Dissertations / Theses on the topic 'Natural selection'
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1
Vick, Jeffrey A. "Natural Selection." VCU Scholars Compass, 2006. http://scholarscompass.vcu.edu/etd/1254.
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My thesis work is about imagination. I use the collaborative efforts of the viewer's mind and my sculptures, or specimens, to make associations of real life animals. I feel this engages the viewer and in turn invites them to inspect the work on closer level. This is my ultimate goal in the work, to take hold of the viewer's curiosity and have them examine the work on a closer level.
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Bourrat, Pierrick Jean-Noel. "Reconceptualising evolution by natural selection." Thesis, The University of Sydney, 2014. http://hdl.handle.net/2123/12942.
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This thesis examines the theoretical and philosophical underpinnings of the concept of natural selection which is pervasively invoked in biology and other ‘evolutionary’ domains. Although what constitutes the process of natural selection appears to be very intuitive (natural selection results from entities exhibiting differences in fitness in a population), this conceals a number of theoretical ambiguities and difficulties. Some of these have been pointed out numerous times; others have hardly been noticed. One aim of this work is to unpack these difficulties and ambiguities; another is to provide new solutions and clarifications to them using a range of philosophical and conceptual tools. The result is a concept of natural selection stripped down from its biological specificities. I start by revisiting the entangled debates over whether natural selection is a cause of evolutionary change as opposed to a mere statistical effect of other causes, at what level this putative cause operates and whether it can be distinguished from drift. Borrowing tools from the causal modelling literature, I argue that natural selection is best conceived as a causal process resulting from individual level differences in a population. I then move to the question of whether the process of natural selection requires perfect transmission of types. I show that this question is ambiguous and can find different answers. From there, I distinguish the process of natural selection from some of its possible products, namely, evolution by natural selection and complex adaptation. I argue that reproduction and inheritance are conceptually distinct from natural selection, and using individual-based models, I demonstrate that they can be conceived as evolutionary products of it. This ultimately leads me to generalise the concepts of heritability and fitness used in the formal equations of evolutionary change. Finally, I argue that concepts of fitness and natural selection crucially depend on the grains of description at and temporal scales over which evolutionary explanations are given. These considerations reveal that the metaphysical status of the process of natural selection is problematic and why neglecting them can lead to flawed arguments in the levels of selection debate.
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Freeland, Stephen J. "Natural selection and the genetic code." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313922.
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Gillespie, Duncan O. S. "Natural selection on female reproduction in humans." Thesis, University of Sheffield, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.556741.
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Nearly all animals show senescent deterioration in physical condition with increasing age but the social and ecological context of how senescence is maintained by natural selection in wild populations remains unclear. I investigated human female reproductive ageing in a multi-generational dataset of pre-industrial Finns, which reconstructed family-lines from dates of birth, marriage and death and also contained information on family economicstatus. Family-building often required many births because not all offspring survived to reproduce themselves, however, high numbers of breeding offspring in landless economicstatus families limited total grand-offspring number (Chapter 1). The likelihood a female was married and thus had an opportunity to reproduce peaked at ages 30-40 years before declining due to female death or widowhood and low re-marriage probabilities for older widows with dependent offspring (Chapter 2). High birth order offspring had lower survival and reproductive success than their elder siblings, especially in landowning families where land inheritance favoured firstborns (Chapter 3). Female reproductive capability improved after the first birth but declined after many previous births, resulting in reduced infant survival and providing evidence for reproductive senescence (Chapter 4). These findings indicate that senescence could be maintained by two processes: declines in the exposure of genetic variation to natural selection at the oldest fertile ages; and because maternal reproductive investment in earlier born offspring has a greater effect on their reproductive success due to the advantage of earlier born offspring in sibling competition. There was also evidence that total lifetime reproduction could be limited by family resource availability. This illustrates how both ecological and social factors can constrain reproductive success while simultaneously maintaining senescence in the female life history.
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Exton, Samantha Jane. "Natural selection in fossil and recent molluscs." Thesis, University of Liverpool, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366482.
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Hu, Min. "Positive natural selection in the human genome." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.607687.
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Bentley, Michael. "The dynamical systems theory of natural selection." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:ff01467a-c1ac-4852-a4b8-9055e9dcb1b0.
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Darwin's (1859) theory of evolution by natural selection accounts for the adaptations of organisms, but, as Fisher (1930) famously said, 'natural selection is not evolution.' Evolutionary theory has two major components: i) natural selection, which involves the underlying dynamics of populations; and ii) adaptive evolutionary change, which involves the optimisation of phenotypes for fitness maximisation. Many of the traditional theoretical frameworks in evolutionary theory have focussed on studying optimisation processes that generate biological adaptations. In recent years, however, a number of evolutionary theorists have turned to using frameworks such as the 'replicator dynamics' or 'eco-evolutionary dynamics', to explore the dynamics of natural selection. There has, however, been little attempt to explore how these dynamical systems frameworks relate to more traditional frameworks in evolutionary theory or how they incorporate the principles that embody the process of evolution by natural selection, namely, phenotypic variation, differential reproductive success, and heritability. In this thesis, I use these principles to provide the formal foundations of a general framework - a mathematical synthesis - in which the future state of an evolutionary system can be predicted from its present state; what I will call a 'dynamical systems theory of natural selection.' Given the state of an existing biological system, and a set of assumptions about how individuals within the system interact, the job of the dynamical systems theory of natural selection is no less than to predict the future in its entirety.
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Svedin, Nina. "Natural and Sexual Selection in a Natural Hybrid Zone of Ficedula Flycatchers." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7372.
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Huisman, Jisca. "Gene Flow and Natural Selection in Atlantic Salmon." Doctoral thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-16991.
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Reardon, James T. "Natural selection and evolutionary ecology in Anolis oculatus." Thesis, Bangor University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297668.
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Beckley, Colin. "Natural selection and natural processes : a philosophical examination of the processes of evolution." Thesis, Oxford Brookes University, 2012. https://radar.brookes.ac.uk/radar/items/76e8697b-c2b8-4d91-8790-08b637fcbc79/1/.
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This thesis concerns evolution and how it is explained. The ambition here is to identify clearly the many aspects of evolution, and to evaluate past and present explanations of evolution for their coherence and validity. Historically natural selection has been taken to be the central and main explanans, with other explanations playing lesser roles. Here it will be argued that the sheer complexity and diversity within nature cannot be accounted for by any single explanatory mechanism and that a plurality of explanatory mechanisms is required. Loading natural selection with the main weight of explanation is an overburden which, far from strengthening its explanatory powers, actually renders it vacuous. A critical historical and philosophical examination of the concept of natural selection reveals that it has never received a formal scientific definition that commands universal respect. This has created a problem of demarcation between that which natural selection can legitimately be said to explain and that which it cannot. In fact, the ontology of natural selection is equivocal, giving rise to the many controversies that have plagued evolutionary biology. The disambiguation of the concept of natural selection is the principle aim of this thesis and guidelines on how this should be accomplished are provided. However, should these reforming guidelines fail to achieve a consensus then a more radical alternative is proposed. It is recommended that the selective terminology is replaced with the less anomalous and demanding principle of ‘meeting the conditions of existence’. Moreover, talk of the evolution and origins by means of natural selection is to be replaced by talk of evolution and origins by means of natural processes. Finally, drawing from a ‘Structuralist’ alternative, it will be demonstrated that biological evolution should not be divorced from general or cosmological evolution. Rather, elucidation should be drawn more deeply from the fields of physics, chemistry, mathematics and topology, without the use of selection-tinted spectacles.
