This work sequenced the placental microbiome of preterm and full-term pregnancies, and related preterm/full-term variations in placental microbiome composition and function to maternal inflammation in order to evaluate the proximate roles of the placental microbiome in responding to maternal immune stress and determining gestation length. These findings were situated in an evolutionary life history framework based on reproductive-immune trade-offs in order to develop an ultimate explanation for why natural selection has left us vulnerable to preterm birth, and why some populations are more affected than others. The preterm placental microbiome was found to be characterized by an inflammatory microbiome, dominated by bacteria that multiply in the context of energetic stress. The presence of such high numbers of these bacteria at the preterm placenta suggests that energetic and immune stresses are occurring in preterm birth, and that there may be a bidirectional relationship between stressful conditions and the microbiome. That is, inflammation or other stressors that contribute to energy imbalance may encourage shifts in the microbiome, which in turn creates more inflammation and energy imbalance. When that happens, pregnancy may become unsustainable before reaching term. Conversely, term pregnancies were characterized by greater numbers of beneficial, anti-inflammatory bacteria, hinting at possible roles for a healthy placental microbiome in nourishing and protecting the fetus. These findings underscore the need for a more holistic view of the role of microbes in pregnancy, as well as the need for health interventions that identify and address root sources of energetic and immune stress. / Anthropology

Two separate but related projects make up the work of this thesis. The growing amount of sequence data available in public databases provides an opportunity to compare species in new ways. It can be shown that there is a systematic change in amino acid composition in a dataset of sequences from 69 species possessing a range of optimal growth temperatures. By creating a phylogenetic tree of all available Archaea, pairs may be selected that contain a relatively closely related mesophile and (hyper)thermophile. In addition, pairs may be selected from Bacteria to include psychrophiles as well as other thermophiles. An evolutionary model is derived here that detects amino acid asymmetries in these species pairs beyond what might be expected to be caused by differences in GC content. This amino acid asymmetry can then be plausibly explained by temperature adaptation occurring in these species since they diverged from a common ancestor. In the second part, similarity searches using molecular sequences are drawn as networks, where open reading frames in one species may be linked to a corresponding sequence in another species if the similarity search score is above a given threshold. This process is similar to that used to identify orthologous sequences for use in evolutionary models. When drawn as a network of distinct clusters of similarity, patterns emerge that can be spurious or have some biological relevance. This work identifies the need to develop better methods of analyzing these network clusters. / Thesis / Master of Science (MSc)

<p> There has been an increasing value in the ability to describe the world's diversity for the purpose of enhancing research and conservatory efforts. Characterizing the level of heterogeneity of particular molecular markers and verifying its suitability as an identifier of new specimens provides a way of quantifying biodiversity. One such molecular marker is the mitochondrial cytochrome c oxidase subunit I (COl). An analysis of the evolutionary rates among and within taxonomic groupings of 13,641 insect COl sequences revealed that the evolutionary rate of some species increased or decreased, sometimes by an order of a magnitude. Furthermore, the increased evolutionary rates of two species, from the Lepidopteran and Orthopteran orders, may be explained by the influence of positive selection but further analyses would be required to rule out other explanations. Overall, we deem that the rate of substitution generates enough change for COl to work sufficiently as a barcode marker in insects. As COl is not suitable for specimen identification in plants, it would be useful to be able to quickly determine if there is enough variation in COl or other molecular markers for specimen identification. In response, a visualization tool, Fingerprint, was developed to graphically depict 11 different types of sequence diversity. An application of the tool to Lepidopteran COl data verified the genetic diversity in insect COl and the tool's ability to sensitively detect different types of heterogeneity. </p> / Thesis / Master of Science (MSc)

