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Intercropping has been suggested as a sustainable alternative to monocropping practice to enhance crop productivity with less fertiliser, pesticide and water inputs. This positive effect of crop diversity on productivity is mainly due to resource partitioning where intercropped species use available resources differently, and thus occupy distinct realised niches in the niche space of this resource. Due to plasticity, species can also shift resource uptake, and thus the realised niches, in response to interactions with other species. Such plant-plant interactions are important for community structure, and persistent interactions can also have evolutionary consequences. In intercropping studies, such persistent interactions and consequent adaptation resulted in enhanced productivity in mixtures. The underlying mechanisms are the differentiation in niches and the reduction of competition among the coexisting plants. In this thesis, I gained an understanding that plant-plant interactions can influence both ecological and evolutionary processes of plant communities. Such ecological and evolutionary changes are only possible when plants are highly plastic to respond to co-occurring plants. This plasticity enabled plants to shift niches when grown in more diverse communities, which in turn was associated with overyielding in mixtures and thus contributed positively to ecosystem functioning. Furthermore, this high plasticity allowed plants to (co)adapt with coexisting plants, where persistent interactions not only reduced competition especially in mixtures but also enhanced the productivity of the plant community. This thesis demonstrates that plant-plant interactions, which are often overlooked in cropping systems, can influence resource use of crop species but also illustrates that persistent interactions among plants and its evolutionary outcomes can affect ecosystem functioning. Furthermore, this thesis underpins the potential that diversification of current cropping systems could provide a more sustainable crop production. The findings presented here could potentially also be interesting for future breeding programs to enhance productivity in intercropping systems.

The present checklist of Swiss rust fungi (basidiomycetes, order Uredinales [or Pucciniales]) comprises 580 taxa belonging to 547 species. For each taxon, the most important synonyms, the life cycle and the host plants recorded in Switzerland are given. It is indicated, furthermore, whether a taxon is adventive in Switzerland and to what extent it has become naturalized. Information is presented on how the accepted rust species are allotted to the rust genera, the different life cycles and host families. A host-rust index and close-up photographs of 144 species supplement the checklist., Die vorliegende Checkliste der Schweizer Rostpilze (Basidiomyzeten, Ordnung Uredinales [oder Pucciniales]) führt 580 Taxa auf, die 547 Arten zugeordnet werden. Für jedes Taxon werden die wichtigsten Synonyme angegeben, der Lebenszyklus und die für die Schweiz nach-gewiesenen Wirtspflanzen. Zusätzlich wird angegeben, ob ein Taxon in der Schweiz adventiv vorkommt und inwieweit es als eingebürgert gelten kann. Eine statistische Analyse zeigt, wie sich die anerkannten Rostpilzarten auf die in der Schweiz vorkommenden Rostpilzgattungen, die verschiedenen Lebenszyklen und die Wirtsfamilien verteilen. Die Checkliste wird durch einen Wirt-Rostpilz-Index und Nahaufnahmen von 144 Arten ergänzt., La présente liste des champignons responsables des rouilles en Suisse (basidiomycètes, ordre des Uredinales [ou Pucciniales]) comprend 580 taxons appartenant à 547 espèces. Pour chaque taxon sont indiqués les synonymes communs, le cycle de vie et les plantes hôtes suisses. En outre, il est indiqué si un taxon est adventive/exotique en Suisse et dans quelle mesure il s’est acclimaté. Des statistiques portant sur la répartition des espèces répertoriées parmi les différents genres de rouilles, leurs différents cycles de vie et leur association avec les familles de plantes hôtes sont présentées. La liste de contrôle est complétée par un index des combinaisons plante hôte-rouille et par de gros plans de 144 espèces.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene ‘icehouse origin’ of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology., bioRxiv

Die vier grössten Schweizer Herbarien beherbergen knapp 12 Millionen Belege. In diesem Artikel zeigen wir Beispiele, wie Pflanzen von gestern in der Forschung von heute genutzt werden. Les quatre plus grands herbiers suisses rassemblent près de 12 millions de spécimens. Dans cet article, nous montrons comment les échantillons d’autrefois sont utilisés dans la recherche d’aujourd’hui., FloraCH, 15

The key to the survival of every organism on the planet is the optimal timing of essential life cycle events. This allows them to first avoid unfavourable periods, which would be harmful to the metabolic functioning or directly threatening the survival of a species (e.g. drought or freezing events). Second, it allows them to synchronize sexual reproduction among individuals of the same species to ensure gene flow in a population. In the case of plants, prominent examples of such ‘phenological events’ include the emergence of leaves in spring as well as flowering, fruit ripening and the abscission of leaves in autumn (senescence). Sensing the optimal time for vegetation onset and completing the phenological cycle requires regular feedback with the environment to adjust investments in vegetative growth, reproduction or preparation of the dormancy – the state in which trees can persist cold periods during winter in temperate and boreal latitudes. The mechanisms for predicting the onset of spring include daylength (photoperiod; PP) and temperatures as the two driving factors. The accumulation of low temperatures ('chilling') followed by an accumulation of a certain amount of thermal forcing in combination with critically PP, at least in some species, are such 'predictive mechanisms' or at least models, that proved to be well usable. The optimal timing of the growing season onset (e.g. leaf-out) marks a trade-off between maximizing the growing season length including competition for resources (e.g. light, nutrients, water) and reducing the risk of damaging late spring frost events. Global warming has changed this trade-off established over a long evolutionary history, increasing the risk of damaging late frosts in many regions of the world, due to a more rapid advancement of leaf emergence compared to the advancement of last spring frost events. This has recently led to large-scale defoliation of the forest canopy in many regions worldwide, which in turn has massive impacts on water, nutrient, and carbon cycling as well as on the overall food web of the forest ecosystem. This PhD aims to address the following three objectives, each presented in one experimental study corresponding to one chapter: i) (Re-)assess the effective chilling temperature range and their efficiency to release temperate deciduous trees from winter dormancy. ii) Disentangle the effects of PP and temperature during the growing season on the timing of senescence and assess the leaf emergence under limiting chilling conditions for provenances from the southern and northern distribution ranges. iii) Quantify the classic trade-off involved in leaf-out timing, i.e. estimating the cost of freezing damages versus the potential gains associated with advanced leaf emergence. An additional chapter is dedicated to a project which aims to foster the exchange of phenological knowledge between researchers, Swiss rangers and the public to promote environmental awareness. In the first study of my thesis (chapter 2), I placed 1,020 twig cuttings of six common European tree species in climatic chambers and exposed them to various chilling temperatures and durations. The experiment revealed a much wider chilling range than was previously assumed, spanning temperatures from minimum -2 up to 10 °C with freezing temperatures revealing equal or highest efficiencies in releasing the dormancy of deciduous trees. Moreover, I showed that species strongly differ in their chilling requirement and that the chilling mediated dormancy progression and release is characterized by three indicators, namely the maximum dormancy depth (a measure for the inability of a species to flush without prior chilling), the temperature-dependent rate of dormancy release (shape of the forcing-chilling-curve) and the minimum forcing requirement after saturating chilling (corresponding to the asymptote of the forcing-chilling-curve). IV In the second study (chapter 3), I exposed 324 saplings of three deciduous tree species originating from the northern and southern distribution ranges to a combination of 3 PP x 2 temperature treatments between the spring and fall equinoxes. Additionally, I extended the warming treatments to exclude critical portions of the chilling range during the subsequent dormancy period. This experiment revealed that a pure PP effect (not altering the amount of light energy for photosynthesis) was evident, generally advancing the timing of senescence in birch and beech (but not in oak) under shorter PPs. The exclusion of temperatures below 5 or 10 °C throughout winter dormancy resulted in consistent advancement of the budburst timing in oak, but weakened or prevented further advances in birch and beech with the latter showing first signs of incomplete leaf development under the most limiting chilling conditions. Provenances from the northern distribution range revealed both earlier senescence as well as budburst dates compared to the southern provenance in birch and beech, reflecting higher temperature sensitivities at higher latitudes. Oak, in contrast, showed the reverse trend with the southern provenance flushing earlier compared to the northern one. In the third study (chapter 4), I used 960 saplings of four deciduous tree species to artificially induce a wide range of realistic leaf-out dates and to subsequently apply a damaging frost event. Except for hornbeam, mortality after the induced damaging frost was negligible for all species. The timing of leaf-out significantly affected the regreening and growth of frozen and non-frozen saplings, with the lowest performance found at the most delayed leaf-out date. I demonstrate that species have different ways to withstand and recover from frost damage, reflecting their risk-taking strategy. Strategies to recover included a clear prioritization of the recovery of sugar reserves over growth (all species), the deployment of dormant reserve buds (oak), regrowth from the stem basis (cherry) and delayed leaf senescence (beech). The ability to recover from frost damage thus becomes an increasingly important functional trait for species persistence in the coming decades, as the frequency of extreme climatic events such as late spring frosts or droughts is expected to increase for wide areas across Europe. In addition to these research goals, I have initiated an Agora Project (still ongoing) entitled ‘PhenoRangers’ (chapter 6). Within this framework, a network has been established to collect high quality data for research to assess how the seasonal activity of different taxa and trophic levels will change in the future (scientific objective). At the same time, this network serves as a basis for communication between researchers, Swiss rangers, and the public to increase awareness of climate change and promote positive attitudes about how to address environmental problems at an individual level (communication objective).

