Domain Adaptation in remote sensing: increasing the portability of land-cover classifiers

Among the types of remote sensing acquisitions, optical images are certainly one of the most widely relied upon data sources for Earth observation. They provide detailed measurements of the electromagnetic radiation reflected or emitted by each pixel in the scene. Through a process termed supervised land-cover classification, this allows to automatically yet accurately distinguish objects at the surface of our planet. In this respect, when producing a land-cover map of the surveyed area, the availability of training examples representative of each thematic class is crucial for the success of the classification procedure. However, in real applications, due to several constraints on the sample collection process, labeled pixels are usually scarce. When analyzing an image for which those key samples are unavailable, a viable solution consists in resorting to the ground truth data of other previously acquired images. This option is attractive but several factors such as atmospheric, ground and acquisition conditions can cause radiometric differences between the images, hindering therefore the transfer of knowledge from one image to another. The goal of this Thesis is to supply remote sensing image analysts with suitable processing techniques to ensure a robust portability of the classification models across different images. The ultimate purpose is to map the land-cover classes over large spatial and temporal extents with minimal ground information. To overcome, or simply quantify, the observed shifts in the statistical distribution of the spectra of the materials, we study four approaches issued from the field of machine learning. First, we propose a strategy to intelligently sample the image of interest to collect the labels only in correspondence of the most useful pixels. This iterative routine is based on a constant evaluation of the pertinence to the new image of the initial training data actually belonging to a different image. Second, an approach to reduce the radiometric differences among the images by projecting the respective pixels in a common new data space is presented. We analyze a kernel-based feature extraction framework suited for such problems, showing that, after this relative normalization, the cross-image generalization abilities of a classifier are highly increased. Third, we test a new data-driven measure of distance between probability distributions to assess the distortions caused by differences in the acquisition geometry affecting series of multi-angle images. Also, we gauge the portability of classification models through the sequences. In both exercises, the efficacy of classic physically- and statistically-based normalization methods is discussed. Finally, we explore a new family of approaches based on sparse representations of the samples to reciprocally convert the data space of two images. The projection function bridging the images allows a synthesis of new pixels with more similar characteristics ultimately facilitating the land-cover mapping across images.

Spatial predictions of land-use transitions and associated threats to biodiversity: the case of forest regrowth in mountain grasslands

Question Can we predict where forest regrowth caused by abandonment of agricultural activities is likely to occur? Can we assess how it may conflict with grassland diversity hotspots? Location Western Swiss Alps (4003210m a.s.l.). Methods We used statistical models to predict the location of land abandonment by farmers that is followed by forest regrowth in semi-natural grasslands of the Western Swiss Alps. Six modelling methods (GAM, GBM, GLM, RF, MDA, MARS) allowing binomial distribution were tested on two successive transitions occurring between three time periods. Models were calibrated using data on land-use change occurring between 1979 and 1992 as response, and environmental, accessibility and socio-economic variables as predictors, and these were validated for their capacity to predict the changes observed from 1992 to 2004. Projected probabilities of land-use change from an ensemble forecast of the six models were combined with a model of plant species richness based on a field inventory, allowing identification of critical grassland areas for the preservation of biodiversity. Results Models calibrated over the first land-use transition period predicted the second transition with reasonable accuracy. Forest regrowth occurs where cultivation costs are high and yield potential is low, i.e. on steeper slopes and at higher elevations. Overlaying species richness with land-use change predictions, we identified priority areas for the management and conservation of biodiversity at intermediate elevations. Conclusions Combining land-use change and biodiversity projections, we propose applied management measures for targeted/identified locations to limit the loss of biodiversity that could otherwise occur through loss of open habitats. The same approach could be applied to other types of land-use changes occurring in other ecosystems.

