The thesis of this dissertation is that not only was Darwin the first Social Darwinist, but that only through appreciation of the roles of confusion, metaphysics, the social and political context, and the work of Alfred Russel Wallace can a better understanding of Darwin's achievement be accomplished. By revealing and then analyzing the Social Darwinist aspects of Darwin's science of transmutation the position of most critics--who hold that Darwin's Social Darwinist followers perverted his "pure" science--is debunked. Darwin's development of a race war theory was done for scientific reasons which cannot be stripped away to reveal a non-political "core" without utterly transforming his ideas. For instance, Darwin developed a biological ranking of indigenous peoples which helped fill in evidential gaps for the theory of evolution as well as provide confirmation for his radical form of reductive materialism. Darwin's Social Darwinism has been noticed by a few critics, but is usually dismissed as either ephemeral or indicative of commonly-held "backround" political biases. The first view is shown to be inadequate by revelation of the deep relation of his metaphysics to his science. The second is exploded through an examination of the work of Alfred Russel Wallace. He opposed Darwin's concept of race war, and his opposition was rooted in his commitment to an emergentist metaphysics. Once the juxtaposition of the social and political aspects of Wallace's work to that of Darwin is provided, the wider context of their work is revealed by an examination of Darwin's use of Malthus, the politics of emerging professional classes, Victorian birth control, and the work of T. H. Huxley. Revelation of the intimate social and political details of the scientific work of Darwin and Wallace helps to create an understanding of how nineteenth century science was constituted and demonstrates that the particular historical relations of science and ideology make the concept of "pure science" an oxymoron.

Within the UK, the continuing biodiversity crisis has led to a policy driven shift in the conservation sector; moving away from localized site scale conservation to a landscape-scale. This approach encourages fragmented habitat patches to be integrated into a much larger habitat network. Epiphytic lichens provide an ideal model system for studying the effectiveness of conservation initiatives within fragmented habitats, due to their metapopulation structures whereby individual trees within woodlands (and woodland stands within wooded landscapes), represent isolated habitat patches. Old-growth woodland in particular provides suitable habitat to a suite of lichens known as the Lobarion community, which are declining throughout Europe. Regeneration within these old growth areas, though essential for future habitat persistence, causes shading and ultimately leads to local extinctions of shade intolerant lichen epiphytes. A landscape scale conservation strategy that relies on habitat permeability to balance colonisation of post-regeneration woodland patches with extinctions in ageing woodland patches elsewhere in the landscape has been proposed as a management strategy to meet the needs of both lichen epiphytes and their woodland habitat. The unique conditions found in western Scotland, combining a relative abundance of high quality old growth habitat (in a European context) coupled with robust populations of some members of the Lobarion community, could provide an ideal opportunity to test such a management strategy. In this thesis, the plausibility of landscape-scale conservation as a management strategy for epiphytic lichens is explored, using a suite of nine target epiphytes of contrasting ecological traits set within Glen Creran, a temperate rainforest on the west coast of Scotland: 1. The habitat requirements of nine target epiphytes were identified and predictions of species distribution made over an entire glen using a species distribution modelling (SDM) approach. The SDM’s were found to apply more generally within the wider biogeographic area for five of the nine species, providing an evidence base for future conservation plans in Scotland’s rainforest zone. 2. A novel method to determine dispersal distance in lichen epiphytes was developed, combining a mechanized propagule trap with molecular techniques. This methodological advance allowed the first direct comparative study of lichen epiphytes in a natural context. 3. An agent based model was developed combining the results of 1. and 2. above to investigate the effect of habitat connectivity on colonisation in six contrasting lichen epiphytes, enabling inferences of species response to landscape-scale conservation scenarios within the study system to be made.

