Dissertations / Theses: 'Adaptive or fitness landscapes'

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SERRELLI, EMANUELE. "Adaptive landscapes: a case study of metaphors, models, and synthesis in evolutionary biology." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19338.

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This dissertation brings a contribution to the philosophical debate on adaptive landscapes, an influent "model" or "metaphor" in evolutionary biology. Some elements of innovation are: the distinction between native and migrant metaphor; a processual and communicational idea on what the Modern Synthesis was, and on what role a metaphor could have played in it; a view (taken by Richard Lewontin) of the disunity and theoretical structure of population genetics; the distinction between “adaptive surfaces” (mainly metaphors) and “combination spaces”, two terms normally conflated in the word “landscape”; an analysis of what bridges (including heuristics) may be cast between equations of gene frequency and the genotype space that, due to its huge dimensionality, cannot be handled by mathematics; a specified vocabulary to be used to clear the adaptive landscapes debate, accompanied by a plea in favor of a pragmatic approach - for example, the plurality of available notions of model forces us to choose one notion and see where it brings, otherwise we get stuck in confused, endless debates; an updated analytical comment of recent landscapes - Dobzhansky, Simpson, Dawkins but also the proliferation of combination spaces used in evolutionary biology to address a great variety of problems; the vision (got by Sergey Gavrilets) of a patchwork of tools finally making Mendelian population suitable model also for speciation; the exact position of holey landscapes in this patchwork, and the idea that scientists’s questions - like “how possibly” questions - matter in accessing this patchwork and in deciding “what explains” and “what describes” what in the world; the direct response to some mistakes Massimo Pigliucci made, I think, in his assessment of the adaptive landscape; an analysis of the Extended Evolutionary Synthesis project at its present stage, and some reflections on the conditions that will allow such a project to give a fair treatment and a good position to tools from the past, like the adaptive landscapes.

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Meer, Margarita V. 1986. "Exploring fitness landscapes." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/402192.

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Fitness landscape is a concept, which describes the dependence of phenotype on genotype. It was proposed almost a hundred years ago but only recent burst of technologies finally allowed exploring it. We studied different aspects of fitness landscape applying both: computational and experimental approaches. Using mammalian mitochondrial tRNAs we proved that evolution can proceed not only along the ridges of high fitness but also cross the low fitness valleys. Functional analysis of more than 56 000 mutants of green fluorescent protein from Aequorea victoria (avGFP) allowed us to describe local fitness landscape around a particular fitness peak. In addition to this we studied a case of population being on a slope – genetic code is undergoing changes in Methanosarcina making them stay in sub-optimum.
El paisaje adaptativo (fitness landscape) es un concepto que describe la dependencia del fenotipo en el genotipo. Hace mas de cien años que éste concepto fue propuesto, pero es sólo con la reciente expansión de tecnologías que finalmente ha podido ser explorado. Hemos estudiado diferentes aspectos del paisaje adaptativo aplicando tanto procedimientos computacionales como experimentales. Utilizando tRNAs mitocondriales de mamíferos hemos comprobado que la evolución puede proceder no sólo a lo largo de las crestas de elevado fitness sino también a través de los valles con reducido fitness. Análisis funcional de mas de 56000 mutantes de la proteína verde fuorescente de Aequorea Victoria (avGFP) nos permitió describir el paisaje adaptativo local alrededor de un punto máximo específico de fitness. Mas aún, hemos estudiado un caso de una población en una pendiente – el código genético está atravesando cambios en Methanosarcina quedándose en sub-óptimo.

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Di, Pietro Anthony. "Optimising evolutionary strategies for problems with varying noise strength." University of Western Australia. School of Computer Science and Software Engineering, 2007. http://theses.library.uwa.edu.au/adt-WU2007.0210.

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For many real-world applications of evolutionary computation, the fitness function is obscured by random noise. This interferes with the evaluation and selection processes and adversely affects the performance of the algorithm. Noise can be effectively eliminated by averaging a large number of fitness samples for each candidate, but the number of samples used per candidate (the resampling rate) required to achieve this is usually prohibitively large and time-consuming. Hence there is a practical need for algorithms that handle noise without eliminating it. Moreover, the amount of noise (noise strength and distribution) may vary throughout the search space, further complicating matters. We study noisy problems for which the noise strength varies throughout the search space. Such problems have generally been ignored by previous work, which has instead generally focussed on the specific case where the noise strength is the same at all points in the search domain. However, this need not be the case, and indeed this assumption is false for many applications. For example, in games of chance such as Poker, some strategies may be more conservative than others and therefore less affected by the inherent noise of the game. This thesis makes three significant contributions in the field of noisy fitness functions: We present the concept of dynamic resampling. Dynamic resampling is a technique that varies the resampling rate based on the noise strength and fitness for each candidate individually. This technique is designed to exploit the variation in noise strength and fitness to yield a more efficient algorithm. We present several dynamic resampling algorithms and give results that show that dynamic resampling can perform significantly better than the standard resampling technique that is usually used by the optimisation community, and that dynamic resampling algorithms that vary their resampling rates based on both noise strength and fitness can perform better than algorithms that vary their resampling rate based on only one of the above. We study a specific class of noisy fitness functions for which we counterintuitively find that it is better to use a higher resampling rate in regions of lower noise strength, and vice versa. We investigate how the evolutionary search operates on such problems, explain why this is the case, and present a hypothesis (with supporting evidence) for classifying such problems. We present an adaptive engine that automatically tunes the noise compensation parameters of the search during the run, thereby eliminating the need for the user to choose these parameters ahead of time. This means that our techniques can be readily applied to real-world problems without requiring the user to have specialised domain knowledge of the problem that they wish to solve. These three major contributions present a significant addition to the body of knowledge for noisy fitness functions. Indeed, this thesis is the first work specifically to examine the implications of noise strength that varies throughout the search domain for a variety of noise landscapes, and thus starts to fill a large void in the literature on noisy fitness functions.

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Karlsen, Ero Stig. "Learning and Evolution in Complex Fitness Landscapes." Thesis, Norwegian University of Science and Technology, Department of Computer and Information Science, 2007. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-8712.

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The Baldwin effect is the notion that life time adaptation can speed up evolution by 1) identifying good traits and 2) by genetic assimilation inscribing the traits in the population genetically. This thesis investigates the Baldwin effect by giving an introduction to its history, its current status in evolutionary biology and by reviewing some important experiments on the Baldwin effect in artificial life. It is shown that the Baldwin effect is perceived differently in the two fields; in evolutionary biology the phenomenon is surrounded by controversy, while the approach in artificial life seems to be more straight forward. Numerous computer simulations of the Baldwin effect have been conducted, and most report positive findings. I argue that the Baldwin effect has been interpreted differently in the literature, and that a more well-defined approach is needed. An experiment is performed where the effect of learning on evolution is observed in fitness landscapes of different complexity and with different learning costs. It is shown that the choice of operators and parameter settings are important when assessing the Baldwin effect in computer simulations. In particular I find that mutation has an important impact on the Baldwin effect. I argue that today's computer simulations are too abstract to serve as empirical evidence for the Baldwin effect, but that they nevertheless can be valuable indications of the phenomenon in nature. To assure the soundness of experiments on the Baldwin effect, the assumptions and choices made in the implementations need to be clarified and critically discussed. One important aspect is to compare the different experiments and their interpretations in an attempt to assess the coherence between the different simulations.

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Herrmann, Sebastian [Verfasser]. "Complex network analysis of fitness landscapes / Sebastian Herrmann." Mainz : Universitätsbibliothek Mainz, 2017. http://d-nb.info/1122760159/34.

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Barnett, Lionel. "Evolutionary search on fitness landscapes with neutral networks." Thesis, University of Sussex, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288614.

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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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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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Abstract:

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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Lu, Guanzhou. "Characterising fitness landscapes with fitness-probability cloud and its applications to algorithm configuration." Thesis, University of Birmingham, 2014. http://etheses.bham.ac.uk//id/eprint/4756/.

