No description available.

No description available.

Pterosaurs represent the earliest appearance of only three clades of flying vertebrates, the pioneers of aerial vertebrate ecospace, and the lineage to produce the largest known flying organisms. The origins of the pterosaurian flight apparatus have been difficult to ascertain, in part, due to incomplete or two-dimensional preservation of the earliest (Triassic—Jurassic) pterosaur remains. An exceptional early pterosaur specimen that is preserved in three dimensions, the holotype and only known specimen of Arcticodactylus cromptonellus (Fleming Fjord Formation, Greenland) may help address these problems. However, it has remained mostly encased within matrix to protect the delicate elements, obscuring external study. Here I present new synchrotron tomographic scan data of the forelimb (wing-forming) elements of Arcticodactylus cromptonellus. I find that the forelimb of Arcticodactylus is a structural intermediate between the forelimb of early archosaurs and derived pterosaurs. In light of this intermediacy, I reexamined the phylogeny of early Pterosauromorpha, completely reviewing forelimb characters with additional consideration given to other important anatomical regions for pterosauromorph phylogeny. I find that the contents of Lagerpetidae represent a grade of non-pterosaur pterosauromorphs and that the pterosauromorph Scleromochlus taylori is actually closely-related to crocodylomorphs. I recover Arcticodactylus as the earliest-diverging pterosaur, with the pterosaurs of the early Mesozoic (Triassic—Early Jurassic) forming a highly-nested, gradational relationship around a monophyletic Late Mesozoic pterosaur clade with very few multispecific groups exclusive of this latter clade. The sum of this work is an understanding of the current pterosaur fossil record as preserving the gradual assembly of the pterosaur bauplan in exquisite detail. / Master of Science / Flight has only evolved three times within animals with backbones. The first of these three is a group of distant relatives of birds called pterosaurs, which evolved flight independently from birds and produced the largest ever flying animals. Flight requires a suite of specialized adaptations, and these can obscure our understanding of how flying animals evolved if all we have are poorly-preserved fossils or only specialized flighted forms. These problems can be found in the origins of pterosaur flight, with well-preserved (non-crushed or deformed) skeletons generally known only from very late forms. An exception to this rule is the early pterosaur Arcticodactylus cromptonellus, represented by three-dimensionally-preserved skeletal remains. Using CT imagery to study the skeletal anatomy obscured by rock, I describe the forelimb anatomy of Arcticodactylus cromptonellus and include it within an analysis of the evolutionary relationships of pterosaurs and other reptiles. Arcticodactylus is found to be the earliest-originating form of pterosaur known, and it possesses a mixture of features found in non-pterosaurs and in pterosaurs. Arcticodactylus demonstrates the gradual acquisition and timing of the assembly of pterosaur flight anatomy.

<p> Much speculation has been made about the relative importance of changes in developmental regulation of gene expression in determining major phylogenetic patterns observed both in extant and extinct species. However, most of these hypotheses have been formulated based on data obtained from the comparison of very distantly related organisms (e.g., between animal phyla). Another approach to answering questions about development (ontogeny) in the context of evolution (phylogeny) is to observe how developmental patterns diverge between closely related species, in order to obtain a better understanding of the population level processes underlying phyletic change. With the intent of addressing this possibility, the principle work outlined in this thesis investigated patterns of divergence between closely related species of Drosophila at the level of both the nucleotide coding sequence as well as gene expression levels in the context of ontogeny. The results show that the stage during which genes are expressed has a significant impact on their patterns of divergence, acting both to constrain (earlier stages) and accelerate (later stages) their rates of evolution - the latter being largely the result of sexual selection pressure. However, we also find that intermediate stages of fly development, such as metamorphosis, may experience a greater degree of conservation of the elements regulating gene expression than other stages. Nonetheless, we do find evidence that both gene expression and coding sequences may be subject to similar selection pressures, yet there also appears to be substantial uncoupling of the two, as evidenced by our observation of stage-specific, autonomous patterns of hybrid misexpression manifested in interspecific hybrids. The data presented herein shed new light on patterns of divergence between species, specifically with regards to how various selection pressures affect different stages of ontogeny.</p> / Thesis / Doctor of Philosophy (PhD)

