This thesis considers the importance of adding stochasticity to models of optimal foraging behaviour. The problem is divided into two elements, risk and information, which are treated separately. Part One: Risk. The theoretical and empirical results concerning animal preferences in risky situations are reviewed. Animals are known to show both risk-averse and risk-prone preferences over food reward. It is shown, theoretically, that a simple optimality model mimimizing the probability of death due to starvation accounts for at least some of the observed patterns of preference. The model is generalized to consider preference from arbitrary combinations of mean and variance. Three limitations of the model are treated in detail, that is the importance of starvation by "ruin", mind-changing about risk preferences, and energetic carry-over are discussed. The implications and limitations of these models are outlined. Part Two: Information. The theoretical literature is reviewed, and the problem of information is divided into three elements. A simple model of environmental tracking is studied. The model suggests that there is a trade-off between sensitivity to change and the costs of sampling. The model is tested using great tits (Parus major) foraging in an aviary. The trend in sampling was as predicted, but the birds were less sensitive to change than predicted. The problem of patch sampling is critically discussed. The value of sampling is defined, and this definition is used to compare the assumptions of previous models. Three such problems are treated: the importance of variance in the mixing distribution of patch sub-types; the importance of alternative and unambiguous patch types; and the importance of patch depression. It is concluded that previous models have often over-valued sampling. A simple and natural model of partial patch recognition is considered, and is shown to have empirical support. Implications and limitations of these models of information are discussed.

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.

The mosquito Aedes polynesiensis, a member of the Aedes scutellaris complex, is the main vector in the South Pacific region of the Wuchereria bancrofti parasite, the causative agent of lymphatic filariasis (LF), and is also a major nuisance biter. Decades of Mass Drug treatment (MDA) have not been successful in elimination LF. Two non-vector species in the Ae. scutellaris complex were introgressed with Ae. polynesiensis to attempt to obtain lines that would produce cytoplasmic incompatibility (CI) with wild populations and/or LF-refractoriness. Despite selection of progeny from Brugia-challenged, non-infective females at each backcross, no refractory line was acquired. However, three lines from crosses between aposymbiotic Ae. polynesiensis and Ae. riversi displayed CI and male mating competiveness suitable for the purpose of population suppression using the incompatible insect technique (IIT). A population study was conducted of potential release sites and the evaluation of monitoring tools for Ae. polynesiensis on Moorea and Tetiaroa, French Polynesia. There was no evidence of active migration between selected islets on the atoll of Tetiaroa, suggesting it is a suitable site for field releases of CI males. The BioGents Sentinel trap was shown to be an efficient and convenient trap suitable for Ae. polynesiensis monitoring. The effects of temperature and larval density on life-table parameters relevant to IIT were examined, including: larval survivorship, developmental time to pupation, male to female ratio, male pupae yield, male size and adult male survival. These findings were used to design and conduct a 14-week field experiment testing CI male strain against an isolated population, using optimized rearing conditions. Approximately 8000 males were released weekly on motu Onetahi, Tetiaroa atoll. Significant sterility was induced by Wolbachia in the targeted female population, supporting the development and scale-up of this approach toward Ae. polynesiensis nuisance and LF transmission reduction.

