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Bancroft, David. "Genetic variation and fitness in Soay sheep." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338112.
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Hietpas, Ryan T. "Experimental Illumination of Comprehensive Fitness Landscapes: A Dissertation." eScholarship@UMMS, 2006. http://escholarship.umassmed.edu/gsbs_diss/667.
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Evolution is the single cohesive logical framework in which all biological processes may exist simultaneously. Incremental changes in phenotype over imperceptibly large timescales have given rise to the enormous diversity of life we witness on earth both presently and through the natural record. The basic unit of evolution is mutation, and by perturbing biological processes, mutations may alter the fitness of an individual. However, the fitness effect of a mutation is difficult to infer from historical record, and complex to obtain experimentally in an efficient and accurate manner.
We have recently developed a high throughput method to iteratively mutagenize regions of essential genes in yeast and subsequently analyze individual mutant fitness termed Exceedingly Methodical and Parallel Investigation of Randomized Individual Codons (EMPIRIC). Utilizing this technique as exemplified in Chapters II and III, it is possible to determine the fitness effects of all possible point mutations in parallel through growth competition followed by a high throughput sequencing readout. We have employed this technique to determine the distribution of fitness effects in a nine amino acid region of the Hsp90 gene of S. cerevisiae under elevated temperature, and found the bimodal distribution of fitness effects to be remarkably consistent with near-neutral theory. Comparing the measured fitness effects of mutants to the natural record, phylogenetic alignments appear to be a poor predictor of experimental fitness.
In Chapter IV, to further interrogate the properties of this region, library competition under conditions of elevated temperature and salinity were performed to study the potential of protein adaptation. Strikingly, whereas both optimal and elevated temperatures produced no statistically significant beneficial mutations, under conditions of elevated salinity, adaptive mutations appear with fitness advantages up to 8% greater than wild type. Of particular interest, mutations conferring fitness benefits under conditions of elevated salinity almost always experience a fitness defect in other experimental conditions, indicating these mutations are environmentally specialized. Applying the experimental fitness measurements to long standing theoretical predictions of adaptation, our results are remarkably consistent with Fisher’s Geometric Model of protein evolution.
Epistasis between mutations can have profound effects on evolutionary trajectories. Although the importance of epistasis has been realized since the early 1900s, the interdependence of mutations is difficult to study in vivo due to the stochastic and constant nature of background mutations. In Chapter V, utilizing the EMPIRIC methodology allows us to study the distribution of fitness effects in the context of mutant genetic backgrounds with minimal influence from unintended background mutations. By analyzing intragenic epistatic interactions, we uncovered a complex interplay between solvent shielded structural residues and solvent exposed hydrophobic surface in the amino acid 582-590 region of Hsp90. Additionally, negative epistasis appears to be negatively correlated with mutational promiscuity while additive interactions are positively correlated, indicating potential avenues for proteins to navigate fitness ‘valleys’.
In summary, the work presented in this dissertation is focused on applying experimental context to the theory-rich field of evolutionary biology. The development and implementation of a novel methodology for the rapid and accurate assessment of organismal fitness has allowed us to address some of the most basic processes of evolution including adaptation and protein expression level. Through the work presented here and by investigators across the world, the application of experimental data to evolutionary theory has the potential to improve drug design and human health in general, as well as allow for predictive medicine in the coming era of personalized medicine.
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Hietpas, Ryan T. "Experimental Illumination of Comprehensive Fitness Landscapes: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/667.
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Evolution is the single cohesive logical framework in which all biological processes may exist simultaneously. Incremental changes in phenotype over imperceptibly large timescales have given rise to the enormous diversity of life we witness on earth both presently and through the natural record. The basic unit of evolution is mutation, and by perturbing biological processes, mutations may alter the fitness of an individual. However, the fitness effect of a mutation is difficult to infer from historical record, and complex to obtain experimentally in an efficient and accurate manner.
We have recently developed a high throughput method to iteratively mutagenize regions of essential genes in yeast and subsequently analyze individual mutant fitness termed Exceedingly Methodical and Parallel Investigation of Randomized Individual Codons (EMPIRIC). Utilizing this technique as exemplified in Chapters II and III, it is possible to determine the fitness effects of all possible point mutations in parallel through growth competition followed by a high throughput sequencing readout. We have employed this technique to determine the distribution of fitness effects in a nine amino acid region of the Hsp90 gene of S. cerevisiae under elevated temperature, and found the bimodal distribution of fitness effects to be remarkably consistent with near-neutral theory. Comparing the measured fitness effects of mutants to the natural record, phylogenetic alignments appear to be a poor predictor of experimental fitness.
In Chapter IV, to further interrogate the properties of this region, library competition under conditions of elevated temperature and salinity were performed to study the potential of protein adaptation. Strikingly, whereas both optimal and elevated temperatures produced no statistically significant beneficial mutations, under conditions of elevated salinity, adaptive mutations appear with fitness advantages up to 8% greater than wild type. Of particular interest, mutations conferring fitness benefits under conditions of elevated salinity almost always experience a fitness defect in other experimental conditions, indicating these mutations are environmentally specialized. Applying the experimental fitness measurements to long standing theoretical predictions of adaptation, our results are remarkably consistent with Fisher’s Geometric Model of protein evolution.
Epistasis between mutations can have profound effects on evolutionary trajectories. Although the importance of epistasis has been realized since the early 1900s, the interdependence of mutations is difficult to study in vivo due to the stochastic and constant nature of background mutations. In Chapter V, utilizing the EMPIRIC methodology allows us to study the distribution of fitness effects in the context of mutant genetic backgrounds with minimal influence from unintended background mutations. By analyzing intragenic epistatic interactions, we uncovered a complex interplay between solvent shielded structural residues and solvent exposed hydrophobic surface in the amino acid 582-590 region of Hsp90. Additionally, negative epistasis appears to be negatively correlated with mutational promiscuity while additive interactions are positively correlated, indicating potential avenues for proteins to navigate fitness ‘valleys’.
In summary, the work presented in this dissertation is focused on applying experimental context to the theory-rich field of evolutionary biology. The development and implementation of a novel methodology for the rapid and accurate assessment of organismal fitness has allowed us to address some of the most basic processes of evolution including adaptation and protein expression level. Through the work presented here and by investigators across the world, the application of experimental data to evolutionary theory has the potential to improve drug design and human health in general, as well as allow for predictive medicine in the coming era of personalized medicine.
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Ricketts, Huw John. "Molecular genetic biomarkers of reproductive fitness in earthworms." Thesis, Cardiff University, 2004. http://orca.cf.ac.uk/55966/.
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When ecotoxicologists assess the environmental impact of pollution they must pose a fundamental question. That is, is the toxicological data produced from any experiment ecologically relevant It has long been thought that a measure of survival of any organism is not sufficient to predict potential population effects. A more sensitive method is the measurement of sub-lethal endpoints, such as growth and reproduction. However, measurement of these parameters may not give an 'early warning' of the impact of complex pollutants within any ecosystem. Therefore, so-called biomarkers have been developed to fill this void. Biomarkers can be used at a number of organisational levels e.g. cellular, protein or DNA, but they all have the sensitivity to act as predictive tools in ecotoxicology and risk assessment. In the past twenty years earthworms have become model organisms in terrestrial ecotoxicology. This is mainly due to the critical role they play within the soil ecosystem in most parts of the world. Therefore the present study utilises three earthworm species (Eisenia fetida, Eisenia andrei and Lumbricus rubellus) to identify, characterise and validate molecular genetic biomarkers of reproduction. To isolate potential reproductive genes a subtractive library was created from the anterior and posterior segments of Lumbricus rubellus. A number of potential biomarker candidate genes were identified, but a putative sperm-specific antigen warranted special attention. The gene fragment of this putative sperm antigen was identified in all three earthworm species used in the study and its potential as a biomarker is discussed. Annetocin has previously been characterised as a member of the mammalian vasopressin/oxytocin superfamily of neuropeptides and has been shown to induce egg-laying behaviours in Eisenia fetida. The annetocin gene was isolated from the three earthworm species and shown to be expressed in the reproductive segments of Eisenia fetida. The expression levels of the annetocin gene were determined in earthworms exposed to metalliferous soils both in laboratory and semi-field exposures using quantitative PCR. A decrease in annetocin gene expression levels correlated with a similar decrease in cocoon production rates of Eisenia fetida after metal exposure. Upon exposure to the mammalian steroid hormones, 17/3-oestradiol and testosterone along with the synthetic oestrogen 17a-ethynylestradiol, annetocin gene expression levels in Eisenia andrei were elevated in some cases, suggesting a role for oestrogens in earthworm reproduction. Eisenia andrei were also exposed to bisphenol A and nonylphenol in artificial soils and annetocin gene expression was determined. Although toxic to Eisenia andrei these two (weakly oestrogenic) compounds did not affect annetocin gene expression. These data strongly suggest that annetocin plays a critical role in earthworm reproduction and that oestrogens may modulate the expression of this gene. The annetocin genomic structure was determined and three oestrogen-responsive elements were identified within the promoter of the gene in Eisenia fetida. What is more, the genomic structure of annetocin conformed to the three exon, two intron model of vasopressin/oxytocin superfamily neuropeptides.