Social interactions can have profound influences on an individual’s fitness. As part of a long-term research program on the mechanisms and functions of social behaviour in fruit flies (Drosophila melanogaster), we addressed two main questions. First, we asked whether social behaviour is positively correlated between the larval and adult stages. We quantified genetic variation in social behaviour by measuring aggregation among larvae and adults taken from each of 29 inbred, wild-derived lines. We found significant genetic variation in social behaviour in both larvae and adults. While these lines also showed significant genetic variation in baseline locomotor activity, it had no significant influence on social behaviour. We found that neither social behaviour nor activity were correlated between larval and adult flies. This is consistent with the hypothesis that metamorphosis adaptively decouples the expression of genes between distinct life stages in animals with complex life cycles. That is, genetic variation in social behaviour during each life stage may reflect adaptation to the specific ecological settings during that stage. Our second question was whether social behaviour in adult flies was influenced by indirect genetic effects (IGEs), defined as the effect an individual’s genotype has on the phenotype of an interacting partner. IGEs can have profound effects on the rate of phenotypic evolution. We found that groups of 6 focal males maintained shorter inter-individual distances among themselves when interacting with 12 males from a line previously identified as highly social than when paired with 12 males from the least social genotype. Overall, our results indicate that heritable genetic variation influences an individual’s predisposition to engage in social behaviour as well as its effect on social interactions among other individuals it encounters. / Thesis / Master of Science (MSc)

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No description available.

No description available.

The relentless evolution of antibiotic resistance in pathogens is one of the most pressing medical concerns of the 21st century. Antibiotic resistance and antibiotic drugs originated in environmental bacteria, where they have been integral to their evolution for millions of years. The application of antibiotics in medicine and agriculture has selected for mobilization and dissemination of resistance genes in pathogens. Understanding their evolution here will aid in combating their evolution in pathogens. This work expands the known mechanistic, functional, and genetic diversity of resistance (i.e. resistomes) in environmental bacteria. I systematically parse the extensively drug-resistant resistome of Paenibacillus sp. LC231, which was sampled from an underground ecosystem spatiotemporally isolated from the surface for over 4 Myr. Paenibacillus sp. LC231 was resistant to 26 of 40 drugs tested. Informatic annotation of resistance genes and functional genomes revealed 18 new resistance elements including five determinants without characterized homologs and three mechanisms not previously known to confer resistance. I investigated the resistome of Brevibacillus brevis VM4 to study the relationship between species diversity and resistance diversity in the Paenibacillaceae family, which includes Paenibacillus sp. LC231. I found that resistome diversity does not correlate with species diversity, consistent with horizontal transfer of resistance genes. In each of Paenibacillus sp. LC231 (MphI) and B. brevis VM4 (MphJ), I identified Mphs with unique substrate specifies. I identified the molecular determinants of substrate discrimination in MphI and in doing so, I developed a general strategy for understanding and predicting the functional evolution of resistance enzymes. Together, this work expands the known diversity of resistance that will enable better detection of resistance in pathogens. / Thesis / Doctor of Philosophy (PhD) / Infections caused by antibiotic resistant bacteria are a significant medical problem. Bacteria will always become resistant to antibiotic drugs. Understanding how resistance evolves is essential for increasing the effective lifetime of these drugs. Antibiotics have been naturally produced by bacteria for millions of years, which caused the spread of resistance in environmental bacteria. Medical and agricultural antibiotic use by humans caused resistance in environmental bacteria to transfer to pathogenic bacteria. My work expands the known causes of resistance in environmental bacteria so that we can better detect the causes of resistance in pathogens. In doing so, I demonstrate that multi-drug resistance is over 4 million years old and that environmental bacteria naturally transfer resistance genes. Furthermore, I develop a way to predict the evolution of new resistance functions by inferring their evolutionary histories.

This dissertation is an attempt of expanding the domain of game theory into the sphere of evolving, potentially non-equilibrium systems. We especially focus our attention on studying the effects of local interactions, using automata networks as a modelling tool. The Chapters 2 and 3 of this dissertation concentrate on applications of the local nature of interactions and rely on automata networks as an investigating and modelling tool for game theory. Chapter 2 is devoted to cooperation and to a smaller extent to the endogenous formation of links between the agents. Chapter 3 is investigating the deterministic and stochastic best response play when interactions are local. / Ph. D.