A national coastal erosion risk assessment for Scotland

The geography of Scotland, with a highly undulating hinterland, long and indented coastline, together with a large number of islands, means that much social and economic activity is largely located at the coast. The importance of the coast is further highlighted by the large number of ecosystem services derived from the coast. The threat posed by climate change, particularly current and future sea level rise, is of considerable concern and the associated coastal erosion and coastal flooding has the potential to have a substantial effect on the socioeconomic activity of the whole country. Currently, the knowledge base of coastal erosion is poor, which serves to hinder the current and future management of the coast. This research reported here aimed to establish four key aspects of coastal erosion within Scotland: the physical susceptibility of the coast to erosion; the assets exposed to coastal erosion; the vulnerability of communities to coastal erosion; and the coastal erosion risk to those communities. Coastal erosion susceptibility was modelled here within a GIS, using data for ground elevation, rockhead elevation, wave exposure and proximity to the open coast. Combining these data produced the Underlying Physical Susceptibility Model (UPSM), in the form of a 50 m2 raster of national coverage. The Coastal Erosion Susceptibility Model (CESM) was produced with the addition of sediment supply and coastal defence data, which then moderates the outputs of the UPSM. Asset data for dwellings, key assets, transport infrastructure, historic assets, and natural assets were used along with the UPSM and CESM to assess their degree of exposure to coastal erosion. A Coastal Erosion Vulnerability Model (CEVM) was produced using Experian Mosaic Scotland (a geodemographic classification which identifies 44 different social groups within Scotland) to classify populations based upon 11 vulnerability variables. Dwellings were assigned a CESM and CEVM score in order to establish their coastal erosion risk. This research demonstrated that the issue of coastal erosion will impact on a relatively low number of properties compared to those impacted by flooding (both coastal and fluvial) as many dwellings are already protected by coastal defences. There is therefore, a considerable future liability, and great pressure for coastal defences to be maintained and upgraded in their current form. The use of the CEVM is a novel inclusion within a coastal erosion assessment for Scotland. Use of the CEVM established that coastal erosion risk is not distributed equally amongst the Scottish coastal population and highlighted that risk can be reduced by either reducing exposure or reducing vulnerability. Thus far in Scotland, reducing exposure has been the primary management approach, which has a number of implications with regards social justice. This research identified the existing data gaps that should be addressed by future research in order to further improve coastal management in Scotland. Future research should focus on assessing historical coastal change rates on a national scale, improve modelling of national scale wave exposure, enhance the information held about current coastal defences and, determine the direct and indirect economic cost associated with the loss of different asset types. It is also necessary to clarify the social justice implications of using adaptation approaches to manage coastal erosion as well as establishing a method to communicate the susceptibility, exposure, vulnerability and risk aspects whilst minimising the potential negative impacts (e.g. property blight) of releasing such information.