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Metaheuristics are approximation optimisation techniques widely applied to solve complex optimisation problems. Despite a large number of developed metaheuristic algorithms, a limited amount of work has been done to understand on which kinds of problems the proposed algorithm will perform well or poorly and why. A useful solution to this dilemma is to use fitness landscape analysis to gain an in-depth understanding of which algorithms, or algorithm variants are best suited for solving which kinds of problem instances, even to dynamically determine the best algorithm configuration during different stages of a search algorithm. This thesis for the first time bridges the gap between fitness landscape analysis and algorithm configuration, i.e., finding the best suited configuration of a given algorithm for solving a particular problem instance. Studies in this thesis contribute to the following: a. Developing a novel and effective approach to characterise fitness landscapes and measure problem difficulty with respect to algorithms. b. Incorporating fitness landscape analysis in building a generic (problem-independent) approach, which can perform automatic algorithm configuration on a per-instance base, and in designing novel and effective algorithm configurations. c. Incorporating fitness landscape analysis in establishing a generic framework for designing adaptive heuristic algorithms.

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Manukyan, Narine. "Analysis and Modeling of Quality Improvement on Clinical Fitness Landscapes." ScholarWorks @ UVM, 2014. http://scholarworks.uvm.edu/graddis/253.

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Widespread unexplained variations in clinical practices and patient outcomes, together with rapidly growing availability of data, suggest major opportunities for improving the quality of medical care. One way that healthcare practitioners try to do that is by participating in organized healthcare quality improvement collaboratives (QICs). In QICs, teams of practitioners from different hospitals exchange information on clinical practices, with the aim of improving health outcomes at their own institutions. However, what works in one hospital may not work in others with different local contexts, due to non-linear interactions among various demographics, treatments, and practices. I.e., the clinical landscape is a complex socio-technical system that is difficult to search. In this dissertation we develop methods for analysis and modeling of complex systems, and apply them to the problem of healthcare improvement. Searching clinical landscapes is a multi-objective dynamic problem, as hospitals simultaneously optimize for multiple patient outcomes. We first discuss a general method we developed for finding which changes in features may be associated with various changes in outcomes at different points in time with different delays in affect. This method correctly inferred interactions on synthetic data, however the complexity and incompleteness of the real hospital dataset available to us limited the usefulness of this approach. We then discuss an agent-based model (ABM) of QICs to show that teams comprising individuals from similar institutions outperform those from more diverse institutions, under nearly all conditions, and that this advantage increases with the complexity of the landscape and the level of noise in assessing performance. We present data from a network of real hospitals that provides encouraging evidence of a high degree of similarity in clinical practices among hospitals working together in QIC teams. Based on model outcomes, we propose a secure virtual collaboration system that would allow hospitals to efficiently identify potentially better practices in use at other institutions similar to theirs, without any institutions having to sacrifice the privacy of their own data. To model the search for quality improvement in clinical fitness landscapes, we need benchmark landscapes with tunable feature interactions. NK landscapes have been the classic benchmarks for modeling landscapes with epistatic interactions, but the ruggedness is only tunable in discrete jumps. Walsh polynomials are more finely tunable than NK landscapes, but are only defined on binary alphabets and, in general, have unknown global maximum and minimum. We define a different subset of interaction models that we dub as NM landscapes. NM landscapes are shown to have smoothly tunable ruggedness and difficulty and known location and value of global maxima. With additional constraints, we can also determine the location and value of the global minima. The proposed NM landscapes can be used with alphabets of any arity, from binary to real-valued, without changing the complexity of the landscape. NM landscapes are thus useful models for simulating clinical landscapes with binary or real decision variables and varying number of interactions. NM landscapes permit proper normalization of fitnesses so that search results can be fairly averaged over different random landscapes with the same parameters, and fairly compared between landscapes with different parameters. In future work we plan to use NM landscapes as benchmarks for testing various algorithms that can discover epistatic interactions in real world datasets.

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Vassilev, Vesselin K. "Fitness landscapes and search in the evolutionary design of digital circuits." Thesis, Edinburgh Napier University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.322508.

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Merz, Peter. "Memetic algorithms for combinatorial optimization problems fitness landscapes and effective search strategies /." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=960860029.

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Franke, Jasper [Verfasser], Joachim [Akademischer Betreuer] Krug, and Heiko [Akademischer Betreuer] Rieger. "Statistical topography of fitness landscapes / Jasper Franke. Gutachter: Joachim Krug ; Heiko Rieger." Köln : Universitäts- und Stadtbibliothek Köln, 2012. http://d-nb.info/1038224721/34.

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Atkinson, Simon Reay. "Engineering design adaptation fitness in complex adaptive systems." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648674.

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Melnyk, Anita H. "Adaptive landscapes in evolving populations of Pseudomonas fluorescens in simple environments." Thesis, University of Ottawa (Canada), 2010. http://hdl.handle.net/10393/28876.

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The adaptive landscape heuristic can be used to answer the question "how predictable is evolution?" because its topology will impact the repeatability of evolution. In my Masters research I addressed this question in two ways: (1) I reviewed empirical adaptive landscape studies in the fields of directed protein evolution and microbial experimental evolution and (2) I performed a selection experiment to characterize adaptive landscape topology by measuring variance in fitness and metabolic phenotype within and among genetically distinct Pseudomonas fluorescens strains in two environments. Empirical studies have found that protein level landscapes are generally smooth, however, population level landscapes are rugged even in simple environments. Experimentally I found that the pattern of variance in fitness and metabolic phenotype was unique to the selection environment. The response to selection was highly repeatable at the level of fitness, but the underlying genetic routes taken were different for each environment and more variable in xylose than in glucose, suggesting a more rugged underlying landscape. More generally, my research suggests that making statements about the predictability of adaptive evolution at the population level may be challenging and wi11likely depend on the specifics of the environment in which selection occurs.

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Mlambo, Nolwazi S. X. "Restoring Curio[City] : An Alternative Adaptive Reuse Approach for the derelict Staatsmuseum building throough Landscape Design." Diss., University of Pretoria, 2020. http://hdl.handle.net/2263/78705.

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Urban relics, memories of bygone eras, sit desolate and disregarded on the Northern and Southern fringes of the City of Tshwane’s inner-city, also known as Pretoria. Flaking facades, uninviting margins and deflected gazes have resulted in forgotten city narratives, narratives that are immortalised in these monuments. These compositions of culture, and remnants of the past, have fallen prey to the swift progress of the city and have been left forgotten as they retreat into the shadows of their former grandeur. Dwarfed by the bustle of the city and it’s towering urban fabric, a generation unknowing pass these urban gems daily, unaware of their past splendour. Existing now only as urban scars, these buildings become spectators to the continued advancing and changing cityscape, they become invisible remnants of the city’s cultural and historical landscape. The dissertation aims to generate a landscape design proposal for the Old Staatsmuseum building as an attempt to reactivate one such urban relic, to return it to some of its historic grandeur, and imagining new ways for old buildings to inject meaning into the cityscape. Drawing inspiration from creative industries, such as art, media and functional creations, the project investigates landscape architecture’s potential to; regenerate and remodel buildings into creative sites, prevent their further decay, celebrate their inherent adaptive history and make them accessible to the new generation of city dwellers and visitors. Furthermore, such an attempt also seeks to connect and enhance the otherwise fragmented urban nature within the City of Tshwane, by connecting the Old Staatsmusem, to its context of the National Zoological Gardens, and further afield to the grassland landscapes of Gauteng. Landscape architecture is therefore used to present an allusion of the “continuation of cultural phenomena through built infrastructure” (Wong 2017:30) and as a catalyst for urban regeneration in the Pretoria inner-city.
Mini Dissertation (ML (Prof))--University of Pretoria, 2020.
Architecture
ML (Prof)
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Keller, George Burleigh. "Modeling and Measuring Affordability as Fitness." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77365.

