I evaluated possible constraints on the evolution of viviparity in the lizard genus Sceloporus by experimentally extending the length of egg retention past the normal time of oviposition for a number of oviparous species. Observations also included a representative of the genus Urosaurus, the sister genus to Sceloporus. I determined the effects of retention on embryonic development, hatchlings, and gravid females. Results indicated that the proximate constraints on longer retention times and viviparity are 1) embryonic development becomes arrested or severely retarded in utero, and 2) the ability to maintain gravidity past the normal time of oviposition is limited in some species. Observations on Urosaurus further showed that extended egg retention results in hatchlings with traits that are associated with lower fitness. I also tested the hypothesis that reproductive Sceloporus lower their body temperatures during activity because their normal body temperatures are detrimental to embryos. Observations on a viviparous species of Sceloporus indicated that the normal body temperature of the female was detrimental to embryonic development. This result is indicates that viviparity would be constrained in some squamate lineages if maternal body temperatures are too high for successful embryonic development. I also evaluated the hypothesis that the evolutionary transition from oviparity to viviparity involves a "reduction" of the eggshell concurrent with longer durations of egg retention. If this hypothesis is correct, then attributes of eggshells that should enhance exchange of respiratory gases (i.e., thickness, density, permeability to water vapor) would be correlated with the maximal developmental stage that embryos are able to attain in the oviducts (i.e., stage of developmental arrest). The results of this study indicated that these features of shells do not determine the stage at which development becomes arrested. Thus, the results do not support the hypothesis that shell reduction occurs concurrently with longer periods of egg retention. The results are consistent with the alternative hypothesis that reduction of the eggshell occurs after viviparity has evolved. / Ph. D.

Macroevolutionary patterns of adaptation are a product of natural selection acting on genetic and developmental variation within populations, the basis of microevolution. In microevolution, an adaptive landscape is used to visualize the relationship between phenotype and fitness, through a series of peaks and valleys. The adaptive landscape, as a concept suggests that there is some phenotypic optimum, or a combination of phenotypes, that result in a maximum fitness. This peak is not stable but is a reflection of interactions between the environment and the flora and fauna within. To expand the adaptive landscape to macroevolutionary scales is to assume that there is some optimum that a species or population is adapted to, and that numerous species can be compared to one another on the same landscape. The world of phylogenetic comparative methods uses the theory of the adaptive landscape in investigating the trajectory of trait change but is often limited to extant organisms. The fossil record often represents a major gap in the use of adaptive landscape theory, due in part to the incomplete nature of specimens or difficulties in untangling evolutionary relationships. Within this gap, the Triassic Period (252.2 – 201.5 MA) is sparsely represented, due to the often highly incomplete nature of Triassic fossils and our constantly evolving understanding of their phylogenetic relationships. However, the Triassic Period is bookended by mass extinctions, and is thus a useful case study to explore the utility of adaptive landscape theory for organisms in a time of rapid environmental change. My dissertation explores convergence and growth through an adaptive landscape framework, to reconstruct how species were evolving, or populations adapting, to a changing environment. The first chapter of my dissertation explores the evolution of a long snout in reptiles, with exploration of convergent evolution for both extant and extinct reptiles across the tree of life. The second chapter of my dissertation explores a statistical method to incorporate variation due to fossilization in estimating and quantifying growth curves. This second chapter was necessary to explore the third chapter of my dissertation, the ontogeny of a large-bodied mammal relative, Exaeretodon argentinus. With my third chapter, I quantify growth curves, compare them across other proto mammals closely related to Exaeretodon, and explore how diet may have changed over the lifetime of a single individual. These chapters focus on the adaptive landscape over different scales (population vs clade), and serve as a basis for future work in estimating dietary evolution. / Doctor of Philosophy / Evolutionary studies are often divided into macroevolution and microevolution. Microevolution can be thought of as the primary process of evolution, such as evolution by natural selection. Macroevolution, however, relates to patterns in evolution, such as the repeated evolution of flight in insects, birds, bats, and many extinct reptiles known only from fossils. Surprisingly, we lack any convincing models that can accurately relate evolution by natural selection with macroevolutionary patterns. One idea to bridge this gap is the adaptive landscape, an 80-year-old concept that relates a trait to the fitness of a population or a species. The adaptive landscape provides a visual representation of evolution through a series of peaks and valleys. Peaks embody high fitness, reflecting a population that is well adapted to their environment. Valleys on the other hand represent extinction traps, where populations are maladapted to their environment, and are in decline and at a higher risk of extinction. The adaptive landscape essentially quantifies how different traits of a population relate to their environment. My dissertation seeks to explore evolution through the lens of the adaptive landscape, to better reconstruct hypotheses about how animals interact with their environments, particularly in extinct animals known from fossils. I view the adaptive landscape with a macroevolutionary lens by redescribing a fossil reptile and investigating the repeated evolution of a long snout in reptiles. I then attempt to look at the adaptive landscape at a microevolutionary scale, by investigating patterns of growth in a 230-million-year-old mammal relative. My dissertation views evolution across scales and sets the stage for future work to better connect those scales.

