European ash trees (Fraxinus excelsior ) are under threat from the fungal pathogen Hy- menoscyphus fraxineus causing ash dieback disease (ADB). Previous research has shown heritable variation in ADB susceptibility in natural ash populations. Prior to this project, very little genetic data were available for ash, thus hampering efforts to identify markers associated with susceptibility. In this thesis, I have presented nuclear and organellar assemblies of the 880 Mbp F. excelsior genome, with a combined N50 scaffold size of over 100 kbp. Using Ks distributions for six plant species, I found evidence for two whole genome duplication (WGD) events in the history of the ash lineage, one potentially shared with olive (Ks 0.4), and one potentially with other members of the Lamiales order (Ks 0.7). Using a further 38 genome sequences from trees originating throughout Europe, I found little evidence of any population structure throughout the European range of F.excelsior, but nd a substantial decrease in effective population size, both in the distant (from 10 mya) and recent past. Linkage disequilibrium is low at small distances between loci, with an r2 of 0.15 at a few hundred bp, but decays slowly from this point. From whole genome DNA methylation data of twenty F. excelsior and F. mandshurica trees, I identi ed 665 Differ- entially Methylated Regions (DMRs) between those with high and low ADB susceptibility. Of genes putatively duplicated in historical WGD events, an average of 25.9% were differen- tially methylated in at least one cytosine context, possibly indicative of unequal silencing. Finally, I found some variability in methylation patterns among clonal replicates (Pearson's correlation coefficient 0.960), but this was less than the variability found between different genotypes ( 0.955). The results from this project and the genome sequence especially, will be valuable to researchers aiming to breed or select ash trees with low susceptibility to ADB.

Forests are a critical biome but are under threat from unprecedented global change. The need to understand forest dynamics across spatial, temporal and biological scales has never been greater. Critical to this will be understanding how the demographic rates of individuals translate into patterns of species diversity, biomass and carbon turnover at much larger scales. In this thesis, I present a modelling framework focussed on demography. In Chapter 2, I introduce methods for translating forest inventory data into population models that account for the size-dependency of vital rates and persistent differences in individual performance. Outbreaks of forest pest and pathogens are increasing in frequency and severity, with consequences for biodiversity and forest structure. In Chapter 3, I explore the impact of ash dieback on the community dynamics of a British woodland, describing a spatially explicit individual based model that captures the effect of an opening of the canopy on local competitive interactions. Chapter 4 introduces methods to infer the impact of historical deer herbivory on the juvenile survival of forest trees. The approach is generalisable and could be applied to any forest in which patterns of regeneration and community structure have been impacted by periodic disturbance (e.g. forest fires). Finding meaningful ways of incorporating species diversity into global vegetation models is increasingly recognised as a research priority. In Chapter 5, I explore the diversity of demographic rates in a tropical forest community and identify groups of species with similar life history strategies. I discuss the potential of integrating demographic and physiological traits as a way to aggregate species for inclusion in global models. In summary, translating measurements of individuals into population dynamics provides opportunities to both explore small-scale community responses to disturbance events, and to feed into much larger scale vegetation models.