Warfare in the West Highlands and Isles of Scotland, c. 1544-1615

Warfare has long been associated with Scottish Highlanders and Islanders, especially in the period known in Gaelic tradition as ‘Linn nan Creach’ (the ‘Age of Forays’), which followed the forfeiture of the Lordship of the Isles in 1493. The sixteenth century in general is remembered as a particularly tumultuous time within the West Highlands and Isles, characterised by armed conflict on a seemingly unprecedented scale. Relatively little research has been conducted into the nature of warfare however, a gap filled by this thesis through its focus on a series of interconnected themes and in-depth case studies spanning the period c. 1544-1615. It challenges the idea that the sixteenth century and early seventeenth century was a time of endless bloodshed, and explores the rationale behind the distinctive mode of warfare practised in the West Highlands and Isles. The first part of the thesis traces the overall ‘Process of War’. Chapter 1 focuses on the mentality of the social elite in the West Highlands and Isles and demonstrates that warfare was not their raison d'être, but was tied inextricably to chiefs’ prime responsibility of protecting their lands and tenants. Chapter 2 assesses the causation of warfare and reveals that a recurrent catalyst for armed conflict was the assertion of rights to land and inheritance. There were other important causes however, including clan expectation, honour culture, punitive government policies, and the use of proxy warfare by prominent magnates. Chapter 3 takes a fresh approach to the military capacity of the region through analysis of armies and soldiers, and the final thematic chapter tackles the conduct of warfare in the West Highlands and Isles, with analysis of the tactics and strategy of militarised personnel. The second part of this thesis comprises five case studies: the Clanranald, 1544-77; the Colquhouns of Luss and the Lennox, 1592-1603; the MacLeods of Harris and MacDonalds of Sleat, 1594-1601; the Camerons, 1569-1614; and the ‘Islay Rising’, 1614-15. This thesis adopts a unique approach by contextualising the political background of warfare in order to instil a deeper understanding of why early modern Gaelic Scots resorted to bloodshed. Overall, this period was defined by a sharp rise in military activity, followed by an even sharper decline, a trajectory that will be evidenced vividly in the final case study on the ‘Islay Rising’. Although warfare was widespread, it was not unrestrained or continuous, and the traditional image of a region riven by perpetual bloodshed has been greatly exaggerated.

Reading Pitscottie's Cronicles: a case study on the history of literacy in Scotland, 1575-1814

This thesis addresses a range of research questions regarding literacy in early modern Scotland. Using the early modern manuscripts and printed editions of Robert Lindsay of Pitscottie’s late sixteenth-century 'Cronicles of Scotland' as a case study on literacy history, this thesis poses the complementary questions of how and why early modern Scottish reading communities were encountering Pitscottie’s 'Cronicles', and how features of the material page can be interpreted as indicators of contemporary literacy practices. The answers to these questions then provide the basis for the thesis to ask broader socio-cultural and theoretical questions regarding the overall literacy environment in Scotland between 1575 and 1814, and how theorists conceptualise the history of literacy. Positioned within the theoretical groundings of historical pragmatics and ‘new philology’ – and the related approach of pragmaphilology – this thesis returns to the earlier philological practice of close textual analysis, and engages with the theoretical concept of mouvance, in order to analyse how the changing ‘form’ of Pitscottie’s 'Cronicles', as it was reproduced in manuscript and print throughout the early modern period, indicates its changing ‘function’. More specifically, it suggests that the punctuation practices and paratextual features of individual witnesses of the text function to aid the highly-nuanced reading practices and purposes of the discrete reading communities for which they were produced. This thesis includes extensive descriptive material which presents previously unrecorded data regarding twenty manuscripts and printed witnesses of Pitscottie’s 'Cronicles', contributing to a gap in Scotland’s literary/historiographical canon. It then analyses this material using a transferable methodological framework which combines the quantitative analysis of micro-data with qualitative analysis of this data within its socio-cultural context, in order to conduct diachronic comparative analysis of copy-specific information. The principal findings of this thesis suggest that Pitscottie’s 'Cronicles' were being read for a combination of devotional and didactic purposes, and that multiple reading communities, employing highly nuanced reading practices, were encountering the text near-contemporaneously. This thesis further suggests that early modern literacy practices, and the specific reading communities which employ them, should be described as existing within a spectrum of available practices (i.e. more or less oral/aural or silent, and intensive or extensive in practice) rather than as dichotomous entities. As such, this thesis argues for the rejection of evolutionary theories of the history of literacy, suggesting that rather than being described antithetically, historical reading practices and purposes must be recognised as complex, coexisting socio-cultural practices, and the multiplicity of reading communities within a single society must be acknowledged and analysed as such, as opposed to being interpreted as universal entities.