Knowing the past to predict the future: land-use change and the distribution of invasive bullfrogs

Biological invasions and land-use changes are two major causes of the global modifications of biodiversity. Habitat suitability models are the tools of choice to predict potential distributions of invasive species. Although land-use is a key driver of alien species invasions, it is often assumed that land-use is constant in time. Here we combine historical and present day information, to evaluate whether land-use changes could explain the dynamic of invasion of the American bullfrog Rana catesbeiana (=Lithobathes catesbeianus) in Northern Italy, from the 1950s to present-day. We used maxent to build habitat suitability models, on the basis of past (1960s, 1980s) and present-day data on land-uses and species distribution. For example, we used models built using the 1960s data to predict distribution in the 1980s, and so on. Furthermore, we used land-use scenarios to project suitability in the future. Habitat suitability models predicted well the spread of bullfrogs in the subsequent temporal step. Models considering land-use changes predicted invasion dynamics better than models assuming constant land-use over the last 50 years. Scenarios of future land-use suggest that suitability will remain similar in the next years. Habitat suitability models can help to understand and predict the dynamics of invasions; however, land-use is not constant in time: land-use modifications can strongly affect invasions; furthermore, both land management and the suitability of a given land-use class may vary in time. An integration of land-use changes in studies of biological invasions can help to improve management strategies.

Land use improves spatial predictions of mountain plant abundance but not presence-absence

Question Does a land-use variable improve spatial predictions of plant species presence-absence and abundance models at the regional scale in a mountain landscape? Location Western Swiss Alps. Methods Presence-absence generalized linear models (GLM) and abundance ordinal logistic regression models (LRM) were fitted to data on 78 mountain plant species, with topo-climatic and/or land-use variables available at a 25-m resolution. The additional contribution of land use when added to topo-climatic models was evaluated by: (1) assessing the changes in model fit and (2) predictive power, (3) partitioning the deviance respectively explained by the topo-climatic variables and the land-use variable through variation partitioning, and (5) comparing spatial projections. Results Land use significantly improved the fit of presence-absence models but not their predictive power. In contrast, land use significantly improved both the fit and predictive power of abundance models. Variation partitioning also showed that the individual contribution of land use to the deviance explained by presence-absence models was, on average, weak for both GLM and LRM (3.7% and 4.5%, respectively), but changes in spatial projections could nevertheless be important for some species. Conclusions In this mountain area and at our regional scale, land use is important for predicting abundance, but not presence-absence. The importance of adding land-use information depends on the species considered. Even without a marked effect on model fit and predictive performance, adding land use can affect spatial projections of both presence-absence and abundance models.

Changing landscapes of Switzerland: assessing effects of historic and future land uses and land covers on the occurrence of selected butterfly species

