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In an attempt to halt species and habitat loss across the continent, many restoration projects have been established across Europe. However, clear scientific insight in the processes governing the success of these restoration projects is currently limited, as traditional ecological restoration research mainly focuses on the species level and the effects of site-level conditions on assembly outcome. In this study, we evaluated several underexplored aspects of community assembly following restoration within several restored calcareous grasslands in the Viroin valley in southern Belgium. In an attempt to contribute to a better understanding of how different processes shape species colonization and community assembly following restoration, we examined the effects of the landscape configuration and contingencies on community assembly at different levels of diversity organization. More specifically, we looked at the species and functional trait level assembly of the above ground vegetation and the soil seed bank, on the one hand, and the population gene level during colonization of the long-lived grassland species, Origanum vulgare, on the other.Progressing assembly of the above ground vegetation was found to consist of a sequential replacement of generalist species with specialist species, which was reflected by a directional assembly at the functional trait level. Landscape configuration significantly affected this assembly, as grassland isolation slowed down assembly at both the species and the trait level. More interestingly, spatial isolation was found to act as a trait filter, independent of assembly age. We found a proportionally higher occurrence of species with light seeds and a high seed attachment potential in more isolated restoration patches, which could indicate that dispersal is likely more limited in isolated grasslands.Furthermore, we compared differentiation among these restored grasslands based on the species and functional trait composition. These analyses showed that trait similarity among grasslands clearly increased with the amount of time since restoration, indicating trait convergence through time. At the species level, we found no evidence of convergence through time, with even a trend towards divergence. These results support the idea that only limited niches occur, which are only filled by species that have the appropriate functional traits, resulting in clear deterministic assembly at the trait level. Species identity, on the contrary, has no role in this niche filling. The first appropriate species to reach a restoration site will be the ones that get established, resulting in divergence of the species composition among restored grasslands. When comparing the genetic diversity of recent populations and old, putative source populations of Origanum vulgare, we did not observe decreased genetic diversity in recent populations, nor inflated genetic differentiation among them.Nevertheless, a significantly higher inbreeding coefficient was observed in recent populations, although this was not associated with negative effects on two measured proxies related to reproductive success. Our analyses indicated that colonization occurred from several source populations, with sufficient gene flow overcoming any large genetic founder effects, which likely increased the overall metapopulation viability of O. vulgare. Gene flow was nonetheless affected by the spatial configuration of the grasslands as gene flow into the recent populations mainly originated from nearby source populations.Comparing the soil seed bank composition of restored and ancient grassland, we observed that the species richness decreased through time. This was reflected at the trait level by a replacement of traits associated with generalist therophytes by traits typical for chamaephytes and grassland specialists. While species differentiation remained relatively constant, trait differentiation was observed to decrease through time. Only the species composition of ancient grasslands was affected by spatial isolation. The seed bank composition of ancient grasslands was furthermore observed to be a nested subset of that of young grasslands. These results suggest that community disassembly occurs in the seed bank. This implicates that directly following restoration, a large and diverse seed bank is formed, followed by a gradual net loss of species. Although theory predicts this species loss to be driven by seed persistence traits, we found that this was not the case in our system, but that species loss was likely governed by functional changes in the above ground community. This disassembly process results in one deterministic end state at the trait level, but not at the species level.Our results suggest that several parallels in assembly patterns exist among the different organizational levels of diversity, most notably among both the species and functional trait level of the above ground community and the soil seed bank. Nevertheless, clear differences among the different organizational levels also remain, illustrating the importance of a multi-level approach to gain in-depth insight in community assembly following restoration. More specifically, restoration monitoring should evaluate the genetic viability of colonizing species in parallel with community assembly since colonization itself is not a guarantee for successful establishment. The soil seed bank can furthermore significantly affect above ground assembly and should for this reason be taken into account. Finally, we observed that the spatial configuration of the study area and priority effects significantly affect assembly patterns, and should therefore be included when designing restoration projects.

