Tesi: "Evolution (Biology) Adaptation (Biology) Insects"

1

Mattsson, Monte Arthur. "The Impeccable Timing of the Apple Maggot Fly, Rhagoletis pomonella (Dipetera: Tephritidae), and its Implications for Ecological Speciation". PDXScholar, 2015. https://pdxscholar.library.pdx.edu/open_access_etds/2627.

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Abstract (sommario):

Speciation is the process by which life diversifies into discrete forms, and understanding its underlying mechanisms remains a primary focus for biologists. Increasingly, empirical studies are helping explain the role of ecology in generating biodiversity. Adaptive radiations are often propelled by selective fitness tradeoffs experienced by individuals that invade new habitats, resulting in reproductive isolation from ancestral conspecifics and potentially cladogenesis. Host specialist insects are among the most speciose organisms known and serve as highly useful models for studying adaptive radiations. We are just beginning to understand the pace and degree with which these insects diversify. The apple maggot, Rhagoletis pomonella, is a well-studied insect whose eastern and southern populations are models for ecological speciation. Recently (40–65 ya), the fly has invaded the Pacific Northwestern United States through human-transported apples infested with larvae. There, populations of R. pomonella have rapidly colonized two novel hawthorn hosts whose fruiting times bracket apple’s (early-season native Crataegus douglasii and introduced C. monogyna, which fruits late in the season). The recent introduction might initiate host shifts, providing opportunities to examine the pace and mechanistic means with which host races (an evolutionary stage preceding speciation) become established. Here, I demonstrate that host-associated populations at a site in southwest Washington are partially allochronically isolated from one another, and life cycles temporally match with natal host fruit ripening times in sympatry. If spatially widespread, these temporal barriers could result in reproductive isolation and possibly cladogenesis. Implications of these findings reach beyond academic import, as R. pomonella is expanding not only its host range, but its geographic range is encroaching upon central Washington, the site of a multi-billion dollar per year apple-growing industry.

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2

Belda, Cuesta Eugeni. "Genome evolution and systems biology in bacterial endosymbionts of insects". Doctoral thesis, Universitat de València, 2010. http://hdl.handle.net/10803/57466.

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Abstract (sommario):

Gene loss is the most important event in the process of genome reduction that appears associated with bacterial endosymbionts of insects. These small genomes were derived features evolved from ancestral prokaryotes with larger genome sizes, consequence of a massive process of genome reduction due to drastic changes in the ecological conditions and evolutionary pressures acting on these prokaryotic lineages during their ecological transition to host-dependent lifestyle. In the present thesis, the process of genome reduction is studied from different perspectives. In the first chapter, genome rearrangements have been studied in a set of 31 complete γ-proteobacterial genomes that includes five genomes of bacterial endosymbionts of insects. This is carried out by comparing the order of a subset of 244 single-copy orthologous genes presents in all the genomes and calculating the number of inversions and breakpoints between each genome pair. This reveals that inversions were the main rearrangement event in γ-proteobacteria evolution, with a progressive increase in the number of rearrangements with increased evolutionary distance. However, significant heterogeneity in different γ-proteobacterial lineages was also detected, with a significant acceleration in the rates of genome rearrangements in bacterial endosymbionts of insects at initial stages of the association. In the second chapter, the structure and functional capabilities of Sodalis glossinidius has been studied. S. glossinidius is the secondary endosymbiont of tsetse flies, and it´s at very initial stages of genome reduction process. It´s genome is experiencing a massive process of gene inactivation, with 972 pseudogenes (inactivated genes) that were described but not annotated in the original annotation of the genome. In this chapter, a complete functional re-annotation of this genome was carried out, that includes the characterization of 1501 pseudogenes though analysis of S. glossinidius intergenic regions. A massive presence of CDSs related with mobile genetic elements and surface proteins were detected, being also the functional classes most affected by pseudogenization. The reconstruction of the metabolic map of S. glossinidius revealed a functional profile very similar to that of free-living enterics, with inactivation of L-arginine biosynthesis pathway, whereas the comparison with Wigglesworthia glossinidia (tsetse primary endosymbiont) reveals possible cases of metabolic complementation between both tsetse endosymbionts at thiamine, coenzyme A and tetrahydrofolate biosynthesis level. Finally, in the third chapter of the thesis, the complete reductive evolution process associated with S. glossinidius was studied from a systems biology perspective through the reconstruction of their genome-scale metabolic networks at different stages of this process and the prediction of their internal reaction fluxes under different external conditions through Flux Balance Analysis. This revealed the decisive role of the pseudogenization of genes involved in L-arginine and glycogen biosynthesis and specially the pseudogenization of the key anaplerotic enzyme phosphoenolpyruvate carboxylase in the ecological transition to a host-dependent lifestyle experienced by S. glossinidius. A progressive decrease in network robustness to gene deletion events and to changes in particular reaction fluxes were detected. Finally, reductive evolution simulations over the functional network of S. glossinidius under different external conditions revealed a higher plasticity in minimal networks evolved in a nutrient-rich environment, and allow defining different sets of essential and disposable genes based on their presence or absence in minimal metabolic networks. These essential genes had more optimized patterns of codon usage and more restricted patterns of sequence evolution than disposable genes that could be lost without affecting the functionality of the network. However, lineage-specific estimates of dN and dS in S. glossinidius and Escherichia coli revealed that common features of ancient bacterial endosymbionts like acceleration in the rates of sequence evolution and the loss of adaptative codon usage were starting to affect S. glossinidius evolution.
En esta tesis doctoral, el proceso de reducción genómica característico de bacterias endosimbiontes de insectos ha sido estudiado utilizando diferentes aproximaciones computacionales basadas en la genómica comparada y la biología de sistemas. Por un lado, las dinámicas de reordenaciones genómicas han sido estudiadas en un subconjunto de 31 genomas completos de γ-proteobacterias que incluyen 5 genomas completos de endosimbiontes bacterianos de insectos, revelando una aceleración significativa de las tasas de reordenaciones en estos genomas en etapas iniciales del proceso de reducción. Posteriormente, el genoma de Sodalis glossinidius, el endosimbionte secundario de la mosca tsétsé, fue re-anotado con el objetivo de evaluar el impacto de los procesos de inactivación génica y proliferación de elementos genéticos móviles en etapas tempranas del proceso de reducción, asi como su impacto sobre las capacidades funcionales de la bacteria en el contexto ecológico de su coexistencia con el endosimbionte primario ancestral Wigglesworthia glossinidia. Finalmente, el proceso completo de reducción genómica en S. glossinidius ha sido estudiado a través de la reconstrucción de su red metabólica a diferentes etapas de este proceso y su análisis funcional mediante Análisis de Balance de Flujos, evaluando la robustez de las redes frente a sucesos de deleción asi como las dinámicas evolutivas de genes esenciales y no esenciales en base a su presencia en redes mínimas evolucionadas a partir de la red funcional. Este análisis permitió identificar sucesos de inactivación génica con efectos drásticos sobre las capacidades funcionales del sistema como los genes implicados en la biosíntesis de arginina y glicógeno, y especialmente la inactivación de la enzima fosfoenolpiruvato carboxilasa, asi como una disminución progresiva de la robustez de las redes frente a diferentes sucesos mutacionales asociada al proceso de pérdida génica. Finalmente, simulaciones de evolución reductiva sobre la red funcional bajo diferentes condiciones de entorno ha permitido definir conjuntos de genes esenciales y delecionables en base a su presencia o ausencia en las redes mínimas producto de las simulaciones, revelando una mayor conservación a nivel de secuencia y un uso de codones más optimizado en genes esenciales frente a genes cuya pérdida no afecta a la funcionalidad del sistema.

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3

Leiby, Nicholas. "Adaptation and Specialization in the Evolution of Bacterial Metabolism". Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11364.

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Abstract (sommario):

Specialization is a balance of evolutionary adaptation and its accompanying costs. Here we focus on the Lenski Long-Term Evolution Experiment, which has maintained cultures of Escherichia coli in the same, defined seasonal environment for 50,000 generations. This dissertation explores the extent and means by which metabolic specialization occurs over an extended period in the same environment.

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4

Simons, Pamela J. "Molecular evolution of the alpha-amylase genes of Bombyx mori and other insects". Thesis, University of Ottawa (Canada), 1993. http://hdl.handle.net/10393/6643.

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Abstract (sommario):

The gene of the ubiquitous starch degrading enzyme $\alpha$-amylase has been chosen to study evolutionary mechanisms and the relationships between several insect groups. In this project, the $\alpha$-amylase gene sequence of a representative of the order Lepidoptera, Bombyx mori, was determined. The coding region of Bombyx and the seven other insect genes are approximately the same size and have at least 60% identity with one another. There are various numbers of introns dispersed throughout the loci but often sites are shared between two or more species. There is evidence of differing codon biases among the genes with Drosophila and Anopheles being very GC rich and Choristoneura and Tribolium having virtually no bias. Biases caused discrepancies between the phylogenetic trees created by several different methods. Representatives of the same order always grouped together as predicted, but the order within the Lepidoptera varied with the method used. (Abstract shortened by UMI.)

