Two of the most challenging goals of evolutionary biology are to reconstruct the evolutionary relationships among all extant species and to understand the process by which new species form. Accomplishing these goals will require accurate computational methods for reconstructing phylogenetic trees, general analytic models of speciation, and powerful statistical tools for studying the process of speciation in natural systems. In the first chapter, I study the effects of improper model assumption on estimates of phylogeny. Using DNA sequence data simulated under a variety of models of sequence evolution, I demonstrate that use of oversimplified models can result in erroneous phylogeny estimates. This result suggests that if the models currently utilized are oversimplified then current estimates of phylogeny may be inaccurate and more complex models need to be developed and employed. In the second and third chapters, I study one process thought to be important in completing the final stages of speciation: reinforcement. Using simulations of a hybrid zone, I show that the process of reinforcement can result in patterns other than reproductive character displacement. I also show that speciation by reinforcement is more likely when the genes involved in reproductive isolation are sex-linked. In the fourth chapter, I develop a statistical method of quantifying the degree of isolation between species undergoing divergence. Using genotype data obtained from natural hybrid zones, this novel method can be used to estimate the fitness of hybrids during different stages of their life cycle. This approach offers a new approach to empirical biologists studying extrinsic postzygotic isolation in natural systems.

published_or_final_version / Education / Master / Master of Education

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The aim of this dissertation is to explore the nature of scientific progress and to broaden existing theories of what constitutes progress in science. I do this by means of a close analysis of the main post-Kuhnian philosophical accounts of scientific progress, namely those put forward by Imre Lakatos, Larry Laudan and Philip Kitcher. I test these three accounts by reconstructing a series of scientific episodes in evolutionary ecology in terms of each account and then assessing the degree to which each account incorporates what is progressive. The episodes I have selected concern the resource competition research of Dolph Schluter on Galapagos finches and related work leading up to it. After distinguishing between macroscopic and microscopic levels in science, I attend carefully to the microscopic level of each episode as it relates to epistemic progress. This investigation demonstrates that some important aspects of scientific progress have been overlooked. I conclude that there are three main ways in which the philosophies of science surveyed do not adequately represent instances of scientific progress. First, the accumulation of factual knowledge is not well accommodated. Second, the role of evidence and argument in scientific theories is not adequately captured. Third, the fine-grained level at which much important epistemic progress in science occurs is often not accounted for. These criticisms relate to a more general tendency of contemporary philosophical accounts to emphasize the macroscopic level of entire research programmes and traditions while failing to attend to the microscopic level of progress inherent in a detailed case study. I end by offering a positive account of scientific progress in light of these criticisms.

In this dissertation, we explore the effect of variable evolutionary rates on phylogenetic inference. In the first half of the thesis are introduced the biological fundamentals and the statistical framework that will be used throughout the thesis. The basic concepts in phylogenetics and an overview of Bayesian inference are presented in Chapter 1. In Chapter 2, we survey the models that are already used for rate variation. We argue that the CIR process---a diffusion process widely used in finance---is the best suited for applications in phylogenetics, for both mathematical and computational reasons. Chapter 3 shows how evolutionary rate models are incorporated to DNA substitution models. We derive the general formulae for transition probabilities of substitutions when the rate is a continuous-time Markov chain, a diffusion process or a jump process (a diffusion process with discrete jumps). / The second half of the thesis is dedicated to applications of variable evolutionary rate models in two different contexts. In Chapter 4, we use the CIR process to model heterotachy, an evolutionary hypothesis according to which positions of an alignment may evolve at rates that vary with time differently from site to site. A comparison the CIR process with the covarion---a widely-used heterotachous model---on two different data sets allows us to conclude that the CIR provides a significantly better fit. Our approach, based on a Bayesian mixture model, enables us to determine the level of heterotachy at each site. Finally, the impact of variable evolutionary rates on divergence time estimation is explored in Chapter 5. / Several models, including the CIR process are compared on three data sets. We find that autocorrelated models (including the CIR) provide the best fits.