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May, Shoshanna. "Fitness and genetic diversity in Bufo calamita populations." Thesis, University of Sussex, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.505908.
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The aims of this DPhil were the characterisation of major histocompatibility complex class II β loci in the amphibian species Bufo calamita, determination of fitness of four Bufo calamita populations and measurement of genetic diversity at both microsatellite loci and MHC class II β loci. The genetic diversity at microsatellite loci is considered to be neutral to selection and the genetic diversity seen at MHC loci is adaptive. Fitness in the four populations was measured using the known larval fitness traits age at metamorphosis, growth rates and survival. A 114 base pair section of MHC class II loci was characterised in this study. It was shown here that the diversity at neutral microsatellite markers was negatively correlated with adaptive MHC class II variation. No correlation was found between microsatellite HE and the larval fitness traits growth rate, survival and age at metamorphosis. However, MHC class II diversity was found to be associated with survival, and individuals that were heterozygous at both MHC loci had a significantly higher chance of survival than individuals homozygous at one or both of the two loci. A separate part of this DPhil project was the population genetics of six Irish Bufo calamita populations. The genetic structure was investigated using nine polymorphic microsatellite markers. It was found that all populations had similar and moderate levels of genetic diversity, comparable with those on the coast of north-west England. Toad populations were substantially differentiated, implying little migration between sites within historical times. Phylogenetics and estimates of divergence times supported the hypothesis that populations on the north coast of Dingle separated from those around Castlemaine Harbour many thousands of years ago, and are not recent introductions.
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Cooper, Jason. "Improving performance of genetic algorithms by using novel fitness functions." Thesis, Loughborough University, 2006. https://dspace.lboro.ac.uk/2134/2271.
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This thesis introduces Intelligent Fitness Functions and Partial Fitness Functions both of which can improve the performance of a genetic algorithm which is limited to a fixed run time. An Intelligent Fitness Function is defined as a fitness function with a memory. The memory is used to store information about individuals so that duplicate individuals do not need to have their fitness tested. Different types of memory (long and short term) and different storage strategies (fitness based, time base and frequency based) have been tested. The results show that an intelligent fitness function, with a time based long term memory improves the efficiency of a genetic algorithm the most. A Partial Fitness Function is defined as a fitness function that only partially tests the fitness of an individual at each generation. Thus only promising individuals get fully tested. Using a partial fitness function gives the genetic algorithm more evolutionary steps in the same length of time as a genetic algorithm using a normal fitness function. The results show that a genetic algorithm using a partial fitness function can achieve higher fitness levels than a genetic algorithm using a normal fitness function. Finally a genetic algorithm designed to solve a substitution cipher is compared to one equipped with an intelligent fitness function and another equipped with a partial fitness function. The genetic algorithm with the intelligent fitness function and the genetic algorithm with the partial fitness function both show a significant improvement over the genetic algorithm with a conventional fitness function.
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Haram, Per Magnus. "Genetic vs. Aquired fitness: Metabolic, Vascular and Cardiomyocyte Adaptations." Doctoral thesis, Norwegian University of Science and Technology, Department of Circulation and Medical Imaging, 2006. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-1921.
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Ali, Mohamed Medhat. "Studying the genetic determinants of Salmonella fitness in vivo." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397816634.
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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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Drahošová, Michaela. "Koevoluce prediktorů fitness v kartézském genetickém programování." Doctoral thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2017. http://www.nusl.cz/ntk/nusl-412587.
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Kartézské genetické programován (CGP) je evoluc inspirovaná metoda strojového učen, která je primárně určená pro automatizovaný návrh programů a čslicových obvodů. CGP je úspěšné v řešen mnoha úloh z reálného světa. Avšak k nalezen inovativnch řešen obvykle potřebuje značný výpočetn výkon. Každý kandidátn program navržený pomoc CGP mus být spuštěn, aby se zjistilo, do jaké mry tento program řeš zadaný problém, a mohla mu být přiřazena fitness hodnota. Právě vyhodnocen fitness bývá výpočetně nejnáročnějš část návrhu pomoc CGP. Tato práce se zabývá využitm koevoluce prediktorů fitness v CGP za účelem zrychlen procesu evolučnho návrhu prováděného pomoc CGP. Prediktor fitness je malá podmnožina trénovacch dat použvaná pro rychlý odhad fitness hodnoty namsto náročného vyhodnocen objektivn fitness hodnoty. Koevoluce prediktorů fitness je optimalizačn metoda modelován fitness, která snižuje náročnost a frekvenci výpočtu fitness. V této práci je koevolučn algoritmus přizpůsoben pro CGP a jsou představeny a zkoumány tři přstupy k zakódován prediktorů fitness. Představená metoda je experimentálně vyhodnocena v pěti úlohách symbolické regrese a v úloze návrhu obrazových filtrů. Výsledky experimentů ukazuj, že pomoc této metody lze významně snžit výpočetn čas, který CGP potřebuje pro řešen zkoumané třdy úloh.
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Mandal, Rabindra Kumar. "Genetic Determinants of Salmonella and Campylobacter Required for In Vitro Fitness." Thesis, University of Arkansas, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10249279.
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Non-typhoidal Salmonella (NTS) and Campylobacter play a major role in foodborne illness caused by the consumption of food contaminated by pathogens worldwide. A comprehensive understanding of the genetic factors that increase the survival fitness of these foodborne pathogens will effectively help us formulate mitigation strategies without affecting the nutrition ecology. The objective of this study was to identify the genetic determinants of Salmonella and Campylobacter that are required for fitness under various in vitro conditions. For the purpose, we used a high throughput Transposon sequencing (Tn-seq) that utilizes next generation sequencing (NGS) to screen hundreds of thousands of mutants simultaneously. In Chapter 1, we reviewed the technical aspects of different Tn-seq methods along with their pros and cons and compressive summary of recently published studies using Tn-seq methods. In Chapter 2, we exposed complex Tn5 library of Salmonella Typhimurium 14028S (S. Typhimurium) to the mimicked host stressors in vitro conditions. Such as low acidic pH (pH 3) found in the stomach, osmotic (3% NaCl) and short chain fatty acid (SCFAs, 100 mM Propionate) found in intestine, and oxidation (1mM H2O2) and starvation (12-day survival in PBS) found in macrophage. There was an overlapping set of 339 conditionally essential genes (CEGs) required by S. Typhimurium to overcome these host stressors. In Chapter 3, we screened of S. Typhimurium Tn5 library for desiccation survival. Salmonella spp. is the most notable and frequent cause of contamination in low-water activity foods. We identified 61 genes and 6 intergenic regions required for fitness during desiccation stress. In Chapter 4, the essential genome of Campylobacter jejuni (C. jejuni) NCTC 11168 and C. jejuni 81-176 was investigated using Tn-seq. We identified 166 essential protein-coding genes and 20 essential transfer RNA (tRNA) in C. jejuni NCTC 11168 which were intolerant to Tn5 insertions during in vitro growth. The reconstructed library C. jejuni 81-176 had 384 protein coding genes with zero Tn5 insertions. The genetic determinants Salmonella and Campylobacter identified in this study have high potential to be explored as food safety intervention, therapeutic and vaccine target to curb the spread of the foodborne pathogens making world a safer place.
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Wahlroos, Heli. "The correlated effects of genetic selection for growth on reproductive fitness." Thesis, University of Edinburgh, 2002. http://hdl.handle.net/1842/13164.
