Dissertations / Theses on the topic 'Genetic adaptations'

In the area of artificial intelligence, the development of Evolutionary Algorithms (EAs) has been very active, especially in the last decade. These algorithms started to evolve when scientists from various regions of the world applied the principles of evolution to algorithmic search and problem solving. EAs have been utilised successfully in diverse complex application areas. Their success in tackling hard problems has been the engine of the field of Evolutionary Computation (EC). Nowadays, EAs are considered to be the best solution to use when facing a hard search or optimisation problem. Various improvements are continually being made with the design of new operators, hybrid models, among others. A very important example of such improvements is the use of parallel models of GAs (PGAs). PGAs have received widespread attention from various researchers as they have proved to be more effective than panmictic GAs, especially in terms of efficacy and speedup. This thesis focuses on, and investigates, cellular Genetic Algorithms (cGAs)-a competitive variant of parallel GAs. In a cGA, the tentative solutions evolve in overlapped neighbourhoods, allowing smooth diffusion of the solutions. The benefits derived from using cGAs come not only from flexibility gains and their fitness to the objective target in combination with a robust behaviour but also from their high performance and amenability to implementation using advanced custom silicon chip technologies. Nowadays, cGAs are considered as adaptable concepts for solving problems, especially complex optimisation problems. Due to their structural characteristics, cGAs are able to promote an adequate exploration/exploitation trade-off and thus maintain genetic diversity. Moreover, cGAs are characterised as being massively parallel and easy to implement. The structural characteristics inherited in a cGA provide an active area for investigation. Because of the vital role grid structure plays in determining the effectiveness of the algorithm, cellular dimensionality is the main issue to be investigated here. The implementation of cGAs is commonly carried out on a one- or two-dimensional structure. Studies that investigate higher cellular dimensions are lacking. Accordingly, this research focuses on cGAs that are implemented on a three-dimensional structure. Having a structure with three dimensions, specifically a cubic structure, facilitates faster spreading of solutions due to the shorter radius and denser neighbourhood that result from the vertical expansion of cells. In this thesis, a comparative study of cellular dimensionality is conducted. Simulation results demonstrate higher performance achieved by 3D-cGAs over their 2D-cGAs counterparts. The direct implementation of 3D-cGAs on the new advanced 3D-IC technology will provide added benefits such as higher performance combined with a reduction in interconnection delays, routing length, and power consumption. The maintenance of system reliability and availability is a major concern that must be addressed. A system is likely to fail due to either hard or soft errors. Therefore, detecting a fault before it deteriorates system performance is a crucial issue. Single Event Upsets (SEUs), or soft errors, do not cause permanent damage to system functionality, and can be handled using fault-tolerant techniques. Existing fault-tolerant techniques include hardware or software fault tolerance, or a combination of both. In this thesis, fault-tolerant techniques that mitigate SEUs at the algorithmic level are explored and the inherent abilities of cGAs to deal with these errors are investigated. A fault-tolerant technique and several mitigation techniques are also proposed, and faulty critical data are evaluated critical fault scenarios (stuck at ‘1’ and stuck at ‘0’ faults) are taken into consideration. Chief among several test and real world problems is the problem of determining the attitude of a vehicle using a Global Positioning System (GPS), which is an example of hard real-time application. Results illustrate the ability of cGAs to maintain their functionality and give an adequate performance even with the existence of up to 40% errors in fitness score cells. The final aspect investigated in this thesis is the dynamic characteristic of cGAs. cGAs, and EAs in general, are known to be stochastic search techniques. Hence, adaptive systems are required to continue to perform effectively in a changing environment, particularly when tackling real-world problems. The adaptation in cellular engines is mainly achieved through dynamic balancing between exploration and exploitation. This area has received considerable attention from researchers who focus on improving the algorithmic performance without incurring additional computational effort. The structural properties and the genetic operations provide ways to control selection pressure and, as a result, the exploration/exploitation trade-off. In this thesis, the genetic operations of cGAs, particularly the selection aspect and their influence on the search process, are investigated in order to dynamically control the exploration/exploitation trade-off. Two adaptive-dynamic techniques that use genetic diversity and convergence speeds to guide the search are proposed. Results obtained by evaluating the proposed approaches on a test bench of diverse-characteristic real-world and test problems showed improvement in dynamic cGAs performance over their static counterparts and other dynamic cGAs. For example, the proposed Diversity-Guided 3D-cGA outperformed all the other dynamic cGAs evaluated by obtaining a higher search success rate that reached to 55%.

Mycobacterium tuberculosis stably adapts to respiratory limited environments by entering into a nongrowing but metabolically active state termed quiescence. This state is inherently tolerant to antibiotics due to a reduction in growth and activity of associated biosynthetic pathways. Understanding the physiology of the quiescent state, therefore, may be useful in developing new strategies to improve drug efficiency. Here, we used an established in vitro model of respiratory stress, hypoxia, to induce quiescence. We utilized metabolomic and genetic approaches to identify essential and active pathways associated with nongrowth. Our metabolomic profile of hypoxic M. tuberculosis revealed an increase in several free fatty acids, metabolite intermediates in the oxidative pathway of the tricarboxylic acid (TCA) cycle, as well as, the important chemical messenger, cAMP. In tandem, a high-throughput transposon mutant library screen (TnSeq) revealed that a cAMP-regulated protein acetyltransferase, MtPat, was conditionally essential for survival in the hypoxic state. Via 13C-carbon flux tracing we show an MtPat mutant is deficient in re-routing hypoxic metabolism away from the oxidative TCA cycle and that MtPat is involved in inhibiting fatty-acid catabolism in hypoxia. Additionally, we show that reductive TCA metabolism is required for survival of hypoxia by depletion of an essential TCA enzyme, malate dehydrogenase (Mdh) both in in vitro hypoxia and in vivo mouse infection. Inhibition of Mdh with a novel compound resulted in a significantly greater killing efficiency than the first-line anti-M. tuberculosis drug isoniazid (INH). In conclusion, we show that understanding the physiology of the quiescent state can lead to new drug targets for M. tuberculosis.

Mycobacterium tuberculosis stably adapts to respiratory limited environments by entering into a nongrowing but metabolically active state termed quiescence. This state is inherently tolerant to antibiotics due to a reduction in growth and activity of associated biosynthetic pathways. Understanding the physiology of the quiescent state, therefore, may be useful in developing new strategies to improve drug efficiency. Here, we used an established in vitro model of respiratory stress, hypoxia, to induce quiescence. We utilized metabolomic and genetic approaches to identify essential and active pathways associated with nongrowth. Our metabolomic profile of hypoxic M. tuberculosis revealed an increase in several free fatty acids, metabolite intermediates in the oxidative pathway of the tricarboxylic acid (TCA) cycle, as well as, the important chemical messenger, cAMP. In tandem, a high-throughput transposon mutant library screen (TnSeq) revealed that a cAMP-regulated protein acetyltransferase, MtPat, was conditionally essential for survival in the hypoxic state. Via 13C-carbon flux tracing we show an MtPat mutant is deficient in re-routing hypoxic metabolism away from the oxidative TCA cycle and that MtPat is involved in inhibiting fatty-acid catabolism in hypoxia. Additionally, we show that reductive TCA metabolism is required for survival of hypoxia by depletion of an essential TCA enzyme, malate dehydrogenase (Mdh) both in in vitro hypoxia and in vivo mouse infection. Inhibition of Mdh with a novel compound resulted in a significantly greater killing efficiency than the first-line anti-M. tuberculosis drug isoniazid (INH). In conclusion, we show that understanding the physiology of the quiescent state can lead to new drug targets for M. tuberculosis.

Systems biology approaches have allowed for comprehensive understanding of complicated biological processes. Here, we’ve developed a global phenotypic profiling method by improving upon transposon mutagenesis methods for identifying genes required for bacterial growth in various conditions. By using the massively parallel power of Illumina sequencing, we precisely redefined the genes required for the growth of Mycobacterium Tuberculosis (Mtb) in vitro. This adapted technique provided more informative data with both increased dynamic range and resolution. As a result, we quantitatively assessed the fitness of individual mutants, as well as identified sub-genic essentiality. Mtb is well adapted to its nutrient-limiting intracellular niche. One important and novel adaptation is its ability to consume cholesterol for both energy and carbon. A combination of this genome-wide phenotypic analysis and global metabolite profiling was used to define the dedicated cholesterol catabolic pathway, as well as important transcriptional and metabolic adaptations required for the consumption of this carbon source. We identified the methylcitrate cycle (MCC) and an unexpected gluconeogenic route as essential pathways. Furthermore, we found that the cholesterol-dependent transcriptional induction of these metabolic enzymes was also essential for growth on this substrate, a function mediated by the Rv1129c regulatory protein. Using a combination of genetic and chemical methods to inhibit these pathways, we show that cholesterol represents a significant source of carbon during intracellular growth in macrophages. Finally, we have begun to define the mechanism by which lipids, such as cholesterol, are imported into the cell by investigating the assembly of the ABC-like lipid transporter, Mce1. The subunits of this system are localized to the cell wall and data is provided to support a novel mechanism for Mce-dependent import of lipids, such as cholesterol. In sum, this global analysis of host cholesterol utilization during infection provides insight into each step of this complicated process; import into the bacterial cell, the degradation of the molecule into primary metabolites, and the transformation of these metabolites into carbon and energy.

