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The British breeding programme (Programme) for Sitka spruce (Picea sitchensis (Bong.) Carr.) began in 1963 by selecting individual plus trees with superior characteristics for construction-grade timber. With the establishment of seed orchards and vegetative propagation programmes, the production of improved forest reproductive material from the Programme intensified. Currently, the vast majority (>90%) of Sitka plants sold in Great Britain come from the Programme. Since the beginnings of genetic improvement of Sitka spruce in GB predates the readily available molecular genotyping methods, little is known about the genetic diversity inside the Programme. The thesis explores genetic diversity inside the different stages of the Programme. Using microsatellite (SSR) markers, chapter Chapter 1 assesses the stepwise reduction of diversity from natural populations to vegetative propagation programmes, differentiation between different seed years/provenances, and considers the origin of plus trees. Chapter 2 focuses on simple, nonmolecular methods for assessing unequal parentage contributions in a seed orchard that lead to the loss of genetic diversity. Chapter 3 utilises SSR markers to assign parents to the seed crop, quantifies and spatially analyses gene flow inside a seed orchard, and provides G-statistics of the seed crop from the orchard. Chapter 4 explores the appropriateness of SNP markers for internal control and tracking of forest reproductive material from clonal archives through seed nurseries and forest plantations. Results presented in Chapter 1 suggest that the breeding population of Sitka spruce in Britain exhibits high levels of genetic diversity. The levels are comparable and sometimes exceed those of unimproved natural populations. The highest average and effective number of alleles (12.58 and 6.27, respectively) were found in the 60 elite plus trees subsample. Similar levels are also found in the natural regeneration cores sampled under unimproved Sitka stands, which is promising for any continuous cover forest management. Genetic transfer from parents inside the studied seed orchard in Chapter 2 was incomplete and varied substantially between years. Effective population sizes based on seed viability of collected crops ranged from 7.6 in 2020 to 29.5 in 2019 (total population size is 35). The general health status of each ramet, male and female cone abundance and frost effect were all significant factors for yearly variations in genetic diversity. A molecular approach for studying the extent of genetic transfer inside the tree orchard in Chapter 3 confirms incomplete transfer and yearly variations. Low contamination rates from beyond the orchard were also detected (5.12%). A strong correlation between male flowering abundance and father contributions in successful pollinations (R2=0.41) suggests that forestry practitioners can use simple non-molecular methods for basic genetic monitoring of orchards. Finally, Chapter 4 reveals worrying levels of genetic diversity in highly improved vegetatively propagated full-sib families (VP FRM). Most samples (98%) inside the VP FRM plantations were assigned to the wrong pedigree due to mislabelled maps, clerical errors, replanting after high mortality and contaminations at the tree nurseries. Discrepancies between clonal identities inside the clonal archives were also found (27% error), suggesting that systematic testing of the breeding population would benefit further improvement efforts. Molecular markers proved to be a helpful tool for internal quality control. Comparison between SSR and SNP markers suggests that SSR markers outperform the SNP Sequenom array in the current state, and further efforts would be needed to optimize the SNP method for internal control of the breeding programme. In each of the chapters, practical advice for forestry practitioners is given. In conclusion, genetic diversity inside the Sitka spruce British breeding programme stores plenty of genetic diversity ready to be deployed. More efforts should be put into optimizing the yearly variation of seed quality from seed orchards by mixing different seed years and maintaining the general health of ramets. Additionally, levels of genetic diversity at the most improved stages of the improvement programme need to be lowered by controlling contaminations and human errors as they undermine breeding efforts to achieve desired high genetic gains.

Mycorrhizal fungi are important mutualistic symbionts of most plant species, exchanging soilbound nutrients with their host plants in exchange for photosynthetically derived sugars. Although generally beneficial, not all mycorrhizal fungi provide the same amount of benefit to their hosts, and in some contexts they can also have negative effects on their hosts. Because of this variation in potential benefit, and because different fungal species are found in different places, host populations may be under selection to modify which fungi they interact with, or how they interact with fungi, in order to increase the amount of benefit they receive from the interaction. If selection occurrs differently at different host populations, this would then also lead to local adaptation. In this thesis, I explore whether evolution in response to ectomycorrhizal (EM) fungi has occurred in the Caledonian pinewoods of Scotland, the remnant fragments of Pinus sylvestris woodland that established in Scotland 10,000 years ago. Firstly, I set up a reciprocal inoculation experiment to estimate the amount of genetic variation present amongst families of Scots pine for response to mycorrhizal inoculation, and to look for potential local adaptation of populations to local fungi. We used seedlings and soil from four populations in the Caledonian pinewoods, measuring seedling total biomass after four months. While I found that ectomycorrhizal responsiveness was highly heritable, there was no evidence that pine populations were locally adapted to fungal communities. Instead, I found a complex suite of interactions between pine population and soil inoculum. These results suggest that while Scots pine has the potential to evolve in response to mycorrhizal fungi, evolution in Scotland has not resulted in local adaptation. Long generation times and potential for rapid shifts in fungal communities in response to environmental change may preclude the opportunity for such adaptation in this species, and selection for other factors such as resistance to fungal pathogens may explain the pattern of interactions found. To explore whether there was genetic variation in the association of pine seedlings with different species of EM fungi, or whether pine defensive compounds (monoterpenes) affected the colonisation of EM fungi, we set up a reciprocal transplant experiment. Seedlings from six populations of Scots pine were grown reciprocally in grids at each of the originating populations. EM communities on each seedling were characterised using a combination of microscopy and molecular barcoding, and we used gas chromatography to characterise the monoterpene chemotype for a subset of seedlings. While there was strong evidence that mycorrhizal communities varied between sites, and among grids within sites, I found no evidence that either maternal family or monoterpene chemotype explained any variation in EM community composition. These results again suggest the importance of life history: if a seedling is too selective, it may impose penalties to competitiveness at an important life stage. Instead, a lack of selectivity may allow a seedling to gain the competitive advantage needed to outcompete conspecifics. Finally, I explored the spatial ecology of EM communities from the dataset collected previously. Although I previously found that EM community composition varied between sites and grids, approximately 30% of the variation remained unexplained. I conducted spatial correlogram analysis on EM communities at the 0 - 70 cm scale, and performed an analysis of co-occurrence of species pairs to find evidence of positive and negative interactions between fungal species. I found that most grids showed no spatial autocorrelation in EM root tips at this scale, suggesting relatively homogeneous EM communities. However, some grids were autocorrelated up to 20 cm in distance, suggesting patchy distributions of some EM fungi. I found evidence for negative interactions between species, with the two most abundant species being involved in over half of negative interactions detected. I also found evidence of positive interactions between species pairs, with most involving the genus Suillus, a group of fungi that have been previously found to host N-fixing bacteria. The presence of positive interactions with these species may suggest a facilitative effect of Suillus on other EM species. Overall, I found that while mycorrhizal traits in Scots pine had a genetic component, in natural conditions ectomycorrhizal interactions may be determined much more strongly by aspects of the ecology of individual mycorrhizal species than by host genetics. More generally, the outcomes of these interactions may depend on the life history strategy of the host, and selection pressures may be stronger in species with shorter lifespans or which occur in competition-heavy environments. Further work investigating these effects of life history should also aim to incorporate more natural conditions, as ecological interactions between fungi may mitigate genetic effects.