academic collection --- 58 --- Botany --- Theses --- 58 Botany --- 58 Botanie --- Botanie

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In the last two decades, genetic data considerably improved our understanding of the phylogenetic history and diversity of species, but the ultimate drivers of speciation remain poorly understood. However, it became clear that evolutionary divergence has a strong ecological component. How ecological factors contribute to evolutionary divergence at historical or contemporary time scales is therefore a key question in evolutionary biology.Parasites represent a strong ecological pressure, which is predominant in all animals. Since parasites influence survival and reproduction, they can also influence adaptation, reproductive isolation and ultimately perhaps even speciation of their host. Whether or not parasites induce local immunogenetic adaptation and hence divergence of their host across landscape, depends on how parasite communities respond to environmental and biogeographic variation, and the strength of host-parasite co-evolution.In this doctoral thesis, we address questions related to parasite infection patterns and parasite driven adaptation in a cichlid radiation in Lake Tanganyika. The African Great Lake cichlids are famous because of their astonishing species-richness, and represent one of the most powerful model systems to study the genetic basis of diversification. Especially the cichlid fishes of Lake Tanganyika are genetically and morphologically very diverse. A diversity that yet has to be explained. The processes, which lead to the emergence of so many species in such an adaptive radiation, are probably manifold and due to an interaction of several extrinsic (e.g. ecological opportunities) and intrinsic factors (e.g. key innovations or genetic propensity of a taxon to diversify). Interestingly, adaptive divergence causing shifts in diet, habitat use or behaviour might directly relate to shifts in parasite infection.We chose three host species for our studies. All of them inhabit rocky outcrops in the littoral zone of Lake Tanganyika. Whereas Tropheus moorii and Variabilichromis moorii are stenotopic and philopatric species, Simochromis diagramma is more eurytopic and may disperse across various habitats. We found this dispersal behaviour to be reflected in genetic connectivity among populations. Furthermore, screening of sympatric populations of the three species for infection with metazoan ecto- and endoparasites revealed that populations face contrasting parasite communities. In S. diagramma, contrasts are weaker, probably as a consequence of homogenization of parasite communities by host dispersal. But host dispersal is only one of many factors determining the spatial structure of parasite communities. Despite these recent advances in our understanding of parasite community structure in Lake Tanganyika, we still lack information on the distribution of intermediate hosts or how parasite communities respond to environmental variation.We observed that ecological differentiation by infection with contrasting parasite communities is paralleled by adaptive immunogenetic divergence among host populations at genes of the major histocompatibility complex (MHC) in all three host species. MHC genes play a pivotal role in the recognition of antigens and are the most polymorphic genes known in jawed vertebrates. In cichlids MHC class IIB genes occur as two clusters (a and b) on two different chromosomes. We found that the loci of the more diverse of these clusters probably originated from a single ancestral gene through a birth and death process of gene evolution after the divergence of cichlids from other percomorph lineages. Some of these loci show elevated levels of polymorphism, whereas others are less variable, indicating the existence of several MHC class IIB b loci with non-classical functions.Cichlid individuals vary in respect to the number of loci within their MHC class IIB b cluster. In our studies we found that T. moorii individuals with an intermediate number of MHC loci can deal more efficiently with their fat reserves than those with few or too many loci. The reason might be that they suffer less from parasite infection or the negative consequences of T-cell selection by a high MHC diversity.At the host species level, we observed parallel parasite infection patterns and parallel immunogenetic adaptation among sympatric populations of T. moorii and S. diagramma. Shared infection patterns might be the ultimate reason for frequent MHC trans-species polymorphism among African cichlids. But detailed information on more species will be necessary to reveal general patterns in multi-host-multi-parasite infection dynamics and how this translates to immunogenetic adaptation.The water level of Lake Tanganyika fluctuates at geological time scales. Previous research suggested that populations of the rock-dwelling cichlids T. moorii and V. moorii along the Zambian shore-line of Lake Tanganyika diverge during isolation at lake level high stands and face increased levels of gene flow at low stands. In this thesis we propose that ecological divergence might be caused by contrasting parasite communities. We speculate that this ecological differentiation significantly contributed to the morphological and genetic diversity found in these two cichlid species today.

