Phytoplankton aggregations come in a wide range of space and time scales and, as such, simulating such behavior is computationally restrictive. I present a Large-eddy simulation of the upper mixed layer, resolving scales of o(1m). I then show how aggregations are promoted by nutrient upwellings (something which macroscale models struggle to emulate), facilitated primarily by Langmuir circulations. I then demonstrate how certain levels of turbulent mixing encourage planktonic thin layering, a phenomenon which is widely observed.

This thesis aims to improve our understanding of the macroevolutionary implications of antipredator defences, particularly with regard to how defence impacts biodiversity (including both species and trait diversity). To do this I took a phylogenetic comparative approach and used multiple study systems in an attempt to ensure the generality of my work. I begin by investigating how chemical defence and protective coloration influence ecology by testing for life history and ecological correlates of these defences (Chapter 1). Upon finding evidence for an increased niche space in chemically-defended species, and to some degree in conspicuously-patterned species, I explore whether this leads to increased diversification by increasing speciation rates and/or lowering extinction rates (Chapter 2), as also predicted by escape-and-radiate theory (a major and highly influential framework for the macroevolution of natural enemy interactions). Both conspicuous coloration and chemical defence increased speciation rates, but extinction rates were also raised in chemically-defended lineages, leading to a reduction in net diversification. Macroevolutionary extinction rates may or may not be related to contemporary extinction risk, but if they are then there may be conservation implications by allowing prediction of threat status of species with limited direct information. Consequently, in Chapter 3 I asked whether chemically-defended species are more threatened than those lacking such a defence. In accordance with the macroevolutionary results from Chapter 2, I found that chemical defence is indeed associated with a higher extinction risk even amongst contemporary species. In addition to factors that promote diversity, in this thesis I also investigated convergent evolution as a means of constraining diversity of phenotypic traits, using mimicry as a case study for antipredator defences. Many antipredator defences are convergent to some degree, with examples in the repeated evolution of chemical defences and warning coloration as well as independently derived similarity in protective mimicry. However, methods of quantifying the strength of convergent evolution are lacking, not to mention a conceptual framework to define 'strength' in this context, I began by developing a new method to do this which I called the Wheatsheaf index (Chapter 4). Subsequently, I (in collaboration with a colleague, Amanda Minter) also designed software in the form of an R package (called 'windex') to enable user-friendly implementation of the Wheatsheaf index in a familiar statistical environment to many biologists (Chapter 5). In the final data chapter of this thesis, I apply this method in a case study to explore the patterns of phenotypic convergence that result from the evolution of Batesian and Müllerian mimicry complexes. I find that these two types of protective mimicry are generally characterised by convergence in different broad types of traits, but that the specific traits which converge in a given mimicry complex are less predictable (Chapter 6). Overall, this thesis provides novel insights into the evolutionary patterns and consequences of antipredator defences, develops a framework and methods for the analysis of convergent evolution, and suggests further avenues of research for future studies.

There is increasing concern about the adverse effects of the road network on wildlife. The impacts of roads in the ecological landscape include habitat loss, habitat fragmentation and habitat degradation. These interrupt and modify natural processes, altering community structures and population dynamics. The large number of animal fatalities from road traffic accidents is also of concern. Only limited work has been carried out to investigate the intensity of these effects in the UK landscape. This study investigates the effects of roads on both small and large mammals and reviews mitigation measures that have been installed to ameliorate some of these effects. Roads of all sizes present a significant barrier to animal movement and they affect it in specific ways. Movement of small mammals is inhibited by lack of cover and the hostile road surface, whilst fragmentation of the road-verge by highway-related structures, impedes dispersal and compromises the benefits of connectivity often ascribed to such areas. Large animals, which use roads to travel through their territory, are more likely to be struck by traffic and are therefore, more directly affected by traffic-intensity. There is room for further mitigation to reduce the worst of the road-related impacts.