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This study addressed the question of effects of growth selection and inbreeding on reproductive fitness in the first parity of mice. A range of components was analysed in a unique set of inbred mouse lines derived from seven genetically high growth lines and four low growth lines, with the average weight at mating of high and low line females respectively 48g and 15g. The collection of ‘replicated’ growth lines allowed more general conclusions to be drawn about the effects that were investigated. A correlated response of growth selection was observed on litter size. Surprisingly the litter size of the growth lines did not greatly decrease over the period of full-sib matings, but some other traits such as the number of infertile matings were suspected to be showing inbreeding depression. Therefore, an experiment was designed to estimate the correlated effects of growth selection on components of reproductive fitness. The effects of inbreeding were removed at a foetus level by crossing inbred lines and at parental level by producing two-way crosses. Growth selection had a strong effect on the component of reproductive fitness, for example the ovulation rate was on average 17 ova in high and 9 ova in low lines. The regression of ovulation rate on body weight was consistent in different size of females and as not greatly affected by the inbreeding. However, the little size did not have such a strong connection with body weight due to positive regression between embryonic mortality and body weight. The heavier the females were, the lower was the survival rate from ovulated egg to foetus. Also lower pregnancy rates were observed among the heavy females, which would further reduce the expected litter size of heavy females.
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Trefilík, Jakub. "Koevoluce obrazových filtrů a prediktorů fitness." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2015. http://www.nusl.cz/ntk/nusl-234952.
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This thesis deals with employing coevolutionary principles to the image filter design. Evolutionary algorithms are very advisable method for image filter design. Using coevolution, we can add the processes, which can accelerate the convergence by interactions of candidate filters population with population of fitness predictors. Fitness predictor is a small subset of the training set and it is used to approximate the fitness of the candidate solutions. In this thesis, indirect encoding is used for predictors evolution. This encoding represents a mathematical expression, which selects training vectors for candidate filters fitness prediction. This approach was experimentally evaluated in the task of image filters for various intensity of random impulse and salt and pepper noise design and the design of the edge detectors. It was shown, that this approach leads to adapting the number of target objective vectors for a particular task, which leads to computational complexity reduction.
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Drahošová, Michaela. "Symbolická regrese a koevoluce." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2011. http://www.nusl.cz/ntk/nusl-236994.
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Symbolic regression is the problem of identifying the mathematic description of a hidden system from experimental data. Symbolic regression is closely related to general machine learning. This work deals with symbolic regression and its solution based on the principle of genetic programming and coevolution. Genetic programming is the evolution based machine learning method, which automaticaly generates whole programs in the given programming language. Coevolution of fitness predictors is the optimalization method of the fitness modelling that reduces the fitness evaluation cost and frequency, while maintainig evolutionary progress. This work deals with concept and implementation of the solution of symbolic regression using coevolution of fitness predictors, and its comparison to a solution without coevolution. Experiments were performed using cartesian genetic programming.
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Jašíčková, Karolína. "Klasifikace obrazů pomocí genetického programování." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2018. http://www.nusl.cz/ntk/nusl-385980.
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This thesis deals with image classification based on genetic programming and coevolution. Genetic programming algorithms make generating executable structures possible, which allows us to design solutions in form of programs. Using coevolution with the fitness prediction lowers the amount of time consumed by fitness evaluation and, therefore, also the execution time. The thesis describes a theoretical background of evolutionary algorithms and, in particular, cartesian genetic programming. We also describe coevolutionary algorithms properties and especially the proposed method for the image classifier evolution using coevolution of fitness predictors, where the objective is to find a good compromise between the classification accuracy, design time and classifier complexity. A part of the thesis is implementation of the proposed method, conducting the experiments and comparison of obtained results with other methods.
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Harbin, Susan Nalani Ching. "Measures of fitness and genetic variation in the endangered Hawaiian Genus Hesperomannia." Thesis, University of Hawaii at Manoa, 2003. http://hdl.handle.net/10125/7031.
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Chapman, Joanne. "Genetic variation, mate choice and fitness in the Wytham Great Tit population." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540088.
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Murray, Skyler James. "Algorithmically Flexible Style Composition Through Multi-Objective Fitness Functions." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3382.
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Creating a fitness function for music is largely subjective and dependent on a programmer's personal tastes or goals. Previous attempts to create musical fitness functions for use in genetic algorithms lack scope or are prejudiced to a certain genre of music. They also suffer the limitation of producing music only in the strict style determined by the programmer. We show in this paper that musical feature extractors that avoid the challenges of qualitative judgment enable creation of a multi-objective function for direct music production. Multi-objective fitness functions enable creation of music with varying identifiable styles. With this system we produced three distinct groups of music which computationally cluster into distinct styles as described by the set of feature extractors. We also show that knowledgeable individuals make similar clusters while a random sample of people make some similar and some different clusterings.
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Mohebbi, Sara. "Measuring the effect of inbreeding on reproductive success in population of friute flies (Raleigh LINES)." Thesis, Uppsala universitet, Zooekologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-173881.
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Borg, Randy Charles. "Phenotypic and genetic evaluation of fitness characteristics in sheep under a range environment." Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/27383.
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The objectives of this dissertation were to evaluate genetic and environmental relationships between lamb and ewe traits including body weight, fleece weight and quality, prolificacy, body condition, ewe stayability and lamb survival. Average heritability estimates for lamb birth weight (BWT), weaning weight (WW), maternal weaning weight, yearling body weight, fleece weight, spinning count and staple length were 0.19, 0.09, 0.08, 0.35, 0.38, 0.25, and 0.31 respectively. Heritability estimates for adult traits averaged 0.43 for body weight (AW), 0.13 for body condition (AC), and 0.12 for number of lambs born per ewe lambing (NLB). Correlations between direct additive AW and direct additive and maternal lamb weights ranged from 0.21 to 0.96 (P < 0.05) and 0.29 to 0.53 (P < 0.05), respectively, with residual correlations ranging from 0.05 to 0.95. Correlations of lamb traits with adult body condition and NLB were generally not different from zero; genetic and residual correlations ranged from -0.52 to 0.69 and -.39 to 0.31, respectively.
Ewe stayability was analyzed as overall stayability (STAYn|2) which indicated the presence or absence of a ewe at n yrs of age, given that she was present at 2 yrs of age, and marginal stayability (STAYn|1-n) recording the presences of a ewe at n yrs of age, given that she was in the flock the previous year. Additive variance in ewe stayability was only found in stayability at 5 and 6 yr of age (P < 0.05). Heritability estimates for STAY5|4 and STAY6|2 from multiple trait analyses with other traits averaged 0.08 and 0.10, respectively. Phenotypic correlations between STAY and all other traits were near zero, ranging from -0.04 to 0.03. The estimated correlations between additive effects on STAY5|4 and STAY6|2 and additive maternal effects on WW were positive (both 0.46; P < 0.05). Genetic correlations between STAY5|4 and WW, adult weight, and NLB were 0.06, 0.13 and -0.06 (P > 0.10), respectively. However, genetic correlations between STAY6|2 and WW, adult weight, and NLB were negative (-0.17, -0.32 (P < 0.05) and -0.03, respectively). Significant genetic variation was thus present in stayability, with nonzero genetic correlations present between STAY, maternal milk, WW, and adult weight.
Survival analysis was performed using a proportional hazards model to measure the probability of lamb death before weaning. Lamb survival was recorded as the day of age at death. Records were censored if a live lamb was artificially removed from their litter before death. Fixed effects on survival included ewe age, litter size, sex, and linear and quadratic BWT. Average age of death was 13.7 d. Censoring of records before weaning occurred in 12.9% of the total lambs born. Risk ratios indicated lambs from yearlings and ewes older than 5 yr had the greater risk of death, as did triplet and quadruplet lambs. Linear and quadratic BWT effects on lamb survival were found (P < 0.05) and accounted for most of the litter size effects in large litters. The influence of informative censoring was considered by assuming that lambs censored by 3 d of age had died at the time of censoring. Heritability of lamb survival at 3 d of age (estimated using an animal model in MTDFREML) was near zero, ranging from 0.00 to 0.01. The lack of additive variance suggests that improvement in lamb survival should be made through changes in management practices.Ph. D.
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Högström, Gabriel. "Cardiovascular disease and all-cause mortality : influence of fitness, fatness and genetic factors." Doctoral thesis, Umeå universitet, Geriatrik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-130312.
