In the present study, I used transcriptomic data to elucidate the role of selection in maintaining genetic cohesion and promoting divergence among wild populations of the annual sunflower Helianthus annuus. I observed that nearly half of the loci displaying high levels of population structure (44%) show allele frequency spectrum skew consistent with recent exposure to natural selection. Among transcriptomic regions at which allele frequency divergence is lowest, fewer loci maintain strong signals of selection (34%). Additionally, I find evidence supporting the maintenance of evolutionarily complex haplotype structure within populations at loci showing high levels of among-population allele frequency divergence.

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.

Master of Science / Particulate ingestion has been an ongoing issue in the aviation industry as aircraft are required to operate in hostile environments. Ingesting particulates such as sand or dust can erode and damage engine components. This damage will affect the life cycle of parts and compromise the safety of the aircraft. This issue is very costly and dangerous. In order to combat these issues, a particle sensor with the ability to monitor in-stream particulate size, shape, and mass flow rate is necessary. Our team with the Advanced Propulsion and Power Laboratory developed a non-intrusive optical sensor that is able to characterize non-spherical particles. This sensor has been used in various applications through the years; however, most recently, the sensor has been demonstrated at the Virginia Tech M250 engine inlet. This was the first time that the sensor was directly attached to an engine's inlet and subjected to engine conditions. For this validation, highly erosive, coarse quartz was used. Utilizing laser and cameras, the sensor is able to deduce the particles' average shape and size distributions. From those measurements, the mass flow rate of the particle can be calculated. The works provided in the thesis show that particle ingestion rates can be measured to an acceptably high accuracy. In contrast, refinement of the processing techniques can provide spatially resolved measurements of particle characteristics as well.

Dispersal influences several ecological and evolutionary processes, such as intraspecific competition, genetic drift and inbreeding. It can lead to phenotypic mismatch with the habitat when a locally adapted individual winds up in an environment with a divergent selection regime compared to the source habitat. The aim of this project was to compare dispersive traits in the freshwater isopod Asellus aquaticus from a cave habitat, with surface dwelling isopods collected upstream and downstream from the cave system. The subterranean stream (cave) represents a rare, geographically limited habitat which has a divergent selective pressure compared to the surrounding habitats. Experiments on dispersal were performed in the laboratory, in darkness with IR-equipment for visualization. Displacement was measured using one-dimensional test arenas. Compared to the surface phenotype, the cave phenotype was expected to have reduced fitness outside of the cave and unlikely to successfully disperse to new areas of similar suitable conditions. The results did not follow my main hypothesis that isopods from the cave would be less dispersive than individuals from the surface. The inconclusive results might derive from large variation in the data and divergent adaptations which yield similar expression of dispersal.

In many habitats, species’ traits correspond strongly to local environmental conditions. The cause of this pattern may be in-situ evolution, where initially mal-adapted resident species evolved traits that increased their fitness. Alternatively, species with suitable traits may have colonized the focal habitat and replaced resident species. Since theories in the fields of evolutionary biology and community ecology developed independently, few guidelines tell us when to expect evolutionary adaptation or ecological species replacement as the primary driver of species and trait composition in a given habitat. The goal of my dissertation research was to explain how evolutionary adaptation and ecological species replacement together determine the composition of pond zooplankton communities. I combined theoretical models with thorough surveys of natural pond communities and manipulative experiments. I discovered that one particular zooplankton species, Daphnia pulex, evolved to have different trait values in ponds with different environments. The evolutionary divergence within D. pulex profoundly affected its ecological interactions with other zooplankton species. D. pulex populations diverged from one another so much that they differed in their ability to successfully colonize ponds full of competing zooplankton species. I also used a computer simulation model to determine when a community’s trait changes were explained by evolutionary adaptation or ecological species replacement. The dispersal rate of species among habitats and the amount of genetic variance within these species both influenced adaptive trait change in a community. The group of research studies that indicate evolutionary and ecological processes operate on a similar time scale is small but growing. My dissertation research provides another crucial demonstration that evolution within individual species, such as D. pulex, influences their community ecological interactions with other species. I also identified key parameters (dispersal rate among and genetic variance within species) that may help biologists predict whether evolution or ecological species replacement explained adaptive trait change. My projects mostly concern the community and trait distributions that result from the assembly of species in new habitats. However, this framework may inform studies of community response to environmental changes such as invasive species or habitat destruction. / text