L’addiction est une pathologie mentale chronique caractérisée par une recherche et une prise compulsive de drogue malgré la perception de conséquences physiques et psychologiques négatives. L’amygdale étendue (EA) est une entité neuroanatomique impliquée dans les réponses comportementales au stress et à l’anxiété et est placée à l’interface des circuits du stress et de la récompense. Les neuroadaptations se produisant dans l’EA durant la consommation chronique de drogue sont impliquées dans l’émergence d’un état émotionnel négatif apparaissant et se développant avec le sevrage. Les modifications se déroulant dans l’AE sont susceptibles d’être impliquées dans les phénomènes de recherche compulsive de drogue et dans la rechute. Les récepteurs aux opioïdes mu font partie du système opioïde endogène et leur activation est cruciale pour la médiation des effets récompensants des drogues. Dans la première partie de cette thèse, nous avons étudié les variations du niveau d’expression des gènes mu-dépendants au niveau de l’EA après un traitement chronique à l’alcool. Nous avons vérifié si l’expression des gènes régulés par l’activation chronique du récepteur mu était également régulée par l’exposition chronique à des drogues non opiacées. Les régulations observées suggèrent que le développement de l’addiction à l’alcool est accompagné d’un remodelage des épines dendritiques et d’une modification de l’activité neuronale dans l’EA. Dans la seconde partie de cette thèse, nous avons créé et caractérisé de nouveaux modèles génétiques qui seront utiles pour améliorer notre compréhension concernant le rôle joué par le récepteur aux opioïdes mu dans l’expression des conduites addictives
Addiction is a chronic relapsing disorder characterized by compulsive drug-seeking and drug-taking despite negative consequences. The extended amygdala (EA) is a neuroanatomical entity that interfaces brain reward and stress systems and that is involved in behavioral responses related to stress and anxiety. Neuroadaptations within this neural circuit during chronic drug of abuse consumption are involved in the emergence of the negative emotional state that appears with drug withdrawal and that increases with the development of addiction. Therefore modifications occurring within this structure are likely involved in molecular mechanisms underlying drug craving and relapse. Mu opioid receptors are part of the endogenous opioid system and its activation was shown to be crucial for the reinforcing and addictive properties of opiate as well as other drugs of abuse. The first aim of this thesis project was to study variations occurring in the expression of mu opioid receptor-dependent genes in the EA following alcohol exposure. We investigated whether the expression of genes whose transcription is modulated by the chronic activation of mu opioid receptor in the EA is also regulated by chronic treatments using non opiate drugs of abuse. The observed transcriptional regulations suggest that the development of alcohol addiction is accompanied with dendritic spine remodeling and modifications in neuronal activity in the EA. The second aim of this thesis work consisted in the generation and characterization of novel murine genetic models that would be useful to expand our understanding on mu opioid receptor implication in addictive behaviors

Modern humans originated in Africa around 200,000 years ago and today have settled in nearly every corner of earth. During migrations humans became exposed to new pathogens, food sources and have encountered vastly different environments. Natural selection likely contributed to the survival under such diverse conditions by promoting the raise in frequency of advantageous alleles. Thereby natural selection leaves genetic footprints that we can identify. The thesis at hand is about understanding how natural selection has shaped different human populations by analyzing these genetic footprints. In the first study, I infer the evolutionary history of an insertion-substitution variant using present-day human genomic data. This variant is interesting because the ancestral allele encodes a previously unannotated open-reading frame for a gene with antiviral ac- tivity (IFNL4 ), while the derived allele truncates this open-reading frame and is strongly associated with improved clearance of Hepatitis C, a major health care problem. Using an approximate bayesian computation approach I infer a complex evolutionary history, where the derived, truncating allele evolved under weak positive selection in Africa, with selection strength increasing in non-African populations, especially in East Asian popu- lations where the truncating allele is nearly fixed today. Hence, the changes in selection and resulting population differences in allele frequency contribute to the variation in Hep- atitis C clearance observed across human populations today. In the second study, I use ancient human genomes to estimate genome-wide allele frequencies in the past to understand present-day population differentiation. I develop a new statistic and incorporate the genome of Ust’-Ishim, a modern human that lived 45,000 year ago in Siberia, to study to what extent natural selection and drift have contributed to human population differentiation. The results suggest that European populations carry high frequency alleles in protein-coding (genic) regions that evolved under strong, recent positive selection. Further, the genic alleles that rose in frequency recently in Europeans were already present in ancient hunter-gatherers more often than in ancient farmers. This suggests that during the colonization of Europe local, positive selection changed the frequency of advantageous alleles in hunter-gatherer populations prior to the influx of farming individuals and those alleles remained beneficial also in the later admixed populations.

Prédire les réponses de la biodiversité aux changements climatiques anthropiques est devenu un champ de recherche avec des enjeux scientifiques et sociétaux majeurs. Mon travail de thèse a consisté à évaluer les impacts du réchauffement climatique sur un parasitoïde de drosophiles, Leptopilina boulardi, à une petite échelle géographique, le sud-est de la France. L'objectif était non seulement d'examiner l'évolution de la distribution du parasitoïde en réponse à une hausse des températures qu'il fallait préciser à cette échelle géographique, mais aussi d'appréhender les adaptations mises en place dans la zone de progression de l'espèce. Dans un premier temps, l'analyse de données d'échantillonnages et de données météorologiques m'ont permis de mettre en évidence une rapide expansion de l'aire de répartition du parasitoïde vers le nord, à un taux moyen de 90km/décennie, simultanément à une augmentation moyenne de la température de 1,57°C ces 30 dernières années, dans l'aire d'étude. Après avoir identifié les principaux facteurs environnementaux, structurant la répartition spatiale de L. boulardi, j'ai modélisé sa distribution potentielle dans le sud-est de la France, sous conditions climatiques actuelles et pour 2050, pour deux scénarios d'émission de CO2. En 2050, la distribution géographique de L. boulardi devrait considérablement s'étendre vers le nord sous l'effet des changements climatiques. Ensuite, en mesurant plusieurs traits d'histoire de vie selon 4 régimes thermiques fluctuants, j'ai montré que les populations de L. boulardi situées en limite d'aire de répartition sont génétiquement différenciées de celles situées dans l'aire centrale de répartition. Le fait que les populations marginales aient une valeur sélective plus importante à faible température suggère une adaptation locale des parasitoïdes dans la zone de progression de l'aire de répartition. La dernière partie de ce travail de thèse a pour objectif de mieux comprendre le processus de colonisation de L. boulardi. Pour cela, j'ai entrepris le développement de marqueurs RAD-sequencing sur 15 populations de cette espèce, distribuées le long d'un cline de latitude dans le sud-est de la France. Les nombreuses données issues du séquençage Illumina me permettront de connaître la structuration génétique de ces populations. L'ensemble de ces résultats obtenus au cours de ma thèse révèlent la force avec laquelle les changements climatiques peuvent impacter les espèces, principalement celles de haut niveau trophique, en provoquant des changements très rapide de distribution et des modifications génotypiques et phénotypiques permettant une meilleure adaptation locale
Predicting biodiversity responses to anthropogenic climate change has become a field of research with major scientific and societal issues. The main goal of my thesis was to evaluate the impacts of global warming on a Drosophila parasitoid, Leptopilina boulardi, at a small geographical scale, the South-East of France. The aim was not only to examine the change in the distribution of the parasitoid in response to rising temperatures, but also to understand the adaptations associated with this change. First, the analysis of insect sampling and meteorological data allowed me to demonstrate a rapid expansion of the parasitoid range to the north with an average rate of 90km/decade as well as a simultaneous temperature increase of 1.57°C on average over the past 30 years in the studied area. Following the identification of the main environmental factors structuring the spatial distribution of L. boulardi, I fitted a model predicting its potential distribution in the south-east of France, under the current climate and in 2050, for two CO2 emission scenarios. In 2050, the geographical distribution of L. boulardi should significantly extend northward as a result of climate change. Then, by measuring several life history traits under four fluctuating temperature regimes, I have shown that populations of L. boulardi located on the border of the range are genetically differentiated from those in the central range. The fact that marginal populations have a greater fitness at low temperature suggests local adaptation of parasitoids in the area of progression of range. The last part of this thesis aimed to better understand the process of colonization of L. boulardi. For this, I undertook the development of RAD-sequencing markers to genotype 15 populations of this species distributed along a cline of latitude in the southeast of France. Numerous data from Illumina sequencing will allow me to characterize the genetic structure of the populations. All the results obtained in my thesis highlight the force with which climate change may impact species, in particular those of high trophic level, causing rapid changes in distribution along with genotypic and phenotypic changes underlying local adaptation