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Background Low aerobic fitness and obesity are associated with atherosclerosis, and thereforegreatly increase the risk of cardiovascular disease (CVD) and early death. It has long been known that atherosclerosis my begin early in life. Despite this fact, it remains unknown how obesity and aerobic fitness early in life influence the risks of atherosclerosis, CVD and death. Furthermore, it is unknown whether high aerobic fitness can compensate for the risks associated with obesity, and how genetic confounding affects the relationshipsof aerobic fitness with CVD and all-cause mortality. Thus, the main aims of this thesis were to investigate the associations of aerobic fitness in late adolescence with myocardial infarction (Study I), stroke (Study II) and all-cause mortality (Study III), and how genetic confounding influences the relationshipsof aerobic fitness with CVD, diabetes and death (Study IV). Methods The study population comprised up to1.3 million men who participated in mandatory Swedish military conscription. During conscription, all conscripts underwent highly standardized tests to assess aerobic fitness, body mass index, blood pressure and cognitive function. A physician also examined all conscripts. Data on subjects’ diagnoses, death and socioeconomic status during follow-up were retrieved using record linkage. Subjects were subsequently followed until the study endpoint, date of death or date of any outcome of interest. Associations between baseline variables and the risks of adverse outcomes were assessed using Cox’s proportional hazard models. Genetic confounding of the relationships between aerobic fitness and diabetes, CVD and death was assessed using a twin population and a paired logistic regression model. Results In Study I, low aerobic fitness at conscription was associated with an increased risk of myocardial infarction (MI) during follow-up (hazard ratio [HR] 0.82 per standard deviation increase). Similarly, in Study II, high aerobic fitness reduced the risk of stroke (HR 0.84 for ischemic stroke, HR 0.82 for hemorrhagic stroke; P < 0.001 for all), and obesity was associated with an increased risk of stroke (HR 1.15 for ischemic stroke, HR 1.18 for hemorrhagic stroke; P < 0.001 for all). In Study III, high aerobic fitness was also associated with reduced all-cause mortality later in life (HR 0.49, P < 0.001). High aerobic fitness exerted the strongest protection against death from substance and alcohol abuse, suicide and trauma (HRs 0.20, 0.41 and 0.52, respectively; P < 0.001 for all). Obese individuals with aerobic fitness were at higher risk of MI and all-cause mortality than were normal-weight individuals with low fitness (Studies I and III). In Study IV, fit twins had no reduced risk of CVD or death during follow-up compared with their unfit twin siblings (odds ratio 1.11, 95% confidence interval 0.88–1.40), regardless of how large the difference in fitness was. However, the fitter twins were protected against diabetes during follow-up. Conclusions Already early in life, aerobic fitness is a strong predictor of CVD and all-cause mortality later in life. In contrast to the “fat but fit” hypothesis, it seems that high aerobic fitness cannot fully compensate for the risks associated with obesity. The associationsof aerobic fitness with CVD and all-cause mortality appear to be mediated by genetic factors. Together, these findings have implications for the view of aerobic fitness as a causal risk factor for CVD and early death.
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Li, Geng. "Tuning genetic programming performance via bloating control and a dynamic fitness function approach." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/tuning-genetic-programming-performance-via-bloating-control-and-a-dynamic-fitness-function-approach(ba24d28d-6fd4-4832-9cca-e1132dd9755e).html.
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Inspired by Darwin's natural selection, genetic programming is an evolutionary computation technique which searches for computer programs best solving an optimization problem. The ability of GP to perform structural optimization at the same time of parameter optimization makes it uniquely suitable to solve more complex optimization problems, in which the structure of the solution is not known a priori. But, as GP is applied to increasingly difficult problems, the efficiency of the algorithm has been severely limited by bloating. Previous studies of bloating suggest that bloating can be resolved either directly by delaying the growth in depth and size, or indirectly by making GP to find optimal solutions faster. This thesis explores both options in order to improve the scalability and the capacity of GP algorithm. It tackles the former by firstly systematically analyzing the effect of bloating using a mathematical tool developed called activation rate. It then proposes depth difference hypothesis as a new cause of bloating and investigates depth constraint crossover as a new bloating control method, which is able to give very competitive control over bloating without affecting the exploration of fitter individuals. This thesis explores the second option by developing norm-referenced fitness function, which dynamically determines the individual's fitness based on not only how well it performs, but also the population's average performance as well. It is shown both theoretically and empirically that, norm-referenced fitness is able to significantly improve GP performance over the standard GP setup.
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Tour, Samir R. "Parallel Hybrid Clustering using Genetic Programming and Multi-Objective Fitness with Density(PYRAMID)." NSUWorks, 2006. http://nsuworks.nova.edu/gscis_etd/886.
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Clustering is the art of locating patterns in large data sets. It is an active research area that provides value to scientific as well as business applications. There are some challenges that face practical clustering including: identifying clusters of arbitrary shapes, sensitivity to the order of input, dynamic determination of the number of clusters, outlier handling, high dependency on user-defined parameters, processing speed of massive data sets, and the potential to fall into sub-optimal solutions. Many studies that were conducted in the realm of clustering have addressed some of these challenges. This study proposes a new approach, called parallel hybrid clustering using genetic programming and multi-objective fitness with density (PYRAMID), that tackles several of these challenges from a different perspective. PYRAMID employs genetic programming to represent arbitrary cluster shapes and circumvent falling in local optima. It accommodates large data sets and avoids dependency on the order of input by quantizing the data space, i.e., the space on which the data set resides, thus abstracting it into hyper-rectangular cells and creating genetic programming individuals as concatenations of these cells. Thus the cells become the subject of clustering, rather than the data points themselves. PYRAMID also utilizes a density-based multi-objective fitness function to handle outliers. It gathers statistics in a pre-processing step and uses them so not to rely on user-defined parameters. Finally, PYRAMID employs data parallelism in a master-slave model in an attempt to cure the inherent slow performance of evolutionary algorithms and provide speedup. A master processor distributes the clustering data evenly onto multiple slave processors. The slave processors conduct the clustering on their local data sets and report their clustering results back to the master, which consolidates them by merging the partial results into a final clustering solution. This last step also involves determining the number of clusters dynamically and labeling them accordingly. Experiments have demonstrated that, using these features, PYRAMID offers an advantage over some of the existing approaches by tackling the clustering challenges from a different angle.
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Bortel, Martin. "Evoluční algoritmy." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2012. http://www.nusl.cz/ntk/nusl-219807.
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Thesis describes main attributes and principles of Evolutionary and Genetic algorithms. Crossover, mutation and selection are described as well as termination options. There are examples of practical use of evolutionary and genetic algorithms. Optimization of distribution routes using PHP&MySQL and Google Maps API technologies.
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Beraldi, Dario. "Genetic variation in natural populations : linkage mapping of fitness related traits in Soay sheep." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/10789.
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The Soay sheep on St Kilda, the free-living population which is the subject of this project, offers an unprecedented opportunity to dissect the architecture of fitness related traits. In this project, 588 animals belonging to a larger pedigree (882 animals) were genotyped to build a complete genetic map comprising 251 markers. Consequently, a whole genome scan was carried out to detect qualitative and quantitative trait loci. Different morphological and physiological traits were chosen on the basis of their relationship to fitness. The loci affecting the Mendelian polymorphisms of horn type and two aspects of coat colour were mapped with good reliability (Horn type mapped to chromosome 10, Coat colour to chromosome 2, Coat pattern to chromosome 13; LOD scores >3). Several quantitative traits were analyzed and one genomic region showed significant linkage with the variation in jaw length (chromosome 11, LOD = 3.59). In addition, suggestive linkages were detected for hind leg length (chromosome 15, LOD = 2.89), birth weight (chromosome 8, LOD = 2.54), and timing of birth (chromosome 2, LOD = 2.70). Finally, two suggestive linkages were scored for resistance to the gastrointestinal parasite coccidian (chromosome 3 and X, LOD = 2.68 and 2.21 respectively). This project is one of the first attempts to dissect the genetic architecture of complex traits in the wild through linkage mapping. The results reported here will improve our understanding of the evolution and genetics of natural populations by allowing a more realistic modelling of the study traits and by opening the way towards the molecular characterisation of the genomic regions of interest.
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Xue, Feng. "Fitness effects of natural genetic variation on the Ras signalling network in Caenorhabditis elegans." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/fitness-effects-of-natural-genetic-variation-on-the-ras-signalling-network-in-caenorhabditis-elegans(1d3ecc50-2fd5-4f5f-9fdc-147282cd73b8).html.