As sessile organisms, plants had to develop various biochemical and physiological mechanisms to respond and adapt to abiotic stress conditions such as salt and drought and thus acquire stress tolerance. A particular interesting mechanism is the so called “priming effect”: an application of a mild short stress to plants at an early stage of development appears to enable them to cope better when stressed again at mature stage. However, the molecular effects of salt priming have not been systematically quantified and as a consequence the molecular basis of priming remains unknown. In this study an experimental procedure was established that allowed to test whether salt priming of young Arabidopsis thaliana plants had an effect on plants exposed to more severe salt stress at a later stage of development. To quantify how primed and non-primed plants responded to the second salt stress, global changes in their transcriptional expression profiles were monitored using Affymetrix GeneChip ATH1 microarray. Results showed that both primed and non-primed plants responded to the salt treatment modulating the same set of known stress responsive genes. However, primed plants differentially regulated a smaller set of genes. Furthermore, the vast majority of the stress responsive genes showed a weaker response in primed than in nonprimed plants. These results suggested that primed plants channelled the stress response using only selected genes. The next question addressed was how primed plants could “remember” the priming treatment after a period of extensive growth. Several studies had indicated that environmental stress induces changes in the chromatin structure thereby modifying the accessibility of the DNA for transcription factors and other regulatory proteins. This suggested a link between epigenetic modification and exposure of plants to stressful conditions, where the chromatin status might act as an epigenetic mark that could be maintained during plant growth and development. To investigate this hypothesis I carried out a comparative analysis of the epigenetic landscapes of primed and non-primed plants combining Chromatin Immuno-Precipitation with Illumina sequencing (ChIP-Seq). Genome-wide profiles of H3K4me2, H3K4me3, H3K9me2 and H3K27me3 were generated for roots and shoots of plants harvested immediately after the priming treatment. Roots of primed plants showed indeed numerous differences in their epigenetic profiles compared to non-primed roots, in particular at the level of H3K27me3. Therefore, I carried out an additional ChIP-Seq experiment before the application of the second stress to test if the priming induced changes in H3K27me3 were maintained over this period of extensive growth. Results showed that several epigenetic differences caused by priming were still maintained. Finally, to elucidate the relationship between epigenetic modifications and transcriptional responses the ChIP-Seq profiles were coupled with genome wide transcript profiles obtained by RNA-seq. Results shown that in the non-steady state there was no clear correlation between the differences detected at the transcriptional and at the epigenetic level. The results identified H3K27me3 as a potential mark for salt stress memory and they call for future studies extending both temporal and spatial resolution of epigenetic and transcriptional changes after salt priming.

A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) are a family of proteins that are closely related to the matrix metalloproteinases (MMPs). It has been suggested that the proteins have a critical role in the breakdown of articular cartilage during osteoarthritis (OA). More recently it has been suggested that their actions could potentially regulate atherosclerotic plaque stability. Atherosclerosis is a chronic, inflammatory disorder characterised by lipid and cholesterol accumulation and the development of fibrotic plaques within the walls of large and medium arteries. The stability of the plaques is very important because clinical symptoms are only presented after rupture of the unstable plaques, leading to thrombosis and ischemia. During the current study, immunohistochemical analysis confirmed that ADAMTS-­1, -­4 and -­5 were being expressed within human carotid atherosclerotic lesions; macrophages were identified as major contributors to their expressions. Following on from this THP-­1 macrophages were stimulated with transforming growth factor-­β (TGF-­β), interferon-­γ (IFN-­γ), TNF-­like protein 1A (TL1A), interleukin (IL)-­17A and IL-­33. The regulation of ADAMTS-­1, -­4 and -­5 expressions were analysed using quantitative polymerase chain reactions (QPCR) and western blots. It was shown that TGF-­β increased the expressions of ADAMTS-­1 and -­5 and decreased the expression of ADAMTS-­4. IL-­33 decreased the expressions of ADAMTS-­1, -­4 and -­5 and IFN-­γ also decreased the expression of ADAMTS-­1. TL1A and IL-­17A stimulation of macrophages had no regulatory actions over ADAMTS-­1, -­4 or -­5 expressions. Looking at evidence from previous studies, TL1A and IL-­17A were identified as agents that could potentially act in synergy to amplify pro­inflammatory cytokine responses. To investigate this further, THP-­1 macrophages were stimulated with TL1A and IL-­17A, TL1A and IFN-­γ and also IL-­17A combined with IFN-­γ. TL1A and IL-­17A were shown to act in synergy to increase the expressions of ADAMTS-­1, -­4 and -­5 in macrophages. The regulation of ADAMTS-­1, -­4 and -­5 expressions in macrophages by IL-­33 was studied further. The mechanism of signal transduction was studied using RNA interference (RNAi) targeting extracellular signal-­‐regulated kinases (ERK)-­1, ERK-­2, p38, c-­Jun N-­terminal kinases(JNK)-­1/2, c-­Jun, phosphoinositide 3-­kinase(PI3K)-­γ, PI3K-­δ, p50, p65 and Janus kinase(JAK)-­1/2. It was determined that the attenuation of ADAMTS-­1, -­4 and -­5 expressions occurred through transcriptional regulation that was dependent on the ST2 receptor. ERK-­1, ERK-­2, JNK-­1/2, c-­Jun, PI3K-­γ and PI3K-­δ were also involved in the signal transduction of the response. The cellular roles of ADAMTS activity within atherosclerotic disease progression remain poorly understood. During the current study adenoviral vectors were created that delivered shRNA-­targeting ADAMTS-­1, -­4 and -­5. The adenoviral vectors were utilised in studies designed to investigate the roles of ADAMTS-­1, -­4 and -­5 during macrophage migration and foam cell formation. The studies showed that knockdown of ADAMTS-­1, -­4 and -­5 had no effect on macrophage migration or foam cell formation. More research is required into the cellular roles that ADAMTS proteases play during atherosclerotic disease progression. The field of research is now growing and could potentially provide some exciting opportunities for novel therapeutics of the future.

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.

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.

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.

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.