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Conservation biology, defined by its goal—to halt or repair the undeniable, massive damage that is being done to ecosystems, species, and the relationships of humans to the environment, can help to understand how native species respond to the main threats to biodiversity. The tropical Andes is one of the most important mountainous hotspots of biodiversity, and the ecosystems above the forest line contain one of the most threatened ecosystems in South America, the Polylepis woodlands. The main threats to these ecosystems are fire, overcutting, overgrazing with cattle and sheep, and reforestation with exotic tree species, as well as habitat fragmentation, and global warming effects. In Bolivia, core area for the genus’ diversity, there is little or no information about the effects of exotic species, fragmentation and climate change on Polylepis species. Our research aims to describing the species diversity inhabiting Polylepis woodlands in Bolivia, and studying how Polylepis trees and populations may respond to three major threats: global warming, the introduction of exotic species and habitat fragmentation. We used literature reviews, observational studies, and field and laboratory experiments to understand how the regeneration, growth and population genetics of the native trees Polylepis (P. besseri and P. subtusalbida) respond to these threats. The Bolivian high Andes holds 13 species and three subspecies of the genus Polylepis, which including plants, birds, mammals, butterflies and reptiles, at least contain 780 species. Ten of the 13 Polylepis species, as well as 7 other plants, 14 birds and 4 mammals were categorized as threatened or near threatened according to IUCN criteria, showing it is time to act to conserve these species. Herbs and shrubs were most common plants found in the Polylepis woodlands in Bolivia, whereas insectivorous birds, mammals, and reptiles were the most dominant guilds for animals. However, we found only one study dealing with insects in the Polylepis woodlands. Increasing the length of the growth season and precipitation, both increased plant and bird species richness. Regarding the effect of global warming on P. besseri’s regeneration, and based on the hydrothermal time modelling of germination, we found that an increase of 0.3°C of the current minimum field temperature may release P. besseri from the limit imposed by its base temperature (3°C). As temperatures rise, germination will be the result of the balance between increased temperatures and reduced water potential. Finally, when maximum temperature surpasses the optimum temperature for P. besseri (21.7°C), germination will start to decrease. P. besseri seeds from high elevations might become maladapted to warm conditions, given their home-site advantage for cold environments. If this pattern of local adaptation is supported through different years, then the translocation of individuals from low to high elevation has to be considered. Regarding Polylepis’ regeneration with exotic trees, we found that P. subtusalbida’s seedlings may coexist with the exotic trees Pinus radiata and Eucalyptus globulus. Likely, this coexistence occurs under low plant densities and low canopy cover. Although it depended on the locations, exotic species increased the frequency of the lateral growth form in P. subtusalbida, which in turn have the lowest survival. Thus, any measure for sustainable management of these forests should be contingent to specific locations. As for what concerns the effects of global warming on Polylepis growth, we found that an increase of temperature before the growth season (October) would increase P. besseri’s growth at Uypa fragment but not at Chutu Senega because trees from both fragments respond in different ways to regional climate. Our literature survey on the effects of habitat fragmentation on population genetics of Polylepis woodlands showed that offspring lost genetic diversity and increased its differentiation compared to the adult generation. These results show fragmentation effects are only becoming apparent, and suggest the main fragmentation event occurred c. 400yr ago. Manual introduction of pollen or seed from other fragments can be an efficient conservation strategy that needs to be initially evaluated through field experiments. Finally, we present unsolved problems and suggestions for further research, which include and are not limited to the modelling of germination below the base temperature for P. besseri, the confirmation of the local adaptation pattern to high elevations of the germination, the identification of the limiting factors for grassland colonization, and field surveys through the country to complete accounts of species diversity of Polylepis woodlands.