The Arctic is warming at twice the rate of the rest of the planet with dramatic consequences for Northern ecosystems. The rapid warming is predicted to cause shifts in plant phenology and increases in tundra vegetation productivity. Changes in phenology and productivity can have knock-on effects on key ecosystem functions. They directly influence plant-herbivore and plant-pollinator interactions creating the potential for mismatches and changes in food web structure, and they alter carbon and nutrient cycling, which in turn influence feedback mechanisms that couple the tundra biome with the global climate system. Improving our understanding of changes in tundra phenology and productivity is therefore critical to projecting not only the future state of Arctic ecosystems, but also the magnitude of potential feedbacks to global climate change. In this thesis, I combine observations from ground-based ecological monitoring, satellites and drones (also known as unmanned aerial vehicles or remotely piloted aircraft systems) to investigate how tundra plant phenology and productivity are changing across space and time, and to test how observational scales influences our ability to detect these changes. Spring plant phenology is tightly linked to temperatures, and advances in spring phenology are one of the most well documented effects of climate change on global biological systems. With rapid and near-ubiquitous Arctic warming, the absence of consistent trends in tundra spring phenology among sites suggests that additional environmental factors may exert important controls on tundra plant phenology. Indeed, further to temperature, snowmelt and sea-ice have been reported to strongly influence tundra phenology. Yet, the relative influence of these three factors has yet to be evaluated in a single cross-site analysis. In Chapter 2, I tested the importance of local average spring temperatures, local snowmelt and the timing of the drop in regional spring sea-ice extent as controls on variation in spring leaf out and flowering of 14 plant species from long-term records at four coastal sites in Arctic Alaska, Canada and Greenland. I found that spring phenology was best explained by snowmelt and spring temperature. In contrast to previous studies, sea-ice did not predict spring plant phenology at these study sites. This contrasting finding is likely explained by differences in the scale of the sea-ice measures employed. While many previous studies used descriptors of circum-polar sea-ice conditions that serve as aggregate measures for global weather conditions, I tested for the indirect effects of sea-ice conditions at a regional scale. My findings (re)emphasize the importance of snowmelt timing for tundra spring plant phenology and therefore highlight the localised nature of some of the key drivers of tundra vegetation change. Discrepancies between conventional scales of observation and underlying ecological processes could limit our ability to explain variation in tundra plant phenology and vegetation productivity. In the remote biome, ground-based monitoring is logistically challenging and restricted to comparably few sites and small plot sizes. Multispectral satellite observations cover the whole biome but are coarse in scale (tens of meters to kilometres) and uncertainties persist in how trends in vegetation indices like the Normalised Differential Vegetation Index (NDVI) relate to in situ ecological processes. Recent advances in drone technologies allow for the collection of multispectral fine-grain imagery at landscape level and have the potential to bridge the gap in observational scales. However, collecting high-quality multispectral drone imagery that is comparable across sensors, space and time remains challenging particularly when operating in extreme environments such as the tundra. In Chapter 3 of this thesis, I discuss the key error sources associated with solar angle, weather conditions, geolocation and radiometric calibration and estimate their relative contributions to the uncertainty of landscape level NDVI measurements at Qikiqtaruk in the Yukon Territory of Canada. My findings show that these errors can lead to uncertainties of greater than ± 10% in peak season NDVI, but also demonstrate they can be accounted for by improved flight planning, meta-data collection, ground control point deployment, use of reflectance targets and quality control. Satellite data suggest that vegetation productivity in the Arctic tundra has been increasing in recent decades: the tundra is greening. However, the observed trends show a lot of variation: although many parts of the tundra are greening, others show reductions in vegetation productivity (sometimes known as browning), and the satellite-based trends do not always match in situ records of change. Our ability to explain this variation has been limited by the coarse grain sizes of the satellite observations. In Chapter 4, I combined time-series of multispectral drone and satellite imagery (Sentinel 2 and MODIS) of coastal tundra plots at my focal study site Qikiqtaruk to quantify the correspondence among satellite and drone observations of vegetation productivity change across spatial scales. My findings show that NDVI estimates of tundra productivity collected with both platform types correspond well at landscape scales (10 m - 100 m) but demonstrate that the majority of spatial variation in NDVI at the study sites occurs at distances below 10 m and is therefore not captured by the latest generation of publicly available satellite products, like those of the Sentinel 2 satellites. I observed strong differences in mean estimates and variation of vegetation productivity between the dominant vegetation types at the field site. When comparing greening observations over two years, I detected differences in the amount of variation amongst years and a within-season decline in variation towards peak growing season for both years. These results suggest that not only the timing, but also the heterogeneity of tundra landscape phenology can vary within and among years, and if lowered by warming could alter trophic interactions between species. The findings presented in this thesis highlight the importance of the localised processes that influence large-scale patterns and trends in tundra vegetation phenology and productivity. Localised snowmelt timing best explained variation in tundra plant phenology and drone imagery revealed meter-scale heterogeneity in tundra productivity. Research that identifies the most relevant scales at which key biological processes occur is therefore critical to improving our forecasts of ecosystem change in the tundra and resulting feedbacks on the global climate system.

Rapid climate change is a significant threat to the long-term persistence of native tree populations. Concern has been expressed that tree populations might fail to adapt due to rate of change, insufficient adaptive variation in tree populations and limits to dispersal. In contrast, others have contended that most tree species have high phenotypic plasticity, maintain high levels of within-population genetic variation and exhibit effective gene dispersal capability, all characteristics which should enable an adaptive response. To assess the potential adaptability of tree populations we need to understand their genetic diversity and phenotypic plasticity to build on the currently limited evidence base and guide decisions about seed sourcing for establishment of new woodlands desired to meet ambitious planting targets. Currently the seed sourcing system divides the island in four regions of similar size although it is not based on any genetic or ecological information. We discuss the suitability of this system with the insight of the data collected from native tree populations growing in experimental trials. In this thesis we study genetic diversity and phenotypic plasticity patterns in over 30 native tree populations across all Great Britain for three broadleaved species: ash (Fraxinus excelsior), rowan (Sorbus aucuparia), and silver birch (Betula pendula). To obtain these data we assessed the variation in multiple traits in several common garden experiments for each species, which were grown in contrasting environments. There is a tendency in provenance experiments to consider height as a proxy for fitness. We demonstrate that tree height is not enough to understand tree fitness and its adaptability capacity. We assessed our tree populations for growth (survival, tree height, DBH), stem form (number of forks), leaf phenology (leaf flushing and senescence) and leaf anatomical traits (leaf area, stomatal density and stomatal size).Great Britain has very distinct and heterogeneous environments likely to have given rise to adaptive differentiation. Knowing the geographical pattern of the genetic differences we can see the direction selective pressures have had on each of the traits studied, and we compare differences in patterns across the traits and species. Comparing populations growing in different environments we assessed the variation in phenotypic plasticity by trait and the direction of these plasticity. We found that tree populations across Great Britain are highly genetically variable and show genetic differences which have a geographical pattern, and that the patterns and size of the differences vary by species. Phenotypic plasticity varies across traits and interactions between genotype and environment make plasticity in some traits more unpredictable than others. We conclude that tree populations of ash, rowan and birch are well adapted to the diverse and oceanic climate of Great Britain, and that levels of genetic diversity and phenotypic plasticity provide a high capacity to respond to environmental change.