The purpose of this thesis was to analyze the rhetoric of the Creationist-evolutionist textbook controversy. In Chapter II, Leland Griffin's approach to the study of historical movements was used concomitantly with Thomas Kuhn's ideas concerning scientific revolution to explore the first research question: What changes have occurred in the persuasive success rate of the Creationists' textbook battle as it has moved from its stance of "the good versus the evil" toward the stance of the scientist, (including scientific methods of reasoning and observation)?Chapter III explored the second research question: Do the new persuasive tactics, the use of scientific vocabulary, grammar, and forms of argument, provide more effective persuasive persuasive methods than did the earlier approaches. This chapter examined the evolutionary content of secondary school biology textbooks, and in particular, estimated the impact of change in Creationist persuasive tactics used since 1968 upon the content and marketing of secondary biology textbooks. The textbook studies supported the contention that the bifurcated movement has been highly successful. Evolutionary coverage has decreased in biology textbooks since 1968 while biblical creation has seen a definite increase.Currently, however, the two Creationist fronts face a new challenge as their polar views have been observed together in recent legal battles. This polarity in approach has already proven detrimental to the Creationists in recent trials. Chapter IV discussed the implications of this bifurcation of the Creationist Movement. Further, the implications of the current rhetorical crisis were examined. It was recommended that research be continued examining the rhetorical strategies used by the Creationists since 1963. Also, further research in the area of textbook analysis was deemed necessary. / Department of Speech Communication

The purpose of this dissertation was to explore the status of and relationships among the variables of teacher acceptance of evolutionary theory, teacher understanding of evolutionary theory, and teacher understanding of the nature of science among Indiana public high school biology teachers. The relationships between these variables and the emphasis evolution receives in the classroom and teacher academic variables were investigated. Teacher knowledge structure of the concept of evolution was also explored.To answer the questions and hypotheses delineated in the study, a 68-item questionnaire and concept mapping activity was administered to the population of 989 teachers. The response rate was 53%.The teachers exhibited only a moderate level of acceptance and a marginal level of understanding of evolutionary theory. Teacher understanding of the nature of science was moderately high. Evolution played only a minor role in the curriculum. While the teachers had completed considerable course work in biology, the vast majority lacked specific course work in evolution and the nature of science.The data revealed a significant relationship between teacher acceptance and teacher understanding of evolutionary theory and between teacher acceptance of evolutionary theory and teacher understanding of the nature of science. The data also revealed significant associations between teacher allocation of instructional time to evolution and teacher level of acceptance of evolutionary theory, teacher level of understanding of evolutionary theory, teacher level of understanding of the nature of science, and teacher completion of a course in evolution. Additionally, the data revealed significant associations between teacher level of understanding of evolutionary theory and teacher completion of a course in evolution and teacher academic background in biology. Significant associations were revealed between teacher level of acceptance of evolutionary theory and both teacher completion of a course in evolution and teacher completion of a course in the nature of science.A significant amount of the variance in teacher acceptance of evolutionary theory was explained by the other variables delineated. The concept mapping activity revealed that teacher acceptance and understanding of evolutionary theory was reflected in teacher knowledge structure of evolution and that teachers' knowledge structures were characterized by an unsophisticated organizational framework. / Department of Biology