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Natural genetic variation within populations is an important determinant of susceptibilities to complex diseases like cancer. Cryptic genetic variation refers to a particular type of genetic variation that remains silent unless perturbed by a genetic or environmental change. Understanding the role of this 'hidden' genetic variation in signalling networks can provide insights into how individuals of differing genetic backgrounds might respond to perturbations that cause disease. The well-characterized Ras signalling network is ideal for such studies as it is conserved in nature and regulates a multitude of biological processes that include cellular differentiation, proliferation and survival. I developed a novel approach for studying the effects of cryptic alleles on signalling pathways, which I applied to determine if cryptic genetic variation, influencing the Ras signalling pathway, was a ubiquitous property found in natural populations of C. elegans. This approach utilized mutant alleles to expose cryptic genetic variation in different genetic backgrounds, which were then systematically screened for variations in response to RNAi treatments targeting the Ras signalling network. A population-level fitness phenotype, based on population feeding behaviour, was used to quantify the effects of mutant alleles and RNAi knockdowns. The mechanistic basis of this dynamic phenotype was further explored using an in silico model that I constructed. My findings indicate that cryptic genetic variation is a ubiquitous feature of the Ras signalling network in the six natural isolate backgrounds examined. Specific genes that mediate response variation to elevated Ras signalling in these natural isolates were also identified and found to consist of a mixture of common and unique components from Ras, Notch and Wnt pathways.
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Holleley, Clare Ellen Biological Earth & Environmental Sciences Faculty of Science UNSW. "Testing hypotheses in molecular ecology: genetic exchange and hybrid performance." Publisher:University of New South Wales. Biological, Earth & Environmental Sciences, 2009. http://handle.unsw.edu.au/1959.4/43361.
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Population structure, gene flow and dispersal are some of the most commonly estimated population parameters in population genetics, evolutionary biology and conservation genetics. The primary aim of thesis is to test the precision and accuracy of genetic estimates of population structure, gene flow and dispersal. The controlled replicated Drosophila melanogaster experiments of known effective population size (Ne = 14.3) and dispersal rate (m = 0.0025 - 0.04) all adhered to Wright??s demographic island model. Three statistical approaches were empirically tested: 1) the conversion of population structure to gene flow using FST, RST, SHUA and PhiST ; 2) the private alleles method to estimate gene flow; 3) a Bayesian assignment method to estimate dispersal (BAYESASS 1.2). Even in the best-case scenario, almost all current methods except SHUA significantly underestimate population structure, and consequently overestimate gene flow and dispersal when applied to real populations. It was crucial to ensure that the manipulated rate of gene flow was correctly defined. This led to three supporting investigations of hybrid performance, inversion polymorphisms and effective population size. The hybrid performance investigation demonstrated that the manipulated rate of gene flow had not been unexpectedly inflated by hybrid vigour or reduced by breakdown. These experiments also demonstrated that close inbreeding is not a necessary precondition for hybrid vigour or breakdown, which is important for conservation strategies involving induced dispersal. The investigation of inversion polymorphisms ensured that the manipulated rate of gene flow was not affected by selection on inverted regions. The effective population size investigation used a temporal estimation method to confirm that the Ne was accurately predicted by an N:Ne ratio of 0.286. Additionally this experiment showed that the single-sample estimation methods implemented by ONeSAMP or LDNE resulted in downwardly biased estimates of Ne in structured populations. In conclusion these results call into question the confidence that biologists may have in some of the most widely used molecular tools in conservation biology.
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Spong, Goran. "Genetic Consequences of Dispersal and Social Behavior in Lions, Panthera leo." Doctoral thesis, Uppsala universitet, Institutionen för evolutionsbiologi, 2001. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1424.
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This thesis combines behavioral observations of African lions (Panthera leo) with genetic analyses, in an attempt to clarify causes and consequences of lion group living. The numerous complex cooperative behaviors of lions present an excellent opportunity to investigate the evolution and maintenance of group living. This thesis focuses on female group living and male dispersal patterns. Lion sociality is found to be more complex than previously thought. Short dispersal distances result in strong kinship ties among prides, creating the potential for kin selection to operate among prides. Simultaneously, some prides contained unrelated females, depriving females in such prides of inclusive fitness benefits from group living. Concurrent with short dispersal distances in both males and females, significant genetic differentiation could be detected over relatively short distances in analyses of males. Extensive behavioral observations showed that territorial behaviors were unaffected by kinship ties to intruders. Instead, favorable odds and several environmental conditions were important factors. Space use analyses showed large overlap among prides. Again, kinship did not affect degree of overlap. Conclusively, these results show that the ultimate causes of lion sociality remain elusive, but that kin selection may be less important than generally thought. Lion sociality seems to be explicable mainly in terms of direct fitness benefits, which therefore should be given more attention.
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Johansson, Markus. "Effects of Agriculture on Abundance, Genetic Diversity and Fitness in the Common Frog, Rana temporaria." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4619.
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Hammerly, Susan C. "The Effects of Inbreeding on Fitness Traits in the Critically Endangered Attwater’s Prairie-chicken." Thesis, University of North Texas, 2014. https://digital.library.unt.edu/ark:/67531/metadc699930/.
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The goals of captive breeding programs for endangered species include preserving genetic diversity and avoiding inbreeding. Typically this is accomplished by minimizing population mean kinship; however, this approach becomes less effective when errors in the pedigree exist and may result in inbreeding depression, or reduced survival. Here, both pedigree- and DNA-based methods were used to assess inbreeding depression in the critically endangered Attwater’s prairie-chicken (Tympanuchus cupido attwateri). Less variation in the pedigree-based inbreeding coefficients and parental relatedness values were observed compared to DNA-based measures suggesting that errors exist in the pedigree. Further, chicks identified with high parental DNA-based relatedness exhibited decreased survival at both 14- and 50-days post-hatch. A similar pattern was observed in later life stages (> 50 days post-hatch) with birds released to the wild; however, the pattern varied depending on the time post-release. While DNA-based inbreeding coefficient was positively correlated with mortality to one month post-release, an opposite pattern was observed at nine months suggesting purging of deleterious alleles. I also investigated whether immunocompetence, or the ability to produce a normal immune response, was correlated with survival; however, no significant correlation was observed suggesting that inbreeding was a more important factor influencing survival. Pairing individuals for breeding by minimizing DNA-based parental relatedness values resulted in a significant increase in chick survival. This study highlights the importance of using DNA-based methods to avoid inbreeding depression when errors exist in the pedigree.
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Mota, Filho Francisco Osvaldo Mendes. "Aplicação de modelos de estimação de fitness em algoritmos geneticos." [s.n.], 2005. http://repositorio.unicamp.br/jspui/handle/REPOSIP/261755.
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Orientador: Fernando Antonio Campos GomideDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Eletrica e de Computação
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Resumo: Para obter uma solução satisfatória, algoritmos genéticos avaliam, em geral, um número grande de indivíduos durante o processo evolutivo. É comum, em aplicações práticas, encontrar funções de avaliação computacionalmente complexas e caras. Porém, nesses casos, o tempo é um fator determinante no desempenho de algoritmos genéticos. Dessa forma, os algoritmos genéticos devem encontrar soluções adequadas em curto intervalo de tempo. Uma alternativa promissora para contornar os custos computacionais referentes à função de avaliação considera o fato de que pode ser mais atrativo avaliar diretamente somente indivíduos selecionados e estimar os fitness dos restantes do que avaliar diretamente toda a população. Este trabalho propõe o uso de modelos de estimação de fitness em algoritmos genéticos. Especificamente, são sugeridos modelos de estimação baseados em agrupamento nebuloso supervisionado (Fuzzy C-Means) e não supervisionado (Aprendizagem Participativa). O objetivo é aproximar as funções de avaliação por meio de modelos de estimação de fitness, sem afetar significativamente a qualidade das soluções. Inicialmente, os modelos de estimação propostos são comparados e analisados experimentalmente com alternativas sugeri das por outros autores, utilizando, para isso, problemas de otimização considerados na literatura de algoritmos genéticos. A seguir, os modelos de estimação de fitness são aplicados em um problema real de engenharia, o planejamento de circulação de trens em ferrovias. Este é um caso típico onde o desempenho de cada planejamento exige um tempo significativo. A eficiência dos modelos propostos é verificada e comprovada experimentalmente comparando com os resultados, em instâncias mais simples, fornecidos por modelos de programação matemática e, em instâncias complexas, fornecidos pelo algoritmo genético clássico
Abstract: Genetic algorithms usually need a large number of fitness evaluations before a satisfying result can be obtained. In many real-world applications, fitness evaluation may be computationally complex and costly. In these cases, time is an essential subject in performance analysis of genetic algorithms. Therefore, genetic algorithms should provide good solutions in a short period of time. A promising approach to alleviate the computational cost of evaluations considers the fact that sometimes it is better to evaluate only selected individuals and estimate the fitness of the remaining individuals instead of evaluate a whole population. This work suggests the application of fitness estimation models in genetic algorithms. More specifically, it deals with estimation models based on supervised fuzzy clustering (Fuzzy C-Means) and unsupervised fuzzy clustering (Participatory Learning). The goal is to approximate the evaluation functions through the use of fitness estimation models, without significantly affect the quality of solutions. Initially, the fitness estimation models are compared and analyzed experimentally with other models already proposed in the literature. Their performance are evaluated using benchmark optimization problems found in the genetic algorithms literature. Next, the fitness estimation models are used to solve a real-world engineering problem, namely the train scheduling in a freight rail line. This is a typical case where the performance measure of each schedule demands a considerable amount of time. Once again, the performance of the fitness estimation models are evaluated experimentally, comparing their results with the results provided, for simple instances, by linear programming models and, for complex instances, by the classic genetic algorithm
Mestrado
Engenharia de Computação
Mestre em Engenharia Elétrica
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Annavi, Geetha. "Genetic, socio-ecological and fitness correlates of extra-group paternity in the European badger (Meles meles)." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:8d7304b2-84a2-4d5d-bbbc-63270d309e2e.