The World Health Organization estimates that vector-borne diseases account for 17% of the global burden of all infectious diseases and has identified the mosquito as the most dangerous of all disease-transmitting insects, being responsible for several million deaths and hundreds of millions of cases each year. The study of mosquito genomics provides a deeper understanding of the molecular mechanisms involved in every aspect of vector biology, such as sex determination, host-parasite interaction, ecology, feeding behavior, immunity and evolutionary trends and can be used for the development of new strategies for vector control. We developed the first map of the mitotic chromosomes of the major vector for West Nile fever and lymphatic filariasis, Culex quinquefasciatus. The map was then successfully utilized for mapping of approximately 90% of available genetic markers to their precise positions on the chromosomes. Idiograms were integrated with 140 genetic supercontigs representing 26.5% of the genome. A linear regression analysis demonstrated good overall correlation between the positioning of markers on physical and genetic linkage maps. This will improve gene annotation and help in distinguishing potential haplotype scaffolds and regions of segmental duplications. It will also facilitate identification of epidemiologically important genes that can be used as targets for the vector control and provide a better framework for comparative genomics that will help understanding of the evolution of epidemiologically important traits. In another study, we confirmed the presence of the newly described species, Anopheles daciae, in regions of Russia using molecular data. Although sympatric with its sibling species, Anopheles messeae, five nucleotide substitutions in the internal transcribed spacer 2 of ribosomal DNA can be used to distinguish the morphologically similar species. Chromosome rearrangements have a significant impact on mosquito adaptation and speciation. Using sequencing data in combination with karyotyping, we demonstrated that significant differences in inversion frequencies distinguish An. messeae from An. daciae, suggesting that these inversions are actively involved in adaptation and speciation. It is essential to have reliable toolbox for correct identification of these species and to know their range for future possible malaria outbreaks prevention. / Ph. D. / The more you study, the more you know The more you know, the more you forget The more you forget, the less you know So why study? According to the World Health Organization, mosquitoes are one of the deadliest animals in the world. They spread disease to humans resulting in hundreds of millions of illnesses and several million deaths every year. Study of the mosquito genome can help us understand vector biology and speciation and can be used to develop new strategies for vector control. Culex quinquefasciatus, the southern house mosquito, is one of the major vectors for the West Nile virus in the U.S. and for lymphatic filariasis, a disabling and disfiguring disease, worldwide. The traditional methods of control are of limited effectiveness because of high insecticide resistance in many populations of the mosquito. To enhance our resources for the control strategies, we developed physical maps of the chromosomes for this mosquito and effectively integrated it with available genetic linkage map. This work will help to identify epidemiologically important genes that can be used as targets for the vector control. Malaria vectors, mosquitoes from the genus Anopheles, are known for their ecological plasticity, which can be partially explained by chromosome rearrangements called inversion. A global malaria eradication program significantly reduced the number of deaths related to malaria, especially in Europe and the U.S. However, malaria outbreaks can occur anywhere competent vectors occur. We studied Anopheles messeae, one of the major European malaria vectors and its closely related species, Anopheles danciae. We report for the first time the presence of An. daciae in Russia and demonstrate that its distribution overlaps with that of An. messeae. Using genetic sequence data in combination with chromosome structure, we demonstrated that significant differences in inversion frequencies reliably distinguish An. messeae from An. daciae. These inversions may be involved in adaptation and speciation of these two species. It is essential to have reliable toolbox for correct identification of these species and to know their range for future possible malaria outbreaks prevention.

