The study of animal personality, i.e. consistent individual differences in animal behaviour, is a rapidly growing research field. The construct of personality has been studied in many different scientific disciplines including ethology, behavioural ecology, psychology, animal management and physiology. Studying personality using a comparative framework is important for establishing whether phylogeny and/or ecology are a driving force in personality development. The applied use of personality assessments to aid captive animal management could also have far reaching ramifications, as recent studies have demonstrated that personality has relationships with variables such as health, welfare and breeding success. Within the animal personality literature three main methods of assessing personality have been developed: i) coding behavioural data under natural conditions, ii) coding animals’ responses during novelty tests and iii) rating animals on sets of behaviourally defined traits. In the current study personality was investigated in three primate species, Sulawesi black crested macaques (Macaca nigra), barbary macaques (Macaca sylvanus) and common squirrel monkeys (Saimiri sciureus). The two macaque species are closely related, being from the same genus, but show some differences in their ecology and behaviour while S. sciureus are phylogentically distinct but exhibit some similarities to the two macaque species in certain aspects of their ecology and behaviour. The aims of the study were twofold: i) establish whether phylogeny or socioecology has an impact on the development of personality structure by comparing the study species with other primate species, and ii) evaluate the use of personality assessments as a tool for the management of the study species in captivity. Personality was assessed using the trait rating method. Questionnaires consisting of 38 personality traits, with accompanying definitions, were sent to all European institutions holding any of the study species. Keepers were required to rate animals on each trait using a 1 – 7 interval scale. Personality assessments were tested for inter-observer reliability. For each species a Principal Components Analysis (PCA) was carried out using only traits that exhibited good inter-observer reliability and scores for animals on each of the resulting components (personality dimensions) were calculated. Construct validity of the personality dimensions was assessed by evaluating the relationships between personality dimension scores and, i) behaviour under natural conditions, and ii) behaviour during a novel object test. In order to assess the management implications of personality assessments further analyses were carried out using the personality dimension data, i) a MANOVA was used to assess whether personality dimension scores were affected by Zoo, Age and Sex, ii) Generalised Linear Mixed Models (GLMMs) were used to assess which, if any, specific Zoo variables effect mean personality scores, iii) multiple regression and ANOVA analyses were carried out to establish whether personality dimension scores could predict breeding variables in M. nigra, iv) parent-offspring regressions were used to assess the heritability of personality dimensions in M. nigra, and v) correlation and General Linear Model (GLM) analyses were used to assess whether personality dimension scores effected behavioural measures of enrichment use in aM. nigra group. Twenty four traits in M. nigra (N= 64), 25 traits in M. sylvanus (N= 62) and 18 traits in S. sciureus (N= 69)were rated reliably by human observers. When reliable traits were entered into a PCA for each species, results revealed three personality dimensions for M. nigra, Sociability, Dominance, and Emotionality; four personality dimensions for M. sylvanus, Sociability, Dominance, Emotionality and Human-Animal Sociability (HA-Sociability); and three personality dimensions for S. sciureus, Sociability, Dominance, and Cautiousness. Construct validity of each species personality ratings, in terms of relationships with observable behaviour, was demonstrated for each species. Validity was affected by contextual variables such as Zoo, Age and Sex, which, as personality can vary with the variables (see below) was to be expected. MANOVA results showed that the variable ‘Zoo’ had significant effects on personality dimension scores in all three species. Further investigation using GLMMs revealed that i) in M. nigra mean Sociability scores were higher in groups with a lower mean age, ii) in S. sciureus mean Sociability scores were higher in groups where keepers had a high mean experience (months) working with the animals, and iii) again in S. sciureus mean Cautiousness scores were higher in groups with a small total group size. Multiple regression showed that personality dimension scores could not predict breeding success variables in either male or female M. nigra individuals. Of the three variables that could affect the breeding success of a male/female partnership, Male, Female and Zoo, only Male identity significantly affected breeding success but this could not be assessed