The genetic basis of phenotypes that have contributed to the adaptation of species and organisms to new environments is a central question in evolutionary genetics. The recent accumulation of genetic variability data has allowed a genome-wide search for different signatures of positive selection which has led to the discovery of hundreds of putative candidate genes that may have played a role in adaptation. However, such hypothesis-free approaches do not reveal either causal variants or the actual biological mechanisms that have made each adaptation possible. Furthermore, the detection of molecular signatures is limited both by the complex architecture of the genome and by the possible polygenic nature of the selected trait. In this thesis, through different evolutionary and functional approaches, we have disentangled the adaptive role of two non-synonymous variants in two different candidate genes encoding for a lymphocyte receptor and a zinc transporter, respectively. In past human adaptation, they were most likely selected as more effective means to fight pathogens. We have also revealed differences in the action of natural selection between different pathways and different coding and non-coding genomic elements in the chimpanzee lineage by analyzing polymorphisms and divergence data together. Thus, the results of this PhD thesis have contributed to detect new instances of genetic adaptation and provide biological explanation to them.
La base genética de los carácteres que han contribuido a la adaptación de los organismos y las especies ha sido siempre una pregunta central en biología evolutiva. Gracias a la acumulación masiva de datos de variabilidad genética, en los últimos años se ha podido detectar en el genoma diferentes señales de selección positiva y también localizar cientos de genes candidatos que han podido tener un papel en la adaptación de las poblaciones a diferentes ambientes. Sin embargo en estos estudios, donde no hay una hipótesis a priori, se desconoce qué variantes dentro de estos genes fueron realmente las que proporcionaron una ventaja selectiva y por qué. Además, la compleja arquitectura del genoma y la naturaleza poligénica de muchos carácteres hace que sea difícil detectar casos más complejos de adaptación. En esta tesis se intenta resolver algunos de estos problemas. En primer lugar, mediante un enfoque evolutivo y funcional, hemos descifrado el rol adaptativo de dos variantes genéticas, una en un receptor linfocitario y la otra en un transportador de zinc, que probablemente fueron seleccionadas por conferir resistencia a patógenos. En segundo lugar, mediante el análisis de datos de polimorfismo y divergencia conjuntamente, también hemos detectado distintos mecanismos de acción de la selección natural en distintos pathways y entre elementos codificantes y elementos no codificantes reguladores en chimpancé.

Evolution frequently plays out over ecological timescales. Local adaptation under the joint action of evolutionary and ecological processes frequently leads to novel outcomes, as is evidenced by the theoretical work on adaptation at species' borders. However, to date this body of work does not have a theory for the effect of stochastic processes on local adaptation. The primary goal of this thesis is to show that demographic and genetic fluctuations can significantly impact upon local adaptation. In addition, the effect of polygenic evolution is also analysed. Specifically, three types of models are considered. First a deterministic mainland-island, subject to hard directional selection, maladaptive gene flow and density regulation is solved for two different trait architectures: an explicit multilocus trait and a quantitative trait. The maladaptive and adaptive steady states can be bistable. This depends on the underlying architecture of the trait, as well as locus number and ploidy. Sourcesink structure can emerge, accompanied by a novel, upper critical threshold above which maladaptation occurs. The most favourable condition for local adaptation occurs for few loci and low migration. Second, a stochastic version of the mainland-island model is analysed as a diffusion process. This is the central premise of the thesis and is explored by examining properties of the stationary distributions of both trait architectures, and the first-passage properties of the single locus case. It is found that across a range of migration rates that depend on locus number and migrant polymorphism, local adaptation may be reversed or escape from maladaptation becomes possible at varying transition rates. The diffusion model is compared to a similar discrete model. The continuous model is in good qualitative agreement with the discrete model. Third, the stochastic model is generalised to the infinite island model, which evolves deterministically. Under deterministic dynamics a range of equilibria are possible, depending on whether habitat size varies or is fixed. Multilocus dynamics restrict the conditions for polymorphism. Stochastic dynamics can have potentially detrimental consequences for the persistence of the island population when drift is strong. The relevance of the stochastic model to border populations is discussed. Although the diffusion process imposes severe constraints on the permissible parameter ranges, it is still able to provide a good qualitative understanding of the impact demographic and genetic fluctuations have on local adaptation.

Population Genetics has led to countless numbers of fruitful studies of evolution, due to its abilities for prediction and description of the most important evolutionary processes such as mutation, genetic drift and selection. The field is still growing today, with new methods and models being developed to answer questions of evolutionary relevance and to lift the veil on the past of all life forms. In this thesis, I present a modest contribution to the growth of population genetics. I investigate different questions related to the dynamics of populations, with particular focus on studying human evolution. I derive an upper bound and a lower bound for FST, a classical measure of population differentiation, as functions of the homozygosity in each of the two studied populations, and apply the result to discuss observed differentiation levels between human populations. I introduce a new criterion, the Gain of Informativeness for Assignment, to help us decide whether two genetic markers should be combined into a haplotype marker and improve the assignment of individuals to a panel of reference populations. Applying the method on SNP data for French, German and Swiss individuals, I show how haplotypes can lead to better assignment results when they are supervised by GIA. I also derive the population size over time as a function of the densities of cumulative coalescent times, show the robustness of this result to the number of loci as well as the sample size, and together with a simple algorithm of gene-genealogy inference, apply the method on low recombining regions of the human genome for four worldwide populations. I recover previously observed population size shapes, as well as uncover an early divergence of the Yoruba population from the non-African populations, suggesting ancient population structure on the African continent prior to the Out-of-Africa event. Finally, I present a case study of human adaptation to an arsenic-rich environment.

Understanding the process of adaptation requires elucidating the mechanisms through which natural selection alters the genetic variation underlying phenotypic traits. Here, I explore the genetics of adaptive evolution empirically, using lab and field experiments with threespine stickleback fish, and theoretically, using population genetic models. Freshwater stickleback populations are derived from ancestral marine populations that colonized lakes and streams at the end of the last ice age. These derived populations exhibit remarkable parallel divergence in a number of morphological and physiological traits. The parallel nature of these changes suggests the influence of natural selection, because genetic drift is unlikely to produce a strong correlation between phenotype and environment. Adaptive evolution in some of these traits is due to selection on standing genetic variation present in the ancestral marine population. I investigate the ecological, ontogenetic and behavioural mechanisms that contribute to the maintenance of this variation. I present evidence of extremely strong selection acting at phenotypic and genotypic levels over short time scales. Population genetic theory typically assumes much smaller selection coefficients than those measured in this work. I derive population genetic theory to describe the distribution of fitness effects of beneficial mutations without this restriction of weak selection, and test the analytical theory with numerical simulations. Collectively, this research is helping to identify some of the primary functional mechanisms that maintain genetic variation within and between natural populations.

Revolutions in sequencing technology have provided an unprecedented opportunity to uncover the genetic basis of traits of adaptive importance, enabling researchers not only to merely describe the means of inheritance of traits but also to establish the genetic changes under selection. This thesis examines the loci involved in two recent episodes of strong selection, namely the suppression of Wolbachia-induced male-killing in the butterfly Hypolimnas bolina and the evolution of melanism in moths. H. bolina has evolved the ability to suppress the male-killing effects of the heritable endosymbiont Wolbachia. This thesis demonstrates firstly that this results from a single locus trait that doesn't involve genetic variants beyond chromosome 25. This simple genetic basis explains in part the speed of spread of the suppressor in natural populations. The hypothesis that the insect sex determination gene doublesex is the target of selection is then examined. Compatible with this hypothesis, doublesex variants were found to cosegregate with suppression, and that the peak of a selective sweep is located within doublesex region. An unusual pattern of inheritance was uncovered at the doublesex locus, suggestive of a duplication event. These data are consistent with, though not proof of, Wolbachia driving the evolution of this key sex determination gene. The progression of a selective sweep for the suppression, as it travelled in space across Independent Samoa, was then examined. The sweep across Independent Samoa corroborated the genomic region immediately around doublesex as the target of selection. The sweep was very broad but weakened as it progressed across Samoa. The thesis then examines the genetic basis of melanism in Lepidoptera, and compares the genomic region associated with a naturally selected melanistic form to a laboratory mutant. The 'natural' example corresponded to a known genomic hotspot for colour pattern evolution, whereas this region was excluded in the laboratory mutants. These data support the pleiotropic view of convergence - that involvement of a single region is associated with minimized non-target effects. The thesis ends with a discussion of these data and a programme for future research in the area.

The human colonization of worldwide landmasses occurred through complex patterns of dispersal and admixture. At the same time, the survival in the different areas of the world depended on the adaptation to new habitats that imposed novel selective challenges. With the advent of high-throughput genotyping technologies and dense catalogues of human genetic variation, the demographic history of many human populations has been unraveled from genomic data, with important implications in medical genetics. However, several human groups are yet to be genetically characterized. These incomplete past histories include the determination of ancestries of the current Cuban population, as well as the origins and dispersal of European Romani, whose demographic history is aimed to be reconstructed in this work. Finally, the present study also aims to describe the genetic basis and evolution of one of the most striking human phenotypes, the African Pygmy height.
La colonización humana de las diferentes masas continentales se produjo mediante complejos patrones de dispersión y mezcla. La supervivencia en las diversas regiones del planeta ha dependido de la adaptación a las presiones selectivas impuestas por los nuevos hábitats. Con el desarrollo de tecnologías de genotipado masivo y las bases de datos de la diversidad genética humana, la historia demográfica de muchas poblaciones humanas, y sus implicaciones médicas, han sido descritas. Sin embargo, algunas poblaciones todavía no han sido caracterizadas genéticamente. Por ejemplo, tanto la descomposición de la ancestría genética de la población cubana actual como los orígenes y la dispersión de los gitanos europeos siguen siendo historias incompletas que se han reconstruido en esta tesis. Finalmente, este estudio también tiene como objetivo describir la evolución y las bases genéticas de uno de los fenotipos humanos más llamativos, la altura de los pigmeos africanos.