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Sikora, Martin. "Evolutionary genetics of malaria: genetic susceptibility and natural selection." Doctoral thesis, Universitat Pompeu Fabra, 2010. http://hdl.handle.net/10803/7220.
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Una de les forces selectives més fortes que han afectat a les poblacions humanes en la història més recent és el paràsit de la malària: Plasmodium falciparum, que és la causa de varis exemples d'adaptació induïda per patògens en els éssers humans. Una forma especial de malària és l'associada a l'embaràs, que es caracteritza per l'acumulació d'eritròcits infectats en la placenta, i que pot arribar a causar fins a 200.000 morts maternoinfantils cada any. L'objectiu d'aquest treball és descriure com aquesta forma peculiar de malària ha afectat la variació genètica humana. Amb aquesta finalitat, hem utilitzat mètodes tant de la genètica evolutiva com de l'epidemiologia molecular, resultant en la primera investigació a gran escala de la base genètica de la malària placentària. Els resultats ofereixen una nova visió sobre els gens que modulen el risc d'infecció, ,així com de la selecció natural actuant sobre les vies cel·lulars implicades en la patogènesi de la malaltia. Finalment, també aportem noves dades sobre l'estructura genètica de les poblacions sub-saharianes analitzades.One of the strongest selective forces affecting human populations in recent history is the malaria parasite Plasmodium falciparum, which is the cause of a variety of well-established examples of pathogen-induced adaptation in humans. A special form of malaria is pregnancy-associated malaria, which is characterised by the accumulation of infected erythrocytes in the placenta, and causes up to 200,000 maternal and infant deaths every year. The aim of this work is to characterise how this particular form of malaria has shaped human genetic variation. To that end we use methods of both evolutionary genetics and molecular epidemiology, reporting the first large-scale investigation of the genetic basis of placental infection. Our results provide new insights into genes modulating the risk of infection, as well as natural selection acting on cellular pathways involved in the pathogenesis of the disease. Finally, we also provide new data on the genetic structure of affected populations in Sub-Saharan Africa.
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Lorente, Galdós Maria Belén. "The Action of natural selection in recently duplicated genes." Doctoral thesis, Universitat Pompeu Fabra, 2011. http://hdl.handle.net/10803/53562.
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Identification of signatures of positive selection has long been a major issue for
understanding the unique features of any given species. However, only a fraction of
human genes have been interrogated. Genes within segmental duplications are usually
omitted due to the limitations of draft genome assemblies and the methodological
reliance on accurate gene trees. In this work, we show the feasibility of a new method
that does not need accurate gene trees or individual high-quality assemblies. We applied
the concept to study exon evolution in the human genome, identifying 74 exons with
evidence for rapid coding sequence evolution during human and Old World monkey
evolution. Our results suggest abundant accelerated coding sequence evolution within
duplicated regions of the genome and provide a more comprehensive view of the role of
selection on the human genome.La identificación de señales debidas a la acción de la selección positiva es de gran relevancia para desvelar características únicas de las especies. A pesar de ello, solo una fracción de genes humanos han sido analizados. Los genes incluidos en duplicaciones segmentarias son normalmente ignorados debido a limitaciones impuestas por la naturaleza preliminar de los genomas distintos al humano, así como por la dependencia en adecuados árboles filogenéticos. En este proyecto, demostramos la viabilidad de un nuevo método que no necesita árboles filogenéticos correctos ni ensamblajes de genomas de alta calidad. Hemos aplicado el concepto al genoma humano y hemos identificado 74 exones que muestran evidencia de haber evolucionado más rápidamente desde la separación de los humanos y los monos del viejo mundo. Nuestros resultados sugieren que ha habido abundante evolución acelerada dentro de las regiones duplicadas y ofrece una visión más esclarecedora del rol de la selección en la evolución del genoma humano.
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Andrews, Tessa Marie. "Natural selection in the field and in the classroom." Diss., Montana State University, 2012. http://etd.lib.montana.edu/etd/2012/andrews/AndrewsT0512.pdf.
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This dissertation examined natural selection in westslope cutthroat trout (Oncorhynchus clarkii lewisi) and undergraduate learning in the subject area natural selection. Translocation-moving individuals to a new habitat to establish, re-establish or supplement a population-is a crucial management strategy for cutthroat trout. One of the major questions managers face in a translocation is which population(s) should contribute individuals? Unfortunately, we often know little about the differences among potential contributing population. The goal of the first half of this dissertation was to look for differences in performance among individuals from five populations of westslope cutthroat trout. I assessed survival, growth, and condition (Chapter 2) and dispersal (Chapter 3) following the translocation of embryos from these five populations to six introduction sites in Cherry Creek. No differences existed among these populations in relative survival, growth, or condition at age 1 or 2. In contrast, statistically significant differences existed in dispersal distance among these populations. These differences were consistent across some, but not all, introduction locations. As our knowledge of evolutionary biology has continued to grow, so too has our knowledge of how students learn evolution. Students taught using active learning strategies can learn substantially more about complex scientific concepts than students taught using primarily lectures. The goal of the second half of this dissertation was to further examine how students learn natural selection and how instructors facilitate that learning. I conducted a national survey of the relationship between an instructor's use of active learning strategies and how much students learned about natural selection (Chapter 4). I used a random sample of instructors from the largest and most prestigious universities in the country so that my results could be inferred to this large population of instructors. The degree to which instructors used active learning was NOT associated with student learning in this population of typical biology instructors. However, I found that a discussion of contemporary human evolution that used active learning strategies could effectively facilitate student learning of natural selection (Chapter 5). 'Co-authored by Bradley B. Shepard, Andrea R. Litt, Carter G. Kruse, Lee M. Nelson, Patrick Clancey, Alexandar V. Zale, Mark L Taper, Steven T. Kalinowski, Mary J. Leonard, and Clinton A. Colgrove.'
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Hoffman, Michael M. "Quantifying evolution and natural selection in vertebrate noncoding sequence." Thesis, University of Cambridge, 2008. https://www.repository.cam.ac.uk/handle/1810/245947.
