We examine the evolution of globular star clusters, modelled as spherically symmetric stellar systems, using various techniques. Such clusters possess a central region of approximately uniform density which is referred to as the core. We concentrate our analysis on the evolution of the cluster after the core has undergone core collapse; a process where its radius decreases and its density increases. After this collapse, the system as a whole can expand in a self-similar fashion (homologous post-collapse evolution) which has long been thought to be due to gravitational interactions between different populations of single stars and binary stars in the core. We confirm this assumption by constructing a simple analytical model which combines much of the theoretical knowledge of previous research in the field. This model consists of two stellar populations, each defined by the mass of the individual stars, and a separate core. Our simple model is itself constructed from two simpler models – a twocomponent model without a core and a single mass model with a core – and takes into account the main gravitational interactions thought to drive the post-collapse evolution. To ensure that no important mechanisms have been neglected in our simple model, we will compare it with an N-body simulation. We compute our N-body models with NBODY6 (using a GPU version for large N). When we compare the N-body model with the simple model, we find qualitative agreement between them for most cases. Even though some mechanisms (e.g. escape of stars) are neglected in our simple model, we find that both models show homologous post-collapse evolution. We also review the homologous post-collapse Fokker-Planck model in the case of equal stellar masses derived by H´enon (1961) with the intention of extending this for the two-component case. We present our numerical solutions for H´enon’s model and find that our numerical solutions are in satisfactory agreement with the results shown in this paper. When we extend this work for a general two-component model (i.e. with no restriction on the number of heavier stars), we find that a homologous solution cannot be found with this approach. By contrast, we suggest that it would be possible to find a homologous two-component solution by extending the one-component solution published later by H´enon (1965), which differs from the earlier model by neglecting the external tidal field of the parent galaxy. Much of the work shown in this thesis would be relevant for such future study.

Cultural artifacts, such as language, survive and replicate by passing from mind to mind. Cultural evolution always proceeds by an inductive process, where behaviors are never directly copied, but reverse engineered by the cognitive mechanisms involved in learning and production. I will refer to this type of evolutionary change as inductive evolution and explain how this represents a broader class of evolutionary processes that can include both neutral and selective evolution. This thesis takes a mechanistic approach to understanding the forces of evolution underlying change in culture over time, where the mechanisms of change are sought within human cognition. I define culture as anything that replicates by passing through a cognitive system and take language as a premier example of culture, because of the wealth of knowledge about linguistic behaviors (external language) and its cognitive processing mechanisms (internal language). Mainstream cultural evolution theories related to social learning and social transmission of information define culture ideationally, as the subset of socially-acquired information in cognition that affects behaviors. Their goal is to explain behaviors with culture and avoid circularity by defining behaviors as markedly not part of culture. I take a reductionistic approach and argue that all there is to culture is brain states and behaviors, and further, that a complete explanation of the forces of cultural change can not be explained by a subset of cognition related to social learning, but necessarily involves domain-general mechanisms, because cognition is an integrated system. Such an approach should decompose culture into its constituent parts and explore 1) how brains states effect behavior, 2) how behavior effects brain states, and 3) how brain states and behaviors change over time when they are linked up in a process of cultural transmission, where one person's behavior is the input to another. I conduct several psychological experiments on frequency learning with adult learners and describe the behavioral biases that alter the frequencies of linguistic variants over time. I also fit probabilistic models of cognition to participant data to understand the inductive biases at play during linguistic frequency learning. Using these inductive and behavioral biases, I infer a Markov model over my empirical data to extrapolate participants' behavior forward in cultural evolutionary time and determine equivalences (and divergences) between inductive evolution and standard models from population genetics. As a key divergence point, I introduce the concept of non-binomial cultural drift, argue that this is a rampant form of neutral evolution in culture, and empirically demonstrate that probability matching is one such inductive mechanism that results in non-binomial cultural drift. I argue further that all inductive problems involving representativeness are potential drivers of neutral evolution unique to cultural systems. I also explore deviations from probability matching and describe non-neutral evolution due to inductive regularization biases in a linguistic and non-linguistic domain. Here, I offer a new take on an old debate about the domain-specificity vs -generality of the cognitive mechanisms involved in language processing, and show that the evolution of regularity in language cannot be predicted in isolation from the general cognitive mechanisms involved in frequency learning. Using my empirical data on regularization vs probability matching, I demonstrate how the use of appropriate non-binomial null hypotheses offers us greater precision in determining the strength of selective forces in cultural evolution.