The dominantly held view in evolutionary theory focuses on gradual or punctuated change, primarily via natural selection, as the mechanism by which novel traits arise and evolution occurs. Noticeably absent from this portrayal of evolution is mention of the conservation of general characteristics, such as homologous morphological features or conserved nucleotide sequences, commonly observed across even distantly related groups at both the molecular and organismal levels. This raises at least the following questions: a) How does the evolution of conserved traits fit into an evolutionary theory that emphasizes change? b) What components of an evolving system provide the capacity for adaptation in spite of this apparent conservation of general traits? And c) How do these components affect the evolution of lineages? Here I suggest that heritable traits such as DNA methylation and histone modifications provide one place to look when addressing these questions. Current quantitative and population genetic models reflect the dominant view of evolution described above, and act as the foundation for both formal and informal descriptions and predictions of evolutionary change. Using results from recent work in molecular epigenetics, I consider the evolutionary implications for these traits, and show how current models of evolution fail to accurately capture this influence. In doing so, I also address some of the philosophical implications for how we conceptualize evolution, and what potential changes might be necessary for a more complete theory. / Master of Arts

Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / This study employs a suite of geophysical, sedimentological, and chronostratigraphic tools to investigate the complex interactions among changes in sea level, climate, and sedimentation processes that have driven Holocene coastal evolution. These interrelationships were explored in investigations of three coastal sites with diverse sea-level and sedimentation histories: the Egyptian Red Sea (Wadi Gawasis), southern Brazil (Pinheira) and the Western Gulf of Maine (Plum Island). This study demonstrates the need to quantify the integrated impacts of spatially-diverse changes in global (sea level), regional (climate, sea level), and local (sedimentation) factors if we are to predict large-scale coastal evolution in response to the ongoing acceleration in sea-level rise. The mid-Holocene in both the Red Sea and southern Brazil was characterized by higher-than-present stands of sea level. Sedimentological, malachological, foraminiferal, and rheological studies at Wadi Gawasis reveal that this resulted in the formation of a shallow bay that reached its maximum extent prior to a 1.5-m highstand at 5 ka, demonstrating a dominance of sedimentation processes despite contrary sea-level change. Early bay closure was driven by sediment inputs enhanced by a wetter climate. Slowly falling sea level and coincidental climatic aridization allowed for the establishment of an Egyptian harbor 4 ka, followed by late-stage progradation dominated by sea-level fall. In southern Brazil, an abundant sediment supply and sea-level fall following the mid-Holocene highstand were responsible for the development of the 5-km wide Pinheira strandplain, composed of regular beach and dune ridges. Identification of anomalous barrier, lagoonal, and tidal fill deposits within this plain demonstrates the complex nature of the sedimentological response to a small-scale change in the rate of sea-level fall. By contrast, Plum Island formed in a regime of rapid sea-level rise that reworked shallow shelf and fluvial deposits. Geophysical and sedimentological studies reveal a complex barrier formation (aggradation, spit accretion and progradation), including evidence for inlet migration and closure. Time-transgressive backstripping of backbarrier facies shows that bay sedimentation in a regime of slowly rising sea level reduced tidal-prism and produced inlet closure. This is first study to demonstrate that the direct impact of backbarrier processes influencing barrier island development. / 2999-01-01

The central goal of this thesis is to provide additional criteria towards implementing open-ended evolution in an artificial system. Methods inspired by biological evolution are frequently applied to generate autonomous agents too complex to design by hand. Despite substantial progress in the area of evolutionary computation, additional efforts are needed to identify a coherent set of requirements for a system capable of exhibiting open-ended evolutionary dynamics. The thesis provides an extensive discussion of existing models and of the major considerations for designing a computational model of evolution by natural selection. Thus, the work in this thesis constitutes a further step towards determining the requirements for such a system and introduces a concrete implementation of an artificial evolution system to evaluate the developed suggestions. The proposed system improves upon existing models with respect to easy interpretability of agent behaviour, high structural freedom, and a low-level sensor and effector model to allow numerous long-term evolutionary gradients. In a series of experiments, the evolutionary dynamics of the system are examined against the set objectives and, where appropriate, compared with existing systems. Typical agent behaviours are introduced to convey a general overview of the system dynamics. These behaviours are related to properties of the respective agent populations and their evolved morphologies. It is shown that an intuitive classification of observed behaviours coincides with a more formal classification based on morphology. The evolutionary dynamics of the system are evaluated and shown to be unbounded according to the classification provided by Bedau and Packard’s measures of evolutionary activity. Further, it is analysed how observed behavioural complexity relates to the complexity of the agent-side mechanisms subserving these behaviours. It is shown that for the concrete definition of complexity applied, the average complexity continually increases for extended periods of evolutionary time. In combination, these two findings show how the observed behaviours are the result of an ongoing and lasting adaptive evolutionary process as opposed to being artifacts of the seeding process. Finally, the effect of variation in the system on the diversity of evolved behaviour is investigated. It is shown that coupling individual survival and reproductive success can restrict the available evolutionary trajectories in more than the trivial sense of removing another dimension, and conversely, decoupling individual survival from reproductive success can increase the number of evolutionary trajectories. The effect of different reproductive mechanisms is contrasted with that of variation in environmental conditions. The diversity of evolved strategies turns out to be sensitive to the reproductive mechanism while being remarkably robust to the variation of environmental conditions. These findings emphasize the importance of being explicit about the abstractions and assumptions underlying an artificial evolution system, particularly if the system is intended to model aspects of biological evolution.