Summary Landscapes are continuously changing. Natural forces of change such as heavy rainfall and fires can exert lasting influences on their physical form. However, changes related to human activities have often shaped landscapes more distinctly. In Western Europe, especially modern agricultural practices and the expanse of overbuilt land have left their marks in the landscapes since the middle of the 20th century. In the recent years men realised that mare and more changes that were formerly attributed to natural forces might indirectly be the result of their own action. Perhaps the most striking landscape change indirectly driven by human activity we can witness in these days is the large withdrawal of Alpine glaciers. Together with the landscapes also habitats of animal and plant species have undergone vast and sometimes rapid changes that have been hold responsible for the ongoing loss of biodiversity. Thereby, still little knowledge is available about probable effects of the rate of landscape change on species persistence and disappearance. Therefore, the development and speed of land use/land cover in the Swiss communes between the 1950s and 1990s were reconstructed using 10 parameters from agriculture and housing censuses, and were further correlated with changes in butterfly species occurrences. Cluster analyses were used to detect spatial patterns of change on broad spatial scales. Thereby, clusters of communes showing similar changes or transformation rates were identified for single decades and put into a temporally dynamic sequence. The obtained picture on the changes showed a prevalent replacement of non-intensive agriculture by intensive practices, a strong spreading of urban communes around city centres, and transitions towards larger farm sizes in the mountainous areas. Increasing transformation rates toward more intensive agricultural managements were especially found until the 1970s, whereas afterwards the trends were commonly negative. However, transformation rates representing the development of residential buildings showed positive courses at any time. The analyses concerning the butterfly species showed that grassland species reacted sensitively to the density of livestock in the communes. This might indicate the augmented use of dry grasslands as cattle pastures that show altered plant species compositions. Furthermore, these species also decreased in communes where farms with an agricultural area >5ha have disappeared. The species of the wetland habitats were favoured in communes with smaller fractions of agricultural areas and lower densities of large farms (>10ha) but did not show any correlation to transformation rates. It was concluded from these analyses that transformation rates might influence species disappearance to a certain extent but that states of the environmental predictors might generally outweigh the importance of the corresponding rates. Information on the current distribution of species is evident for nature conservation. Planning authorities that define priority areas for species protection or examine and authorise construction projects need to know about the spatial distribution of species. Hence, models that simulate the potential spatial distribution of species have become important decision tools. The underlying statistical analyses such as the widely used generalised linear models (GLM) often rely on binary species presence-absence data. However, often only species presence data have been colleted, especially for vagrant, rare or cryptic species such as butterflies or reptiles. Modellers have thus introduced randomly selected absence data to design distribution models. Yet, selecting false absence data might bias the model results. Therefore, we investigated several strategies to select more reliable absence data to model the distribution of butterfly species based on historical distribution data. The results showed that better models were obtained when historical data from longer time periods were considered. Furthermore, model performance was additionally increased when long-term data of species that show similar habitat requirements as the modelled species were used. This successful methodological approach was further applied to assess consequences of future landscape changes on the occurrence of butterfly species inhabiting dry grasslands or wetlands. These habitat types have been subjected to strong deterioration in the recent decades, what makes their protection a future mission. Four spatially explicit scenarios that described (i) ongoing land use changes as observed between 1985 and 1997, (ii) liberalised agricultural markets, and (iii) slightly and (iv) strongly lowered agricultural production provided probable directions of landscape change. Current species-environment relationships were derived from a statistical model and used to predict future occurrence probabilities in six major biogeographical regions in Switzerland, comprising the Jura Mountains, the Plateau, the Northern and Southern Alps, as well as the Western and Eastern Central Alps. The main results were that dry grasslands species profited from lowered agricultural production, whereas overgrowth of open areas in the liberalisation scenario might impair species occurrence. The wetland species mostly responded with decreases in their occurrence probabilities in the scenarios, due to a loss of their preferred habitat. Further analyses about factors currently influencing species occurrences confirmed anthropogenic causes such as urbanisation, abandonment of open land, and agricultural intensification. Hence, landscape planning should pay more attention to these forces in areas currently inhabited by these butterfly species to enable sustainable species persistence. In this thesis historical data were intensively used to reconstruct past developments and to make them useful for current investigations. Yet, the availability of historical data and the analyses on broader spatial scales has often limited the explanatory power of the conducted analyses. Meaningful descriptors of former habitat characteristics and abundant species distribution data are generally sparse, especially for fine scale analyses. However, this situation can be ameliorated by broadening the extent of the study site and the used grain size, as was done in this thesis by considering the whole of Switzerland with its communes. Nevertheless, current monitoring projects and data recording techniques are promising data sources that might allow more detailed analyses about effects of long-term species reactions on landscape changes in the near future. This work, however, also showed the value of historical species distribution data as for example their potential to locate still unknown species occurrences. The results might therefore contribute to further research activities that investigate current and future species distributions considering the immense richness of historical distribution data. Résumé Les paysages changent continuellement. Des farces naturelles comme des pluies violentes ou des feux peuvent avoir une influence durable sur la forme du paysage. Cependant, les changements attribués aux activités humaines ont souvent modelé les paysages plus