Dissertation presented to obtain the Ph.D degree in Evolutionary Biology
Understanding the genetic basis of adaptation is crucial to explain the emergence and maintenance of the multitude of life forms we find on Earth today. Perhaps even more importantly, gaining knowledge about how fast organisms can cope with environmental changes may prove crucial in a world being altered at increasing speed due to the human actions. The study of adaptive evolution may therefore have major implications (and applications) in Agriculture, Conservation of endangered species and even Human Health. Natural selection has long been appreciated as one of the predominant evolutionary mechanisms and it enjoys a solid theoretical framework regarding its requirements, its effects and its limitations. Empirically, however, it has proved quite challenging to study. In wild populations natural selection is particularly difficult to characterize and measure since in these settings other evolutionary mechanisms (such as genetic drift or gene flow) often occur simultaneously. In addition to this, the different evolutionary mechanisms may vary greatly in time and in space with respect to their relative influences on the evolutionary dynamics of populations.(...)

Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations. Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci. The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry. This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.

The processes driving and maintaining variable immune responses are poorly understood compared with other aspects of an organism’s ecology. This is particularly true from an evolutionary perspective, as the evolutionary relationships between immune responses and other traits and processes in nature remain inadequately explored. I investigated these associations in this thesis using the three-spined stickleback system as an evolutionary and immunological model. I combined sampling of wild individuals with genomic analyses to demonstrate phenotypic and genomic associations between immune responses and life history evolution across multiple populations. I also observe how experimental changes in daylength, a seasonal cue, modulate immune responses and increase parasite susceptibility in a controlled laboratory experiment. These findings occur independently of natural variation in parasite resistance. Stickleback are also a model for studies of speciation. I used sampling of wild hybrids to assess the significance of immune variation in postzygotic isolating mechanisms between diverging ecotypes; although my findings suggest a minor role. Finally, I demonstrate that genomic responses to parasitism and abiotic environmental variation are repeatable across independent, intercontinental adaptive radiation events in sticklebacks; conferring a repeatability of the evolutionary relationships of immune variation documented in this thesis. The findings within this thesis therefore provide novel insights into poorly explored or open areas of research regarding how variable immune responses evolve in nature.

Drug efflux represents an important protection mechanism against antibiotics and environmental toxic compounds in bacteria. Efflux genes constitute from 6% to 18% of all transporters in bacterial genomes, yet their regulation, natural substrates, and physiological functions are poorly understood. Among the 20 chromosomally encoded efflux genes in Escherichia coli K-12, only the AcrAB-TolC efflux system is constitutively expressed under the ordinary laboratory growth of E. coli. To explore conditions and circumstances that trigger the expression of additional efflux genes as well as their physiological functions, I examined the expression of all 20 efflux genes under a physiologically relevant circumstance for E. coli, which is anaerobic condition in this study. I found that expression of an RND type efflux pump MdtEF is up-regulated more than 20 fold when E. coli is cultured under anaerobic conditions. Mutagenesis studies revealed that the anaerobically induced expression of mdtEF is subject to the regulation of the anaerobic global transcription factor ArcA. Direct drug efflux and tolerance assay showed that anaerobically grown E. coli cells display an increased efflux activity and enhanced drug tolerance in an MdtEF dependent manner, confirming the functional up-regulation of the efflux pump MdtEF in the anaerobic physiology of E. coli. Since the up-regulation of mdtEF by anaerobic growth occurs in the absence of antibiotics and drugs, I speculate that MdtEF has physiological functions under the anaerobic growth of E. coli. To explore this, I first compared the viability of ΔmdtEF and WT MG1655 strains and found that ΔmdtEF caused a decreased cell survival during prolonged anaerobic growth of E. coli. Interestingly, this defect became more pronounced when cells grow in the presence of 10 mM nitrate, but no defect was observed in ΔmdtEF strain when cells grow in the presence of 40 mM fumarate under the same anaerobic conditions, suggesting that MdtEF has physiological roles relevant to the anaerobic respiration of nitrate. I further found that E. coli cells harboring the deletion of mdtEF are susceptible to indole nitrosative derivatives, a class of toxic by-products formed and accumulated within E. coli when the bacterium respires nitrate under anaerobic conditions, and deletion of the genes responsible for the biosynthesis of indole, tnaAB, restores the growth defect of the ΔmdtEF strain during anaerobic respiration of nitrate. Taken together, I conclude that the multidrug efflux pump MdtEF expels the nitrosated indole derivatives out of E. coli cells under anaerobic conditions. Since the production and accumulation of nitrosyl indole derivatives is ascribed to the reactive nitrogen species elicited when E. coli consumes nitrate, I propose that the up-regulated multidrug efflux pump MdtEF functions to protect E. coli from nitrosative damage in its anaerobic ecological niches.
published_or_final_version
Biological Sciences
Master
Master of Philosophy

Evolutionary Algorithms are search algorithms based on the Darwinian metaphor of “Natural Selection”. Typically these algorithms maintain a population of individual solutions, each of which has a fitness attached to it, which in some way reflects the quality of the solution. The search proceeds via the iterative generation, evaluation and possible incorporation of new individuals based on the current population, using a number of parameterised genetic operators. In this thesis the phenomenon of Self Adaptation of the genetic operators is investigated. A new framework for classifying adaptive algorithms is proposed, based on the scope of the adaptation, and on the nature of the transition function guiding the search through the space of possible configurations of the algorithm. Mechanisms are investigated for achieving the self adaptation of recombination and mutation operators within a genetic algorithm, and means of combining them are investigated. These are shown to produce significantly better results than any of the combinations of fixed operators tested, across a range of problem types. These new operators reduce the need for the designer of an algorithm to select appropriate choices of operators and parameters, thus aiding the implementation of genetic algorithms. The nature of the evolving search strategies are investigated and explained in terms of the known properties of the landscapes used, and it is suggested how observations of evolving strategies on unknown landscapes may be used to categorise them, and guide further changes in other facets of the genetic algorithm. This work provides a contribution towards the study of adaptation in Evolutionary Algorithms, and towards the design of robust search algorithms for “real world” problems.