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5

Banks, John E. "The effects of landscape heterogeneity on insect populations : a study of pattern and scale /". Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/5166.

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6

Kingsley, Evan Prentice. "Adaptation in the forest deer mouse: evolution, genetics, and development". Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467192.

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Abstract (sommario):

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

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7

Lieberman, Tami Danielle. "Genomic insights into bacterial adaptation during infection". Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11312.

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Abstract (sommario):

Bacteria evolve during the colonization of human hosts, yet little is known about the selective pressures and evolutionary forces that shape this evolution. Illumination of these processes may inspire new therapeutic directions for combating bacterial infections and promoting healthy bacteria-host interactions. The advent of high-throughput sequencing has enabled the identification of mutations that occur within the human host, and various tools from computational and evolutionary biology can aid in creating biological understanding from these mutations. Chapter 1 describes recent progress in understanding within-patient bacterial adaption, focusing on insights made from genomic studies.

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8

Kwan, Lucia. "Adaptation to desiccation resistance fails to generate pre- and postmating isolation in Drosophila melanogaster". Thesis, University of Ottawa (Canada), 2009. http://hdl.handle.net/10393/28210.

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Abstract (sommario):

Many laboratory speciation experiments have raised allopatric populations in different environments to determine whether reproductive isolation evolves as a by-product of adaptation. Few, however, have controlled for the effects of genetic drift, addressed the evolution of both pre- and postmating isolation, or investigated the conditions that promote or hamper the process. I present results of a long-term evolution experiment in which 12 replicate populations of Drosophila melanogaster independently evolved for more than 57 generations under alternative desiccation treatments (six control and six desiccation-selected populations). Specifically, I demonstrate the divergence between the desiccation and control populations of cuticular hydrocarbons, key traits that have been implicated in mate choice and sexual isolation in Drosophila. Despite this divergence, there was no detectable pre- or postmating isolation between the desiccation and control populations. Novel environments are generally thought to promote the evolution of reproductive isolation. Understanding the conditions that favour or hamper this remains a key challenge for speciation research.

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9

Maher, Keri Renee. "A geographically constrained molecular phylogeny of Panamanian Aechmea species (Bromeliaceae, subfamily bromelioideae)". CSUSB ScholarWorks, 2007. https://scholarworks.lib.csusb.edu/etd-project/3280.

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Abstract (sommario):

This study lends strong support to the idea that members of Bromeliaceae have undergone a recent adaptive radiation, and therefore show that, at least in part, diversity in the tropics is due to a fast speciation rate and that the tropics can be a "cradle" for new diversification and exploitation of varying ecological niches through the diversification of ecophysiological traits within a lineage.

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10

Smith, Jeramiah James. "AMBYSTOMA: PERSPECTIVES ON ADAPTATION AND THE EVOLUTION OF VERTEBRATE GENOMES". Lexington, Ky. : [University of Kentucky Libraries], 2007. http://lib.uky.edu/ETD/ukybiol2007d00627/JJSmith_Dissertation.pdf.

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Abstract (sommario):

Thesis (Ph. D.)--University of Kentucky, 2007.
Title from document title page (viewed on September 4, 2007). Document formatted into pages; contains: vii, 182 p. : ill. (some col.). Includes abstract and vita. Includes bibliographical references (p. 164-180).

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11

Crumière, Antonin. "Developmental mechanisms of adaptive phenotypes and associated ecological relevance in the semiaquatic bugs". Thesis, Lyon, 2017. http://www.theses.fr/2017LYSEN095/document.

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Abstract (sommario):

Comprendre comment est générée la diversité biologique est un enjeu majeur de la biologie évolutive. Chaque espèce vit dans un environnement écologique qui lui est propre et dans lequel elle s’est adaptée au cours de l’évolution par les moyens de la sélection naturelle. Chaque espèce est également soumise à la sélection sexuelle contribuant au dimorphisme entre les sexes. Les traits phénotypiques associés au succès évolutif sont formés lors du développement par l’action de gènes qui sont transmis de génération en génération. Ces traits et ces gènes varient d’une espèce à une autre et contribuent directement à la diversité morphologique. La compréhension des interactions entre les mécanismes développementaux et les pressions écologiques permettent de mieux comprendre les processus qui influent sur la diversité morphologique et l’évolution des espèces. Obtenir une vision intégrative est un réel défi et demande de combiner diverses approches. Au cours de ma thèse, j’ai utilisé les insectes semi-aquatiques (Gerromorphes) qui sont un modèle permettant de lier évolution, écologie et développement. En utilisant différentes approches j’ai pu mettre en évidence des gènes impliqués dans le développement de divers traits adaptatifs, l’importance de ces traits dans un contexte écologique et leur impact sur l’évolution du groupe des Gerromorphes. L’ensemble des résultats obtenus améliore notre compréhension de comment sélection naturelle et sélection sexuelle, en agissant sur les mécanismes génétiques, génèrent de la diversité morphologique
Understand how biodiversity is generated is a major goal in evolutionary biology. Every species live in a specific ecological habitat where they adapted during evolution by the mean of natural selection. Every species is also under sexual selection that generates dimorphism between the sexes. Adaptive traits contributing to evolutionary success are shaped during development by the action of genes that are transmitted through generations. These traits and genes vary across species and directly contribute to generate morphological diversity. The study of the interactions between developmental genetic mechanisms and selective ecological pressures allow a better understanding of the processes generating morphological diversity and driving the evolution of species. Obtain an integrative view is a challenge and required the combination of different approaches. During my PhD, I used the semiaquatic bugs (Gerromorpha) that are model systems allowing to link evolution, ecology and development. By using various approaches I could highlight genes involved in the development of different adaptive traits, the relevance of these traits in an ecological context and their impact on the evolution of the group of Gerromorpha. Altogether these results improve our understanding of how natural and sexual selection, by acting on genetic mechanisms, generate morphological diversity

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12

Baverstock, P. R. "Studies in the adaptation and evolution of the Australasian fauna : a collection /". Title page, introduction and index only, 1987. http://web4.library.adelaide.edu.au/theses/09SD/09sdb353.pdf.

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Thesis (D. Sc.)--University of Adelaide, 1988.
Collection of previously published articles. Includes Allozyme electrophoresis / B.J. Richardson, P.R. Baverstock and M. Adams (1986). Includes bibliographical references.

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13

Sheeley, Sara Lynn. "Investigating patterns of parallel genetic change in repeated adaptation". Diss., University of Iowa, 2010. https://ir.uiowa.edu/etd/600.

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Abstract (sommario):

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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14

Mena, Paulina Alejandra. "The Role of chromosomal rearrangements in adaptation in Drosophila americana". Diss., University of Iowa, 2009. https://ir.uiowa.edu/etd/310.

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Abstract (sommario):

Natural environments expose organisms to multifarious selective pressures involving numerous aspects of the overall phenotype, therefore eliciting a response from multiple correlated loci. It has been hypothesized that chromosomal rearrangements can play a role in facilitating local adaptation by establishing new linkage relationships and modifying the recombination patterns between the different chromosomal forms, allowing coordinated adaptation of several loci. The central aim of the work presented here is to test this hypothesis using Drosophila americana as a model system. This species segregates several inversions and an X-4 centromeric fusion which makes it an excellent model to study the role of chromosomal rearrangements on local adaptation. This hypothesis was tested using several approaches. The geographic distribution of the chromosomal rearrangements was determined through sampling of wild populations from a broad geographic range. It was found that several of the chromosomal rearrangements exhibit clinal variation. Furthermore, many of these are found in high linkage disequilibrium. The X-4 fusion is highly associated with inversions on the X and 4th chromosome. Also, two inversions on chromosome 5 are in strong negative linkage disequilibrium. The sequence variation associated with rearrangements of the X was studied using inbred lines. The results show that the inversion and the fusion strongly influence variation on this chromosome. Regions of significant population differentiation and linkage with the rearrangements are found interspersed with loci showing neutral variation indicating that in spite of recombination, allelic associations are maintained on this chromosome. The analysis was also extended to flies directly collected from the wild sampled from a region encompassing a large part of the species' range. Loci throughout chromosome X and 4 were genotyped. Sites in high linkage disequilibrium with the rearrangements and with other assayed sites were found in close proximity with sites that did not show this pattern. In conclusion, the clinal distribution of chromosomal rearrangements and associated genetic variation in conjunction with the detection of islands of linkage disequilibrium among the rearrangements and loci on both chromosomes indicate that chromosomal rearrangements are facilitating local adaptation in D. americana.

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15

Wyatt, Gregory Alan Kenneth. "Coevolutionary adaptation in mutualisms". Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:c3318211-a893-432e-a52e-35a6c60b76ce.

