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This thesis investigates the novel idea of using a computer to create and optimise conceptual designs of a range of differently-shaped three-dimensional solid objects from scratch. An extensive literature review evaluates all related areas of research and reveals that no such system exists. The development of a generic evolutionary design system, using a genetic algorithm (GA) as its core, is then presented. The thesis describes a number of significant advances necessitated by the development of this system. Firstly, a new low-parameter spatial-partitioning representation of solid objects is introduced, which allows a wide range of solid objects to be appropriately defined and easily manipulated by a GA. Secondly, multiobjective optimisation is investigated to allow users to define design problems without fine-tuning large numbers of weights. As a result of this, the new concepts of acceptability, range-independence and importance are introduced and a new multiobjective ranking method is identified as being most appropriate. Thirdly, variable-length chromosomes in GAs are addressed, to allow the number of primitive shapes that define a design to be variable. This problem is overcome by the use of a new hierarchical crossover operator, which uses the new concept of a semantic hierarchy to reference chromosomes. Additionally, the thesis describes how the performance of the GA is improved by using an explicit mapping stage between genotypes and phenotypes, steady-state reproduction with preferential selection, and a new lifespan limiter. A library of modular evaluation software is also presented, which allows a user to define new design problems quickly and easily by picking combinations of modules to guide the evolution of designs. Finally, the feasibility of the generic evolutionary design of solid objects is demonstrated by presenting the successful evolution of both conventional and unconventional designs for fifteen different solid-object design tasks, e.g. tables, heatsinks, penta-prisms, boat hulls, aerodynamic cars.

abstract: Evolution is the foundation of biology, yet it remains controversial even among college biology students. Acceptance of evolution is important for students if we want them to incorporate evolution into their scientific thinking. However, students’ religious beliefs are a consistent barrier to their acceptance of evolution due to a perceived conflict between religion and evolution. Using pre-post instructional surveys of students in introductory college biology, Study 1 establishes instructional strategies that can be effective for reducing students' perceived conflict between religion and evolution. Through interviews and qualitative analyses, Study 2 documents how instructors teaching evolution at public universities may be resistant towards implementing strategies that can reduce students' perceived conflict, perhaps because of their own lack of religious beliefs and lack of training and awareness about students' conflict with evolution. Interviews with religious students in Study 3 reveals that religious college biology students can perceive their instructors as unfriendly towards religion which can negatively impact these students' perceived conflict between religion and evolution. Study 4 explores how instructors at Christian universities, who share the same Christian backgrounds as their students, do not struggle with implementing strategies that reduce students' perceived conflict between religion and evolution. Cumulatively, these studies reveal a need for a new instructional framework for evolution education that takes into account the religious cultural difference between instructors who are teaching evolution and students who are learning evolution. As such, a new instructional framework is then described, Religious Cultural Competence in Evolution Education (ReCCEE), that can help instructors teach evolution in a way that can reduce students' perceived conflict between religion and evolution, increase student acceptance of evolution, and create more inclusive college biology classrooms for religious students. / Dissertation/Thesis / Doctoral Dissertation Biology 2018

This thesis questions whether sympatric divergence, brought about by disruptive selection in a spatially heterogeneous environment, can occur under natural conditions and in the laboratory. I. An investigation, to detect micro-differentiation, was made on a Plantago lanceolata population, comprising a gradation of phenotypes and occurring in a small area (lx 5m) of dune pasture, heterogeneous by virtue of different vegetation heights. The prostrate phenotype with shorter leaves and inflorescences was correlated with low vegetation} the erect phenotype was correlated with taller vegetation. Vegetative propagules in standard conditions of garden and greenhouse showed persistent genotype differences of growth habit, leaf length and inflorescence length. Growth habit and leaf length also correlated with the original environment, indicating adaptive micro-differentiation. Some phenotypic plasticity was apparent. Investigation of the field population revealed flowering time differences between the phenotypes and rapid turnover of individuals less than six months old, particularly in low vegetation where the Plantago population was the most dense. Selection pressures appeared to be operating to maintain differentiation within this heterogeneous environment. Population control was evident, with mortality matching recruitment, but the chances of survival of an individual were independent of the season of establishment. II. In a second series of experiments, a population of randomly- mating Drosophila melanogaster was maintained for 20 generations in small 'population cages', heterogeneous because they contained two types of food medium, viz. normal food and normal food plus peppermint essence. The founder population yielded 40£ more progeny on the normal food. There were three control populations feeding on (l) normal food only, (2) peppermint food only, (3) homogeneous half-strength peppermint only. The experimental population initially responded to the heterogeneous environment (with its choice of food media), by yielding numbers of progeny and biomass in excess of expectation, which was calculated from the controls. This was thought to be an environmental response. The difference between the observed yield and expectation increased steadily for 10 generations, implying adaptation to the heterogeneity, but, after 17 generations of selection, the yield was significantly less than expectation. This persisted for a generation of lapsed selection on normal food, indicating a genetic response to some factor within the heterogeneous environment. Because females reared on peppermint showed a behavioural change and tended to choose this less palatable medium on which to lay their eggs, it is suggested that a genetic component of behavioural flexibility contributed to this result. There was also evidence of improved adaptation to normal food, possibly a genetic response to highly competitive conditions on this densely- populated medium. Although sympatric divergence was not conclusively demonstrated, a measure of habitat selection for egg-laying sites developed and the population became non-random. Peppermint retards the life-cycle of the flies living on it by approximately one day. Therefore, the heterogeneous population was experiencing conditions which might promote assortative mating. It was concluded from the two experiments, that a heterogeneous environment may act disruptively on a small, randomly-breeding population within a small area. The Plantago population, in an environment where selection pressures were probably high, showed evidence of micro-differentiation, indicating that sympatric divergence had occurred, although phenotypic plasticity was also evident in some morphological characters. The Drosophila population, in a heterogeneous environment where selection pressures may have been relatively low, also became non-random and evolved habitat-choice. In both investigations, forces enhancing assortative mating, helping to maintain genetic variation by reducing gene flow, were apparent. Therefore, it is concluded that sympatric divergence may be brought about by disruptive selection in a heterogeneous environment.