Blood donor motivation and recruitment : a comparative study in West of Scotland and the Sudan

In modern society, blood donor motivation and recruitment is a fundamental part of health care delivery. Well defined and documented programmes exist throughout the world but new ideas are always welcome. The situation in the Sudan is different and much remains to be done by way of comparison with elsewhere. This thesis outlines the objectives of a study, how it was supported, sponsored and achieved. It describes briefly the geography of the Sudan, the source of Sudanese economy, climate, culture and historical backgrounds. The problems of existing services in the Sudan are reviewed and a brief account of the demographic characteristics of the Sudanese population is given. Two surveys done in West of Scotland and in the Sudan are described in detail. This work discloses and compares the positive motives that enhances giving of blood and the negative motives that hinders its donation. The comparison is between an Eastern Society with a voluntary motivation not fully activated because of lack of understanding and awareness of the need to give blood voluntarily for strangers and Western Society with a well established voluntary system of donation. An addition to this research was the investigation into the immunity to tetanus and hepatitis in the Sudanese population. An estimate of the percentage of individuals with detectable levels of hepatitis A and B antibodies and tetanus antibodies is included since there is a need to establish a plasmapheresis programme as part of a good Blood Transfusion Service for the procurement of specific immunoglobulin's. This work has revealed major differences between the West of Scotland and the Sudan and suggestions are made for their resolution. The main conclusion and comparison are summarised in Chapter 7. It is hoped that many of the suggestions in this thesis can be introduced in the Sudan at an early date.

Epidemiology and genetic architecture of blood pressure: a family based study of Generation Scotland

