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Cooperative coevolutionary algorithms (CCEA) are a form of evolutionary algorithm that is applicable when the problem can be decomposed into components. Each component is assigned a subpopulation that evolves a good solution to the subproblem. To compute an individual's fitness, it is combined with collaborators drawn from the other subpopulations to form a complete solution. The individual's fitness is a function of this solution's fitness. The contributors to the comprehensive fitness formula are known as collaborators. The number of collaborators allowed from each subpopulation is called pool size. It has been shown that the outcome of the CCEA can be improved by allowing multiple collaborators from each subpopulation. This results in larger pool sizes, but improved fitness. The improvement in fitness afforded by larger pool sizes is offset by increased calculation costs. This study targeted the pool size parameter of CCEAs by devising dynamic strategies for the assignment of pool size to regulate selection pressure. Subpopulations were rewarded with a larger pool size or penalized with a smaller pool size based on measures of their diversity and/or fitness. Measures for population diversity and fitness used in this study were derived from various works involving evolutionary computation. This study showed that dynamically assigning pool size based on these measures of the diversity and fitness of the subpopulations can yield improved fitness results with significant reduction in calculation costs over statically assigned pool sizes.

This work further elucidates processes involved in promoting and sustaining evolutionary diversification within the gall-inducing thrips that specialise on Australian Acacia. A phylogenetic approach was taken to determine modes of diversification available to these insects. The extension and revision of the gall-thrips phylogeny is central to the work and primarily focuses on cryptic populations of the Kladothrips rugosus and Kladothrips waterhousei species complexes. Parallel diversification, where the radiation of the K. rugosus and K. waterhousei lineages broadly mirror one another, offered a rare opportunity to test hypotheses of coevolution between gall-thrips and their Acacia hosts. In the absence of a reliable host Acacia phylogeny, indirect inference of insect/plant cospeciation can be arrived at as these two complexes share the same set of host species. The expectation is that if the phylogenies for the gall-thrips complexes show a significant level of concordance, then cospeciation between insect and host-plant can be inferred. Results indicate that the K. rugosus species complex comprise populations at species level. A significant level of phylogenetic concordance between the two species complexes is consistent with gall-thrips lineages tracking the diversification of their Acacia hosts. Given the less than strict form of insect/host cospeciation, factors impacting host diversification become important to gall-thrips diversification. Gall-thrips radiated over a period during the expansion of the Australian arid-zone. Cycles of host range expansion and fragmentation during the Quaternary could have played a major role in gall-thrips diversity. An interesting feature of resourse sharing amongst the K. rugosus and K. waterhousei complex members is the apparent absence of competitive exclusion between them. The persistence of this sympatry over millions of years is an unusual feature and merits further investigation.

Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2008. / Committee Chair: Fathianathan, Mervyn; Committee Member: Melkote, Shreyes; Committee Member: Paredis, Chris

For my dissertation research, I used a model system of bacteria and bacteriophage to study patterns of genome evolution. I performed whole-genome sequencing of replicate populations to determine the genetic changes responsible for a repeatable pattern of coevolution between bacteria and phage. I found that genetic changes conferring resistance in bacteria negatively impacted other traits such as growth rates and sensitivity to antibiotic. Different resistance mutations varied in the magnitude of their pleiotropic costs, and this resulted in a fixation bias favoring mutations that minimized pleiotropic effects. I manipulated the environment and found that differential pleiotropy between environments drove repeatable evolution at different genetic scales. Finally, I explored theoretically how bacteria, phage, and resource interact through a dynamic system of feedbacks. I used a mathematical model to describe priority effects in evolution, where the expected fate of a beneficial mutation varies depending upon whether it appears before or after a competing mutation. / 10000-01-01

Symbioses between cool-season grasses (Subfamily Pooideae) and endophytic fungi in the genera Epichlo and Neotyphodium straddle a continuum of interactions from antagonistic to highly mutualistic. Although these two genera of endophytes are closely related, Neotyphodium endophytes are strictly seed-transmitted and provide many physiological and defensive benefits to their hosts, while Epichlo spp. have an obligately sexual contagious stage wherein host inflorescences are replaced by fungal sexual structures (stromata), effectively sterilizing the plant. Between these two extremes of interactions are Epichlo spp. with a mixed strategy, where some grass tillers are sterilized while others develop normally and yield healthy endophyte-infected seeds. These symbioses offer a unique opportunity to dissect evolutionary mechanisms that may drive movement along this continuum. The research presented characterizes distinct hybridization processes in endophytes and grasses that result in the generation of astounding genetic diversity for the symbiosis. Interspecific hybridization via hyphal anatomosis is a common feature of Neotyphodium endophytes, and may promote mutualism by combining suites of defensive alkaloid genes and ameliorating the adverse evolutionary effects of an asexual lifestyle. My results demonstrate that several genetically distinct hybrid endophytes infect grass species in tribe Poeae. Further, I show that a highly mutualistic asexual endophyte infecting tall fescue (=Festuca arundinaceum Schreb.), Neotyphodium coenophialum, also infects two closely related and interfertile relatives of this host. My findings suggest that this seed-borne endophyte may have been introgressed into these grasses through sexual grass hybridization events. These findings highlight interspecific hybridization as a means of generating tremendous genetic variability in both endophytes and their hosts, thus magnifying the adaptive evolutionary potential of these symbioses. Further, I establish a phylogenetic framework for grasses naturally harboring Epichlo and Neotyphodium endophytes. I show that patterns of genetic divergence among grass lineages are emulated by those of their fungal symbionts. These results suggest that endophytes have co-evolved with grasses in subfamily Pooideae, and may have played a critical role in the evolutionary success and radiation of this group of grasses.

