Theropod dinosaurs are an iconic and familiar group of extinct species that include predators such as Tyrannosaurus and Velociraptor, as well as an array of other Mesozoic taxa. Carnivorous theropods are the evolutionary ancestors of birds, and the evolutionary transition between theropods and birds is a textbook example of a major evolutionary transformation in the history of life. Despite a flurry of research on early birds and their dinosaurian relatives, however, several questions still remain. First, the anatomy of some major theropod groups has yet to be described in detail. Second, there is little consensus on the phylogenetic relationships of the basal members of a theropod subgroup called Coelurosauria: the clade of birds and their closest relatives (defined as all taxa closer to birds than to Allosaurus). Third, there has been little synthetic work on large-scale macroevolutionary patterns during theropod evolution. This dissertation includes three chapters that touches on these three major issues. Chapter 1 is a detailed description of the Late Cretaceous tyrannosaurid theropod Alioramus altai, based on its holotype specimen from the Tsaagan Khuushu locality in the Maastrichtian Nemegt Formation of Mongolia. This monographic description provides further evidence that Alioramus is an unusual long-snouted, gracile, and slender-limbed taxon with an unpredecented degree of cranial ornamentation among tyrannosaurids and an extremely pneumatized skeleton. Anatomical comparisons indicate that the long skull of Alioramus is an autapomorphic feature that is proportionally longer (relative to femur length) than in any other known tyrannosaurid specimen, including juveniles, and that Alioramus is morphologically distinctive relative to similarly-sized individuals of the contemporary and sympatric Tarbosaurus. The coexistence of the long-snouted Alioramus and robust and deep-snouted Tarbosaurus, which are found together at the Tsaagan Khuushu locality, demonstrate that multiple large tyrannosaurids were able to live in sympatry, likely because of niche partitioning due to differences in craniofacial morphology and functional behavior. Chapter 2 presents a comprehensive new phylogenetic analysis of coelurosaurian theropods, which is an updated version (and thus the latest iteration) of the long-standing Theropod Working Group (TWiG) analysis. The new analysis incoroporates a wealth of new taxa and character data into the TWiG matrix for the first time, most of which is relevant to basal (non-maniraptoran) coelurosaurs such as tyrannosauroids and ornithomimosaurs, which had previously been the subject of only cursory character and taxon sampling in TWiG studies. The full dataset was analyzed under parsimony, and the resulting phylogeny includes several well supported relationships and agrees with previous analyses in many aspects. As a result, it is argued that a consensus view of basal coelurosaurian relationships has emerged, including: 1) the monophyly of major subclades such as Tyrannosauroidea, Compsognathidae, and Ornithomimosauria; 2) the position of the singleton genera Bicentenaria, Zuolong, and Tugulusaurus near the base of Coelurosauria; 3) the placement of Tyrannosauroidea as the most basal major coelurosaurian subclade; 4) the inclusion of Guanlong, Dilong, and Proceratosaurus within Tyrannosauroidea; 5) the existence of a derived maniraptoran clade that includes alvarezsauroids, therizinosauroids, oviraptorosaurs, and paravians to the exclusion of ornithomimosaurs and tyrannosauroids. Remaining areas of uncertainty include the phylogenetic position of Compsognathidae and the singleton genus Ornitholestes, and relationships at the base of the Ornithomimosauria + Maniraptora clade and Maniraptora itself. The phylogeny indicates that much of the early history of Coelurosauria has yet to be sampled in the fossil record, that coelurosaurs originated at small body size, and that the evolution of the iconic Tyrannosaurus-like bauplan occurred only towards the end of the Cretaceous. Chapter 3 presents a geometric morphometric analysis that is used to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). The analysis finds that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and that oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.

With the number of sequenced microbial species soon to be in the tens of thousands, we are in a unique position to investigate microbial function, ecology, and evolution on a large scale. In this dissertation I first describe the use of hundreds of in silico models of bacterial metabolic networks to study the long-term the evolution of growth and gene-essentiality phenotypes. The results show that, over billions of years of evolution, the conservation of bacterial phenotypic properties drops by a similar fraction per unit time following an exponential decay. The analysis provides a framework to generate and test hypotheses related to the phenotypic evolution of different microbial groups and for comparative analyses based on phenotypic properties of species. Mapping of genome sequences to phenotypic predictions -such as used in the analysis just described- critically relies on accurate functional annotations. In this context, I next describe GLOBUS, a probabilistic method for genome-wide biochemical annotations. GLOBUS uses Gibbs sampling to calculate probabilities for each possible assignment of genes to metabolic functions based on sequence information and both local and global genomic context data. Several important functional predictions made by GLOBUS were experimentally validated in Bacillus subtilis and hundreds more were obtained across other species. Complementary to the automated annotation method, I also describe the manual reconstruction and constraints-based analysis of the metabolic network of the malaria parasite Plasmodium falciparum. After careful reconciliation of the model with available biochemical and phenotypic data, the high-quality reconstruction allowed the prediction and in vivo validation of a novel potential antimalarial target. The model was also used to contextualize different types of genome-scale data such as gene expression and metabolomics measurements. Finally, I present two projects related to population genetics aspects of sequence and genome evolution. The first project addresses the question of why highly expressed proteins evolve slowly, showing that, at least for Escherichia coli, this is more likely to be a consequence of selection for translational efficiency than selection to avoid misfolded protein toxicity. The second project investigates genetic robustness mediated by gene duplicates in the context of large natural microbial populations. The analysis shows that, under these conditions, the ability of duplicated yeast genes to effectively compensate for the loss of their paralogs is not a monotonic function of their sequence divergence.