against personality.Of the three M. nigra personality dimensions only one, Sociability, appears to have a heritable component. There were no significant correlations between personality dimension scores of individual M. nigra and measures of enrichment use across a range of enrichment devices. Repeated measures GLM revealed that while the individuals did spend significantly different amounts of time interacting with each of the enrichment devices this did not vary as a function of either repetition number or personality. When comparing the three study species with other primate species, the Sociability and Dominance dimensions were comparable with previous research on non-human primates (NHP), except that aggressive-type traits found in other studies were not present in the Dominance dimension in M. nigra and M. sylvanus. This may be attributed to data suggesting they have more tolerant social systems compared to other primate species. The Emotionality dimension was similar across the two macaque species and was comparable to analogous dimensions in other NHP species. The Cautiousness dimension in S. sciureus was found to be similar to dimensions such as fearfulness and bold/shy in other NHP species. The HA-Sociability dimension found in M. sylvanus could not be compared with other primate studies as, to date, there has been limited investigation of human-directed personality dimensions in captive primates. Quantitative analyses using partial Mantel tests were conducted to evaluate if either phylogenetic similarity or similarity in socioecological variables significantly correlated with similarities in personality structure for 11 primate species (including the three study species). The results of this analysis were inconclusive as neither phylogenetic similarity nor socioecological similarity had a significant correlation with personality similarity. However the effect of socioecology was approaching significance, indicating that, selection pressures related to socioecology may play an important role in shaping personality structure but further data collection on a wider range of species is needed to explore these relationships further. In terms of the management of the study species in the current study, it was demonstrated that the captive environment, particularly the social environment and human-animal relationships (HARs), has a significant impact on personality and so personality could prove to be a valuable management tool. Breeding success of M. nigra could not be predicted by personality and this could be an indicator that M. nigra actually adapt to life in captivity relatively well compared to some other species.

The structure of direct-current microdischarges is investigated using a detailed two-dimensional multi-species continuum model. Microdischarges are directcurrent discharges that operate at a relatively high pressure of about 100 Torr and geometric dimensions in the 10-100 micrometer range. Our motivation for the study of microdischarges comes from a potential application of these devices in microthrusters for small satellite propulsion. The Micro Plasma Thruster (MPT) concept consists of a direct-current microdischarge in a geometry comprising a constant area flow section followed by a diverging exit nozzle. A detailed description of the plasma dynamics inside the MPT including power deposition, ionization, coupling of the plasma phenomena with high-speed flow, and propulsion system performance is reported in this study. A two-dimensional model is developed as part of this study. The model consists of a plasma module coupled to a flow module and is solved on a hybrid unstructured mesh framework. The plasma module provides a self-consistent, multispecies, multi-temperature description of the microdischarge phenomena while the flow module provides a description of the low Reynolds number compressible flow through the system. The plasma module solves conservation equations for plasma species continuity and electron energy, and Poisson’s equation for the self-consistent electric field. The flow module solves mass, bulk gas momentum and energy equations. The coupling of energy from the electrostatic field to the plasma species is modeled by the Joule heating term which appears in the electron and heavy species energy equations. Discretization of the Joule heating term on unstructured meshes requires special attention. We propose a new robust method for the numerical discretization of the Joule heating term on such meshes using a cell-centered, finite volume approach. A prototypical microhollow cathode discharge (MHCD) is studied to guide and validate the modeling effort for theMPT. Computational results for the impedance characteristics as well as electrodynamic and chemical features of the discharge are reported and compared to experimental results. At low current (< 0.1 mA), the plasma activity is localized inside the cylindrical hollow region of the discharge operating in the so-called “abnormal regime”. For larger currents, the discharge expands over the outer flat surface of the cathode and operates in the “normal regime”. Transient