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Abstract (sommario):

Natural selection favours those individuals that respond best to novel features of their selective environment. For many, a critical challenge is responding to evolutionary change in mutualistic species. These responses create complex feedbacks, so only coevolutionary approaches are able to fully answer key questions about the maintenance or disruption of mutualistic behaviour, and explain the range of mechanisms that allow individuals to benefit from these associations. I first consider the hypothesis that economic models studying multiple classes of traders, where each trader seeks to optimise its own payoffs will yield insights into mutualistic systems. I show that individuals can be favoured to discriminate amongst potential partners based on the price for which they provide resources. Then, I show that market mechanisms can maintain cooperation and drive specialisation in mutualistic systems. I extend this market model to allow individuals to restrict a mutualistic partner's access to resources, and show that this strategy can stabilise cooperation and increase the fitness of both partners. I also explicitly incorporate relatedness in my market model. I show that high relatedness sometimes increases cooperativeness in members of a mutualistic species, but sometimes decreases cooperativeness as it narrow the scope for partner choice to maintain cooperation. Having studied market mechanisms, I consider indiscriminate costly help to members of another species. I discover that this trait can be favoured by natural selection and can be classified as either altruism between or altruism within species. Finally, I consider a framework for analysing coevolved phenotypic responses to a partner's cooperativeness, a challenging process to model. I demonstrate that this framework can yield firm predictions about behaviour whenever partners hold private information about their costs and benefits.

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16

Thézé, Julien. "Diversification et adaptation génomique des virus entomopathogènes". Thesis, Tours, 2013. http://www.theses.fr/2013TOUR4006.

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À différentes échelles de temps, le but de ma thèse a été de comprendre l'évolution des virus entomopathogènes à travers l’étude de la diversification et de l’adaptation génomique de grands virus à ADN d’insectes. Dans un premier temps, j’ai pu estimer les âges de diversifications des baculovirus et des nudivirus, et proposer un scénario de coévolution à long terme entre ces virus et leurs hôtes insectes. Puis, me plaçant sur une échelle de temps moindre, j’ai montré que les hôtes insectes sont le facteur principal de la diversification des baculovirus, et de façon surprenante, j’ai également observé que l'environnement biotique de ces virus, c’est-à-dire les plantes hôtes des insectes, joue un rôle central dans leur évolution. Dans un second temps, des mutations ponctuelles ont pu être reliées à l’adaptation locale de populations différentiées du baculovirus SeMNPV. Enfin, l’étude de l'adaptation génomique convergente entre les entomopoxvirus et les baculovirus a mis en évidence que les transferts horizontaux de gènes sont une source importante de variabilité pour les grands virus à ADN, pour l'adaptation aux mêmes niches écologiques. Les gènes et les mécanismes identifiés dans ce travail de thèse apportent des éléments nouveaux pour comprendre comment les génomes sont façonnés par l’écologie
At different timescales, the purpose of my PhD was to understand insect virus evolution through the study of the genomic diversification and adaptation of insect large DNA viruses. Firstly, I was able to estimate the ages of baculovirus and nudivirus diversifications, and to propose a long-term coevolutionary scenario between these viruses and their insect hosts. Then, on a narrower timescale, I showed that insect hosts are the major factor in baculovirus diversification, and surprisingly, I also observed that the virus biotic environment, i.e. insect host plants, plays a central role in their evolution. Secondly, punctual mutations have been linked to the local adaptation of differentiated populations of the baculovirus SeMNPV. Finally, the study of convergent genomic adaptation between entomopoxviruses and baculoviruses highlighted that horizontal gene transfers are an important source of variability for large DNA viruses, for the adaption to the same ecological niches. Genes and mechanisms identified in this PhD work provide new insights to understand how genomes are shaped by ecology

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17

Piri, Rebecca D. "Spatial Genetic Structure and Local Adaptation within and among Foxtail Pine (Pinus balfouriana subsp. balfouriana) Populations Located in the Klamath Mountains, California". VCU Scholars Compass, 2019. https://scholarscompass.vcu.edu/etd/6018.

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Abstract (sommario):

Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated (FST= 0.000644) and there is weak isolation-by-distance structure, but ongoing gene flow is unlikely. Within populations, stand density and competitor effects contribute to inbreeding. I also show that previously measured traits are predominantly determined by genetics. Analyzing by sliding window in the genome, I show that connectivity patterns vary widely throughout the genome and identify several areas that are important to the genetic architecture of the phenotypic traits and plasticity (GxE). Overall, there is high connectivity, genetic similarity, and genetically based trait variation among and within populations of the northern subspecies of foxtail pine due to historical processes, despite biotic interactions driving inbreeding. Persistent genetic isolation, however, may make adaptation to future climate a challenge for the subspecies.

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18

Ogden, Thomas H. "Evolution and phylogeny of basal winged insects with emphasis on mayflies (Ephemeroptera)". BYU ScholarsArchive, 2004. https://scholarsarchive.byu.edu/etd/207.

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Ephemeroptera (mayflies) is a monophyletic group of semi-aquatic pterygote insects, comprising 3083 species, 376 genera, and 37 described families and are present on all continents, excluding Antarctica, being associated with freshwater and brackish water habitats. The order is unique among pterygote insects in possessing functional wings at the penultimate molt (subimago stage), prior to the full development of genitalia; in all other insects the presence of functional wings occurs only after the final molt. The purpose of this dissertation is to use molecular and morphological data, in order to investigate the position of the order Ephemeroptera among other insect orders, the higher-level relationships among the major lineages of mayflies, and a detailed analysis of the family Ephemerellidae. Ephemeroptera has been considered by many to be sister to Odonata + Neoptera although alternate hypotheses have been suggested. Data from three molecular loci ambiguously resolve basal pterygote relationships, however, total evidence analysis (combined molecular and morphological data) strongly supports the position of mayflies as sister to all other extant pterygotes. These results and methodologies were recently criticized, and, therefore, the response to the author is included following the manuscript. The phylogenetic relationships among mayfly families is debatable and in some groups unknown. Prior studies have produced phylogenies based on morphological characters mixed with intuition. The first molecular phylogeny for the Order Ephemeroptera is presented. The analyses include 31 of the 37 families, representing ~24% of the genera. The suborders Furcatergalia and Carapacea are supported as monophyletic while Setisura and Pisciforma are not supported as monophyletic. The evolution of the wings, mandibular tusks, burrowing lifestyle, and fishlike body are investigated. Topological sensitivity analysis is used as a tool to examine patterns concerning the stability of relationships across a parameter landscape, providing additional information that may not have been acquired otherwise. The Pannote family Ephemerellidae is comprised of 16 genera and over 300 species and is distinguished from other mayfly families by the absence of the second pair of abdominal gills. The position of Ephemerellidae relative to other closely related pannote mayflies is unclear as are the relationships of the genera within the family. The combined molecular and morphological analyses resulted in a monophyletic Ephemerellidae as sister to the other ephemerelloid families. The subfamily Ephemerellidae was supported as monophyletic, while Timpanoginae had conflicting results.

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19

Ridout, Kate E. "Genome-wide analysis of selection in mammals, insects and fungi". Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:5a894760-9240-4e79-a50f-37547f108a00.

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Characterising and understanding factors that affect the rate of molecular evolution in proteins has played a major part in the development of evolutionary theory. The early analyses of amino acid substitutions stimulated the development of the neutral theory of molecular evolution, which later evolved into the nearly neutral theory. More recent work has lead to a better understanding of the role selection plays at the molecular level, but there is still limited understanding of how higher levels of protein organisation affect the way natural selection acts. The investigation of this question is the central aim of this thesis, which is addressed via the analysis of selective pressures in secondary protein structures in insects, mammals and fungi. The analyses for the first two groups were conducted using publically available datasets. To conduct the analyses in fungi, genome sequence data from the fungal genus Microbotryum (sequenced in our laboratory) was assembled and annotated, resulting in the development of a number of bioinformatics tools which are described here. The fungal, insect and mammalian datasets were interrogated with regard to a number of structural features, such as protein secondary structure, position of a site with regard to adaptively evolving sites, hydropathy and solvent-accessibility. These features were correlated with the signals of positive and purifying selection detected using phylogenetic maximum likelihood and Bayesian approaches. I conclude that all of the factors examined can have an effect on the rate of molecular evolution. In particular, disordered and hydrophilic regions of the protein are found to experience fewer physiochemical constraints and contain a higher proportion of adaptively evolving sites. It is also revealed that positively selected residues are ‘clustered’ together spatially, and these trends persist in the three taxa. Finally, I show that this variation in adaptive evolution is a result of both selective events and physiochemical constraint.

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20

Lettieri, Liliana B. "The evolution of cleaning mutualism and predator cooperation in a radiation of Caribbean fishes". Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/34690.

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The steps by which neutral, random and/or negative biological interactions evolve into mutualistic ones remain poorly understood. Here, we study Elacatinus gobies and the fishes from which they clean parasites, termed 'clients'. Colorful stripes are common to mutualist cleaners and non-cleaning sister species. Blue stripes are unique to obligate cleaners. We quantified the contrast potential of ancestral and novel stripe colors, using fish color vision models, and determined that color stripes have become more visible to clients over evolutionary time. In turn, we focused on the role of color as a potentially specialized signal. We show that cleaners possess a putative chemical defense (one multimedia file in .mov format included) and demonstrate that stripes are sufficient to elicit client stereotypical posing behavior and to deter attack. Analysis of previously published records show that yellow cleaners tend to predators less than expected, compared to green and blue cleaners. Our results highlight evolution from predator avoidance to tolerance with conspicuous advertising reinforced by chemical defense in cleaners. Similar trajectories, via recognizable signals to risky partners, may be common in other diffuse mutualisms. We discuss the generality of defense and signal traits in other species rich lineages of mutualists.