Understanding the genetic basis of adaptive evolution, and how natural selection has shaped patterns of polymorphism and divergence within and between species are enduring goals of evolutionary genetics. In this thesis, I used whole genome re-sequencing data to characterize the genomic signatures of natural selection along different evolutionary timescales in three Populus species: Populus tremula, P. tremuloides and P. trichocarpa. First, our study shows multiple lines of evidence suggesting that natural selection, due to both positive and purifying selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. Second, we characterize the evolution of genomic divergence patterns between two recently diverged aspen species: P. tremula and P. tremuloides. Our findings indicate that the two species diverged ~2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. We further explore different mechanisms that may explain the heterogeneity of genomic divergence, and find that variation in linked selection and recombination likely plays a key role in generating the heterogeneous genomic landscape of differentiation between the two aspen species. Third, we link whole-genome polymorphic data with local environmental variables and phenotypic variation in an adaptive trait to investigate the genomic basis of local adaptation in P. tremula along a latitudinal gradient across Sweden. We find that a majority of single nucleotide polymorphisms (SNPs) (&gt;90%) identified as being involved in local adaptation are tightly clustered in a single genomic region on chromosome 10. The signatures of selection at this region are more consistent with soft rather than hard selective sweeps, where multiple adaptive haplotypes derived from standing genetic variation sweep through the populations simultaneously, and where different haplotypes rise to high frequency in different latitudinal regions. In summary, this thesis uses phylogenetic comparative approaches to elucidate how various evolutionary forces have shaped genome-wide patterns of sequence evolution in Populus. / <p>The research in this thesis was supported by the Swedish research council (to Pär K. Ingvarsson) and the JC Kempe Memorial Scholarship Foundation (to Jing Wang). The PhD study of Jing Wang in Sweden was funded by the State Scholarship from China Scholarship council.</p>

For insects that develop inside discrete hosts both host size and host quality constrain offspring growth, influencing the evolution of body size and life history traits. This dissertation examines the effects of host size, host quality, and intraspecific competition on life history and associated traits of populations of the seed-feeding beetle S. limbatus adapted to different host plants, and quantifies population differences in phenotypic plasticity. Populations of the study correspond to divergent clades of the species phylogeography (Colombia and United States). Clades compared differ genetically for all traits when beetles were raised in a common garden. Contrary to expectations from the local adaptation hypothesis, beetles from all populations were larger, developed faster and had higher survivorship when reared in Acacia greggii, the larger host. Two host-plant mediated maternal effects were found: offspring matured sooner, regardless of their rearing host, when their mothers were reared on Pseudosamanea guachapele and females laid larger eggs on Ps. guachapele. These results also show that this species in addition to be a smaller is a low quality host. Females also laid more eggs and sooner on A. greggii than in Ps. guachapele and, laid more eggs on P. guachapele when A. greggii seeds were small than when they were large. Eggs were larger when laid on Ps. guachapele and Parkinsonia florida, two hosts that reduce survivorship in all populations. However, Colombia females laid eggs of similar size on Ps. guachapele and Pa. florida, while USA females laid the largest eggs on Pa. florida. Larger beetles were most affected when larval competition was increased and seed size decreased. The responses of different body sized females were asymmetrical showing significant variation in plasticity. Although differences between populations in growth and life history traits appear to be adaptations to the size and quality of their host plants, host-associated maternal effects, partly mediated by maternal egg size plasticity play an important role in the evolution of S. limbatus’ diet breadth. More generally, phenotypic plasticity mediates the fitness consequences of using novel hosts, likely facilitating colonization of new hosts but also buffering herbivores from selection post-colonization.