Since the beginning of agriculture, approximately 10’000 years ago, plant pathogens have posed a major threat to global food production. Great progress has been made in agricultural practices to improve quality and crop yield. However, pathogens still pose a threat to crop production, and many aspects of the biology and the ecology of pathogens remain unexplored or not fully understood. A major knowledge gap is represented by the little comprehension of pathogen-pathogen interactions in natural infections. The following doctoral thesis aims to shed light on infections involving more than one pathogen, which greatly affect the population dynamics of plant pathogens. The final objective is to improve our understanding of pathogens and design better control strategies to prevent the damage produced by diseases and to hinder pathogen spread. An optimal model to study pathogen-pathogen-plant interactions is represented by the heterothallic ascomycete fungus Zymoseptoria tritici and its host wheat. Septoria tritici blotch (STB) caused by this fungus is one of the most damaging diseases of wheat cultivars in Europe and in the world. Remarkably during conducive years, it can lead to up to 50% yield losses. Characterized by its high evolutionary potential and by its genotypic and phenotypic plasticity, Z. tritici is highly diverse. In certain wheat fields, it has been described that more than several millions of different genotypes occur per hectare. A direct consequence of this extremely high diversity is that mixed infections in wheat fields are extremely frequent. To explore how pathogen-pathogen interactions affect the transmission of Z. tritici, we serial passaged a mixture of four different strains through the same host. The results obtained demonstrated that competition between strains leads to strain exclusion, and after several cycles of transmission, only one strain remains. Remarkably, the outcome of the serial passages depended on the cultivar genotype, indicating that the competitive ability of the strains is cultivar-specific. Against what has been previously described for other pathosystems, virulence does not positively affect the competitive ability of Z. tritici strains, while reproductive potential does. Overall, these findings suggest that mixed infections potentially affect the population structure and the evolution of virulence of pathogens. Mixed infections involve at least two pathogens and the host. Some pathogens harboring avirulence factors (Avrs) are recognized by resistance proteins (R) expressed in the plant. Consequently, the infection and the reproduction of those pathogens are hindered by the resistant host, resulting in incompatible interactions. How avirulent pathogens behave in mixed infection with a virulent pathogen remained largely unexplored. To investigate the interaction between avirulent strains and their resistant host in the presence of virulent strains, transcriptomic analysis of single and mixed infections was pursued. Results demonstrated that virulent strains of Z. tritici suppress the plant immune system enabling the infection and the reproduction of the co-infecting avirulent strain locally and distally. The prior arrival (priority effect) of the virulent strain did not increase the reproductive capacity of the avirulent strains, while infection on detached leaves revealed that competition for resources significantly affected the reproduction of the avirulent strains. We demonstrated that host immune suppression by virulent strains favors infection by avirulent strains, and we speculate that this could potentially also benefit colonization by opportunistic microorganisms. The results obtained during this doctoral thesis indicate that mixed infections importantly impact the dynamic of pathogen populations and their composition. This could have consequences for the evolution of pathogens and the survival and spread of avirulent pathogens.

Understanding the large-scale biodiversity distribution is one of the greatest challenges in macroecology and biogeography today. The observed patterns are the result of a combination of ecological factors (e.g., past and contemporary environment) on the one hand, and evolutionary processes (e.g., species interactions and evolution) on the other. A major outstanding question in biodiversity research is the relative role of contemporary and historic environments in the formation of distribution patterns. A crucial step in answering this question is first, the reconstruction, and second, the simulation of eco-evolutionary processes. In this thesis, I focused on both steps and target the distribution patterns of Fagales, a plant lineage with wide distribution and long evolutionary history. More specifically, first, I constructed high-resolution distribution and biodiversity distribution maps for Fagales and second, I explored the mechanisms behind the formation of these patterns with a process-based simulation model (Gen3sis). Moreover, I focused on the phylogenetic patterns of Fagales and explore how past and contemporary climate conditions shaped these patterns. Specifically: In the first chapter, I presented a novel approach to mapping species ranges at a global scale, integrating polygon mapping and species distribution modelling (SDM). The polygon mapping applies a new algorithm by considering distances and nestedness of occurrences. In addition, the SDM approach considers multiple modelling algorithms, complexity levels, and pseudoabsence selections to map the species at a high spatial resolution. The final maps are the intersection of both the SDM and generated polygon maps. Using this approach, I constructed range maps for all available 1957 species of Fagales and Pinales. Using these maps, I constructed high-resolution global species richness maps of these important plant clades, and documented diversity hotspots for both clades in southern and southwestern China, eastern and western North America, and Borneo. I compared two representative genera, Quercus and Pinus, from the two orders with previously published coarser range maps and find a good match. By efficiently producing high-resolution range maps, this mapping approach offers a new tool in the field of macroecology for studying global species distribution patterns and supporting ongoing conservation efforts. In the second chapter, I used Gen3sis, a process-based model, to reconstruct the evolutionary history and contemporary species richness of Fagales. In total, I ran 100 simulations from 17 different model structures (n = 1700) combined with different settings in the four main modules (dispersal, ecological processes, adaptation, and divergence). The models that performed best show hotspots of species richness consistent with the observed distribution of Fagales, where the highest species richness was found in eastern Asia, followed by southern North America, Central America, and southern Europe, with nearly no species in Africa, Central Asia, and few species in South America, Australia, and Siberia. The simulated evolutionary rates (speciation, extinction, and diversification) are coherent with the empirical rates from fossil evidence. These coherences show the powerful simulation ability of Gen3sis and provide deep insight into understanding the evolution of Fagales. In the third chapter, I investigated the global distribution of phylogenetic alpha diversity by computing Faith’s phylogenetic diversity (PD) and standardized PD, neighbourhood phylogenetic beta diversity (phylo-β), and phylogenetic endemism (PE) in Fagales, a diverse taxon and important component in temperate and subtropical ecosystems. I found that the hotspots of PD occur in southern China and the eastern US, while the hotspots of PE are in southern China and Central America. Metrics of phylogenetic alpha diversity (PD, PE) are well correlated with modern climate, where the most diverse locations occur in subtropical to temperate regions, where precipitations are more frequent. In contrast, hotspots of phylo-β occur mostly in specific mountain and plateau regions and these hotspots are weakly correlated with the environmental variables considered in this study, suggesting the combined effects of multiple complex processes. These results suggest that the diversification of Fagales lineages has occurred within well-defined climatic conditions, which further favoured the co-existence of these species in subtropical and temperate climates. Yet, in the regions with the highest heterogeneity in lineages, small-ranged endemic species occur in mountains, which may have prompted the local speciation while reducing extinction. This study documenting the determinants of phylogenetic diversity of global Fagales sheds light on the environmental conditions and processes that formed this important and structuring tree clade. Together, my thesis contributes to a better documentation of the distribution of biodiversity of a tree clade that is functionally important for temperate ecosystems as well as a better understanding of the ecological and evolutionary processes that have shaped them.

Viscum album L., known as European mistletoe, is a hemiparasite that can infect various host tree species across the European continent. Infection by V. album has become more and more apparent with climate change during the last decades. In some drought-prone regions, mistletoe infection has been found to aggravate drought stress, leading to increasing tree mortality. It is well known that mistletoe relies on water and nutrients from its host. It is still unclear, however, whether there is carbon exchange between mistletoe and its host, as mistletoe connects only to the host xylem and not to the phloem. This Ph.D. thesis concentrates on two common subspecies of European mistletoe (i.e. V. album ssp. austriacum and V. album ssp. album) and their host trees, exploring the relationship between mistletoe and its host from a comprehensive perspective. Two controlled labeling experiments (Chapters I, II) and a field assessment (Chapter III) were conducted to investigate the carbon, water and nutrient relationship between V. album and its hosts under various growing conditions. In Chapter I, a dual-labeling (i.e. 13C and 18O) experiment was conducted on pine mistletoe (V. album ssp. austriacum) and its host Scots pine (Pinus sylvestris L.) growing in dry and irrigated plots of a long-term irrigation experiment in Pfynwald, Valais. Compared with the dry control, irrigation resulted in a lower natural abundance of 18O and a lower concentration of non-structural carbohydrates (NSC) in V. album ssp. austriacum but not in Scots pine, indicating that mistletoe and its host may differ in their strategies to deal with water stress. Further, Scots pine branches and detached mistletoes (i.e. preventing resource exchange between mistletoe and host branch) were labeled with 13C-enriched CO2 and 18O-enriched water vapor over 4 hours in closed chambers. Both mistletoe and its host had a weaker 13C-signal but an unchanged 18O signal in irrigated plots compared with values in dry control plots. Irrespective of the irrigation treatment, the 13C and 18O labeling of the assimilates was 50% weaker in mistletoe than in its host, indicating a lower incorporation capacity in the former than in the latter. Chapter II is based on two experiments, a wrapping experiment and a removal experiment, conducted under the ‘umbrella’ of a whole-tree 13C-pulse labeling experiment with mature Scots pine infected by V. album ssp. austriacum growing in the dry and irrigated plots in Pfynwald. In the wrapping experiment, mistletoe clusters were selected and wrapped with gas-tight plastic and aluminum foil before the whole-tree 13C-pulse labeling was started, to prevent uptake of 13CO2 from the labeling. Hence, any 13C labeling signals potentially measured in these wrapped mistletoe clusters would provide direct evidence for carbon transfer from host to mistletoe. To investigate carbon exchange in relation to changes in carbon and water availability of the host, a tissue removal experiment was conducted on girdled pine branches infected by mistletoe, i.e. preventing carbon translocation via the phloem. Before the whole-tree 13C-pulse labeling, these branches were treated with either: (1) removal of all pine needles, (2) removal of all mistletoe tissues, or (3) intact control without needle or mistletoe tissue removal. Results of the wrapping experiment indicate that there is no carbon transfer from the host to the mistletoe, as no labeled 13C signal was found in the wrapped mistletoe tissue. Also, no carbon transfer was observed from the mistletoe to the carbon-limited host (i.e. pine branch with needles removed). However, the increase in local water availability with pine needle removal resulted in more pronounced 13C signals and higher NSC concentrations in mistletoes in dry plots, suggesting that the assimilation capacity of mistletoes is constrained by the availability of water to the host. Therefore, it can be concluded that V. album ssp. austriacum assimilates carbon independently assimilates carbon independently but that its capacity to assimilate carbon depends on the availability of water to the host tree. Chapter III focuses on the carbon, water and nutrient relationships between V. album ssp. album and its various host tree species growing under different environmental conditions. It is based on a field sampling assessment of nine mistletoe–host pairs in central Switzerland. Consistent with the results in the first two chapters, the concentrations of NSC and its compounds in mistletoe and the host tissues showed no significant correlations among the different mistletoe–host pairs, suggesting a carbon independency of V. album ssp. album and its hosts. In contrast, leaf δ13C, leaf water content, and leaf concentrations of almost all nutrient elements were consistently positively correlated among all nine mistletoe–host pairs, indicating an adaptation strategy of mistletoe to co-exist with its host under varying water and nutrient availability. Overall, the aim of this thesis is to investigate the carbon, water and nutrient relationships between V. album and its host trees. It provides novel direct evidence that no carbon transfer occurs between V. album and its host. Furthermore, it demonstrates that the water and nutrient status of V. album is directly impacted by the availability of water and nutrients to its host. Hence, this thesis deepens the mechanistic understanding of mistletoe–host coexistence in various and changing environmental conditions, including ongoing global environmental change.