relaxation oscillations are predicted in the plasma properties for intermediate discharge currents ranging from 0.1 mA to 0.3 mA; a phenomenon that is reported in experiments. The MPT, in its present configuration, is found to operate as an electrothermal, rather than as an electrostatic thruster. A significant increase in specific impulse, compared to the cold gas micronozzle, is obtained from the power deposition into the expanding gas. For a discharge voltage of 750 V, a power input of 650 mW, and an argon mass flow rate of 5 sccm, the specific impulse of the device is increased by a factor of 1.5 to a value of 74 s. The microdischarge remains mostly confined inside the micronozzle and operates in an abnormal regime. Gas heating, primarily due to ion Joule heating, is found to have a strong influence on the overall discharge behavior. The study provides crucial understanding to aid in the design of direct-current microdischarge based thrusters. / text

Alcohol use disorders (AUDs) are major health issues with few known genetic explanations. This project used the fruit fly (Drosophila melanogaster) model to identify genes and gene networks that influence alcohol intoxication, a phenotype related to alcohol abuse in humans. We used bioinformatic tools to build gene networks based on 24 published Drosophila ethanol-responsive genes with human orthologs. We then assessed the role of these networks in ethanol sedation by testing two of the networks seeded on IP3K2, a gene that regulates calcium signaling, and CG14630, a gene involved in carnitine biosynthesis. We knocked down several genes in each of the networks using RNAi and tested the knockdown flies in a behavioral assay for ethanol sedation. Nervous system RNAi expression against 7 of 20 genes in the IP3K2 network and 4 of 30 genes in the CG14630 network significantly affected the sensitivity of flies to ethanol. To determine whether the hit rates in these two networks were greater than would be expected by random chance alone, we also assessed the effects of nervous system RNAi targeting a random set of fly genes. Unexpectedly, the fraction of randomly selected genes that affected ethanol sensitivity in a primary screen was comparable to or even larger than that from bioinformatically-derived gene networks. Our data are consistent with two possibilities that are not mutually exclusive. One possibility is that there are a very large number of genes that impact ethanol sedation and our bioinformatic analyses did not substantially enrich for these genes. A second possibility is that expression of RNAi could influence ethanol sedation independent of target gene knock-down. These two possibilities will be examined in future experiments.

I carried out several large, manipulative greenhouse and controlled-setting experiments to elucidate Panicum hemitomon growth response as influenced by environmental conditions associated with restoring thick-mat floating marsh. Initially, Panicum hemitomon growth response was assessed in conjunction with manipulated nutrient availability and hydrology. Next, I assessed Panicum hemitomon growth response in conjunction with a suite of substrate and mat or containment materials. Finally, I evaluated Panicum hemitomon growth response, as well as overall created floating marsh vegetated development, using both a multi-species planting approach and a suite of Panicum hemitomon establishment techniques. All partitions of Panicum hemitomon biomass (shoot, rhizome, and root material) were enhanced under nitrogen, and to a lesser extent, phosphorous enrichment. Saturated (not inundated) hydrologic conditions were most conducive for robust growth by all partitions of Panicum hemitomon biomass. Substrate and mat or containment materials had a significant effect on Panicum hemitomon vigor, with peat and peat-containing blended substrate materials being most conducive for vigorous Panicum hemitomon growth. Duralast coconut fiber was the most suitable mat or containment material based not only on measures of plant vigor, but also for reasons associated with strength and stability, as well as buoyancy. The combination of Panicum hemitomon and Ludwigia peploides was superior to any other multi-species treatment tested. Ludwigia peploides was highly resilient to transplanting, grew vigorously in a lateral fashion, produced significantly more biomass than any other secondary species, and enhanced overall mat buoyancy, all key metrics regarding successful floating marsh restoration. Equally as important, the large amount of biomass attained by Ludwigia peploides was not totally at the expense of vigorous Panicum hemitomon growth. With respect to establishment technique, the positive response of Panicum hemitomon rhizome growth to humic acid amendment warrants further study. This research generated data that not only advance the body of general ecological knowledge pertaining to Panicum hemitomon, the dominant macrophyte of thick-mat floating marsh, but equally as important, data that are likely to augment or enhance the creation and restoration of this important freshwater marsh type.