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Ash dieback is a severe disease of ash trees (Fraxinus spp.), caused by the invasive fungus Hymenoscyphus fraxineus. In its native East Asia, H. fraxineus is a harmless endophyte, but since its accidental import into Europe in the early 1990s it has infected over 90% of ash trees in some areas, with long-term mortality sometimes exceeding 90%. The disease was discovered in Great Britain in 2012, and has since spread rapidly. This thesis investigates some of the possible impacts on biodiversity, ecosystem functioning, and society, and in doing so identifies ways to alleviate some impacts. Britain has only 13% tree cover (among the lowest in Europe), so may be particularly vulnerable to ash loss. Better understanding of the effects and how to minimise them is critical to deliver an evidence-based response. First, we investigated impacts in woodlands by experimentally killing woodland ash trees by ring-barking. We found no short-term effect of ash loss on ground flora or earthworm communities, or on the regeneration or growth of other woody species. Observational evidence suggested that remaining canopy trees rapidly filled gaps left by ash, perhaps contributing to stability. Our woodlands appeared to be remarkably resilient to ash loss, although there may be long-term effects or impacts on other species that this experiment failed to observe. To investigate broader-scale impacts, we required high-quality abundance maps for ash and other trees across Britain. Using species distribution modelling and random forest regression, we developed a protocol to produce abundance maps from readily available data. We tested the predictive power of the resulting maps using cross validation. Our maps are the best available for abundance of British tree species, and will be useful across a wide range of disciplines. We then used them to model ecosystem vulnerability to ash loss, based on the abundance of ash and other tree species, and their ecological trait similarity. We identified areas at risk of the largest impacts, and produced guidance for positive management actions to minimise ecological change. Lastly, we investigated the financial impacts of ash dieback, estimating the total cost to Britain at £9.2 billion. This figure is many times larger than the value of lost trade if biosecurity were improved to prevent future invasions, questioning the validity of financial arguments against biosecurity. We also found that loss of ecosystem services accounted for less than a third of the total cost, suggesting that ecosystem service assessments may miss a large proportion of the true cost of biodiversity loss. Overall, we found that some impacts may be less than expected, such as local effects on woodland ground flora, and others, such as the economic cost, may be much larger than expected. However, the resilience of ecosystems to a major shock such as loss of a common species, and actions to mitigate the impacts, depend on having a diversity of other trees present. The ash dieback outbreak highlights the importance of preventing other severe pests and diseases of trees from being introduced; something that has been increasing exponentially, largely due to international trade in trees. This thesis provides further firm evidence that there is an ecological and social imperative to halt this trend.

Sun-exposed broad leaved deciduous trees have a great species diversity of epiphytic lichens. In Europe, these trees have decreased dramatically in number as wooded pastures have become overgrown with trees and bushes, and broad leaved deciduous stands have been replaced by planted coniferous trees. These are the main reasons for many lichens depending on deciduous trees being red-listed. Epiphytic lichens in overgrown areas could benefit from conservation thinning, but few studies have been performed on how this type of cutting affects the lichens. In a previous study, the presence of red-listed epiphytic lichens in a broad leaved deciduous forest was examined. After the study, thinning of trees and bushes was made. Here we study the effects of this thinning on Lobaria pulmonaria. We tested possible factors that may affect the growth of L. pulmonaria, and if there were any differences in incidence and vitality of the lichen between managed and unmanaged stands. Since Dutch elm disease and ash dieback are well spread in the area, we wanted to see if they also affected the growth of L. pulmonaria. There were no differences in incidence and growth between managed and unmanaged stands. The results were unexpected since other studies show that, for instance, increased sun exposure often has a great effect on the growth of lichens. Many elms and ashes were dead or dying and had a significant negative effect on the change of number of lobes and the lobe surface. The diseases of the trees can thus be assumed to be the greatest cause of why the lichens in the managed stand did not benefit from thinning.

No / Characterising the future risk to biodiversity across multiple environmental drivers is fraught with uncertainty and is a major conservation challenge. Scenario planning - to identify robust decisions across a range of plausible futures - can aid biodiversity conservation when tactical decisions need to be made in the present-day, yet consequences are realised over many decades. Management responses to the impact of tree disease are an excellent candidate for scenario planning, because actions to reduce an imminent biodiversity threat need to be effective in the long-term by accounting for concomitant factors such as a changing climate. Lichen epiphytes were used to exemplify a guild sensitive to woodland change, such as a tree disease impact. Bioclimatic models for 382 British epiphytes were combined with species-specific tree association values, to explore scenarios of tree disease (ash dieback), climate change, and range-filling under a lower SO2 pollution regime, for northern Britain focussed on Scotland. Results indicated: 1. Exposure of lichen diversity to projected climate change is spatially structured and expected to be greater in continental northeast Scotland, compared to oceanic western Scotland. 2. Impact of tree disease showed analogous geographic trends, evidencing a critical interaction between the climatic and local ecological setting. On average, the loss of ash could have an effect on epiphyte assemblages comparable in magnitude to that of climate change under a 2080s high emissions scenario. 3. In general, tree disease impacts can be mitigated by increasing the diversity of substitute tree species within a stand, to generate complementarity among epiphyte communities. However, the effectiveness of alternate management scenarios varied locally between sites and temporally with the progression of climate change. Given this variability, scenario analysis is recommended to effectively manage for resilience, by scoping how local factors (e.g. managed woodland composition) can reduce epiphyte assemblage turnover beyond that uniquely associated with larger-scale environmental impacts. (C) 2014 Elsevier Ltd. All rights reserved.