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Affordability of products and services is an economic benefit that should accrue to consumers, whether they are corporations, government agencies or individuals. This concept of affordability goes beyond conventional wisdom that considers affordability as the ability to pay the price of a product or service. This dissertation defines and explores a broader concept of affordability – one of fitness to perform at the level of quality required by the consumer, to perform at that level whenever the product or service is used, and to do so with minimum consumption of resources. This concept of affordability is applied to technological systems by using the complexity sciences concept of fitness as the metaphor for technological systems' fitness. During a system design evolution, the specific design outcome is determined by that set of design search paths followed – it is path dependent. Dynamic mechanisms create, dictate and maintain path dependence. Initial conditions define the start and direction of a path. During subsequent design steps, positive feedback influences the designer to continue on that path. This dissertation describes underlying mechanisms that create, dictate and maintain path dependence; discusses the effects of path dependence on system design and system affordability; models these effects using system dynamics modeling; and suggests actions to address its effects. This dissertation also addresses several types of fitness landscapes, and suggests that the Data Envelopment Analysis (DEA) solution space is a form of fitness landscape suitable for evaluating the efficiency, and thus the fitness, of research and development (R&D) projects. It describes the use of DEA to evaluate and select Department of Defense (D0D) R&D projects as a new application of DEA.
Ph. D.

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Neidhart, Johannes [Verfasser], Joachim [Akademischer Betreuer] Krug, and Anton [Akademischer Betreuer] Bovier. "Fitness Landscapes, Adaptation and Sex on the Hypercube / Johannes Neidhart. Gutachter: Joachim Krug ; Anton Bovier." Köln : Universitäts- und Stadtbibliothek Köln, 2014. http://d-nb.info/1064693423/34.

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Kousathanas, Athanasios. "Fitness effects of new mutations and adaptive evolution in house mice." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/8250.

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Knowledge of the distribution of fitness effects of new mutations (DFE) can enable us to quantify the amount of genetic change between species that is driven by natural selection and contributes to adaptive evolution. The primary focus of this thesis is the study of methods to infer the DFE and the study of adaptive evolution in the house mouse subspecies Mus musculus castaneus. Firstly, I extended previous methodology to model the DFE based on polymorphism data. Methods that have previously been used to infer the DFE from polymorphism data have relied on the assumption of a unimodal distribution. I developed new models that can be used to fit DFEs of arbitrary complexity, and found that multimodality can be detected by these models given enough data. I used these new models to analyse polymorphism data from Drosophila melanogaster and M. m. castaneus, and found evidence for a unimodal DFE for D. melanogaster and a bimodal DFE for M. m. castaneus. Secondly, I investigated the contribution of change in coding and non-coding DNA to evolutionary adaptation. I used a polymorphism dataset of ~80 loci from M. m. castaneus sequenced in 15 individuals to investigate selection in protein-coding genes and putatively regulatory DNA close to these genes. I found that, although protein-coding genes are much more selectively constrained than non-coding DNA, they experience similar rates of adaptive substitution. These results suggest that change in functional non-coding DNA sequences might be as important as protein-coding genes to evolutionary adaptation. Thirdly, I used whole genome data from 10 M. m. castaneus individuals to compare the rate of adaptive substitution in autosomal and X-linked genes. I found that, on average, X-linked genes have a 1.8 times faster rate of adaptive substitution than autosomal genes. I also found that faster-X evolution is more pronounced for male-specific genes. I used previously developed theory to show that these observations can be explained if new advantageous mutations are recessive, with an average dominance coefficient less than or equal to 0.25. These results can help to explain the long-studied phenomenon of the large effect of the X chromosome in speciation.

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Rendel, Mark D. "The evolutionary dynamics of neutral networks : lessons from RNA." Thesis, University of Oxford, 2008. http://ora.ox.ac.uk/objects/uuid:85107ca7-fada-4582-95e7-17b5bbb038cd.

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The evolutionary options of a population are strongly influenced by the avail- ability of adaptive mutants. In this thesis, I use the concept of neutral networks to show that neutral drift can actually increase the accessibility of adaptive mu- tants, and therefore facilitate adaptive evolutionary change. Neutral networks are groups of unique genotypes which all code for the same phenotype, and are connected by simple point mutations. I calculate the size and shape of the networks in a small but exhaustively enumerated space of RNA genotypes by mapping the sequences to RNA secondary structure phenotypes. The qual- itative results are similar to those seen in many other genotype–phenotype map models, despite some significant methodological differences. I show that the boundary of each network has single point–mutation connections to many more phenotypes than the average individual genotype within that network. This means that paths involving a series of neutral point–mutation steps across a network can allow evolution to adaptive phenotypes which would otherwise be extremely unlikely to arise spontaneously. This can be likened to walking along a flat ridge in an adaptive landscape, rather than traversing or jumping across a lower fitness valley. Within this model, when a genotype is made up of just 10 bases, the mean neutral path length is 1.88 point mutations. Furthermore, the map includes some networks that are so convoluted that the path through the network is longer than the direct route between two sequences. A minimum length adaptive walk across the genotype space usually takes as many neutral steps as adaptive ones on its way to the optimum phenotype. Finally I show that the shape of a network can have a very important affect on the number of generations it takes a population to drift across it, and that the more routes between two sequences, the fewer generations required for a population to find an advantageous sequence. My conclusion is that, within the RNA map at least, the size, shape and connectivity of neutral networks all have a profound effect on the way that sequences change and populations evolve, and by not considering them, we risk missing an important evolutionary mechanism.

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Gifford, Danna R. "Scaling fitness optima-Studying adaptive evolution with multiple genotypes of Aspergillus nidulans." Thesis, University of Ottawa (Canada), 2011. http://hdl.handle.net/10393/28888.

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Adaptation involves the successive substitution of beneficial mutations by selection, a process known as an adaptive walk. Theoretical models of adaptation have made predictions regarding the properties of adaptive walks, but we know little empirically about how adaptation differs between different genotypes faced with the same environment, knowledge that is critical to a broad understanding of natural adaptation. Furthermore, as the body of theoretical knowledge continues to grow, it is becoming apparent that the conventional model systems used to study adaptation, chiefly single-celled organisms, are not well-suited for studying adaptation in spatially structured environments, and, barring yeasts, cannot be used to study the effects of sex on adaptation. This thesis tackles both questions using the fungus Aspergillus nidulans , first demonstrating that the selection coefficients of mutations, but not the total number, are affected by initial adaptedness to an environment and then developing a mathematical growth model that will allow for further development of theoretical models of adaptation in spatially structured environments.

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Posani, Lorenzo. "Inference and modeling of biological networks : a statistical-physics approach to neural attractors and protein fitness landscapes." Thesis, Paris Sciences et Lettres (ComUE), 2018. http://www.theses.fr/2018PSLEE043/document.

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L'avènement récent des procédures expérimentales à haut débit a ouvert une nouvelle ère pour l'étude quantitative des systèmes biologiques. De nos jours, les enregistrements d'électrophysiologie et l'imagerie du calcium permettent l'enregistrement simultané in vivo de centaines à des milliers de neurones. Parallèlement, grâce à des procédures de séquençage automatisées, les bibliothèques de protéines fonctionnelles connues ont été étendues de milliers à des millions en quelques années seulement. L'abondance actuelle de données biologiques ouvre une nouvelle série de défis aux théoriciens. Des méthodes d’analyse précises et transparentes sont nécessaires pour traiter cette quantité massive de données brutes en observables significatifs. Parallèlement, l'observation simultanée d'un grand nombre d'unités en interaction permet de développer et de valider des modèles théoriques visant à la compréhension mécanistique du comportement collectif des systèmes biologiques. Dans ce manuscrit, nous proposons une approche de ces défis basée sur des méthodes et des modèles issus de la physique statistique, en développent et appliquant ces méthodes au problèmes issu de la neuroscience et de la bio-informatique : l’étude de la mémoire spatiale dans le réseau hippocampique, et la reconstruction du paysage adaptatif local d'une protéine
The recent advent of high-throughput experimental procedures has opened a new era for the quantitative study of biological systems. Today, electrophysiology recordings and calcium imaging allow for the in vivo simultaneous recording of hundreds to thousands of neurons. In parallel, thanks to automated sequencing procedures, the libraries of known functional proteins expanded from thousands to millions in just a few years. This current abundance of biological data opens a new series of challenges for theoreticians. Accurate and transparent analysis methods are needed to process this massive amount of raw data into meaningful observables. Concurrently, the simultaneous observation of a large number of interacting units enables the development and validation of theoretical models aimed at the mechanistic understanding of the collective behavior of biological systems. In this manuscript, we propose an approach to both these challenges based on methods and models from statistical physics. We present an application of these methods to problems from neuroscience and bioinformatics, focusing on (1) the spatial memory and navigation task in the hippocampal loop and (2) the reconstruction of the fitness landscape of proteins from homologous sequence data

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23

Kinkaid, Eden. "The architecture of ecology: Systems design for sustainable agricultural landscapes." Ohio University Honors Tutorial College / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1366983104.