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21

Hoostal, Matthew John. "Local Adaptation of Microbial Communities along Geochemical Spatial Gradients in Sediments of the Lake Erie Region". Bowling Green State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1375187243.

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22

Holding, Matthew Landon. "Evolution of Rattlesnake Venom involves Geographically Structured Coevolution and Local Adaptation to Prey". The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1494248063332041.

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23

Peña, Jacqueline J. "Plant Evolutionary Response to Climate Change: Detecting Adaptation Across Experimental and Natural Precipitation Gradients". DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/7340.

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Global climate change is a real-time problem that presents threats to many species. Climate change can alter ecosystems and may lead to species extinction. Species can respond to climate change by moving to a better environment or adapting. Therefore, it is necessary to rely on several approaches and perspectives to anticipate ecological impacts of climate change. A common strategy uses models to understand how populations respond to different climate scenarios. Ecological models have helped usunderstand population persistence, but they often ignore how populations adapt to environmental stress. Adaptive evolution has been ignored because it was assumed that evolution was too slow to have any effect on ecology. Current research has shown that some populations are able to rapidly adapt to novel environments and this is essential for population persistence. We used a population genomics approach to understand how different precipitation regimes affect the perennial bunchgrass, Pseudoroegneria spicata, in the eastern Idaho sagebrush steppe. Our objective was to determine how genetic diversity changes under manipulated precipitation regimes and whether these changes were consistent with patterns of genetic diversity under natural precipitation regimes. The manipulated precipitation regimes consist of three precipitation treatments: control, drought with 50% ambient precipitation, and irrigation with 150% ambient precipitation. The natural precipitation regimes consist of two treatments: low elevation (drier than the experimental site) and high elevation (wetter). We collected plant tissue to isolate plant DNA and then used sequenced DNA for analyses. We used a hierarchical Bayesian model to estimate genotypes and allele frequencies across all loci. We found that there were low levels of genetic variation across all experimental precipitation treatments. When examining genetic differentiation, we found there was stronger differentiation in the natural precipitation regimes. Our study focuses on the short-term responses to climate to understand how environmental stress influences genetic diversity.

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Presloid, John B. "Characterization of Vesicular Stomatitis Virus Strains with Adaptability". University of Toledo Health Science Campus / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=mco1225313889.

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25

Ammunet, Tea. "Evolution and diversification of secreted protein effectors in the order Legionellales". Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-357800.

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The evolution of a large, diverse group of intracellular bacteria was previously very difficult to study. Recent advancements in both metagenomic methods and bioinformatics has made it possible. This thesis investigates the evolution of the order Legionellales. The study concentrates on a group of proteins essential for pathogenesis and host manipulation in the order, called effector proteins. The role of effectors in host adaptation, evolutionary history and the diversification of the order were investigated using a multitude of bioinformatics methods. First, the abundance and distribution of the known effector proteins in the orderwas found to cover newly discovered clades. There was a clear distinction between the proteins present in Legionellales and the outgoup, indicating the important role of the effectors in the order. Further, the effectors with known functions found in the new clades, particularly in Berkiella, revealed potential modes of host manipulation of this group. Secondly, the evolution of the effector gene content in the order shed light on theevolution of the order, as well as on the potential evolutionary differences between Legionellaceae and Coxiellaceae. In general, most of the effectors were gained early in the last common ancestor of Legionellales and Legionellaceae, as further indication of their role in the diversification of the order. New effector genes were acquired in the Legionellaceae even up to recent speciation events, whereas Coxiellacea have lost more protein coding genes with time. These differences may be due to horizontal gene transfer in the case of gene gains in Legionellaceae and loss of selection in the case of gene losses in Coxiellaceae. Third, the early evolution of core gained effector proteins for the order was studied.Two of the eight investigated core effectors seem to have a connection to eukaryotes, the rest to other bacteria, indicating both inter-domain and within bacteria horizontal gene transfer. In particular, one effector protein with eukaryotic motif gained at the last common ancestor of Legionellales, was found in all the clades and is therefore an important evolutionary link that may have allowed Legionellales to utilize eukaryotic hosts.

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26

Bengston, Sarah Elizabeth. "A Colony-Level Behavioral Syndrome In Temnothorax Ants: Explaining Risk-Taking Variation Across A Latitudinal Gradient". Diss., The University of Arizona, 2015. http://hdl.handle.net/10150/556615.

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Between individual behavioral variation has been described in nearly every animal taxa where it has been measured. Often, these behavioral variations correlate across contexts, forming a behavioral syndrome. Despite a recent push to better understand the origins and consequences of behavioral syndromes, there still is no cohesive framework that describes this phenomenon. Here, I develop a social insect species into a model for measuring and testing behavioral syndromes at a new level of biological organization; the colony. This builds upon the rich literature describing between-colony variation in behavior and provides novel insights into the evolution of behavioral syndromes. In my first chapter I show that colonies do not vary from one another in foraging distance, nor is foraging distance directly associated with colony size. This was my first step in demonstrating that colony behavioral variation is not simply a byproduct of colony size. In chapter two, I expanded upon this finding by testing colonies both in the lab and in the field for a variety of ecologically relevant behaviors. Here, I found that there was a behavioral syndrome that reflected foraging distance, foraging effort to novel and familiar resources, response to threat and aggression. While there is a gradient of phenotypes, some colonies either travel farther to forage for food and respond more aggressively when confronted with a conspecific invader, but appear to invest less in each given incident or food source. I consider this to be more risk-tolerant; they increase their risk of external mortality for potentially larger pay-offs. On the other hand, risk-averse colonies deploy more foragers to exploit closer resources, increase their overall activity in the response to threat, but avoid travelling farther distances or aggressively engaging invaders. Additionally, there is between population variations in risk-taking phenotype. Across the western United States, colonies at more northern latitudes are more risk-tolerant than colonies at more southern latitudes. In chapter 3, I expand upon this latitudinal gradient in behavioral phenotype by investigating what ecological factors predict a colonies level of risk-tolerance. Specifically, I focused on ecological traits that reflected predation, competition, food resource availability and abiotic stress. I found that competition for nest sites and spatial clustering predicted behavioral type; colonies at high levels of nest site competition or spatial clustering were more risk-tolerant than colonies at lower levels of competition or were more spatially dispersed. In chapter 4, I used a common garden and brood transfer experiment to investigate if the relationship between the ecological environment and behavior was the result of phenotypic plasticity or local adaptation. I show that local adaptation is the most likely explanation, as colonies with more workers from the donor colony are more, behaviorally, like the donor colony than colonies with fewer donor workers. In chapter 5 I test if the risk-taking behavioral syndrome is the result of life history strategy variation. I test the growth rate and energy allocation towards either somatic effort or reproductive effort. I found that colonies which are risk-tolerant also grow faster and dedicate more energy towards reproductive effort, which is consistent with predictions built from life history theory. This body of work shows that behavioral syndromes can exist at a new level of organization, the colony, and that variation in behavioral type is the result of differential selection pressure between populations. This directly connects behavioral syndrome research to life history strategy research. As life history strategy theory is a well-understood field, this represents a true advancement in the field of behavioral syndromes.

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27

Bair, Elizabeth Ashley. "The Consequences of Phenotypic Plasticity on Adaptive Rate in Escherichia coli". University of Akron / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=akron1416855604.

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28

Zhang, Mingcai. "The Role of New Mutations in Evolution: Identifying the Deleterious Effect of Heterozygotes and the Beneficial Effect on Adaptation to Salt-Stressed Environments in Drosophila Melanogaster". Bowling Green State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1276892040.

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29

Caro, Quintero Alejandro. "The role of horizontal gene transfer in bacterial evolution". Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/48979.

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Horizontal gene transfer (HGT) is probably the most important mechanism for functional novelty and adaption in bacteria. However, a robust understanding of the rates of HGT for most bacterial species and the influence of the ecological settings on the rates remain elusive. Four whole-genome comparative studies of free-living bacteria will be described that integrated physiological and ecological data with novel detection bioinformatic pipelines to elucidate the magnitude of HGT at three distinct levels of genetic relatedness: i) the species level, where overlapping ecological niche among co-occurring bacteria in the water column of the Baltic Sea has caused HGT to have been so rampant that it has served as the force of species cohesion; ii) the genus level, where HGT appeared to predominantly mobilize a limited number of genes with ecological/selective advantage (e.g., antibiotic resistance genes) among distinct pathogenic Campylobacter species and hence, did not lead to species convergence; and iii) the phylum level, where HGT was found to be, in general, less frequent than the genus level but, over evolutionary time, has assembled a large part of the metabolic functions of natural microbial communities, especially within organic matter rich, anaerobic habitats. In conclusion, this work advances the methods to link ecological relationships with HGT and suggests that HGT among very divergent organisms may have been more frequent than previously thought and led to successful adaptation.

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30

Feldman, Chris R. "Evolutionary Genetics of Tetrodotoxin (TTX) Resistance in Snakes: Tracking a Feeding Adaptation from Populations Through Clades". DigitalCommons@USU, 2008. https://digitalcommons.usu.edu/etd/159.