Hypertension is a major risk factor for cardiovascular disease and mortality, and a growing global public health concern, with up to one-third of the world’s population affected. Despite the vast amount of evidence for the benefits of blood pressure (BP) lowering accumulated to date, elevated BP is still the leading risk factor for disease and disability worldwide. It is well established that hypertension and BP are common complex traits, where multiple genetic and environmental factors contribute to BP variation. Furthermore, family and twin studies confirmed the genetic component of BP, with a heritability estimate in the range of 30-50%. Contemporary genomic tools enabling the genotyping of millions of genetic variants across the human genome in an efficient, reliable, and cost-effective manner, has transformed hypertension genetics research. This is accompanied by the presence of international consortia that have offered unprecedentedly large sample sizes for genome-wide association studies (GWASs). While GWAS for hypertension and BP have identified more than 60 loci, variants in these loci are associated with modest effects on BP and in aggregate can explain less than 3% of the variance in BP. The aims of this thesis are to study the genetic and environmental factors that influence BP and hypertension traits in the Scottish population, by performing several genetic epidemiological analyses. In the first part of this thesis, it aims to study the burden of hypertension in the Scottish population, along with assessing the familial aggregation and heritialbity of BP and hypertension traits. In the second part, it aims to validate the association of common SNPs reported in the large GWAS and to estimate the variance explained by these variants. In this thesis, comprehensive genetic epidemiology analyses were performed on Generation Scotland: Scottish Family Health Study (GS:SFHS), one of the largest population-based family design studies. The availability of clinical, biological samples, self-reported information, and medical records for study participants has allowed several assessments to be performed to evaluate factors that influence BP variation in the Scottish population. Of the 20,753 subjects genotyped in the study, a total of 18,470 individuals (grouped into 7,025 extended families) passed the stringent quality control (QC) criteria and were available for all subsequent analysis. Based on the BP-lowering treatment exposure sources, subjects were further classified into two groups. First, subjects with both a self-reported medications (SRMs) history and electronic-prescription records (EPRs; n =12,347); second, all the subjects with at least one medication history source (n =18,470). In the first group, the analysis showed a good concordance between SRMs and EPRs (kappa =71%), indicating that SRMs can be used as a surrogate to assess the exposure to BP-lowering medication in GS:SFHS participants. Although both sources suffer from some limitations, SRMs can be considered the best available source to estimate the drug exposure history in those without EPRs. The prevalence of hypertension was 40.8% with higher prevalence in men (46.3%) compared to women (35.8%). The prevalence of awareness, treatment and controlled hypertension as defined by the study definition were 25.3%, 31.2%, and 54.3%, respectively. These findings are lower than similar reported studies in other populations, with the exception of controlled hypertension prevalence, which can be considered better than other populations. Odds of hypertension were higher in men, obese or overweight individuals, people with a parental history of hypertension, and those living in the most deprived area of Scotland. On the other hand, deprivation was associated with higher odds of treatment, awareness and controlled hypertension, suggesting that people living in the most deprived area may have been receiving better quality of care, or have higher comorbidity levels requiring greater engagement with doctors. These findings highlight the need for further work to improve hypertension management in Scotland. The family design of GS:SFHS has allowed family-based analysis to be performed to assess the familial aggregation and heritability of BP and hypertension traits. The familial correlation of BP traits ranged from 0.07 to 0.20, and from 0.18 to 0.34 for parent-offspring pairs and sibling pairs, respectively. A higher correlation of BP traits was observed among first-degree relatives than other types of relative pairs. A variance-component model that was adjusted for sex, body mass index (BMI), age, and age-squared was used to estimate heritability of BP traits, which ranged from 24% to 32% with pulse pressure (PP) having the lowest estimates. The genetic correlation between BP traits showed a high correlation between systolic (SBP), diastolic (DBP) and mean arterial pressure (MAP) (G: 81% to 94%), but lower correlations with PP (G: 22% to 78%). The sibling recurrence risk ratio (λS) for hypertension and treatment were calculated as 1.60 and 2.04 respectively. These findings confirm the genetic components of BP traits in GS:SFHS, and justify further work to investigate genetic determinants of BP. Genetic variants reported in the recent large GWAS of BP traits were selected for genotyping in GS:SFHS using a custom designed TaqMan® OpenArray®. The genotyping plate included 44 single nucleotide polymorphisms (SNPs) that have been previously reported to be associated with BP or hypertension at genome-wide significance level. A linear mixed model that is adjusted for age, age-squared, sex, and BMI was used to test for the association between the genetic variants and BP traits. Of the 43 variants that passed the QC, 11 variants showed statistically significant association with at least one BP trait. The phenotypic variance explained by these variant for the four BP traits were 1.4%, 1.5%, 1.6%, and 0.8% for SBP, DBP, MAP, and PP, respectively. The association of genetic risk score (GRS) that were constructed from selected variants has showed a positive association with BP level and hypertension prevalence, with an average effect of one mmHg increase with each 0.80 unit increases in the GRS across the different BP traits. The impact of BP-lowering medication on the genetic association study for BP traits has been established, with typical practice of adding a fixed value (i.e. 15/10 mmHg) to the measured BP values to adjust for BP treatment. Using the subset of participants with the two treatment exposure sources (i.e. SRMs and EPRs), the influence of using either source to justify the addition of fixed values in SNP association signal was analysed. BP phenotypes derived from EPRs were considered the true phenotypes, and those derived from SRMs were considered less accurate, with some phenotypic noise. Comparing SNPs association signals between the four BP traits in the two model derived from the different adjustments showed that MAP was the least impacted by the phenotypic noise. This was suggested by identifying the same overlapped significant SNPs for the two models in the case of MAP, while other BP traits had some discrepancy between the two sources

Evaluating consumer price perception: a mental accounting and frame dependent perspective

In this thesis, we evaluate consumer purchase behaviour from the perspective of heuristic decision making. Heuristic decision processes are quick and easy mental shortcuts, adopted by individuals to reduce the amount of time spent in decision making. In particular, we examine those heuristics which are caused by framing – prospect theory and mental accounting, and examine these within price related decision scenarios. The impact of price framing on consumer behaviour has been studied under the broad umbrella of reference price, which suggests that decision makers use reference points as standards of comparison when making a purchase decision. We investigate four reference points - a retailer's past prices, a competitor's current prices, a competitor's past prices, and consumers' expectation of immediate future price changes, to further our understanding of the impact of price framing on mental accounting, and in turn, contribute to the growing body of reference price literature in Marketing research. We carry out experiments in which levels of price frame and monetary outcomes are manipulated in repeated measures analysis of variance (ANOVA). Our results show that where these reference points are clearly specified in decision problems, price framing significantly affects consumers' perceptions of monetary gains derived through discounts, and leads to reversals in consumer preferences. We also found that monetary losses were not sensitive to price frame manipulations.