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SNYDER, GREGORY HOWARD. "SUSTAINABILITY THROUGH ADAPTIVE REUSE: THE CONVERSION OF INDUSTRIAL BUILDINGS." University of Cincinnati / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1115644591.

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Stultz, Bailey E. "Mnemonic Futures: Exploring the future of place-based memory in post-industrial landscapes." University of Cincinnati / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1522340029293925.

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Toubiana, William. "Towards an adaptive and genomic understanding of an exaggerated secondary sexual trait in water striders." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSEN058/document.

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Les nombreuses différences qui existent entre les organismes illustrent que le processus de variation est un phénomène universel en biologie. Ces variations sont particulièrement observables chez les espèces sexuées, entre mâles et femelles. Comprendre les différents facteurs biologiques, environnementaux et génétiques, à l'origine de ce dimorphisme sexuel est le cœur de mon sujet de thèse. Pour cela, j’ai établi un nouveau modèle d'étude, l’insecte semi-aquatique Microvelia longipes. Ces insectes ont évolué un dimorphisme sexuel spectaculaire où les mâles présentent une croissance extrême et hypervariable spécifiquement au niveau de la troisième paire de pattes. Pour étudier ce phénomène, nous avons, en premier lieu, émis l’hypothèse que cette croissance exagérée était associée à des pressions de sélection sexuelle. Nous avons mis en évidence la présence de compétition intense entre males, qui utilisent leurs pattes arrière comme arme, pour s’accoupler avec les femelles. Les males à pattes plus longues gagnent souvent dans ces combats, expliquant l’importance adaptative de ces pattes exagérées chez les mâles. De plus, nous montrons que l’intensité que mettent les mâles à se battre est associée aux variations de taille de pattes chez les mâles, de la même espèce ou d’espèces différentes. Nous avons également développé un génome et une approche transcriptomique comparant les sexes et les pattes afin d’identifier les gènes responsables de cette croissance exagérée. Ceci a permis de dresser une liste de gènes dont l’expression corrèle avec l’exagération de la croissance des pattes chez les mâles et d’identifier des régions génomiques associées à la sélection sexuelle
From the DNA molecule to the more complex phenotypes, variation is a universal process in life and living organisms. The innumerable differences that exist between species are probably one of the most manifest examples. Yet, all this diversity would never have occurred in nature without some pre-existing divergence within species. One of the most striking examples of intraspecies variation appears in sexual organisms, between males and females. Understanding the environmental and genetic factors influencing sexual divergence is a longstanding question in evolutionary biology. To this end, I focus here on a new insect model system, Microvelia longipes, which has the particularity to have evolved an extreme case of sexual dimorphism in the rear legs. Males display exaggerated long rear legs compared to females but also an extreme variability in these leg lengths from one male to another. We identified that M. longipes males use their exaggerated legs as weapons during male-male competition. Males with longer legs have more chance to access females on egg-laying sites and therefore increase their reproductive success. Moreover, fitness assays and comparative studies between Microvelia species revealed that the intensity of male competition was associated with the exaggeration and hypervariability of the rear legs in M. longipes males. In a second approach, we studied the developmental and genomic basis of this sexual dimorphism through a comparative transcriptomic analysis and identified genes and genomic regions associated with male exaggerated legs and ultimately with sexual selection. Overall, the integrative approach used in this work allows to establish Microvelia longipes as a promising new model system to study the influence of sexual selection in adaptive evolution

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Price, Brian. "The application of modified adaptive landscapes to heuristic modelling of engine concept designs using sparse data." Thesis, Aston University, 2017. http://publications.aston.ac.uk/37624/.

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The automotive internal combustion engine industry operates in a sector that relies on high production volumes for economies of scale, and dedicated production equipment for efficiency of operations and control of quality, yet is subject to the vagaries of a dynamic marketplace, with the need for constant change. These circumstances place pressure on engine designs to be optimised at launch to be competitive and meet market needs, yet be adaptable to uncertain requirements for change over their production life. Engine designers therefore need concept configuration evaluation tools that can assess architectures for resilience to geometric change over the production life of the product. The problem of being resource efficient whilst having the capacity to adapt tochanging environments is one that has been addressed in nature. Natural systems have evolved strategies of satisficing conflicting requirements whilst being resource efficient. The theory of adaptive landscapes helps us to visualise the adaptive capacity of potential morphological forms. A concept attribute analysis methodology based on satisficing and adaptive landscapes has been developed and tested for application to engine concept design. The Plateau, Flooded Adaptive Landscape technique (PFAL),has been evaluated against exemplar engine life histories and shows merit in aiding the decision-making process for concept designers working with sparse data. The process lets the designer visualise the attribute map, enabling them to make better trade-off decisions and share these with non-expert stakeholders to gain their input in final concept choices.

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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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Tierney, Lauren. "An Agent-Based Model of Wildlife Migratory Patterns in Human-Disturbed Landscapes." Thesis, University of Oregon, 2015. http://hdl.handle.net/1794/19266.

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In recent years, human decision-making has led to significant landscape impacts in the western United States. Specifically, migratory wildlife populations have increasingly been impacted by rural urban development and energy resource development. This research presents the application of agent-based modeling to explore how such impacts influence the characteristics of migratory animal movement, focusing on mule deer (Odocoileus hemionus) in Western Wyoming. This study utilizes complex adaptive systems and agent-based modeling frameworks to increase understanding of migratory patterns in a changing landscape and explores thresholds of interference to migration patterns due to increased habitat degradation and fragmentation. The agent-based model utilizes GPS-collar data to examine how individual processes lead to population-level patterns of movement and adaptation. The assessment incorporates elements from both human and natural systems to explore potential future scenarios for human development in the natural landscape and incorporates adaptive behaviors, as well as animal-movement ecology, in changing landscapes.

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Horstkotte, Tim. "Contested Landscapes : social-ecological interactions between forestry and reindeer husbandry." Doctoral thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-66386.

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Throughout northern Fennoscandia, reindeer husbandry is a central part in the cultural heritage of the Sámi people. In its history, Sámi culture and reindeer husbandry have undergone significant adaptations to environmental, social and political challenges. Landscape changes on the winter grazing grounds were mainly driven by resource exploitation, especially by industrialized forestry. Important grazing resources were lost, i.e. terrestrial and arboreal lichens that constitute essential key elements in the herding year. In my thesis, I explore the consequences of these transformations in Swedish boreal forests for reindeer husbandry. The multi-disciplinary approach integrates interview studies, ecological fieldwork and theoretical modeling of forest development. I emphasize the understanding of landscapes as multi-dimensional concepts with ecological, social and economic components. They interact in determining the amount of landscape fragmentation in physical or administrative ways, or in enabling reindeer herders to move between different landscape elements. These elements, e.g. forest stands of different ages, can react differently to winter weather. Thus, they enable reindeer herders to adjust their grazing grounds according to the availability of forage, mediated by snow conditions. However, forestry practices have reduced the abundance of old-growth forests, and therewith the functionality of the landscape. By comparing snow conditions in different forest types, I show that multi-layered canopies can offer a more diverse pattern of snow hardness. However, the interaction between forest characteristics with snow is strongly dependent on weather conditions, e.g. the timing and intensity of warm spells. The prevalence of single-layered forest stands therefore can lead to a reduction in snow variability and potentially restricts the availability of suitable grazing grounds for reindeer. If snow conditions hinder reindeer in foraging on terrestrial lichens, old forests formerly supplied reindeer with arboreal lichens. I show how industrial forestry has reduced the availability of this emergency forage by the reduction of old forests and increased landscape fragmentation and analyze the consequences of different management strategies on future habitat availability for arboreal lichens. By integrating these results into a model of forest management, I offer insights into consequences arising from different priorities that either favor timber production or the development of lichen-rich grazing grounds. In conclusion, I emphasize the importance of landscape diversity, as well as the ability to make use of this diversity, as a source of adaptability of reindeer husbandry to changes in grazing conditions by e.g. winter weather dynamics. A shared future of reindeer husbandry and forestry could be fostered by encouraging the social-ecological co-evolution of multiple use landscapes and the enhancement of the cultural and biological significance of the Swedish boreal forests.