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The evolution of extra-group paternity (EGP) is a contentious issue in evolutionary biology. This thesis examines the factors and adaptive benefits driving EGP in a high-density, group-living population of European badgers (Meles meles). To improve power to assign parentage, I isolated and characterised 21 new polymorphic microsatellite markers. I genotyped 83% of 1410 badger trapped 1987‒2010 using 35 autosomal microsatellite markers. Maternity and paternity were assigned at 80% confidence ca. 82% of individuals. 48% of paternities were extra-group, where 85% were attributable to neighbouring-group males and EGP was detected in 47% of litters; thus badger social group do not correspond with a breeding unit. I tested whether indirect genetic benefits explain these high EGP rates. (1) ‘Good-gene-as-heterozygosity Hypothesis’: Paternal heterozygosity, but not maternal or an individual’s own heterozygosity, associated positively with first-year survival probability. Under benign environmental conditions, cubs fathered by more heterozygous males had a higher first year survival probability. Despite this correlation, the EGP rate per litter correlated with neither average nor maximum within-group heterozygosity of candidate fathers. (2) Fitness benefit Hypothesis: Extra-group offspring (EGO) had lower first-year survival probability and lived 1.3 years less than within-group offspring (WGO). Female WGO produced more litters and offspring over their lifetime than female EGO, whereas male EGO produced more offspring than male WGO. (3) Inbreeding avoidance hypothesis: The EGP rate within a litter increased with greater average pair-wise relatedness between mothers and within-group candidate fathers. No inbreeding depression on first-year survival probability was detected, but small sample sizes limited statistical power. Socio-ecologically, at the litter level, EGP correlated negatively with the number of within-group candidate fathers, and positively with neighbouring-group candidate fathers. In conclusion, EGP in badgers may reduce inbreeding and be maintained in the population through a sex-specific antagonistic selection and indirect genetic benefits may occur when the total fitness benefits of producing extra-group sons outweigh the costs of producing extra-group daughters. These indirect genetic benefits only partially explain the evolution of promiscuity in European badgers, highlighting that evolutionary factors underlying promiscuity remain unclear.
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Saxon, Andrew Dougal. "The effects of ecological and genetic variation on fitness in the rainforest fruit fly, Drosophila birchii." Thesis, University of Bristol, 2018. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.752809.
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Le, Cocq Kate Frances. "Engineering the biological control and plant growth promotion fitness of Trichoderma hamatum GD12 through genetic manipulation." Thesis, University of Exeter, 2012. http://hdl.handle.net/10036/4161.
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Trichoderma species are ubiquitous soil saprotrophs and well-characterized biological control agents. Certain strains have also been shown to stimulate plant growth through the production of bioactive secondary metabolites, and are therefore receiving increased attention as natural plant growth stimulants. Previous research at the University of Exeter (Ryder et al. (2012) Microbiology 158, 84-97) has shown that the Plant Growth Promotion activity of a biocontrol strain of Trichoderma hamatum (strain GD12) can be dramatically enhanced by targeted mutation of the N-acetyl-β-D-glucosaminidase-encoding gene nag. However, due to the loss in chitinase activities, the mutant (ΔThnag::hph) displays loss of saprotrophic competitiveness and reduced fitness as a biocontrol agent. We set out to investigate how we can use genetic manipulation to improve strain GD12 in the context of biological control and plant growth promotion. We approached this by firstly sequencing the whole genome of GD12 and then using the information available from this to produce a targeted deletion mutant in the GD12 background disrupting one of the most down regulated proteins in the ΔThnag::hph, a branched chain amino acid transaminase (bcat), implicated in the production of secondary metabolites. Secondly, we aimed to engineer hyper-secretion and enhanced PGP activities in GD12 without impairing biocontrol activity. Over-expression of the S. cerevisiae gene dolichol-phosphate mannose synthase (dpm1) in T. reesei leads to altered cell wall architecture and increased secretory potential. Using the constitutive promoter ToxA, we over-expressed the dpm1 gene in T. hamatum GD12 and assessed its effects on the biocontrol and PGP activities of the fungus. The data presented herein, shows, that bcat deletion in T. hamatum GD12 results in a detrimental effect of germination of lettuce seedlings grown in the presence of ∆Thbcat::hph. We show that single copy insertions of ToxA-dpm1 leads to improved PGP activities, while biocontrol fitness is unaffected. However, while multiple copy insertions similarly lead to enhanced PGP, such strains display impaired biocontrol of soil-borne pathogens such as the plurivorous damping-off pathogen Sclerotinia sclerotiorum. This work demonstrates that while significant improvements in crop productivity can be achieved through genetic modification of the beneficial rhizosphere fungus T. hamatum GD12, it can have important consequences for other aspects of its biology and ecology and competence as a soil-borne microorganism.
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Allard, David M. "A Multi-Objective Genetic Algorithm to Solve Single Machine Scheduling Problems Using a Fuzzy Fitness Function." Ohio University / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1180968613.
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Banger, Nicola A. "Consequences of Multiple Paternity for Female Fitness in an Ontario Population of Northern Map Turtles, 'Graptemys geographica'." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/22881.
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Although sexual stereotypes paint males as being promiscuous and females as being choosy in order to increase their reproductive success, multiple mating by females is widespread and females of many taxa often produce progeny sired by multiple males – but why? In species in which there are no direct benefits associated with mating, females may adopt promiscuous mating strategies to increase their fitness through the acquisition of genetic benefits. Here, I examine the genetic mating system of map turtles, Graptemys geographica in Lake Opinicon. Based on the most conservative estimate, at least 71% of clutches in this population are sired by multiple males. There did not appear to be any relationship between female body size and frequency of multiple paternity. There was a marginally significant effect of multiple paternity on hatching success and survival of clutches, but there was no effect on hatchling morphology or locomotor performance.
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Veřmiřovský, Jakub. "Koevoluce v evolučním návrhu obvodů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2016. http://www.nusl.cz/ntk/nusl-255429.
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This thesis deals with evolutionary design of the digital circuits performed by a cartesian genetic programing and optimization by a coevolution. Algorithm coevolves fitness predictors that are optimized for a population of candidate digital circuits. The thesis presents theoretical basis, especially genetic programming, coevolution in genetic programming, design of the digital circuits, and deals with possibilities of the utilization of the coevolution in the combinational circuit design. On the basis of this proposal, the application designing and optimizing logical circuits is implemented. Application functionality is verified in the five test tasks. The comparison between Cartesian genetic programming with and without coevolution is considered. Then logical circuits evolved using cartesian genetic programming with and without coevolution is compared with conventional design methods. Evolution using coevolution has reduced the number of evaluation of circuits during evolution in comparison with standard cartesian genetic programming without coevolution and in some cases is found solution with better parameters (i.e. less logical gates or less delay).
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Everman, Elizabeth R. "The evolution and genetic control of stress tolerance in a complex world." Diss., Kansas State University, 2017. http://hdl.handle.net/2097/35437.