A revolution is taking place in education today at all levels from kindergarten through college, in virtually all subject matter areas. This revolution is due, in part, to research in learning theory and technological advances. Changes in attitudes have led to the concept of "accountability"--that educators must perform and produce educational programs that are meaningful and interesting as well as informative. The fact that private industry has had satisfactory results in the academic marketplace has also provided impetus for the current educational revolution which has resulted in several innovations.A general education biology course, Man and the Life Sciences, has been taught with an audiotutorial component at Ball State University since 1965. Quarterly evaluations by the students provided the staff with evidence that three of the units should be redesigned 1) to have more appeal to the students; 2) to meet their expectancy of relevance; and 3) to have a higher level of academic quality.The problem for the present research investigation was twofold: 1) to design three audiotutorial units for a college general education biology course titled Aggression, Territoriality and Survival; Time, Adaptation and Change; and Man, Communication and Behavior, with innovative approaches and 2) to evaluate the effectiveness of the newly developed materials.In designing these three units, specific goals of the research undertaking were 1) to integrate the three units in such a way that concepts of organismal biology, evolution and behavior are pervasive throughout all three units; 2) to develop a list of performance objectives for each of the three units; 3) to determine learning strategies which will help the students achieve each of these objectives; and 4) to determine learning strategies which will help make these objectives interesting and relevant to the students.In order to meet these criteria, the principles of systems management were employed bys 1) specifying goals, 2) specifying desired outcomes for students, 3) planning instruction, 4) evaluating student achievement, and 5) revising instructional procedure in light of experience. In planning the instruction, the method used to facilitate the accomplishment of the desired outcomes was the audiotutorial approach which allowed the student to learn at his own pace. Each unit actively involved the student in sequential multimedia learning activities. A learning guide was designed for the student to use in responding to questions posed as he progressed through the audiotutorial learning activities.After development, the unit materials were first tested with a group of ten students. Feedback on the basis of achievement tests and individual interviews provided the rationale for revisions in preparation for field testing. After completion of the field testing, which involved approximately 650 students, additional revisions were made, resulting in the final version which was evaluated to determine the overall effectiveness of the learning materials.Final measurement of student accomplishment was effected by the use of pre-tests and post-tests consisting of parallel quiz items which had been validated in preliminary testing. Forty-five objectives were final tested; difficulty levels from the pre-test indicated that twenty-four of the objectives were achieved by seventy percent or more of the students. Chi square applied to the results of the remaining items indicated that seven additional objectives probably were also achieved at this same level; fourteen of the objectives were not achieved during the final evaluation. Standard item analysis was used to assist in determining why these objectives were not accomplished; this information can be used in making future revisions.Student opinions were solicited in the form of a student unit evaluation. At least forty percent of the students rated each unit's interest level as high and fifty percent rated each as average; thus, the units accomplished what was expected.A program of instruction should evolve with new ideas and innovations with an effort toward continual improvement. Data collected from this research investigation can be used to pinpoint specific areas where additional research would be beneficial.

DNA methylation is an epigenetic modification in which a methyl group is covalently added to the DNA. In vertebrate genomes methylation occurs almost exclusively at cytosines immediately followed by a guanine (CpG dinucleotides). Two important aspects of DNA methylation have inspired several recent scientific investigations including those in this dissertation. First, methylated cytosines are hotspots of point mutation due to a methylation-dependent mutation mechanism, which has caused a deficiency of CpGs in vertebrate genomes. Second, DNA methylation in promoters is linked with transcriptional silencing of the associated genes. This dissertation presents the results of four studies in which I investigated the impacts of DNA methylation on the neutral and functional evolution of vertebrate genomes. The results of the first two studies demonstrate that DNA methylation has profound impacts on both inter- and intra-genomic neutral substitution rate variation. The third and fourth studies demonstrate that DNA methylation has played critical roles in shaping the evolution of vertebrate promoters and gene regulation.