profondément. Depuis les années 1950 surtout, les pratiques agricoles modernes ou l'expansion des surfaces d'habitat et d'infrastructure ont caractérisé le développement du paysage en Europe de l'Ouest. Ces dernières années, l'homme a commencé à réaliser que beaucoup de changements «naturels » pourraient indirectement résulter de ses propres activités. Le changement de paysage le plus apparent dont nous sommes témoins de nos jours est probablement l'immense retraite des glaciers alpins. Avec les paysages, les habitats des animaux et des plantes ont aussi été exposés à des changements vastes et quelquefois rapides, tenus pour coresponsable de la continuelle diminution de la biodiversité. Cependant, nous savons peu des effets probables de la rapidité des changements du paysage sur la persistance et la disparition des espèces. Le développement et la rapidité du changement de l'utilisation et de la couverture du sol dans les communes suisses entre les années 50 et 90 ont donc été reconstruits au moyen de 10 variables issues des recensements agricoles et résidentiels et ont été corrélés avec des changements de présence des papillons diurnes. Des analyses de groupes (Cluster analyses) ont été utilisées pour détecter des arrangements spatiaux de changements à l'échelle de la Suisse. Des communes avec des changements ou rapidités comparables ont été délimitées pour des décennies séparées et ont été placées en séquence temporelle, en rendrent une certaine dynamique du changement. Les résultats ont montré un remplacement répandu d'une agriculture extensive des pratiques intensives, une forte expansion des faubourgs urbains autour des grandes cités et des transitions vers de plus grandes surfaces d'exploitation dans les Alpes. Dans le cas des exploitations agricoles, des taux de changement croissants ont été observés jusqu'aux années 70, alors que la tendance a généralement été inversée dans les années suivantes. Par contre, la vitesse de construction des nouvelles maisons a montré des courbes positives pendant les 50 années. Les analyses sur la réaction des papillons diurnes ont montré que les espèces des prairies sèches supportaient une grande densité de bétail. Il est possible que dans ces communes beaucoup des prairies sèches aient été fertilisées et utilisées comme pâturages, qui ont une autre composition floristique. De plus, les espèces ont diminué dans les communes caractérisées par une rapide perte des fermes avec une surface cultivable supérieure à 5 ha. Les espèces des marais ont été favorisées dans des communes avec peu de surface cultivable et peu de grandes fermes, mais n'ont pas réagi aux taux de changement. Il en a donc été conclu que la rapidité des changements pourrait expliquer les disparitions d'espèces dans certains cas, mais que les variables prédictives qui expriment des états pourraient être des descripteurs plus importants. Des informations sur la distribution récente des espèces sont importantes par rapport aux mesures pour la conservation de la nature. Pour des autorités occupées à définir des zones de protection prioritaires ou à autoriser des projets de construction, ces informations sont indispensables. Les modèles de distribution spatiale d'espèces sont donc devenus des moyens de décision importants. Les méthodes statistiques courantes comme les modèles linéaires généralisés (GLM) demandent des données de présence et d'absence des espèces. Cependant, souvent seules les données de présence sont disponibles, surtout pour les animaux migrants, rares ou cryptiques comme des papillons ou des reptiles. C'est pourquoi certains modélisateurs ont choisi des absences au hasard, avec le risque d'influencer le résultat en choisissant des fausses absences. Nous avons établi plusieurs stratégies, basées sur des données de distribution historique des papillons diurnes, pour sélectionner des absences plus fiables. Les résultats ont démontré que de meilleurs modèles pouvaient être obtenus lorsque les données proviennent des périodes de temps plus longues. En plus, la performance des modèles a pu être augmentée en considérant des données de distribution à long terme d'espèces qui occupent des habitats similaires à ceux de l'espèce cible. Vu le succès de cette stratégie, elle a été utilisée pour évaluer les effets potentiels des changements de paysage futurs sur la distribution des papillons des prairies sèches et marais, deux habitats qui ont souffert de graves détériorations. Quatre scénarios spatialement explicites, décrivant (i) l'extrapolation des changements de l'utilisation de sol tels qu'observés entre 1985 et 1997, (ii) la libéralisation des marchés agricoles, et une production agricole (iii) légèrement amoindrie et (iv) fortement diminuée, ont été utilisés pour générer des directions de changement probables. Les relations actuelles entre la distribution des espèces et l'environnement ont été déterminées par le biais des modèles statistiques et ont été utilisées pour calculer des probabilités de présence selon les scénarios dans six régions biogéographiques majeures de la Suisse, comportant le Jura, le Plateau, les Alpes du Nord, du Sud, centrales orientales et centrales occidentales. Les résultats principaux ont montré que les espèces des prairies sèches pourraient profiter d'une diminution de la production agricole, mais qu'elles pourraient aussi disparaître à cause de l'embroussaillement des terres ouvertes dû à la libéralisation des marchés agricoles. La probabilité de présence des espèces de marais a décrû à cause d'une perte générale des habitats favorables. De plus, les analyses ont confirmé que des causes humaines comme l'urbanisation, l'abandon des terres ouvertes et l'intensification de l'agriculture affectent actuellement ces espèces. Ainsi ces forces devraient être mieux prises en compte lors de planifications paysagères, pour que ces papillons diurnes puissent survivre dans leurs habitats actuels. Dans ce travail de thèse, des données historiques ont été intensivement utilisées pour reconstruire des développements anciens et pour les rendre utiles à des recherches contemporaines. Cependant, la disponibilité des données historiques et les analyses à grande échelle ont souvent limité le pouvoir explicatif des analyses. Des descripteurs pertinents pour caractériser les habitats anciens et des données suffisantes sur la distribution des espèces sont généralement rares, spécialement pour des analyses à des échelles fores. Cette situation peut être améliorée en augmentant l'étendue du site d'étude et la résolution, comme il a été fait dans cette thèse en considérant toute la Suisse avec ses communes. Cependant, les récents projets de surveillance et les techniques de collecte de données sont des sources prometteuses, qui pourraient permettre des analyses plus détaillés sur les réactions à long terme des espèces aux changements de paysage dans le futur. Ce travail a aussi montré la valeur des anciennes données de distribution, par exemple leur potentiel pour aider à localiser des' présences d'espèces encore inconnues. Les résultats peuvent contribuer à des activités de recherche à venir, qui étudieraient les distributions récentes ou futures d'espèces en considérant l'immense richesse des données de distribution historiques.