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When studying genomic evolution, biologists find it important to identify varying patterns of natural selection. Many traditional methods of classifying directional selection have relied on models that categorize mutations as function-altering or neutral, and then comparing the rates of the two categories of mutations. The most well-known methods specifically compare nonsynonymous and synonymous substitutions in protein-coding sequence. The recent availability of whole genome sequences, especially those of various mammals and other vertebrates, enables us to develop alternative methods for analyzing molecular evolution and selection that rely on noncoding sequence. Furthermore, our greater understanding of the importance of noncoding DNA demands such methods. This thesis contains the results of the first in-depth genomic-scale analysis using intron substitutions to estimate the neutral rate of evolution. Performing this analysis across several genomes requires the development of a new model of gene evolution and related methods. I find strong correlation between estimates of the neutral rate made with intron methods and estimates made with synonymous coding nucleotides for both human–dog and mouse–rat comparisons. However, the two estimates cannot be considered directly equivalent. This thesis also describes a novel method that estimates a rate of function affecting evolution in promoter regions by inspecting the effect of simulated mutations on transcription factor binding. This involves the development and use of a probabilistic method that uses a hidden Markov model to predict the binding of transcription factors. I report the results of applying these new methods to the human genome for the identification of transcription factor binding sites, and for the identification of natural selection.
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Spencer, Christopher C. A. "Human genetic variation and the evidence for natural selection." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436963.
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Pichler, Peter-Paul. "Natural selection, adaptive evolution and diversity in computational ecosystems." Thesis, University of Hertfordshire, 2009. http://hdl.handle.net/2299/4006.
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The central goal of this thesis is to provide additional criteria towards implementing open-ended evolution in an artificial system. Methods inspired by biological evolution are frequently applied to generate autonomous agents too complex to design by hand. Despite substantial progress in the area of evolutionary computation, additional efforts are needed to identify a coherent set of requirements for a system capable of exhibiting open-ended evolutionary dynamics. The thesis provides an extensive discussion of existing models and of the major considerations for designing a computational model of evolution by natural selection. Thus, the work in this thesis constitutes a further step towards determining the requirements for such a system and introduces a concrete implementation of an artificial evolution system to evaluate the developed suggestions. The proposed system improves upon existing models with respect to easy interpretability of agent behaviour, high structural freedom, and a low-level sensor and effector model to allow numerous long-term evolutionary gradients. In a series of experiments, the evolutionary dynamics of the system are examined against the set objectives and, where appropriate, compared with existing systems. Typical agent behaviours are introduced to convey a general overview of the system dynamics. These behaviours are related to properties of the respective agent populations and their evolved morphologies. It is shown that an intuitive classification of observed behaviours coincides with a more formal classification based on morphology. The evolutionary dynamics of the system are evaluated and shown to be unbounded according to the classification provided by Bedau and Packard’s measures of evolutionary activity. Further, it is analysed how observed behavioural complexity relates to the complexity of the agent-side mechanisms subserving these behaviours. It is shown that for the concrete definition of complexity applied, the average complexity continually increases for extended periods of evolutionary time. In combination, these two findings show how the observed behaviours are the result of an ongoing and lasting adaptive evolutionary process as opposed to being artifacts of the seeding process. Finally, the effect of variation in the system on the diversity of evolved behaviour is investigated. It is shown that coupling individual survival and reproductive success can restrict the available evolutionary trajectories in more than the trivial sense of removing another dimension, and conversely, decoupling individual survival from reproductive success can increase the number of evolutionary trajectories. The effect of different reproductive mechanisms is contrasted with that of variation in environmental conditions. The diversity of evolved strategies turns out to be sensitive to the reproductive mechanism while being remarkably robust to the variation of environmental conditions. These findings emphasize the importance of being explicit about the abstractions and assumptions underlying an artificial evolution system, particularly if the system is intended to model aspects of biological evolution.
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Siska, Veronika. "Human population history and its interplay with natural selection." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/284164.
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The complex demographic changes that underlie the expansion of anatomically modern humans out of Africa have important consequences on the dynamics of natural selection and our ability to detect it. In this thesis, I aimed to refine our knowledge on human population history using ancient genomes, and then used a climate-informed, spatially explicit framework to explore the interplay between complex demographies and selection. I first analysed a high-coverage genome from Upper Palaeolithic Romania from ~37.8 kya, and demonstrated an early diversification of multiple lineages shortly after the out-of-Africa expansion (Chapter 2). I then investigated Late Upper Palaeolithic (~13.3ky old) and Mesolithic (~9.7 ky old) samples from the Caucasus and a Late Upper Palaeolithic (~13.7ky old) sample from Western Europe, and found that these two groups belong to distinct lineages that also diverged shortly after the out of Africa, ~45-60 ky ago (Chapter 3). Finally, I used East Asian samples from ~7.7ky ago to show that there has been a greater degree of genetic continuity in this region compared to Europe (Chapter 4). In the second part of my thesis, I used a climate-informed, spatially explicit demographic model that captures the out-of-Africa expansion to explore natural selection. I first investigated whether the model can represent the confounding effect of demography on selection statistics, when applied to neutral part of the genome (Chapter 5). Whilst the overlap between different selection statistics was somewhat underestimated by the model, the relationship between signals from different populations is generally well-captured. I then modelled natural selection in the same framework and investigated the spatial distribution of two genetic variants associated with a protective effect against malaria, sickle-cell anaemia and β⁰ thalassemia (Chapter 6). I found that although this model can reproduce the disjoint ranges of different variants typical of the former, it is incompatible with overlapping distributions characteristic of the latter. Furthermore, our model is compatible with the inferred single origin of sickle-cell disease in most regions, but it can not reproduce the presence of this disorder in India without long-distance migrations.
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Gossmann, Toni Ingolf. "Investigating genome wide patterns of natural selection in eukaryotes." Thesis, University of Sussex, 2012. http://sro.sussex.ac.uk/id/eprint/43293/.
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Mutations are the ultimate source of new genetic information and they can be neutral, harmful or beneficial. The ultimate fate of all mutations is either to be lost or to eventually become fixed in a population. In this thesis I investigate genome wide traces of natural selection in eukaryotes. I focus on the most common type of mutations, point mutations, in protein coding genes. I investigated whether there is adaptive evolution in 11 plant species comparisons by applying an extension of the McDonald Kreitman (MK) test and found little evidence of adaptive evolution. However, most of the investigated plant species have low effective population sizes (Ne) and the rate of adaptive evolution is thought to be correlated to Ne. I therefore extended my study using additional data from mammals, drosophilids and yeast to investigate the relationship between the rate of adaptive evolution and Ne. I found a highly significant correlation between the rate of adaptive evolution relative to the rate of neutral evolution (!a) and Ne. It has been proposed that evidence of adaptive evolution can be an artifact of fluctuating selection. I simulated a model of fluctuating selection, in which the average strength of selection acting upon mutations is zero. Under this model adaptive evolution is inferred using MK-type tests. However, the mutations which become fixed are on average positively selected. The signal of adaptive evolution is therefore genuine. Ne can not only vary between species but also across genomes. However, how much variation there is, and whether this affects the efficiency of natural selection, is unknown. I analysed 10 species and show that variation in Ne is widespread. However, this variation is limited, amounting to a few fold variation in Ne between most genomic regions. This is never-the-less sufficient to cause variation in the efficiency of selection.
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Yi, Jon Rong-Wei 1975. "Corpus-based unit selection for natural-sounding speech synthesis." Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/16944.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.Includes bibliographical references (p. 179-196).