本研究主要探討企業如何透過組織間跨疆域知識移轉，強化組織的核心能耐。其研究方法採行質化研究，以統一超商公司為研究對象，透過深度訪談，詳盡報導統一超商跨疆域知識移轉的活動與過程，並結合文獻探討以及研究者個人理解，發展十三個命題。主要研究結論如下： (1) 知識特性與移轉模式的關係 經營知識可依內隱性與地區鑲嵌性劃分四個知識群組。知識的內隱性影響移轉媒介，內隱程度高者以人員為主；反之以物件為主。知識的地區鑲嵌程度則影響移轉深度，地區鑲嵌程度較低，知識提供者同時移轉知識架構與知識內容；反之，知識提供者移轉知識架構，知識接受者建構知識內容。 (2) 移轉雙方特質與移轉模式的關係 知識提供者與接受者的目標結合程度會影響知識移轉的涉入程度。當目標結合程度愈高，知識移轉的內容愈具廣度與深度、互動頻率愈高、移轉機制愈多元且參與成員體系愈龐大，愈有利於移轉內隱知識，亦愈需要設置知識移轉的統籌窗口，負責最新營運情報的即時傳遞、個別移轉專案的協調整合、建立知識移轉之責任分工體系與推動計劃性移轉機制。 知識接受者的先前基礎會影響知識的移轉順序。當知識接受者不具先前基礎，知識提供者移轉各項核心營業活動的入門知識。當知識接受者具備先前基礎，知識移轉涉及組織改變，優先移轉快速展現績效的經營知識；又先移轉後勤支援系統，後移轉核心營業活動。 (3) 跨疆域知識移轉之本土化調適 針對外部機構配合問題，可利用知識提供者原有網絡關係加以調適；針對社會型態與消費習慣迥異問題，可透過知識接受者觀摩民情風俗較為相近的第三國做法加以調適。此外，知識接受者可透過內化、共同化、外化與結合之知識螺旋循環，在知識提供者的知識架構下，自行建構與當地社會情境鑲嵌的知識內容。

Tout observateur peut constater la diversité des milieux sur Terre. La compréhension des liens entre cette diversité des habitats et la biodiversité est l'un des thèmes centraux en Écologie, en Évolution et en Biologie de la conservation. Je m'intéresse dans cette thèse aux conséquences écologiques (à court terme) et évolutives (à plus long terme) de la structuration spatiale et de l'hétérogénéité de l'environnement. Je développe et analyse plusieurs modèles mathématiques, combinant différents formalismes théoriques (dynamiques adaptatives, génétique des populations, génétique quantitative). Ces modèles permettent d'explorer les conséquences de l'hétérogénéité spatiale de l'environnement sur (1) les conditions de persistance des populations ; (2) la coexistence entre différents phénotypes et (3) la dynamique évolutive des populations. Je montre ainsi l'importance (i) de l'intensité et de la place de la migration dans le cycle de vie ; (ii) du type de structure spatiale (explicite ou implicite, continu ou discret) ; (iii) de la forme du compromis évolutif, et donc des coûts d'adaptation à une autre ressource ; et enfin (iv) des éventuels rétrocontrôles démographiques. J'illustre à l'aide des interactions entre hôtes et parasites l'importance des hétérogénéités spatiales. Un premier exemple concerne leur utilisation dans la gestion des pharmacorésistances ou des résistances aux insecticides : une répartition hétérogène du traitement permet d'éviter la propagation de parasites ou de nuisibles résistants. Un second exemple, enfin, illustre comment les hétérogénéités dues à l'auto-structuration spatiale influencent l'évolution de stratégies de défense des hôtes, et permettent l'évolution de défenses altruistes. / Any observer can notice the diversity of habitats on Earth. Understanding the links betweenthis diversity of habitats and biodiversity is a core topic in Ecology, Evolution andConservation Biology.In this thesis, I study the ecological (short-term) and evolutionary (long-term) consequencesof spatial structuring and environmental heterogeneities. I develop and analyzeseveral mathematical models, which combine different theoretical frameworks (adaptivedynamics, population genetics, and quantitative genetics). I explore the consequences ofspatial heterogeneities on (1) the conditions for population persistence; (2) the coexistenceof different phenotypes, and (3) evolutionary dynamics of populations. I show that theresults depend on (i) the life-cycle, and in particular whether migration influences local regulation;(ii) the choice of the spatial structure (explicit or implicit, continuous or discrete);(iii) the shape of the trade-off, and hence the costs of adaptation to another resource, andfinally (iv) the potential demographical feedbacks.I use the specific case of hosts and parasites interactions to illustrate the importanceof spatial heterogeneities. As a first example, I show that a heterogeneous application oftreatments can help prevent the spread of resistant parasites or pests. Secondly, I show howspatial heterogeneities due to self-structuring influence the evolution of host defense strategies,and allow for the evolution of altruistic defense strategies.

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.