Evolution is an ubiquitous feature of living systems. The genetic composition of a population changes in response to the primary evolutionary forces: mutation, selection and genetic drift. Organisms undergoing rapid adaptation acquire multiple mutations that are physically linked in the genome, so their fates are mutually dependent and selection only acts on these loci in their entirety. This aspect has been largely overlooked in the study of asexual or somatic evolution and plays a major role in the evolution of bacterial and viral infections and cancer. In this thesis, we put forward a theoretical description for a minimal model of evolutionary dynamics to identify driver mutations, which carry a large positive fitness effect, among passenger mutations that hitchhike on successful genomes. We examine the effect this mode of selection has on genomic patterns of variation to infer the location of driver mutations and estimate their selection coefficient from time series of mutation frequencies. We then present a probabilistic model to reconstruct genotypically distinct lineages in mixed cell populations from DNA sequencing. This method uses Hidden Markov Models for the deconvolution of genetically diverse populations and can be applied to clonal admixtures of genomes in any asexual population, from evolving pathogens to the somatic evolution of cancer. To understand the effects of selection on rapidly adapting populations, we constructed sequence ensembles in a recombinant library of budding yeast (S. cerevisiae). Using DNA sequencing, we characterised the directed evolution of these populations under selective inhibition of rate-limiting steps of the cell cycle. We observed recurrent patterns of adaptive mutations and characterised common mutational processes, but the spectrum of mutations at the molecular level remained stochastic. Finally, we investigated the effect of genetic variation on the fate of new mutations, which gives rise to complex evolutionary dynamics. We demonstrate that the fitness variance of the population can set a selective threshold on new mutations, setting a limit to the efficiency of selection. In summary, we combined statistical analyses of genomic sequences, mathematical models of evolutionary dynamics and experiments in molecular evolution to advance our understanding of rapid adaptation. Our results open new avenues in our understanding of population dynamics that can be translated to a range of biological systems.

Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 91-103). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 91-103). Also available on the Internet.

A synthetic proto-organism could be self-assembled by integrating a lipid proto-container with a proto-metabolic subsystem and a proto-genetic subsystem. This three-component system can use energy and nutrients by means of either redox or photo-chemical reactions, evolve its proto-genome by means of template directed replication, and ultimately die. The evolutionary dynamics of the proto-organism depends crucially on the chemical kinetics of its sub-systems and on their interplay. In this work the template replication kinetics is investigated and it is found that the product inhibition inherent in the ligation-like replication process allows for coexistence of unrelated self-replicating proto-genes in the lipid surface layer. The combined catalytic effects from the proto-genes on the metabolic production rates determine the fate of the strain protocell.

Software Product Lines (SPLs) are a successful approach to software reuse in the large. Even though tools exist to create SPLs, their evolution is widely unexplored. Evolving an SPL manually is tedious and error-prone as it is hard to avoid unintended side-effects that may harm the consistency of the SPL. In this thesis, the conceptual basis of a system for the evolution of model-based SPLs is presented, which maintains consistency of models and feature mapping. As basis, a novel classification is introduced that distinguishes evolutions by their potential to harm the mapping of an SPL. Furthermore, multiple remapping operators are presented that can remedy the negative side-effects of an evolution. A set of evolutions is complemented with appropriate remapping operations for the use in SPLs. Finally, an implementation of the evolution system in the SPL tool FeatureMapper is provided to demonstrate the capabilities of the presented approach when co-evolving models and feature mapping of an SPL.:1 Introduction 1.1 Motivation for Evolving Software Product Lines 1.2 Outline of the Thesis 2 Background and Scope 2.1 Concepts and Terminology 2.1.1 Software Product Lines 2.1.2 Model-Driven Software Development 2.1.3 FeatureMapper 2.2 Scope 2.3 Related Work 3 Evolution of Software Product Lines 3.1 Evolutions 3.1.1 Evolutions in the Problem Space 3.1.2 Evolutions in the Solution Space 3.2 Classification Systems for Evolutions 3.2.1 Classification by Behavior Preservation 3.2.2 Classification Systems in the Literature 3.2.3 Classification by Semantical Extent of Model Changes 3.3 Remapping Operations 3.3.1 Remapping in the Problem Space 3.3.2 Remapping in the Solution Space 3.4 Classification and Remapping of Evolutions 3.4.1 Classification and Remapping of Problem Space Evolutions 3.4.2 Classification and Remapping of Solution Space Evolutions 4 A Framework for Evolutions in FeatureMapper 4.1 Relevant Technology 4.1.1 Refactory 4.1.2 EMFText 4.2 Implementation 4.2.1 Implementation of the Evolutions System 4.2.2 Implementation of the Remapping System 4.2.3 Implementation of the User Interface System 4.2.4 Implementation of the Test Suite 4.3 Possibilities for Extension 4.3.1 Adding New Evolutions 4.3.2 Adapting Existing Evolutions 5 Example Project 5.1 Initial Situation in 2001 5.2 First Revision in 2006 5.2.1 Removing the Cassette Player 5.2.2 Adding an MP3 CD Player 5.2.3 Adding a Personal Navigation Device 5.2.4 Changing the Implementation of the UI Builder 5.2.5 Summary of the Changes of the First Revision in 2006 5.3 Second Revision in 2011 5.3.1 Creating a Multi-Format CD Player 5.3.2 Enhancing Voice Recognition to Control the Audio Player 5.3.3 Restructuring Personal Navigation Maps 5.3.4 Changing the Implementation of the CD Player 5.3.5 Summary of the Changes of the Second Revision in 2011 5.4 Conclusion of the Example Project 6 Conclusion 6.1 Summarized Findings 6.2 Limitations and Drawbacks 6.3 Possibilities for Future Work 6.4 Theoretical and Practical Contributions A Object Remapping Specification (*.orspec) A.1 Object Remapping Specification Model A.2 Object Remapping Specification Syntax B DocBooklet (*.docbooklet) B.1 DocBooklet Model B.2 DocBooklet Syntax C NavMap (*.navmap) C.1 NavMap Model C.2 NavMap Syntax List of Figures List of Tables List of Listings Bibliography