Galaxies in the Universe are primarily blue and star-forming or red and passively evolving. Here we study an outlier population of red, star-forming galaxies in the local Universe which we call Red Misfits. These galaxies are classified based on inclination-corrected optical colours and specific star formation rates derived from the Sloan Digital Sky Survey Data Release 7. We find that $\sim$11 per cent of galaxies at all stellar masses are classified as red in colour yet actively star-forming. Using the wealth of information provided by the SDSS and related products we explore a number of properties of these galaxies and demonstrate that Red Misfits are a distinct population of galaxies in the Universe and not simply blue star-forming galaxies whose colours are reddened by intrinsic dust extinction. Red Misfit galaxies exhibit intermediate, bulge-dominated disk morphologies, intermediate stellar ages, slightly enhanced dust extinction and gas-phase metallicities, and an enhanced likelihood of hosting an active galactic nucleus. The proportion of Red Misfits in galaxy groups remains constant irrespective of group halo mass or projected distance to the group centre. We conclude that Red Misfits are a transition population being gradually quenched on their way to the red sequence and that this quenching is dominated by internal mechanisms rather than environmentally-driven processes. / Thesis / Master of Science (MSc)

The genome of the a-proteobacterium Sinorhizobium meliloti has been completely sequenced and annotated. providing a wealth of information about this endosymbiotic N2 fixing organism. Although the structure of the genome, consisting of a circular chromosome and two smaller pSymA and pSymB replicons, has long been known, only a small portion of ORFs have previously been characterized. Sequence analysis of pSymB has revealed that a large portion of the 1570 ORFs code for solute uptake systems and polysaccharide biosynthesis. The pSymB replicon been referred to as a "megaplasmid," implying that pSymB is non-essential for viability of the organism. However, coded on pSymB are several essential genes, including a tRNA ArgCCG gene and the minCDE genes, which are not found elsewhere in the genome. Replication of pSymB is controlled by repABC genes, a typical property of plasmids among Rhizobiaceae. Therefore, the genome signature, a compositional analysis that allows comparison of whole replicons rather than focusing on particular genes, was used to provide support for designation of pSymB as a second chromosome in S. mdiloti. It was found that among a-proteobacteria, plasmids and chromosomes have distinctive patterns of dinucleotide biases, and in this respect, pSymB is chromosome-like while pSymA is plasmid-like. This brings into question how the pSymB replicon came to acquire chromosome-like properties while appearing to be maintained as a plasmid in the genome. Whole-genome nearest neighbor analysis shows that the linear chromosome of Agrobacterium tumefaciens and pSymB may have a common origin. Despite conservation of gene order within small groups of genes, it is evident that rearrangements, duplications, and horizontal transfer of genes since the divergence of these species have contributed to the mosaic nature of pSymB. Since synteny between the S. meliloti chromosome and A. tumefaciens circular chromosome is highly conserved, it appears that the instability of pSy mB has played a key role in the adaptation and evolution of S. meliloti. / Thesis / Master of Science (MS)

In the early 1980s Anderson and May showed that parasite virulence (host mortality rate when infected) and parasite transmission are positively correlated because of their joint dependence on host exploitation (e.g. replication rate). This correlation often results in maximum parasite fitness at intermediate virulence, which has important implications for both parasite evolution and transmission. Anderson and May's observation has led to nearly four decades of work on the ecology and evolution of host-parasite interactions, which focuses on making either general predictions for a range of simplified host-parasite systems or detailed predictions for a single host-parasite system. Yet, despite decades of research, we know comparatively little about parasite evolution and transmission in heterogeneous and/or small host populations. Additionally, much previous work has distanced itself from empirical data, either by outpacing the collection of data or under-utilizing available data. My work focuses on the evolution and transmission of parasites in heterogeneous host populations; I rely on tradeoff theory, but adopt a case-study approach to maximize the use of empirical data. Using West Nile virus infections of birds I show that a continent-wide strain displacement event cannot be explained by current data (Chapter 2), and that transmission in heterogeneous host communities can be estimated using data from citizen scientists, laboratory experiments, and phylogenetic comparative analysis (Chapter 3). Using Myxoma virus infection of European rabbits, I show that tradeoff theory can help us to understand parasite evolution in host populations with heterogeneous secondary infection burden (Chapter 4). In Chapter 5 I show that poorly evolved parasites invading new host populations experience transient evolution away from optimal virulence. In addition to my biological focus, I emphasize clarity and rigor in statistical analyses, including the importance of appropriate uncertainty propagation, as well as reproducible science. / Thesis / Doctor of Philosophy (PhD) / In their work in the late 1970s and early 1980s, Anderson and May demonstrated that pathogen induced host harm and pathogen transmission ability are intimately linked. This work clearly showed that pathogens maximize their reproductive potential by causing some harm their hosts, contrary to the established belief that pathogens shouldn't harm their hosts at all. I extend this work to study pathogen evolution and transmission in heterogeneous host populations, using two model host-pathogen systems: birds infected with West Nile virus, and European rabbits infected with the myxoma virus, as well as a general model for the evolution of poorly adapted pathogens in small host populations. I show that pathogen transmission in heterogeneous host populations can be estimated using citizen science data, that pathogen transmission is lower in heterogeneous populations, and that pathogens invading naive host populations may experience short-term evolution to higher-than-optimal virulence, increasing infection burden.