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Oba, Takuji. "Mathematical foundation of invasion exponents associated with adaptive dynamics." Kyoto University, 2019. http://hdl.handle.net/2433/242439.

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Gaunersdorfer, Andrea, and Cars H. Hommes. "Nonlinear adaptive beliefs and the dynamics of financial markets. The role of the evolutionary fitness measure." SFB Adaptive Information Systems and Modelling in Economics and Management Science, WU Vienna University of Economics and Business, 2001. http://epub.wu.ac.at/434/1/document.pdf.

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We introduce a simple asset pricing model with two types of adaptively learning traders, fundamentalists and technical traders. Traders update their beliefs according to past performance and to market conditions. The model generates endogenous price fluctuations and captures some stylized facts observed in real returns data, such as excess volatility, fat tails of returns distributions, volatility clustering, and long memory. We show that the results are quite robust w.r.t. to different choices for the performance measure. (author's abstract)
Series: Report Series SFB "Adaptive Information Systems and Modelling in Economics and Management Science"

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Nowak, Stefan [Verfasser], Joachim [Akademischer Betreuer] Krug, and Anton [Akademischer Betreuer] Bovier. "Properties of Random Fitness Landscapes and Their Influence on Evolutionary Dynamics. A Journey through the Hypercube / Stefan Nowak. Gutachter: Joachim Krug ; Anton Bovier." Köln : Universitäts- und Stadtbibliothek Köln, 2015. http://d-nb.info/1084169762/34.

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Leandersson, Dennis. "The role of copulatory wound infliction on fitness in Drosophila melanogaster." Thesis, Karlstads universitet, Fakulteten för hälsa, natur- och teknikvetenskap (from 2013), 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-84494.

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One of the more fascinating Darwinian puzzles in sexual selection is that of copulatory wounding. For those taxa displaying this behavior, and that does not engage in traumatic insemination, the function of wound infliction during copulation remains unknown. In this study, the intention was to evaluate the purpose of copulatory wounding in Drosophila melanogaster and the consequences it might have for male and female fecundity. The present study measured the size and number of wounds that males from different stocks of Darwinian fitness imposed on females, as well as the copulation duration and the resulting fecundity. The number of wounds and the total wound size showed no apparent correlation to fecundity, but a significant difference in variation of the number of wounds inflicted on females was observed between males from two different lines of fitness. Wounded females were also considerably more common than non-wounded females, as were wounds that were paired compared to non-paired copulatory wounds. The results suggests that wounding might be an adaptive male trait and a copulatory courtship interpretable to females, implying a possible case of cryptic female choice. Since most wounds were paired, this implies that a bilaterally symmetrical organ is causing these wounds. Also, wounding was not as important for fecundity as previously thought.
Ett av de mer fascinerande Darwinistiska pusslen inom sexuell selektion är skadande under kopulationen. För de taxa som uppvisar detta beteende, och inte engagerar sig i traumatisk insemination, så är funktionen av kopulationsskador okänd. I denna studie så var avsikten att utvärdera syftet av kopulationsskador hos Drosophila melanogaster och de konsekvenser beteendet kan ha för det resulterande antalet avkomma. Denna studie uppmätte storleken och antalet skador som hanar av olika Darwinistisk fitness vållade honor, samt kopulationstiden och antalet avkomma. Antalet skador och den totala storleken av skador visade ingen signifikant korrelation till antalet avkommor, däremot uppvisades signifikanta variationsskillnader mellan hanar av två olika fitnessnivåer. Skadade honor visade sig också vara betydligt vanligare än icke skadade honor och parade skador var även vanligare än icke parade skador. Resultaten indikerade att kopulationsskador kan vara en adaptiv egenskap hos hanar och en form av uppvaktning som honorna kan tyda, vilket kan antyda ett möjligt fall av ”kryptiskt honligt val”. Eftersom de flesta skador var parade, så antyder detta att ett bilateralt symmetriskt organ orsakar skadorna. Kopulationsskador visade sig heller inte vara så viktiga som man tidigare antagit.

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Chan, Yvonne H. "The Complex Role of Sequence and Structure in the Stability and Function of the TIM Barrel Proteins." eScholarship@UMMS, 2011. http://escholarship.umassmed.edu/gsbs_diss/934.

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Sequence divergence of orthologous proteins enables adaptation to a plethora of environmental stresses and promotes evolution of novel functions. As one of the most common motifs in biology capable of diverse enzymatic functions, the TIM barrel represents an ideal model system for mapping the phenotypic manifestations of protein sequence. Limits on evolution imposed by constraints on sequence and structure were investigated using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Exploration of fitness landscapes of phylogenetically distant orthologs provides a strategy for elucidating the complex interrelationship in the context of a protein fold. Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape. These results suggest that fitness landscapes of point mutants can be successfully translocated in sequence space, where knowledge of one landscape may be predictive for the landscape of another ortholog. Analysis of a surprising class of beneficial mutations in all three IGPS orthologs pointed to a long-range allosteric pathway towards the active site of the protein. Biophysical and biochemical analyses provided insights into the molecular mechanism of these beneficial fitness effects. Epistatic interactions suggest that the helical shell may be involved in the observed allostery. Taken together, knowledge of the fundamental properties of the TIM protein architecture will provide new strategies for de novo protein design of a highly targeted protein fold.

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Chan, Yvonne H. "The Complex Role of Sequence and Structure in the Stability and Function of the TIM Barrel Proteins." eScholarship@UMMS, 2017. https://escholarship.umassmed.edu/gsbs_diss/934.

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Sequence divergence of orthologous proteins enables adaptation to a plethora of environmental stresses and promotes evolution of novel functions. As one of the most common motifs in biology capable of diverse enzymatic functions, the TIM barrel represents an ideal model system for mapping the phenotypic manifestations of protein sequence. Limits on evolution imposed by constraints on sequence and structure were investigated using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Exploration of fitness landscapes of phylogenetically distant orthologs provides a strategy for elucidating the complex interrelationship in the context of a protein fold. Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape. These results suggest that fitness landscapes of point mutants can be successfully translocated in sequence space, where knowledge of one landscape may be predictive for the landscape of another ortholog. Analysis of a surprising class of beneficial mutations in all three IGPS orthologs pointed to a long-range allosteric pathway towards the active site of the protein. Biophysical and biochemical analyses provided insights into the molecular mechanism of these beneficial fitness effects. Epistatic interactions suggest that the helical shell may be involved in the observed allostery. Taken together, knowledge of the fundamental properties of the TIM protein architecture will provide new strategies for de novo protein design of a highly targeted protein fold.

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37

Peterson, Michael Ray. "Evolutionary Methodology for Optimization of Image Transforms Subject to Quantization Noise." Wright State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=wright1214303970.

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38

Wenger, Jacob A. "The Adaptive Evolution and Control of Biotypic Virulence in North American SoybeanAphids (Aphis glycines)." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1437564434.

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Pace, Bruno. "Rhythms and Evolution: Effects of Timing on Survival." Doctoral thesis, Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-213241.