• Non-timber forest products offer a critical opportunity for supporting sustainable development of rural communities and conservation of natural ecosystems. The Brazil nut (Bertholletia excelsa) is arguably the most prominent NFTP from the Neo-tropics, as a globallytraded product from a hyperdominant carbon-rich tree and cornerstone species for rainforest conservation with potential for restoration. Hence, this species has the capacity to contribute to resilient stewardship of forest landscapes, while generating income and improving the livelihood of a vast number of people and local communities throughout the Amazon basin, as well as playing a role in climate change mitigation. • Although it is a protected species, the habitat where Brazil nuts occur is being degraded due to logging of other tree species and land conversion from forest to unsustainable agricultural systems. In this thesis I adopt an interdisciplinary approach across ecosystem management and applied molecular ecology and genomics to 1) Explore the reproductive vulnerability of natural Brazil nut populations in a categorized forest-degradation gradient in the highly biodiverse region of Madre de Dios; 2) Increase our understanding of the role of forest genetic resources as a foundation for resilient oroduction and a vital source of material for forest enrichment and Brazil-nut based restoration; and 3) Provide evidence-based recommendations for management practices that have demonstrated positive effects on the sustainability of Brazil nut populations and its value for restoration. • For genetic analyses, I used a combination of traditional microsatellite SSR loci and developed ddRAD-generated SNPs novel to the species. I place the overall results in the context of patterns of fine-scale genetic structure (FSFS), comparisons genetic-diversity and pollen geneflow patterns, signs of inbreeding through genetic erosion, heterozygosity-fitness correlations related to survival, growth and fruit productivity, monitoring of the success of planting initiatives, and exploration of cost-efficient management practices from collaborative research components. • These findings are detailed and discussed in three main chapters, followed by an additional genome-size technical note and information from co-authored studies related to similar topics within sustainable forest management. Together, they aim to contribute to our holistic understanding of approaches required for resilient management of this vulnerable and socioecologically valuable Amazon rainforest species.

Understanding P uptake in soil–plant systems requires suitable P tracers. The stable oxygen isotope ratio in phosphate (expressed as δ18OP) is an alternative to radioactive labelling, but the degree to which plants preserve the δ18OP value of the P source is unclear. We hypothesised that the source signal will be preserved in roots rather than shoots. - In soil and hydroponic experiments with spring wheat (Triticum aestivum), we replaced irrigation water by 18O-labelled water for up to 10 d. We extracted plant inorganic phosphates with trichloroacetic acid (TCA), assessed temporal dynamics of δ18OTCA-P values after changing to 18O-labelled water and combined the results with a mathematical model. - Within 1 wk, full equilibration of δ18OTCA-P values with the isotope value of the water in the growth medium occurred in shoots but not in roots. Model results further indicated that root δ18OTCA-P values were affected by back transport of phosphate from shoots to roots, with a greater contribution of source P at higher temperatures when back transport was reduced. - Root δ18OTCA-P partially preserved the source signal, providing an indicator of P uptake sources. This now needs to be tested extensively for different species, soil and climate conditions to enable application in future ecosystem studies., New Phytologist, 230 (5), ISSN:0028-646X, ISSN:1469-8137

The present checklist of Swiss rust fungi (basidiomycetes, order Uredinales [Pucciniales]) comprises 576 taxa belonging to 543 species. For each taxon, the most important synonyms, the life cycle and the host plants recorded in Switzerland are given. It is indicated, furthermore, whether a taxon is adventive in Switzerland and to what extent it has become naturalized. Information is presented on how the accepted rust species are allotted to the rust genera, the different life cycles and host families. A host-rust index and close-up photographs of 127 species supplement the checklist.

Tree mortality is a key factor for understanding forest dynamics. So far, however, only few studies have focused on the mortality of tree regeneration. Thus, more research is needed in this context to better understand the underlying ecological processes and predict more reliably how forest ecosystems will respond to ongoing climate change. As the current and future changes are expected to either favor or impair the growth and survival of large trees, it is pivotal to investigate the effects on the next generation, i.e. young and small trees. A better understanding of tree regeneration allows to extend or adapt the findings from the already well-studied adult, large trees to small-sized trees, for which sparse empirical data are available. Particularly relevant questions relate to the drivers of survival probabilities and of horizontal spatial patterns (i.e. the distribution in space) of tree regeneration. The aims of this PhD thesis therefore were (i) to improve the understanding of natural mortality processes of tree regeneration at different developmental stages and spatio-temporal scales, (ii) to investigate the effect of various abiotic and biotic factors on the mortality of tree regeneration, and (iii) to study the relationship between mortality, growth and site conditions. For this purpose, I assessed 1) the effect of emergence time, height and number of leaves of seedlings, light availability, temperature, precipitation, seedbed and microsite conditions on the survival time of seedlings; 2) the effect of light availability on the growth of saplings and its relationship with mortality; and 3) the effect of topography and of large neighboring trees on the spatial pattern of living and dead small trees. These effects were investigated for small-sized trees (diameter at breast height < 10 cm) of both conifer and deciduous species at several study sites in Switzerland across elevational gradients that represent distinct climate regimes and growth conditions. In Chapter 1, I studied the effects of emergence time on the mortality of seedlings. The underlying rationale was that global warming is expected to advance the timing of germination, leading the seedlings to potentially experience more severe damage and mortality due to late frost events in spring. Thus, I monitored the emergence, characteristics, and survival of seedlings across ten tree species in temperate mixed deciduous forests around Zurich (Switzerland) over one and a half years. For each seedling, I recorded characteristics such as height, number of cotyledons and euphylls, cause and severity of possible damages, and extent of missing foliar tissue due to herbivory. Moreover, I documented the seedbed type of each seedling and that of the microsite at the plot level. For each plot, I also determined light availability using hemispherical canopy photographs, logged the temperature curve, and measured soil moisture. Based on the empirical data, I conducted a survival analysis using the Kaplan-Meier method to estimate survival curves and Cox’s proportional hazards model to assess the effects of the explanatory variables on survival time. I tested whether the timing of emergence represents a trade‐off for seedling survival between minimizing frost risk and maximizing the length of the growing period. Seedlings that emerged early faced a severe late frost event. Nevertheless, they benefited from the overall longer growing period, resulting in increased overall survival. Larger seedling height and higher number of leaves positively influenced survival. Seedlings growing on moss had higher survival compared to those growing on mineral soil, litter, or in herbaceous vegetation. Since almost two‐thirds of the monitored seedlings died during the first growing season and early-emerging seedlings were more likely to survive, this chapter highlights how the first months of life together with an early emergence time of seedlings are decisive for successful tree regeneration, which will ultimately have an impact on the future development of forest stands. In Chapter 2, I investigated whether radial and vertical growth rates are suitable indicators of impending mortality in young trees, as previous research on adult, large trees had suggested, and whether light availability and tree size have an influence on mortality probability. Thus, I sampled an equal number of living and dead saplings of four conifer species (Swiss stone pine, European larch, Norway spruce and silver fir) in nine mountain forests along an elevational gradient of the Swiss Alps. I performed a tree-ring analysis, calculated both radial and vertical growth rates and compared them between living and dead saplings based on tree-ring widths reconstructed from stem disks at multiple tree heights. I observed a divergent pattern in radial growth of living and dead saplings, with reduced growth of dead saplings starting several years prior to death, which emphasizes the importance of long-term predisposing factors for tree mortality. Then, I quantified the combined effects of light availability, growth and tree size on mortality, using species- and site-specific conditional logistic regression models, by previously matching living and dead saplings of similar ages. Light availability influenced positively the survival probabilities of conifer saplings in mountain forests, although the positive effect decreased with increasing elevation. Recent radial growth rate and diameter had only minor effects on sapling mortality. By highlighting the importance of long-term predisposing factors for the mortality of conifer saplings in mountain forests, this chapter extends well-established findings of the adult stage to the so far little investigated sapling stage. In Chapter 3, I analyzed the horizontal spatial patterns of small living and dead Norway spruce trees in two subalpine forest reserves of Switzerland, Scatlè and Bödmerenwald, by nearest neighbor-based and distance-based analyses. I accounted for spatial inhomogeneity by investigating how the local densities of living and dead small trees depend on environmental covariates. I found that the local density of living and dead small trees is influenced by latitude, elevation and aspect. Yet, the influence of these covariates varied between the two forest reserves due to their different topography and peculiar site conditions. Then, I considered neighborhood interactions between trees based on the vicinity and size of trees, by analyzing how small trees are influenced by large neighboring trees over a range of spatial scales. Both tree vicinity and size were important for the spatial patterns of small trees in both reserves. Small living trees showed a random pattern around large dead trees over a range of distances and, at certain distances in one reserve, even dispersion. Small living trees further showed clustering around large living trees at short distances and dispersion at large distances. Small dead trees featured mainly a random pattern, even though with a tendency to cluster at short distances around large neighbors, irrespective of whether these were living or dead. Yet, the fading of clustering with increasing distance indicates that the influence of large trees on small trees varies with the distance and thus that the neighborhood interactions between trees are scale-dependent. I further found that the influence of large neighboring trees on small trees varied with topography, revealing a relationship between spatial inhomogeneity and neighborhood interactions, as I expected due to the strongly different tree sizes and environmental gradients in mountain forests. Overall, this chapter emphasizes the importance of considering both spatial inhomogeneity and neighborhood interactions when investigating the spatial ecology of mortality of small-sized trees in uneven-aged and unmanaged mountain forests. Throughout this PhD thesis, I extended well-established ecological findings from the adult, large trees to the regeneration stage of trees, which is an important bottleneck of forest dynamics. The empirical findings of my PhD thesis represent a considerable contribution towards a better understanding of the temporal and spatial patterns of mortality in tree regeneration as well as of the relationship between mortality, growth and site conditions.