A house, not a home? Examining the use of the private rented sector to resolve homelessness in Scotland

Changes to homelessness legislation in post-devolution Scotland have resulted in an expansion of rights for homeless households seeking formal assistance from local authorities. These changes have led to Scotland’s homelessness arrangements being considered among the most progressive in Europe. In recent years, however, the Scottish Government has increasingly promoted homelessness prevention and Housing Options approaches as a means by which homelessness might be avoided or resolved without recourse to statutory rights. As part of that, they have promoted greater use of the private rented sector (PRS) as a key housing option, with the potential to meet the needs of homeless households. The arguments made to support use of the PRS have much in common with arguments for privatisation in other areas of social policy, notably greater choice for the individual promoting better welfare outcomes, and competition among providers encouraging improvements in quality of service provision. Critics have argued that such benefits may not be realised and that, on the contrary, privatisation may lead to exclusion or act to worsen households’ outcomes. This thesis considers the extent to which the PRS has been utilised in Scotland to accommodate homeless households, and the consequences of this for their welfare. The thesis uses a combination of quantitative and qualitative methods. To examine trends in the use of the PRS, it presents quantitative analysis of the data on the operation of the statutory system and Housing Options arrangements, and of data from a survey of local authority homelessness strategy officers. To examine the consequences of this for homeless households, the thesis uses qualitative research involving face-to-face interviews with 35 homeless households across three local authority areas. This research considers the extent to which households’ experiences of homelessness, housing need and the PRS reflect the arguments presented in the literature, and how settled accommodation has impacted on households’ ability to participate fully in society. The research found an increasing but still limited role for the PRS in resolving statutory homelessness in Scotland, with indications that the PRS is being increasingly used as part of the Housing Options approach and as a means of resolving homelessness outside the statutory system. The PRS is being utilised to varying degrees across different local authority areas, and a variety of methods are being used to do so. While local authorities saw clear advantages to making greater use of the sector, a number of significant barriers including affordability, available stock and landlord preferences - made this difficult in practice. Research with previously homeless households in the PRS similarly found broadly positive experiences and views of the sector, particularly with regard to enabling households to access good quality accommodation in desirable areas of their choosing, with many households highlighting improvements relating to social inclusion and participation. Nevertheless, concerns around the security of tenure offered by the sector, repairs, service standards and unequal power relations between landlord and tenant persisted. As such, homeless households frequently expressed their decision to enter the sector in terms of a trade-off between choice and security.

Africans in Scotland: heterogeneity and sensitivities to HIV

Aim: To investigate how diversity within the African migrant population in Scotland affects their understandings of HIV and uptake of HIV testing and treatment, in order to improve HIV-related outcomes. Background: In the UK, Africans have the worst outcomes for HIV infection, primarily due to late diagnosis. Improvement requires better understanding of the barriers to healthcare engagement. This PhD study investigates how diversity among first generation African migrants in Scotland could affect engagement with general healthcare and HIV related interventions and services. Methods: I conducted qualitative research, involving participant observation at two sites (an African religious group and an asylum seeker/refugee drop-in centre) and interviews with African migrants attending these and three additional sites (two advocacy charities and a student association). Data were collected in two cities (Glasgow and Edinburgh) and two smaller towns (Paisley and Kirkcaldy). I interviewed 27 Africans, including economic migrants (n=8), students (n=9) and asylum seeker/refugees (n=10) and 14 representatives from organisations with high levels of African attendees (e.g., country associations, community organisations, advocacy groups, commercial establishments and religious based organisations). Thematic data analysis was carried out. Results: Diversity of the population and related issues of identity: Participants were highly diverse and reported considerable heterogeneity in the African diaspora in Scotland. The identity of “African” was bound with various negative stereotypes and appeals to this identity did not necessarily have relevance for participants. Nature of African affiliated organisations in Scotland: There were a wide range of organisations that advertised their remit as catering for the African diaspora. They varied in consistency and sustainability and contributed towards healthcare engagement to different degrees. Engagement with healthcare: There were multiple experiences and understandings of the healthcare system within the sample as a whole, and to an extent by migrant type. Whilst the majority reported successful and satisfactory service use, distinct barriers emerged. These included: understandings of rights and access to care based on African models of healthcare; the interplay of religious based understandings with ideas about access to healthcare; and assumptions and anxiety about the connections between visa status and health status. Knowledge of HIV and engagement with HIV related services: Participants had good knowledge about HIV, with some notable exceptions, but there was no patterning by migrant type. They had diverse views about risk of HIV infection, most of which did not align with the HIV epidemiology that identifies African migrants as an at risk group. Most of the sample did not think targeting African migrants for HIV interventions would be successful and were hostile to the proposal for various reasons, especially because they believed it would perpetuate stigma and prejudice towards the African diaspora. There were mixed experiences of HIV related services, and prompts to test for HIV had elicited a range of reactions, the majority negative. Conclusion: Diversity within the African diaspora in Scotland should be taken into account to improve the salience and relevance of future HIV interventions. Attitudes towards current HIV testing promotion suggest that a more cooperative approach could be taken with African communities to build on existing relationships of trust and understandings of HIV.

