This dissertation explores the experiential quality of zoological garden enclosures and the threshold between man and animal. This exploration manifests within the context of man’s act of demarcation represented in zoological gardens. The National Zoological Gardens in Pretoria situated on the periphery of the Central Business District form the proposed context of this study. The zoological gardens provide a platform to explore the ill-defined threshold between man and animal, the lack of experiential levels and the quality of the enclosures as habitat. The study investigates landscape design as a medium for design intervention to enhance the experience of zoo enclosures for both the visitor and animal. Through a methodological approach, the dissertation aims to establish design stratagems grounded in theory of landscape architecture, zoo design theory and case study review. The stratagems will serve as catalyst to challenge current zoo design principles in order to determine a new set of principles for landscape intervention. The design will follow a hypothetical process that implements the principles as spatial explorations, followed by pragmatic considerations. The outcome will demonstrate on a spatial and experiential level how landscape design can combine ecology and aesthetics to create a hybridised interactive experience with nature, animals and humans in a detail enclosure design. Technical and programmatic requirements will test and refine the final proposal of the enclosure design. / Dissertation (ML(Prof))--University of Pretoria, 2014. / Architecture / ML(Prof) / Unrestricted

The guiding principles of polytechnic education, as developed at the École Polytechnique in Paris from 1794, aimed at practical application and democratization. Accordingly, great value was attached to the practical experience of technology. At that time, it was possible to acquire these primarily through drawing exercises, demonstrations and experiments, as well as through geometric methods. In order to synthesize new technical means, it was supremely important to be able to determine from a drawing those connections that were both constructive and related to manufacturing technology. Therefore, the educational goals at the emerging polytechnic schools involved training spatial powers of imagination, conveying design thinking and encouraging precision skills. Such precision and reproducibility were required by the developing mechanized production in factories.

The subject of this dissertation is the Zoological Gardens of the Zoological Society of London (f. 1826) in the nineteenth century. Located in Regent s Park, it was the express purpose of the Gardens (f. 1828) to function as a testing-ground for acclimatisation and to demonstrate the scientific impor­tance of various animal species. The aim is to analyse what the Gardens signified as a recreational, educational and scientific institution in nineteenth-century London by considering them from four different perspectives: as a pan of a newly-founded society, as a part of the leisure culture of mid-Victorian London, as a medi­ator of popular zoology and as a constituent of the Zoological Society's scientific ambitions. After an introduction which describes the devlopment of European zoos, Chapter two recapitu­lates the early years of the Society and the Gardens. The original aims of the Society—science and acclimatisation located in a museum and zoological garden—as stated in various prospectuses, are examined. The implications of acclimatisation, it being a problematic practice, are outlined and the connections between acclimatisation, the Society, the Gardens and the British Empire are also briefly considered. The founding of the Gardens is extensively described as well as how the animals were obtained and how exhibits were arranged. Chapter three is based primarily on the popular response to the Gardens in the 1850s when, after a period of decline, the institution once again became a common London visiting-place. The most important questions of this chapter concern the public and how it reacted to the Gardens of this period. The financial problems preceding the five years between 1850 and 1855 ^ described as well as how the Society managed to regain its popularity. This process was closely linked to the decision in 1847to let non-members of the Society enter the Gardens, and the implications of this resolution are discussed. As a background to the Gardens' popularity, two other London recreations are also described: the Colosseum Panorama and the Surrey Zoological Garden. The Surrey Zoological Gar­den especially is interesting, as it was a rival of the Society's Gardens, and the different attractions of these establishments are considered. Chapter four focuses on the official and non-official guidebooks to the Gardens and the implica­tions of these as mediators of popular zoology. The historical and cultural connection between the guidebooks and travel handbooks is oudined and also how the genre as a whole is constructed. The progress and development of the Society's guidebooks during the nineteenth century is described and the differences between these guidebooks and the non-official ones are examined. Finally, with the aid of Victorian children's books, I argue that the guidebooks can literally be considered as travel handbooks since a visit to the Gardens may be regarded as a journey of knowledge. Chapter five is an in-depth study of the zoological science of the Gardens. The scientific work of the Society is briefly described, starting with the Committee of Science and Correspondence, and the Proceedings of the Zoological Society of London. The Proceedings reports that base their findings on animals in the Gardens are then described together with minor detours into the history of taxonomy and morphology. / digitalisering@umu