Understanding the evolution of biological diversity is of fundamental interest to molecular ecologists and conservation biologists. In particular in biodiversity hotspots, major knowledge gaps exist regarding the numbers of species, their morphological distinction, ecology, distribution and risk of extinction, as well as their possible commercial value and use. The pantropical genus Dalbergia L.f. (Fabaceae) includes precious timber species known as rosewoods or palisanders, many of which are threatened by habitat degradation and often illegal selective logging. The use of existing species circumscriptions and application of available identification keys is particularly challenging in Madagascar, where a large number of closely related species co-occur and where the reliance on flower and fruit characters for identification is high, even though these structures are often absent on living specimens. The resulting taxonomic uncertainties have important implications for national and international trade regulations and impede the setting of conservation priorities. The aim of this Ph.D. thesis was to increase our understanding of the number, morphological distinction and phylogenetic relationships between the Dalbergia species present in Madagascar. Towards this goal, I developed a genome-wide DNA analysis approach that I used in combination with morphological and eco-geographic analyses. In the first chapter, my collaborators and I explored the utility of target enrichment sequencing to assess genetic variation in Dalbergia at the level of populations and closely related species, and between divergent species within the genus. Specifically, we assessed the sequence capture sensitivity and specificity of 7,201 candidate genomic regions with a conserved core across available genomes of Papilionoideae, and identified 2,396 regions that can be efficiently recovered for genomic analyses across Dalbergia. We also explored the performance of the 7,201 candidate regions across legumes, and identified 1,005 target regions that can be efficiently recovered for analyses at the family level. These confirmed high levels of gene tree discordance, previously reported also by other authors, especially near the root of the family. Furthermore, our analyses resulted in the development of a general-purpose bioinformatics pipeline for scalable, streamlined and reproducible analysis of such genome-wide and complex datasets. In the second chapter, we employed the developed genomic and bioinformatic resources for species discovery within the genus Dalbergia from Madagascar and the Comoros. This led to the confirmation of 46 out of 49 already described and accepted species as separately evolving lineages, while three currently accepted species were identified as potential synonyms. Furthermore, we discovered 49 new candidate species, of which 14 could be delimited as separately evolving from one another and from the confirmed described species. Lineage separation could not be conclusively assessed for the remaining 35 candidate species because of a currently insufficient availability of high-quality collections. Phylogenomic analysis confirmed the existence of two diverse clades of Malagasy Dalbergia, one of which appears to be associated with a clade of species from continental Africa, as well as an isolated lineage, which also occurs in continental East Africa. It further revealed a fourth lineage present in Madagascar, which is connected to another clade of species from continental Africa, and a biogeographic connection between species of West Madagascar and the Comoros. In the third chapter, we completed the integrative taxonomic workflow for three confirmed evolutionary species of high conservation concern. Specifically, we newly described D. pseudomaritima Crameri, Phillipson & N. Wilding and D. razakamalalae Crameri, Phillipson & N. Wilding as distinct species occurring in littoral and low-elevation evergreen humid forests in southeast Madagascar, and emended the description of D. maritima R. Vig. from central-east Madagascar to exclude the two south-eastern species, with which it had previously been confused. For all three species we also performed conservation assessments according to the IUCN Red List categories and criteria, and assigned the category Endangered (EN) to all of them. A major result from this dissertation is the finding that the diversity of Dalbergia species in Madagascar has hitherto been vastly underestimated. Thanks to major recent efforts to sample and document Dalbergia species, and the developed sequence capture and high-throughput DNA sequencing approach, which provides unprecedented phylogenomic resolution, part of the species diversity existing in Madagascar could be uncovered. In combination with morphological and eco-geographic data we were able to show that several threatened species are not currently represented in existing protected areas and that some highly exploited species with presumably large distribution ranges are actually composed of several species with much narrower distribution ranges. These findings call for further investigations and conservation action, and provide scientific evidence that will hopefully foster science-based conservation efforts.

One of the most pressing tasks faced by environmental scientists and society is to predict how climate and other environmental factors shape the distribution of biological species at the global scale. Whether a region houses many or few species affects ecosystem functions, including productivity and stability, through complementarity in species’ niches. Phytoplankton have evolved ecological niches that fill the entire near-surface global ocean. Despite being some of the tiniest organisms on Earth, they drive as much as half of global primary production. However, the functional and ecological consequences of phytoplankton species diversity have been poorly known, as global diversity patterns of these microbes have been among the least characterized throughout the history of ecology. To determine global patterns and drivers of phytoplankton diversity, this thesis combines ocean-sourced data with statistical models, developed specifically to address data sparseness.

Transposons are genetic foreign elements that constitute large parts of eukaryotic genomes by virtue of their ability to make copies of themselves. Retroelements, the predominant class of plant transposons, must regulate their protein expression from highly compact sequences to successfully transpose. They have evolved unique strategies to optimize their gene expression, which relies on the transcriptional and translational machinery of the host. Here, by studying the transcriptome and translatome in two DNA methylation mutants of Arabidopsis thaliana we have generated a genome-wide map of intact and active transposons. In-depth analysis of this map has led to the discovery of a conserved expression strategy to balance the protein levels of Ty1/Copia elements, a family of young and active retroelements. An alternative splicing event coupled to premature termination prompts the production of a subgenomic mRNA solely dedicated to the production of a structural protein, required in molar excess to the catalytic components for transposition. Preferential translation of the subgenomic mRNA concludes the establishment of appropriate protein levels, but also marks the onset of de novo RNA silencing of the prototypical and autonomous element ÉVADÉ (EVD). The short and spliced mRNA is not only the sole substrate of siRNA production but also the unique target of RNA silencing effectors. Mutations introduced in transgenic EVD versions revealed that splicing and premature termination are dispensable for the silencing initiation. Furthermore, engineering the EVD intron and terminator sequence between two reporter genes fully reconstitutes its transcriptional and translation features and is sufficient to confer silencing on the subgenomic mRNA, suggesting a purely innate response. Further inspections of the translational dynamics by ribosomal profiling of EVD indicates that suboptimal translation initiates RNA silencing. Subsequent genetic analyses have revealed unexpected links between co-translational mRNA decay and RNA silencing in transposon silencing, reminiscent of anti-viral activities of RNA quality control. Collectively, this study furthers the understanding of how constraints in transposon gene expression provide entry points for foreign element recognition of their host.

Natural selection is acting on the genome of individuals that are experiencing particular abiotic and biotic conditions, resulting in adaptation to local habitat. Accordingly, local genotypes will show higher fitness in their local habitats than genotypes from a foreign habitat introduced at this site (“local vs. foreign” sensu Kawecki & Ebert 2004). Understanding, how individuals are adapted to their environment is especially interesting and valuable in the context of climate change, which is thought to increase the frequency of disturbances that individuals have to cope with. Therefore, evolutionary biologist have a particular interest in genes involved in local adaptation to understand which biological functions are important in which environments and to comprehend how species will react to future climate change. The capacity of species to cope with changes will rely on sufficient genetic variation upon which selection can act. Different methods exist to detect signals of adaptation. Landscape genomics (for example environmental association analysis) has the potential to find genes under adaptation by associating genomic variation with environmental data, hence linking signatures of selection with their potentially underlying environmental drivers. In this study, the alpine rock cress, Arabis alpina, was used to investigate signals of adaptation in heterogeneous alpine environments. The high-quality reference genome available and previous studies in ecological genetics make this species suitable as model system to study which parts of the genome show signals of adaptation and investigate key functions involved. When studying local adaptation, it is important to take into account the neutral genetic structure of the studied populations as it may mimic signals of local adaptation. These patterns come from neutral processes like gene flow, genetic drift and mutation, but not from non-neutral processes like selection. The phylogeographic structure of alpine species, predominantly shaped by these neutral demographic processes, can be complex, as the recurrent glaciations during the Pleistocene confined species to refugial areas from where they repeatedly recolonized their current range. Thus, in the first chapter of this thesis, I aimed to investigate the population structure of A. alpina across the Alps (372 individuals from 127 populations) and at the regional scale (364 individuals from 22 populations) in the western Swiss Alps—the study region of the subsequent landscape genomic investigations. Based on nuclear microsatellite data, I found that the pattern of genetic clusters across the Alps was coherent with that of previous phylogeographic analyses using anonymous molecular markers. In the western Swiss Alps, I discovered that the populations from this region showed several genetic clusters associated to different putative refugia, as presumably observed in other species. Moreover, the four study regions sampled for the environmental association analysis appeared to descend from the same original population, indicating a largely common genetic background. Our results not only substantiated the congruence of large-scale genetic structure using alternative types of molecular markers, but also set a helpful basis for further studies on ecological genomics in A. alpina. Studying local adaptation at small scale requires highly resolved and accurate genomic data. Therefore, I re-sequenced the whole genomes of 304 individuals from four nearby populations sampled in the western Swiss Alps. The second chapter describes the genomic diversity of the four sampled populations based on single-nucleotide polymorphisms (SNPs) and transposable elements (TEs). The latter corresponds to a major fraction of plant genomes, but has hitherto been largely ignored regarding their role in adaptive responses to the environment. After stringent bioinformatic filtering, 291,396 SNPs and 20,548 polymorphic TEs were identified. Few SNPs were shared among the populations, unlike the TEs that were shared among populations to a large degree. Through the genomic context of both types of sequence variants, I described their potential impact on functional genes. Almost 5% of the SNPs were non-synonymous and 43% of the TEs were present within or next to 7,475 genes of A. alpina. These genes were enriched in functional categories related to reproduction and responses to biotic and abiotic stress. Overall, in addition to SNPs, TEs are likely to shape adaptive genetic variation in A. alpina as they might affect genes by their close vicinity. Finally, in the third chapter, I studied the extent of local adaptation in A. alpina. In order to capture signals of local adaptation at small scale, I ran association analyses of environmental factors, derived from digital elevation models based on high-resolution Light Detection And Ranging (LiDAR) data, with the genomic variants previously described (SNPs and TEs). Latent factor mixed models indicated that both types of variants showed significant signals of local adaptation within gene flow distance, after controlling for neutral genetic population structure. The significantly associated high-impact SNPs were mainly involved in metabolic and cellular processes, and few were involved in reproduction. TE families responding to heat stress were highlighted, but their impact is difficult to assess given the lack of functional information. The observed signals of local adaptation in response to alpine environments seem to be mainly driven by humidity and solar radiation. The impact of the reproductive strategy (predominant selfing) and the demographic history of A. alpina on the observed signals of adaptation were finally discussed. In conclusion, this thesis presents the phylogeographic diversity of A. alpina over the Alps and in a region presumably at the junction of several glacial refugia, the western Swiss Alps. The re-sequencing of the whole genome of 304 individuals of four populations sampled from this region showed that TEs and not only SNPs evidenced genomic variation, some of which are apparently involved in adaptation to the local environment. These results open new perspectives on genome architecture and the role of variants in driving evolution within natural populations, highlighting the complexity of the genomics of adaptation.

