosis. The prevalence of phenotypic findings, teratogen exposure, birth complications, congenital malformations, surgical interventions and results of genetic testing in this cohort is described. Descriptive statistical analysis was used. Results: A total of 47 children with craniosynostosis were included in this study. Twenty-five individuals of the cohort were male, and one patient has a disorder of sexual development. Eighteen patients had non-syndromic synostosis. Twelve of these had sagittal type synostosis and five had metopic type synostosis with one unspecified. Thirteen had syndromic synostosis. Eight were clinically diagnosed with Crouzon syndrome of which three were molecularly confirmed. Four patients had Apert syndrome and one had Pfeiffer syndrome, these were clinically diagnosed without molecular confirmation. Sixteen patients had craniosynostosis with some additional findings but no syndromic diagnosis. The suture involved in the majority of patients was the sagittal suture. Ten patients had an additional structural brain abnormality and 13 had signs of raised intracranial pressure. The average age at confirmation of diagnosis of craniosynostosis by CT scan was 22.5 months (SD = 31.4, range: 0.1 – 140.9). Thirty of the 47 patients had craniosynostosis surgery. The average age of surgery was 22.4 months (SD = 19; range: 5-79). The anthropometric, phenotype and developmental features indicate that this is a highly heterogenous group of disorders. Conclusion: Craniosynostosis has been widely reported worldwide, especially in individuals of European descent with only a few reports on craniosynostosis in South African or African populations. Knowledge of the phenotypic spectrum will aid in understanding and documenting this group of disorders in our local population. This study also highlights that this is a complex condition best managed by a multidisciplinary team that should include a medical geneticist. The recognition of specific craniosynostosis syndromes together with appropriate molecular testing can be cost effective even in a limited resource setting and aid in accurate prognosis and recurrence risk information for families.
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Sawyer, Sarah Lynn. "Using SNPs to study complex genetic disease : a population and evolutionary genetics perspective /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-967-6/.
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Härnström, Karolina. "Bloom dynamics and population genetics of marine phytoplankton : community, species and population aspects /." Göteborg : Department of Marine Ecology, University of Gothenburg, 2009. http://gupea.ub.gu.se/dspace/bitstream/2077/20913/1/gupea_2077_20913_1.pdf.
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Agarwala, Vineeta. "Integrating empirical data and population genetic simulations to study the genetic architecture of type 2 diabetes." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11120.
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Most common diseases have substantial heritable components but are characterized by complex inheritance patterns implicating numerous genetic and environmental factors. A longstanding goal of human genetics research is to delineate the genetic architecture of these traits - the number, frequencies, and effect sizes of disease-causing alleles - to inform mapping studies, elucidate mechanisms of disease, and guide development of targeted clinical therapies and diagnostics. Although vast empirical genetic data has now been collected for common diseases, different and contradictory hypotheses have been advocated about features of genetic architecture (e.g., the contribution of rare vs. common variants). Here, we present a framework which combines multiple empirical datasets and simulation studies to enable systematic testing of hypotheses about both global and locus-specific complex trait architecture. We apply this to type 2 diabetes (T2D).