Aquatic polyculture has been recognised as a potential way of increasing the costeffectiveness of farming marron (Cherax tenuimanus), as it can lower average costs of production, increase system yields, and reduce economic risks associated with monoculture operations. Polyculture also increases ecological stability and assists recycling processes, which can result in synergistic benefits to participating species. In aquaculture, this synergism can result in increased profitability through advanced growth rates and/or reduced feed input. However, many of the inherent advantages of aquatic polyculture rely on cohabitants occupying distinct ecological niches within the system. In Western Australia, opportunities to multi-crop aquatic species are limited by species choice due to low natural diversity and strict translocation policies. This creates a situation where available aquaculture species exhibit overlaps in occupied niches. Effects of this overlap can include direct predation, increased intraspecific conflict, and competition for resources such as shelter and food. Prior to this study, silver perch (Bidyanus bidyanus) were identified as a prime candidate for duoculture with marron, based on favourable schooling and feeding characteristics, and preliminary trials demonstrated commercial benefits, including synergistic growth advantages to marron. However, investigations also showed that silver perch will predate on both small and moulting crayfish under certain conditions, and that growth of silver perch was inhibited when held in cages to prevent predation. The work reported in this thesis was undertaken to address the niche overlap existing between marron and silver perch, and therefore assist the marron industry in Western Australia in implementing appropriate management strategies for diversification. / Research focussed on investigating the ecological issues underlying interspecific interactions in marron polysystems, with the eventual aim of presenting information that could assist system managers in determining optimal conditions required to reduce antagonistic relationships and maximise synergism, ultimately leading to higher yields. Seven trials were conducted in three culture systems (54L aquaria, 250L aquaria and 720m2 experimental ponds) examining the ability of marron to detect, recognise and respond to a range of information cues (chemical, visual, tactile) from two potential predators (silver perch and Murray cod), with and without competition from conspecific and heterospecific crayfish (Cherax albidus). The ability of marron to interpret and respond appropriately to these variables was tested under a range of system-specific conditions, including stocking density, stocking size, shelter/habitat complexity, food availability, light intensity and life stage. Cage culture conditions were also examined to determine if the addition of shelter would mediate growth inhibition previously recorded, and to determine the desired stocking regime to return market sized fish in one growth season (8 months). Results from laboratory research and field-based trials did not support the free-range culture of marron and silver perch, even where turbidity and habitat complexity is high. Although both male and female marron (various sizes) demonstrated an ability to detect and differentiate between chemical and visual cues from potential predators, avoidance responses were only displayed upon attack from predators, or following predation of conspecifics; and avoidance strategies employed by marron were relatively ineffective. / Although marron showed some capacity to recognise an impending predatory threat, high initial mortalities and growth inhibition due to reduced foraging, would greatly reduce system yields. In addition, intraspecific competition between marron is likely to increase as avoidance responses would lead to high relative densities within shelters. The lack of avoidance behaviour displayed by marron when only visual and chemical cues from predators are present strongly supports cage culture of silver perch in marron ponds. As marron did not appear to alter their general behaviour (e.g. foraging) based on cues associated with silver perch held in cages they stand to benefit from cohabitation. Field-trials examining the pond culture of marron and caged silver perch demonstrated synergistic growth advantages to marron, compared to monoculture, and also identified several system variables that appear to improve polyculture production. The addition of bank shelters (within 1m of waters edge) was suggested to give marron a competitive advantage when moulting, expressed through growth and survival. Survival of marron was also increased in caged polyculture ponds, compared to monoculture, most likely due to increased health status (due to improved recycling) and/ or increased habitat complexity owing to the presence of fish cages. Growth inhibition previously reported when silver perch are held in cages was mediated to some degree by cage shelters, which appeared to increase feeding behaviour, reduce general anxiety and resulted in increased growth. The introduction of advanced silver perch fingerlings in order to produce market-sized fish in one growth season was also supported. However, it is recommended that cage culture dynamics require further