This thesis examines the evolutionary biology of the RNA viruses, a diverse group of pathogens that cause significant diseases. The focus of this work is the relationship between the processes driving the evolution of virus populations within individual hosts and at the epidemic level. First, Chapter One reviews the basic biology of RNA viruses, the current state of knowledge in relevant topics of evolutionary virology, and the principles that underlie the most commonly used methods in this thesis. In Chapter Two, I develop and test a novel framework to estimate the significance of phylogeny-trait association in viral phylogenies. The method incorporates phylogenetic uncertainty through the use of posterior sets of trees (PST) produced in Bayesian MCMC analyses. In Chapter Three, I conduct a comprehensive analysis of the substitution rate of hepatitis C virus (HCV) in within- and between-host data sets using a relaxed molecular clock. I find that within-host substitution rates are more rapid than previously appreciated, that heterotachy is rife in within-host data sets, and that selection is likely to be a primary driver. In Chapter Four I apply the techniques developed in Chapter Two to successfully detect compartmentalization between peripheral blood and cervical tissues in a large data set of human immunodeficiency virus (HIV) patients. I propose that compartmentalization in the cervix is maintained by selection. I extend the framework developed in Chapter Two in Chapter Five and explore the Type II error of the statistics used. In Chapter Six I review the findings of this thesis and conclude with a general discussion of the relationship between within- and among-host evolution in viruses, and some of the limitations of current techniques.

Understanding the conditions that favour the evolution and maintenance of spiteful bacteriocin production combines two important questions from the fields of social evolution and microbiology. Spiteful behaviours, though, initially thought to be rare represent an important class of interactions between bacteria through the production of bacteriocins. Bacteriocins can be considered spiteful as they are costly to produce (in many cases requiring lysis) and are costly to sensitive bacteria (i.e. they are lethal). However, much about the ecology of spiteful behaviours and bacteriocin production remains unclear. Mathematical models have given us important insights into some conditions that should favour bacteriocin production, but few empirical studies exist supporting these results. In this thesis I use the bacterium Pseudomonas aeruginosa (a prolific producer of bacteriocins), to examine conditions that favour bacteriocin production. I also investigate more specific elements about this system and toxin production in general. I find that bacteriocin production in P. aeruginosa closely follows predictions made from mathematical models under a range of different conditions (e.g. frequency, scale of competition, multiple social traits). I also find that resistance can evolve to bacteriocins and biological mechanisms such as the neutralisation of one’s own toxin can have important consequences. Finally, I consider bacteriocin as a policing trait testing predictions about the role that linkage plays in policing. This work represents a comprehensive study into the importance of bacteriocin production in bacteria.

The chimpanzee (Pan troglodytes, Pongidae) among all other living species, is our closest relation, with whom we last shared a common ancestor less than five million years ago. These African apes make and use a rich and varied kit of tools. Of the primates, and even of the other Great Apes, they are the only consistent and habitual tool-users. Chimpanzees meet the criteria of working definitions of culture as originally devised for human beings in socio-cultural anthropology. They show sex differences in using tools to obtain and to process a variety of plant and animal foods. The technological gap between chimpanzees and human societies living by foraging (hunter-gatherers) is surprisingly narrow, at least for food-getting. Different communities of chimpanzees have different tool-kits, and not all of this regional and local variation can be explained by the varied physical and biotic environments in which they live. Some differences are likely customs based on non-functionally derived and symbolically encoded traditions. Chimpanzees serve as heuristic, referential models for the reconstruction of cultural evolution in apes and humans from an ancestral hominoid. However, chimpanzees are not humans, and key differences exist between them, though many of these apparent contrasts remain to be explored empirically and theoretically.