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Doctor of PhilosophyDepartment of Biology
Theodore J. Morgan
Natural populations are highly complex and consist of genetically variable individuals that belong to continuously varying age classes. Genotype and age interact to determine how individuals respond to environmental stress, which ultimately determines the evolutionary trajectories and persistence of populations in variable environments. For small ectothermic species, seasonal and diurnal variation in temperature is an important source of environmental stress that impacts activity patterns and suites of phenotypes directly related to whole organism fitness. I used the genetic and ecological model Drosophila melanogaster to investigate the influence of seasonal and diurnal thermal variability on survival and reproduction in genetically diverse populations. First, I characterized changes in cold tolerance and phenotypic plasticity within a natural population as it responded to seasonal shifts in developmental and short-term acclimation and thermal selection. I found that seasonal variation in cold tolerance was significantly influenced by developmental acclimation that occurred in the field as well as in the lab, where flies that developed under warmer conditions had reduced cold tolerance relative to flies that developed under cooler conditions. Second, I characterized the effect of variation in age on stress response phenotypes in a genetically variable population. I measured genotype- and age-specific responses to multiple environmental stressors, and identified regions of the genome that were associated with age-specific stress tolerance. Genome-wide association mapping revealed that age-specific phenotypes were influenced by distinct sets of polymorphisms and genes, suggesting that the evolution of age-related decline in phenotypes is driven by mutation accumulation within phenotypes, but both mutation accumulation and antagonistic pleiotropy between phenotypes. Next, I characterized the costs and benefits of acclimation for survival and reproduction to understand how physiological and behavioral plasticity interact to determine fitness. I found that phenotypic plasticity and the capacity for acclimation significantly influenced behavioral reproductive success, but the thermal cues that led to adaptive acclimation response in survival also led to decreased reproductive success. However, genotypes with the capacity to acclimate were more likely to survive thermal variation and more likely to reproduce, suggesting that genetic capacity for phenotypic plasticity has important implications for whole organism fitness. Finally, I measured the effect of acclimation on the induction of diapause and ability to survive cold stress in the recently introduced invasive species Drosophila suzukii. D. suzukii is endemic to Asia and was first detected in California in 2008 and in Topeka, KS in 2013. Its recent invasion history thus provides an interesting model to understand the role of plasiticy in the response to a novel and variable environment. I found that diapause was induced through a plastic response to acclimation and short photoperiod, though diapause was more drastically induced by acclimation. Overall, my research provides critical insights into how organisms respond to thermal variation by intergrating quantitative genetics, ecology, evolution, and life history tradeoffs. Collectively, my research demonstrates that the ability of organisms to survive thermal stress is a function of genetic capacity to tolerate stress, genetic capacity for phenotypic plasticity, prior exposure to thermal variation, and the age of the individual.
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Baker, Karis Helen. "Population genetic history of the British roe deer (Capreolus capreolus) and its implications for diversity and fitness." Thesis, Durham University, 2011. http://etheses.dur.ac.uk/897/.
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The first part of this study examined post glacial recolonisation by UK roe. Previous studies established three main roe deer lineages exist across Europe: a western (Iberian Peninsula), an eastern (Balkan region) and a central lineage (which spans across central Europe). It was unknown which group British roe deer populations belonged. Using a 419 bp region of the mt-DNA d-loop (HVR1) amplified from ancient and modern UK samples a direct comparison was made with previously published European data. Results showed that UK populations belong to the central lineage, indicating a post glacial re-colonisation that is likely to have occurred via an eastern route. The estimation of a substitution rate, which was applied to coalescent based methods, detected a signal for divergence of UK roe from continental roe at 5,600 YBP (HPD 3,500 - 11, 200 YBP), not long after the proposed date for the land bridge split (7,500 YBP). Since post glacial re-colonisation, roe were known to have undergone severe fluctuations in population size. Perhaps the most significant fluctuation began during the medieval period, when roe suffered severe declines (bottlenecking) due to over hunting and deforestation. These declines were so severe that, by the 16th century, roe were believed to have been extirpated (locally extinct) from all southern areas of UK and considered scarce in northern areas. However, by the 19th century roe began to recover. Recovery in the south may have resulted solely from re-introductions (involving both native and non-native stocks) whilst, in the north, recovery resulted from natural re-colonisation from remnant native stocks. The second part of this study investigated the impacts of this more recent history. This was first investigated using a 750 bp of the mt-DNA d loop region (HVR), 16 microsatellite loci and 18 skull traits from modern roe from across the UK to examine structure and diversity. Results based on both DNA and morphology revealed strong differentiation. Northern roe appeared least impacted by recent events; maintaining patterns of isolation by distance (IBD) and high genetic diversity (compared to southern populations). In contrast, southern roe appeared more strongly impacted by recent events; in particular, IBD was non-significant (although this may have been due to a sample size effect) and genetic diversity was lower (compared to northern populations). The roe re-introduction records indicated that the south western population was native in origin (Perthshire). Genetic data showed that this population was, however, highly differentiated from its proposed source; which could reflect the powerful impact of genetic drift resulting from small founder populations. Alternatively, it may be that the ancestry of the south western population is more complex than previously assumed. For the other southern population (Norfolk), re-introduction records indicate a non-native (German) origin. In line with this, both genetic and morphological data implied that these roe were highly distinct. The impacts of bottlenecks (including medieval declines and founder events) on roe populations were also examined. Bottleneck analyses examined ‘signatures’ in modern populations based on 16 microsatellites. The strongest evidence of bottlenecking was detected in the Norfolk population, consistent with the small founder group size introduced into this location relatively recently. For the other populations bottleneck signatures tended to be weak and non-significant. Direct comparisons of ancient (pre-bottleneck) and modern (post –bottleneck) populations were made based on 419 bp of mt-DNA d –loop (HVR1). Results showed considerable losses in genetic diversity between time frames consistent with medieval declines. Northern populations were also found to harbour the highest number of ‘native’ haplotypes and southern populations the lowest. The southern population of Norfolk exhibited only one ‘novel’ haplotype confirming its non-native origin. The impacts of bottlenecks on populations are of concern because they have been shown to reduce population fitness and increase the risk of extinction. Therefore, fitness of roe was examined using fluctuating asymmetry (FA) of 10 skull traits as an indicator of developmental stability. Correlations of FA and genetic diversity indices were examined at the level of individuals within populations, across all populations and among populations. All correlations existed in expected directions; however, correlations tended to be weak and non-significant. Furthermore, among population level FA did not vary significantly across populations providing no indication as to whether fitness has been impacted by past population history.
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Weyrauch, Shauna L. "Habitat fragmentation and woodland amphibians consequences for distribution, genetic diversity and fitness responses to UV-B radiation /." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1092668394.
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Thesis (Ph. D.)--Ohio State University, 2004.Title from first page of PDF file. Document formatted into pages; contains xiv, 138 p. : ill. Advisor: Thomas C. Grubb, Dept. of Evolution, Ecology, and Organismal Biology. Includes bibliographical references (p. 129-138).
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Mony, Vinod Kurumathurmadam Namboothiripad. "The genetic architecture underlying the Caenorhabditis elegans response to grassland soil bacteria and its effects on fitness." Diss., Kansas State University, 2013. http://hdl.handle.net/2097/16752.
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Doctor of PhilosophyDepartment of Biology
Michael Herman
Soil nematode communities are important components of the micro fauna in grassland ecosystems and their interaction with soil microbes affects important ecological processes such as decomposition and nutrient recycling. To study genetic mechanisms underlying ecologically important traits involved in the response of nematode communities to soil microbes, we employed genomic tools available for the model nematode, Caenorhabditis elegans. Previous work identified 204 C. elegans genes that were differentially expressed in response to growth on four different bacteria: Bacillus megaterium, Pseudomonas sp., Micrococcus luteus and Escherichia coli. For many of the genes the degree of differential gene expression between two bacterial environments predicted the magnitude of the effect of the loss of gene function on life-history traits in those environments. Mutations can have differential effects on fitness in variable environments, which can influence their maintenance in a population. Our fitness assays revealed that bacterial environments had varying magnitude of stress, defined as an environment in which the wild-type has a relatively low fitness. We performed fitness assays as part of a comprehensive analysis of life history traits on thirty five strains that contained mutations in genes involved in the C. elegans response to E. coli, B. megaterium, Pseudomonas sp. We found that many of the mutations had conditionally beneficial effects and led to increased fitness when nematodes bearing them were exposed to stressful bacteria. We compared the relative fitness of strains bearing these mutations across bacterial environments and found that the deleterious effects of many mutations were alleviated in the presence of stressful bacteria. Although transcriptional profiling studies can identify genes that are differentially regulated in response to environmental stimuli, how the expressed genes provide functional specificity to a particular environment remains largely unknown. We focused on defense and metabolism genes involved in C. elegans-bacterial interactions and measured the survivorship of loss-of-function mutants in these genes exposed to different bacteria. We found that genes had both bacteria-specific and bacteria-shared responses. We then analyzed double mutant strains and found bacteria-specific genetic interaction effects. Plasticity in gene interactions and their environment-specific modulation have important implications for host phenotypic differentiation and adaptation to changing environments.