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Speech synthesis is an automatic encoding process carried out by machine through which symbols conveying linguistic information are converted into an acoustic waveform. In the past decade or so, a recent trend toward a non-parametric, corpus-based approach has focused on using real human speech as source material for producing novel natural-sounding speech. This work proposes a communication-theoretic formulation in which unit selection is a noisy channel through which an input sequence of symbols passes and an output sequence, possibly corrupted due to the coverage limits of the corpus, emerges. The penalty of approximation is quantified by substitution and concatenation costs which grade what unit contexts are interchangeable and where concatenations are not perceivable. These costs are semi-automatically derived from data and are found to agree with acoustic-phonetic knowledge. The implementation is based on a finite-state transducer (FST) representation that has been successfully used in speech and language processing applications including speech recognition. A proposed constraint kernel topology connects all units in the corpus with associated substitution and concatenation costs and enables an efficient Viterbi search that operates with low latency and scales to large corpora. An A* search can be applied in a second, rescoring pass to incorporate finer acoustic modelling. Extensions to this FST-based search include hierarchical and paralinguistic modelling. The search can also be used in an iterative feedback loop to record new utterances to enhance corpus coverage. This speech synthesis framework has been deployed across various domains and languages in many voices, a testament to its flexibility and rapid prototyping capability.
(cont.) Experimental subjects completing tasks in a given air travel planning scenario by interacting in real time with a spoken dialogue system over the telephone have found the system "easiest to understand" out of eight competing systems. In more detailed listening evaluations, subjective opinions garnered from human participants are found to be correlated with objective measures calculable by machine.
by Jon Rong-Wei Yi.
Ph.D.
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Stewart, A. J. "The construction of transcription factor networks through natural selection." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/19895/.
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Transcription regulation plays a key role in determining cellular function, response to external stimuli and development. Regulatory proteins orchestrate gene expression through thousands of interactions resulting in large, complex networks. Understanding the principles on which these networks are constructed can provide insight into the way the expression patterns of different genes co-evolve. One method by which this question can be addressed is to focus on the evolution of the structure of transcription factor networks (TFNs). In order to do this, a model for their evolution through cis mutation, trans mutation, gene duplication and gene deletion is constructed. This model is used to determine the circumstances under which the asymmetrical in and out degree distributions observed in real networks are reproduced. In this way it is possible to draw conclusions about the contributions of these different evolutionary processes to the evolution of TFNs. Conclusions are also drawn on the way rates of evolution vary with the position of gene in the network. Following this, the contributions of cis mutations, which occur in the promoters of regulated genes, and trans mutations, which occur in the coding reign of transcription factors, to the evolution of TFNs are investigated. A space of neutral genotypes is constructed, and the evolution of TFNs through cis and trans mutations in this space is characterised. The results are then used to account for large scale rewiring observed in the yeast sex determination network. Finally the principles governing the evolution of autoregulatory motifs are investigated. It is shown that negative autoregulation, which functions as a noise reduction mechanism in haploid TFNs, is not evolvable in diploid TFNs. This is attributed to the effects of dominance in diploid TFNs. The fate of duplicates of autoregulating genes in haploid networks is also investigated. It is shown that such duplicates are especially prone to loss of function mutations. This is used to account for the lack of observed autoregulatory duplicates participating in network motifs. From this work, it is concluded that the relative rates of different evolutionary processes are responsible for shaping the global statistical properties of TFN structure. However, the more detailed TFN structure, such as network motif distribution, is strongly influenced by the population genetic details of the system being considered. In addition, extensive neutral evolution is shown to be possible in TFNs. However, the effects of neutral evolution on network structure are shown to depend strongly on the structure of the space on neutral genotypes in which the TFN is evolving.
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Bhatt, Samir. "Statistical analysis of natural selection in RNA virus populations." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:64341c38-f09e-48ed-84e8-7ab9f171a753.
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A key goal of modern evolutionary biology is the identification of genes or genome regions that have been targeted by natural selection. Methods for detecting natural selection utilise the information sampled in contemporary gene sequences and test for deviation from the null hypothesis of neutrality. One such method is the McDonald Kreitman test (MK test), which detects the the molecular 'footprint' left by natural selection by considering the frequency of observed mutations within the sampled population. In this thesis I investigate the applicability of the MK test to viral populations and develop several new methods based on the original MK test. In chapter 2, I use a combination of simulation and methodological improvements to show that the MK test can have low error when applied to analysis of RNA virus populations. Then, in chapter 3, I develop an extension of the MK test with the purpose of estimating rates of adaptive fixation for all genes of the human influenza A virus subtypes H1N1 and H3N2. My results are consistent with previous studies on selection in influenza virus populations, and provide a new perspective on the evolutionary dynamics of human influenza virus. In chapter 4 I develop a formal statistical framework based, on the MK test, for calculating the number of non neutral sites at any frequency range in the site frequency spectrum. In this framework, I introduce a new method for reconstructing the site frequency spectrum that incorporates sampling error and allows for the inclusion of prior knowledge. Using this new framework I show that the majority of nucleotide sites in hepatitis C virus sequences sampled during chronic infection represent deleterious mutations. Finally, in chapter 5 I use the generalised framework introduced in chapter 4 to develop a statistic for evaluating the deleterious mutation load of a population. I apply this test sequences that represent 96 RNA virus genes and show that my approach has comparable power to equivalent phylogenetic methods. In this thesis I have developed computationally efficient methods for analysis of genetic data from virus populations. It is my hope that these methods will become useful given the explosion in sequence data that has accompanied recent improvements in sequencing technology.
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Ramey, Holly Rene. "Mapping natural and artificial selection events in animal genomes." Thesis, University of Missouri - Columbia, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10182613.
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Baker, Joanne. "The varying rate of phenotypic evolution and natural selection." Thesis, University of Reading, 2017. http://centaur.reading.ac.uk/69463/.
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Changes in the rate at which biological evolution proceeds are widespread and common. Advancements in methodology make it possible to characterize such historical evolution more accurately and reveal complex scenarios where rates vary among organismic groups and even between individual lineages. The work presented here embraces such complexity, seeking to exploit phenotypic rate variation to reconstruct patterns and processes of evolution deep in time with unprecedented accuracy. Chapters 1 and 2 demonstrate for the first time that it is possible to reveal historical, directional trends in morphology that played out over millions and millions of years using only data from living species. These trends arose as a consequence of rapid and repeated instances of directional evolutionary change and the approach employed to detect them may be the only way to study historical adaptive trends in morphology that cannot otherwise be observed in the fossil record. Where evolution is fastest, natural selection has acted more strongly; this idea is developed further in Chapter 3 which presents a novel way to characterize an exceptional subclass of rates of morphological evolution that can be defined as positive phenotypic selection. In both Chapters 3 and 4 it is shown that such intense episodes of natural selection have punctuated the evolution of diverse groups including plants, dinosaurs and hominins. Chapter 5 demonstrates that it is possible to uncover explicit underlying causes of positive phenotypic selection and takes us one step closer to being able to truly understand the drivers of natural diversity. As a complete work, this thesis harnesses and exploits phenotypic rate heterogeneity to inform inferences about patterns and processes of evolution deep in time and to understand how natural selection has acted to sculpt morphology, giving rise to the diversity we observe today both in living species and the fossil record.
