No description available.

No description available.

Conserving biodiversity in human-dominated landscapes requires protecting networks of ecological reserves and managing the intervening matrix to maintain the potential for species to move among them. This dissertation provides original insights towards (1) identifying areas for protection in reserves that are critical to maintain biodiversity and (2) assessing the potential for species' movements among habitat patches in a reserve network. I develop and test methods that will facilitate conservation planning to promote viable, resilient populations through time. The first part of this dissertation tests and develops reserve selection strategies that protect either a single focal species in a dynamic landscape or multiple interacting species in a static landscape. Using a simulation model of boreal forest dynamics, I test the effectiveness of static and dynamic reserves to maintain spatial habitat requirements of a focal species, American Marten (Martes americana). Dynamic reserves improved upon static reserves but re-locating reserves was constrained by fragmentation of the matrix. Management of the spatial and temporal distribution of land-uses in the matrix will therefore be essential to retain options for re-locating reserves in the future. Additionally, to include essential consumer-resource interactions into reserve selection, a new algorithm is presented for American marten and its two primary prey species. The inclusion of their interaction had the benefit t of producing spatially aggregated reserves based on functional species requirements. The second part of this dissertation evaluates and synthesizes the network-theoretic approach to quantify connectivity among habitat patches or reserves embedded within spatially heterogeneous landscapes. I conduct a sensitivity analysis of network-theoretic connectivity analyses that derive least-cost movement behavior from the underlying cost surface which describes the relative ecological costs of dispersing through different landcover types. Landscape structure is shown to aff ect how sensitive least-cost graph connectivity assessments are to the quality (relative cost values) of landcover types. I develop a conceptual framework to classify network connectivity statistics based on the component of habitat connectivity that they quantify and the level within the network to which they can be applied. Together, the combination of reserve design and network connectivity analyses provide complementary insights to inform spatial planning decisions for conservation.

Many evolutionary game theory papers have obtained their results when the bounded rationality which creates change vanishes. In our first chapter we consider whether such results are actually a good reflection of a population whose bounded rationality is small yet persistent. Our model consists of a two type population with three stable equilibria. Firstly we find that results from the standard vanishing noise approach can be very different from those obtained when noise is small but constant. Secondly when the results differ the small and persistent noise approach selects an equilibrium with a co-existence of conventions. Our second chapter generalises the model of our first chapter to a population of many player types and several stable equilibria. Firstly we produce the characteristics of the long run equilibria under vanishing noise analysis. Secondly we find that the introduction of a small neutral group into a divided society can produce a welfare improving switch in the long run equilibrium towards social co-ordination. Our third chapter combines the model of the second chapter with the message of the first. We show numerically that the long run location of a heterogenous population with extremely low levels of bounded rationality can be completely different to the equilibria selected through vanishing noise analysis. We also show that such an event is not a rare occurrence and find that over a third of populations are misrepresented by stochastic stability. Our final chapter conducts a review of the literature on social threshold models. We give a thorough description of each paper and discuss the main assumptions that drive the key results.

How parasites influence the population dynamics of their hosts depends on 1) theproportion of individuals that carry the infection in the population, 2) what type of individuals aremost susceptible to infection and 3) the fitness effects of infection. In this study I first investigate thefrequency of malaria strains transmitted in the African winter quarters or at the European breedinggrounds in collared flycatchers (Ficedula albicollis). I then zoom in on the relationship between avianmalaria infection status and condition, expression of sexually selected ornament and reproductiveperformance of male collared flycatchers. I found that female flycatchers are more likely to beinfected than males and that both sexes have a large bias towards infection with European strains ofmalaria. Infected male flycatchers have higher reproductive success and tend to have largerornaments but there was no detected relationship between malaria infection and male condition.This is the first example, that I am aware of, of a positive relationship between malaria infection andreproductive success.

This thesis is concerned with problems of variable selection, influence of sample size and related issues in the applications of various techniques of exploratory multivariate analysis (in particular, correspondence analysis, biplots and canonical correspondence analysis) to archaeology and ecology. Data sets (both published and new) are used to illustrate these methods and to highlight the problems that arise - these practical examples are returned to throughout as the various issues are discussed. Much of the motivation for the development of the methodology has been driven by the needs of the archaeologists providing the data, who were consulted extensively during the study. The first (introductory) chapter includes a detailed description of the data sets examined and the archaeological background to their collection. Chapters Two, Three and Four explain in detail the mathematical theory behind the three techniques. Their uses are illustrated on the various examples of interest, raising data-driven questions which become the focus of the later chapters. The main objectives are to investigate the influence of various design quantities on the inferences made from such multivariate techniques. Quantities such as the sample size (e.g. number of artefacts collected), the number of categories of classification (e.g. of sites, wares, contexts) and the number of variables measured compete for fixed resources in archaeological and ecological applications. Methods of variable selection and the assessment of the stability of the results are further issues of interest and are investigated using bootstrapping and procrustes analysis. Jack-knife methods are used to detect influential sites, wares, contexts, species and artefacts. Some existing methods of investigating issues such as those raised above are applied and extended to correspondence analysis in Chapters Five and Six. Adaptions of them are proposed for biplots in Chapters Seven and Eight and for canonical correspondence analysis in Chapter Nine. Chapter Ten concludes the thesis.

