There are an overwhelming number of biodiversity indices and indicators available for ecologists and conservationists to use when seeking to understand how biodiversity responds to human disturbance. In choosing between measures there is often an underlying assumption that if a measure works well for one group it will be equally applicable to another. In this study, I use multiple taxa to explore the performance of a wide range of alpha and beta diversity measures for studying biodiversity responses to human disturbance in tropical forest. I sampled 18 sites along a gradient of human disturbance from primary tropical forest to banana monocultures in Peru. I chose three taxonomic groups and one audio approach, which have all been suggested to be useful indicators for studying biodiversity responses to disturbance: orchid bees (n = 1783), dung beetles (n = 3787), butterflies (n = 2506) and soundscape samples (n = 6600). This allowed me to identify how these groups responded to disturbance, which diversity measures were most sensitive for detecting those changes and whether the same measures were suitable for all groups. I used Hill numbers to measure alpha diversity and explored beta diversity by looking at changes in community composition and two new measures of beta diversity: redundancy and representativeness. To see how the diversity patterns changed when taxonomic similarity was considered, I used a recently developed family of similarity-sensitive diversity measures and compared the results of these against more traditional measures. I found that the diversity indices that were best for detecting disturbance patterns varied widely among taxonomic groups. For dung beetles, species richness and community composition were the most effective measures, whereas these performed poorly for orchid bees. Abundance and redundancy were more sensitive for detecting a response to disturbance in orchid bees. Using the butterfly dataset, I show that the inclusion of species similarity completely changed the diversity patterns found across the disturbance gradient. The similarity of species present in a community is likely to be important for the preservation of evolutionary adaptability and the provision of ecosystem functions and I therefore suggest that diversity measures based on similarity will be a useful additional tool for conservation and impact assessments. Acoustic diversity showed unintuitive responses to disturbance, with higher diversity detected in more disturbed forest, and more research is required to assess the performance of different acoustic indices in rainforest environments. Overall, my results demonstrate the importance of choosing diversity indices carefully to suit the taxa being studied to avoid missing important ecological responses, including a consideration of species similarity. I recommend that, where possible, multiple diversity indices and taxonomic groups should be used to reduce this risk and provide a comprehensive understanding of ecosystem patterns in response to environmental change.

This study reviews and evaluates the current status of management planning and policy in Protected Areas (PAs) in Bangladesh via a case study of two Wildlife Sanctuaries and one National Park. Using a mixed method approach, the research evaluates the perceptions and attitudes of local residents and other stakeholders towards the effectiveness of protected area planning and management, specifically co-management plans for the case study areas. The research was based on semi-structured and in-depth interviews with key informants, focus group discussions, and questionnaire surveys of village residents. The study revealed a complex socio-economic context characterised by poverty; within this, a diverse range of stakeholders exist whose interests in, and perceptions of, protected area management do not necessarily coincide with those of the Forest Department officials, leading to situations of conflict and difficulty for the Forest Department in enforcing the law over areas of forest in Bangladesh, a situation that has not been helped by the limited availability of manpower and modern equipment. It is concluded that the co-management approach, by taking into account the interests, wishes, and aspirations of the local communities, holds out better prospects of protecting the forest, meeting the objectives of the protected area management plans, and development ambitions of local communities. However, the findings suggest that community participation needs to be improved if effective forms of co-management are to be achieved, in turn improving the chances of conserving the forest for future generations while permitting the present generation to pursue sustainable livelihoods. Based on this study, it is clear that not only is action required to increase the participation of the local community, but human resource development is required to produce parallel institutional capacity building within the Forest Department. Moreover, programmes designed to support the generation of alternative livelihood opportunities are required to reduce dependency on forest resources. All of these lines of development are essential to increase the capacity of the local communities and officials to work together to develop and implement the management objectives of the National Parks and Wildlife Sanctuaries. However, without genuine political will to act it will be difficult to achieve the aforementioned ambitions/objectives.