Learning to construct our identities over the life course: a study with lesbian, gay, bisexual and transgender adults in Scotland

To date, adult educational research has had a limited focus on lesbian, gay, bisexual and transgendered (LGBT) adults and the learning processes in which they engage across the life course. Adopting a biographical and life history methodology, this study aimed to critically explore the potentially distinctive nature and impact of how, when and where LGBT adults learn to construct their identities over their lives. In-depth, semi-structured interviews, dialogue and discussion with LGBT individuals and groups provided rich narratives that reflect shifting, diverse and multiple ways of identifying and living as LGBT. Participants engage in learning in unique ways that play a significant role in the construction and expression of such identities, that in turn influence how, when and where learning happens. Framed largely by complex heteronormative forces, learning can have a negative, distortive impact that deeply troubles any balanced, positive sense of being LGBT, leading to self- censoring, alienation and in some cases, hopelessness. However, learning is also more positively experiential, critically reflective, inventive and queer in nature. This can transform how participants understand their sexual identities and the lifewide spaces in which they learn, engendering agency and resilience. Intersectional perspectives reveal learning that participants struggle with, but can reconcile the disjuncture between evolving LGBT and other myriad identities as parents, Christians, teachers, nurses, academics, activists and retirees. The study’s main contributions lie in three areas. A focus on LGBT experience can contribute to the creation of new opportunities to develop intergenerational learning processes. The study also extends the possibilities for greater criticality in older adult education theory, research and practice, based on the continued, rich learning in which participants engage post-work and in later life. Combined with this, there is scope to further explore the nature of ‘life-deep learning’ for other societal groups, brought by combined religious, moral, ideological and social learning that guides action, beliefs, values, and expression of identity. The LGBT adults in this study demonstrate engagement in distinct forms of life-deep learning to navigate social and moral opprobrium. From this they gain hope, self-respect, empathy with others, and deeper self-knowledge.

The difference of Being in the early modern world: a relational-material approach to life in Scotland in the period of the witch trials