The morphological and ecologicalevolution of middle-upper Eocene planktonic foraminiferal family Hantkeninidae is investigated in the context of the dramatic palaeoceanographic and climatic changes that marked the transition from Paleogene "greenhouse" to Neogene "icehouse" climatic conditions. Morphometric analysis proves that evolution in family Hantkeninidae was gradual but complex in detail with periods of relative stasis. Multiple lines of evidence demonstrate that Hantkenina evolved from planispiral clavate genus Clavigerinella and not, as was previously believed, from Pseudohastigerina micra. The ancestor of Clavigerinella was probably a low trochospiral form Paragloborotalia sp., which has been recognized for the first time in this study at a number of sites. Trends in chamber inflation, tubulospine angle and the position of the tubulospine on each chamber show the most dramatic evolutionary changes, indicating that these are the most useful characters for taxonomy. These morphological changes correlate well with known palaeoceanographic changes as well as the shift in hantkeninid ecology from a deep to a surface water habitat. Hantkeninids underwent pronounced adaptive evolution in depth habitats during the initial phase of the climatic transition. Lower middle Eocene forms lived in a cool deep-water environment within or below the oceanic thermocline and shifted to warmer surface waters in the late middle Eocene. They evolved in the low latitudes and were primarily. a tropical-subtropical group. The occurrence of Hantkenma australis at relatively high northerly and southerly latitudes during the middle Eocene may record a temporary expansion of warmer water conditions into these regions, possibly representing a hitherto unknown "hyperthermal" event. Clavigerinella is rare in middle Eocene open-ocean sequences but occasionally occurs in relative abundance in other localities (such as on continental margins and oceanic seamounts), suggesting that it was specialized for living in upwelling regions. A revised taxonomy of family Hantkeninidae is presented that reflects new understanding ofhantkeninid evolution. The reconstructed phylogeny demonstrates that the tubulospine-bearing genera Hantkenina and Cribrohantkenina represent a monophyletic clade. Multivariate analysis suggests that more than one morphological population existed at several times and that these may represent biological species. The results demonstrate that the hantkeninids are not merely passive recorders of ocean conditions but have instead evolved morphology and changed habitat in response to climate change.

<p> Natural selection, the driving force behind evolution, acts on individual phenotypes. Phenotypes are the result of an individual&rsquo;s genotype, but the development from genotype to phenotype is not always accurate and precise. Developmental instability (DI: random perturbations in the microenvironment during development) can result in a phenotype that misses its genetic target. In the current study I assert that developmental instability may itself be an evolvable trait. Here I present evidence for DI&rsquo;s heritability, selectability, and phenotypic variation in the form of empirical data and evidence from the literature from the years 2006 through 2016. Phenotypic variation contributed by DI was estimated using fluctuating asymmetry and was found to contribute up to 60% of the phenotypic variation in certain trait types. I suggest that selection against developmental instability in some traits may result in higher evolvabilities (i.e., rates of evolution) for those traits or for entire taxonomic groups.</p><p>