Natural disturbances such as windthrow and bark beetle outbreaks are important drivers of long-term forest dynamics. While they are expected to promote tree species diversity, they can also negatively affect the provisioning of ecosystem goods and services (EGS). Especially in the face of climate change and altered disturbance regimes, the ability of forests to provide EGS is increasingly threatened. The maintenance or enhancement of tree species diversity is seen as a possibility to increase the resistance and resilience of forests and to secure the provisioning of EGS for the future. Thus, unravelling the relationship between tree species diversity and EGS under multiple disturbances and climate change has become increasingly important in ecology over the last decades. However, little is known on this relationship at large spatio-temporal scales due to the limitations of empirical studies. Dynamic vegetation models (DVM) can be used to assess the proposed benefits of tree species diversity in a holistic way. Forest landscape models, one important type of DVMs, are especially suitable to simulate forest dynamics and tree species diversity under changing climatic conditions and over large spatial and temporal scales. They also allow to study the complex relationship between tree species diversity and interacting disturbances while controlling for site history and environmental conditions. The forest landscape model LandClim was used to address the following objectives: (1) to assess how tree species diversity can influence the ability of a forest to provide single and multiple EGS, (2) to evaluate the impact of multiple disturbances on tree species diversity, and (3) to quantify the resistance and resilience of mixed-species forests to multiple disturbances and climate change. In Chapter I, I systematically evaluated the suitability of monocultures and mixed-species forests to provide single and multiple EGS at the landscape scale. To this end, I simulated all possible combinations of dominant tree species in two mesic landscapes in Central Europe (region around the Mt. Feldberg in the Black Forest in Germany, and the Dischma valley in the Canton of Grisons in Switzerland). To quantify their ability to provide EGS, several EGS metrics were examined: protection against natural hazards (avalanche and rockfall protection), aboveground biomass and habitat quality for birds. Simulation results indicated that mixed-species forests were generally better in providing multiple EGS whereas monocultures were often best for single EGS. Moreover, changing environmental conditions along an elevational gradient had a strong impact on the structure of the different species combinations and therefore on the provisioning of EGS. Thus, tree species diversity per se is not a good predictor of multifunctionality, but it is important to select species as part of the mixtures that occupy different ecological niches and that are best suited for the local environmental conditions. Forest disturbances can act as important drivers for biodiversity. In Chapter II, I evaluated the relative contribution of two distinctive disturbance agents (i.e., windthrow and ungulate browsing) for tree species diversity at the landscape scale and assessed the shape of the diversity-disturbance relationship. Simulations were run with varying browsing intensities and wind severities in four landscapes in Central Europe, differing in species pools and landscape complexity. My findings showed that tree species diversity in all four landscapes was influenced strongly by understorey (browsing) and overstorey (wind) disturbances, and their relative contribution depended highly on species composition, species-specific vulnerabilities to the disturbance, and forest structure, particularly tree size structure, mediated by growing conditions within the landscape. Tree species diversity was found to peak at intermediate browsing pressure, as dominant but browsing-intolerant species disappeared from the landscape. By contrast, more frequent and more severe wind regimes increased tree species diversity almost linearly by generating a mosaic of uneven-aged forest patches. Thus, the pattern and diversity of forest landscapes in Central Europe are shaped by understorey and overstorey disturbances. Tree species diversity may help to enhance forest resistance and resilience to disturbances and climate change. In Chapter III, I systematically explored the influence of multiple factors on the resistance and resilience to multiple disturbances and climate change at the landscape scale. To this end, I simulated a wide range of mixtures of three major Central European tree species (i.e., Norway spruce, European beech and Silver fir) under current and future climate, including wind and bark beetle disturbances. Simulation results indicated that even though spruce-dominated forests were least resistant to wind disturbance, increasing spruce proportion had a positive influence on resilience under current climate. Moreover, in the absence of climate change, forest resilience generally decreased with elevation and the co-occurrence of bark beetle outbreaks. Under climate change, elevation and spruce proportion reversed their influence on forest resilience, with elevation becoming an important positive factor and spruce proportion a negative factor. In interaction with bark beetle outbreaks, enhanced wind disturbances had a negative influence, particularly under water-limited conditions caused by climate change. As high resistance did not necessarily imply high resilience, the two properties should be considered separately in further studies. Additionally, especially the resistance and resilience of spruce-dominated forests to interacting disturbances and climate change could be enhanced if admixed with more drought- and disturbance tolerant species. Based on these findings, I recommend the following future research to further enhance our knowledge about the influence of tree species diversity on EGS provisioning and the diversity-disturbance relationship: (1) to assess the influence of subdominant species on EGS provisioning, (2) to evaluate EGS at multiple time points so as to increase the robustness of the findings, (3) to corroborate the wind module e.g. using a model comparison, and (4) to develop a more dynamic representation of browsing at the landscape scale in order to be able to assess more systematically interaction effects of windthrow and browsing on tree species diversity. Overall, this thesis demonstrated the usefulness of forest landscape models for biodiversity studies at spatial and temporal scales that are not accessible to either observation or experimentation. The findings highlighted the importance to focus on species with different functional traits in EGS studies, rather than on species diversity itself. Moreover, due to altered growth patterns of tree species under climate change, forest managers need to adapt forests continuously to maintain their resilience to disturbances under changing environmental conditions.

Diverse rainforests in the tropics are being rapidly modified and fragmented for human use. Plants that persist in remnant forest patches are threatened by many biotic and abiotic changes that are associated with fragmentation. Several of these fragments consequently contain fewer plant species than they once did but, in the absence of contiguous forest, remain the only strongholds of plant and animal diversity in many parts of the world. However, the future of diversity in forest fragments may be uncertain as fragmentation can influence plant-animal interactions that shape plant communities. Some of these changes may already be apparent in the youngest life stages of fragmented plant communities, which would then form the template for the future of those fragments. By examining the compositions of differently aged plant communities in forest fragments, we may be able to identify interactions that are especially influenced by fragmentation, as various plant-animal interactions play structuring roles during different stages of a plant’s life cycle. In this thesis, we primarily investigate relationships between fragment area and processes that structure plant communities in a tropical forest. In the first data chapter (the second chapter of this thesis), we examine the compositions of four life stages of woody plants across a gradient of fragment size. We show that plant species are primarily affected by fragment size during their transitions from seeds to saplings. We discuss several possible explanations for the observed patterns but suggest that altered interactions between plants and their natural enemies (insects and fungal pathogens) may be particularly important drivers. Such plant-enemy interactions have the potential to maintain plant diversity by causing the negative density-dependent mortality of locally abundant plant species, and by allowing the persistence of locally rare species (the Janzen-Connell Hypothesis). As the modification of diversity-maintaining interactions can have catastrophic long-term consequences for the plant diversity in small fragments, it was important to investigate whether plant-enemy interactions are indeed sensitive to fragment size. In the second data chapter (the third chapter of this thesis), we investigate the relationship between fragment area and (soil-borne) fungus-induced mortality of six woody plant species in a shadehouse experiment. We present evidence that the pathogenic effects of fungi on one plant species increased with increasing fragment size. Although we show that plant fungus-interactions can be influenced by fragment size, further experiments are required to investigate whether such effects (even when spread across the community) can influence the diversity maintained in a forest fragment. In the third data chapter (the fourth chapter of this thesis), we first examine the roles of insects and fungi in maintaining woody plant seedling diversity in an Indian rainforest. We then investigate whether the diversity-maintaining abilities of these natural enemies are influenced by fragment size. We present evidence that insects play important roles in maintaining gamma diversity primarily by suppressing common plant species independent of density. We show that they maintain more diversity in large fragments than in smaller fragments, as smaller fragments were dominated by insect-resistant species. We present evidence that fungi caused the density-dependent mortality of one plant species but infer the presence of more such interactions in the community. We show that fungi may be sensitive to fragment size, and that fungi maintain more beta diversity of woody plant seedlings in large fragments than in small fragments. In conclusion, I show in my thesis that insects and fungi play important roles in maintaining woody plant seedling diversity. I further show that these essential plant-enemy interactions are predictably influenced by the size of a forest fragment, and that the plant diversity in small fragments may consequently be at risk from the breakdown of such interactions.