This thesis investigates how ways of being in different ontologies emerge from material and embodied practice. This general concern is explored through the particular case study of Scotland in the period of the witch trials (the 16th and 17th centuries C.E.). The field of early modern Scottish witchcraft studies has been active and dynamic over the past 15 years but its prioritisation of what people said over what they did leaves a clear gap for a situated and relational approach focusing upon materiality. Such an approach requires a move away from the Cartesian dichotomies of modern ontology to recognise past beliefs as real to those who experienced them, coconstitutive of embodiment and of the material worlds people inhabited. In theory, method and practice, this demands a different way of exploring past worlds to avoid flattening strange data. To this end, the study incorporates narratives and ‘disruptions’ – unique engagements with Contemporary Art which facilitate understanding by enabling the temporary suspension of disbelief. The methodology is iterative, tacking between material and written sources in order to better understand the heterogeneous assemblages of early modern (counter-) witchcraft. Previously separate areas of discourse are (re-)constituted into alternative ontic categories of newly-parallel materials. New interpretations of things, places, bodies and personhoods emerge, raising questions about early modern experiences of the world. Three thematic chapters explore different sets of collaborative agencies as they entwine into new things, co-fabricating a very different world. Moving between witch trial accounts, healing wells, infant burial grounds, animals, discipline artefacts and charms, the boundaries of all prove highly permeable. People, cloth and place bleed into one another through contact; trees and water emerge as powerful agents of magical-place-making; and people and animals meet to become single, hybrid-persons spread over two bodies. Life and death consistently emerge as protracted processes with the capacity to overlap and occur simultaneously in problematic ways. The research presented in this thesis establishes a new way of looking at the nature of Being as experienced by early modern Scots. This provides a foundation for further studies, which can draw in other materials not explored here such as communion wares and metal charms. Comparison with other early modern Western societies may also prove fruitful. Furthermore, the methodology may be suitable for application to other interdisciplinary projects incorporating historical and material evidence.

Mixed genotype Hepatitis C virus infections: incidence in Scotland and methods for detection

The diagnosis of mixed genotype hepatitis C virus (HCV) infection is rare and information on incidence in the UK, where genotypes 1a and 3 are the most prevalent, is sparse. Considerable variations in the efficacies of direct-acting antivirals (DAAs) for the HCV genotypes have been documented and the ability of DAAs to treat mixed genotype HCV infections remains unclear, with the possibility that genotype switching may occur. In order to estimate the prevalence of mixed genotype 1a/3 infections in Scotland, a cohort of 512 samples was compiled and then screened using a genotype-specific nested PCR assay. Mixed genotype 1a/3 infections were found in 3.8% of samples tested, with a significantly higher prevalence rate of 6.7% (p<0.05) observed in individuals diagnosed with genotype 3 infections than genotype 1a (0.8%). An analysis of the samples using genotypic-specific qPCR assays found that in two-thirds of samples tested, the minor strain contributed <1% of the total viral load. The potential of deep sequencing methods for the diagnosis of mixed genotype infections was assessed using two pan-genotypic PCR assays compatible with the Illumina MiSeq platform that were developed targeting the E1-E2 and NS5B regions of the virus. The E1-E2 assay detected 75% of the mixed genotype infections, proving to be more sensitive than the NS5B assay which identified only 25% of the mixed infections. Studies of sequence data and linked patient records also identified significantly more neurological disorders in genotype 3 patients. Evidence of distinctive dinucleotide expression within the genotypes was also uncovered. Taken together these findings raise interesting questions about the evolutionary history of the virus and indicate that there is still more to understand about the different genotypes. In an era where clinical medicine is frequently more personalised, the development of diagnostic methods for HCV providing increased patient stratification is increasingly important. This project has shown that sequence-based genotyping methods can be highly discriminatory and informative, and their use should be encouraged in diagnostic laboratories. Mixed genotype infections were challenging to identify and current deep sequencing methods were not as sensitive or cost-effective as Sanger-based approaches in this study. More research is needed to evaluate the clinical prognosis of patients with mixed genotype infection and to develop clinical guidelines on their treatment.