Multi environment trials conducted over mapping population are often used to test genotypes in a set of environments that represent the target environmental range. The first part of this work is the evaluation of the ‘Nure’ x ‘Tremois’ double-­‐haploid mapping population, together with an association panel comprising 185 barley varieties representative of the barley germplasm cultivated in the Mediterranean basin. Plant material was tested across eighteen site by year field trials combination, in six countries across the Mediterranean basin. Trials were growth at sites contrasting for natural rainfall (high vs low on the base of past meteorological data) or at the same site with one being rainfed and the other with supplementary irrigation. Trials conducted for two years in each one of the sites and this allowed tocollect a huge data series comprising agronomical traits defining grain yield and yield components, phenological and environmental data, subsequently used to identify genomic regions involved in barley adaptation. The 118 doubled haploid lines of the mapping population were genotyped with Diversity Array Technology® (DaRT) marker assay and subsequently a total of 15 CAPS and SSCP marker for candidate genes involved in phenology regulation and abiotic stress response were added to the linkage map based on DaRT markers. Data collected were firstly used to perform QTLs analysis with composite interval mapping for any environment/ trait combination, results showed eight QTLs for grain yield, days to heading and grain yield components. . The two mostly frequents QTLs for grain yield and days to heading were located on barley chromosome 1H (3 trials), 2H (8 trials) and 5H (5 trials) overlapping respectively HvFT3 gene, the earliness per se locus (eam6/Eps-­‐2) and the vernalization gene Vrn_H1. A further QTL multi-­‐environment analysis was performed and revealed that across the 18 field trials QTL for eam6/Eps-­‐2 (2H) and Vrn-­‐H1 (5H) were commons for days to heading and grain yield. We use all the environmental information collected to check QTLs sensitivities to co-­‐environmental co-­‐variables. Most of significant associations collected were related to temperature and temperature-­‐based variables troughtout the growing cycle. Eam6/Eps-­‐2 showed non-­‐crossover QTL.E interaction, while for Vrn-­‐H1 crossover interactions were revealed. The 185 barley accession were genotyped with 1536 SNPs and data collected for this population for cold resistance in two field trials in Spain an Italy, the first trial was characterized by an exceptional winter, while the second was previously know has frost-­‐prone environment. Results from genome wide association analysis showed 13 positive associations with specific genomic regions. Interestingly several of these QTL were coincident with the position of previously mapped loci for cold tolerance, on chromosomes 2HL, 4HL and 5HL.
Els assajos en localitats múltiplas de poblacions de mapeo s'utilitzen freqüentment per a testar genotips en un conjunt d'ambients representatius de la condicions climàtiques on es volen introduir aquests genotips. La primera part d'això treball ha estat l'avaluació de la població de mapeo ‘Nure x Tremois’ constituïda de 118 de doble haploides d'ordi, juntament amb panell d'associació que comprèn 185 varietats d'ordi representatives del germoplasma conreat en la conca Mediterrània. El material vegetal ha estat assajat en una combinació de divuit camps per any desllorigats en sis països de la conca mediterrània. Els assajos s'han portat a terme en camps amb diferent disponibilitat d'aigua, classificats sobre la base de les dades relatives a les freqüència i quantitat de les precipitacions o en el mateix lloc amb un camp en secà i altre regat. Els assajos es van portar a terme per dos anys en cada localitat i això va permetre la recollida d'un gran volum de dades que comprenen caràcters agronómicos relacionats amb rendiment i components del rendiment, dades fenológicos i ambientals. Aquestes dades es van utilitzar després per a la identificació de regions genomicas involucrades en l'adaptació de l'ordi a l'ambient. Els 118 dobles haploides de la població ‘Nure x Tremois’ es genotiparon amb marcadors DaRT (Diversity Array Technology), després un set de 15 marcadors CAPS I SCCP per a gens candidats involucrats en la regulació de les fases fenológicas van ser afegits al mapa de lligament construït amb els marcadors DaRT. Les dades van ser utilitzats per a fer una anàlisi de QTL amb procediment ‘Composite Interval Mapping’ para cada combinació ambienti/ caràcter. Es van trobar diversos QTLs per rendiment i data d'espigolat i components del rendiment. Els QTL mes freqüents trobats per rendiment i data de floració i components del rendiment estan localitzats en els cromosomes 1H (3 camps), 2H (8 camps) i 5H (5 camps) coincidents respectivament amb HvFT3 locus, eam6/Eps-­‐2 (earliness per se) locus i amb el locus de vernalización Vrn-­‐H1. Una ulterior anàlisi de QTL feta amb el mètode “Multi Environment Trial” ha revelat que els QTL localitzats en el locus eam6/Eps-­‐2 (cromosoma 2H) i Vrn-­‐H1 (cromosoma 5H) són comunes per rendiment i data de floració en els 18 camps d'assaig. Per això utilitzem tots el dades ambientals col·leccionades durant tot el cicle del cultiu per a investigar la sensibilitat de dites QTL a les co-­‐variables ambientals. La majoria de les associacions oposades estan relacionades amb temperatures i variables relacionades amb aquestes. Eam6/Eps-­‐2 mostra una interacció de tipus quantitatiu amb aquestes variables mentre Vrn-­‐H1 mostra una interacció de tipus qualitatiu amb aquestes variables. Les 185 varietats assajades van ser genotipadas amb 185 SNPs i fenotipadas per resistència a fred en dos assajos uneixo a Espanya i altre a Itàlia. El primer assaig va ser caracteritzat per un hivern excepcionalment fred, mentre el d'Itàlia ha estat utilitzat en passat per testar resistència a fred a causa de els hiverns rígids que solen registrar-­‐se en aquesta localitat. Les dades van ser utilitzats per a portar a terme la analisis GWAS “Genome Wide Association Analysis” . Els resultats van permetre identificar 13 regions genomicas involucrades en la resistència a frio. Entre elles tres regions coincideixen amb loci ja mapeados i coneguts per ser involucrats en la resposta a frio en los cromosomes 2HL, 4HL i 5HL.
Los ensayos en localidades múltiplas de poblaciones de mapeo se utilizan frecuentemente para testar genotipos en un conjunto de ambientes representativos de la condiciones climáticas donde se quieren introducir dichos genotipos. La primera parte de esto trabajo ha sido la evaluación de la población de mapeo ‘Nure x Tremois’ constituida de 118 de doble haploides de cebada, junto con panel de asociación que comprende 185 variedades de cebada representativas del germoplasma cultivado en la cuenca Mediterránea. El material vegetal ha sido ensayado en una combinación de dieciocho campos por año dislocados en seis países de la cuenca mediterránea. Los ensayos se han llevado a cabo en campos con diferente disponibilidad de agua, clasificados en base a los datos relativos a las frecuencia y cantidad de las precipitaciones o en el mismo sitio con un campo en secano y otro regado. Los ensayos se llevaron a cabo por dos años en cada localidad y esto permitió la recogida de un gran volumen de datos que comprenden caracteres agronómicos relacionados con rendimiento y componentes del rendimiento, datos fenológicos y ambientales. Dichos datos se utilizaron después para la identificación de regiones genomicas involucradas en la adaptación de la cebada al ambiente. Los 118 dobles haploides de la población ‘Nure x Tremois’ se genotiparon con marcadores DaRT (Diversity Array Technology), después un set de 15 marcadores CAPS Y SCCP para genes candidatos involucrados en la regulación de las fases fenológicas fueron añadidos al mapa de ligamento construido con los marcadores DaRT. Los datos fueron utilizados para hacer una análisis de QTL con procedimiento ‘Composite Interval Mapping’ para cada combinación ambiente/ carácter. Se encontraron varios QTLs por rendimiento y fecha de espigado y componentes del rendimiento. Los QTL mas frecuentes encontrados por rendimiento y fecha de floración y componentes del rendimiento están localizados en los cromosomas 1H (3 campos), 2H (8 campos) y 5H(5 campos) coincidentes respectivamente con HvFT3 locus, eam6/Eps-­‐2 (earliness per se) locus y con el locus de vernalización Vrn-­‐H1. Una ulterior análisis de QTL hecha con el método “Multi Environment Trial” ha revelado que los QTL localizados en el locus eam6/Eps-­‐2 (cromosoma 2H) y Vrn-­‐H1 (cromosoma 5H) son comunes por rendimiento y fecha de floración en los 18 campos de ensayo. Por esto utilizamos todos lo datos ambientales coleccionadas durante todo el ciclo del cultivo para investigar la sensibilidad de dichos QTL a las co-­‐variables ambientales. La mayoría de las asociaciones encontradas están relacionadas con temperaturas y variables relacionadas con estas. Eam6/Eps-­‐2 muestra una interacción de tipo cuantitativo con dichas variables mientras Vrn-­‐H1 muestra una interacción de tipo cualitativo con dichas variables. Las 185 variedades ensayadas fueron genotipadas con 185 SNPs y fenotipadas por resistencia a frío en dos ensayos uno en España y otro en Italia. El primer ensayo fue caracterizado por un invierno excepcionalmente frío, mientras el de Italia ha sido utilizado en pasado por testar resistencia a frío debido a los inviernos rígidos que suelen registrarse en dicha localidad. Los datos fueron utilizados para llevar a cabo la analisis GWAS “Genome Wide Association Analysis”. Los resultados permitieron identificar 13 regiones genomicas involucradas en la resistencia a frio. Entre ellas tres regiones coinciden con loci ya mapeados y conocidos por ser involucrados en la respuesta a frio en los cromosomas 2HL, 4HL y 5HL.

The phenomenon of repeated evolution runs counter to expectations about the role of contingency in adaptation. However, many examples of independently acquired similar traits show that evolution sometimes does follow the same path. Factors influencing the probability of such an event include selection, trait complexity and relatedness. Previous investigations of repeated adaptation have primarily focused on low-complexity traits subject to strong selection. Studies of systems with varying levels of trait complexity, selection, and relatedness are needed to evaluate the relative contributions of these factors. The series of studies reported here 1) establishes a system for inquiry into the role of parallel adaptation among hosts and parasites and 2) provides an assessment of the role of parallel genetic change in the evolution of a complex trait. In Chapter 2, I show that all-female broods in a line of Drosophila borealis are caused by infection with a male-killing strain of Wolbachia that is very closely-related to another male-killing strain infecting a geographically and evolutionarily distant species of Drosophila. This host-parasite system, together with two other known male-killing Wolbachia strains infecting Drosophila provides a framework for investigating the role of parallel evolution in the independent acquisition of the male-killing trait among Wolbachia, as well as in the adaptation of divergent hosts to similar male-killing parasites. In Chapters 3-5, I investigate the role of parallel genetic change in a complex trait in two species of Drosophila by searching for evidence of adaptation in the Drosophila americana homologs of genes thought to underlie adaptation to climate in Drosophila melanogaster. In Chapter 3, I investigate the D. americana homolog of Alcohol dehydrogenase (Adh). In contrast with D. melanogaster, which segregates functionally distinct variants in Adh that represent local adaptation to climate, D. americana segregates little variation. This is surprising, especially because Adh of D. americana is found near a polymorphic chromosomal rearrangement that does segregate geographically-structured alleles across the species' range. In Chapter 4, I report similarities at the Phosphoglucomutase (Pgm) locus in the two species, including a shared excess of nonsynonymous variants and the presence of clinal alleles. However, while variation at Pgm of D. melanogaster is proposed to underlie local adaptation, variation at Pgm of D. americana appears to be predominantly neutral. In Chapter 5, I investigate the role of positive selection in sequence evolution in the D. americana homologs of a group of genes thought to underlie local adaptation to climate in D. melanogaster. The two species share a large geographic range and exhibit levels of sequence variation that indicate a similar effective population size, but D. melanogaster appears to undergo more frequent fixation of advantageous alleles. Approximately half of all amino acid divergence in D. melanogaster is attributable to positive selection, but I find no signs of positive selection in the investigated genes in D. americana. Overall, the results reveal little or no parallel evolution at the single genes analyzed. This lack of parallel evolution is likely a result of the high complexity of adaptation to climate as well as contingency.