1. Insect pollinators have been shown to alter their foraging patterns in response to habitat and landscape composition, particularly in relation to changes in the availability of floral resources which provide essential pollen and nectar provisions. Changes to pollinator behaviour and community composition, may alter the distance, directness and frequency of pollen movement and thus, the compatibility and genetic relatedness of pollen transferred between plants. We still lack good understanding of how variation in the spatial and temporal availability of floral resources drives pollinator responses and in turn, affects the fitness of outcrossing plants. Knowledge in this area could contribute to improved management interventions to enhance pollination services for plant conservation. 2. Through a combination of habitat and landscape scale field experiments, I explored how the availability of floral resources at different spatial scales affected plant-pollinator interactions, pollen transfer and mating success in plant populations, particularly those isolated from conspecifics. This involved introducing different species of plants in experimental arrays across a range of study systems that varied in structure and floral availability. Over the course of the thesis, I measured the community composition and behaviour of pollinators visiting experimental arrays; focusing on traits considered important for pollen transfer (e.g. Inter-tegular ('IT') span). Pollen movement was quantified within and between populations (5-150m) and the resulting plant outcrossing rates were measured using different methods including paternity analysis and the use of a dominance inheritance system. In addition, the implications of variations in pollinator foraging and pollination services can be attributed to pollen and gene flow and subsequently the reproduction and fitness of plants were assessed as a means of predicting the impacts on longer-term plant survival. 3. Findings from this thesis demonstrate reductions in the activity density (the abundance of actively foraging pollinators) and richness of pollinators and thus, the potential for plant visitation in response to a high abundance of floral resources within a habitat. This led to disruptions in pollen transfer, illustrated through a lower incidence of intra and inter-population pollen movement, and ultimately, reduced plant outcrossing rates. In parallel, plant seed set and germination rates were also reduced in habitats with high resource availability. Changes to pollinator communities and pollination services varied with the spatial scale at which floral resources were measured. Pollinator communities (activity density, richness and IT span) were most affected by floral resource abundance at a local scale (1-50m), particularly within a 20m radius of a plant population. Intra-population pollen movement was similarly affected by floral resources at a local spatial scale (within a 1m radius of a plant population). In contrast, no effect was observed on pollinator communities, intra-population pollen movement or plant reproduction when floral resources were measured at a landscape scale (within a 100-1500m radius of a plant population). However, findings were variable across different experiments at the same scale of measurement. For instance, the availability of floral resources at a local scale did not always elicit an effect on plant reproduction. This reflects differences in plant species identity and the effects of breeding system and floral traits, illustrated through variations in visitation rates between plant species. Inconsistencies were further observed with pollinator activity density and richness, which were not related to floral resources at a habitat scale in one chapter. 4. This thesis highlights the importance of the availability of floral resources at a local scale on plant-pollinator interactions and pollination services to plants. Co-flowering plants within florally rich habitats compete for pollinators and subsequently, visitation and pollen transfer between individuals of low density plant populations is diluted rather than facilitated. This suggests that although pollinator abundance and diversity may be enhanced through florally rich habitats (e.g. habitats implemented under the agri-environment scheme), pollination services are not automatically improved for plants which are present at low frequency in the landscape. This needs to be considered when designing and implementing management for threatened or isolated plants where plants may instead benefit from focused interventions. For instance, pollination services may be increased by efforts to maximise the facilitative effect of surrounding habitats, while increasing the ability of threatened or isolated plants to withstand competition from co-flowering plants.

Integrated Pest Management (IPM) has long been promoted as a means of reducing reliance on pesticide inputs as compared to conventional farming systems. Reduced pesticide application could be beneficial due to the links between intensive pesticide use and negative impacts upon biodiversity and human health as well as the development of pesticide resistance. Work assessing the potential of IPM in cereal production is currently limited, however, and previous findings have generally covered the subject from the perspective of either field trial data or social science studies of farmer behaviour. This thesis attempts to help to address this knowledge gap by providing a more holistic assessment of IPM in Scottish spring barley production (selected because of its dominance in Scotland’s arable production systems), in relation to three of its most damaging fungal pathogens: Rhynchosporium commune, Blumeria graminis f.sp. hordei, and Ramularia collo-cygni. Several IPM techniques of potential relevance to the sector were identified, and the prospects of three in particular – crop rotation, varietal disease resistance, and forecasting disease pressure – were assessed in several ways. Preliminary analysis of experimental field trial data collected from 2011 – 2014 across Scotland found that the majority of spring barley trials in this period (65%) did not show a statistically significant impact of fungicide treatment on yield, with the average yield increase due to fungicide application being 0.62 t/ha. This initial analysis was expanded upon using stepwise regressions of long-term (1996 – 2014) field trial data from the same dataset. Here, the difference between treated and untreated yields could be explained by disease resistance, average seasonal rainfall (whereby wetter seasons saw an increased impact of fungicide use on yield), and high combined disease severity. Stakeholder surveying provided information about current practice and attitudes towards the selected IPM techniques amongst a group of 43 Scottish spring barley farmers and 36 agronomists. Stakeholders were broadly open to taking up IPM measures on farm; sowing of disease resistant varieties was most frequently selected as the best technique in terms of both practicality and cost, though individual preference varied. However, a disparity was seen between farmer perception of their uptake of IPM and actual, self-reported uptake for both varietal disease resistance and rotation. Farmers and agronomists also overestimated the impact of fungicide use as compared with the field trials results – the majority of stakeholders believed fungicide treatment to increase yields by 1 - 2 t/ha, while the majority of 2011 – 2014 field trials had a yield difference of under 1 t/ha. The reasons behind these differences between perception and practice are not currently known. Finally, an annual survey of commercial crops, gathered from 552 farms across Scotland (from 2009 – 2015), highlighted two gaps where IPM practice could be improved upon. Firstly, relatively few of the varieties listed in the commercial crops database were highly resistant to the three diseases – 26.1% were highly resistant to Ramularia, 14.2% to Rhynchosporium, and 58.1% to mildew. Secondly, 71% of the farms included in the database had planted barley in at least two consecutive seasons, indicating that crop rotation practices could be improved. The overarching finding of this project is that there is scope for IPM uptake to be improved upon and fungicide use to be reduced while maintaining high levels of yield in Scottish spring barley production. Incorporating experimental field data, stakeholder surveying, and commercial practice data offered a unique view into the potential for IPM in this sector, and provided insights which could not have been gained through the lens of a single discipline.

Current and emerging threats to trees and forest ecosystems require a re-evaluation of the way forest genetic resources are managed. Governments in the United Kingdom and elsewhere are committed to the restoration, expansion and creation of new woodlands. Tree populations are often adaptively differentiated from one another, so a key question underpinning the success of planting schemes is the choice of seed origin. A long held understanding is that locally sourced seeds will have the best opportunity to tolerate conditions of the planting site (local provenancing). However, the rate at which the environment is changing introduces a great deal of uncertainty into decision making and there is concern that climate change is proceeding at rates faster than those with which locally adapted trees would be able to cope. As such, there are suggestions that seed collected from areas already experiencing the anticipated future conditions will improve the adaptability of forests (predictive provenancing). This thesis investigated outstanding questions relating to the merits of the local provenancing and predictive provenancing approaches, and the practical implementation of seed sourcing policy in British forestry. The validity of existing seed zone boundaries used under local provenancing was analysed for ancient semi-natural Scots pine Pinus sylvestris L. forests of Scotland. Vegetation description and analyses of climatic covariates revealed that the existing series of seed zones used to guide selection of planting stock for restoration do not necessarily environmentally match seed sources to planting sites under current conditions. Additional disparity is introduced when edaphic variation (or proxies for this) is considered. To determine whether future adaptation under local provenancing may be restricted by limited pollen flow among populations of native Scots pine in Scotland, the timing of pollen production in five populations was estimated by repeatedly measuring strobilus development on a series of twenty trees over three consecutive springs. Differences in the mean predicted date of pollen production were found, with populations in the warmer west shedding pollen earliest each year, although the timing and differences in timing among populations varied from year to year, with shedding taking place earliest in the warmest of the three years and latest in the coolest year. A theoretical multi-patch, ecological genetic individual-based model (IBM) was developed to investigate the utility of different seed sourcing strategies (local versus non local provenance) and their capacity to help populations adapt to directional climate change. As well as being adapted to climate, which varied in a clinal pattern, individuals also had to be well adapted to the habitat conditions of the planting site in order to survive hard selection at the seedling stage. The model showed that population size of a new planting was reduced when planting stock adapted to the future conditions but not to current conditions was deployed. The differences were most severe when selection acted simultaneously on both the climate-related and the habitat-related phenotype. Finally, a series of in-depth qualitative surveys conducted with members of the domestic forest nursery and seed supply sector in Great Britain found that there are many difficulties associated with seed sourcing and the supply of trees. These problems arise due to a very limited ability to predict demand at the time of seed sowing, and lead to waste when demand is overestimated and importation of planting stock when demand is underestimated. Confidence and competitiveness in the domestic sector could be greatly improved by updating seed sourcing guidelines and by simplifying certain aspects of the process by which forest planting projects are funded.