Understanding the origin of biodiversity is a central question in evolutionary biology. Ecological specialisation, including the repeated rapid and parallel evolution of ecological specialists (‘ecotypes’), is a major source of biodiversity. The parallel evolution of ecotypes in salmonid fishes, such as Arctic charr, brown trout and European whitefish, has resulted in extensive diversity in northern postglacial freshwater ecosystems. Despite their ecological diversity and importance for northern ecosystems, the knowledge on the genetic basis of ecological specialisation, the evolutionary history of adaptive divergence, and the factors shaping the underlying genetic architecture are still not well understood in salmonids. Over the last decade many studies have investigated the genetic basis of ecologically relevant phenotypic traits in a wide range of salmonid species using genetic mapping approaches. However, knowledge on the conservation of the genetic basis for particular traits, or suits of traits, across species is limited, mainly due to a lack of genomic resources. Similarly, little is known about the genomic architecture of phenotypic diversity within species, such as the organisation of species-specific quantitative trait loci across the genome and the frequency of potential pleiotropy or genetic linkage. To understand how conserved the genomic basis for particular traits is across species and how quantitative trait loci (QTL) are organised within the genome, we analysed the genetic basis for a wide range of phenotypic traits (N=18) in six salmonid species using a dataset comprising of 943 QTL markers. We developed a novel analytical approach to analyse the colocalisation and synteny of QTL within and across species using a hetero-specific reference genome, in this case the Atlantic salmon (Salmo salar) genome. We found that QTL were not randomly distributed across the genome and that gene-density determined the distribution of QTL across chromosomes. By comparing QTL across species, we further identified genomic regions that were enriched for QTL for morphological and physiological traits (synteny blocks) in a range of species. Within three of the species, we also detected the significant colocalisation of QTL for different traits. Overall, the detection of synteny blocks and colocalised traits suggests a small but detectable role of pleiotropy and genetic linkage in trait evolution in salmonids and a conserved genetic basis for some traits across species. However, the observed patterns of conserved genetic basis and colocalisation were relatively weak, as QTL were mostly not conserved across species or colocalised within species. In general, the repeated evolution of similar ecotypes across populations and species implies a certain predictability of evolution. However, it is not well understood how phenotypic evolution overcomes the contingencies of heterogeneous genomic backgrounds of natural populations. To investigate the repeatability and predictability of parallel evolution, we used eco-morphological, genome-wide SNP and transcriptome data within and across lakes and evolutionary lineages of Arctic charr (Salvelinus alpinus). We found significant parallelism across replicated ecological specialists in foraging-associated traits. This phenotypic parallelism evolved despite population-specific variation in demographic histories, varying genomic response to selection and the non-parallel genetic basis of ecotype divergence. However, the regulatory molecular basis of ecological specialisation, inferred from gene expression and biological pathways, was highly parallel across ecotypes, bridging non-parallel genomic patterns and parallel eco-morphology. These findings suggest that parallel phenotypic evolution is possible despite non-parallel evolutionary routes when the functional molecular basis of ecological specialisation compensates for non-parallel genomic basis and histories. Evolutionary and genomic contingencies, such as demographic histories and genomic features can strongly influence the genomic architecture of adaptive divergence and reproductive isolation. To investigate how genomic features and demographic history influence the genetic architecture of adaptation and reproductive isolation, we reconstructed the demographic history and analysed the genetic architecture of divergence in brown trout (Salmo trutta) from the Maree Catchment in Scotland. Brown trout display reproductively isolated and divergent life histories and ecological specialisation, including a large piscivorous life-history form (ferox trout) and a smaller benthivorous life-history form. We found that ferox trout and benthivorous brown trout most likely diverged under a secondary contact of at least two distinct postglacial lineages and identified 33 genomic islands across the genome differentiating life-history forms. We demonstrated that some of these genomic islands formed under selection, and contained genes and biological pathways related to growth, development and immune response. Overall, we found strong genomic signals of divergence that were partially driven by selection on divergent phenotypes, and not only caused by genetic drift or through underlying genomic features, such as reduced recombination. The identification of the underlying evolutionary history and genetic architecture highlights the strength of genomic studies using species pairs for understanding the driving factors of adaptive divergence and reproductive isolation. Despite extensive knowledge on the genomic mechanisms underlying adaptive divergence over longer time scales and under the influence of phases of geographic isolation, less is known about the mechanisms underlying rapid ecological and phenotypic divergence. Rapid evolution plays an important role in the adaptation of species to human-induced environmental changes. However, it has been shown that in some cases human-driven environmental changes can lead to rapid loss of species and functional diversity, e.g. through species collapse and hybridization. Even though theoretical models predict that species can rapidly re-diverge under the right conditions following a species collapse and hybridization, the underlying mechanisms of rapid re-divergence remain to be elucidated. Empirical evidence for re-divergence following a species collapse is also lacking. We found evidence for the rapid evolution of ecologically-relevant phenotypic diversity in a European whitefish subspecies from Lake Constance, the gangfisch (Coregonus lavaretus macrophthalmus) after the recovery of pristine ecosystem conditions, following human-driven eutrophication, and speciation reversal. We found that a key functional trait, gill raker number, rapidly diversified within less than 10 generations following ecosystem recovery, allowing the use of vacant trophic niches. Variation in gill raker number is controlled by a sparse genetic architecture, as predicted by theory, and we further found evidence suggesting that introgression potentially provided the underlying adaptive variants. Several biological pathways that are known to be involved to ecological specialisation in fishes, such as metabolism, immune response and neural development, were identified based on coexpressed gene modules and genes under selection associated with gill raker number. Overall, our results demonstrate that functional diversity can rapidly re-emerge, given the right combination of genetic architecture, genetic diversity, and selection. In summary, this thesis demonstrates the evolutionary and genomic routes underlying phenotypic evolution and ecological specialisation in salmonid fishes. Comparing across different study systems, we find that secondary contact and historical gene flow played an important role in the evolution of salmonid species. Despite strong variation in the genomic basis of phenotypic traits across species and the genomic patterns of divergence across populations within species, we find some molecular parallelism across populations and species. Parallel ecotypes most likely evolved through parallel regulatory evolution and involvement of similar functional biological pathways. Furthermore, we find biological pathways that are repeatedly involved in adaptive divergence in different species. / Overall, our results indicate that despite the flexibility of rapid and parallel phenotypic evolution on the genomic level, it is relatively conserved on the level of regulatory mechanisms and functional biological pathways.