The trophy hunting of African leopards Panthera pardus pardus may generate revenue to help foster their conservation. However, leopards are sensitive to hunting and populations decline if overharvested. The practice therefore requires careful management grounded in robust estimates of population density/status. Camera-trap surveys are commonly used to establish leopard numbers, and may guide harvest quotas. However, such surveys are limited over wide spatial scales and many African governments lack resources to implement them. In this thesis I explore the potential use of a harvest composition scheme applied to puma Puma concolor in North America, to monitor leopards. The method hinges on the susceptibility of different leopard cohorts to hunting and if this varies, then predictions can be made about harvest composition. Susceptibility is likely to be governed by space use, encounter rates with bait lures (a common method used to attract leopards to hunting hides) and hunter selectivity. Thus in this thesis I explore leopard susceptibility to these factors using a protected leopard population in northern Zululand, South Africa. In my first chapter I examine using scent lures in camera-trapping. Against a backdrop of a passive survey I show adult males, females and sub-adults are captured at similar rates compared to a passive survey using lures. The use of lures does not appear to violate closure assumptions or affect spatio-temporal patterning, but their use appears limited as density estimate precision is not improved. My second chapter examines ecological (likelihood of encountering a hunter) and anthropogenic (attractiveness to hunters) susceptibility of leopards to trophy hunting. I show that adult males are the most susceptible cohort to hunting (sub-adults least susceptible). I then take the incident rates from ecological and anthropogenic models and create a theoretical harvest composition using population parameters of protected leopards. My third data chapter departs from hunting susceptibility and examines determinants of leopard trophy package price across Africa. I show that factors such as trophy quality, outfitter leopard hunting reputation and hunt success have little impact on price determination. Instead, overall outfitter reputation and the number of charismatic species in a package are positively correlated with price. These results have important consequences on several sustainable leopard hunting schemes proposed in the literature.

This thesis focuses on conflict resolution and collective decision-making in co-navigating pigeons, Columba livia. These birds have a remarkable homing ability and frequently fly in flocks. Group navigation demands that group members reach consensus on which path to follow, but the mechanisms by which they do so remain largely unexplored. Pigeons are particularly suitable for studying these mechanisms, due to their sociality and the fact that their possession of information can easily be altered and quantified. I present the results of a series of experiments that manipulated the experience of homing pigeons in various ways so as to observe the effect of information they had previously gathered on their group behaviour. Key findings were: Previous navigational experience contributes to the establishment of leader-follower relationships. The larger the difference in experience between two co-navigating pigeons, the higher the likelihood the more experienced bird will emerge as leader. Shared homing experience through repeated joint flights can allow two pigeons to develop into a “behavioural unit”. They form spatial sub-groups when flying with less familiar birds, and perform a similar transition between compromise- and leadership-dominated flights as single birds, although they are more likely to accept compromise routes. Such previous association histories between birds can thus affect collective decision-making in larger flocks. There is a trade-off between the amount of spatial information handled and the efficiency with which such information can be applied during homing. Leading/following behaviour is influenced by the recency of the route memories. Leadership hierarchies in pigeon flocks appear resistant to changes in the navigational knowledge of a subset of their members, at least when these changes are relatively small in magnitude. The stability of the hierarchical structure might be beneficial during decision-making. Mathematical modelling suggests that underlying hierarchical social structures can increase navigational accuracy. Hierarchically organised groups with the smallest number of strong connections achieve highest accuracy. Group leader-follower dynamics resemble the underlying social structure.

The study of social evolution and virulence in parasites is concerned with fitness consequences of trade-offs between parasite life history traits and interactions between parasite species and/or genotypes with their hosts. I develop our understanding of social evolution and virulence in parasites in several ways. (1) I review empirical evidence for the fundamental predictions of virulence-transmission trade-off theory and demonstrate that the fit between theory and data is primarily qualitative rather than quantitative; that parasites differ in their degree of host generalism, and this is likely to impact virulence in four ways. (2) I take a comparative approach to examine the underlying causes of an observed statistical variation in the size of parasite infectious doses across taxa, revealing that mechanisms used by parasites to infect hosts are able to explain variation in both infectious dose and virulence. (3) I formally compare data on human pathogens to explain variation in virulence across taxa, revealing that immune subversion and not growth rate, explains variation in virulence. This allows me to predict that immune subverters and not fast growing parasites are likely to cause the most virulent clinical infections. (4) Using bacteria and their naturally infecting viruses (bacteriophage), I take an experimental approach to investigate the consequences of coinfection for parasite life history traits, and find that viruses cultured under a mix of single infections and coinfections evolved plasticity; they killed hosts more rapidly when coinfecting, and this resulted in high fitness under both single infection and coinfection conditions. (5) I experimentally investigate how selection within and between hosts and patches of hosts affects the fitness and virulence of populations of these viruses. I find that limited host availability favours virulent, faster killing parasites with reduced transmission; suggesting high, rather than low, virulence may be common in spatially structured host-parasite communities.

Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen responsible for >1.6 million annual deaths globally. Pneumococcal penicillin-resistance is conferred by acquisition of ‘altered’ penicillin-binding protein (pbp) genes. The first penicillin-nonsusceptible pneumococci were identified in the late 1960s. Global pneumococcal penicillin-nonsusceptibility rates rapidly increased in the 1980s/90s. Since 2000, protein-conjugate vaccines, targeting 7, 10 or 13 of the ≥94 different pneumococcal capsule types (serotypes), have been introduced in many countries. Following vaccine implementation there has been a decline in vaccine-type pneumococcal disease and an increase in non-vaccine-type disease. These epidemiological changes result from “serotype replacement” and/or “serotype switching”. The former describes the expansion of non-vaccine-type clones in the absence of vaccine-type pneumococci. The latter describes serotype change following recombination at the capsule polysaccharide synthesis (cps) locus. To fully understand how pneumococci respond to vaccine- and antibiotic-induced selective pressures, we must better understand the evolutionary history of this pathogen. This thesis describes the study of a global collection of 426 pneumococci, dated 1937 - 2007. Serotype, genotype and penicillin-susceptibility data were collected. Nucleotide sequences of three pbp genes (for 389 isolates) and whole-genome sequences (for 96 isolates) were also generated. The data demonstrated the long-term persistence of certain clones within pneumococcal populations, and that pbp and large-fragment (>30 kb) cps ± pbp recombination was occurring prior to both widespread antibiotic use and vaccine implementation. The data highlighted the promiscuous nature of the globally-distributed PMEN1 clone and its contribution to the spread of pneumococcal penicillin-resistance. PMEN1 also donated multiple, large regions (1.7 - 32.3 kb) of its genome to at least two un-related clones. Finally, six “Tn916-like” genetic elements, conferring resistance to non-penicillin antibiotics, were newly identified. These included two of the oldest ever described. These results provided a unique insight into the history of pneumococcal evolution and the importance of genetic recombination.

Silks are biomaterials made by spiders and silkworms, evolved for natural functions ranging from protection to predation. The research presented in this Thesis combines principles and methods from engineering, physics and biology to study the material properties of single silk fibres from a biological perspective. In particular, the factors that contribute to the variation in properties of single silk fibres are investigated. The first part of the Thesis focuses on silks made by silkworms. Whether naturally spun or forced reeled, the mechanical properties of these silks are sensitive to a range of environmental and processing conditions, such as humidity, stretching and reeling speed. The research presented in this section contributes to the understanding of how these applied conditions affect silk mechanical properties, which can be understood in terms of silk’s protein structure and biological context. The second section compares both silkworm and spider silk single fibres to other materials in terms of their sonic properties – how the materials propagate sound waves, whether following impact, or propagating vibrations. The results are discussed in the context of the silk’s natural function for impact resistance (silkworm cocoon or spider web) and vibrational signalling (spider silks). The Thesis ends with a discussion of how the presented techniques can be applied to help further our understanding of orb web function through studying spider silks. Overall, this interdisciplinary Thesis contributes to our understanding of the structure-property-function links of these fascinating biomaterials.

This thesis explores the potential of new substrates for ancient DNA studies and addresses novel questions that can now be asked. It also highlights an additional use of ancient DNA extracted from a traditional source.

Centrioles and basal bodies with their characteristic 9+2 structure are found in all major eukaryotic lineages. The correlation between the occurrence of centrioles and the presence of cilia/flagella, but not centrosome-like structures, suggests that the ciliogenesis function of centrioles is ancestral. Here, it is demonstrated that the centriole domain of centrosomes emerged within the Metazoa from an ancestral state of possessing a centriole with basal body function but no functional association with a centrosome. Centrosome structures involving a centriole are metazoan innovations. When an axoneme is still present but no longer fully functional, such as the sensory cilia of Caenorhabditis elegans or, as depicted here, the flagellum of the intracellular amastigote stage of the Leishmania mexicana parasite, the basal body structure is less constrained and can depart from the canonical structure. A general view has emerged that classifies axonemes into canonical motile 9+2 and noncanonical, sensory 9+0 structures. This study reveals this view to be overly simplistic, and additional axonemal architectures associated with potential sensory structures should be incorporated into prevailing models. Here, a striking similarity between the axoneme structure of Leishmania amastigotes and vertebrate primary cilia is revealed. This striking conservation of ciliary structure, despite the evolutionary distance between Leishmania and mammalian cells, suggests a sensory function for the amastigote flagellum. Adding weight to a sensory hypothesis, close examination of Leishmania positioning inside the parasitophorous vacuole revealed frequent contact between the flagellum tip and the vacuole membrane. A sensory function could also explain the retention of a flagellum in Trypanosoma cruzi amastigotes, an intracellular stage that, as shown in this study, emerged independently to the Leishmania amastigote. Basal body appendages, such as pro-basal bodies and microtubule rootlets, also vary widely in their structure. Choanoflagellates, a sister group to the Metazoa, posses an extensive microtubule rootlet system that provides support for their characteristic collar tentacles. This atypical structure is reflected in the underlying molecular components of the choanoflagellate basal body. The importance of choanoflagellates as the closest known relative of metazoans was first revealed by their similarity to choanocytes, the feeding cells of sponges. Although phylogenetic analyses leave little doubt that choanoflagellates are a sister group of animals, comparisons of molecular and structural components of appendages associated with the collar tentacles highlight significant differences and questions the extent to which the collar structures of choanoflagellates and choanocytes can be assumed to be homologous. Finally, the confinement of a centriole-based centrosome to the Metazoa provides little support for the flagellar synthesis constraint as an explanation for the origin of multicellularity. There is, indeed, an apparent constraint; no flagellated or ciliated metazoan cell ever divides. This constraint, however, did not arise until after the incorporation of centrioles into the centrosome in the metazoan lineage and the co-option of centrioles as a structural and functional component of the centrosome. The flagellar synthesis constraint is therefore not an explanation for the origin of multicellularity but a consequence of it.