Crop yields are coming under pressure to continue to grow in the face of climate change, competition, disease and pressure to reduce inputs. Photosynthetic efficiency is being targeted for improvement to increase yields. This study examined the variation in parameters of photosynthetic efficiency including canopy structure (leaf length, canopy angle, and chlorophyll content and growth rate) and gas exchange (photosynthetic rate, stomatal density and chlorophyll fluorescence) in Spring Barley (Hordeum vulgare ssp vulgare). These were first established for modern cultivars representing the most widely grown lines in the last 60 years. As cultivars are developed from a small pool of parents they may have limited genetic variation available for breeding. Landraces have been suggested as sources of variation. Using field and growth cabinet based studies the photosynthetic efficiencies of canopy structure and gas exchange were established for a range of European landraces under high and low nutrient inputs. This study demonstrated that in modern cultivars the leaf length increased with year of release from 23.2 to 29.6 cm and the chlorophyll content decreased from 46.9 to 34.8 SPAD units. Once the ear had emerged no difference was seen in canopy structure or photosynthetic rate. There was variation in landrace canopy establishment rate, leaf angle and number of leaves present within the canopy. The landraces from Northern European latitudes pushed though booting and reached full canopy establishment up to 8 days sooner than those from Southern Europe. This may be a response to a shorter growth season at Northern latitudes requiring the canopy to be established quickly. The landraces held the leaves within their canopy in a more horizontal position than the Southern European lines with leaf angle ranging from 18-45 degrees at GS39 and 31-84 degrees at GS59. This regressed negatively with temperature so it may be that a vertical canopy structure is beneficial in areas with higher temperatures. The photosynthetic rate of the landraces showed no variation but when chlorophyll fluorescence examined the efficiency of photosystem II (PSII) there was a positive regression of Fv/Fm ratio with latitude. This suggested that lines from Southern Europe were experiencing a greater stress with a ratio of up to 0.822 compared to those lines from the North with ratios from 0.767. The stomatal density of the landraces showed a large difference in ranges from 22-41 stomata between the lines. When high and low nutrient inputs were compared reductions from a ratio of 0.48 to 0.47 in Harvest Index and from 55g to 52g in 1000 grain weight were seen. The chlorophyll content of the lines was also reduced from 41.7 to 39.2 SPAD units at GS39 and from 44.9 to 39.8 SPAD units at GS59 by the reduction in nutrient inputs which may be a result of less N available for the production of chlorophyll. In conclusion there is variation present in canopy structure in European landraces that may be useful for future breeding or in identifying landrace collections which could be targeted for traits of interest in photosynthetic efficiency. These landraces may provide traits which could be used to develop cultivars which are locally adapted to climate and environmental conditions.

Trees and forests are under increasing threat from pathogens which cause huge economic and ecological damage. The unprecedented global movement of pathogens into new areas creates novel pathosystems, while the changing climate affects the dynamics of endemic pathosystems. Co-evolution within endemic pathosystems affects the genetic composition of hosts and pathogens. Spatial heterogeneity in pathogen pressure leads to genetic variation in disease-related traits among host populations. In contrast, novel hosts or populations are expected to be highly susceptible to exotic pathogens as there has been no evolution of defence responses. Host response to disease can therefore be an indicator of a novel or endemic pathosystem. The long term resilience of forests to pathogens depends on the adaptive capacity of both the host and pathogen species. Establishing the extent of genetic and phenotypic variation within both the host and pathogen is therefore fundamental in understanding past, current and future pathosystem dynamics. The most significant current threat to Scots pine (Pinus sylvestris) is Dothistroma needle blight (DNB) caused by the foliar pathogen Dothistroma septosporum which is assumed to be exotic to Great Britain. This study aimed to increase understanding of the genetic and phenotypic variation in this pathosystem. Results from this study show that there are high levels of variation in the Dothistroma – Pinus pathosystem. Genetic variation, elucidated using neutral genetic markers, mating type specific markers and in vitro analysis of phenotypic variation in D. septosporum collected from Scottish pinewoods, was found to be high: there was high allelic diversity, particularly within plantation forests outside the native pinewood range, and high phenotypic plasticity in response to different temperature treatments. Both mating type idiomorphs were found in one forest which demonstrates their potential for sexual as well as asexual reproduction. There is also tentative evidence from this study that the pathogen is either introduced to Great Britain or that endemic pathogen populations have been augmented with introduced pathogens. Artificial and natural inoculations of native Scots pine provenances with D. septosporum indicate that there is considerable variation in susceptibility to DNB across the native range in Scotland and that variation in this trait is both highly heritable and evolvable. Furthermore, provenance mean susceptibility to DNB is negatively and significantly associated with water-related variables at site of origin, a finding that is potentially indicative of a co-evolutionary history between host and pathogen. Genetic differences among individuals which are ‘resistant’ or ‘susceptible’ to DNB were identified in Pinus radiata for which there has been extensive research in this pathosystem, by comparing the transcriptome sequences of the two phenotypic groups. Nearly half of the genetic differences identified among phenotypes were found in genes with a putative defence function. In conclusion, native Scots pine provenances contain the necessary heritable genetic diversity to evolve a decrease in their susceptibility to D. septosporum through natural selection in response to elevated prevalence of this pathogen. However, implementation of key native pinewood management strategies, including encouraging regeneration in particular, are necessary in order to facilitate the adaptive evolution of native forests to increased levels of DNB. The effectiveness of this response will depend on the rapidity of adaptation of the pathogen. Measures to limit adaptation where possible, including the use of pathogen monitoring and control in nurseries and the limitation of pathogen movement into native pinewoods, should be continued.

It is common for pigs to engage in physical aggression when mixed into new social groups, in order to establish dominance relationships. Phenotyping aggression is time consuming, however skin lesions resulting from physical aggression are quick to record, are genetically correlated with aggressive behavioural traits, and have low to moderate heritability (0.19 to 0.43). Reducing aggression via selection on skin lesion traits would provide a socially acceptable, long-term solution to the problem. Barriers to implementing selection against skin lesions lie in the lack of understanding regarding the underlying genetic basis of aggression, and its relationship with other behaviour and production traits. This thesis has focused on dissecting the phenotypic and genetic relationship between skin lesions recorded 24 hours after mixing (SL24h), and either 3 or 5 weeks later (SL3wk/SL5wk, respectively), with aggression performed at mixing, and several production traits. Chapter 2 provided evidence of a potential trade-off between involvement in aggression upon first mixing, and receipt of aggressive attacks several weeks after mixing. In particular, animals that avoid aggression at mixing had the highest fresh skin lesion numbers at 3 weeks. This suggests that reciprocal fighting at mixing may be beneficial for long-term group social stability. It also suggests that it may be possible to phenotype the least aggressive individuals in a group using SL3wk. In Chapter 3, I quantified the magnitude of reduction in complex aggressive behavioural traits when using SL24h or SL3wk as selection criteria, to identify the optimum skin lesion trait for selection purposes. The results of Chapter 3 provided evidence that selection against anterior SL24h would result in the greatest genetic and phenotypic reduction in aggressive behaviour recorded at mixing. Although there is evidence that selection for increased SL3wk would reduce aggression at mixing, current understanding of aggressive behaviour under stable group conditions is insufficient to recommend using this trait for selection purposes. Chapter 4, presented genetic associations between skin lesion traits as a measure of short- and long-term aggression, and commonly used commercial performance measures: growth, feed intake, feed efficiency, and carcass traits. The results suggested that, genetically, animals that receive many lesions show improved performance compared to those with few lesions, except for anterior SL24h, which have been shown to be genetically positively correlated with the initiation of nonreciprocal attacks. The aim of Chapter 5, was to determine whether skin lesion traits are phenotypically or genetically associated with behavioural measures of fearfulness. As found in Chapter 4, there was some evidence of an association between SL5wk and the traits, however this was not the case for anterior SL24h. For the 6th and final Chapter, we used skin lesion data from 1,840 pigs to perform genome wide association studies (GWAS), which detected a single SNP significantly associated with SL5wk on a genome wide level, as well as several SNPs associated with both SL24h and SL5wk on a chromosome wide level.