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Fedder, Joshua C. "Causal Complexity and Comprehension of Evolution by Natural Selection." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1461145729.
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Adam, Kwame Asamoah. "Tree selection in selective logging : ecological and silvicultural considerations for natural forest management in Ghana." Thesis, University of Aberdeen, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400673.
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This thesis was to examine selective logging practices in Ghana and to gather and apply relevant ecological and silvicultural knowledge to rules governing the selection of trees for felling (specifically minimum felling diameters and harvest intensities) and seed tree retention. The work involved reviews of historical data as well as field-based studies, including experimental and descriptive work. A review of forest regulation between 1900 and 1989 revealed that timber harvesting in permanent forest reserves has primarily been regulated through minimum felling limits. These regulations appear to have been insufficient to ensure regeneration of the valuable species, as suggested by examination of stem stocking and species composition data from six reserves that differ in levels of historical exploitation. The stock of timber trees in the logged forest is dominated by shade tolerant species indicating a need for silvicultural interventions. Census of seedlings and saplings within 50m of mother trees for 15 species revealed that more than 60% of their seedlings occur within 30m of parents indicating spatial limitation to seedling recruitment. The result also indicated that 14 of the species have reproductive size threshold lower than their respective minimum felling diameter (MFD) suggesting that decisions about seed tree retention could be uncoupled from MFDs. Logging studies to compare logging damage (ground area disturbed, stems damaged and canopy change) between two levels of harvest intensities (26.3m3 ha-1 and 52.6m3 ha-1) and two sizes (large and small) of tree selected for felling showed that doubling of harvest intensity increased the ground area disturbed by only 40%, but the higher felling intensity was associated with greater amount of canopy opening (mean loss of 21%) than the low intensity (mean loss of 9%).
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Boarman, McKaila J. S. "Trade-offs and Temporal Variation in Predator-Mediated Natural Selection and Sexual Selection on the Wings of the Damselfly Calopteryx splendens." Ohio University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1491746850419119.
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Glinka, Sascha. "Population Genetic Approaches to Detect Natural Selection in Drosophila melanogaster." Diss., lmu, 2005. http://nbn-resolving.de/urn:nbn:de:bvb:19-37102.
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Bolstad, Geir Hysing. "Evolution of Signals: Genetic Architecture, Natural Selection and Adaptive Accuracy." Doctoral thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for biologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-12514.
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Riihimäki, M. A. (Mona-Anitta). "Flowering time and natural selection in Arabidopsis lyrata." Doctoral thesis, University of Oulu, 2005. http://urn.fi/urn:isbn:9514277945.
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Abstract
Arabidopsis lyrata is a close outcrossing relative of Arabidopsis thaliana, the model organism of plant physiology and molecular biology. I studied variation in flowering time and the factors shaping the variation within and between A. lyrata populations in different environments. The role of the two important proximate factors determining flowering time, day length and temperature, were studied in climate chambers. The southern A. lyrata populations were found to flower in high frequency and quicker than northern A. lyrata populations in all studied environments, but the reaction of northern populations on long day length was found to be stronger than that of southern populations. Differences in vernalization requirement between A. lyrata populations were found in outdoor common garden, but in the climate chambers the results of vernalization experiments were not consistent. Strength and direction of selection on flowering time and other life history traits were studied in alpine and lowland A. lyrata populations in Scandinavia. Differences in selection were found both between populations and between years. Grazing sheep caused high levels of damage in inflorescences in the alpine population. In the lowland population there was less herbivory, caused by insects and hares. The difference in selection on flowering traits in the two study populations might be partly caused by selective grazing. Completely outcrossing mating system in A. lyrata is due to well developed self-incompatibility system. However, biparental inbreeding is likely to exist in natural populations and it may lead to spatial structuring of genetic variation within populations. I studied the effects of biparental inbreeding on components of fitness in A. lyrata in three different environments. I found inbreeding depression after sib-mating to be substantial. Stressful environment reduced the overall performance of the plants, but had no effect on the magnitude of inbreeding depression. A literature survey indicates that the observed levels of inbreeding depression in self-incompatible A. lyrata were higher than those of self-compatible species. This suggests that self-compatible species have purged some of their genetic load. The genetic basis of flowering time variation in A. lyrata can be further studied by using A. thaliana molecular tools.
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Merl, Daniel M. "Detecting patterns of natural selection using bayesian generalized linear models /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2006. http://uclibs.org/PID/11984.
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Tamuri, A. U. "Using phylogenetic models to characterise natural selection from molecular data." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1378602/.
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Molecular phylogenetics is the application of mathematical and computational techniques to analyse molecular sequences and make inferences about their evolutionary relationships. There is substantial interest in developing probabilistic models of evolution that effectively detect, locate and characterise different type of selection in genes, driven by the relationship of selection to protein structural constraints and function. In this thesis we propose novel approaches that can be used not only to detect the presence of selection but also to characterise its kind and strength. We first develop a phylogenetic method to identify changes in selective constraints and use it to identify those mutations that allow influenza viruses from avian origin to spread successfully in the human population. The model explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We then use these results to develop a measure of the level of adaptation of any given influenza virus sequence to the selective constraints imposed by avian or human hosts. We show that adaptation to the human host has been gradual when applied to historical data. Our results also indicate that the 1918 influenza virus had undergone a period of pre-adaptation prior to 1918 when compared to the adaptation of other avian influenza viruses. Finally, we develop a codon-based model of mutation-selection to estimate the distribution of selection coefficients and find that we can recover distributions similar to those expected by population genetics theory. We show that the distribution of mammalian mitochondrial proteins is bimodal with the majority of mutations being deleterious. When we apply the model to the PB2 influenza polymerase protein following a host shift from birds to humans, we find a trimodal distribution with a significant proportion of advantageous substitutions.
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Teitz, Levi S. (Levi Shmuel). "The effects of natural selection on human Y chromosome amplicons." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/117785.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged student-submitted from PDF version of thesis.
Includes bibliographical references.
The Y chromosome is unique among the mammalian chromosomes: it determines sex, and is therefore normally present in a single copy, unlike all other chromosomes that can recombine with an identical homolog. These two facts have had profound effects on the fate of the Y chromosome, subjecting it to unique evolutionary pressures that caused the loss of most of its genes. Because of this lack of functional genes, speculation abounded that natural selection is ineffective on a chromosome that lacks a homolog with which to recombine, and that the Y chromosome is doomed to eventually fade away. In recent years, evidence has been building that the Y chromosome is indeed shaped by evolutionary forces acting to maintain its functional genes. However, these studies bypassed the amplicons-large, highly identical segmental duplications-which are a prominent feature of mammalian Y chromosomes and contain many genes crucial for spermatogenesis. In this thesis, we present evidence that natural selection acts on the ampliconic regions of the human Y chromosome. We first develop computational tools to detect amplicon copy number changes from whole genome sequencing data of 1216 men, and find that many men have such changes. By projecting those changes onto a phylogenetic tree of the analyzed Y chromosomes, we find that the reference copy number of each amplicon is ancestral to all modern human Y chromosomes. We then use simulations and novel analytical methods to demonstrate that the ancestral copy number of each amplicon is maintained by selection within diverse human lineages, even in the face of extremely high rates of mutation. Finally, we find that deleted amplicons are preferentially restored to their previous copy number by subsequent duplications. These results are another step forward in the ongoing reframing the history of the mammalian Y chromosome: the Y chromosome is not the victim of random neutral processes, but is the carefully calibrated result of complex interplay between various selective forces.
by Levi S. Teitz.