Climate variability and landscape characteristics interact to define specific catchment hydrological response. Catchments are considered fundamental landscape units to study the water cycle, since all aspects of the land surface component of the hydrological cycle come together in a defined area, which enables scientific research through mass, momentum and energy budgets. The role of climate-landscape interactions in defining hydrologic partitioning, particularly at the catchment scale, however, is still poorly understood. In this study, a catchment scale process-based hydrologic model (hillslope storage Boussinesq- soil moisture model, hsB-SM) was developed to investigate such interactions. The model was applied to 12 catchments across a climate gradient. Dominant time scales (T.S.) of catchment response and their dimensionless ratios were analyzed with respect to climate and landscape features to identify similarities in catchment response. A limited number of model parameters could be related to observable landscape features. Several T.S. and dimensionless numbers show scaling relationships with respect to the investigated hydrological signatures (runoff coefficient, baseflow index, and slope of the flow duration curve). Some dimensionless numbers vary systematically across the climate gradient, pointing to the possibility that this might be the result of systematic co-variation of climate, vegetation and soil related T.S. Each of 12 behavioral hsB-SM models were subsequently subjected to each of 12 different climate forcings. Mean deviations from Budyko's hypothesis controlling long-term hydrologic partitioning (represented by the evaporation index, E/P, dependence on the aridity index, PET/P) were computed per catchment and per climate. The trend observed per catchment could be explained by the dimensionless ratio of perched aquifer storage-release T.S. and mean storm duration T.S. The trend observed per climate could be explained by an empirical relationship between fraction of rainy days and average daily temperature during those days. Catchments that produce more E/P have developed in climates that produce less E/P, when compared to Budyko's hypothesis. Also, climates that give rise to more E/P are associated with catchments that have vegetation with less efficient water use parameters. These results suggest the possibility of vegetation and soil co-evolution in response to local climate leading to (catchment scale) predictable hydrologic partitioning.

Immune responses are presumed to contribute to host fitness, either by fighting off infections or via immunopathology. Research in this thesis sought to relate the magnitude of a putative immune response to infection and host and parasite fitness. The experiments and field studies presented here all focus on the interactions between the freshwater crustacean, Daphnia magna and its sterilizing bacterial endoparasite, Pasteuria ramosa, using the number of circulating haemocytes as a measure of host immune activity. I found substantial genetic variation in Daphnia’s cellular response to P. ramosa, and that Daphnia genotypes that mount the strongest cellular responses are the most likely to get infected and suffer sterilization. Thus, a strong cellular response is associated with low, as opposed to high host fitness potential. There were also some host genotypes that mounted a weaker cellular response and did not go on to suffer infection, and some that lacked a cellular response and also never suffered infection with P. ramosa. These findings led to a heuristic two-stage model for infection, where the parasite has to (1) pass from the host gut to haemolymph and then (2) successfully overcome haemolymph-based immune effectors to reproduce and achieve fitness. I also demonstrate that both the magnitude of host cellular response and likelihood of infection increases with initial parasite dose in susceptible host genotypes, and that host cellular response is associated with likely infection under both host and parasite genetic variation. Parasitised Daphnia also have substantially more circulating haemocytes than their healthy counterparts in both the laboratory and in the wild, where there is substantial genetic and environmental variation. This is one of the very few examples of how an immune response designates low host and high parasite fitness potential in a wild system. Finally, using a mixture of field study and common garden experiment, I demonstrate evolution in parasite infection traits over the course of an epidemic in a wild population, and that this evolution is associated with a decline in host abundance.

A series of recent studies using Drosophila melanogaster suggest that while males may benefit from having access to many partners, female fitness is reduced by extended cohabitation and sexual interaction with males. Yet, even if repeated sexual interactions are harmful to females, limited male exposure will ultimately be detrimental due to sperm-depletion and infertility. Females are therefore expected to balance mating opportunities and sperm storage capacity to maximize lifetime reproductive success. I introduced extended mating deprivation as a selective pressure to experimentally evolve lines of D. melanogaster for characters related to mating and postcopulatory sexual selection. Evolution of the mate-deprived lines over several dozen generations demonstrated that restricted sexual access was indeed a potent selective pressure. I consistently found that when males were removed for an extended time period, female fitness declined substantially, suggesting that mate-deprivation over nine days was harmful. Under these conditions, selected-line males responded to mate-reduced conditions and demonstrated a 13% increase in reproductive success compared to controls. Experimental females had a 15% increase in fertility compared to controls. I investigated a series of developmental characteristics that may have been altered by the selection regime, and while there was some evidence of evolved change, these results were not consistent. Although the data at hand do not substantiate a detailed characterization, both sexes in the experimental populations demonstrated increased fitness after extended mate-deprivation, thus evolutionary change appears to have occurred via selection on one or both relevant male ejaculate characteristics: sperm number and survival, and factors affecting female late-life fertility. / Thesis (Master, Biology) -- Queen's University, 2008-04-28 23:05:42.835