The Middle Ordovician to Late Silurian represents an interval of approximately 50 million years, which has been recognised as the initial, cryptic, period in the evolutionary history of chondrichthyan fish. The fossil remains attributed to early chondrichthyans are dominated by isolated dermal scales that predate the appearance of undisputed chondrichthyan teeth and articulated skeletons in the Lower Devonian. Investigation of the inter-relationships of these scale taxa and their systematic position relative to high- ranked chondrichthyan clades has been hampered by the lack of developed scale-based classification schemes for jawed gnathostomes, coupled with the limited use of scale characters in phylogenetic studies of Palaeozoic Chondrichthyes. Here, all previously documented scale types of alleged Lower Palaeozoic chondrichthyans were examined using a combination of X-ray microtomography, SEM and Nomarski DIC optics. These were found to exhibit a set of characteristics (symmetrical trunk scales, areal crown growth and lack of hard-tissue resorption, cancellous bone and enamel) recognised as specific to the dermal skeleton of chondrichthyans among derived gnathostomes. The collected data permitted the establishment of a hierarchy of scale characters for separate taxonomic ranks, leading to the recognition of three Orders (Mongolepidida, Elegestolepida ordo nov. and Altholepida ordo nov.) of early chondrichthyans, differentiated by distinct types of scale-crown morphogenesis. A scale-based cladistic analysis of jawed gnathostomes corroborated these results by recovering a chondrichthyan clade that incorporates all examined taxa and ‘acanthodians’ with non-superpositional crown growth patterns. It is thus proposed that chondrichthyan dermoskeletal characters carry a phylogenetic signal, allowing to interpret the documented diverse types of scale morphogenesis as evidence for a major radiation of chondrichthyan lineages in the Lower Palaeozoic.

The eggshells of many avian species are spotted in appearance but the functional significance of such maculation is poorly understood. Protoporphyrin, responsible for brownish-red colouring on eggshells, is postulated to reinforce the structural integrity of eggshells under conditions when dietary calcium (Ca) is scarce. Within the context of this hypothesis, this thesis documents the use of Ca supplementation of two common British passerine species, blue (Cyanistes caeruleus) and great tits (Parus major), to explore the relationships between eggshell Ca and protoporphyrin content and visible pigment spotting. It further assesses the diversity of avian eggshell coloration using museum eggshells of 73 British passerine species. Despite low soil Ca availability, females were not necessarily Ca-limited but Ca-supplements may still influence eggshell traits and breeding behaviour, possibly by providing females with more time to invest in other activities. The importance of quantifying eggshell pigment concentrations directly, rather than using a proxy, is highlighted. Finally, this thesis shows that passerine eggshell pigment concentrations are highly phylogenetically conserved, thereby encouraging future studies testing key hypotheses to compare eggshell pigmentation of closely related species. This phylogenetic association may be essential to explain the functional significance of eggshell coloration of avian species.

Dramatic loss of biodiversity in the last two decades has been associated with human activities. Yet, we understand little of the mechanisms that enable species persistence to anthropogenic environmental changes over evolutionary time. Here, we measured ecological and evolutionary responses of a population of Daphnia magna to multiple anthropogenic stressors over evolutionary time, and assessed the role of historical exposure in adaptive response to recurring environmental stress. D. magna is a keystone grazer in freshwater standing waters and a driver of ecosystem dynamics. As part of its life cycle, Daphnia produces dormant embryos that arrest their development entering dormancy and creating a long-term documentation of evolutionary responses to environmental change. Resurrected dormant stages are maintained as clonal lines in the laboratory, providing us with the unique opportunity of disentangling the role of phenotypic plasticity and genetic adaptation in population responses to environmental stress. We studied phenotypic, physiological, and molecular responses that enabled a population of D. magna to persist across major pollution events. We found that adaptive responses to multiple environmental stressors are not predictable from the responses to single stressors. We also discovered that historical exposure to stress prior to dormancy provides an evolutionary advantage when the stress recurs. However, this advantage is contingent upon the type and severity of environmental stressor. We discovered that response to environmental stress is underpinned by extensive epistasis and pleiotropy, suggesting that standing genetic variation is the clay of evolution in this species.

Avian eggshell colouration fulfills multiple adaptive functions, including egg camouflage. The potential role of the two main eggshell pigments in oxidative stress, biliverdin and protoporphyrin, may be behind a relationship between female immunocompetence and eggshell pigment investment strategies. In this study, environmental conditions were manipulated during different life cycle stages, via a variety of methods, including food-restriction and stress hormone exposure in female Japanese quails (Coturnix coturnix japonica), in order to experimentally test the condition-dependence of eggshell pigmentation, and to give first insights into the possible implications for egg crypsis. I demonstrated that eggshell pigmentation strategy is not only affected by female current body condition, but is also shaped by its early life experience such as exposure to stress, and that eggshell colouration is a key factor involved in egg crypsis in Japanese quail. Eggshell colour and maculation were both independently affected by breeding conditions; which stresses the complexity of the relationship between eggshell pigment concentrations and its appearance. My findings imply that eggshell appearance is a female extended phenotypic trait, and that trade-offs between eggshell pigmentation and immune-functions may lead to inter-females differences in their ability to maximise egg crypsis.