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Understanding the nature of adaptive evolution has been the recent focus of research detailing the genetic basis of adaptation and theoretical work describing the mechanics of adaptive evolution. Nevertheless, key questions regarding the process of adaptive evolution remain. Ultimately, a detailed description of the ecological context, evolutionary history, and genetic basis of adaptations is required to advance our understanding of adaptive evolution. To address some of the contemporary issues surrounding adaptive evolution, I examine phenotypic and genotypic changes in a snake feeding adaptation. Adaptations can arise through fixation of novel mutations or recruitment of existing variation. Some populations of the garter snakes Thamnophis sirtalis, T. couchii, and T. atratus possess elevated resistance to tetrodotoxin (TTX), the lethal toxin of their newt prey. I show that TTX resistance has evolved independently through amino acid changes at critical sites in a voltage-gated sodium channel protein (Nav1.4) targeted by TTX. Thus, adaptive evolution has occurred multiple times in garter snakes via de novo acquisition of beneficial mutations. Detailing the genetic basis of adaptive variation in natural populations is the first step towards understanding the tempo and mode of adaptive evolution. I evaluate the contribution of Nav1.4 alleles to TTX resistance in two garter snake species from central coastal California. Allelic variation in Nav1.4 explains 29% and 98% of the variation in TTX resistance in T. atratus and T. sirtalis, respectively, demonstrating that Nav1.4 is a major effect locus. The simple genetic architecture of TTX resistance in garter snakes may significantly impact the dynamics of trait change and coevolution. Patterns of convergent evolution are cited as some of the most compelling examples of the strength of natural selection in shaping organismal diversity. Yet repeated patterns may tell us as much about the constraints that restrict evolution as about the importance of natural selection. I present data on convergent molecular adaptations in parallel arms races between diverse snakes and amphibians from across the globe. Six snake species that prey on TTX bearing amphibians have independently acquired amino acid changes in Nav1.4. The derived mutations are clustered in two portions of the gene, often involving the same sites and substitutions. While a number of amino acid changes can make Nav1.4 insensitive to TTX, most of these negatively impact or abolish the ion-conducting function of the protein. Thus, intramolecular pleiotropy likely prevents most replacements from becoming fixed and imposes limits on protein evolution.

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Marchini, Gina Lola. "Mechanisms of Adaptation in the Newly Invasive Species Brachypodium sylvaticum (Hudson) Beauv". PDXScholar, 2015. https://pdxscholar.library.pdx.edu/open_access_etds/2640.

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It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) Beauv. to determine mechanisms contributing to adaptation and success in the novel habitat. The first study used simulations and experiments to test the hypothesis that genetic purging, the process where genetic load is reduced by selection against the recessive deleterious alleles expressed in the homozygous state, promotes invasive range expansion. I found that homozygous populations on B. sylvaticum's range periphery displayed lower inbreeding depression compared to heterozygous populations near introduction sites. Empirical tests with B. sylvaticum further demonstrate that purging of genetic load is a plausible scenario promoting range expansion during invasion. Next, I explored how the interaction between population genetic diversity and the environment contributed to the establishment and spread of Brachypodium sylvaticum. I found that nitrogen application increases both final size and shoot biomass for B. sylvaticum individuals from source populations with low HS levels to levels found in individuals from populations with high HS. A coefficient of relative competition intensity index (RCI) displayed reduced effects of interspecific competition on B. sylvaticum biomass in high nitrogen plots. Results show that elevated nitrogen deposition is a factor that increases establishment of introduced species with historically small effective population sizes. Thirdly, I investigated phenotypic differentiation during the establishment and range expansion of Brachypodium sylvaticum. Utilizing a novel approach, unique alleles were used to determine the genetic probability of contribution from native source regions to invasive regions. These probabilities were integrated into QST-FST comparisons to determine the influence of selection and genetic drift on twelve physiological and anatomical traits associated with drought stress. Phenotypic divergence greater than neutral expectations was found for five traits between native and invasive populations, indicating selective divergence. Results from this study show that the majority of divergence in B. sylvaticum occurred after introduction to the novel environment, but prior to invasive range expansion. The final chapter of my dissertation investigates the adaptive role of genetic differentiation and plasticity for Brachypodium sylvaticum invasion. Plasticity was measured across treatments of contrasting water availability. Linear and nonlinear selection gradients determined the effect of directional and quadratic selection on plasticity and genetic differentiation. Invasive trait divergence was a consequence of post-introduction selection leading to genetic differentiation, as there were no plastic responses to contrasting water availability for any measured traits. Genetic divergence of invasive plants was not consistently in the direction indicated by selection, suggesting limitations of selection that may be a consequence of physical constraints and/or tradeoffs between growth and abiotic tolerance. Results suggest that selection, rather than plasticity, is driving phenotypic change in the invaded environment. The combined volume of these studies contributes significantly to the field of invasion and plant biology by providing novel insights into the processes underlying range expansion, adaptation, and ultimately, evolution of introduced species.

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Handel, Kevin. "Testing Local Adaptation Of The Federally Endangered Karner Blue Butterfly (Lycaeides Melissa Samuelis) To Its Single Host Plant The Wild Lupine (Lupinus Perennis)". Bowling Green State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1429214530.

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33

Weglarz, Kathryn M. "Investigating the Roles of Bacterial Endosymbionts in the Evolution of Adelgidae (Hemiptera: Sternorrhyncha)". DigitalCommons@USU, 2019. https://digitalcommons.usu.edu/etd/7645.

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Abstract (sommario):

Insects form close partnerships, or symbioses, with bacteria. These partnerships allow the insects to use resources that would be unavailable to them otherwise. Certain insects, hemipterans, are able to feed on nutrient-poor plant-sap because these bacteria supplement their diets. While this association is beneficial for both the insect and bacteria, it also comes with consequences: the genomes of bacterial symbionts typically undergo extreme degradation, becoming small and lacking many genes necessary for typical bacterial functioning. In the Hemiptera, aphids, mealybugs, cicadas, true bugs,and their relatives, these bacterial partnerships tend to be stable over millions of years. However, adelgids (Aphidoidea: Adelgidae) are highly unusual in that their symbiotic bacteria have been frequently replaced. These replacements offer a unique opportunity to explore the effects of symbiont role and age on symbiont genome degradation. My dissertation uses the pattern of adelgid symbiont gains and losses to understand the process of symbiont replacements and co-symbiont gain. I accomplished this by sequencing and annotating the genomes of adelgid symbionts from across the family, first focusing on the symbionts from a pest species, then expanding to representatives from across the family, and finally conducting an in-depth exploration of how the genomes of a symbiont found in two branches of the adelgids varies between species. Through this work I demonstrate that adelgid symbionts are nutritional providers, they have a unique pattern for distributing the work of providing nutrients between the symbiont pairs, and that a symbiont’s precedence, whether it was there first or whether it joined another symbiont, has an impact on genome degradation.

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Lind, Brandon M. "NATURAL AND ANTHROPOGENIC DRIVERS OF TREE EVOLUTIONARY DYNAMICS". VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5359.

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Species of trees inhabit diverse and heterogeneous environments, and often play important ecological roles in such communities. As a result of their vast ecological breadth, trees have become adapted to various environmental pressures. In this dissertation I examine various environmental factors that drive evolutionary dynamics in threePinusspecies in California and Nevada, USA. In chapter two, I assess the role of management influence of thinning, fire, and their interaction on fine-scale gene flow within fire-suppressed populations of Pinus lambertiana, a historically dominant and ecologically important member of mixed-conifer forests of the Sierra Nevada, California. Here, I find evidence that treatment prescription differentially affects fine-scale genetic structure and effective gene flow in this species. In my third chapter, I describe the development of a dense linkage map for Pinus balfouriana which I use in chapter four to assess the quantitative trait locus (QTL) landscape of water-use efficiency across two isolated ranges of the species. I find evidence that precipitation-related variables structure the geographical range of P. balfouriana, that traits related to water-use efficiency are heritable and differentiated across populations, and associated QTLs underlying this phenotypic variation explain large proportions of total variation. In chapter five, I assess evidence for local adaptation to the eastern Sierra Nevada rain shadow within P. albicaulisacross fine spatial scales of the Lake Tahoe Basin, USA. Here, genetic variation of traits related to water availability were structured more so across populations than neutral variation, and loci identified by genome-wide association methods show elevated signals of local adaptation that track soil water availability. In chapter six, I review theory related to polygenic local adaptation and literature of genotype-phenotype associations in trees. I find that evidence suggests a polygenic basis for many traits important to conservation and industry, and I suggest paths forward to best describing such genetic bases in tree species. Overall, my results show that spatial and genetic structure of trees are often driven by their environment, and that ongoing selective pressures driven by environmental change will continue to be important in these systems.

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Batista, Marcos Roberto Dias. "Estudos citogeneticos em dipteros = inversões cromossomicas em Drosophila mediopunctata e fotomapa dos cromossomos politenicos de Cochliomyia hominivorax". [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316982.