Zum Erhalt vom Aussterben bedrohter Papageienvögel (Psittaciformes) ist die Nachzucht in Menschenobhut neben dem Erhalt freilebender Populationen von großer Bedeutung, die Reproduktion bestimmter Arten gelingt allerdings nur unzureichend. Als Hauptgrund dafür gilt die Zwangsverpaarung im Rahmen von Zuchtprogrammen (Beispiel: Europäisches Erhaltungszuchtprogramm, EEP), hier werden Brutpaare hauptsächlich nach genetischen Aspekten zusammengestellt. Der reproduktive Erfolg ist bei den meisten Papageienarten, die in dauerhaften Paarbindungen leben (perennial monogamy), eng der Paarbindung korreliert. Eine freie Partnerwahl ist demnach von großer Bedeutung für die Zucht in Menschenobhut, im Rahmen von Erhaltungszuchtprogrammen jedoch nur selten möglich. Das Ziel der Untersuchung war, eine wissenschaftlich begründete Methode zu entwickeln, durch die es möglich sein soll, das Fortpflanzungspotential von Brutpaaren der Gattung Ara anhand der Paarbindung zu bestimmen. Dafür wurde die Bedeutung der Qualität der Paarbindung der Brutpaare für den Lebens-Reproduktionserfolg (Lifetime-reproductive success, LRS) untersucht. Die Datenaufnahme erfolgte in dem Zuchtzentrum 'La Vera' der Loro Parque Fundación auf Teneriffa/ Spanien. Hier wurden in den Jahren 2006 und 2007 21 Brutpaare der Gattung Ara untersucht. Die Paarbindung wurde zum Einen durch typisches Paarbindungsverhalten und zum Anderen durch die physiologische Abstimmung der einzelnen Brutpaare anhand der Ausschüttung des Steroidhormons Testosteron dargestellt. Das Paarbindungsverhalten setzte sich aus der ‚Abstimmung der Tagesaktivität’, dem ‚Kontaktverhalten’ und den ‚sozialen Interaktionen’ zusammen. Zur Abstimmung der Tagesaktivität zählten die Verhaltensweisen Ruhen, Sitzen, Nahrungsaufnahme, Gefiederpflege, Beschäftigung und Lokomotion. Unter Kontaktverhalten wurden das Überschreiten der Individualdistanz bei bestimmten Verhaltensweisen und die Rollenverteilung der Geschlechter untersucht. Unter ‚sozialen Interaktionen’ wurden die Dauer und der Häufigkeit der sozialen Gefiederpflege und der Sozialen Index zusammengefasst. Bei der sozialen Gefiederpflege wurde die Dauer und die Häufigkeit der Phasen erhoben, sowie der jeweilige Initiator dieser Interaktion. Zusätzlich wurde untersucht, welches Geschlecht, wie häufig und mit welcher Dauer aktiv an der sozialen Gefiederpflege beteiligt war. Aus den Beobachtungen wurde der soziale Index berechnet, der angibt, wie das Verhältnis sozio-positiver zu agonistischen Interaktionen für jedes Individuum, sowie das Paar an sich ist. Zur Messung der Testosteron-Ausschüttung der Partnertiere wurden von September bis November 2007 über einen Zeitraum von 9 Wochen jede Woche einmal für jedes Individuum Kotproben gesammelt. Mit der Analyse der Proben wurde das Veterinär-Physiologisch-Chemische-Institut der Universität Leipzig unter der Leitung von Prof. Dr. Almuth Einspanier beauftragt. Zur Ermittlung des Hormongehalts in den gewonnenen Kotproben diente ein kompetitiver Doppelantikörper-Enzymimmunoassay (EIA). Das Fortpflanzungspotential wurde über die Anzahl der Eier, Gelege und Jungtiere, sowie über die Gelegegröße dargestellt. Diese Daten geben, bezogen auf die Dauer der Paarbindung, Auskunft über die Produktivität eines Brutpaares, anhand dessen zusätzlich ein Produktivitäts-Koeffizient berechnet wurde. Des weiteren sollte die Anzahl der von einem Brutpaar selbständig großgezogenen Jungtiere Auskunft über die Fähigkeit zur kooperativen Jungenaufzucht geben. Zur Untersuchung der Bedeutung der Paarbindungsqualität wurden Diskriminanzfunktionsanalysen und Regressionsanalysen durchgeführt, wozu die untersuchten Brutpaare anhand ihres Fortpflanzungspotentials in verschiedene Gruppen eingeteilt wurden. Anhand der Ergebnisse der Studie konnte gezeigt werden, dass das Fortpflanzungspotential von Brutpaaren von verschiedenen Kriterien, die die Paarbindungsqualität charakterisieren, abhängt. Dabei ist zwischen der Produktivität und der Fähigkeit zur kooperativen Jungenaufzucht zu unterscheiden. Die Produktivität eines Paares wurde hinsichtlich der abgestimmten Tagesaktivität positiv vom synchronen Ruhen mit dem Partner beeinflusst, sowie von der Häufigkeit und Dauer der vom Weibchen ausgehenden sozialen Gefiederpflege. Brutpaare mit hoher Produktivität waren zudem über eine hohe ‚intra-Paar Fluktuation’ des Steroidhormons Testosteron gekennzeichnet. Die Brutpaare, die in der Lage sind, ihre Jungtiere in Kooperation großzuziehen, zeigten ebenfalls einen hohen Anteil zeitlich mit dem Partner abgestimmter Ruhephasen, zudem häufiges Ruheverhalten in Körperkontakt zum Partner und ein hohes zeitliches Investment der Männchen bei der Initiierung und Durchführung sozialer Gefiederpflege. Darüber hinaus zeigten Männchen, die einen Beitrag zur kooperativen Jungenaufzucht leisten, eine wesentlich geringere durchschnittliche Testosteron-Konzentration – bezogen auf den Untersuchungszeitraum, als Männchen, die Brutpaaren angehören, die nicht zur selbständigen Jungenaufzucht fähig sind. Dieses Ergebnis spiegelt die Bedeutung von Testosteron bei der elterlichen Fürsorge wider und bietet einen Anhaltspunkt für weitere Untersuchungen. Die Untersuchung konnte zeigen, dass es möglich und sinnvoll ist, das individuelle Verhalten von