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The SnRK1 (SNF1-related kinase1) protein kinase, the ortholog of the yeast SNF1 (Sucrose non-fermenting1) kinase and animal AMP-activated kinase (AMPK), acts as a key metabolic sensor in plants. It integrates both endogenous developmental cues and diverse environmental stress conditions, that affect photosynthesis, respiration, or carbon allocation, triggering a coordinated response to ensure the maintenance of cellular energy homeostasis and survival. This involves metabolic and transcriptional reprogramming, also affecting plant growth. However, how exactly SnRK1 is activated upon increased energy demand or decreasing energy supply and how this affects growth and development is still largely unknow. To address these questions, we first developed and optimised a novel reporter to assess in vivo SnRK1 activity. The reporter is based on a peptide sequence of the well-known AMPK target Acetyl CoA Carboxylase 1 (ACC1) with S79 phosphorylation site, that is fused to an enhanced Green Fluorescent Protein (eGFP) tag (for subcellular localisation) and a double hemagglutinin (HA) tag (for protein expression analysis). The phosphorylation status of the reporter is evaluated using a commercially available phospho-ACC antibody. This construct can be used to study SnRK1 activity in vivo in isolated leaf mesophyll protoplasts or in intact Arabidopsis reporter plants constitutively expressing the reporter. After heterologous expression in bacteria and purification, it can also be used for in vitro kinase assays. Specific and conserved phosphorylation of the reporter was also confirmed in yeast using the S. cerevisiae snf1 mutant. Trehalose-6-phosphate (T6P), an intermediate of plant trehalose biosynthesis and an important novel growth regulator, was suggested to repress SnRK1 activity in young tissues under optimal growth conditions (Zhang et al., 2009). A major objective of this work is to study the molecular mechanisms involved. Using cellular (transient expression) and in vitro assays (using the ACC reporter), we confirmed that T6P regulates SnRK1 especially in younger tissues, and that T6P is not a direct regulator of the heterotrimeric SnRK1 complex, but requires an additional intermediary protein. We then explored the possible conserved regulation of yeast SNF1 by T6P, which would enable the use of powerful yeast genetics to elucidate the underlying molecular mechanisms in more detail. T6P regulation of SNF1 was suggested by the observation that the additional mutation of Snf1 in the tps1 mutant rescued the growth defect of this mutant on rapidly fermentable carbon sources. However, SNF1 T-loop phosphorylation, ACC reporter phosphorylation, and Mig1 (SNF1 target transcription factor) localisation in the WT and tps1 mutant indicated that T6P does not regulate SNF1 activity. Further investigation of gene expression, protein stability and activity of two SNF1 regulated enzymes fructose-1,6-bisphosphatase (encoded by FBP1) and phosphoenolpyruvate carboxykinase (PCK1), revealed a role for T6P in the regulation of gluconeogenesis, downstream and independent of SNF1 activity. The involvement of two SNF1-regulated transcription factors, Cat8 and Sip4, was assessed, but neither transcription factor seems to be involved in mediating the T6P regulation.The role of SnRK1 signalling in growth and development was investigated by gene expression profiling of growing leaves. Previous analyses in Arabidopsis rosette leaf series identified a remarkable peak in the expression of DIN6 (DARK-INDUCIBLE 6), a well-characterized SnRK1 target, suggesting a SnRK1-mediated metabolic and/or developmental transition, coinciding with the growth of the petiole and reduced sugar accumulation. Early leaf development involves a transition from cell division to cell expansion. Using the mesophyll protoplast assay, we found that SnRK1 can repress cyclin (CYCD3;1 and CYCB1;1) promoter activity, providing a direct link with growth control. Interestingly, transient expression of regulatory components in fully differentiated mesophyll leaf cells system can be used as a tool to study cell cycle regulatory machinery. However, the observed peak in DIN6 expression in developing leaves occurs after the transition from cell division to cell expansion. It also does not correspond to the juvenile-adult transition in larger rosettes. The expression of genes involved in sink and source activities indicate that the peak in DIN6 expression (and thus SnRK1 activity) might rather be associated with the transition from sink (net sucrose importing) to source (active photosynthesis and net sucrose exporting) activity, although in cellular assays overexpression of the SnRK1 catalytic subunit KIN10 mainly induced genes involved in sink activities.Finally, given its vital role in plant growth and development, further analyses of SnRK1 function are highly needed and would greatly benefit from specific direct small molecule SnRK1 activators and inhibitors. We therefore optimised the protoplast transient expression system for high throughput compound screening. New luciferase reporter constructs, using the deep sea shrimp nanoluciferase, were made resulting in an increased bioluminescence signal and simplification of the protocol to a one step process and optimal protoplast concentrations were determined.

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The proposed research has the aim to better understand eco-evolutionarydynamics and investigates methods to describe these dynamics adequately. The three methods that will be used in this research is the Price equation (Price 1970), the method developed by Ellner et al. (2011) and 'integral projection models' (Coulson et al. 2011). The insight in a mathematical structure of these methods allow us to apply these methods on datasets already available at the KU Leuven, and in a further stage the extension to analyses on community level and in space. This extension contains inserting indirect effects and implementing of a multivariate approach. In a later stage we investigate if we can find a continuous version of the equation of Collins and Gardner (2009) and if we canimplement this in an analogous method developed by Ellner et al. (2011). Implementing of this allows us to determine the relative importance ofpopulation dynamics (evolution and phenotypic plasticity) and communitydynamics. To validate our methods we will perform simulations. During my mandate I will search for agriculture- and industrial production systems where we can apply our developed methods.