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Orientadores: Louis Bernard Klaczko, Galina Ananina
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-15T15:35:04Z (GMT). No. of bitstreams: 1 Batista_MarcosRobertoDias_D.pdf: 1499232 bytes, checksum: f14f9f280608caee726a8954c332d6b9 (MD5) Previous issue date: 2010
Resumo: Nesta tese, estudamos uma questão básica e uma aplicada: os determinantes da variação geográfica e temporal do polimorfismo de inversões do segundo cromossomo em populações naturais de Drosophila mediopunctata; ainda, adaptamos a técnica para análise de politênicos de Drosophila para estudos em Cochliomyia hominivorax e assim elaboramos um mapa dos cromossomos politênicos desta praga da pecuária. Duas décadas depois de estudos anteriores, realizamos cinco novas coletas no Itatiaia e observamos inesperadas mudanças nas frequências dos arranjos mais comuns e em sua variação microgeográfica em relação àquelas antes descritas. No segundo cromossomo, o arranjo DA continua sendo o mais frequente, porém não detectamos mais uma correlação significativa com a altitude. Para os arranjos DS e DP, além de não haver mais correlações significativas com a altitude, suas frequências se mostram ainda mais baixas, principalmente no inverno. Entretanto, o ciclo sazonal observado para estas inversões se mantém. O arranjo DI aumentou sua frequência significativamente e agora mostra uma correlação positiva e significativa com a altitude. Estes resultados sugerem que, depois de duas décadas, houve mudanças ambientais incluindo alterações climáticas e provavelmente fatores bióticos que devem ter afetado a arquitetura genética das populações. Observamos uma diferenciação entre o padrão das frequências de inversões do cromossomo II de populações vizinhas de D. mediopunctata. As matas estudadas estão situadas em duas diferentes unidades geomorfológicas, que apresentam diferenças marcantes em relação ao solo, relevo, paisagem, vegetação e fauna. Nossos resultados sugerem que a diferenciação geográfica observada nas frequências de inversões pode ser resultado de uma adaptação local às diferenças florísticas e climáticas. Entretanto, outros marcadores genéticos devem ser pesquisados para analisar os efeitos da fragmentação florestal sobre as populações. Cochliomyia hominivorax, conhecida no Brasil como a mosca-da-bicheira, é considerada uma das principais moscas causadoras de miíases primária na região Neotropical. Apesar de um fotomapa preliminar de seus cromossomos politênicos ter sido publicado anteriormente, com resultados encorajadores, não havia um mapa dos cromossomos politênicos com boa resolução para a espécie. Desta forma, elaboramos um novo fotomapa dos cinco autossomos com uma resolução total de 1450 bandas
Abstract: In this thesis, we studied a basic and an applied issue: the determinants of geographical and temporal variation of the second chromosome inversion polymorphism in natural populations of Drosophila mediopunctata; and, adapting the squashing technique used for Drosophila to Cochliomyia hominivorax, we made a map of the polytene autosomes of this livestock pest. Two decades after previous studies, we carried out five collections in Itatiaia, RJ. We observed unexpected changes in the frequencies of the most common inversions of the second chromosome. The DA gene arrangement is still the most common, but we no longer detect a significant correlation between its frequency and altitude. Furthermore, the frequencies of DS and DP inversions became even lower, especially in winter; and didn't show a significant correlation with altitude. However, the previously observed seasonal cycle for these inversions is still present. DI frequency increased significantly, and it is now significantly positively correlated with altitude. These results suggest that, after two decades, there were modifications in the climate, but other variables - such as biotic factors -have also probably changed and may be correlated with the changes in the genetic architecture of the Itatiaia population. Furthermore, we report a differentiation between frequencies of inversions of the second chromosome in neighboring populations of D. mediopunctata. The forests studied are located over two geomorphologic units that have marked differences regarding landscape, topography, soil, vegetation, and fauna. Our results suggest that the observed geographical variation in the inversion frequencies may be a result of local adaptation to climate and floral and faunal changes. However, further analysis with other genetic markers must be performed to assess the possible effects of forest fragmentation on different populations. Cochliomyia hominivorax, the New World screwworm fly is one of the main flies causing primary myiasis in the Neotropical region. Although a preliminary photomap of the polytene chromosomes of C. hominivorax was previously published, a good resolution map of the polytene chromosomes was not available for this species. Here, we present a new photomap of the five autosomes of this species with a total resolution of 1450 bands
Doutorado
Genetica Animal e Evolução
Doutor em Genetica e Biologia Molecular

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Herman, Jonathan David. "Halofuginone: A Story of How Target Identification of an Ancient Chinese Medicine and Multi-Step Evolution Informs Malaria Drug Discovery". Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11540.

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Malaria is a treatable communicable disease yet remains a common cause of death and disease especially among pregnant women and children. Most of malaria's worldwide burden disproportionately lies in Southeast Asia and Sub-Saharan Africa. Western medicine's 100+ year history of combating Plasmodium falciparum has taught us that the global population of malaria parasites has a unique and dangerous ability to rapidly evolve and spread drug resistance. Recently it was documented that resistance to the first-line antimalarial artemisinin may be developing in Southeast Asia.

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37

Løe, Geir. "Ecology and Evolution of Resistance to Herbivory : Trichome Production in Arabidopsis lyrata". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6359.

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38

Palacio, Lopez Kattia Paola. "Effects Of Plasticity And Hybridization On Life History Traits In Arabidopsis Thaliana Ecotypes". ScholarWorks @ UVM, 2017. http://scholarworks.uvm.edu/graddis/816.

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Understanding the strategies that plant populations implement to increase evolutionary responsiveness to better survive environmental changes induced by climate change is a critical challenge for ecology and evolutionary studies. This dissertation investigates the role of hybridization, local adaptation, and phenotypic plasticity in plant population responses to environmental change. Specifically, I utilized meta-analysis techniques to investigate the prevalence of local adaptation and phenotypic plasticity as the two main mechanisms used to adapt to heterogeneous environments, and experimentally explored the genetic pathway of plasticity in phenology traits such as bolting time in Arabidopsis thaliana under high temperatures. Furthermore, A. thaliana was used to create artificial hybrids to test if novel trait combinations allow hybrids to outperform their parental source in novel and stressful environments. In the second chapter, I included reciprocal transplant plant studies and found that local adaptation is more common than adaptive plasticity as an evolutionary response to environmental heterogeneity. Although local adaptation was more common, plastic responses have been reported as a mechanism to tolerate increases in global temperature; however, the underlying genetic and developmental mechanisms are only starting to be elucidated. To address this, the third chapter determined whether alternative splicing of the ambient temperature flowering pathway gene FLOWERING LOCUS-M (FLM), and expression of SHORT VEGETATIVE PHASE (SVP), can explain flowering time plasticity in ecotypes of A. thaliana under 18°C and 26°C. Although the expression of SVP and FLM-β tracks reaction norms, I failed to find evidence that alternative FLM splicing plays a role in phenotypic plasticity in intraspecific flowering time variation. Intraspecific hybridization (admixture) disrupts divergent genetic architectures between populations to generate phenotypic novelty and raw material for environmental selection to act upon. In order to understand the effect of this disruption to local adaptation of A. thaliana ecotypes separated along geographic and locally adaptive genetic distances, the fourth chapter used experimentally created F1-hybrids between geographically distant ecotypes, and used single nucleotide polymorphism (SNP) data to estimate (putatively neutral) background and adaptive genetic distances. My results suggest that disruption of locally adaptive genomic loci decreases the performance of offspring between distantly related parents, but that crosses between very closely related parents also reduce performance, suggesting that during admixture selection may have to balance the consequences of disrupting local adaption while also avoiding inbreeding depression. Lastly, I examined the effect of recombination events under limiting and novel growing conditions (i.e. drought, high temperatures, and freezing field over-wintering conditions) in A. thaliana F2-hybrids. I provide empirical data for the effect of limiting growing environment on phenology, growth, and fitness traits on the admixed and parental ecotypes. I found that recombination events generate novel phenotypes. Generally, offspring phenotypic variation increases and shifts from the parental ecotype phenotypes, and in some cases, offspring display transgressive segregation, heterosis, or outbreeding depression. This work provides a novel contribution towards understanding mechanisms that plant implement to deal with rapid environmental changes. Specifically, plastic responses and hybridization events may interplay to maintain and increase genotypic diversity.

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Thomann, Michel. "Evolution des stratégies de reproduction des plantes à fleurs face aux changements globaux et au déclin des pollinisateurs". Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20230.

