This thesis presents two novel algorithms for the evolutionary optimisation of agent populations through divergent search of low dimensional phenotypic landscapes. As the eld of Evolutionary Robotics (ER) develops towards more complex domains, which often involve deception and uncertainty, the promotion of phenotypic diversity has become of increasing interest. Divergent exploration of the phenotypic feature space has been shown to avoid convergence towards local optima and to provide diverse sets of solutions to a given objective. Novelty Search (NS) and the more recent Multi-dimensional Archive of Phenotypic Elites (MAP-Elites), are two state of the art algorithms which utilise divergent phenotypic search. In this thesis, the individual merits and weaknesses of these algorithms are built upon in order to further develop the study of divergent phenotypic search within ER. An observation that the diverse range of individuals produced through the optimisation of novelty will likely contain solutions to multiple independent objectives is utilised to develop Multiple Assessment Directed Novelty Search (MADNS). The MADNS algorithm is introduced as an extension to NS for the simultaneous optimisation of multiple independent objectives, and is shown to become more e ective than NS as the size of the state space increases. The central contribution of this thesis is the introduction of a novel algorithm for rapid and thorough divergent search of low dimensional phenotypic landscapes. The Spatial, Hierarchical, Illuminated NeuroEvolution (SHINE) algorithm di ers from previous divergent search algorithms, in that it utilises a tree structure for the maintenance and selection of potential candidates. Unlike previous approaches, SHINE iteratively focusses upon sparsely visited areas of the phenotypic landscape without the computationally expensive distance comparison required by NS; rather, the sparseness of the area within the landscape where a potential solution resides is inferred through its depth within the tree. Experimental results in a range of domains show that SHINE signi cantly outperforms NS and MAP-Elites in both performance and exploration.

The annual killifish, Austrofundulus limnaeus, may enter embryonic diapause at three distinct points of development, termed diapause I, II, and III. Previous studies suggest a role for steroid hormones in the regulation of diapause in annual killifish. This study concerns the hormonal and genomic components involved in the developmental decision to enter or escape diapause II from both a maternal and embryonic perspective. Steroid hormone levels were measured in tissues isolated from adult female fish that were producing either high or low proportions of escape embryos. Levels of steroid hormones were also measured in new fertilized embryos that were known to be on either an escape or diapausing developmental trajectory. In addition, cDNA microarray gene expression analysis was used to identify gene sequences that may be associated with the regulation of entry into diapause in this species. Decreases in maternal estrogen levels associated with aging are correlated with decreasing escape embryo production, but there is no direct association between measured steroid hormone levels and escape embryo production. However, maternal production of escape embryos is correlated with increased ratios of 17 ß-estradiol to testosterone in ovary tissue, and cDNA microarray gene expression analysis indicates differentially regulated sequences associated with escape embryo production in maternal tissues. Both of these independent measures suggest hormonal involvement in the regulation of diapause. Embryonic levels of steroid hormones in newly fertilized embryos are not correlated with entry or escape from diapause II, although incubation in exogenous cortisol and 17 ß-estradiol causes an increase in the proportion of escape embryos. Gene expression analysis again suggests hormonal involvement. Interestingly, genes involved in epigenetic control of gene expression though chromatin condensation are differentially regulated in both maternal tissues producing escape embryos, and in embryos on the different developmental trajectories. These data suggest that hormonal control of gene expression through alterations of chromatin condensation may regulate the decision to enter or escape diapause II.

The hybridizing Daphnia mendotae and D. dentifera (Crustacea: Cladocera) are sympatric throughout much of North America, and are considered a cryptic species complex due to their lack of phylogenetically informative morphological characters. They appear to have no biological mating barriers: hybrids may dominate or coexist with either or both parental species, and are sexually competent, forming both F2 hybrids and back-crosses. Nevertheless, the two species remain distinct. There is observational evidence that separation may be enforced by adaptation to different predation regimes: D. mendotae, with its greater anti-predator morphological plasticity, may out-compete D. dentifera under intense invertebrate predation, while the smaller D. dentifera may be better adapted to avoid predation by visually feeding fish. We tested this idea by examining whether D. mendotae and D. dentifera differ in ecologically relevant life history and morphological traits. We performed a replicated life history experiment involving 6 replicates of 6 clones within each species, and measured time until first reproduction, fecundity, and juvenile and population growth rates. In parallel, we examined whether these species differed in morphological traits predicted to arise from adaptation to different predator types, and tested the ecological relevance of these traits by exposing Daphnia to predation by the invasive cladoceran Bythotrephes longimanus. Finally, we examined the plasticity of life history, morphology, and susceptibility to predation by rearing Daphnia under exposure to Bythotrephes chemical cues for two generations. D. mendotae and D. dentifera differed across almost all measured life history and morphological traits in directions that accord with our hypotheses, strongly suggesting that their species boundaries are maintained by adaptation to different predation regimes. Plastic reaction to Bythotrephes, however, was weak and inconsistent, suggesting that these species either do not detect or respond to this recent invader, or that their responses are manifested in other ways. / Thesis (Master, Biology) -- Queen's University, 2011-12-23 20:31:14.76

Thesis (M.A.) -- Central Connecticut State University, 2008. / Thesis advisor: Jeremiah Jarrett. "... in partial fulfillment of the requirements for the degree of Master of Arts in Biology." Includes bibliographical references (leaves 27-29). Also available via the World Wide Web.