This thesis is an evaluation of the hypothesis that the spennathecae of spiders affects the sperm precedence patterns in a predictable way (Austad 1984). Spermathecae come in two varieties: cul-de-sac and conduit. Cul-de-sac spennathecae, according to the hypothesis, are supposed to lead to second male sperm priority and conduit to first male sperm priority . The hypothesis was evaluated both directly and indirectly. Direct measurements were made of paternity in two species, Pholcus phalangioides and Tetragnatha montana, both of which are cul-de-sac species. It was found that P. phalangioides complies with the predicted precedence pattern and thus does not disprove the hypothesis. This second male priority pattern was despite a much shorter mating time by second mating males. In T. montana no precedence pattern was found, with equal likelihood of first or second mating males of gaining paternity. There was in T. montana a possible influence of the duration of mating affecting the precedence pattern, with longer mating males gaining a higher paternity no matter what order they mated in. It is discussed whether or not this is due to sperm loading or genitalic stimulation (Eberhard 1985). Indirect evaluation of the hypothesis included an analysis of mating behaviour in Zygiella x-notata which is a conduit species and was chosen as a comparison to the two cul-de-sac species. In Z. x-notata it was found that there was no difference between mating duration in first and second mating males. Mating persistence is thus the same in first and second mating males, suggesting that the males cannot detect that the female is a denuded resource to second mating males. Hence first male priority may not be a factor in this species. Other indirect methods of evaluating the hypothesis involved charting the incidence of mate-guarding and mating-plugs. The expected pattern of mate-guarding was for conduit species to pre-mate guard and for cul-de-sac species to post-mate guard, because of the predicted sperm precedence patterns associated with the spermathecae. The predicted pattern was not found. In the case of mating-plugs it was predicted that these should be deployed by cul-de-sac species because it is in these species that second males are able to usurp paternity to a large extent. The opposite pattern was found with mating-plugs of various design being utilized by conduit species. It is postulated that mating-plugs are the mechanism by which first male priorities are established in conduit species, where this pattern is found. The absence of plugs in cul-de-sac species is possibly the reason that second males can cuckold. The additional data collected since 1984 reveal that patterns of paternity found in spiders seem to be more complex than was originally assumed by Austad (1984). Spermathecae are species-specific in character and this may reflect a species specificity in sperm precedence patterns. Thus the conduit I cul-de-sac dichotomy may not reflect a useful prediction of paternity patterns.

The investigation examines the effects of three contexts (strong easily discriminable colors, shifting strong to weak colors, and a homogeneous white background) on cue selection in a paired associate study. Stimuli employed were high similarity consonant-consonant-consonant trigrams, and the responses were high imagery value nouns. Each S learned two lists.

Parasites have detrimental effects on an animal's fitness and could play a significant role in shaping the adaptive behaviour of animals. Natural selection may favour those behaviours utilised by animals that minimise the risk and intensity of infections. Animals use a range of behavioural strategies associated with grooming, social, mating, migratory and foraging behaviours to minimise their parasite burdens. Herbivores have two means available for reducing the effects of parasites while foraging. They may avoid parasites or consume plants with anti-parasitic properties. Sheep (Ovis aries) were shown to avoid foraging in areas of the sward contaminated with O. circumcincta infective larvae but could only do so when larvae were associated with faeces. The ability of sheep to avoid contaminated patches of the sward increased as the size of contaminated sward patches increased. This avoidance behaviour resulted in a reduction in the numbers of parasites ingested. Animals infected with O. circumcincta were more selective in their grazing behaviour than uninfected animals with respect to faeces avoidance. In order to determine which plants possess anti-parasitic properties Lotus pedunculatus, Pinus sylvestris, Tanacetum vulgare and Artemisia absinthium extracts were screened against Trichostrongylus colubriformis infections in the Mongolian gerbil (Meriones unguiculatus). Only A. absinthium merited further investigation as it appeared to suppress worm burdens when administered in a high single dose. A. absinthium extracts were subsequently administered to sheep infected with T. colubriformis.

Recent advances in sequencing technology and computing power mean that we are in an unprecedented position to analyse large viral sequence datasets using state-of-the-art methods, with the aim of better understanding pathogen evolution and epidemiology. This thesis concerns the evolutionary analysis of rapidly evolving RNA viruses, with a focus on avian influenza and the use of Bayesian methodologies which account for uncertainty in the evolutionary process. As avian influenza viruses present an epidemiological and economic threat on a global scale, knowledge of how they are circulating and evolving is of substantial public health importance. In the first part of this thesis I consider avian influenza viruses of haemagglutinin (HA) subtype H7 which, along with H5, is the only subtype for which highly pathogenic influenza has been found. I conduct a comprehensive phylogenetic analysis of available H7 HA sequences to reveal global evolutionary relationships, which can help to target influenza surveillance in birds and facilitate the early detection of potential pandemic strains. I provide evidence for the continued distinction between American and Eurasian sequences, and suggest that the most likely route for the introduction of highly pathogenic H5N1 avian influenza to North America would be through the smuggling of caged birds. I proceed to apply novel methods to better understand the evolution of avian influenza. Firstly, I use an extension of stochastic mutational mapping methods to estimate the dN/dS ratio of H7 HA on different neuraminidase (NA) subtype backgrounds. I find dN/dS to be higher on the N2 NA background than on N1, N3 or N7 NA backgrounds, due to differences in selective pressure. Secondly, I investigate reassortment, which generates novel influenza strains and precedes human influenza pandemics. The rate at which reassortment occurs has been difficult to assess, and I take a novel approach to quantifying reassortment across phylogenies using discrete trait mapping methods. I also use discrete trait mapping to investigate inter-subtype recombination in early HIV-1 in Kinshasa, the epicentre of the HIV-1 group M epidemic. In the final section of the thesis, I describe a method whereby epidemiological parameters may be inferred from viral sequence data isolated from different infected individuals in a population. To conclude, I discuss the findings of this thesis in the context of other evolutionary and epidemiological studies, suggest future directions for avian influenza research and highlight scenarios in which the methods described in this thesis might find further application.