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The evolution of metabolism regulation is an intertwined process, where different strategies are constantly being developed towards a cognitive ability to perceive and respond to an environment. Organisms depend on an orchestration of a complex set of chemical reactions: maintaining homeostasis with a changing environment, while simultaneously sending material and energetic resources to where they are needed. The success of an organism requires efficient metabolic regulation, highlighting the connection between evolution, population dynamics and the underlying biochemistry. In this work, I represent organisms as coupled information-processing networks, that is, gene-regulatory networks receiving signals from the environment and acting on chemical reactions, eventually affecting material flows. I discuss the mechanisms through which metabolism control is improved during evolution and how the nonlinearities of competition influence this solution-searching process. The propagation of the populations through the resulting landscapes generally point to the role of the rhythm of cell division as an essential phenotypic feature driving evolution. Subsequently, as it naturally follows, different representations of organisms as oscillators are constructed to indicate more precisely how the interplay between competition, maturation timing and cell-division synchronisation affects the expected evolutionary outcomes, not always leading to the \"survival of the fastest\".

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Fritsch, Coralie. "Approches probabilistes et numériques de modèles individus-centrés du chemostat." Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20062/document.

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Dans une première partie, nous proposons un nouveau modèle de chemostat dans lequel la population bactérienne est représentée de manière individu-centrée, structurée en masse, et la dynamique du substrat est modélisée par une équation différentielle ordinaire. Nous obtenons un processus markovien que nous décrivons à l'aide de mesures aléatoires. Nous déterminons, sous une certaine renormalisation du processus, un résultat de convergence en loi de ce modèle individu-centré hybride vers la solution d'un système d'équations intégro-différentielles. Dans une seconde partie, nous nous intéressons à des modèles de dynamiques adaptatives du chemostat. Nous reprenons le modèle individu-centré étudié dans la première partie, auquel nous ajoutons un mécanisme de mutation. Sous des hypothèses de mutations rares et de grande population, les résultats asymptotiques obtenus dans la première partie nous permettent de réduire l'étude d'une population mutante à un modèle de croissance-fragmentation-soutirage en milieu constant. Nous étudions la probabilité d'extinction de cette population mutante. Nous décrivons également le modèle déterministe associé au modèle individu-centré hybride avec mutation et nous comparons les deux approches, stochastique et déterministe; notamment nous démontrons qu'elles mènent au même critère de possibilité d'invasion d'une population mutante dans une population résidente.Nous présentons des simulations numériques illustrant les résultats mathématiques obtenus
In the first part, we propose a new chemostat model in which the bacterial population is mass structured and individual-based and the substrate dynamics are modelized by an ordinary differential equation. We obtain a Markovian process which we describe as random measures. We determine, under a certain normalization of the process, a result of convergence in distribution towards the solution of a system of integro-differential equations. In the second part, we are interested in adaptive dynamic models of the chemostat. We add a mutation mechanism to the individual-based model which was studied in the first part. Under rare mutations and large population size hypotheses, the asymptotical result of the first part allows us to reduce the study of the mutant population to a growth-fragmentation-washout model in a constant environment. We study the extinction probability of this mutant population. We also describe the deterministic model related to the hybrid individual-based model with mutations and we compare these two approaches (stochastic and deterministic). In particular we prove that the two approaches lead to the same invasion criteria of a mutant population in a resident population.We present numeric simulations in order to illustrate the mathematical results

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Torrents, Pau. "Farmers' participation in conservation of rural landscapes : A case study of the Menorca Biosphere Reserve (Spain)." Thesis, Stockholms universitet, Stockholm Resilience Centre, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-99774.

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In an European context of agricultural land abandonment, the role of the farming community as landscape stewards is crucial for maintaining the rural landscape as well as the ecosystem services provided by this landscape. Such stewardship is studied here by assessing the participation of the farming community in the management of Menorca Biosphere Reserve, a small Mediterranean island with very well conserved and rich rural landscape which is not escaping this tendency of land abandonment. A survey of 41 farms and interviews with 15 stakeholders were performed in order to assess the role of the farming community in participatory management processes and the effectiveness of the Menorca Biosphere Reserve Agency (MBRA) in facilitating their participation.The results show that the participatory activities of the MBRA are effective and highly valued by participating stakeholders but could be improved by: 1) engaging non-associated farmers and traditional farmers in the MBRA activities 2) finding a consensual and long-term solution on issues related to the access to private rural land 3) providing rapid feedback to participants after meetings and 4) transforming the MBRA structure in order to deal with changes and an uncertain future. Failing to do this could illegitimate further participatory activities, erode trust among stakeholders and alienate the farming community and the society, thereby affecting the maintenance of the rural landscape.This case study highlights the importance of appropriate management structure for adaptive co-management to benefit from the participation of stakeholders in general and farmers in particular. The findings should be of interest to managers, scholars and practitioners using adaptive co-management approaches to manage complex social-ecological systems such as rural, cultural landscapes.

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Köhler, Alexander [Verfasser], and Stephan [Akademischer Betreuer] Becker. "The species-specific effects of guinea pig adaptive mutations in Marburg virus VP40 and L on the protein’s functions and viral fitness / Alexander Köhler ; Betreuer: Stephan Becker." Marburg : Philipps-Universität Marburg, 2017. http://d-nb.info/1135385483/34.

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Köhler, Alexander Verfasser], and Stephan [Akademischer Betreuer] [Becker. "The species-specific effects of guinea pig adaptive mutations in Marburg virus VP40 and L on the protein’s functions and viral fitness / Alexander Köhler ; Betreuer: Stephan Becker." Marburg : Philipps-Universität Marburg, 2017. http://d-nb.info/1135385483/34.

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Duncan, Kayleigh E. "Islands of Fitness Compact Genetic Algorithm for Rapid In-Flight Control Learning in a Flapping-Wing Micro Air Vehicle: A Search Space Reduction Approach." Wright State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=wright1578065644405701.

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45

Kemble, Henry. "The genotype-phenotype relationship across different scales." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC178/document.

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Avec la révolution moléculaire en biologie, une compréhension des mécanismes de la relation génotype-phénotype est devenue possible. Récemment, les progrès réalisés dans la synthèse et le séquençage de l’ADN ont permis le développement d’expériences de deep-mutational scanning capable de quantifier divers phénotypes pour un ensemble de génotypes sur toute la longueur d’un gène. Ces ensembles de données sont non seulement intéressants en eux-mêmes, mais permettent également de tester de manière rigoureuse des modèles phénotypiques quantitatifs. Nous avons utilisé cette technologie pour caractériser les cartes séquence-fitness de 3 systèmes bactériens modèles: un régulateur global, la CRP, une enzyme de résistance aux antibiotiques, la β-lactamase, et une petite voie métabolique constituée des enzymes AraA et AraB. Ces systèmes ont été choisis pour éclairer les rôles de différentes caractéristiques dans la formation de la relation génotype-fitness (réseaux de régulations, stabilité des protéines et flux métabolique). Nous constatons que la tendance globale des effets sur le fitness semble prévaloir sur les tendances spécifiques. Ceci nous conduit à penser qu’une grande partie de la relation entre le génotype et le fitness pourrait être expliquée à partir de la forme des fonctions de phénotype-fitness. Par ailleurs, nous voyons que la caractérisation de la relation génotype-fitness dans différents systèmes peut être un moyen puissant d’obtenir des informations sur les phénotypes pertinents
With the molecular revolution in Biology, a mechanistic understanding of the genotype-phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep-mutational scanning experiments, capable of scoring comprehensive libraries of genotypes for a variety of phenotypes over the length of entire genes. Such datasets are not only interesting in themselves, but also allow rigorous testing of quantitative phenotypic models. We used this technology to characterise sequence-fitness maps for 3 model bacterial systems: a global regulator, CRP, an antibiotic-resistance enzyme, β-lactamase, and a small metabolic pathway, consisting of the enzymes AraA and AraB. These different systems were chosen to illuminate the roles of different mechanistic features in shaping the genotype-fitness relationship (regulatory wiring, protein stability and metabolic flux). We find that smooth patterns of fitness effects tend to prevail over idiosyncrasy, indicating that much of the genotype-fitness relationship could be understood from the global shape of smooth underlying phenotype-fitness functions. On the flip side, we see that characterising the genotype-fitness relationship in different systems can be a powerful way to glean phenotypic insights

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Matysek, K. "Resilience and Social-Ecological Systems: The UNESCO Biosphere Reserve Program in Australia and Canada." Thesis, Royal Society of Tasmania, University of Tasmania Library Special and Rare Materials Collection, 2009. https://eprints.utas.edu.au/11207/1/01front.pdf.