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O comportamento diferencial de um grupo de genótipos avaliados em diferentes ambientes ocorre devido às interações entre genótipos e ambientes. Essas interações são amplamente estudadas, pois o seu entendimento pode caracterizar os ambientes de experimentação, podendo agrupar locais semelhantes e também identificar ambientes que possam levar a maior ou menor expressão das características de interesse de cada genótipo. Além disso, a compreensão da interação genótipo x ambiente é importante para que os métodos de seleção sejam calibrados para reduzir os seus efeitos e proporcionar resultados eficientes na identificação dos genótipos superiores, sejam eles estáveis ou de ampla ou específica adaptação. Assim, o presente trabalho teve como objetivo avaliar o resultado de produção de grãos e podridão de colmo de 36 genótipos de milho em 22 ambientes na safra 2012/2013. Os ambientes fazem parte da rede de experimentação da empresa Dow AgroSciences. A estratificação formou 24 grupos para produção de grãos e 21 para podridão de colmo. E a interação genótipo x ambiente foi predominantemente do tipo complexa para ambas as características. Utilizando os dois métodos em conjunto foi possível reduzir 3 pares de ambientes (1,03%) ) para produção de grãos e 10 pares de ambientes (4,33%) para podridão de colmo. Essa baixa redução demonstra a baixa similaridade entre os locais avaliados garantindo uma boa eficiência na seleção de genótipos de milho. Os genótipos mais estáveis, de adaptabilidade ampla e alta média de Produção de Grãos foram: HE30PW, HE12PW e HE22PW. E os mais estáveis, de adaptabilidade ampla e baixa média de Podridão de Colmo foram: HE31PW, HE16PW e HE17PW. Pelo teste de média os genótipos com o maior número de vitorias foram para Produção de Grãos: HE28PW, HE10PW, HE02PW, HE29PW e HE16PW e para Podridão de Colmo: HE29PW, HE27PW, HE16PW, HE08PW e HE02PW
The differential behavior of a group of genotypes at different environments is due to the interaction between genotypes and environment. These interactions are widely studied, because its understanding can distinguish the environments for experimentation, by gathering similar environments and also to identify environments that can lead the genotype to express more or less its main phenotypes. Furthermore, the comprehension of the interaction it is important to calibrate the methods for selection of superior genotypes: stables one, or with specific or wide adaptability. Therefore, our objective was to evaluate the results of yield and stalk rots of 36 corn genotypes at 22 locations during the season 2012/2013. All the experiments are part of the Dow AgroSciences evaluation fields. Stratification formed 24 groups for yield and 21 for stalk rot. The interaction was mainly of the complex type for both traits. Analyzing both methods at the same time 3 environments pair (1,03%) could be reduced for yield and 10 pairs (4,33%) for stalk rot. This low location reduce capacity, shows the low similarity between locations and is an indication of the efficiency of the locations for corn selection. The most stable, with wide adaptability and highest yield were the genotypes: HE 30 PW, HE12PW and HE22PW. The most stable, with wide adaptability lowest stalk rot were: HE31PW, HE16PW and HE17PW. The Scott-Knott test showed that the genotypes with no significant difference to the checks in a higher number of locations for yield were: HE 28PW, HE 10PW, HE 02PW, HE 29PW and HE 16PW. For Stalk Rot the genotypes were: HE 29PW, HE 27PW, HE 16PW, HE 08PW and HE 02PW

Genetic algorithm and artificial life techniques are applied to the development of challenging and interesting opponents in a combat-based computer game. Computer simulations are carried out against an idealized human player to gather data on the effectiveness of the computer generated opponents.

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2007.
Title from dissertation home page (viewed May 28, 2008). Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7090. Adviser: Loren H. Rieseberg.

Northern fringe populations generally have low amounts of genetic variation and inhabit habitats where specific adaptations are needed. On the Swedish west coast, the natterjack toad (Bufo calamita) inhabits skerry islands. I have examined: I) adaptation to two environmental stressors in this habitat; II) the genetic population structure within the skerry habitat; III) the effects of neutral genetic variation, selection and genetic drift on trait divergence within the skerry habitat; and IV) the effects of genetic variation on fitness under three thermal conditions of varying stressfulness. V) I have also studied the impact of putative local adaptations on the Scandinavian green toad (Bufo viridis) conservation programme. The results suggest that the skerry natterjack toads are locally adapted to the desiccation risk in their habitat. However, despite inhabiting a more saline habitat, they had a lower salinity tolerance when compared to their conspecifics in the more general habitat. The lowered salinity tolerance is most likely explained by the presence of negative genetic correlations between salinity tolerance and desiccation avoidance and suggests that the occurrence of multiple environmental stressors may constrain adaptation. Within the skerry habitat, the toads exhibited a strong population structure with populations differing in their levels of genetic variation. Moreover, within the skerry habitat, the results suggest uniform selection pressures. However, correlations between trait values and neutral genetic variation suggest that inbreeding depression may affect trait values and thus potentially constrain adaptation. In the natterjack toad, fitness costs associated with lack of genetic variation were only present under benign conditions and not under more natural conditions. This suggests that environmental stress masks inbreeding depression in these traits under natural conditions. In the study regarding the Scandinavian green toads, I found that one population inhabiting a saline habitat had a higher salinity tolerance than other populations in less saline habitats. This suggests the presence of local adaptation, which should be acknowledged in the green toad conservation programme. Several of the northern fringe populations of toads fulfill the criteria of being Evolutionary Significant Units and their conservation thus should be prioritized.

There is growing evidence that disruptive selection generated by intraspecific resource competition may be a common mechanism for generating biological diversity. Adaptive dynamics models provide a framework describing how frequency dependent selection drives such diversification, but these models don’t consider the complexities that arise as a result of gene interactions. Here, we explore the relative effects of ecological and genetic constraints on diversification using an experimental system of Escherichia coli in which diversification is driven by frequency dependence based on resource use. Diversified populations consist of ecotypes that consume glucose and ac- etate at different rates, and a mutation in the arcA gene has been identified that has a large effect on this phenotype. By isolating clones of each eco- type from a previously diversified population, we find that the effect of the arcA mutation on rediversification depends on both the ecotype and the genetic background. While some of these observations are consistent with predictions made by adaptive dynamics models, others cannot be explained without also accounting for epistasis and genetic constraints, highlighting the importance of considering both ecological and genetic factors when pre- dicting diversification. Adaptation in this system also provides an example of an interaction between ecological and evolutionary processes, adding to a growing number of studies that exhibit a clear feedback between these two processes.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 215-223).
When different cells thrive across diverse environments, their genetic differences can reveal what genes are essential to survival in a particular environment. Prochlorococcus, a cyanobacterium that dominates the open ocean, offers an opportunity to explore such differences. Its diversity is examined here, beginning with an overview and comparison of 12 fully sequenced Prochlorococcus genomes. The Prochlorococcus core genome, that set of genes shared by all cultured Prochlorococcus, appears to be well defined by the set shared by these isolates. The flexible genome, that set of genes found in some isolates but not shared by all Prochlorococcus, was found to be much larger and open-ended. Most laterally-acquired genes were found to be located in highly variable islands such as those described in previous studies of Prochlorococcus. Those lateral gene transfer events can also be placed on the Prochlorococcus phylogenetic tree: each Prochlorococcus isolate possesses a significant number of genes that even its closest sequenced cousin does not. A particular gene family may define a Prochlorococcus ecotype if those genes are possessed by all members of that ecotype, and if their presence gives that ecotype a selective advantage in some circumstance, thus contributing to the determination of its niche. One gene family is conspicuous for appearing in many copies per genome in one Prochlorococcus clade, referred to as eNATL. The sequenced strains belonging to this clade each possess over 40 copies of genes encoding high light inducible proteins (HLIPs), compared to only 9-24 in the other Prochlorococcus genomes. Other studies suggest these genes may be involved in resistance to sudden increases in light intensity, among other stresses. This becomes especially interesting as recent field studies also found that eNATL cells may survive changes in light intensity more easily than other lowlight adapted Prochlorococcus. Here, the effects of light shocks on an eNATL strain and on other Prochlorococcus strains are studied. eNATL cultures do recover from light shock conditions that are lethal to other low light-adapted Prochlorococcus. Measurements of bulk in vivo chlorophyll fluorescence, fluorescence per cell, and variable fluorescence, along with preliminary gene expression data, suggest that the early, rapid response of high light-adapted cells and of eNATL cells distinguish them from other low light-adapted cells, possibly explaining their subsequent survival. The possible role of HLIPs in this response is discussed. The discussion of HLIPs and eNATL is based on the complete sequences of only two eNATL genomes, both sampled from the same part of the ocean at the same time. That dataset is expanded by the inclusion of Global Ocean Survey environmental shotgun reads, from which are identified several thousand HLIP genes. Past work has shown that HLIPs are divided into two distinct clades: the core, freshwater cyanobacteria-like HLIPs and the flexible, phage-like, island-bound copies. That distinction is examined in the metagenomic data, demonstrating that the separate types are consistently found in distinct chromosomal neighborhoods.
(cont.) The evolution of HLIPs is also explored by the analysis of large-insert environmental clones containing islands from a variety of eNATL cells. Here, not even all island-bound, HLIP-encoding genes appear to be alike, as only a subset are consistently found in the same locations across the whole eNATL clade. Ecotype-defining genes are those genes, shared by all members of an ecotype, that provide an ecologically significant advantage, thus helping to define the ecotype's niche. It can be expected that, as environmental data accumulates (including additional measurements of Prochlorococcus abundance and newly sequenced genomes from uncultured cells), additional such genes can be identified. This work should represent a model for searching for and examining such genes. Hopefully, future experiments will be able to test the physiological significance of candidate ecotype-defining genes, while feeding back to the environmental data to verify their importance in the open ocean.
by Gregory C. Kettler.
Ph.D.