Di nitrogen (N) fixation of legume-rhizobia symbiosis represents a relevant N source for agricultural systems and has the potential to reduce the input of synthetic N fertiliser. Legumes in mixture with grass constitutes an important component of cropping systems of crop-livestock farms. In recent years, these mixtures became an interesting alternative in stockless farms as feedstock for biogas production. Clover growing in association with grass receives 80% of its N from symbiotic N2 fixation. Estimations of fixed N have usually considered neither belowground clover N nor clover N transferred to the associated grass. One reason might be that the assessment of belowground N is laborious, since roots have to be recovered from the soil and N derived from rhizodeposition has to be estimated. Rhizodeposition N, composed of particulate and non-particulate compounds, is released into the soil from living roots via exudation and root turnover. Rhizodeposition has been studied by stable isotope 15N enrichment techniques. Likewise, N transfer from clover to grass has been assessed with 15N techniques using both the 15N enrichment and 15N natural abundance method. Fixed N contained in above- and belowground N of clover-grass swards potentially presents a significant N input in both conventional and organic cropping systems. These systems differ in fertilisation and crop protection strategies. The amount and the quality of applied fertilisers result in differences in soil nutrientavailability. Organically cropped soils often have a greater soil microbial biomass both in size and in activity compared to conventionally cropped ones. There is a lack of understanding on how these factors affect the input of symbiotically fixed N and on the fate of legume N remaining in the soil. To examine these relations, a microplot study was conducted in the DOK long-term field experiment, since 33 years of organic vs. conventional cropping with respective fertilisation and plant protection strategies resulted in soils with a gradient in nutrient-availability, soil microbial biomass both in size and in activity, and 15N natural abundance of soil N. Red clover (Trifolium pratense L.) above- and belowground N was quantified in model clover-grass swards. Swards were cultivated in microplots over two consecutive years. Microplots were located in DOK field plots with different fertilisation strategies. In general, the fertilisation increased in the order zero-fertilisation control (NOFERT), organic cropping system with half dose fertilisation (BIOORG1), organic cropping system with regular dose fertilisation (BIOORG2), and conventional cropping system (CONMIN2) with regular dose fertilisation. The organic cropping system at level 1 and 2 was fertilised with farmyard manure (manure and slurry) while the conventional cropping system was supplied by mineral fertiliser exclusively. Red clover rhizodeposition N was determined by 15N multiple-pulse leaf labelling (chapter 1). All roots were carefully removed from the soil. Subsequently, the fate of N derived from rhizodeposition being still present in the soil was investigated at different points of time using a sequential extraction. This procedure allows to extract soluble N and microbial biomass N from the soil. The remaining soil organic matter pools were separated in low and high density occluded particulate organic matter and silicate and quartz mineral-organic associations using a sequential density fractionation. Cropping system related effects from the size and activity of the microbial biomass on the General introduction 4 incorporation of N derived from rhizodeposition in soil pools and soil organic matter pools were assessed (chapter 2). Furthermore, different 15N natural abundance and 15N enrichment procedures were compared to determine the transfer from red clover N to perennial ryegrass (Lolium perenne L.). Subsequently, the 15N natural abundance method was verified with cropping systems under identical environmental and management conditions but differing in 15N natural abundance of the applied N fertilisers. One 15N natural abundance procedure was selected to quantify red clover N and symbiotically fixed red clover N being transferred to perennial ryegrass (chapter 3). Finally, the results from chapter 1 to 3 were scaled up from the microplot level to the field plot level of the DOK experiment. For this, N yields and clover proportions of clover-grass swards of field plots were used. Results were synthesised to present an overall picture on symbiotically fixed N in the plant-soil system of clover-grass swards under different cropping systems (general discussion). Red clover belowground N developed proportional to aboveground N at a ratio of 0.4 to 1 irrespective of the fertilisation strategy and the time of cultivation. However, the ratio N derived from rhizodeposition to root N changed with time. More than 90% of rhizodeposition N was incorporated into soil organic matter pools. Thereof, about 40% was found in silicate mineral-organic associations, 40% to 50% in both occluded particulate organic matter fractions, and the remainder in quartz mineralorganic associations irrespective of the fertilisation strategy related organic matter input. The proportions of grass N transferred from red clover N being estimated by 15N natural abundance procedures were within the range of that being estimated by 15N enrichment based procedures. About 40% of perennial ryegrass N was transferred from red clover in the low N fertilised swards (< 50 kg mineral N ha-1 a-1) NOFERT, BIOORG1 and BIOORG2. This corresponds to more than one third of perennial ryegrass N if related to symbiotically fixed red clover N. Up scaled from the microplot level to the field plot level of the DOK experiment, the sward plant-soil system obtained 300 to more than 400 kg N ha-1 from the symbiotic N2 fixation of clover after two years of cultivation. From that symbiotically fixed clover N, nearly 50% was present in the clover yield, about one third was transferred to grass, nearly 15% was accumulated in soil organic matter pools, 5% remained in the stubble and the root, and less than 1% was found in the both soil pools soluble N and microbial biomass N. Subsequent to the last harvest at the end of the 2nd year, on average 100 kg ha-1 symbiotically fixed clover derived N remained in the stubble and the roots of clover and grass and in the soil pools. Remaining N increased in the order NOFERT, CONMIN2, BIOORG2, and BIOORG1 at a ratio of 0.9 to 0.9 to 1.1 to 1.2 related to the average of the four cropping systems. In conclusion, red clover belowground N could be estimated from aboveground N by a factor of 0.4 irrespective of the fertilisation strategy and the cultivation time. Allocation of red clover rhizodeposition N to the silicate mineral-organic association was the dominant process N derived from rhizodeposition remaining in the soil was exposed. This process proceeded within months, but remained unaffected by the cropping system related microbial size and activity. 15N natural abundance procedures resulted in somewhat less variable estimates of N transfer from red clover to perennial ryegrass than 15N enrichment General introduction 5 procedures. Cropping systems affected the amount of red clover and perennial ryegrass N accumulation, red clover N derived from rhizodeposition, and N transfer to grass, but hardly affected the partitioning of N derived from rhizodeposition to soil pools. The partitioning of red clover N between above- and belowground and the partitioning within soil organic matter pools was not affected by cropping systems in the studied plant-soil system. Up scaled from the microplot to the field plot level of the DOK experiment, about 50% of symbiotically fixed clover N was deposited into the soil (≈15%) or transferred to grass (≈35%) at the end of the 2nd cultivation year. Hence, clover belowground N and N transfer to grass may represent important and considerable N inputs to agricultural systems.

Just about all plants are colonized by fungal endophytes. Dark septate endophytes (DSE) are a diverse group of ascomycetes colonizing roots of a vast number of plants in many different ecosystems. Considering the Northern hemisphere, the majority of DSE belong to the Phialocephala fortinii s.l. - Acephala applanata species complex (PAC), consisting of at least 21 morphologically indistinguishable cryptic species (CSP), to seven of which species rank was formally assigned. CSP are reproductively isolated and so far no teleomorphic form of the fungus has been found, even tough evidence exists that sexual reproduction occurs or has occurred in the past. PAC communities are highly diverse and still little is known about the factors influencing community formation. Even though PAC are highly successful root colonizers, their ecological function is poorly understood. Therefore, community structure and dynamics, competition and possible modes of transmission were investigated within the scope of this thesis. In a first study, spatial and temporal dynamics of a PAC community in an undisturbed Norway spruce (Picea abies) forest, originally assessed in 2004, were reassessed ten years later. The spectrum of species remained virtually the same over this period. In both years, a majority of isolates belonged to Phialocephala turicensis, Phialocephala letzii, Phialocephala europaea, and Phialocephala helvetica and a trend towards fewer species per sampling plot could be observed. Microsatellite analysis revealed that none of the PAC genotypes detected in 2004 were present at the same grid points in 2014. Furthermore, only four of the 22 genotypes detected in 2004 were found again in 2014, indicating recombination. Recognizing that the PAC community is subjected to both spatial and temporal changes, the competitiveness of three P. subalpina strains and two P. fortinii s.s. strains was tested under laboratory conditions in living roots of inoculated Norway spruce saplings. Saplings were first colonized by a “resident” strain (“primary colonizer”) followed by transplantation into a substrate colonized by the “invading” strain (“secondary colonizer”). Power of retention and power of colonization were calculated for each strain. Overall, the strains clearly differed in their ability to colonize roots, as well as in their capability of offering resistance against an invading strain, and also in their power of suppressing an already established “resident” strain within living roots. With the possibility of inoculating Norway spruce saplings, transmission of PAC was tested using three different set-ups in a semi-sterile substrate: (I) without root contact by separating inoculated and non-inoculated saplings with a fine mesh, (II) confrontation of a non-inoculated sapling wrapped in fine mesh with a colonized substrate without contact, and (III) direct root contact between inoculated and non- inoculated spruce. PAC was transmitted most successfully via direct root contact between saplings, followed by saplings confronted with the inoculated substrate. But also contact-less transmission from tree to tree through the semi-sterile soil could be demonstrated for short distances of 0.5 cm. In the last study, transmission of PAC was investigated under more near-natural conditions in mesocosms containing natural Norway spruce regeneration, partly in a climate chamber and partly outside in the forest. The effects of disturbance (clear-cutting and drought) on a resident PAC community along with the ability of an alien PAC strain to invade a well established ecosystem were tested. The overall PAC community structure remained similar, despite successful introduction of the alien strain into the mesocosms. Only A. applanata was found to profit from clear-cutting, while the general PAC presence was significantly reduced. Drought did not have any significant influence on the PAC community. Our results show that the PAC community is subjected to spatial and temporal changes. These changes are, however, comparatively slow. Colonization of unsterile but PAC-free Norway spruce saplings, as well as the competitive strength of PAC were shown to be strain dependent. Together with the demonstration of PAC transmission by root contact and successful integration of an alien PAC strain into well-established communities, these findings are a first step towards understanding the processes shaping PAC assemblages in natural forest ecosystems.