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United Nations Educational, Scientific and Cultural Organisation (UNESCO) Biosphere Reserves (BRs) provide an example of an integrated sustainability framework that allows for connection between international, national, state / provincial and local levels of conservation and capacitybuilding. The three major functions of a BR are conservation of biodiversity, sustainable development and support for logistics. As coupled social-ecological systems, BRs explicitly acknowledge that human systems and ecological systems are inextricably linked, and have the potential to bridge ecological and social-political spheres that have been viewed as predominantly disparate entities, rather than as interconnected or nested systems. The aim of this thesis is to identify the key features (assets, process and outcome) required to enhance the fit between governance systems and ecosystems using the UNESCO BR model, and develop a framework for establishing BRs as resilient working landscapes. By identifying features that seem critical for linking civil society, institutions and government dynamically across multiple levels, the research addresses the governance dimension of ecosystem management and the social factors that enable such management. The scope of the thesis is limited to developed country contexts. Data are derived from focus groups, site visits, 52 key informant interviews and literature reviews. The research process utilised an emergent, naturalistic inquiry, characterised by abductive, deductive and inductive methods. Four Australian and four Canadian qualitative case studies support and demonstrate the three phases of the BR resilience conceptual framework developed herein. UNESCO BRs originated in the early 1970s as international examples of biodiversity conservation and sites of scientific research and monitoring. Since this time, the international program has broadened to include more complex notions of social-ecological systems, reflecting shifts in environmental discourse and praxis. The Australian BR Program is characterised by governmentinitiated BRs and those generated though community-derived stewardship. Over the same period, the Canadian BR Program has consistently developed through community capacity and the Canadian Biosphere Reserve Association. Capital assets and ‘new governance’ processes are two of the three key phases of developing a successful (resilient) BR. Adaptive capacity is a key component of the final phase; the achievement of a resilient working landscape. In the framework, evolution and devolution of a BR occurs in response to social and ecological variables. However, maintenance and renewal of capital assets are crucial to sustaining the first and most fundamental phase of BR resilience. Specific guidelines for the application of the BR resilience conceptual framework are provided to inform individual BRs and their national programs more generally, and provide any party interested in the BR concept with a means to develop a resilient BR, from its inception. Avenues for future research are suggested, with a recommended focus upon harnessing greater understanding of resilience factors in social-ecological systems, and the relationship of these to BRs.

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Mangueira, Julia Raquel de Sá Abilio. "A regeneração natural como indicadora de conservação, de sustentabilidade e como base do manejo adaptativo de fragmentos florestais remanescentes inseridos em diferentes matrizes agrícolas." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/11/11150/tde-04072012-102118/.

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O cenário atual do estado de São Paulo reflete o cenário de degradação observado na Floresta Atlântica do país, onde os remanescentes florestais estão muito fragmentados, degradados e imersos em uma paisagem agrícola, dominada predominantemente por matrizes de cana de açúcar e pastagens. Neste contexto, objetivamos investigar se a regeneração natural da borda de fragmentos florestais tem características distintas nessas duas matrizes agrícolas dominantes. Nossa hipótese foi que de a regeneração natural em fragmentos inseridos em matrizes de cana de açúcar e pastagem são distintas, porque essas matrizes definem diferentes trajetórias de degradação sobre a flora de fragmentos naturais. Este trabalho foi desenvolvido na bacia do rio Corumbataí, onde indivíduos de espécies arbustivo e arbóreas do estrato regenerante (mínimo de 30cm de altura até 15 cm de perímetro à altura do peito) foram amostrados em 60 transectos de 30x2m (subdivididos em transectos contíguos de 10x2m) sistematicamente distribuídas a partir da borda de 12 fragmentos selecionados na bacia. Primeiramente, foi feita uma caracterização florística geral da regeneração natural das bordas de fragmentos florestais inseridos nas duas matrizes agrícolas. Posteriormente, foram utilizadas as variáveis número de indivíduos.hectare-1 (RN_HA) e número de espécies/m2 (NESP_M2) e diversidade florística (ISHANNON) para analisar as diferenças da estrutura e composição da regeneração natural nas duas matrizes. Essas mesmas variáveis foram utilizadas para analisar estatisticamente o efeito de indicadores de conservação dos fragmentos, como entrada de gado, presença de eucaliptos no dossel e abundância de gramíneas e lianas, sobre a regeneração natural. A similaridade florística entre remanescentes das paisagens foi calculada através do Índice de Similaridade de Jaccard. Em todos os transectos, foram amostrados 5886 regenerantes, divididos em 58 famílias, 220 espécies e 18 morfoespécies. O índice de Jaccard mostrou que houve similaridade florística (45%) entre os regenerantes dos fragmentos da matriz de pastagem e cana de açúcar. Nos fragmentos inseridos na matriz de pastagem, a entrada de gado foi o indicador de conservação de fragmentos que apresentou maior interferência sobre a regeneração natural, diminuindo tanto o número de indivíduos por unidade de área quanto a diversidade florística. Para a paisagem de cana, a fonte de variação que mais interferiu na estrutura da regeneração foi a presença de eucaliptos no dossel, que aumentou o número de indivíduos por unidade de área. A abundância de gramíneas e lianas e a presença de epífitas não apresentaram influência sobre a regeneração quando analisados tipo de matriz ou tamanho do fragmento. Entre os sub-transectos contíguos de 10m, não houve variação na estrutura e composição da regeneração natural, indicando que nesta profundidade de borda a vegetação regenerante é homogênea quanto à florística, diversidade e classificação sucessional. Os resultados indicam que, mesmo inseridos em paisagens agrícolas profundamente antropizadas, os remanescentes florestais ainda detém elevada diversidade florística. A regeneração natural mostrou-se um bom indicador de qualidade atual e futura dos remanescentes florestais, e demonstrou, juntamente com os indicadores de conservação, que os fragmentos são passíveis de manejo, o que poderá potencializar o papel de conservação da biodiversidade exercido pela regeneração natural.
At São Paulo state, Brazil, the scenario of the Atlantic Forest reflects the scenario of degradation of the biome in the country, where forest remnants are embedded in an agricultural landscape, dominated by sugar cane fields and pasture fields. In this context, we aimed to investigate if natural forest regeneration responds differently to each agricultural matrix. Our hypothesis was that forest regeneration composition in remnants surrounded by sugar cane fields is different of forest regeneration composition in remnants surrounded by pasture fields, because these agricultural matrices impact differently forest biota. The present research was developed in Corumbataí river basin, in the countryside of São Paulo state. Shrub and tree individuals, from regeneration layer, were sampled in 60 plots 30x2 meters long (subdivided in plots 10x2 meters long) systematically distributed on the edges of 12 fragments. Firstly, we characterized the natural regeneration of the edges of forest remnants embedded in agricultural landscapes. Then we used the variables number of individuals.ha-1 (RN_HA), number of species/m2 (NESP_M2) and floristic diversity (ISHANNON) to analyze the differences in structure and composition of forest natural regeneration between sugar cane fields and pasture fields. These variables were used to analyze the statistical effects of conservation indicators, such as cattle entrance on forest remnants, abundance of woody-vines and grasses, and presence of eucalyptus trees on forest canopy, on natural regeneration. Floristic similarity between forest remnants was assessed by Jaccard Similarity Index. 5886 saplings were sampled among the 60 plots, divided in 57 families, 214 species and 31 morphospecies. Jaccard index indicated floristic similarity (45%) among the fragments inserted in sugar cane field and pasture field. Among the fragments inserted in pasture field, cattle entrance was the conservation indicator with the strongest interference over natural regeneration, decreasing both the number of plants per area and the floristic diversity. At sugar cane landscape, presence of eucalyptus on forest canopy increased the number of individuals per area. Grass and woody-vines abundance and presence of epiphytes were not significant for any variable, when analyzed with matrix type or fragment size. Among the subplots of 10m long, there was no variation of structure and composition of natural regeneration, what indicates that, in relation to floristic, diversity and sucessional classification, the regenerant vegetation is homogeneous in the first 30 meters of the edge. The results indicate that, even embedded in anthropogenic agricultural landscapes, the remnants studied still retain high floristic diversity. Natural regeneration has shown to be a good indicator of actual and future quality of forest remnants, and, together with conservation indicators, demonstrated that the fragments studied are subject to management actions, which may improve the role of biodiversity conservancy developed by natural regeneration