Comparison of seven isolates of rust from leek (Allium porrum), three from chives (Allium schoenoprasum), one from A. scorodoprasum and one from A. babingtonii on the basis of telial and uredinial morphology showed there to be three morphologically distinct species. Application of these criteria to herbarium material confirmed these findings and showed the rust on leeks in the U.K. to be the same species found on European leeks, garlic and certain wild Allium spp. from the Mediterranean. It is suggested that the following names be adopted, viz. Puccinia allii (DC.) Rud. for the rust on leeks, Puccinia mixta Fuck. for the rust on chives and Uromyces ambiguus (DC) Lev. for the rust on A. babingtonii. Infection studies on isolates of each rust supported the morphological evidence, and showed the three species to have different, extensive but overlapping host ranges within the genus Allium. In the ampeloprasum complex, A. kurrat accessions were highly susceptible to leek rust whereas some accessions of A. ampeloprasum and A. babingtonii had high levels of quantitative resistance. There was no evidence of 'hypersensitive-type' resistance in the complex. Tests within one leek cultivar (Musselburgh) showed older plants to be more resistant than seedlings in at least two quantitative components. However leaf tissue appeared to become more susceptible to infection with age, except in the leaf tips, which did not change in susceptibility over time. Inoculation of 16 leek cultivars with leek rust isolates from different geographical areas, and subsequent analysis during the disease cycle of several components of resistance (viz; latent period, pustule density and pustule length) showed that some cultivars performed consistently better against all isolates. However, in most cases there was a considerable and complex cultivar-isolate-component interaction. There was no evidence of physiologic specialisation in the isolates, but low levels of specialisation could have been hidden by the high level of variation in the experiments. Comparison of field cultivars of garlic with equivalent virus-free material using an isolate of leek rust gave inconclusive results, and further study of the rust-garlic-virus interaction is recommended. Major trends in the infection/resistance studies included a high level of environmentally-dependent variation and a lack of 'hypersensitive-type' resistance, even in host species quite distantly related to the normal host.

Supplementary feeding wild birds is a widespread phenomenon. Recently, non-governmental organisations have recommended that the bird-feeding public should feed wild birds throughout the breeding season. Currently, such recommendations are not supported by a large body of research findings to suggest that food supplementation has benefits for breeding birds. To investigate this further I provided two commercially available wild bird foods (peanut cake and mealworms [Tenebrio molitor]) to Blue Tits (Cyanistes caeruleus) and Great Tits (Parus major) breeding in a woodland in Central England from 2007 to 2009. Supplementary feeding significantly advanced nest construction and decreased brood provisioning rates for both species. Supplemented Blue Tits significantly decreased daily incubation activity and increased both the proportion of extra-pair young and proportion of males per brood while supplemented Great Tits decreased incubation recess lengths. Analyses of data from the British Trust for Ornithology’s Nest Record Scheme suggested that probable widespread supplementary feeding of both Blue and Great Tits in urban habitats from 1962 to 2008 influenced breeding parameters across the study period but measuring food availability across wide spatial scales remains problematic. I discuss the implications of my results within an urban garden bird feeding context and provide suggestions for future research.

Trilobites from the Ludlow and Přídolí of England and Wales are described. A total of 15 families; 36 genera and 53 species are documented herein, including a new genus and seventeen new species; fourteen of which remain under open nomenclature. Most of the trilobites in the British late Silurian are restricted to the shelf, and predominantly occur in the Elton, Bringewood, Leintwardine, and Whitcliffe groups of Wales and the Welsh Borderland. The Elton to Whitcliffe groups represent a shallowing upwards sequence overall; each is characterised by a distinct lithofacies and fauna. The trilobites and brachiopods of the Coldwell Formation of the Lake District Basin are documented, and are comparable with faunas in the Swedish Colonus Shale and the Mottled Mudstones of North Wales. Ludlow trilobite associations, containing commonly co-occurring trilobite taxa, are defined for each palaeoenvironment. Trilobites in the British Přídolí are too rare and sporadic to systematize them into distinct associations. A preliminary study on the global diversity of Silurian trilobites is presented also. A total of six trilobite bioevents are recognised for the Silurian occurring in the argenteus-leptotheca, sedgwickii, centrifugus-murchisoni, nilssoni, formosus, and bouceki-transgrediens graptolite biozones, characterised by elevated extinction rates.