The remnants of the Caledonian Pine Forest represent the north western boundary of the Eurasian Pinus sylvestris (L.) distribution. Remnant populations occupy a diverse range of environments within Scotland, subject to a steep rainfall gradient, and previous investigations have found evidence of local adaptation. Additionally, studies of biochemical and molecular markers have indicated that Scotland’s native pinewoods originated from more than one glacial refugium. Whole-genome-shotgun (WGS) sequencing was employed for the discovery of mitochondrial (mt) variants that may provide further insight into the origins of P. sylvestris populations both in Scotland and mainland Europe. DNA extractions were performed on megagametophyte tissue from Scottish, Finnish, and Spanish populations. Three members of the closely related P. mugo species complex were also sequenced. Using similarity-based approach, 160kbp of putative mitochondrial sequence was recovered by comparison of de novo assembled contigs with the mtgenome of the gymnosperm Cycas taitungensis. In total, 16 novel variants were identified among samples, which may be used in future phylogeographic studies. A study of needle characters was performed for eight native populations of P. sylvestris in an outdoor provenance/progeny trial of 192 saplings. A negative correlation was detected between longitude and the number of stomatal rows present on needle surfaces. It was posited that this may be an adaptive response to lower water availability in eastern pinewoods, possibly in conjunction with increasing altitude. The west coast of Scotland is one of the wettest regions in Europe: western pinewoods may receive in excess of 3,000mm of rainfall in a year, compared with an average of 800mm eastern sites. To determine whether native pinewoods are differentially adapted to waterlogging, a glasshouse based provenance/progeny trial of 432 saplings from nine native populations was undertaken, in which 50% were subject to a long-term waterlogging treatment, and the remainder used as a control. Two studies were then conducted. In the first, responses to the treatment were assessed in terms of phenological and growth traits. Bud flush was delayed in response to waterlogging, and growth was impeded relative to the control. Although population differences were observed, treatment × population interactions were not detected. In the second study physiological traits known to be sensitive to plant stress and water balance were measured at intervals throughout the experiment. Prior to the commencement of the treatment needle δ13C was found to exhibit interpopulation differentiation, and was positively correlated with longitude. This seems likely to represent differential selection for water use efficiency between eastern and western pinewoods. Photochemical efficiency and stomatal conductance were found to be reduced by waterlogging, and needle δ13C was increased. After generalising populations into ‘high’ and ‘low’ rainfall groups (monthly averages of 214.9mm and 72.8mm, respectively), high rainfall populations were observed to maintain consistently higher photochemical efficiency under waterlogging the low rainfall populations. In addition, the low rainfall group exhibited greater variability in response to flooding (in terms of phenotypic and additive genetic variance) which may be indicative of a lack of past selection pressure.

Ramularia collo-cygni (Rcc) is a damaging fungal pathogen of barley (Hordeum vulgare). It is a causal agent of Ramularia Leaf Spot (RLS), which contributes to significant economic yield losses worldwide. Protection against the disease has been, and is currently, based on foliar fungicide applications as available seed treatments are not effective and there are no fully resistant barley varieties. Two groups of systemic fungicides, Succinate Dehydrogenase Inhibitors (SDHIs) and DeMethylation Inhibitors in sterol biosynthesis (DMIs), are used and in addition a protectant multisite inhibitor chlorothalonil has been used to minimise the damaging effects of RLS in barley. SDHI fungicides have been extensively used in cereals since 2005 in the UK. Resistance outbreaks to SDHIs have been reported in several plant pathogenic fungi. The risk of resistance in Rcc was unstudied and so this study aimed to develop the methodologies needed to screen populations, establish baseline sensitivity data, evaluate the risk of evolution of fungicide resistance to SDHIs in the population of Rcc and make recommendations on appropriate anti-resistance strategies to minimise the risk. A combined approach of SDHIs’ field performance under different application regimes, sensitivity testing in vitro, molecular analysis of resistance mutations and studies of the genetic structure of populations was used. The results in this study demonstrated that currently SDHI foliar applications remain effective in controlling RLS in barley. The most consistent control was observed when applying them in mixtures with DMIs. All of the tested field isolates were in the range of baseline sensitivity to SDHIs and no shifts between years and different applications regimes were observed. The molecular characterisation of Rcc resistant mutants developed in UV mutagenesis studies revealed that in four out of five mutants a single amino acid change in a target succinate dehydrogenase (Sdh) protein was associated with decrease in sensitivity to SDHIs. All of these mutations, with the exception of one mutant, were stable in the absence of SDHI fungicide. The analysis of fitness components indicated that mutated strains did not confer a fitness penalty associated with the mutation when measuring the growth in vitro. Additionally a detached leaf assay performed for two selected mutants with high or moderate resistant factors showed that the resistant phenotypes were able to colonise the leaf surface and reproduce successfully. Thus if the resistance was to develop due to these point mutations in the target Sdh gene, mutated phenotypes are likely to be fit enough to outcompete the sensitive population. Analysis of the genetic structure of the Rcc populations demonstrated that the pathogen is highly diverse, is likely to undergo sexual reproduction over the growing season (the sexual stage remains undiscovered) and has a potential for extensive spore dispersal across the field. Thus Rcc has a high evolutionary potential and could adapt to different control measures relatively quickly. In the 2012 growing season, two field phenotypes with reduced sensitivity to SDHIs were identified as a consequence of sensitivity monitoring in vitro. Neither of the isolates had any nucleotide or amino acid changes in the target Sdh gene and the mechanism responsible for the resistance in these two strains remains unknown. One of the field isolates was tested in planta and exhibited abnormal growth on the leaf surface. This could result either from fitness costs incurred due to resistance or the fact that this isolate does not belong to the Rcc species, a possibility which must be further investigated. In conclusion, SDHI fungicides remain effective in controlling RLS in barley, however this study demonstrated that there is a risk of measurable loss of efficacy in field conditions. Thus monitoring studies should be intensified and integrated crop management practices applied to prolong the life span of SDHI fungicide treatments.