elucidation if silver perch are to be commercially successful as a stand-alone crop using this growout strategy. / Significantly, the synergistic growth advantages experienced by marron when grown with fish demonstrate value from polyculture even if fish are not depended on as a secondary income. In this case, other species may also provide similar advantages, and a native candidate such as freshwater cobbler (Tandanus bostocki) would also redress problems associated with translocation laws restricting the use of silver perch in some areas of Western Australia. As no density effects were recorded in any of the trials conducted for either species, further investigation into increased system loads is required. In addition, as nutrient loads, and thus phytoplankton density, usually increases proportionately with pond biomass it is recommended that an additional herbivorous species, for example white eye mullet (Mugil cephalus), be examined in conjunction with increased density trials. Field research reported in this thesis was carried out in earthen ponds utilising remediated water from a acidified mine lake. Over a three-year period water quality parameters were maintained within optimal ranges for marron and silver perch, and survival and growth of both species was comparable to industry levels. These results validate the effectiveness of mine-water treatment technology; and accordingly, results support commercial viability of crayfish polyculture utilising remediated acid mine water. The large water resources offered by the numerous artificial lakes created from open cut mining has the potential to sustain a large successful aquaculture industry for Collie (Western Australia), and in other areas with extension of water treatment technology. / The incorporation of caged silver perch into marron ponds not only takes advantage of the inherent economic and risk-spreading benefits from a diversified management strategy, but also incorporates a number of within-system benefits due to synergism between species. The ecological approach to aquatic polyculture research reported in this thesis has elucidated key communication factors underlying interactions within crayfish polysystems, which is critical to a knowledge-based approach to system management.

The Stefan-Maxwell equations are a system of nonlinear partial differential equations that describe the diffusion of multiple chemical species in a container. These equations are of particular interest for their applications to biology and chemical engineering. The nonlinearity and coupled nature of the equations involving many variables make finding solutions difficult, so numerical methods are often used. In the engineering literature the system is inverted to write fluxes as functions of the species gradient before any numerical method is applied. In this thesis it is shown that employing a mixed finite element method makes the inversion unnecessary, allowing the numerical solution of Stefan-Maxwell equations in their primitive form. The plan of the thesis is as follows, first a mixed variational formulation will be derived for the Stefan-Maxwell equations. The nonlinearity will be dealt with through a linearization. Conditions for well-posedness of the linearized formulation are then determined. Next, the linearized variational formulation is approximated using mixed finite element methods. The finite element methods will then be shown to converge to an approximate solution. A priori error estimates are obtained between the solution to the approximate problem and the exact solution. The convergence order is then verified through an analytic test case and compared to standard methods. Finally, the solution is computed for another test case involving the diffusion of three species and compared to other methods.

The Stefan-Maxwell equations are a system of nonlinear partial differential equations that describe the diffusion of multiple chemical species in a container. These equations are of particular interest for their applications to biology and chemical engineering. The nonlinearity and coupled nature of the equations involving many variables make finding solutions difficult, so numerical methods are often used. In the engineering literature the system is inverted to write fluxes as functions of the species gradient before any numerical method is applied. In this thesis it is shown that employing a mixed finite element method makes the inversion unnecessary, allowing the numerical solution of Stefan-Maxwell equations in their primitive form. The plan of the thesis is as follows, first a mixed variational formulation will be derived for the Stefan-Maxwell equations. The nonlinearity will be dealt with through a linearization. Conditions for well-posedness of the linearized formulation are then determined. Next, the linearized variational formulation is approximated using mixed finite element methods. The finite element methods will then be shown to converge to an approximate solution. A priori error estimates are obtained between the solution to the approximate problem and the exact solution. The convergence order is then verified through an analytic test case and compared to standard methods. Finally, the solution is computed for another test case involving the diffusion of three species and compared to other methods.