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Notice, Joaquim [UNESP]. "Sistemas socioecológicos, resiliência e as comunidades locais de Cateme: os impactos da mineração do carvão em Moatize, Moçambique, no período de 2010-2014." Universidade Estadual Paulista (UNESP), 2017. http://hdl.handle.net/11449/152358.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Esta pesquisa resulta da perspectiva de verificação dos efeitos degradantes da ação das mineradoras concessionadas para a exploração do carvão em Moatize, Moçambique, com objetivo de analisar os impactos adversos sobre as comunidades locais de Cateme, fruto da relação direta entre livrar-se da pobreza que o país se encontra mergulhado desde a sua independência, e o quadro legal do processo em território moçambicano, que envolvessem investimentos privados, nacionais e estrangeiros, suscetíveis de contribuir para o desenvolvimento e o bem-estar social do país. A hipótese é de que as comunidades locais de Moatize acreditam na possibilidade do aparecimento de mais empresas, tal como a Vale Moçambique, para a extração dos recursos naturais nos seus lugares de origem, gerando assim piores condições de vida para elas. A metodologia do interacionismo simbólico, articulado principalmente por uma abordagem etnográfica, nos permitiu junto das populações abrangidas pelo processo de reassentamento em Cateme, mesmo nas cidades de Moatize e Tete, constatar a situação deplorável derivada da exploração desequilibrada e não sustentável do carvão na província de Tete. Diante disso, como forma de oferecer informações para o resgate da concordância e o conforto das comunidades locais, trabalhamos com a presente tese, fundamentados nas teorias de resiliência de comunidades e dos sistemas socioecológicos, justificada no contexto de um processo atual que envolve a superação de condições adversas das comunidades locais em suas vidas, fortalencendo os processos de resiliência comunitária. Entendemos, ao partirmos deste estudo, buscar uma relação socioecológica mais justa e responsável, contemplando a sustentabilidade das diversas comunidades locais, por meio de uma gestão ambiental participativa e adaptativa, integrando as instituções governamentais, as multinacionais e a população, na tomada de decisões e de políticas públicas voltadas à conservação dos recursos naturais e à preservação das raízes socioculturais tradicionais, cooperando no desenvolvimento da resiliência das comunidades envolvidas, a fim de proporcionar uma qualidade de vida e ambiental adequada para a população em Moçambique, diante das transformações referentes às multifuncionalidades de suas paisagens.
This research results from the perspective of verifying the degrading effects of coal mining operations in Moatize, Mozambique, in order to analyze the adverse impacts on the local communities of Cateme, as a result of the direct relationship between getting rid of poverty The country has been immersed since its independence and the legal framework of the process, in Mozambican territory, involving private investments, national and foreign, likely to contribute to the development and social welfare of the country. The hypothesis is that the local communities of Moatize believe in the possibility of the appearance of more companies, such as Vale Moçambique, to extract natural resources in their places of origin, thus generating worse living conditions for them. The methodology of symbolic interactionism, articulated mainly by an ethnographic approach, allowed the populations affected by the resettlement process in Cateme, even in the cities of Moatize and Tete, to note the deplorable situation derived from the unbalanced and unsustainable exploitation of coal in the province of Tete. Therefore, as a way to offer informations to the recovery of the concordance and comfort of local communities, we work with the present thesis, based on the resilience theories of communities and socioecological systems, justified in the context of a current process that involves overcoming conditions Local communities in their lives, strengthening community resilience processes. We intend to seek a more just and responsible socioecological relationship, taking into account the sustainability of the various local communities, through participatory and adaptive environmental management, integrating governmental institutions, multinationals and the population, in decision-making and of public policies aimed at the conservation of natural resources and the preservation of traditional socio-cultural roots, cooperating in the development of the resilience of the communities involved, in order to provide a suitable quality of life and environmental for the population in Mozambique, in face of the transformations regarding the multifunctional Its landscapes.
CNPq: 190668/2013-0

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Cote-Hammarlof, Pamela. "Investigating Evolutionary Innovation in Yeast Heat Shock Protein 90." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1103.

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The Heat Shock Protein 90 (Hsp90) is an essential and highly conserved chaperone that facilitates the maturation of a wide array of client proteins, including many kinases. These clients in turn regulate a wide array of cellular processes, such as signal transduction, and transcriptional reprogramming. As a result, the activity of Hsp90 has the potential to influence physiology, which in turn may influence the ability to adapt to new environments. Previous studies using a deep mutational scanning approach, (EMPIRIC) identified multiple substitutions within a 9 amino acid substrate-binding loop of yeast Hsp90 that provides a growth advantage for yeast under elevated salinity conditions and costs of adaptation under alternate environments. These results demonstrate that genetic alterations to a small region of Hsp90 can contribute to evolutionary change and promote adaptation to specific environments. However, because Hsp90 is a large, highly dynamic and multi-functional protein the adaptive potential and evolutionary constraints of Hsp90 across diverse environments requires further investigation. In this dissertation I used a modified version of EMPIRIC to examine the impact of environmental stress on the adaptive potential, costs and evolutionary constraints for a 118 amino acid functional region of the middle domain of yeast Hsp90 under endogenous expression levels and the entire Hsp90 protein sequence under low expression levels. Endogenous Hsp90 expression levels were used to observe how environment may affect Hsp90 mutant fitness effects in nature, while low expression levels were used as a sensitive readout of Hsp90 function and fitness. In general, I found that mutations within the middle domain of Hsp90 have similar fitness effects across many environments, whereas, under low Hsp90 expression I found that the fitness effects of Hsp90 mutants differed between environments. Under individual conditions multiple variants provided a growth advantage, however these variants exhibited growth defects in other environments, indicating costs of adaptation. When comparing experimental results to 261 extant eukaryotic sequences I find that natural variants of Hsp90 support growth in all environments. I identified protein regions that are enriched in beneficial, deleterious and costly mutations that coincides with residues involved in co-chaperone-client-binding interactions, stabilization of Hsp90 client-binding interfaces, stabilization of Hsp90 interdomains and ATPase chaperone activity. In summary, this thesis uncovers the adaptive potential, costs of adaptation and evolutionary constraints of Hsp90 mutations across several environments. These results complement and extend known structural and functional information, highlighting potential adaptive mechanisms. Furthermore, this work elucidates the impact environment can have on shaping Hsp90 evolution and suggests that fluctuating environments may have played a role in the long-term evolution of Hsp90.

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Hurta, Martin. "Koevoluční algoritmy a klasifikace." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2021. http://www.nusl.cz/ntk/nusl-445529.

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The aim of this work is to automatically design a program that is able to detect dyskinetic movement features in the measured patient's movement data. The program will be developed using Cartesian genetic programming equipped with coevolution of fitness predictors. This type of coevolution allows to speed up a design performed by Cartesian genetic programming by evaluating a quality of candidate solutions using only a part of training data. Evolved classifier achieves a performance (in terms of AUC) that is comparable with the existing solution while achieving threefold acceleration of the learning process compared to the variant without the fitness predictors, in average. Experiments with crossover methods for fitness predictors haven't shown a significant difference between investigated methods. However, interesting results were obtained while investigating integer data types that are more suitable for implementation in hardware. Using an unsigned eight-bit data type (uint8_t) we've achieved not only comparable classification performance (for significant dyskinesia AUC = 0.93 the same as for the existing solutions), with improved AUC for walking patient's data (AUC = 0.80, while existing solutions AUC = 0.73), but also nine times speedup of the design process compared to the approach without fitness predictors employing the float data type, in average.

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Dissertations / Theses on the topic 'Adaptive or fitness landscapes'

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