With the advent of sequencing technologies, a variety of methods have been available day by day. Each of these methods have helped scientists to for a deeper understanding of the biological function and evolutionary constraints on the relevant genes, which can be gained through the use of modern computational approaches. Numerous approaches have being developed to advance these goals, and interaction network mapping is one of them. This method has been employed to study a variety of organisms to illustrate shared (conserved) or individual (unique) properties, and is mainly based on identifying and visualizing modules of co-expressed genes. As being a very strong candidate for such tools, co-expression gene network was used in this study to indentify the genes in wood formation of Populus trichocarpa with the help of the other novel bioinformatics tools such as Gene Ontology and Cytoscape. In order to booster the accuracy of the findings, we have combined it with an evolutionary approach, synonymous and non-synonymous ratio (dN/dS) of the proteins to show the selective patterns of the genes in a comparative fashion between woody and non-woody plants. This thesis is proposed to help plant scientists to gain insights into the genes that are involved in wood formation. By taking advantage of the computational studies have been done on this paper, one can validate the experiments along with reducing the cumbersomeness of the lab trials on the topic of wood formation in plants / Master of Science

No

The relationship between a farmer and their cultivated crops in agriculture is multifaceted, with pathogens affecting both the farmer and crop, and weeds that take advantage of resources provided by farmers. For my doctoral thesis, I aimed to gain a comprehensive understanding of the ecology and symbiosis of fungus farming ambrosia beetles. Through my research, I discovered that the microbial composition of fungus gardens, particularly the mutualists, is significantly influenced by the presence of both adults and larvae. The recognition of both beneficial and harmful symbionts is crucial for the success of ambrosia beetles, who respond differently depending on their life stage and the microbial species they encounter, which can contribute to the division of labour among family groups. The presence of antagonists and pathogens in the fungus garden depends on habitat and substrate quality, and beetle response to their introduction results in behavioural and developmental changes. Individual and social immunity measures, as well as changes in bacterial and fungal communities, were detected as a result of pathogen introduction. Additionally, the ability of ambrosia beetles to establish two nutritional fungal species depends on several factors. These insects must strike a balance between their essential functions and adapt to the constantly changing ecological and social conditions, which demonstrates their adaptive flexibility. However, interpreting data from laboratory studies should be approached with caution, as the natural environment allows for more flexibility and the potential for other beneficial symbionts to become more prominent if required. To aid in my research, I designed primers that use the ‘fungal large subunit’ (LSU) as genetic marker to identify and differentiate mutualistic and antagonistic fungi in X. saxesenii. The primers were able to distinguish closely related species of the Ophiostomataceae and other fungal symbionts. This allowed me to associate the abundance of key fungal taxa with factors such as the presence of beetles, the nest's age and condition, and the various developmental stages present. My primers are a valuable tool for understanding fungal communities, including their composition and the identification of previously unknown functional symbionts. However, some aspects should be approached with caution due to the exclusion of non-amplified taxa in the relative fungal community compositions. / Die Beziehung zwischen einem Landwirt und der von ihm angebauten Nahrung in der Landwirtschaft ist vielschichtig: Pathogene, die sowohl den Landwirt als auch die Pflanzen befallen, und Unkräuter, die sich die von Landwirten bereitgestellten Ressourcen zunutzen machen. In meiner Doktorarbeit wollte ich ein umfassendes Verständnis der Ökologie und der Symbiose von pilzzüchtenden Ambrosiakäfern erlangen. Im Rahmen meiner Forschung fand ich heraus, dass die mikrobielle Zusammensetzung von Pilzgärten, insbesondere der Mutualisten, durch die Anwesenheit sowohl der erwachsenen Tiere als auch der Larven erheblich beeinflusst wird. Die Erkennung sowohl nützlicher als auch schädlicher Symbionten ist entscheidend für den Erfolg der Ambrosiakäfer, die je nach Lebensstadium und den angetroffenen Mikrobenarten unterschiedlich reagieren, was zur Arbeitsteilung zwischen Familiengruppen beitragen kann. Das Vorhandensein von Antagonisten und Krankheitserregern im Pilzgarten hängt von der Qualität des Lebensraums und des Substrats ab, und die Reaktion der Käfer auf ihre Einschleppung führt zu Veränderungen im Verhalten und in der Entwicklung. Individuelle und soziale Immunitätsmaßnahmen sowie Veränderungen der Bakterien- und Pilzgemeinschaften wurden als Folge der Einführung von Krankheitserregern festgestellt. Darüber hinaus hängt die Fähigkeit von Ambrosiakäfern, zwei Nährpilzarten zu etablieren, von mehreren Faktoren ab. Diese Insekten müssen ein Gleichgewicht zwischen ihren lebenswichtigen Funktionen herstellen und sich an die ständig ändernden ökologischen und sozialen Bedingungen anpassen, was ihre Anpassungsfähigkeit zeigt. Bei der Interpretation von Daten aus Laborstudien ist jedoch Vorsicht geboten, da die natürliche Umgebung mehr Flexibilität zulässt und die Möglichkeit bietet, dass andere nützliche Symbionten bei Bedarf stärker in Erscheinung treten. Um meine Forschung zu unterstützen, habe ich Primer entwickelt, die die ‘fungal large subunit‘ (LSU) als genetischen Marker verwenden, um mutualistische und antagonistische Pilze in X. saxesenii zu identifizieren und zu unterscheiden. Die Primer waren in der Lage, eng verwandte Arten der Ophiostomataceae und andere Pilzsymbionten zu unterscheiden. Auf diese Weise konnte ich die Häufigkeit der wichtigsten Pilztaxa mit Faktoren wie dem Vorhandensein von Käfern, dem Alter und Zustand des Nests und den verschiedenen Entwicklungsstadien in Verbindung bringen. Meine Primer sind ein wertvolles Instrument für das Verständnis von Pilzgemeinschaften, einschließlich ihrer Zusammensetzung und der Identifizierung von bisher unbekannten funktionellen Symbionten. Einige Aspekte sind jedoch mit Vorsicht zu genießen, da nicht amplifizierte Taxa in den relativen Zusammensetzungen der Pilzgemeinschaften nicht berücksichtigt werden.