Avian species are known to have the capacity to respond to environmental changes through physiological adjustments. The process whereby organisms adjust their phenotype without genetic change is termed phenotypic plasticity and it is mostly observed to be a phenotypic improvement to ecological challenges. Metabolic rate (MR), which is the rate of energy expenditure in a species, is a highly flexible physiological parameter which results in a great diversity of avian standardised metabolic rates. Like birds from high latitudes, Afrotropical bird species are expected to have the capacity to adjust their energy expenditure to match the availability of resources. Previous studies on the flexibility of physiological parameters in birds have focused on the magnitude of change of physiological adjustments and the cues inducing these changes. Comparative research has furthermore investigated metabolic rates across aridity, altitude, latitude and temperature gradients. Recently, a clear dichotomy has become evident with elevated metabolic rates observed in high latitude birds in winter and a down-regulation of metabolic rates observed in birds exposed to low latitude mild winters. In this study, the shape of the reaction norm, the magnitude, the reversibility, the direction and the rate of change of two physiological parameters, basal metabolic rate (BMR) and summit metabolic rate (Msum), were investigated in a coastal and an inland population of Southern Red Bishops (Euplectes orix) through seasonal acclimatisation and laboratory acclimation. Summer and winter basal metabolic rates as well as body mass, were highly flexible traits in free-ranging coastal and inland Red Bishops. Birds acclimatised to a mild coastal climate in winter exhibited reduced basal and summit metabolic rates, whereas birds originating from a more variable inland climate increased basal metabolic rate in winter, but did not show increases of Msum in winter. Red Bishops responded to short term thermal acclimation under laboratory conditions by gradually changing body mass. Acclimation periods of 21 days revealed a negative relationship between body mass and acclimation air temperature. Peak responses of basal metabolic rate to ambient temperature change were observed in both coastal and inland birds between two and eight days after the change in acclimation air temperature. The influences of seasonal acclimatisation on energy expenditure differed between coastal and inland birds, however, during laboratory acclimation individuals from the two populations showed no difference in response. Within the individuals of the coastal and inland Southern Red Bishops, phenotypic flexibility is observed in body mass, basal metabolic rate and summit metabolic rate as a response to environmental changes. This flexibility is thought to increase thermoregulatory capacities of the Southern Red Bishop in different habitats and climates.

A key factor in studying evolutionary biology is an understanding of the mechanisms organisms utilise in the ongoing process of adaptation. When faced with a heterogeneous and unpredictable environment, we expect organisms to evolve either as specialists or generalists, yet a unifying theory as to which will evolve is still lacking due to conflicting hypotheses based on limited empirical evidence. Phenotypic plasticity allows a single genotype to express different phenotypes, and has been found as an adaptive response to changing environments in all major taxa. With the advent of genomics it has become possible to study the underlying genetics of this phenomenon. It is however becoming clear that there is no single principle governing the plastic response, but rather a complex set of interactions between what appears to be regulatory and structural genes. With empirical data only recently becoming more readily available, the modelling of plastic responses are often still founded on the theoretical predictions and assumptions for which there is little proof. To bridge the gap between theory and nature, the challenge facing scientists today is the construction of experimental systems where theoretical predictions can be scrutinised. Given that phenotypic plasticity is a widespread phenomenon, understanding the magnitude and constraints of this response is an important issue in the study of evolution. Models have predicted a correlation between genome size and phenotypic plasticity, with increased genome size (complexity) linked to higher levels of phenotypic plasticity. Experimental findings, however, increasingly point to plasticity being governed by complicated sets of interactions between various parts of the genome, the adaptive landscape, and environmental cues. In the work presented here, a study was designed to test for a correlation between genome size and the level of plasticity by, looking at the fitness response of phages exposed to varying temperature. Seven phages differing in genome size and genome composition were used. Genome sizes ranged from 5386 bp to 170 000 bp. Taking advantage of the short generation times of phages, fitness could be measured as the growth rate per hour, which was compared among the different phage groups. The growth of large populations within a constant, controlled environment minimized the complications of environmental heterogeneity, and allowed for quantitative measure of the response to different temperatures. This was used to gain insight into how genome size relates to the level of phenotypic plasticity. Limited generation numbers were allowed for, to ensure population growth could be directly related to the plasticity of the genome, since numerous generations would be required for the effects of selection to become apparent. Adsorption rates are influenced by temperature, and were therefore measured to determine if it had a significant effect on the resulting population density. Results showed a marginal interaction between genome size and phenotypic plasticity, with adsorption rate having no significant effect. More experimental work would be required to verify this finding. / Dissertation (MSc (Genetics))--University of Pretoria, 2006. / Genetics / unrestricted