Ph. D.
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Raj, Towfique. "Molecular signatures of natural and artificial selection in mammalian genomes." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609021.
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Yanos, Susan B. "A rhetorical analysis of the current challenges to the evolutionary paradigm." Virtual Press, 1990. http://liblink.bsu.edu/uhtbin/catkey/720347.
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This study explores the establishment of the paradigm of evolution by means of natural selection, asserting that Darwin's theories were not scientifically revolutionary because he established rather than overthrew the existing paradigm in biology. Actually Darwin made three more important contributions than the theory of natural selection. He delivered a blow to essentialism, changing the universe from a product into a process. He established the hypothetico-deductive model of the physical sciences for natural history. And he demonstrated that teleological problems could be studied by scientists. The recent controversies in biology are continuations of the old debate over whether evolution is orderly or irregular, controlled by external or internal forces, continuous or discontinuous. The controversies can be separated into four separate challenges to neo-Darwinism: empirical, epistemological, methodological, and teleological. The study concludes that the empirical and teleological challenges do not pose serious threats to the existing paradigm, but unless the epistemological and methodological challenges can be met satisfactorily, the paradigm may be overthrown.This study also explores the differences between the rhetorical and scientific methods of inquiry. Modern science is considered as predominantly empirical, progressing because of the scientists' system of shared, rational values. Actually both metaphysician and physician ponder the same questions, embrace truth with the same assumptions, and operate with the same epistemology. Science is puzzle solving. Rhetoric deals with ill-defined problems, while science turns ill-defined problems into well-defined ones. The danger in separating the scientific and rhetorical methods is that Western man is split into two irreconcilable points of view: the moral and the scientific. The dichotomy arose because of the two fountainheads of Western culture. Plato "solved" the dichotomy by proposing two worlds of Becoming and Ideas. Darwin's solution depends on a different metaphysical pathos which is only now being realized, due to the rethinking of the paradigm as a result of the challenges. Rather than giving us two worlds, Darwin separated the forces of one, completely naturalistic world into a two-step process: chance and necessity. The problem is that many thinkers focus on only one of the processes, sometimes to the exclusion of the other.Department of English
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Marshall, Rupert Charles. "Song, paternity and genetic diversity in the sedge warbler, Acrocephalus schoenobaenus." Thesis, Royal Holloway, University of London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246800.
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Grieshop, Karl. "Sexual conflict, sexual selection, and genetic variance in fitness." Doctoral thesis, Uppsala universitet, Zooekologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-327304.
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Understanding sex-specific genetic variance for fitness is of fundamental importance to our understanding of evolution. This thesis presents the findings of empirical investigations into sex-specific genetic variance in fitness. The findings are discussed in terms of their implications for our understanding of the classic evolutionary paradoxes of what maintains genetic variance in fitness and what maintains sexual reproduction, as well as more specific implications regarding adaptation and population viability. Males and females reproduce and accrue fitness in fundamentally different ways, which inevitably comes at a detriment to the fitness of individuals of the opposite sex. This is known as sexual conflict, and because males and females use largely the same genome to develop, grow and reproduce, a genetic tug-of-war ensues. Alternative alleles at sexually antagonistic (SA) genes have opposing fitness effects in males and females. The consequence of this genetic tug-of-war is that alternative allelic variants at SA loci can be maintained in the population. Such SA genetic variation can therefore maintain genetic variance for fitness. Variance in fitness can also be maintained by a constant influx of mutations with weakly deleterious effects and weak selection against them, in what is referred to as mutation-selection balance. Because the average deleterious mutation will be detrimental to both sexes, this source of genetic variance in fitness will have predominantly sexually concordant (SC) effects. This thesis uses a wild-caught population of the seed beetle Callosobruchus maculatus to investigate these two mechanisms of maintaining genetic variance in fitness, as well as the consequences they bear on adaptation, population viability, and the maintenance of sexual reproduction. Results largely support much of the theoretical expectations for sexual conflict, sexual selection and maintenance of genetic variance in fitness, as well as stimulate new thoughts and hypotheses about the nature of SA genetic variation and its interaction with weakly deleterious partially recessive mutations.Vår kunskap om könsspecifik selektion och genetisk variation för fitness är central för förståelsen av evolutionära processer. I den här avhandligen presenteras resultaten av empiriska undersökningar av just könsspecifik genetisk variation för fitness. Resultaten diskuteras med fokus på deras betydelse för de klassiska evolutionära paradoxerna angående vad som bibehåller genetisk variation i fitness och varför organismer som förökar sig sexuellt är så vanliga, men även mer specifika konsekvenser för en populations anpassningsförmåga och livskraftighet avhandlas. Evolutionen har ofta gynnat olika reproduktiva strategier hos hannar och honor, och dessa strategier kan medföra kostnader för det motsatta könet. Den könskonflikt som uppstår på grund av detta kan också inbegripa en genetisk dragkamp eftersom könen delar genetisk arvsmassa men gynnas av olika anpassningar. Konsekvensen är att alternativa varianter av gener gynnas hos honor och hanar, vilket resulterar i en form av balanserande selektion som kan bibehålla genetisk variation i en population. Genetisk variation i fitness kan även upprätthållas genom en jämvikt mellan ett konstant inflöde av genetisk variation via mutationer med svagt negativ effekt och svag selektion mot dessa mutationer. Eftersom en negativ mutation normalt kommer vara skadlig för båda könen kommer den här typen av källa till genetisk variation i fitness ha liknande effekt hos könen. I arbetet med denna avhandlig har jag använt en vilt infångad population av fröbaggaen Callosobruchus maculatus för att undersöka dessa två underliggande mekanismer bakom upprätthållandet av genetisk variation för fitness, samt vilka potentiella konsekvenser de kan ha för en populations anpassningsförmåga och för bibehållandet av sexuell reproduktion. Resultaten i denna avhandling stödjer i stort många av de antaganden som ligger till grund för teorin om könskonflikter, sexuell selektion och vad som upprätthåller genetisk variation för fitness. Resultaten ger också upphov till nya idéer och hypoteser angående genetisk variation med könsspecifika effekter och dess interaktion med partiellt recessiva negativa mutationer.
The alternative abstract I uploaded should be used as the Swedish summary.
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Bubb, Kerry Leigh. "The role of balancing selection in maintenance of natural genetic variation /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/10258.
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Baines, John. "Empirical approaches to detecting the action of natural selection in Drosophila." Diss., lmu, 2004. http://nbn-resolving.de/urn:nbn:de:bvb:19-27548.
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Larsson, Sonny. "Mistletoes and Thionins : as Selection Models in Natural Products Drug Discovery." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7705.