Forest ecosystems play an integral role in the earth system (e.g., by regulating biogeochemical cycles) and provide a wide range of services to human societies. It is therefore of crucial importance to understand the effects of a changing climate and changing disturbance regimes on forest dynamics. To date, most studies of forest dynamics have focused on trees, thus neglecting the herbaceous understorey (e.g., grass, ferns, herbs) although an increasing number of empirical studies suggest that the interaction between herbs and trees can profoundly alter forest dynamics. In particular, competition for light and water by the herbaceous understorey has been shown to change the structure and composition of tree regeneration, and thus to delay and potentially even arrest forest succession. When ignoring this interaction, thresholds in ecosystem responses to changing climate and disturbance regimes may remain undetected. However, due to the restrictions of empirical studies little is known on the implications of overstorey-understorey interactions for forest dynamics at larger spatio-temporal scales. Dynamic vegetation models (DVMs) have been developed to overcome this restriction and explore vegetation dynamics at large temporal scales (>100 years). Among the various types of DVMs, forest landscape models (FLMs) are specifically designed to investigate vegetation interactions under changing climate and disturbance regimes at large spatial scales. I used the process-based FLM LandClim to investigate the long-term effect of overstorey-understorey interactions on forest dynamics in central European landscapes, specifically focusing on (1) competition for light in mesic forest landscapes, (2) competition for water under present and future climate conditions in a drought-prone landscape, and (3) the potential of disturbances (browsing, windthrow, timber harvest) to promote delayed and arrested succession. In Chapter I, I implemented an understorey component in the FLM LandClim, with a focus on competition for light as the main mode of interaction. Simulation results for two mesic landscapes in Central Europe (Feldberg in the Black Forest and Dischma valley in the central Alps) showed spatio-temporal patterns that were in line with trends reported in empirical studies from chronosequences and species elevation distributions. The presence of an herbaceous understorey had a strong impact on tree regeneration and forest growth during early succession, but a much smaller effect on the late-successional stage. Also, the strength of overstorey-understorey interactions varied considerably across the landscape, causing large delays in forest growth at low and mid-elevations. Furthermore, the understorey was found to act as a differential filter for tree establishment, inducing a shift towards more shade-tolerant species, which translated into altered overstorey composition for up to 200 years. I was thus able to upscale the effects of understorey competition that are evident from empirical studies at the plot level (i.e., a few square metres) and at the short time scale (

Despite a large unexplained variability in the values, the analysis of the hydrogen (H) isotope composition (δ2H) of plant organic compounds is confidently applied to assess ecohydrological processes in the environment. This is possible because most studies that use the stable H isotopes from plant-derived biomarkers consider the H isotope fractionation that occurs during the biosynthesis of any given compound (2H-εbio) to be constant within a species. Consequently, 2H values in plant organic compounds are assumed to be mainly driven by the plant’s source water 2H values and the leaf water evaporative 2H-enrichment. There are, however, several indications that 2H-εbio of plant organic compounds can vary and that the δ2H values are also related to the plant’s metabolism. In this thesis, the elucidate the puzzling variability in the δ2H values of plant organic compounds, the influence of the plant’s metabolism on the variability of 2H-εbio is specifically explored with regards to the possible biochemical mechanisms underlying this variability. In a first study, based on empirical data produced in two separate experiments, it is shown that the 2H-εbio of different compounds in plants is tightly coupled to a plant’s carbon and energy metabolism. Based on these data, we develop a conceptual biochemical model that explains how and where 2H-fractionation occurs in the biosynthesis of major plant organic compound classes such as carbohydrates and lipids and what the isotope fractionation processes are that introduce a metabolic signal in δ2H values to these compounds. In a second study, with δ2H analyses from heterotrophic plants, it is shown that the hydrogen isotope fractionation occurring during the biosynthesis of different organic compounds in plants can explain part of the variability observed in δ2H values across species. Metabolic effects on 2H values between heterotrophic plants and their autotrophic host plants differed for different compound classes. The remarkable consistency of the compound specific isotope effects between autotrophic host or reference plants and the heterotrophic parasitic or mycoheterotrophic plants points towards a general physiological mechanism that determines these effects and support the model developed in the first study. Finally, with this model, it is mechanistically illustrated that information recorded in the δ2H values of plant organic compounds goes beyond hydrological signals, but also contains important information on the carbon and energy metabolism of a plant. As such we provide the mechanistic basis to introduce hydrogen isotopes in plant organic compounds as new metabolic proxy for the carbon and energy metabolism of plants. Such a new metabolic proxy has the potential to be applied in a broad range of disciplines, including plant and ecosystem physiology, plant breeding, biogeochemistry, paleoecology and Earth system sciences.

Photosynthetic assimilation of atmospheric carbon dioxide (CO2) is the major carbon fixation mechanism. Thereby the captured light energy is used to produce carbohydrates within the Calvin-Benson cycle. A portion of the synthesized carbohydrates is exported out of the chloroplast into the cytosol, where sucrose can be produced. Sucrose is a non-reducing, neutral disaccharide, which can be transported throughout the plant, providing the necessary carbon and energy for development. The Calvin-Benson cycle and cytosolic sucrose metabolism build a complex network consisting of many highly regulated biochemical reactions. One characteristic of primary carbohydrate metabolism in plants is the apparent high level of genetic redundancy, especially among the cytosolic sucrose-metabolic enzymes. While the biochemical reactions are relatively well described, the role of the single isoforms is still unclear, and the apparent redundant isoforms might have a metabolic and physiological role. The aim of this work was to unravel and clarify the function of these (iso)enzymes and, if possible, attribute specific functions to them. First, homozygous single knock-out mutants were screened for phenotypic differences under normal growth conditions. This rarely revealed significant alterations compared to the wild type, suggesting that the isoenzymes may actually be redundant. However, as plants are naturally constantly exposed to environmental fluctuations, the roles of the isoforms may become apparent during acclimation. We therefore established a hydroponic platform, where plants could be grown in well-defined nutrient-deficient media (either without nitrate or phosphate) and under mild long-term abiotic stresses (cold, warm, salt or osmotic stress). This allowed me to perform a comparative proteomic analysis in wild type plants, where the plants’ stress responses to different treatments were examined in both the shoot and the root (Chapter 1). My results suggested that the plants response to the different stresses in a very specific manners. Furthermore, these responses were distinct in the root and the shoot. To link the changes in the proteome with changes at the metabolic level, we also measured carbohydrates in the hydroponically grown plants (Chapter 2). Moreover, I selected promising candidates based on the proteomic analyses, i.e. sucrose-metabolic proteins that were either up- or downregulated in one of the stress responses. The corresponding single mutants were then grown under the stress treatments and analyzed for their growth and early development (Chapter 2). One isoform among the four sucrose phosphate phosphatases (SPP2) and one fructokinase (FRK) turned out to be essential in seed development, the complete knock-out of them resulted in aborted seed development and non-viable plants. The knock-out mutant of another fructokinase (FRK7), which had been downregulated during the salt-stress treatment, grew slower under normal conditions, but was not further impaired during this stress. Further, a cytosolic fructose 1,6-bisphosphate aldolase (FBA8) appeared as the major isoform of its gene family in the cytosol. In the final part of this work (Chapter 3), I characterized additional fructose 1,6-bisphosphate aldolases. The FBA family is known to have diverse functions in plant physiology (i.e. glycolysis, sucrose biosynthesis, Calvin-Benson cycle), but I focused on their role in the Calvin-Benson cycle and investigated the three plastidial isoforms (FBA1, FBA2 and FBA3). While the fba1 mutant was indistinguishable from the wild type, the fba2 and fba3 single mutants grew considerably slower and displayed additional distinct phenotypes: The fba2 mutant showed a marked decrease in total FBA activity and a low level of starch coupled with a high sugar content. The fba3 mutant had an extremely high carbohydrate content, displaying five times elevated sugar and starch levels at the end of the day, but the total FBA activity was altered only little. GUS-reporter lines suggested that FBA3 was predominantly expressed in vascular tissues. This was in contrast to FBA1 and FBA2, which were expressed predominantly in the photosynthesizing cells of the leaf lamina. These data indicate that FBA1 and FBA2 catalyze the canonical reactions in the Calvin-Benson cycle, with FBA2 being the major isoform. By contrast, FBA3 is probably functional in non-photosynthesizing, heterotrophic tissues, especially in the vasculature. The knock-out of FBA3 created a barrier between the photosynthesizing source tissues and the heterotrophic sink tissues.

Agroforestry systems provide multiple ecosystem services and are refuges for diverse flora and fauna. Coffee is one of the main tropical agroforestry crops and of global economic importance. Over recent decades, coffee agroforestry systems have been increasingly intensified by the replacement of native shade tree diversity with one or few, often non-native, tree species. Such reduction in tree diversity might have implications for ecosystem services, such as nutrient cycling, soil fertility, pest control, and coffee production, and ultimately negative effects for the systems’ resilience to climate change. The overall aim of this thesis is to investigate the direct and indirect effects of tree diversity reduction on ecosystem services, to understand the arising management trade-offs for Coffea canephora production in the face of climate change. We therefore studied 25 agroforestry systems in Kodagu, India, across a broad rainfall and management gradient, which experience a gradual transformation of native diverse shade tree canopy to Grevillea robusta dominated shade. Climate change is expected to alter the intense monsoon rainfalls during the short, wet season by an increase in the east and a reduction in the west. The results show that the transformation towards G. robusta dominated shade has not only highly negative effects for tree diversity but also for coffee production and quality. Both coffee production and quality were lower under G. robusta dominating shade. This resulted mainly from the increased development of single-seeded fruits (pea-beans), likely a result from reduced pollination success, and higher infestation rates of the coffee berry borer, Hypothenemus hampei. This suggests that pest control and pollination services are reduced in monospecific agroforestry systems. Grevillea robusta shade reduced nutrient cycling and long-term soil fertility. In contrast to native trees, G. robusta leaf litter shedding was more dependent on the annual rainfall, which reduced litterfall in wet sites to negligible amounts. Low litter quality and reduced decomposition rates characterize G. robusta dominated agroforests, and this led to low soil fertility and a decline in soil carbon contents, particularly in wet sites. The specific characteristic of G. robusta, being a Proteaceae, reduced phosphor cycling by increasing the immobilization of the same. Although, we did not find evidence for increased nutrient limitation in C. canephora leaves under G. robusta shade, the loss of soil carbon reduces soil fertility and nutrient availability over the long-term, which will likely demand higher nutrient inputs in the future. Microclimate and soil moisture was negatively altered under G. robusta monospecific shade compared to native diverse agroforests. Low soil carbon was one of the main drivers for lower soil moisture under G. robusta, which increased nutrient leaching. This, together with higher relative air humidity, reduced coffee production in monospecific shade. While high monsoon rainfall reduced coffee production in all agroforestry types, throughfall reduction benefitted coffee plants less under G. robusta dominated shade, in which high nutrient leaching resulted in a lower final berry-set. In conclusion, we provide strong evidence that there are no trade-offs, but synergies between tree diversity, coffee production and resilience to climate change. A shade cover dominated by G. robusta affects ecosystem resilience by causing: (1) increased pest attacks likely due to a loss of complex multi-trophic interactions; (2) reduced nutrient cycling and loss of soil carbon, reducing soil fertility in the long-term; (3) reduction of soil moisture and increase of nutrient leaching likely via runoff; (4) increased relative humidity potentially due to higher transpiration of the fast-growing G. robusta. These characteristics of G. robusta dominance negatively affect coffee production and quality, and reduce the agroforestry systems’ resilience to climate change.