Facial attractiveness plays a crucial role in human mate choice, with individuals from both sexes using facial attractiveness cues to some degree when choosing a partner. Although some of the general facial attractiveness preferences have been studied in cross-cultural populations, most of the research focused specifically on Western populations. Most previous studies also approached facial attractiveness solely from a psychological point of view. One notable exception was a recent study by Roberts et al. (2005) in which the authors linked the Human Leococyte Antigen (HLA) system to cues for health and facial attractiveness in males. This study provides fascinating evidence that genes involved in the immune response also signal attractiveness and health. But is this true cross-culturally and across genders? Roberts et al. (2005) used a British population, who compared to other populations worldwide, have relatively few pathogens that routinely challenge their immune response. The first objective of our study was to test the role of the HLA system in an African female population with a high pathogen load. We found that common HLA alleles, that seemingly provide resistance against common pathogens, play a more important role in health measures than heterozygosity per se. However, our results showed these individuals were not necessarily rated more attractive. So which facial cues do individuals from our study population find attractive in the opposite sex? According to this study individuals from both sexes prefer neotenous features in the opposite sex. Interestingly, we found no preference for facial symmetry and only a slight preference for femininity in females. Our findings support the hypothesis by Boothroyd et al. (2005) that preference for femininity is a by-product of preference for neotenous cues. To test if ethnic preference could not play a confounding role in facial attractiveness ratings of the ethnically mixed South African population, we tested ethnic recognition in two abundant South African ethnic groups. Our results showed that individuals from both sexes could not reliably assign ethnicity to facial images of the two groups. Ethnic preference could therefore not play a role in our study. But mate choice does not only depend on cues displayed by the person being observed. Conditional dependent factors, inherent to the observer, influence how choosy they are of potential partners and therefore how attractive they rate members of the opposite sex. We tested the role of three condition dependent factors, age self-perceived attractiveness and relationship status in both sexes. We observed no significant difference in choosiness between males and females. Male choice therefore plays a more important role in human mate choice than previously expected. Furthermore, our study showed that condition dependent factors affect choosiness differently in males and females. Females are generally more sensitive to condition dependent factors, especially self-perceived attractiveness, while males showed no correlation between any of the condition-dependent factors and choosiness. Since HIV is so prevalent in the South African population, we also tested the role of self esteem in predicting sexual risky behaviour. Our results showed that high self-esteem males were more likely to be sexually active after the age of 18, but that males with low self-esteem were more likely to start sexual activity prematurely. We observed no significant correlation for females. These results indicate that HIV prevention campaigns should focus more on behavioural outcomes other than abstinence, instead of challenging the cultural norms, as indicated by the behavior of high self-esteem individuals. In conclusion, this dissertation is based on the first comprehensive study of genetic and conditional cues associated with facial attractiveness and health in an African population. This African population, with its high pathogen load, high diversity and novel cultural background provided many novel findings, which would hopefully contribute to a more universal view of human mate choice. / Dissertation (MSc (Genetics))--University of Pretoria, 2006. / Genetics / unrestricted

Competition plays a fundamental role in structuring ecological communities, and is a particularly important interaction for sessile organisms such as plants (Goldberg & Fleetwood 1987; Tilman 1994). To mitigate the negative effects of competition on fitness, plants can alter their phenotypes and reproductive traits through plastic responses. For example, decreases in the red to far-red ratio of light signal the presence of competitors, inducing a suite of responses known as shade avoidance syndrome (Franklin 2008). My thesis examines the impact of the competitive environment on reproductive output, the phenotypes Impatiens capensis produce and natural selection acting on shade avoidance responses. I found that heterospecific competitors affect both the phenotypes of I. capensis, and selection on shade avoidance traits. I also found evidence of population differentiation in hypocotyl lengths and flowering time. My thesis elucidates the influence of competition on the evolution of phenotypic plasticity in Impatiens capensis.

Competition plays a fundamental role in structuring ecological communities, and is a particularly important interaction for sessile organisms such as plants (Goldberg & Fleetwood 1987; Tilman 1994). To mitigate the negative effects of competition on fitness, plants can alter their phenotypes and reproductive traits through plastic responses. For example, decreases in the red to far-red ratio of light signal the presence of competitors, inducing a suite of responses known as shade avoidance syndrome (Franklin 2008). My thesis examines the impact of the competitive environment on reproductive output, the phenotypes Impatiens capensis produce and natural selection acting on shade avoidance responses. I found that heterospecific competitors affect both the phenotypes of I. capensis, and selection on shade avoidance traits. I also found evidence of population differentiation in hypocotyl lengths and flowering time. My thesis elucidates the influence of competition on the evolution of phenotypic plasticity in Impatiens capensis.

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