Evolution proceeds through genetic changes to individuals, which are either propagated or disappear over generations. Adaptation is one of the main mechanisms driving these changes in genetic composition. Speciation can also result from different, and incompatible, genetic changes occurring in different populations. This thesis furthers our knowledge of the genetics of adaptation and speciation using the budding yeast Saccharomyces cerevisiae. My work on the genetic basis of adaptation to high concentrations of copper, when contrasted with a similar experiment using the fungicide nystatin, showed that the environment has a strong influence on both the number of genes that are the targets of selection and the types of potentially beneficial mutations. These results have implications for the repeatability of genetic evolution. In a second study, I found that genetic interactions between individually isolated single-step beneficial mutations from the same selective environment often exhibited the type of epistasis that underlies speciation even though these mutations occurred within a single biosynthetic pathway. These results support the mutation-order model of speciation by adaptation, where the chance order of mutations in separated populations leads to divergence and the build-up of reproductive isolation due to genetic incompatibility. Negative genetic interactions became positive when the level of stress was increased, indicating that genetically-based reproductive isolation can also be environment-dependent. Finally, I found that diploid yeast were generally not able to adapt to a level of fungicide to which haploid yeast can adapt. Diploids have been found to adapt to a lower concentration of the same drug, indicating that the exact environment (type and concentration) and ploidy can have an impact on the likelihood of genetic rescue. Together, these results have implications for our understanding of the genetic basis of adaptation in different types of environments and different levels of the same environmental stressor.
Science, Faculty of
Zoology, Department of
Graduate

Reducing the operating costs of chemical processes is very beneficial in decreasing a company's bottom line numbers. Since chemical processes are usually run in steady-state for long periods of time, saving a few dollars an hour can have significant long term effects. However, the complexity involved in most chemical processes from nonlinear dynamics makes them difficult processes to optimize. A nonlinear, open-loop unstable system, called the Tennessee Eastman Chemical Process Control Problem, is used as a test-bed problem for minimization routines. A decentralized controller is first developed that stabilizes the plant to set point changes and disturbances. Subsequently, a genetic algorithm calculates input parameters of the decentralized controller for minimum operating cost performance. Genetic algorithms use a directed search method based on the evolutionary principle of "survival of the fittest". They are powerful global optimization tools; however, they are typically computationally expensive and have long convergence times. To decrease the convergence time and avoid premature convergence to a local minimum solution, an auxiliary fuzzy logic controller was used to adapt the parameters of the genetic algorithm. The controller manipulates the input and output data through a set of linguistic IF-THEN rules to respond in a manner similar to human reasoning. The combination of a supervisory fuzzy controller and a genetic algorithm leads to near-optimum operating costs for a dynamically modeled chemical process.
Master of Science

Forward progress in empirical population genetics is closely tied to the development of theory which can accomodate and keep pace with the production of genetic data. In recent years, the ability to survey genetic variation at increasingly greater resolution, across the genomes of a variety of species, has prompted new approaches to use this data for population genetic inference. While many models have historically relied on assuming independence among genetic variants in a sample of chromosomes, there are now a variety of methods which can use the non-independence among variants as a source of information. In particular, the unique combination and co-inheritance of variants on a chromosome can be used to define "haplotypes" of linked genetic variation associated with specific populations, individuals, or variants from which they are descended. The work presented here is a contribution to this class of population genetic models which describes: (1) a method to estimate the timing of adaptation for a beneficial allele, including several applications to recent human evolution, (2) an application of the same method to infer the timing of introgression for coat color alleles in North American wolves and high-altitude adaptation in Tibetans, (3) a model to infer the action of purifying selection against genetic incompatibilities in a hybrid zone, and (4) a reanalysis of genomic data from Heliconius butterflies which confirms the role of hybridization in transfering mimicry phenotypes between species.

A l’ordi, la llum i la temperatura controlen la floració a través de la interacció entre els gens de vernalització i fotoperíode. Es coneix menys sobre l’efecte d’altres atributs, com la qualitat de llum. L’objectiu principal d’aquesta tesi és profunditzar en el control genètic del temps de floració a l’ordi, centrant-se en la temperatura, el fotoperíode i la qualitat espectral, afectarà la fenologia i els gens que controlen. Aquest treball es revela la regulació dels principals gèneres de floració sota condicions no inductives, ha presentat nous candidats de la ruta de floració i ha aprofundit en la resposta als canvis de longitud del dia i de qualitat de llum. Les diferències genotípiques trobades i els mecanismes genètics proposats en aquest treball poden ser útils per al disseny d’idiotips d’ordi millor adaptats per a futures condicions climàtiques.
En cebada, la luz y la temperatura controlan la floración a través de la interacción entre los genes de vernalización y fotoperíodo. Se conoce menos sobre el efecto de otros atributos, como la calidad de luz. El objetivo principal de esta tesis es profundizar en el control genético del tiempo de floración en cebada, centrándonos en cómo la temperatura, el fotoperíodo y la calidad espectral, afectan la fenología y los genes que la controlan. En este trabajo se ha revelado la regulación de los principales genes de floración bajo condiciones no-inductivas, se han propuesto nuevos candidatos de la ruta de floración y se ha profundizado en la respuesta a los cambios de longitud de día y de calidad de luz. Las diferencias genotípicas encontradas y los mecanismos genéticos propuestos en este trabajo pueden ser herramientas útiles para el diseño de ideotipos de cebada mejor adaptados para futuras condiciones climáticas.
In barley, temperature and light cues control flowering through the interaction between vernalization and photoperiod genes. Less is known about the effect of other attributes, as light quality. The main objective of this thesis is to increase our knowledge on the genetic control of flowering time in barley, focusing on how temperature, photoperiod and spectral quality, affect to phenology and the flowering time genes. In this work, the regulation of the main flowering genes under non-inductive conditions was revealed, new candidates for the flowering pathway were proposed, and the response to changes in day length and light quality has been deepened. The genotypic differences found and the genetic mechanisms proposed in this work can be useful tools for the design of barley ideotypes better adapted for future climatic conditions.

Abstract Local adaptation is important evolutionary process leading to adaptive population differentiation. Currently, examining its genetic basis is a major goal of evolutionary and ecological genetics. In my thesis I studied local adaptation and its genetic basis in populations of a perennial outcrossing model plant Arabidopsis lyrata by combining common garden experiments at the native field sites and in controlled conditions with quantitative trait locus mapping. Estimates of fitness in the field – both at the level of multiple components as well as hierarchical total fitness – showed that populations of A. lyrata were locally adapted. The studied populations were also phenotypically differentiated in ecologically relevant traits. Different components of fitness were important for the advantage of the locals depending on the environment. Local alleles were associated with high fitness in the field, suggesting that differing directional selection pressures have been involved in phenotypic differentiation. Mostly different genomic regions governed local adaptation in different environments, but the results also suggested that some of these regions could involve rarely documented fitness tradeoffs (antagonistic pleiotropy). Loci governing flowering time differentiation differed between the studied environments, highlighting the need to conduct experiments both in the wild and in controlled conditions. In contrast to most existing studies, F2 hybrids in general had surprisingly high fitness at one study site, largely due to beneficial dominance effects at loci governing survival in that environment. In addition to nuclear genes, cytoplasmic genomes also were found to have a role in local adaptation
Tiivistelmä Luonnonvalinta saa aikaan paikallista sopeutumista ja adaptiivista erilaistumista. Paikallisen sopeutumisen perinnöllisen taustan selvittäminen on tällä hetkellä yksi tärkeimpiä evolutiivisen ja ekologisen genetiikan tavoitteita. Tässä väitöskirjatyössä tutkin paikallista sopeutumista ja sen geneettistä taustaa monivuotisella, ristipölytteisellä mallikasvilla, idänpitkäpalolla (Arabidopsis lyrata). Käytin työssäni geenikartoitusta kasveilla joita kasvatettiin yhdenmukaisissa oloissa sekä populaatioiden luontaisilla kasvupaikoilla että kontrolloiduissa olosuhteissa. Kenttäolosuhteissa arvioitu kelpoisuus osoitti idänpitkäpalkopopulaatioiden olevan paikallisesti sopeutuneita sekä yksittäisten kelpoisuuteen vaikuttavien ominaisuuksien että hierarkkisen kokonaiskelpoisuuden tasolla. Tutkitut populaatiot olivat myös erilaistuneita ekologisesti tärkeissä ominaisuuksissa. Kelpoisuuteen vaikuttavat ominaisuudet myös poikkesivat ympäristöjen välillä. Paikalliset alleelit olivat yhteydessä korkeaan kelpoisuuteen luonnossa, minkä perusteella voitiin päätellä erisuuntaisen luonnonvalinnan vaikuttaneen populaatioden erilaistumiseen. Kromosomiston eri alueet olivat tärkeitä sopeutumisessa eri ympäristöihin, mutta myös joidenkin samojen genomin alueiden havaittiin mahdollisesti vaikuttavan vastakkaisesti kelpoisuuteen eri ympäristöissä. Myös kukkimisajan erilaistumiseen vaikuttavat genomin alueet poikkesivat eri ympäristöjen välillä erityisesti verrattaessa kenttäkokeita kasvatushuone- ja kasvihuonekokeisiin. Toisin kuin useimmissa tutkimuksissa on havaittu, F2-sukupolven jälkeläistön kelpoisuus oli yllättävän korkea yhdessä kenttäkoeympäristössä. Tähän vaikuttivat kelpoisuuden kannalta suotuisat dominoivat geenivaikutukset, jotka paransivat kasvien selviytymistä kyseisessä ympäristössä. Tumassa sijaitsevien geenien lisäksi myös soluelimien perimällä havaittiin olevan yhteys paikalliseen sopeutumiseen