Evolution is a force that has molded human existence since its divergence from chimpanzees about 5.4 million years ago. In that same amount of time, an influenza virus, which replicates every six hours, would have undergone an equivalent number of generations over only a hundred years. The fast replication times of influenza, coupled with its high mutation rate, make the virus a perfect model to study real-time evolution at a mega-Darwin scale, more than a million times faster than human evolution. While recent developments in high-throughput sequencing provide an optimal opportunity to dissect their genetic evolution, a concurrent growth in computational tools is necessary to analyze the large influx of complex genomic data. In my thesis, I present novel computational methods to examine different aspects of influenza evolution. I first focus on seasonal influenza, particularly the problems that hamper public health initiatives to combat the virus. I introduce two new approaches: 1. The q2-coefficient, a method of quantifying pathogen surveillance, and 2. FluGraph, a technique that employs network topology to track the spread of seasonal influenza around the world. The second chapter of my thesis examines how mutations and reassortment combine to alter the course of influenza evolution towards pandemic formation. I highlight inherent deficiencies in the current phylogenetic paradigm for analyzing evolution and offer a novel methodology based on algebraic topology that comprehensively reconstructs both vertical and horizontal evolutionary events. I apply this method to viruses, with emphasis on influenza, but foresee broader application to cancer cells, bacteria, eukaryotes, and other taxa.

Thesis (Ph. D.)--Open University. BLDSC no. DXN116690.

Thesis (Ph.D.) -- University of Texas at Arlington, 2009.

Thesis (Ph. D.)--University of Oregon, 2000. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 150-160). Also available for download via the World Wide Web; free to University of Oregon users.

Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2003. / Vita. Includes bibliographical references (leaves 219-228).

No description available.

Bird Island is a former flood tide delta occurring in the mouth of the River Murray, Encounter Bay, South Australia. The island has experienced a rapid development history; in around 60 years the formerly ephemeral deltaic deposits have rapidly become stabilised, forming a permanent island approximately 1 km in diameter. / It has been possible to place tight time restraints on the progressive development of Bird Island over this 60 year period. Its sand dunes and marshes of different ages can be distinguished clearly from an analysis of successive aerial photographs. Evidence suggests they represent different phases in the growth and development of the island, resulting from an interplay of factors including the position and migration of the Murray Mouth relative to the island as well as the availability of sediment and conditions conducive to aeolian sand transport. / The landforms of Bird Island present a unique opportunity for the assessment and study of progressive plant colonisation and succession on a pristine landscape in a coastal/estuarine setting. Bird Island comprises 19 different dune and marsh vegetation types. Research has identified several trends suggesting that the environmental gradients associated with the marsh-dune landforms has influenced some characteristics of species distribution. It also appears that in a general way, species distributions may represent succession on the sand dunes, but this was not as clearly demonstrated across the marshes of different ages on Bird Island. / Research suggests that the construction of the lower River Murray barrages in 1940, which has reduced the median annual flow to the estuary by nearly 75%, and has reduced the tidal prism by up to 90%; has facilitated the development of Bird Island. Bird Island contributed to the closure of the mouth of the River Murray in 1981; inlet behaviour not demonstrated in the 100 years prior to barrage construction according to the results of this research. / The continuing development of Bird Island suggests considerable potential for more blockages in the future. The continuing sedimentation in the Murray Mouth reflects the inability of the current flow regime and marine processes in maintaining the mouth as they did prior to the construction of regulatory works on the Lower River Murray. / Thesis (MApSc(EnvironmentRecreationMg))--University of South Australia, 2004

Bird Island is a former flood tide delta occurring in the mouth of the River Murray, Encounter Bay, South Australia. The island has experienced a rapid development history; in around 60 years the formerly ephemeral deltaic deposits have rapidly become stabilised, forming a permanent island approximately 1 km in diameter. / It has been possible to place tight time restraints on the progressive development of Bird Island over this 60 year period. Its sand dunes and marshes of different ages can be distinguished clearly from an analysis of successive aerial photographs. Evidence suggests they represent different phases in the growth and development of the island, resulting from an interplay of factors including the position and migration of the Murray Mouth relative to the island as well as the availability of sediment and conditions conducive to aeolian sand transport. / The landforms of Bird Island present a unique opportunity for the assessment and study of progressive plant colonisation and succession on a pristine landscape in a coastal/estuarine setting. Bird Island comprises 19 different dune and marsh vegetation types. Research has identified several trends suggesting that the environmental gradients associated with the marsh-dune landforms has influenced some characteristics of species distribution. It also appears that in a general way, species distributions may represent succession on the sand dunes, but this was not as clearly demonstrated across the marshes of different ages on Bird Island. / Research suggests that the construction of the lower River Murray barrages in 1940, which has reduced the median annual flow to the estuary by nearly 75%, and has reduced the tidal prism by up to 90%; has facilitated the development of Bird Island. Bird Island contributed to the closure of the mouth of the River Murray in 1981; inlet behaviour not demonstrated in the 100 years prior to barrage construction according to the results of this research. / The continuing development of Bird Island suggests considerable potential for more blockages in the future. The continuing sedimentation in the Murray Mouth reflects the inability of the current flow regime and marine processes in maintaining the mouth as they did prior to the construction of regulatory works on the Lower River Murray. / Thesis (MApSc(EnvironmentRecreationMg))--University of South Australia, 2004