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De nombreuses populations voient leurs conditions de vie modifiées par les changements globaux. Au-delà de leurs conséquences écologiques, les changements globaux peuvent également modifier les régimes de sélection des populations. Le déclin récent des pollinisateurs pourrait altérer fortement le succès reproducteur de nombreuses populations de plantes à fleurs. Cependant, ses conséquences évolutives n'ont pas été étudiées jusqu'ici. Cette thèse traite de la possibilité d'adaptation des stratégies de reproduction des plantes face aux changements globaux et plus spécifiquement face au déclin des pollinisateurs. Cette question a été abordée en deux temps. Premièrement, l'analyse de l'abondante littérature théorique et empirique sur les systèmes de reproduction des plantes et dans un moindre mesure la construction d'un modèle d'évolution des traits floraux d'attraction ont permis de clarifier des scénarios d'évolution à court terme. Deuxièmement, une approche empirique originale a été menée, consistant à comparer directement les traits de populations ancestrales et descendantes de trois espèces annuelles, à partir de la culture en jardin commun de graines anciennes et récentes en provenance de régions où des indices de déclin des pollinisateurs existent. Cette approche permet de mettre clairement en évidence l'évolution génétique. Les données existantes indiquent que le déclin des pollinisateurs peut accentuer la limitation pollinique et par conséquent augmenter la sélection sur les traits floraux. Par ailleurs, la variation génétique substantielle dans les populations suggère que l'évolution rapide des populations de plantes est possible. L'analyse de la littérature et notre étude théorique suggèrent que l'accroissement de la capacité d'autofécondation autonome ou l'accroissement de l'attraction des pollinisateurs sont deux scénarios d'évolution possibles. Deux types de réponses évolutives ressortent de nos travaux expérimentaux. D'abord, une avancée du calendrier de floraison a été retrouvée chez les trois espèces étudiées. Ce résultat souligne le rôle de l'évolution génétique, et pas seulement de la plasticité phénotypique, dans les avancées de phénologies de printemps que l'on retrouve chez de très nombreux organismes. Ensuite, contrairement aux traits de phénologie, les traits floraux ont évolué dans des directions opposées selon les espèces. Ainsi, des traits floraux a priori plus attractifs ont évolué chez une des espèces tandis que pour une autre, des traits floraux a priori moins attractifs ont évolué, mais s'accompagnent d'une meilleure capacité d'autofécondation autonome. Cette étude confirme que les traits de reproduction des plantes peuvent évoluer en quelques décennies seulement. La possibilité du sauvetage évolutif des populations, par l'évolution rapide des traits et des stratégies de reproduction des plantes, est une perspective de recherche qui découle de ces résultats
Global change alters life conditions of numerous populations. Beyond ecological consequences, global change can also modify selection regimes in populations. While the recent pollinator decline may specifically affect the reproductive success of flowering plants, its evolutionary consequences have not been studied yet. This thesis deals with the possibility of adaptation of plant reproductive strategies under global change and more specifically under pollinator decline. This question was addressed in two steps. First, the analysis of the extensive literature on plant mating systems, and, to a lesser extent, the construction of a model for the evolution of attractive floral traits, allowed us to clarify evolutionary scenarios at short-time scales. Second, we conducted an original empirical approach, consisting in the direct comparison of ancestral and descendant populations by re-growing old and recent seeds under identical conditions. This approach allowed us to test whether genetic evolution of reproductive traits occurred in the context of pollinator decline for three annual plant species. Data from the literature indicates that pollinator decline likely increases pollen limitation and thus selection on floral traits. Moreover, the substantial genetic variation within populations suggests that rapid evolution is possible. Increased autonomous selfing or increased pollinator attraction are two possible routes of plant adaptation to pollinator decline emerging from the analysis of the literature and from our theoretical study. Our empirical work brings out two types of evolutionary trends. Firstly, earlier flowering phenology was found in all three studied species. This result shows that genetic evolution, not only phenotypic plasticity; certainly contribute to the spring phenological advancements reported for numerous species. Secondly, unlike phenological traits, floral traits evolved in opposite directions depending on the species. Showy floral traits evolved in a species while joint evolution of autonomous selfing with a reduction of floral attractiveness seemed to evolve in another species. This study shows that plant reproductive traits can evolve in a few decades. Whether or not rapid evolution of plant reproductive traits can act as an evolutionary rescue for threatened populations is a research question that arises from these results

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Nyrén, Karl. "Phylogenetic analysis of secretion systems in Francisellaceae and Legionellales : Investigating events of intracellularization". Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-448062.

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Host-adapted bacteria are pathogens that, through evolutionary time and host-adaptive events, acquired the ability to manipulate hosts into assisting their own reproduction and spread. Through these host-adaptive events, free-living pathogens may be rendered unable to reproduce without their host, which is an irreversible step in evolution. Francisellaceae and Legionellales, two orders of Gammaproteobacteria, are cases where host-adaptation has lead to an intracellular lifestyle. Both orders use secretion systems, in combination with effector proteins, to invade and control their hosts. A current view is that Francisellaceae and Legionellales went through host-adaptive events at two separate time points. However, F. hongkongensis, a member of Francisellaceae shares the same secretion system as the order of Legionellales. Additionally, two host-adapted Gammaproteobacteria, Piscirickettsia spp. and Berkiella spp., swaps phylogenetic positions between Legionellales and Francisellaceae depending on methods applied - indicating shared features of Francisellaceae and Legionellales. In this study, we set up a workflow to screen public metagenomic data for candidate host-adaptive bacteria. Using this data, we attempted to assert the phylogenetic position and possibly resolve evolutionary events that occurred in Legionellales, F. hongkongensis, Francisellaceae, Piscirickettsia spp. and Berkiella spp. We successfully acquired 23 candidate host-adapted MAGs by (i) scanning for genes, among reads before assembly, using PhyloMagnet, and (ii) screening for complete secretion systems with MacSyFinder. The phylogenetic results turned out indecisive in the placement ofBerkiella spp. and Piscirickettsia. However, results found in this study indicate that, contrary to previous beliefs, it is possible that it was one intracellularization event of a common ancestor that gave rise to the intracellular lifestyle of Francisellaceae and Legionellales.

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41

Seshadri, Chitra. "Genome wide epigenetic analyses of Araptus attenuatus, a bark beetle". VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4167.

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Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This research examines spatial genetic structure using paired nucleotide and methylation genetic markers in the Sonoran bark beetle, Araptus attenuatus, for which we have a considerable knowledge about its neutral demographic history, demography, and factors influencing ongoing genetic connectivity. Using the msAFLP approach, we attained 703 genetic markers. Of those, 297 were polymorphic in both nucleotide (SEQ) and methylation (METH) were assayed from 20 populations collected throughout the species range. Of the paired SEQ and METH locis, the METH were both more frequent (16% vs. 7%), maintained more diversity (Shannon IMeth = 0.361 vs. ISeq=0.272), and had more among-population genetic structure (ΦST; Meth = 0.035 vs. ΦST; Seq= 0.008) than their paired SEQ loci. Interpopulation genetic distance in both SEQ and METH markers were highly correlated, with 16% of the METH loci having sufficient signal to reconstruct phylogeographic history. Allele frequency variation at five loci (two SEQ and three METH) showed significant relationships with at-site bioclimatic variables suggesting the need for subsequent analysis addressing non-neutral evolution. These results suggest that methylation can be as informative as nucleotide variation when examining spatial genetic structure for phylogeography, connectivity, and, identifying putatively adaptive genetic variance.

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42

Barrabé, Laure. "Systématique et Evolution du genre Psychotria (Rubiaceæ) en Nouvelle-Calédonie, adaptation aux terrains ultramafiques". Phd thesis, Université de Nouvelle Calédonie, 2013. http://tel.archives-ouvertes.fr/tel-00967108.

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La Nouvelle-Calédonie est un archipel du Pacifique Sud-Ouest. Sa flore est riche, unique, et dysharmonique. L'origine temporelle et géographique de cette flore constitue une des problématiques majeures des botanistes. Une étude systématique a été menée sur le genre Psychotria (Rubiaceae), et ses genres alliés (clade Psychotrieae-Palicoureeae), afin de comprendre les modes d'établissement et de diversification des plantes dans l'archipel. Les deux tribus comportent 86 espèces néo-calédoniennes réparties entre les genres Geophila (une espèce), Margaritopsis (quatre espèces) et Psychotria (81 espèces). L'étude taxonomique a permis de déterminer pour chacun d'eux les noms d'espèces valides, et d'identifier 26 espèces nouvelles de Psychotria et Margaritopsis. Neuf combinaisons et noms spécifiques nouveaux sont proposés.La Nouvelle-Calédonie a été colonisée au moins quatre fois par les Psychotrieae-Palicoureeae. Bien que leurs arrivées soient simultanées durant le Néogène, ces quatre lignées ont des histoires évolutives différentes à mettre en lien avec leurs modes propres d'établissement et de diversification. Le genre Geophila n'a pas diversifié. Les Margaritopsis ont eu une diversification modeste, à l'image des autres espèces des îles du Pacifique. Les Psychotria clade NC1 constituent une lignée relique, ayant probablement subit une extinction, et qui se serait uniquement maintenue dans les maquis miniers. Les Psychotria cladeNC2 constituent la plus large, jeune et rapide radiation de plantes de la Nouvelle-Calédonie, probablement originaire des forêts humides d'Australie.Le clade NC2 est en pleine expansion évolutive. Il est constitué de 12 lignées internes. Sa capacité à tolérer les substrats ultramafiques, acquise avant son arrivée dans l'archipel, a favorisé son établissement local. Sa large diversité a probablement différentes origines : une labilité vis-à-vis de la nature des substrats géologiques, des changements éventuels de pollinisateurs, un changement de niche écologique amorcé, lié à l'acquisition d'adaptations à la sécheresse et à l'avènement d'un climat plus aride en Nouvelle-Calédonie durant le Pliocène.