Dairy production systems are an important global contributor to anthropogenic greenhouse gas (GHG) emissions including methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2). Due to the role GHG play in climate change, it is important to investigate ways to minimise their global warming potential (GWP) and to maximise the efficiency of dairy production systems. Finding a balance between improving productivity and suppressing the range and quantity of GHG produced in dairy production is crucial in order to maintain sustainability in the future. The Langhill herd is part of a long term genetic x feeding systems study, representative of a range of dairy production systems which may be found in the UK. Two feeding regimes (low forage (LF) and high forage (HF)) were applied to each of two genetic lines (control (C) and select (S) genetic merit for milk fat plus protein) giving four contrasting dairy production systems (LFC, LFS, HFC, HFS). Biological efficiency (production and energetic) and environmental efficiency (GWP) were assessed by way of life cycle analysis (LCA), accounting for dairy system inputs and outputs from off-farm production of imported feeds and fertilisers to raw milk leaving the farm gate over a period of seven years. Calculations were conducted using the Intergovernmental Panel on Climate Change (IPCC) methods, with system specific data implemented where possible. Select genetic line under low forage regime (LFS) had the highest gross production and energetic efficiencies (p<0.001). In LFS, milk yields were 56% higher per cow than the lowest ranked HFC system, representing a difference of around 3500kg per cow. Milk solids yield per kg dry matter intake was 18% higher in LFS compared to HFC. High forage with control genetic line required 17% more net energy intake than LFS to produce each kg of milk solids. LFS allocated the highest proportion of net energy to lactating after accounting for body maintenance (p<0.001). Rate of change in efficiency throughout lactation varied significantly (p<0.001) amongst systems, with loss of efficiency minimised in LFS and greatest in HFC. However, LFS involuntary culling rate was significantly higher than other systems (p<0.001). LFS was the most environmentally efficient system and HFC the least (p<0.001), both per unit productivity and per unit total land use. Implementing low forage regime with select genetic line lowered GWP per kg energy corrected milk (ECM) by 24% compared to HFC (p<0.001). GWP of LFC was around 8% lower per kg ECM than HFS (p<0.001). Methane from enteric fermentation contributed the greatest proportion of overall GWP (46-49%) in all systems. However, key factors in the differences amongst systems were higher off-farm CO2 equivalent emissions under low forage, and higher on-farm N2O emissions under high forage regime. HFC produced 91% more nitrous oxide per kg ECM from animal manures compared to LFS, and 65% more N2O from applied manufactured fertilisers (p<0.001). Conversely GWP associated with off-farm production of imported feeds in LFS was 11% higher than in HFC (p<0.001). In low forage systems high gross emissions were offset by high productivity but this was not the case for the high forage systems. Cows of high genetic merit managed under a Low Forage feeding regime had improved production, energetic and environmental efficiencies. However, issues with animal health and fertility raise questions about long term sustainability of the LFS dairy production system, emphasising the importance of examining trade offs between systems.

On-farm assessment of cattle health, behaviour and welfare is often a logistical challenge but necessary for ensuring high standards of welfare and production. Recently, technological advances in engineering have allowed the mass manufacture of biotelemetry systems for use in research and industry. A commercial dairy farm may now have many different systems recording information about each individual animal in the herd. One such biotelemetry system is the collection of activity data via activity monitors. These devices were initially used by farmers to detect oestrus bouts through the resulting rise in activity and over the years have been improved to collect highly accurate and specific data about lying, standing and steps recorded over long periods of time. Long term, unobtrusive recording of individual cattle activity patterns is now becoming a reality on several farms. This raises the possibility of utilising sensors to remotely quantify aspects of cattle behaviour and welfare across different farms relatively quickly, allowing for the improvement of management and breeding strategies. Before this can be achieved, there needs to be a solid understanding of how behaviour affects activity patterns and how such data should be handled. In this project, the IceTag (IceRobotics Ltd., South Queensferry, UK), was used as a biotelemetry system for recording the activity of cattle. The IceTag is a tri-axial accelerometer activity monitor with a sample rate of 16Hz which has been shown to be sensitive (i.e. few false negatives) and specific (i.e. few false positives) when recording lying and standing behaviour on adult cattle. Cattle’s individual variation in behaviour was used as a case study to investigate the usage of this type of biotelemetry system. There were two phases to the study. In the first phase, the capabilities and limitations of the IceTag sensor were investigated. This involved assessing the extent of behavioural reactions to the IceTag in cattle. The behaviour of 28 lactating dairy cattle at the SRUC Dairy Research Centre was assessed for an adverse behavioural effect of the tags. The results of this study recommended a period of 48 hours from attachment before cattle grew accustomed to wearing the tag. Following this, the capabilities of the tags were assessed. Activity traits calculated directly from the tag and derived from tag data were analysed with respect to performance in four short term tests of temperament in 67 beef steers at the SRUC Beef Unit. From this work, the good repeatability of activity traits including average bout length, daily MotionIndex and daily step count encouraged their further usage. Steers which responded fearfully in a temperament test had higher MotionIndex in the home pen (rs = 0.35, P = 0.004) and steers which were more capable of displacing other steers at feeding stations also had longer average standing bouts (rs = 0.26, P = 0.036) and were more variable in their total daily standing duration (rs = 0.27, P = 0.030). This suggested that fear and sociability related behaviours can be detected through analysis of activity patterns. This work was continued at Wageningen University’s Dairy Research Centre where activity was recorded in over 100 dairy cattle. Activity recorded over a forty day period could explain some of the variation in behaviours seen during a subsequent fear test, but not in a social motivation test. The trait ‘neophobia’ was associated with more lying bouts and a greater variation in lying bout duration in dairy cows (R2 adj = 0.15, F3,75 = 5.32, P = 0.002) and bold cows also showed less variation in their lying bout durations (R2 adj = 0.11, F2,75 = 5.63, P = 0.005). In conclusion, remote sensors are a useful addition to the ethologist’s toolbox, enabling researchers to gain some insight into how fearfully a cow may react without assessing this through on-farm behavioural testing. Moreover, this work has found that the effects of personality which can be observed in behavioural testing can also be observed in spontaneous behaviour in the home pen away from testing environments. Biotelemetry systems can be utilised as a welfare assessment tool as they record repeatable activity traits which relate to underlying behavioural dimensions linked to the cow’s behavioural response to stimuli.

In the UK, nearly half of the plants short listed for high conservation priority in the UK Biodiversity Action Plan are found in taxonomically complex groups. It is thought that a shift from species- to process-based conservation strategies, aimed at conserving the processes that generate diversity as opposed to simply the end product of these dynamic interactions, may benefit these groups. One group for which this strategy has been proposed is tetraploid Euphrasia. The underlying taxonomic complexity in this group is hypothesised to arise via breeding systems, hybridisation and local ecotypic adaptation. The goal of this thesis is to use morphological, ecological and molecular marker data to examine taxon limits and evolutionary processes in order to further understand the mechanisms involved in maintaining species boundaries and generating taxonomic complexity in tetraploid Euphrasia. This will not only make conservation in this group more effective, but will also provide a broader insight into some of the processes involved in plant speciation. A detailed study of two widespread, small flowered, tetraploid taxa, E. micrantha and E. scottica, showed that offspring are almost exclusively the result of self-fertilization. These taxa maintain distinctive morphologies, habitat preferences and chloroplast DNA variation throughout their range, suggesting that they represent coherent lineages within Scotland. As in other widespread inbreeding species, there are high levels of microsatellite differentiation among different populations of the same species. In northwest Scotland three complex populations of tetraploid Euphrasia were identified which comprised an array of many different morphs (recognised species, and putative hybrids). Analysis of chloroplast and microsatellite markers suggests that these different morphs represent distinct genetic groups. Within each site there is evidence both for habitat heterogeneity, and for association of morphs with this habitat variation. Intermediate morphs were not simple F1 hybrids, but are likely to have originated via hybridisation and subsequent selfing, surviving as independent recombinant lines, perhaps specialised for habitat types different from that of their progenitor parents. These stable morphs of hybrid origin could represent groups with adaptive potential that may result in the origin of a novel Euphrasia species. It will be important to further examine the processes involved in generating novel diversity in Euphrasia. For the time being, these complex populations must be recognised as sites requiring special protection within the context of a process-based conservation strategy.