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Pace, Brian A. "Physiology, Photochemistry, and Fitness of Mexican Maize Landraces in the Field." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1545421491370678.
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Troyer, Ryan M. "Genetic diversity, evolution, and fitness of infectious hematopoietic necrosis virus within an endemic focus in rainbow trout aquaculture /." Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/9288.
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Wiglasz, Michal. "Souběžné učení v koevolučních algoritmech." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2015. http://www.nusl.cz/ntk/nusl-234912.
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Cartesian genetic programming (CGP) is a form of genetic programming where candidate programs are represented in the form of directed acyclic graphs. It was shown that CGP can be accelerated using coevolution with a population of fitness predictors which are used to estimate the quality of candidate solutions. The major disadvantage of the coevolutionary approach is the necessity of performing many time-consuming experiments to determine the best size of the fitness predictor for the particular task. This project introduces a new fitness predictor representation with phenotype plasticity, based on the principles of colearning in evolutionary algorithms. Phenotype plasticity allows to derive various phenotypes from the same genotype. This allows to adapt the size of the predictors to the current state of the evolution and difficulty of the solved problem. The proposed algorithm was implemented in the C language and optimized using SSE2 and AVX2 vector instructions. The experimental results show that the resulting image filters are comparable with standard CGP in terms of filtering quality. The average speedup is 8.6 compared to standard CGP. The speed is comparable to standard coevolutionary CGP but it is not necessary to experimentally determine the best size of the fitness predictor while applying coevolution to a new, unknown task.
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Wong, Phillip Lee-Ming. "Removing redundancy and reducing fitness evaluation costs in genetic programming : a thesis submitted to the Victoria University of Wellington in fulfilment of the requirements for the degree of Master of Science in Computer Science /." ResearchArchive@Victoria e-Thesis, 2008. http://hdl.handle.net/10063/541.
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Myburg, Alexander Andrew. "Genetic Architecture of Hybrid Fitness and Wood Quality Traits in a Wide Interspecific Cross of Eucalyptus Tree Species." NCSU, 2001. http://www.lib.ncsu.edu/etd/public/etd-23521723610112031/etd.pdf.
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Schinn, Song Min. "Cell-Free Synthesis of Proteins with Unnatural Amino Acids: Exploring Fitness Landscapes, Engineering Membrane Proteins and Expanding the Genetic Code." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6496.
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Unnatural amino acids (uAA) expand the structural and functional possibilities of proteins. Numerous previous studies have demonstrated uAA as a powerful tool for protein engineering, but challenges also remain. Three notable such challenges include: (1) the fitness of uAA-incorporated proteins are difficult to predict and time-consuming to screen with conventional methods, (2) uAA incorporation in difficult-to-express proteins (e.g. membrane proteins such as G-protein coupled receptors) remain challenging, and (3) the incorporation of multiple types of uAA are still limited. In response, we pose cell-free protein synthesis (CFPS), a rapid and versatile in vitro expression system, as a platform to explore solutions to these challenges. The "cell-free" nature of CFPS enables it to accelerate protein expression and tolerate extensive modifications to its translational environment. In this work, these advantages were utilized to address the aforementioned challenges by: (1) rapidly expressing and screening uAA-containing proteins, (2) incorporating uAA in functional G-protein coupled receptor in the presence of membrane-mimicking lipid additives, and (3) engineer the translational environment extensively towards multiple uAA incorporation.
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Söylemez, Onuralp 1985. "On the prevalence and role of epistasis in shaping fitness within and between populations." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/398380.
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The role of epistasis – inter-dependent contributions of alleles to fitness – in shaping genetic variation within and between populations is an important question in evolutionary biology with significant implications for our understanding of the factors contributing to phenotypic variation. While epistasis has been shown to play an important role in evolutionary processes such as speciation and adaptive evolution, many aspects of this role remains poorly understood. In particular, there is much debate on whether observing prevalent epistasis in evolution can be taken as evidence for functional epistasis that is relevant to selectable variation. Here, we studied the nature of epistasis in protein evolution, and found a high prevalence of epistatic interactions between amino acid sites in the human genome. We showed that these interactions can help improve accuracy of predicting the impact of genetic variation on the protein structure and function. We also showed that hypothesis-driven search for epistasis in natural populations can detect genomic signatures of epistasis in humans.El papel de la epistasia - contribuciones interdependientes de alelos a la adecuación biológica - en la conformación de la variación genética dentro y entre poblaciones es una cuestión importante en la biología evolutiva con importantes implicaciones para nuestra comprensión de los factores que contribuyen a la variación fenotípica. Mientras la epistasia se ha demostrado que desempeña un papel importante en los procesos evolutivos como la especiación y evolución adaptativa, muchos aspectos de esta función siguen siendo poco conocidos. En particular, hay mucho debate sobre si la observación de epistasia frecuente en la evolución puede ser tomada como evidencia de epistasia funcional que es relevante a la variación heredable. Aquí, se estudió la naturaleza de la epistasia en la evolución de proteínas, y encontramos una alta prevalencia de interacciones epistaticas entre sitios de aminoácidos en el genoma humano. Hemos demostrado que estas interacciones pueden ayudar a mejorar la precisión de predecir el impacto de la variación genética en la estructura y función de las proteínas. También se puso de manifiesto que la búsqueda de investigación basada en hipótesis por epistasia en poblaciones naturales puede detectar firmas genómicas de epistasia en los humanos.
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Sztepanacz, Jacqueline L. P. "The Genetic Limits to Trait Evolution for a Suite of Sexually Selected Male Cuticular Hydrocarbons in Drosophila Serrata." Thesis, Université d'Ottawa / University of Ottawa, 2011. http://hdl.handle.net/10393/20385.
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Directional selection is prevalent in nature yet phenotypes tend to remain relatively constant, suggesting a limit to trait evolution. The genetic basis of evolutionary limits in unmanipulated populations, however, is generally not known. Given widespread pleiotropy, opposing selection on a focal trait may arise from the effects of the underlying alleles on other fitness components, generating net stabilizing selection on trait genetic variance and thus limiting evolution. Here, I look for the signature of stabilizing selection for a suite of cuticular hydrocarbons (CHCs) in Drosophila serrata. Despite strong directional sexual selection on CHCs, genetic variance differed between high and low fitness individuals and was greater among the low fitness males for seven of eight CHCs. Univariate tests of a difference in genetic variance were non-significant but have low power. My results implicate stabilizing selection, arising through pleiotropy, in generating a genetic limit to the evolution of CHCs in this species.
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Nielsen, Janne Thoft. "Population Structure and the Mating System of Loggerhead Turtles (Caretta caretta)." Scholarly Repository, 2010. http://scholarlyrepository.miami.edu/oa_dissertations/507.
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Studies of the maternally inherited mitochondrial DNA in loggerhead sea turtles (Caretta caretta) demonstrate that females are philopatric, returning to nest in the region where they hatched. Eleven genetic stocks of maternal lineages have been identified in the Atlantic Ocean. An analysis of the conventionally-used 380 bp of the mitochondrial control region of a sample of individuals from the genetic stock of loggerheads in Mexico (N = 175) revealed 13 haplotypes. When a longer sequence read of 815 bp was analyzed, 17 haplotypes were uncovered. In the genetic stock of loggerheads in northwestern Florida (N = 25), three haplotypes were identified with both control region sequence lengths. Based on the currently known distributions of the three long CC-A1 and CC-A2 haplotypes, two of each are unique to Mexico. This makes the longer sequence reads useful for stock identification. Within Mexico, there was evidence of significant population structuring between Cozumel and the northern region of the sampling area on mainland Mexico (pairwise ϕST = 0.1003, p = 0.0197), but not after Bonferroni correction. A direct comparison of female and male nuclear microsatellite genotypes indicated male-biased dispersal between Mexico and northwestern Florida. Within Mexico, microsatellite analysis indicated significant structuring of females between sampling years and between the northern and the southern region of the sampling area on the mainland. Consequently, this genetic stock, while perhaps not in equilibrium, shows signs of female natal homing. An analysis of clutches indicated that significantly more clutches in Mexico had multiple paternity compared to the northwestern Florida (66% and 23%, respectively). The frequency of multiple paternity was not correlated with female abundance, nest density or sex ratio of reproductively successful individuals. There was no evidence of females benefiting through increased reproductive success from multiple paternity. This is consistent with other studies of sea turtles.