No description available.

Biological systems involve features/behaviours of individuals and populations that are influenced by a multitude of factors. To explore the dynamics of such systems, a statistical description offers the possibility of testing hypotheses, drawing predictions and more generally, assessing our understanding. In the work presented, I analyse the properties of various biological systems of two very different organisms: Pharaoh‟s ants (Monomorium pharaonis) and badgers (Meles meles). The basis of the work, in the two projects on these biological systems, relies heavily on data collection and explaining observations using quantitative methods such as statistical analysis and simulations. In the first part of this thesis, I describe animal movement in space and time using data collected on the foraging behaviour of ants. A new model is presented which appears to reflect, with a high degree of accuracy, the behaviour of real organisms. This model constitutes the basis of the second chapter in which the qualities of searching strategies are explored in the context of optimal foraging. The final chapter of first part of this thesis concludes with a detailed analysis of the rate of exploration of individuals. As an essential part of foraging, the rate of individuals leaving their nest is analysed using collected data, and contrasted with results derived from a mathematical model. The second part of this thesis focuses on badgers. A first chapter explores the significance of palate maculation that is observed in badgers and relates their symmetry to parasitic infection. I then explore the population dynamics of a population of badgers subject to natural variation in climatic conditions. A first analysis is based on local climatic conditions, while a second analysis focuses on a more general property of climate (i.e. its unpredictability) to infer population dynamics.

The purpose of this work was to study the effects of reactive oxygen species (ROS) on DNA and to investigate the relevance of ROS-induced DNA damage in systemic lupus erythematosus (SLE). Using model systems of ROS generation, it was found that DNA was damaged by ROS at all levels of its structure, causing strand breaks, base modifications and conformational changes. Hydrogen peroxide, a ROS generated during inflammation in vivo, produced a characteristic type of site-specific damage dependent on the DNA-bound metal ion catalysis of its degradation. 8-hydroxydeoxyguanosine (8OHDG), a modified DNA base, was used as a marker of oxidative damage to investigate the role of DNA damage in the aetiopathogenesis of SLE. Excretion of this adduct was detected in normal urine and is believed to arise from normal oxidative metabolic processes. In patients with active rheumatoid arthritis, this level of 8OHDG excretion was significantly elevated. In contrast, in SLE patients with inflammatory activity, 8OHDG was undetectable in the urine. Investigation of the mechanism responsible for this showed that SLE cells had aberrant removal of 8OHDG from DNA following oxidative stress in vitro compared to normal cells, and that ROS-denatured DNA accumulated in circulating immune complexes associated with the disease. SLE is also characterised by circulating anti-DNA antibodies. These antibodies were found to bind better to ROS-DNA than to native double-stranded DNA. Furthermore, ROS-DNA was able to stimulate lymphocytes to produce anti-DNA antibodies. The pattern of DNA damage seen in SLE patients was typical of that induced by hydrogen peroxide in vitro. This suggests that inflammation generates ROS which cause DNA damage. As a result of defective repair within cells, ROS-DNA is released into the circulation following cell death which can form complexes with anti-DNA antibodies. In addition, the ROS-DNA can stimulate further anti-DNA antibody production by acting directly on cells thus perpetuating the disease process and contributing to immune complex deposition, a deleterious manifestation of the disease process.