The evolutionary status of the hot R CrB stars has long remained a matter of conjecture, primarily because of the relative dearth of relevant observational material. Previously the group had been thought to occupy a position intermediate in status between the EHe and R CrB classes as they have (at least at first glance) observational properties in common with both types of object. The photosphere of DY Cen has been quantitatively confirmed to be hydrogen-deficient and photometric variations suggest the star undergoes short period pulsations. Using a period-temperature relation applicable to hydrogen-deficient stars it would appear that this object has similar physical properties to both the EHe and R CrB stars. Narrow band imaging of V348 Sgr has shown that the associated nebula exhibits a bipolar structure and therefore must be closely related to planetary nebulae rather than H II regions. Spectroscopic observations have proved that the star in its present evolutionary state is incapable of ionising the nebula. Several scenarios for this behaviour are briefly discussed. The large helium enrichment found in the nebula indicates that processed material must have been ejected during the last major episode of mass loss. Evidence is presented that suggests a strong hydrogen abundance gradient exists within the nebula. A novel technique has been developed for determining reddening distances. Its main advantage over other similar methods is that both early and late-type stars may be used to establish the reddening-distance relationship. With more development this technique may prove to be an important tool in distance determinations for objects such as planetary nebulae etc. This technique was used to derive a distance of (4. 7±1.0) kpc for V348 Sgr. Using the core-mass relation for hydrogen-deficient stars implies that both V348 Sgr and MV Sgr are lower mass and luminosity objects than EHe and R CrB stars. The evidence presented in this thesis indicates that the hot R CrB group is not a homogeneous one. DY Cen is much more luminous and massive than the other members. The mass and luminosity of V348 Sgr and MV Sgr are consistent with the scenario that both have recently suffered a thermal pulse (causing re-ignition of a helium burning shell) and are currently looping back to the R CrB domain of the H R diagram.

Gnathostome novelties include jaws, paired appendages, and true teeth. Dlx genes encode transcription factors indispensable for embryonic development of these novelties. Gnathostomes possess at least 6 Dlx genes organized in 3 bi-gene clusters, a physical arrangement which is proposed to affect their expression though shared enhancer elements. I studied the Dlx genes of Cyclostomes, the evolutionary sister group of Gnathostomes. I identified 4 novel members of the Dlx gene family in hagfish (Eptatretus stoutii), and confirmed the presence of 6 Dlx genes in lamprey ( Petromyzon marinus). I found that Cyclostomes have only 1 gene cluster and several orphan genes. This lack of conserved arrangement is coincident with an absence of conserved Dlx enhancers. Irregardless, some regulatory conservation is still apparent as lamprey non-coding DNA is able to drive dlx specific expression patterns of reporter genes in zebrafish. Therefore Cyclostome and Gnathostome Dlx are both organized and regulated differently. The causes and consequences of these changes in Chordate evolution are discussed.

<p> The earliest-diverged multicellular animals are decentralized organisms capable of growing to indeterminate sizes and highly variable morphologies. These organisms must coordinate activity among their constitutive cells at the scale of the organism in order to to leverage the benefits of multicellularity, and must do so using decentralized mechanisms that are robust to uncertainty in size and shape. This thesis investigates how coordination within the Placozoa&mdash;arguably the simplest animals&mdash;scales with organism size, quantifies the extent to which different developmental processes affect size regulation, and creates a framework for measuring morphological variability in what had been considered amorphous animals. In Chapter 1 I develop a method by which one can measure coordination and information propagation within an animal's body plan, and investigate how this propagation is affected by changes in size. I argue that such animals are poised at criticality, with evidence presented to suggest that this facilitates optimal information transmission, but that the physical constraints of multicellularity create a size-coordination trade-off in such decentralized organisms. The presence of size-induced trade-offs brings forth the question of how size is regulated, which in Placozoa occurs through growth and asexual fission. In Chapter 2 I investigate whether size is regulated in response to changing environmental nutrient conditions and find that animals adjust their sizes to match their environments. I further find that this change comes about primarily due to changing dynamics of growth rather than fission, and identify that growth is highly dependent on nutrient conditions, but find evidence that asexual fission could be an emergent phenomenon of poor coordination beyond certain sizes. Finally, in Chapter 3 I investigate the morphological variability in Placozoa and find evidence for allometric growth in such animals. In addition, Chapter 3 sets the groundwork for future comparative morphological studies between individuals and for behavioral stereotyping by developing a size and rotation invariant shape representation, which I use to identify the presence of idiosyncratic morphologies. I close the thesis with some remarks regarding future directions in exploring the effects of scaling on coordination, morphology, and behavior in this small yet evolutionarily significant Metazoa phylum.</p><p>

The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adelie penguin (Pygoscelis adeliae) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares similar to 64 per cent genome-wide identity to a previously described Adelie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota, associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.