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Lind, Emma. "Genetic response to pollution in sticklebacks; natural selection in the wild." Doctoral thesis, Stockholms universitet, Zoologiska institutionen, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-89486.
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The last century, humans have been altering almost all natural environments at an accelerating rate, including the Baltic Sea that has highly eutrophicated areas and many coastal industries such as Pulp-mills. For animals living in a habitat that changes there are basically two alternatives, either to cope with the change or become locally extinct. This thesis aims to investigate if recent anthropogenic disturbance in the Baltic Sea can affect natural populations on a genetic level through natural selection. First, we found a fine-scale genetic structure in three-spine sticklebacks (Gasterosteus aculeatus) populations along the Swedish coast (paper I), indicating limited gene-flow between populations in geographic proximity. Different genetic markers, specifically Amplified Fragment Lenght Polymorpism (AFLP, and microsatellites, gave different results, highlighting the heterogeneous character of genomes which demonstrates that it is important to choose a genetic marker that is relevant for the question at hand. With a population genomic approach, and a multilocus genetic marker (AFLP), we detected convergent evolution in genotype composition in stickleback populations living in environments affected by pulp-mill effluent (paper II) and in highly eutrophicated environments (paper III), compared to adjacent reference populations. We found loci, in both studies (paper II, III), that were different from a neutral distribution and thus probably under divergent selection for the habitat differences investigated. The selective effect from pulp-mill effluents were more pronounced, but the two different habitats had mutual characters (AFLP loci). In paper IV, we converted five anonymous AFLP loci to sequenced markers and aligned them to the stickleback genome. Four out of five loci aligned within, or close to, coding regions on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the loci, located on chromosome VIII and identified as under divergent selection in both paper II and III, has been identified in other studies as to be under selection for fresh water adaptation, including Baltic Sea stickleback populations. In conclusion, anthropogenic alterations of natural environments can have evolutionary consequences, probably adaptive, for the animals living there and the evolutionary response exhibited by natural populations can be very fast.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.
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Ulf-Hansen, Peter Fleming. "The dynamics of natural selection for herbicide resistance in grass weeds." Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240807.
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Smith, Chelsea Elizabeth. "The Roles of Natural Selection, History and Chance in Escherichia coli." University of Akron / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=akron1478272123989472.
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Ragsdale, Aaron, and Aaron Ragsdale. "Multi-Allele Population Genomics for Inference of Demography and Natural Selection." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/622993.
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The demographic and evolutionary history of a population leaves an identifiable signature on patterns of genetic variation, so we can learn about demography and natural selection through inference on contemporary polymorphism data. The distribution of sample allele frequencies, known as the allele frequency spectrum (AFS), is an informative statistic that has been used to infer single- and multi-population demographic histories and distributions of fitness effects of new mutations. AFS-based methods typically rely on the infinite sites model, in which loci are assumed to evolve independently and mutations always arise at a previously unmutated site. However, many loci are seen to violate these assumptions. Most obviously, loci occupy a physical space on the genome, and neighboring mutations will have correlated allele frequencies. Additionally some SNPs are found to be multi-allelic, with more than two alleles simultaneously segregating. The assumptions of the infinite sites model forces one to ignore or exclude such loci, but these loci are rich in information not captured by standard AFS approaches. With this in mind, I developed a numerical approach for solving a class of multi-allelic diffusion equations that allow for novel inferences on genomic sequence data. First, I considered selection at triallelic nonsynonymous data to infer the correlation of fitness effects for same-site mutations. I then explored the increase in power afforded to demographic inferences by two-locus allele frequency statistics, in which two biallelic loci are separated by a known recombination distance so the joint distribution of allele frequencies and linkage disequilibrium may be modeled by a diffusion approximation. Finally, I considered the same two-locus diffusion model but with selection placed on one of the two loci. This allows for the direct modeling of the effects of linked selection on neutral variants, and for potential inference applications such as the parameters of a selective sweep or the distribution of fitness effects.
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He, Zhangyi. "Natural selection on two linked loci : Wright-Fisher perspectives and applications." Thesis, University of Bristol, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.702447.
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In the age of next-generation sequencing, an increasing amount of high-quality genomic time-series data is becoming available. This has created new opportunities to provide a more precise inference of population genetic parameters and more accurate hypotheses-testing about the recent action of natural selection. However, most existing population genetic inference procedures are only applicable to one-locus problems or multi-locus problems assuming no linkage between different loci due to the difficulty of computing the likelihood of the time-series data of allele frequencies sampled from multiple linked loci. To address this, we propose a hidden Markov model to characterise the time-series data of allele frequencies and develop an efficient simulated based method to evaluate the likelihood. In the hidden Markov model, the underlying population is assumed to evolve under natural selection at two linked loci according to the Wright-Fisher diffusion, and the observations are implicitly modelled through independent multinomial sampling from the underlying population at each given time point. We evaluate the transition probability density of the Wright-Fisher diffusion and the likelihood of the time-series data of allele frequencies sampled from two linked loci through importance sampling. Our simulation-based method enables us to jointly estimate the selection coefficient, recombination rate, and other population genetic quantities of interest from the two-locus time-series data of allele frequencies and can be naturally extended to analyse the multi-locus time-series data of allele frequencies.
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Anderson, Dianne L. "Natural selection theory in non-majors' Biology : instruction, assessment, and conceptual difficulty /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 2003. http://wwwlib.umi.com/cr/ucsd/fullcit?p3112820.
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Halvarsson, Peter. "Host-Parasite Interactions in Natural Populations." Doctoral thesis, Uppsala, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-300023.
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Parasitism is one of the most common ways of living and it has arised in many taxa. Parasites feed and live inside or on their hosts resulting in both long and short term consequences for the host. This thesis is exploring the phenotypic and genotypic effects of animals living with parasitic infections. I have been studying three different parasite groups and their associated host species: the great snipe, a lekking freshwater wader bird that migrates between Africa and Northern Europe; the tree sparrow, a stationary passerine found close to human settlements and lastly the water vole, a large rodent living in riparian habitats. Avian malaria is one of the most commonly studied parasites affecting birds. Atoxoplasma, an intestinal protozoan parasite is less studied but is thought to be endemic in free-ranging birds. Given the freshwater habitat great snipes inhabit, a prevalence of 30% avian malaria infections is not high and that the prevalence fluctuated among years. Sequencing of the avian malaria cytochrome b gene revealed that parasites are similar to avian malaria parasites found in African birds suggesting that they were infected on the wintering grounds in Africa. Tree sparrows had few malaria infected individuals, a result that is consistent with other studies of stationary birds at high latitudes. Atoxoplasma infections were common in tree sparrows and capture-recapture analyses show decreased survival in infected compared to uninfected birds and signs of lower mating success among infected. Genetic analyses comparing the transcriptome between mated and unmated great snipe males revealed that the genotype is important for mating success and health status for some of the expressed genes. That variations in some of these genes are involved in maintaining a good health status and mating success supports handicap models for sexual selection in this lek mating system. The major histocompatibility complex (MHC) is a part of the immune system and it contains genes involved in immune response. In water voles, a number of new MHC alleles were identified. Based on their in silico phenotype they were grouped into supertypes to facilitate studies on how helminth infections affect the MHC diversity in the water voles. Some of these MHC supertypes provided resistance to one helminth species, but the same supertype caused the opposite effect for other helminth parasites. Overall, parasites are a driving force for maintaining genetic diversity and parasite infections lowers survival rate, which would lead to a lower lifetime breeding success.