Exposure to high environmental pH is physiologically stressful for fish. In British Columbia, this has led to low survivorship among Rainbow Trout stocked into alkaline lakes. Early studies have shown promising results for stocking the progeny of brood stock collected in high pH lakes into similar alkaline environments. Here I follow up by characterizing the high pH tolerance of fish with parents collected from an alkaline lake, Stump Lake. I also look at the effects of acclimation and rearing fish at pH 8.8 on subsequent pH 9.5 tolerance. I found that this population had a short time to loss of equilibrium, with only 10% of fish remaining after a 3 day exposure to pH 9.5. Acclimation resulted in significant improvements to tolerance and rearing resulted in almost none of the fish losing equilibrium over a 3 day exposure. A genome wide association study on non-acclimated and acclimated individuals did not show any significant genetic marker associations with high pH tolerance. However this analysis did identify some potential SNPs associated with genes involved in acid-base regulation, muscle function, neural signaling, and DNA transcription in the non-acclimated fish. The pH 8.8 acclimated fish only showed association with genes involved in neural signaling and DNA transcription. These data suggest that acclimation may remove limitations associated with some of these other processes. Overall the Stump Lake population does not appear to have genetic adaptations that improve tolerance to high pH exposure, but can improve tolerance through acclimation to moderately high pH.
Science, Faculty of
Zoology, Department of
Graduate

The adaptation of an IIR filter is a very difficult problem due to its non-quadratic performance surface and potential instability. Conventional adaptive IIR algorithms suffer from potential instability problems and a high cost for stability monitoring. Therefore, there is much interest in adaptive IIR filters based on alternative algorithms. Genetic algorithms are a family of search algorithms based on natural selection and genetics. They have been successfully used in many different areas. Genetic algorithms applied to the adaptation of IIR filtering problems are studied in this thesis, and show that the genetic algorithm approach has a number of advantages over conventional gradient algorithms, particularly, for the adaptation of high order adaptive IIR filters, IIR filters with poles close to the unit circle and IIR filters with multi-modal error surfaces. The conventional gradient algorithms have difficulty solving these problems. Coefficient results are presented for various orders of IIR filters in this thesis. In the computer simulations presented in this thesis, the direct, cascade, parallel and lattice form IIR filter structures have been used and compared. The lattice form IIR filter structure shows its superiority over the cascade and parallel form IIR filter structures in terms of its mean square error convergence performance.

As the demand for energy rises, Populus species are increasingly grown as bioenergy crops. Meanwhile, due to global change, predictions indicate that summer droughts will increase in frequency and intensity over Europe. This study was carried out to evaluate the adaptation to drought in Populus, at different levels: genetic, genomics and physiology. Forests trees such as poplar are very important ecologically and economically but the Populus genus is known to be drought sensitive. Consequently, it is essential to understand drought response and tolerance for those trees. Two populations of poplar were used for this study, a mapping population (Family 331) and a natural population of Populus nigra. The F2 mapping population obtained from a cross of Populus deltoides and Populus trichocarpa, showed differences in stomatal conductance and carbon isotope composition in both clones and the F2 progeny. It was also used to discover QTL related to water use efficiency highlighting interesting areas of the genome. Combining QTL discovery and microarray analysis of the two clones in response to drought, a list of candidate genes was defined for water use efficiency. The natural population of Populus nigra consisting of 500 genotypes of wild black poplar showed variation in numerous physiological measurements such as leaf development and carbon isotope discrimination in well-watered conditions depending on their latitude of origin. The drier genotypes (from Spain and South France) had the smallest leaf area which could be linked to an adaptation to drought. Physiological measurements of extreme genotypes in leaf size of this population revealed differences in response to water depending on their latitude of origin. Stomatal conductance rapidly decreased and water use efficiency improved for Spanish genotypes after a slow and moderate drought stress. Direct comparisons between the transcriptome of extreme genotypes from Spain and North Italy in well watered and drought conditions provided an insight into the genomic pathways induced during water deficit. Six candidate genes were selecting for further analysis using real-time PCR: two stomatal development genes (ERECTA and SPEECHLESS), two ABA related genes (ATHVA22A and CCD1), a second messenger (IP3) and a NAC transcription factor (RD26)

Starch digestion begins in the mouth where it is hydrolysed into smaller polysaccharides by the enzyme salivary amylase. Three salivary amylase genes (AMY1A, B & C) and a pseudogene (AMYP1) have been described and are located in tandem on chromosome 1. Polymorphic variation has been demonstrated in Caucasians in the form of the number of repeats of the AMY1 genes, as follows: (lA-lB-Pl)n-lC. This variation has been reported to result in differing levels salivary amylase enzyme production and, as a result, differences in the efficiency of starch digestion in the mouth. It is proposed in this thesis that an increase in salivary gene copy number may be an adaptation to high starch diets as a result of the adoption of agriculture. Reliable high-throughput multiplex PCR based methods have been designed to quantify AMY1 gene copy number and to also to type 6 microsatellite markers closely linked to the AMY gene cluster. Data have been collected for 14 human populations, with different histories of cereal agriculture and ancestral levels of starch in the diet. Data have also been collected on AMY1 gene copy number in 5 chimpanzees (Pan troglodytes). The AMY1 allele frequency difference (measured using FST) between the two most extreme populations, the Mongolians and Saami, was not an outlier on a distribution of FST based on presumed neutral 11,024 SNPs from the human genome. The chimpanzee data suggest that the most frequent allele (AMY1*H1) in humans may not be the ancestral allele, as all chimpanzee chromosomes tested carried the AMY1*H0 allele (containing only one copy of the AMY1 gene). A more sensitive selection test, the analysis of the intra-allelic variability of the AMY1 repeat alleles using closely linked microsatellites, showed no compelling evidence for recent positive selection at the AMY1 locus in humans. As a result, genetic drift could not be ruled out as an explanation for the observed AMY1 allele frequency differences among populations. Alanine:glyoxylate aminotransferase (AGT) is an intermediary metabolic enzyme that is targeted to different organelles in different species. Previous studies have shown that there is a clear relationship between the organellar distribution of AGT and diet. Non-human primates show the herbivorous peroxisomal distribution of AGT. In humans a point mutation and insertion deletion polymorphism have been associated with peroxisome-to-mitochondria AGT mis-targeting. Data have been collected using a PCR/RFLP based method, in 11 human populations. In a comparison with FST values from 11.024 SNP loci, 94.5% of SNPs had a lower FST than a comparison of AGT allele frequencies for Saami and Chinese. This unusually high allele frequency difference between Chinese and Saami is consistent with the signature of recent positive selection driven by the unusually high meat content in the Saami diet.

Variation in the shape, size, and number of segments along the vertebral column underlies a vast amount of vertebrate diversity. Although the molecular pathways controlling vertebrate segmentation during normal development are well understood, the genetic and developmental underpinnings responsible for the tremendous variation in size and number of vertebrae are relatively unexplored. The main goal of this dissertation is to explore the genetic and developmental mechanisms influencing naturally occurring variation in the vertebral column. To this end, I focus on intraspecific skeletal variation, with an emphasis on tail length, in the deer mouse, Peromyscus maniculatus. In Chapter 1, I employ a phylogeographic framework to show that longer tails have evolved independently in different populations of forest-dwelling mice. Closer investigation of the underlying morphology shows that long-tailed mice have both (1) a greater number of tail vertebrae and (2) individually longer vertebrae, compared to ancestral short-tailed mice. Chapter 2 explores the genetic basis of tail length variation. I use quantitative trait locus mapping to uncover six loci that influence differences in total tail length (3 associated with vertebral length and 3 with vertebrae number). Finally, in Chapter 3 I combine comparative data from quantitative measurements of tissue dynamics during somitogenesis in fixed embryos and ex vivo explant culture to show that embryos of forest mice make more segments because they produce more presomitic mesoderm, and not because of any significant difference in the timing of somitogenesis. Together, this work integrates phylogeographic, genetic, and developmental studies to pinpoint the ways that natural selection modifies development to produce the repeated evolution of an evolutionarily important trait, and suggests that there are a limited number of ways that long tails can evolve.
Biology, Organismic and Evolutionary