The objective of this study was to evaluate the nutritional profile of mono- or multi-species pastures of native warm season grasses. One of four treatments were randomly assigned to Twelve pastures: 1) BG; 2) IG; 3) Mix G; 4) Mix NG. Growing steers (n = 225) were randomly assigned to one of nine pastures. Grass samples were taken from all pastures every 28 days during a four-month period and were analyzed for nutrient composition. Bermudagrass pastures had greater crude protein and ADF, but less NDF concentrations compared with the native warm-season grasses. Crude protein, IVDMD, and NDF IVDMD concentration decreased while NDF, ADF, and Hemicellulose concentration increased as grasses matured. Steers grazing IG and Mix G pastures gained more weight and consumed more forage than those on BG pastures. It appears that native warm-season grasses may offer a viable alternative to BG for grazing cattle during the summer.

Overfishing of stock and decreasing biodiversity are grave concerns for the U.S. and the rest of the world. Understanding and applying spatial and temporal information of marine species’ reproductive ecology and critical life habitat is vital to the development of effective strategies for marine resource management. In the Caribbean, one of the critical science gaps hindering effective management is the lack of information on how environmental factors may make fish spawning aggregation (FSA) sites optimal for spawning. Understanding the patterns of seafloor characteristics of spawning aggregation sites is of great interest to managers who need a means to efficiently design marine protected areas to help rebuild regional fish stocks. The specific goals of the study were: (1) to map the seafloor at historically known grouper and snapper spawning aggregation sites in three different countries, and (2) to characterize quantitatively the geomorphology of the sites including horizontal and vertical curvature profiles of the reefs, bottom depth at spawning sites, distance between spawning sites and shelf-edges/reef promontory tips, and the shortest distance between the spawning sites and 100 m water depth. These data were field-collected with a GPS and single-beam eco-sounder that provided latitude/longitude and depth. The point data were interpolated to surfaces in GIS to determine slope, aspect, curvature, and distance from spawning sites and three-dimensional reef structures. This study revealed that all 12 known Nassau grouper spawning aggregation sites in Belize and 5 known sites in the Cayman Islands were located at convex-shaped seaward extending reefs (reef promontories) jutting into deep water, within 1 km of reef promontory tips. However, spawning aggregations did not always occur at the tips of reef promontories, though all were found along the shelf edges within 1 km of promontory tips. Sixteen sites were multi-species spawning sites. These general characteristics were used to predict an undiscovered multi-species spawning aggregation in Belize. A successful prediction in Belize, together with the compiled data from multiple sites indicate: 1) reef promontories are vital locations for transient reef fish spawning aggregations, and 2) this study provides a potential tool for prediction of unknown spawning sites in the Caribbean.

The amount of biological sequence data is increasing rapidly, a promising development that would transform biology if we can develop methods that can analyze large-scale data efficiently and accurately. A fundamental question in evolutionary biology is building the tree of life: a reconstruction of relationships between organisms in evolutionary time. Reconstructing phylogenetic trees from molecular data is an optimization problem that involves many steps. In this dissertation, we argue that to answer long-standing phylogenetic questions with large-scale data, several challenges need to be addressed in various steps of the pipeline. One challenges is aligning large number of sequences so that evolutionarily related positions in all sequences are put in the same column. Constructing alignments is necessary for phylogenetic reconstruction, but also for many other types of evolutionary analyses. In response to this challenge, we introduce PASTA, a scalable and accurate algorithm that can align datasets with up to a million sequences. A second challenge is related to the interesting fact that various parts of the genome can have different evolutionary histories. Reconstructing a species tree from genome-scale data needs to account for these differences. A main approach for species tree reconstruction is to first reconstruct a set of ``gene trees'' from different parts of the genome, and to then summarize these gene trees into a single species tree. We argue that this approach can suffer from two challenges: reconstruction of individual gene trees from limited data can be plagued by estimation error, which translates to errors in the species tree, and also, methods that summarize gene trees are not scalable or accurate enough under some conditions. To address the first challenge, we introduce statistical binning, a method that re-estimates gene trees by grouping them into bins. We show that binning improves gene tree accuracy, and consequently the species tree accuracy. To address the second challenge, we introduce ASTRAL, a new summary method that can run on a thousand genes and a thousand species in a day and has outstanding accuracy. We show that the development of these methods has enabled biological analyses that were otherwise not possible.