Begonia L. is one of the largest plant genera, comprising over 1500 species. Weak species cohesion, and the rapid evolution of reproductive barriers in allopatry, are two processes that have been postulated to explain the generation of such hyper-diversity of taxa within a single genus of plants. The aim of this thesis is to investigate whether these factors are likely to have been important contributors to the diversity of species found in Central American Begonia. Species cohesion was analysed in the widespread Central American species Begonia heracleifolia and B. nelumbiifolia. Interpopulation seed flow was estimated with seven plastid microsatellites. Breeding system estimates and measures of genetic differentiation at nine nuclear microsatellites were used to infer levels of interpopulation pollen flow. Controlled crosses were employed to assess the strength of reproductive barriers both between populations within species, and between species differing in ecology. The potential for gene flow between species in the wild was assessed in natural hybrid zones using molecular markers. Finally a quantitative trait locus (QTL) approach was employed to investigate the genetic basis of reproductive traits that differ between species. No plastid polymorphisms were found in B. nelumbiifolia, suggesting it has been through a recent population bottleneck. In contrast, B. heracleifolia possessed many plastid haplotypes that were strongly differentiated between populations (G’ST = 0.829). Nuclear microsatellites showed high genetic differentiation within species, and both species were self-compatible and self-fertilize at a moderate rate (B. heracleifolia F’ST = 0.506, FIS = 0.249; B. nelumbiifolia F’ST = 0.439, FIS = 0.380). F1s between ecologically similar B. heracleifolia and B. sericoneura were partly fertile (2-5% seed set), and F1s and early generation backcrosses were found in a hybrid swarm. F1s between B. heracleifolia and the ecologically contrasting B. nelumbiifolia were pollen sterile, and 3 hybrid swarms showed no evidence of hybrids beyond the F1 generation. Seven QTL were found for reproductive traits, including: sex ratio, pollen sterility and stamen number. The population biology of Begonia, with limited seed and pollen dispersal, small population sizes and frequent self-fertilization predisposes them to genetic isolation, increasing the chances that reproductive barriers evolve. These characteristics may underlie the large number of endemics in Begonia.

Species interactions are recognised as an important evolutionary process, with foundation species in particular being of exceptional importance. Foundation species are those species exhibiting dynamic physical traits, under strong genetic control, that shape the natural processes of habitats and ecosystems. These traits lead to extended consequences for the associated organisms in their community. Therefore, intra-specific variation of a foundation species can have important evolutionary consequences for habitats, communities and entire ecosystems. One such foundation species is aspen (Populus tremula L.), which has important conservation value, particularly for the high diversity of associated species. In Scotland aspen exists in fragmented clonal patches, but has been found to contain a high diversity of associated organisms some of which have a UK Biodiversity Action Plan (BAP). One such group of organisms of high diversity and conservation value in Scotland are the epiphytic cryptogams (i.e. mosses, liverworts, lichens). To date more than 300 species have been recorded on aspen in Scotland, comprising approximately 40% of the epiphyte flora of Europe. The research presented here uses a combination of natural aspen system and two aspen common gardens to test the effects of aspen genetic diversity on physical traits potentially important for epiphyte diversity. The traits investigated were bark texture and bark phenolic chemistry. Bark texture in the wild clones was found vary significantly between clones and under strong genetic control (up to 40%). Bark phenolic chemistry also showed significant genotypic variation, but could not be correlated with patterns of epiphyte species richness and diversity. Nevertheless, epiphytes showed significant patterns related to aspen genotype, particularly along a gradient of bark texture. The results indicate that epiphyte communities are part of the ‘extended phenotype’ of native aspen populations in Scotland are very important for maintaining current levels of epiphyte diversity. A greater diversity and abundance of aspen genotypes in the landscape are essential for increasing epiphyte species richness and diversity, and for ecosystem health as a whole.

This thesis is a phylogeographic investigation into plant species from Patagonia, and aims to infer their past distributions from the study of genealogical lineages. These species have gone through several events such as glacial periods, volcanism and topographical change which are expected to contribute to the divergence of genetic lineages by shaping distributions, isolating populations and therefore changing their genetic structure. So understanding how these processes have affected populations is important to get information on how the biodiversity in the region has been assembled, to identify hotspots of intra-specific diversity and therefore to establish potential conservation priorities. Several multi-species phylogeographic studies have been done in the northern hemisphere, but only few are published for South America and even less for the studied area. Patagonia is an area of a great interest because is the only area in the southern hemisphere apart from Antarctica that have been covered buy a thick layer of ice within the glacial periods. It has high levels of endemism, due to its natural boundaries and environmental processes, and is a biodiversity hotspot for conservation. Its varied topography (two big mountain ranges with a north-south distribution divided by a low flat area) also makes Patagonia interesting to study, due to the likelihood of this impacting on phylogeographic patterns. This study encompass seven different Patagonian species of which one is a range restricted conifer and the rest are all angiosperms and include trees, shrubs and herbs with a broad distributions. The reason why I have chosen so many different species is to look for general phylogeographic patterns in species in this region. The thesis was constructed in five chapters. The first is an introductory chapter that provides background to the study system and concepts. Chapters 2, 3, and 4 are empirical phylogeographic studies. These are written as self-contained chapters with the intention that each will be submitted as a separate paper. This leads to some repetition between chapters, but this is intentional as each will need to ‘stand alone’ when submitted for publication. Chapter 2 is a general investigation into five different Patagonian plant species: Discaria chacaye, Donatia fascicularis, Escallonia virgata, Tepualia stipularis and Weinmannia trichosperma. Chapter 3 describes the phylogeographic structure of Gentianella magellanica an annual, cold tolerant species with a wide distribution throughout Patagonia. This species was treated separately and in more detail than the previous five species due to its marked phylogeographic structure. Chapter 4 describes the phylogeographic structure of a Chilean endemic conifer Prumnopitys andina. This has a small distribution in the Andes and only one known population in the coastal cordillera. It was treated separately due to its restricted distribution and different mode of chloroplast inheritance (paternal). Chapter 5, is a general summary, bring all of the results together and giving a wider explanation of the phylogeographic patterns for all species and an outline of future research areas.

Genetic differentiation in phenotypic traits among populations from heterogeneous environments is often observed in common-garden studies on forest trees, but data on adaptive variation in Scots pine (Pinus sylvestris L.) in Scotland are limited. As a result, current seed transfer guidelines are based on earlier molecular marker studies and do not take into account environmental or adaptive genetic variation. An analysis of spatial variation in climate showed substantial differences in temperature and precipitation among the native Scots pine sites in Scotland. To investigate whether differentiation in response to environmental variation has occurred in Scotland, a glasshouse-based common-garden trial of ~3,360 seedlings from 21 populations and 84 open-pollinated families was established in 2007. At the beginning of the 2nd growing season, timing of bud flush showed evidence of genetic differentiation among populations, with those from cooler origins generally flushing earlier. Variation was also found among families within populations, suggesting that the trait is genetically controlled. Populations and families showed different levels of variability in this trait which could be partly due to variable levels of temporal climate fluctuation in different parts of Scotland. Chlorophyll fluorescence was used to examine drought response in three-year old seedlings from five populations on sites that experience contrasting levels of annual rainfall. It was found that the response was not related to rainfall, but possibly to more complex moisture variables that also take into account additional factors such as evaporation. Also, photosynthetic capacity in response to cold winter temperatures varied significantly among eight populations that were kept outdoors, and the largest reduction was seen in seedlings from the mildest, most maritime coastal site. The following spring, height growth and needle flush started earlier in seedlings from cooler locations. Earlier studies on genetic diversity of native pinewoods have shown high levels of selectively neutral variation in this predominantly outcrossing conifer, and a mating system analysis with a limited number of microsatellite markers supported this pattern. Together, these data suggest that despite significant historic population size decrease, environmental gradients have resulted in genetic differentiation among native pinewoods. In order to minimise the risk of planting poorly-adapted stock and to maximise the success of replanting programmes, it is important that the origins of planting stock are carefully considered in management guidelines for the species.