As urbanisation continues to fragment and degrade habitats there is a need to ensure that cities are managed to sustain ecosystem function and high biodiversity. Ecological theories suggest that areas with higher levels of functional connectivity sustain a more diverse avian population. By identifying the key habitat features that dictate the distribution and abundance of avian populations it is possible to inform planning policy to maximise biodiversity. Bird species presence and abundance across an urban gradient in Birmingham (UK) was surveyed at 70 sites over three sampling periods (between 2009 and 2010), in combination with a tree survey and digital analysis of land use. Functional connectivity was shown to increase the abundance of bird species and to ameliorate the impacts of urban development. Bird species were found to vary with their associations with vegetation structure and a proxy for invertebrate productivity. There was clear evidence for increasing native tree species in the urban matrix to support more bird species. Ringing data collected between 2008 and 2011 were used to examine bird movements through the city and the influence of habitat factors such as connectivity and built space in the matrix. Bird movements between ringing sites demonstrated the permeability of the city and the importance of connectivity in the landscape. This work showed that the composition of the matrix influences bird occupancy and turnover of sites. The novel findings presented in this thesis on the influence of the urban landscape on urban avian ecology should make an important contribution to urban conservation methods.

This study sought to discover whether summer cutting of fenlands changes the biodiversity of invertebrates in managed areas as compared to control areas. Following preliminary sampling reedbeds were chosen for the investigation. The invertebrates studied were Mollusca, Araneae and Coleoptera. Species level changes were investigated in order to identify any specific level responses to management. All the groups studied were shown to be habitat specific and sensitive to management at the species level, for some, but not all species. Overall biodiversity and similarity, in terms of presence and absence of species within each group, and in terms of numbers of individuals, was not shown to be affected by cutting management. All three groups studied contained species which reacted positively to cutting management, increasing in abundance. There were also species in each group which responded negatively to cutting management, decreasing in abundance. Overall response was positive in the short term.

The evolutionary history of archosauromorphs is of particular interest because it includes the origins of two of the best-known and most distinctive extant tetrapod groups: crocodylians and birds. In this thesis, the anatomy, taxonomy and systematics of the Permo-Triassic non-archosaur archosauromorphs are revised. A revision of the Permo-Triassic archosauromorph record indicates that only four Permian species are known and there are three valid proterosuchid species immediately after the Permo-Triassic boundary in South Africa. Analyses of cranial ontogenetic variation in \(Proterosuchus\) \(fergusi\) found that ontogenetic modification events (e.g. heterochrony) may have been key drivers of the evolution of the general shape of the skull at the base of Archosauriformes. A comprehensive quantitative phylogenetic analysis recovered a polyphyletic “Prolacertiformes”, restricted the taxonomic content of Proterosuchidae to only six species, Erythrosuchidae was composed of eight nominal species, and \(Euparkeria\) \(capensis\) was found as the sister-taxon of the clade that includes proterochampsians (doswelliids + proterochampsids) and archosaurs. The results obtained here suggest that the evolutionary history of the archosauriforms during the Early Triassic can be subdivided into a first phase characterized by the short-lived “disaster-clade” Proterosuchidae and a second phase that witnessed the initial morphological and probably palaeoecological diversification of the group.

Research Doctorate - Doctor of Philosophy (PhD) / How may ancient Hebrew texts be presented to a contemporary audience, remaining faithful to the original and at the same time relevant yet timeless? I am painting four series of watercolours, each focussing on a particular Australian habitat. These artworks form decorative borders to the four biblical texts of Lamentations, Ruth, Ecclesiastes and Esther, four of the Jewish Scrolls, and act as visual metaphors of underlying themes and indicators of structure and literary devices. My research is into the texts themselves, reading and responding to them; into natural subjects that express my response; and into the art-making process from which the final artworks are created. The end product of my research is an exhibition of these watercolour works and an A4-sized book combining the complete printed text of the Scrolls in the English Standard Version (ESV) as I have formatted it, with my illustrations as border designs. My aim is that through the manuscripts’ overall design, I honour the authors’ literary artistry, including symmetry, acrostic and reversal. Through my choice of subjects for each illustration, I aim to suggest themes in the adjoining text.