The human prefrontal cortex (PFC) is associated with complex cognitive behaviors such as planning for the future, memory for serial order, social information processing and language. Understanding how the PFC has changed through time is central to the study of human neural evolution. Here we investigate the expansion of the PFC by measuring relative surface area of the PFC in Pan troglodytes and Homo sapiens. Magnetic resonance images (MRI's) from 8 preserved chimpanzee brains (3 male and 5 female adults) were segmented and measured. The results of this study indicate that there are gross anatomical differences between the chimpanzee and human prefrontal cortex beyond absolute size. The lower surface area to volume ratio in PFC of the chimpanzee when compared to a human indicates less gyral white matter in this region and thus, less associative connectivity. This anatomical evidence of a difference corresponds with the lesser cognitive complexity observed in chimpanzees. / by Ian D. George. / Thesis (M.A.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

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.

Herbivory is thought to be nutritionally inefficient relative to carnivory and omnivory. But, herbivory evolved from carnivory in many lineages, suggesting that there are advantages to eating plants. To understand the adaptive significance of the transition from carnivory to herbivory, I proposed five hypotheses for the adaptive evolution of herbivory and reviewed the current freshwater literature to identify conditions where eating plants might be adaptive over eating animals. I tested three of these ideas (Suboptimal Habitat, Heterotroph Facilitation, and Lipid Allocation) using the herbivorous Sailfin Molly (Poecilia latipinna)and identified each as a potential mechanism for the evolution of herbivory. To understand the origins of herbivory in Sailfin Mollies, I reconstructed ancestral habitats and dietsacross a phylogeny of the genus Poeciliaand then used phylogenetically independent contrasts to identify patterns of diet evolution. I found that the degree of herbivory increases with increasing salinity affiliation, suggesting that in this genus, herbivory evolved as an adaptation for invading less productive saline habitats from freshwaters. This result is consistent with the Suboptimal Habitat hypothesis, which states that herbivory allows organisms to invade and persist in ‘suboptimal’ habitats. To understand how herbivory is maintained in extant populations, I raised juvenile Sailfin Mollies in mesocosms and enclosure cages placed in the Everglades to document that dietary autotrophic lipids play a role in early life history by supporting rapid growth (Lipid Allocation). However, dietary bacterial fatty acids promoted fish survival, consistent with the Heterotroph Facilitation hypothesis, which states that indirect detritivory supplements the herbivorous diet. Finally, I quantified periphyton quality/availability and consumer density across the Everglades landscape to examine the correlates of trophic dynamics in nature. Results revealed that herbivores can persist in diverse habitats and survive on varying resources when habitats are unfavorable, supporting the Suboptimal Habitat hypothesis.

Observations of textual document management by individuals and organizations have suggested the popularity of using categories to organize, archive and access documents. The adequacy of an existing category understandably may diminish as it includes influxes of new documents over time or retains only a part of existing documents, bringing about significant changes to its content. Thus, the existing document categories have to be evolved over time as new documents are acquired. Following an evolution-based approach for document-category management, this dissertation extends Category Evolution (CE) technique by addressing its inherent limitations. The proposed technique (namely, CE2) automatically re-organizes document categories while taking into account those previously established. Furthermore, we propose the Ontology-based Category Evolution technique (namely, ONCE) to overcome the problems of word mismatch and ambiguity encountered by the lexicon-based category evolution approach (e.g., CE and CE2). Facilitated by a domain ontology, ONCE can evolve document categories on the conceptual rather the lexical level. Finally, this dissertation further considers the evolution of category hierarchy and proposes Category Hierarchy Evolution technique (CHE) and Ontology-based Category Hierarchy Evolution technique (OCHE) to evolve from an existing category hierarchy. We empirically evaluate the effectiveness of our proposed CE2, ONCE, CHE, and OCHE in different category evolution scenarios, respectively. Our analysis results show CE2 to be more effective than CE and the category discovery approach (specifically, HAC). The ontology-based category evolution approach, ONCE, shows its advantage over CE2 which represents the lexicon-based approach. Finally, the effectiveness attained by CHE and OCHE are satisfactory; and similarly, the ontology-based approach, OCHE, also outperforms the lexicon-based one. This dissertation has contributed to the text mining, document management, and ontology learning research and practice.