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Battisti, Bryce T. "Prevalence of Teleological and Lamarckian Misconceptions of Natural Selection Among College Students." BYU ScholarsArchive, 2004. https://scholarsarchive.byu.edu/etd/3151.
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Science teachers and researchers note that students must correctly understand the role of natural selection in evolution to make sense of biology. The level of understanding of natural selection can be assessed using the Conceptual Inventory of Natural Selection (CINS) which is a 20-item multiple-choice test that incorporates student misconceptions as distractors. In the present study, Item Response Theory (IRT) was used to analyze the occurance of misconceptions on the CINS among 1192 students in an introductory non-majors biology course. The four most difficult topics in the CINS are: (a) how change occurs in a population; (b) origin of variation; (c) heritability of variation; and (d) the origin of species. Students with an average level of understanding of natural selection favored Teleological explanations for why organisms adapt to their environment, namely that organisms change because they need or want to change. These same students favored the Lamarckian explanation for how organisms adapt, namely by passing on acquired traits to offspring. Presence of such misconceptions in students with an average understanding of natural selection highlights the need for biology teachers to make an added effort to create dissatisfaction with teleological and Lamarckian explanations in the minds of their students.
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Sironi, M. "POPULATION GENETIC APPROACHES FOR THE STUDY OF COMPLEX TRAITS: FOCUS ON INFECTIOUS AND AUTOIMMUNE DISEASES." Doctoral thesis, Università degli Studi di Milano, 2010. http://hdl.handle.net/2434/150065.
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It is commonly believed that infectious diseases have represented one of the major threats to human populations and have therefore acted as a powerful selective force. Therefore, several human genes have evolved in response to infectious agents. Indeed, it has been suggested that human populations may have adapted to pathogens to such a degree that the lower exposure to infectious agents in modern developed societies results in immune imbalances, with autoimmune and allergic conditions being the outcome (hygiene hypothesis). Quite obviously, the presence of a functional variant is a prerequisite for selection to act, and the identification of non-neutrally evolving genes has been regarded as a strategy complementary to classical clinical and epidemiological studies to provide insight into the mechanisms of host defense. Similarly, analysis of the evolutionary history of genes involved in immune defense might provide novel insights into the delicate balance between efficient response to pathogens and autoimmune/allergic manifestations. In this work population genetics approaches are applied to study the evolutionary patterns of specific groups of genes such as those encoding blood group antigens and interleukins/interleukin receptors. Several of these latter genes have evolved in response to parasitic worms, but a subset of disease alleles for inflammatory bowel disease and celiac disease have increased in frequency in response to non-helminthic pathogens (i.e. viruses and bacteria). At the genome-wide level, the identification of selective signatures was exploited to identify novel susceptibility variants for virus-, protozan-, and helminth-borne infections. These analyses allowed the identification of several variants that may modulate infection susceptibility and we noticed a partial overlap between genes involved in the response to helminths and those carrying susceptibility alleles for asthma/atopy; similarly, a number of genes subjected to virus-driven selective pressure have been involved in the pathogenesis of multiple sclerosis and type 1 diabetes. One of these, namely IFIH1, was studied in detail: we revealed a complex selective pattern in human populations distributed in different geographic locations. Nonetheless, the analysis of IFIH1 variants involved in the susceptibility to type 1 diabetes indicated that they have evolved neutrally. Finally, we show that the identification of gene regions subjected to natural selection can provide information on the location of functional variants and these, in turn, may be regarded as strong candidates to prioritize on in case/control association studies. In the case of ERAP2 we carried out one such study and verified that a nonsynonymous variant subjected to natural selection affects the natural resistance to HIV-1 infection. In summary we show that selective events leave a signature on human genes that can be detected using population genetics approaches and exploited for the identification of variants that influence complex phenotypic traits such as susceptibility to infections. These studies can also shed light on the relationship between past selective events and predisposition to common diseases in modern populations.
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Bohlin, Gustav. "Evolving germs – Antibiotic resistance and natural selection in education and public communication." Doctoral thesis, Linköpings universitet, Medie- och Informationsteknik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-138657.
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Bacterial resistance to antibiotics threatens modern healthcare on a global scale. Several actors in society, including the general public, must become more involved if this development is to be countered. The conveyance of relevant information provided through education and media reports is therefore of high concern. Antibiotic resistance evolves through the mechanisms of natural selection; in this way, a sound understanding of these mechanisms underlies explanations of causes and the development of effective risk-reduction measures. In addition to natural selection functioning as an explanatory framework to antibiotic resistance, bacterial resistance as a context seems to possess a number of qualities that make it suitable for teaching natural selection – a subject that has been proven notoriously hard to teach and learn. A recently suggested approach for learning natural selection involves so-called threshold concepts, which encompass abstract and integrative ideas. The threshold concepts associated with natural selection include, among others, the notions of randomness as well as vast spatial and temporal scales. Illustrating complex relationships between concepts on different levels of organization is one, of several, areas where visualizations are efficient. Given the often-imperceptible nature of threshold concepts as well as the fact that natural selection processes occur on different organizational levels, visual accounts of natural selection have many potential benefits for learning. Against this background, the present dissertation explores information conveyed to the public regarding antibiotic resistance and natural selection, as well as investigates how these topics are presented together, by scrutinizing media including news reports, websites, educational textbooks and online videos. The principal method employed in the media studies was content analysis, which was complemented with various other analytical procedures. Moreover, a classroom study was performed, in which novice pupils worked with a series of animations explaining the evolution of antibiotic resistance. Data from individual written assignments, group questions and video-recorded discussions were collected and analyzed to empirically explore the potential of antibiotic resistance as a context for learning about evolution through natural selection. Among the findings are that certain information, that is crucial for the public to know, about antibiotic resistance was conveyed to a low extent through wide-reaching news reporting. Moreover, explanations based on natural selection were rarely included in accounts of antibiotic resistance in any of the examined media. Thus, it is highly likely that a large proportion of the population is never exposed to explanations for resistance development during education or through newspapers. Furthermore, the few examples that were encountered in newspapers or textbooks were hardly ever visualized, but presented only in textual form. With regard to videos purporting to explain natural selection, it was found that a majority lacked accounts of central key concepts. Additionally, explanations of how variation originates on the DNA-level were especially scarce. These and other findings coming from the content analyses are discussed through the lens of scientific literacy and could be used to inform and strengthen teaching and scientific curricula with regards to both antibiotic resistance and evolution. Furthermore, several factors of interest for using antibiotic resistance in the teaching of evolution were identified from the classroom study. These involve, among others, how learners’ perception of threshold concepts such as randomness and levels of organization in space and time are affected by the bacterial context