Patterns in the space use of the Bearded Reedling, Panurus biarmicus, on the Tay Reedbeds, Scotland

This thesis presents research into the space use of a specialist reedbed Passerine, the Bearded Reedling, or Bearded Tit, Panurus biarmicus, with a view to inform the conservation of this species and reedbeds as a whole. How a species uses space, and how space use changes between individuals or over time, can influence: the ability to forage and hunt effectively, breeding success, susceptibility to predation, genetic health, disease spread, robustness against environmental change and ultimately, colonisation or extinction. Thus, understanding the space use of animals can provide critical insight into ecological systems. Birds offer interesting models when studying animal space use, as, by being intrinsically mobile, many bird species can occupy multiple spatial scales. As a consequence of being completely dependent on patchy and ephemeral reedbed habitats, the Bearded Reedling, has a clustered, inhomogeneous distribution throughout its range. This drives the existence of distinct spatial scales upon which space use studies should be characterised. Distribution and movement within a single reedbed can be considered local-scale, while spatial processes between reedbeds can be considered wide-scale. Temporal processes may act upon both of these scales. For example, changing interactions with predators may influence nest positioning at a local-scale, while seasonal changes in resource requirements might drive processes such as migration at a wide-scale. The Bearded Reedling has a wide temperate breeding range, extending over much of Eurasia. On the IUCN’s red list, it is listed as ‘of least concern’, with an estimated European population between 240,000-480,000 breeding pairs. Despite its relatively favourable conservation status, its dependence on reedbed habitats drives a fragmented distribution, with populations being concentrated in small, isolated, stands. Over the last century reedbed wetlands have suffered rapid declines caused by drainage schemes undertaken to improve land for development or agriculture. Additionally, many remaining reed stands are subject to extensive commercial management to produce thatch or biofuel. Conversely, in other areas, management is driven by conservation motives which recognise the present threats to reedbeds, and aim to encourage the diversity of species associated with these habitats. As the Bearded Reedling is fundamentally linked to the quality and structure of a reed stand, understanding the space use of this species will offer information for the direct conservation of this specialist species, and for the effects of reedbed management as a whole. This thesis first presents studies of space use at a local-scale. All local-scale research is conducted at the Tay Reedbeds in eastern Scotland. Mist netting and bird ringing data are used within capture recapture models, which include an explicit spatial component, to gain insight into the abundance of the Bearded Reedling on the Tay. This abundance estimation approach suggests the Tay reedbeds are a stronghold for this species on the British Isles, and that, as a high latitude site, the Tay may have importance for range expansion. A combination of transect surveys and radio-tracking data are then used to establish the local-scale space use of this species during the breeding and autumnal seasons. These data are related to changes in the structure of reed caused by local management in the form of mosaic winter reed cutting. Results suggest that birds exploit young and cut patches of reed as foraging resources when they are available, and that old, unmanaged reed is critical for nesting and winter foraging. Further local-scale studies concern the spatial patterns in the nesting habits of this species. Mosaic reed cutting creates clear edges in a reedbed. Artificial nests placed in the Tay Reedbeds demonstrate increased nest predation rates closer to the edges of cut patches. Additionally, high predation rates become reduced as the cut reed re-grows, suggesting that reed cutting may increase accessibility of the stand to predators. As Bearded Reedling nests are uncommon and difficult to locate, the timing, site selection and structure of a sample of real nests from the Tay is then detailed. These demonstrate an early, and relatively rigid breeding onset in this species, the importance of dense, compacted reeds as nesting sites and a degree of flexibility in nest structure. Conservation efforts will also benefit from studies into wide-scale spatial processes. These may be important when establishing how colonisation events occur and when predicting the effects of climatic change. The Bearded Reedling has been traditionally considered a resident species which only occasionally undertakes wide-scale, between-reedbed, movements. Indeed, the ecology of this species suggests strict year round local residency to reedbeds, with distinct seasonal changes in diet allowing occupation of these habitats year round. The European ringing recoveries of this species, since the 1970s are investigated to better characterise the wider movements of specialist resident. These suggest residency in southern populations, but higher instances of movement than expected in more northerly regions. In these regions wide-scale movement patterns resemble those of partial regular migratory species. An understanding of local and wide-scale spatial processes can offer a strong foundation on which to build conservation strategies. This thesis aims to use studies of space use to provide this foundation for the Bearded Reedling and offer further insight into the ecology of reedbed habitats as a whole. The thesis concludes by proposing an effective strategy for the conservation management of reedbeds that will especially benefit the Bearded Reedling.