Theoretical considerations predict that hybridization between plants with different breeding systems could potentially be a powerful evolutionary force but very few studies have been carried out to investigate hybridization among outcrossing and selfing species in natural populations. The objective of this thesis was to use G. urbanum and G. rivale, two freely hybridizing species with putatively different breeding systems, and study the processes that take place when the two different mating systems meet. To establish the extent of the morpholofical and genetic marker differences, the breeding system and levels of inbreeding depression in these two species, I examined reference populations from various locations in Great Britain using morphological (nine phenotypic traits) and genetic analyses of a long standing hybrid swarm between G. urbanum and G. rivale, the results revealed that the two parental species differed signigicanly in all nine traits measured and were clearly separated by 616 AFLP markers, of which 8% were species-specific. The breeding system analysis confirmed the highly selfing nature of G. urbanum and the outcrossing nature of G. rivale. No inbreeding depression was discovered in G. urbanum and very low levels in G. rivale. The AFLP analysis (203 loci) of the hybrid swarm showd that four distinct genetic groups can be distinguished (1) a parental G. urbanum life group (2) an F1 like group (3) a Backcross Rivale group and (4) a parental G. rivale like group. No Backcross Urbanum individuals were detected. Morphological data were hightly correlated with genetic data (Spearman Rank Order Correlation = 0.08,p<0.0001) but less informative as morphological data could not separate the Backcross Rivale samples from G. rivale. Analysis of seed progeny from the hybrid swarm showed that there were clear differences in the genotypic composition of the seed porgeny and the plants from which they were collected, revealing additional genetic classes such as Backcross Urbanum individuals which were not represented in the adult plant state. The Backcross Rivale parental group was the only one in which the average offspring position did not differ signigicantly from the mean parental psition in a PCO plot using 203 AFLP markers, indicating that this group might be reporductively isolated from other groups in the hybrid swarm. Taken together the results suggest that hybridization between G. urbanum and G. rivale results in the production of a range of genotypic and phenotypic classes, some of which are selected against. There is evidence for introgression between these two species, and tentative evidence for partial reporduction isolation of some hybrids suggestion that hybridisation between these outcrossing and selfing Geum species may represent a creative evolutionary force.

The genus Cochlearia is a taxonomically complex genus with a circumpolar distribution. In common with many other post-glacial colonisers it exhibits complex patterns of morphological and ecological variation. The genus has been the subject of continued taxonomic controversy, especially within the species complex C. officinalis s.l. The focus of this study was to investigate whether the three rare putative endemic Cochlearia officinalis s.l. taxa in Britain: C. micacea, C. officinalis subsp. scotica and C. atlantica were sufficiently distinctive to warrant endemic species or taxon status at any rank. Furthermore, to make conservation recommendations for the species complex based on the outcome of this investigation. The patterns of differentiation in Cochlearia were studied to gain insight into the processes that have driven morphological and ecological diversification in the group. The six putative taxa in Cochlearia officinalis s.l. were considered in this study: C. officinalis s.s., C. officinalis subsp. scotica, C. pyrenaica subsp. pyrenaica, C. pyrenaica subsp. alpina, C. atlantica and C. micacea. Samples of C. danica, a member of the wider genus Cochlearia, were also included for comparison. The samples were screened for variation in AFLP fragments, morphological characters and chloroplast haplotypes. This is the first study focussed on the British Cochlearia to use the amplified fragment length polymorphism (AFLP) technique. Many qualitative morphological characters differences between populations were maintained in cultivation under standard conditions. Variation in some quantitative morphological characters was significantly different between taxon groups. The morphological characters combined did not distinguish between taxonomic groups. Variation was found in samples from the uplands only. Although there were three chloroplast haplotypes all but 6 out of 96 samples had the same haplotype and the chloroplast was not taxonomically informative. The AFLP data did not vary significantly between taxonomic groups, ploidy levels, habitats or geographical regions. There was significant AFLP variation between populations. The morphological and ecological diversity present among populations of Cochlearia officinalis s.l. in Britain is most likely to result from local ecotypic differentiation. The variation in Cochlearia officinalis s.l. could not be divided satisfactorily into taxa of species rank and so specific conservation of taxa within the complex is not recommended. Instead the maintenance of Cochlearia diversity can be achieved by the continued protection of the habitats in which the ecotypes grow.

Increased interest in native woodlands has exposed gaps in our knowledge of our native species. Aspen (Populus tremula L.), one such species, is of considerable conservation value though has been subject to very little previous research. It is widely distributed in Scotland at low density occupying a marginalised niche. Aspen is dioecious but reproduces mainly by asexual means and recruitment is reputed to occur only very rarely. Low population density , a marginal niche and an inability to colonise new sites renders the Scottish aspen resource potentially vulnerable to genetic erosion from natural and anthropogenic disturbance potentially compromising its long term future. Intervention is clearly required. Successful conservation management requires a thorough understanding of genetic structure at the national, regional and stand scale. The genetic structure of the Scottish native aspen resource was therefore investigated at the national, regional and stand scales using selectively neutral molecular markers. Isozyme analysis was used to estimate genetic variation and investigate population structure and genetic differentiation in six Scottish aspen populations. Eight systems, yielding eleven putative loci, were employed in screening 275 aspen samples. Genetic variation was shown to be greater than mean values obtained for species sharing similar characteristics and comparable with the homologous species P. tremuloides (Pp=54.5, Hep=0.174, Ap=2.00. Aes=0.121) suggesting that no significant loss of genetic variation has occurred. Some inbreeding was detected (f=0.153) and attributed to assortive mating between a small subset of clones retaining sexual function. A small but significant amount of structuring was detected (q 0.014) although UPMGA clustering of genetic identity (I) indicated little differentiation amongst populations providing little support of r a multiple origin hypothesis. It is concluded that the genetic structure in the present Scottish native aspen resource (SNAR) is little changed from the genetic structure in the SNAR when aspen ceased widespread flowering. The genetic structure of Tomnagowhan Wood, Strathspey, Scotland's largest aspen dominated woodland, was investigated using the same suite of markers. 186 aspen were samples, mapped and genotyped in an area of 4.6 ha. Twenty one clones were identified using a combination of isozyme analysis and probability theory. Clonal diversity in large aspen stands would appear much greater than is often asserted. A wide variety of clone sizes and strategies were also uncovered and leaf flushing date was shown to be an efficient phenotypic clonal marker. Analysis of the distribution of DBH suggests that aspen ramets flow a 'window of opportunity' mode of regeneration with the last burst of regeneration occurring around World War II in Tomnagowhan. Genotypic diversity in the small relict island apsen population of Orkney was estimated using the same suite of markers. Fifteen aspen locations were sampled. Multi-locus genotyping, probability theory and local knowledge were used to identify 12 independent clones. A review of the literature and legislation on the "safe" minimum number of clones to use in plantations suggests that the twelve Orkney aspen clones are sufficient to be safely used in the expansion of native woodland in Orkney thus enabling only locally derived stock to be used. The findings of the three surveys are discussed within an ecological and historical context providing a basis for recommendations for the future management and genetic conservation of the Scottish native aspen resource including guidelines on the conservation of the existing resources, expansion of the resource, the production and deployment of aspen planting stock and strategic initiatives.