With the transition from water to land in early tetrapods, and with transitions to secondarily aquatic habits in numerous tetrapod lineages, the functions of the vertebral column were transformed. Morphological changes in the vertebral column are a major mechanism by which vertebrates accommodate changes in locomotor forces. Although morphometric measurements from vertebrae have been correlated with axial mechanics and locomotor behaviour in numerous extant taxa, few studies have sought to test or apply these principles in non-mammalian tetrapods. In my thesis, I reconstructed the vertebral mechanics of fossil taxa that represent intermediate stages in water/land transitions of their lineages. Study taxa were the basal tetrapod Pederpes finneyae, which is one of the earliest known tetrapods to show indications of terrestrial adaptation, and three extinct crocodylomorphs, Terrestrisuchus, Protosuchus, and Pelagosaurus, which span the spectrum from fully terrestrial to primarily aquatic. I used a combination of morphometric measurements and 3D virtual models of bone morphology to estimate intervertebral joint stiffness and range of motion. For comparison, I also reconstructed the vertebral mechanics of four related extant taxa. Correlations between vertebral morphometrics and axial stiffness were statistically tested in (cadaveric) modem crocodylians, and I validated my methodology by comparing my results with data from extant taxa. My results reveal similarities and differences between the two lineages. Intervertebral joint compliance and range of motion tended to decrease with adaptation for terrestrial locomotion, as expected, but this trend seems to have reversed in later forms. Additionally, vertebral mechanics may have been largely controlled by different structural mechanisms in different lineages. The relationship between biomechanics of vertebrae and environment appears to be more complex than previously supposed. However, approaches that combine experimental measurements from extant animals, thorough analysis of fossil morphology, and explicit phylogenetic considerations have the potential to greatly improve locomotor reconstructions of extinct taxa.