Tieren in Menschenobhut für den Erhalt bedrohter Tierarten einzusetzen. Weitere, auf dieser Studie aufbauende Untersuchungen sollten zum Ziel haben, zuverlässig die Brutpaare erkennbar zu machen, die über ein gutes Fortpflanzungspotential verfügen. Auf diese Weise kann unzureichender Reproduktionserfolg bedrohter Papageienarten in Menschenobhut infolge von Zwangsverpaarung minimiert werden. / In addition to preserve wild populations, captive breeding of certain species is important for the conservation of endangered parrots (Psittaciformes). However, captive breeding of parrot species is rarely successful. The main reason for this failure is that forced pairings are applied under the context of breeding programs such as European Endangered Species Program, EEP, in which breeding pairs are primarily selected under genetic aspects. Bond quality affects the reproductive success of most perennial monogamous parrot species significantly. A free mate selection is therefore important for successful breeding in captivity; however, it is hard to achieve as a part of conservation breeding programs. The aim of this study is to develop a scientific method to determine the reproductive potential of breeding pairs of the genus Ara based on the pair bond. Therefore, the relationship of the pair bond quality in breeding pairs for lifetime reproductive success (LRS) is investigated in this study. The data of 21 breeding pairs was collected in the breeding facility 'La Vera' of the Loro Parque Fundación in Tenerife, Spain between 2006 and 2007. The pair bond was characterized firstly by the typical pair bonding behaviour and secondly by the physiological adaptation of each breeding pair based on the steroid hormone testosterone releases. The pair bonding behaviour consisted in ‘daily activity', ‘contact behaviour' and 'social interactions'. The ‘daily activity' included the behaviours: resting, sitting, eating, preening, activity and movement. Certain individual behaviours and gender roles were examined for the ‘contact behaviour'. The duration and frequency of social preening and the social index were summarized as 'social interactions'. In the social preening the duration and frequency of the phases was recorded, and the respective initiator of this interaction. In addition, gender of the individual, frequency, and duration of the social preening was recorded. Furthermore the social index was calculated, which indicates the relationship between agonistic and socio-positive interactions. To measure the testosterone release in the pair members over 9 weeks (September to November 2007), faecal samples were collected from each individual once a week. The faecal samples were analyzed at the Institute for Physiological Chemistry at the University of Leipzig under supervision of Prof. Dr. Almuth Einspanier. Competitive double-Antibody Enzyme Immunoassay (EIA) was applied to determine the testosteronecontent of the faecal samples. Reproductive success was represented by number of eggs, nests and chicks, and the clutch size. These data provide, based on the duration of the pair bond, information about the productivity of breeding pairs. Furthermore, the number of chicks reared by one breeding pair independently should provide information about the capacity for cooperative breeding. Breeding pairs were classified into different groups depending on their reproductive potential. This classification was verified by discriminant analysis and regression analysis to investigate the importance of the quality of the pair bond for reproductive success. I found that the reproductive potential of breeding pairs is related to various criteria that characterize the quality of a pair bond, but it is essential to distinguish between the productivity itself and the ability to cooperative breeding. The synchronous resting with a partner according to the daily activity, as well as the frequency and duration of social preening initiated by the female positively influenced the productivity of a pair. Breeding pairs with high productivity also showed a high ‚intra-pair fluctuation' of the steroid hormone testosterone level. The breeding pairs which are able to raise their young in cooperation also showed a high percentage of time with coordinated phases of resting, also frequent resting behaviour in physical contact with the partner and a high investment of males in the initiation and implementation of social preening. In addition, males, which actively contribute to cooperative breeding, showed significantly lower testosterone concentrations than males, which were members of breeding pairs not capable of raising chicks on its own. This result emphasizes the importance of testosterone during the parental care, especially in males, and provides a starting point for further investigations. My investigation shows that it is possible and useful to apply the individual behaviour of animals in captivity for the conservation of endangered species. Based on this study, further research should be aimed to expose reliable breeding pairs with good reproductive potential, by behaviour and by measuring hormonal states. In this way, poor reproductive success of endangered parrot species in captivity as a result of forced parings can be minimized.