Els gens estan sotmesos a forces selectives diferents. Un dels objectius de la Biologia Evolutiva és entendre els factors que determinen aquestes diferències. Els gens rarament actuen de manera aïllada, sinó que normalment funcionen com a elements de xarxes complexes formades per un gran nombre de molècules que interactuen entre si. Tot i la rellevància d’aquestes xarxes per entendre l’evolució dels gens, les propietats evolutives d’aquestes xarxes són encara poc conegudes. En aquesta tesi hem estudiat les forces selectives (selecció positiva i negativa) que han actuat sobre els gens implicats en la via de la insulina/TOR, i hem relacionat aquestes forces amb la posició dels gens a la via. Aquest estudi s’ha realitzat en 12 espècies del gènere Drosophila (primer article de la tesi), i en 6 espècies de vertebrats (humà, ratolí, vaca, opòssum, ornitorinc i pollastre) (segon article). A aquests efectes, s’han identificat i anotat els gens implicats a la via en totes les espècies estudiades, s’ha reconstruït la seva història evolutiva mitjançant tècniques d’anàlisi filogenètica, i s’han caracteritzat les forces evolutives que hi han actuat a partir de la relació la divergència no sinònima (dN) i sinònima (dS), ω = dN/dS. Totes les famílies gèniques estudiades tenen almenys un representant a totes les espècies estudiades. A més, tots els gens estudiats estan sotmesos a selecció purificadora, la qual cosa indica que aquests gens són funcionals. Per tant, tots els organismes estudiats presenten una via de la insulina/TOR completa i funcional. Tant a Drosophila com a vertebrats, observem que el nivell de limitació funcional (o selecció purificadora) sota el que evolucionen els gens es correlaciona amb la posició dels gens a la via (mesurada com el nombre de passos des del receptor de la insulina –posició 0– fins la resta de components –posicions 1 a 10), essent els gens de la part downstream els que evolucionen sota un major grau de limitació funcional. El sentit d’aquesta correlació és contrari al que s’ha trobat generalment en rutes metabòliques, on són els gens de la part upstream es que estan sotmesos a un major grau de limitació funcional. Vam avaluar l’impacte d’una sèrie de factors que es correlacionen amb ω (selecció positiva, nivell d’expressió gènica, nombre de teixits en què un gen s’expressa, grau d’esbiaix en l’ús de codons, longitud de les proteïnes codificades, i connectivitat en la xarxa d’interaccions proteïna-proteïna) sobre aquesta correlació. Aquesta anàlisi demostra que la correlació entre la posició a la via i els graus de limitació funcional és independent d’aquests factors. A més, observem que els gens que codifiquen proteïnes que interactuen físicament evolucionen sota seleccions selectives semblants, la qual cosa indica que aquestes proteïnes co-evolucionen. En global, aquests resultats indiquen clarament que els nivells de limitació funcional als què estan sotmesos els gens de la via de la insulina/TOR depenen de la posició que les proteïnes codificades ocupen a la via. Per tant, l’arquitectura de la via té un impacte sobre l’evolució dels seus gens. / Genes are subject to disparate evolutionary forces. One of the goals in Evolutionary Biology is to understand the factors underlying these differences. Genes rarely act in isolation, but they rather operate as elements of complex networks of interacting molecules. Despite the relevance of these networks for understanding gene evolution, the evolutionary properties of these networks remain poorly understood. In this thesis we have studied evolutionary forces (positive and negative selection) that acted on genes involved in the insulin/TOR pathway, and we have related these forces to the position that genes occupy in the pathway. This study has been performed in 12 species of the genus Drosophila, and in 6 vertebrate species. For that purpose, we have (1) identified and annotated the genes involved in this pathway in these species; (2) reconstructed their evolutionary history using phylogenetic analysis; and (3) characterized evolutionary forces that have acted on these genes from the nonsynonymous (dN) to synonymous (dS) divergence ratio (ω = dN/dS). All the studied gene families have at least one representative in all studied species. Furthermore, all studied genes evolve under purifying selection, indicating that they are functional. Therefore, all studied organisms have a complete and functional insulin/TOR pathway. In both Drosophila and vertebrates, we observed that the strength of purifying selection acting on genes correlates with their positions in the pathway, with downstream genes evolving under stronger selective constraint. We evaluated the impact of a number of factors (positive selection, gene expression level and breadth, codon bias, protein length, and connectivity in the protein-protein interaction network) on the observed correlation. This analysis shows that the correlation between pathway position and the strength of purifying selection is independent of these factors. Furthermore, we observed that genes encoding proteins that physically interact evolve under similar selective pressures, which indicates that these proteins co-evolve. Taken together, these results clearly indicate that levels of selective constraint acting on genes of the insulin/TOR pathway are affected by the position that their encoded products occupy in the pathway. Therefore, the structure of the pathway has an effect on the patterns of molecular evolution of its components.