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Bolte, Constance E. "NICHE CONSERVATISM OR DIVERGENCE: INSIGHTS INTO THE EVOLUTIONARY HISTORIES OF Pinus taeda, Pinus rigida, AND Pinus pungens". VCU Scholars Compass, 2017. http://scholarscompass.vcu.edu/etd/4842.

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Environmentally related selective pressures and community interactions are well-documented drivers for niche differentiation, as natural selection acts on adaptive traits best fit for survival. Here, we investigated niche evolution between and within Pinus taeda, Pinus rigida, and Pinus pungens and sought to identify which climate variables contributed to species divergence. We also sought to describe niche differentiation across genetic groupings previously identified for P. taeda and P. rigida. Ecological niche models were produced using Maximum Entropy followed by statistical testing based on a measure of niche overlap, Schoener’s D. Both niche conservatism and niche divergence were detected, thus leading us to conclude that directional or disruptive selection drove divergence of the P. taeda lineage from its ancestor with P. rigida and P. pungens, while stabilizing selection was associated with the divergence of P. rigida and P. pungens. The latter implies that factors beyond climate are important drivers of speciation within Pinus.

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44

Kastally, Cheldy. "Genome-wide genetic variation in two sister species of cold-resistant leaf beetle: migration and population adaptation". Doctoral thesis, Universite Libre de Bruxelles, 2018. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262911.

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An important goal of biology is to understand the key mechanisms of evolution underlying the diversity of living organisms on Earth. In that respect, the recent innovations in the field of new generation sequencing technologies (NGS) are bringing new and exciting opportunities. This thesis presents results obtained with these tools in the specific context of the study of two sister species of cold-adapted leaf beetles, Gonioctena intermedia and G. quinquepunctata. More specifically, this work is focused around four research directions: the two first explore methods of statistical inference using a spatially explicit model of coalescence, by (1) evaluating the potential of various summary statistics to discriminate phylogeographic hypotheses, and (2) investigating the dispersal abilities of a montane leaf beetle, G. quinquepunctata, using an original method that avoids using summary statistics. The third research direction focuses on the adaptation to cold conditions in this montane leaf beetle, by testing the association between genetic polymorphism across tens of thousands of genetic markers and altitude in samples collected at various elevation levels in the Vosges (France). Finally, the fourth, and last, research axis presents the discovery of mitochondrial heteroplasmy, i.e. the presence in an individual of multiple copies of the mitochondrial genome, in natural populations of G. intermedia. We illustrate, here, how NGS technologies could help identify this phenomenon, probably underestimated in animals, on a large scale.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

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45

Belkorchia, Abdel. "Evolution des génomes microsporidiens et mécanisme d'adaptation moléculaire chez les parasites intracellulaires obligatoires". Phd thesis, Université Blaise Pascal - Clermont-Ferrand II, 2007. http://tel.archives-ouvertes.fr/tel-00718201.

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Les microsporidies sont des parasites intracellulaires obligatoires caractérisés par un mode d'infestation original, et pour certaines espèces, par un très fort degré de compaction du génome nucléaire. Des travaux portant sur les mécanismes de régulation transcriptionnelle chez Encephalitozoon cuniculi montrent qu'une organisation polycistronique des gènes est présente. Une maturation aléatoire des messagers conduit à la formation d'une population d'ARNm comprenant des ARNm monocistroniques et polycistroniques. Afin d'améliorer nos connaissances sur la structure des génomes microsporidiens et leur capacité d'adaptation, le sequençage du génome de Brachiola algerae a été initié : 30 bandes d'ADN chromosomiques ont pu être visualisées (taille du génome estimée à 23Mb). Les premières données de séquence ont révélées la présence de plusieurs classes d'éléments transposables ainsi que des gènes codant des enzymes impliquées dans le processus d'ARN interférence

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Kucharavy, Andrei. "Molecular mechanisms of aneuploidy-mediated stress-resistance". Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066734.pdf.

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L’aneuploïdie a été historiquement associé à des phénotypes nuisibles, notamment le cancer et le syndrome de Down. Cependant, des résultats expérimentaux récents suggèrent que l’aneuploïdie permettrait l'adaptation à des stresseurs variés, notamment résistance aux médicaments, en rendant la compréhension critique au domaine biomédical. Cependant, les mécanismes moléculaires permettant cette adaptation restaient à élucider. Une telle élucidation selon plusieurs axes a été justement l'objet de ce travail. Premièrement, nous avons développé un modèle mathématique représentant l'adaptation aux environnements adverses comme un compromis dans la position dans un espace des traits. L’aneuploïdie y permet une exploration plus rapide. Ce modèle a été validé sur des données expérimentaux et a été utilisé pour prédire une combinaison médicamenteuse ciblant les populations cellulaires hétérogènes dans le cancer du sein. Deuxièmement, nous avons utilisé les concepts du domaine de la biologie en réseaux et des résultats de théorie de graphes pour prédire la distribution des gènes essentiels, des interactions létales et des gènes essentiels évolutifs - des gènes essentiels qui peuvent être supprimés dans des organismes devenus aneuploïdes. Nous avons également construit un algorithme pour prédire les mécanismes moléculaires qui expliquerait les phénotypes associés à des perturbations génétiques à grande échelle. Finalement, nous avons exploré plusieurs mécanismes par lesquels l’aneuploïdie pourrait impacter la régulation génétique, conduisant au développement des outil informatiques publiés
Aneuploidy has historically been associated with detrimental phenotypes and diseases, notably cancer and Down Syndrome. However, recent experimental evidence suggests aneuploidy provides adaptation to numerous stressors, including drug resistance, making aneuploidy study critical to biomedical research. However, the molecular mechanisms underlying this process remained elusive until now. This work focused on exploring several approaches to understanding those mechanisms. Frist, we have developed a general mathematical model of organism adaptation to adverse environments. In our model, the adaptation to environments takes place as a trade-off in the space of traits, of which aneuploidy allows a more efficient and rapid sampling. This model was validated on experimental data and used to predict optimal drug combinations targeting heterogeneous populations breast tumor cells. Second, we used the framework of network biology to model biomolecular networks and apply to them results from the graph theory and existing results on weighted graphs from other domains. We were able to predict the distribution of essential genes, lethal genetic interactions and essential evolvable genes - essential genes that can be deleted in the aneuploid background. We were as well able to build a predictive model for inferring most likely pathways underlying the phenotype of large-scale genetic perturbations. Finally, we attempted to explore several possible modes besides dosage effects by which aneuploidy could impact the gene expression regulation. This required a development of an image analysis toolkit that was validated and released for as open-source software

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47

Philippe, Nadège. "Mécanismes moléculaires de l'adaptation au cours de 20 000 générations d'évolution expérimentale chez Escherichia coli". Phd thesis, Université Joseph Fourier (Grenoble), 2006. http://tel.archives-ouvertes.fr/tel-00108200.

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Les mécanismes d'adaptation d'Escherichia coli à une alternance quotidienne entre des conditions de croissance et de carence ont été étudiés grâce à une stratégie d'évolution expérimentale. Douze populations d'E. coli, dérivant d'un ancêtre commun, ont été propagées pendant plus de 40 000 générations par transferts journaliers dans un milieu minimum contenant une quantité limitante de glucose. L'évolution des 12 populations se caractérise par un degré important de parallélisme phénotypique (augmentation du fitness et du volume cellulaire, ...) et génétique, les mêmes gènes étant ciblés par la sélection naturelle dans la majorité des populations. Des mutations bénéfiques ciblant le gène spoT, acteur majeur de la réponse stringente permettant l'adaptation aux carences, avaient été identifiées dans 8 populations. Nous avons mis en évidence des mutations bénéfiques ciblant des gènes impliqués dans la biosynthèse de la paroi (pbpA-rodA) et la superhélicité de l'ADN (topA, fis). L'étude moléculaire de 2 mutations bénéfiques touchant l'opéron pbpA-rodA révèle qu'elles diminuent la quantité de protéine PBP2. L'analyse de 3 mutations ciblant le gène spoT montre qu'elles atténuent le contrôle stringent lors de l'entrée en phase stationnaire sans modifier les niveaux cellulaires de (p)ppGpp. Différentes mutations d'un même gène ayant les mêmes effets, l'évolution révèle un parallélisme moléculaire important. Près de la moitié des mutations bénéfiques affecte les réseaux de régulation globale de l'expression des gènes (spoT, fis, topA). La plasticité des réseaux de régulation globale joue donc un rôle primordial au cours de l'évolution et l'adaptation des bactéries.

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Smiley-Walters, Sarah Ann. "Interactions between Pigmy Rattlesnakes (Sistrurus miliarius) and a Suite of Prey Species: A Study of Prey Behavior and Variable Venom Toxicity". The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1483455551984898.

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Pace, Brian A. "Physiology, Photochemistry, and Fitness of Mexican Maize Landraces in the Field". The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1545421491370678.

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50

Huestis, Diana Lea. "Ecological genetics of adaptive life-history phenotypes in the cricket Allonemobius socius". 2008. http://hdl.handle.net/10106/1852.

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Tesi sul tema "Evolution (Biology) Adaptation (Biology) Insects"

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