Seed development represents a critical stage for plant reproductive success. This dissertation focuses on phenotypic and molecular correlates of hybrid seed failure between closely-related species. Three main compartments comprise the angiosperm seed, each with different genomic make-up: the seed coat (maternal), the endosperm (2m:1p), and the embryo (1m:1p). The endosperm plays a central role in early seed development because it regulates embryo nutrient acquisition while synchronizing growth between seed compartments. Importantly, hybrid seed abortion is generally associated with an altered endosperm development. Moreover, genomic imprinting, i.e. parent-of-origin–dependent expression, is exceedingly rare in other plant tissues but widespread in the endosperm. Potential functional links between imprinting perturbation or -mismatch and seed abortion are predicted by evolutionary theory based on parental conflict, but have only begun to be elucidated at the molecular level. Wild tomatoes (Solanum sect. Lycopersicon) were chosen to compare seed development and gene expression in the endosperm of seeds from intraspecific and hybrid crosses, and to address the role of genomic imprinting in lineage divergence and hybrid seed failure. To this end, I used three tomato lineages with interesting hybrid seed phenotypes and patterns of genetic divergence: S. arcanum var marañón (A), S. chilense (C), and S. peruvianum (P). A large part of my study was based on laser-microdissected developing endosperm obtained from seeds of intra- and interspecific crosses and subsequent transcriptome sequencing. In Chapter 1, I hypothesized that seed abortion in wild tomatoes is triggered by endosperm failure and that viable hybrid progenies, after seed germination, may reveal additional symptoms of hybrid incompatibility. Jointly with my collaborators, I provided a comprehensive morphological description of seed development in intra- and interspecific crosses. I found that the incidence of hybrid seed failure was variable among species combinations, with marked phenotypic asymmetries between reciprocal crosses with near- complete seed inviability. For the latter, circumstantial evidence pointed to endosperm proliferation defects being responsible for embryo arrest at early globular stages. The reciprocal C×A and A×C hybrid crosses yielded intermediate levels of viable seeds, from which we grew an F1 hybrid cohort showing some developmental abnormalities, interpreted as reflecting post-germination genetic incompatibilities. Chapter 2 focuses on seeds from intraspecific crosses, i.e. those with normal seed development. My hypothesis was that genomic imprinting in the endosperm of normally developing seeds serves specific functions and is nonrandomly shared between recently diverged species. I found that the degree of overlap among imprinted genes across the three wild tomato lineages was significant, and higher for Paternally Expressed Genes (PEGs) than for Maternally Expressed Genes (MEGs). However, variation in imprinting status for many genes is suggestive of an evolutionarily fast turnover of imprinted expression. MEGs and PEGs appear to be associated with distinct functions, but I found evidence that they interact in functional and physical networks. In particular, I inferred that interactions between imprinted genes contribute to cell-cycle control. Candidate imprinted genes identified in this chapter should be representative of the typical imprinting landscape of wild tomato viable endosperm; they were used as a reference to compare parent-specific gene expression in within-lineage- and hybrid endosperms in Chapter 3. Chapter 3 aimed at testing the hypothesis that hybrid seed failure involves imprinting perturbation and/or large gene expression changes in wild tomato hybrid endosperms. When compared to intraspecific endosperms, those from strongly abortive crosses were characterized by extensive gene expression perturbation together with increased maternal expression proportions. Two homogeneous groups of hybrid endosperms were separated by the largest expression differences in the whole dataset, congruent with either maternal-excess-like (P×A and P×C) or paternal-excess-like (A×P and C×P) endosperms at the phenotypic level. I found strong evidence for perturbations of parental dosage mechanisms in these abortive endosperms, particularly the widespread loss of imprinting status of candidate PEGs. Crosses yielding only partial seed abortion (A×C and C×A) had far fewer expression changes than strongly abortive endosperms and also retained the imprinted status of most candidate PEGs. I discuss the potential roles of parental conflict and coadaptation in driving expression perturbation in abortive endosperm. Finally, I hypothesize that different ‘genetic strengths’ evolved since lineage divergence and identify candidate genes, such as AGAMOUS-LIKE transcriptions factors, that may underlie this dosage-related phenomenon. Such genes may significantly contribute to postzygotic reproductive isolation between wild tomato lineages. By revealing the widespread perturbation of imprinted expression in abortive hybrid endosperms, my project accrued molecular evidence for the fundamental role of parental dosage in successful seed development. As a collateral resource, it also provides a large number of candidate genes that are potentially useful for developmental and evolutionary biology and for plant breeding.

The ability to produce doubled haploid plants has found broad application in fundamental and applied research as well as in practical plant breeding. In maize (Zea mays L.) and barley (Hordeum vulgare L.), for instance, routine, large-scale doubled haploid production in a single generation has replaced the 5-7 cycles of repeated self-fertilization formerly required to obtain sufficiently homozygous material. Doubled haploid lines have been invaluable for robust, multi-year phenotyping in quantitative trait loci mapping studies and their complete homozygosity has simplified genome sequence assembly efforts. Furthermore, doubled haploids are directly released as stable, homogeneous cultivars or used as parents of F1 hybrid seed to exploit the phenomenon of heterosis. At this time, however, neither homozygous line nor doubled haploid production can be efficiently applied in the important forage crop perennial ryegrass (Lolium perenne L.). An effective self-incompatibility system as well as a marked sensitivity to inbreeding depression hamper iterations of self-fertilization, while low and highly genotype-specific responses render the available in vitro doubled haploid induction methods unproductive. Major benefits associated with easy access to homozygous germplasm, particularly the straightforward production of high yielding hybrid varieties, are therefore unavailable to those working with this economically significant species. This thesis documents the initiation of a modern reboot of the development of an efficient doubled haploid production system for perennial ryegrass. The main goal was to obtain a level of understanding of the genetic factors, as well as their genomic locations, governing the response to in vitro doubled haploid induction, that would enable rapid and effective introduction of high levels of androgenic ability into recalcitrant germplasm. Four distinct phases of the research are reported in chapters 2 through 5, which are summarised below. First of all, a comprehensive overview of the ways in which haploid and doubled haploid techniques may be exploited to reduce the time, space and investment associated with perennial ryegrass research and breeding, is given in chapter 2. The potential of doubled haploid induction to 1) purge deleterious alleles from germplasm intended for breeding, 2) develop mapping populations for genetic and genomic studies, 3) simplify haplotype mapping, 4) fix transgenes and mutations for functional gene validation and molecular breeding, and 5) hybrid cultivar development is discussed. It is concluded that relatively minor improvements to existing in vitro doubled haploid induction protocols of perennial ryegrass should make some exceedingly useful applications available to the forage grass community. A pilot study to characterize the responses of putative highly androgenic germplasm to a decades old in vitro anther culture protocol is presented in chapter 3. The method proved to be efficient and large numbers of microspore-derived embryo-like structures as well as green and albino plantlets could be recovered. In addition, significant genotype-dependent variation was observed between the individual anther donors, confirming the usefulness of the plant material for further investigations into the androgenic ability of perennial ryegrass. Chapter 4 describes the results of the subsequent large, two year screen of the response to the in vitro anther culture protocol of nine distinct, bi-parental populations, obtained by crossing two genotypes with contrasting androgenic capacities. The variation in embryo production, plant regeneration and green plant production observed between and within the populations was large, and its pattern indicated the presence of different genes and alleles involved in the control of the component traits of androgenic ability. An insignificant association of embryo production with plant regeneration, as well as a low correlation between green and albino plant yield, suggested that distinct genes influence these traits. Furthermore, the environment was found to affect the incidence of albinism to a larger degree than genetic components. Lastly, it was concluded that the evaluated populations could provide rare, beneficial alleles for the introgression of high levels of androgenic capacity into recalcitrant material. Finally, chapter 5 addresses the identification of genetic loci associated with androgenic ability, which were determined via a powerful genotyping-by-sequencing-based genome-wide association study using the plant material and phenotypic data of the previous chapter. Between 1 and 10 quantitative trait loci were identified for anther response, embryo and total plant production, green and albino plant production and regeneration. Interestingly, a locus with a major effect on green plant regeneration was identified on perennial ryegrass linkage group 5 which may prove to be orthologous to loci detected at a similar genomic location in four related Poaceae species. In addition, two intriguing candidate genes, encoding chromatin binding domains of the developmental phase transition regulator, Polycomb Repressive Complex 2, were identified and merit further investigation. Ultimately, these results currently enable the development of molecular markers to rapidly introgress androgenic capacity into recalcitrant perennial ryegrass germplasm. It is hard to overstate the importance of doubled haploid techniques to advance research and increase the speed of genetic gain of breeding programmes. Here, I have demonstrated the effectivity of an in vitro anther culture method for doubled haploid production in perennial ryegrass, a forage species of global importance. In addition, plant material carrying valuable alleles as well as the molecular tools to identify them are now available, so that efficient doubled haploid production may soon be added to the arsenal of research and breeding tools of the perennial ryegrass community. My work will significantly accelerate forage grass breeding and constitute a key step towards the realization of a grass hybrid breeding programme. Finally, the results obtained here may prove to be of significant benefit to research and breeding efforts in related Poaceae species as well.