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice.

Land plants have developed a cuticle preventing uncontrolled water loss. Here we report that an ATP-binding cassette (ABC) subfamily G (ABCG) full transporter is required for leaf water conservation in both wild barley and rice. A spontaneous mutation, eibi1.b, in wild barley has a low capacity to retain leaf water, a phenotype associated with reduced cutin deposition and a thin cuticle. Map-based cloning revealed that Eibi1 encodes an HvABCG31 full transporter. The gene was highly expressed in the elongation zone of a growing leaf (the site of cutin synthesis), and its gene product also was localized in developing, but not in mature tissue. A de novo wild barley mutant named "eibi1.c," along with two transposon insertion lines of rice mutated in the ortholog of HvABCG31 also were unable to restrict water loss from detached leaves. HvABCG31 is hypothesized to function as a transporter involved in cutin formation. Homologs of HvABCG31 were found in green algae, moss, and lycopods, indicating that this full transporter is highly conserved in the evolution of land plants.

Evaluating sampling strategies and logistic regression methods for modelling complex land cover changes

The role of land cover change as a significant component of global change has become increasingly recognized in recent decades. Large databases measuring land cover change, and the data which can potentially be used to explain the observed changes, are also becoming more commonly available. When developing statistical models to investigate observed changes, it is important to be aware that the chosen sampling strategy and modelling techniques can influence results. We present a comparison of three sampling strategies and two forms of grouped logistic regression models (multinomial and ordinal) in the investigation of patterns of successional change after agricultural land abandonment in Switzerland. Results indicated that both ordinal and nominal transitional change occurs in the landscape and that the use of different sampling regimes and modelling techniques as investigative tools yield different results. Synthesis and applications. Our multimodel inference identified successfully a set of consistently selected indicators of land cover change, which can be used to predict further change, including annual average temperature, the number of already overgrown neighbouring areas of land and distance to historically destructive avalanche sites. This allows for more reliable decision making and planning with respect to landscape management. Although both model approaches gave similar results, ordinal regression yielded more parsimonious models that identified the important predictors of land cover change more efficiently. Thus, this approach is favourable where land cover change pattern can be interpreted as an ordinal process. Otherwise, multinomial logistic regression is a viable alternative.

Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are symbiotic soil fungi that are intimately associated with the roots of the majority of land plants. They colonise the interior of the roots and the hyphae extend into the soil. It is well known that bacterial colonisation of the rhizosphere can be crucial for many pathogenic as well as symbiotic plant-microbe interactions. However, although bacteria colonising the extraradical AMF hyphae (the hyphosphere) might be equally important for AMF symbiosis, little is known regarding which bacterial species would colonise AMF hyphae. In this study, we investigated which bacterial communities might be associated with AMF hyphae. As bacterial-hyphal attachment is extremely difficult to study in situ, we designed a system to grow AMF hyphae of Glomus intraradices and Glomus proliferum and studied which bacteria separated from an agricultural soil specifically attach to the hyphae. Characterisation of attached and non-attached bacterial communities was performed using terminal restriction fragment length polymorphism and clone library sequencing of 16S ribosomal RNA (rRNA) gene fragments. For all experiments, the composition of hyphal attached bacterial communities was different from the non-attached communities, and was also different from bacterial communities that had attached to glass wool (a non-living substratum). Analysis of amplified 16S rRNA genes indicated that in particular bacteria from the family of Oxalobacteraceae were highly abundant on AMF hyphae, suggesting that they may have developed specific interactions with the fungi.

A concentric analysis of the impact of urbanization on the threatened European tree frog in an agricultural landscape

Pond-breeding amphibians are affected by site-specific factors and regional and landscape-scale patterns of land use. Recent anthropogenic landscape modifications (drainage, agriculture intensification, larger road networks, and increased traffic) affect species by reducing the suitable habitat area and fragmenting remaining populations. Using a robust concentric approach based on permutation tests, we evaluated the impact of recent landscape changes on the presence of the endangered European tree frog (Hyla arborea.) in wetlands. We analyzed the frequency of 1 traffic and 14 land-use indices at 20 circular ranges (from 100-m up to 2-km radii) around 76 ponds identified in western Switzerland. Urban areas and road surfaces had a strong adverse effect on tree frog presence even at relatively great distances (from 100 m up to 1 km). When traffic measurements were considered instead of road surfaces, the effect increased, suggesting a negative impact due to a vehicle-induced effect. Altogether, our results indicate that urbanization and traffic must be taken into account when pond creation is an option in conservation management plans, as is the case for the European tree frog in western Switzerland. We conclude that our easy-to-use and robust concentric method of analysis can successfully assist managers in identifying potential sites for pond creation, where probability of the presence of tree frogs is maximized.

Spatial predictions of phylogenetic diversity in conservation decision making.

Considering genetic relatedness among species has long been argued as an important step toward measuring biological diversity more accurately, rather than relying solely on species richness. Some researchers have correlated measures of phylogenetic diversity and species richness across a series of sites and suggest that values of phylogenetic diversity do not differ enough from those of species richness to justify their inclusion in conservation planning. We compared predictions of species richness and 10 measures of phylogenetic diversity by creating distribution models for 168 individual species of a species-rich plant family, the Cape Proteaceae. When we used average amounts of land set aside for conservation to compare areas selected on the basis of species richness with areas selected on the basis of phylogenetic diversity, correlations between species richness and different measures of phylogenetic diversity varied considerably. Correlations between species richness and measures that were based on the length of phylogenetic tree branches and tree shape were weaker than those that were based on tree shape alone. Elevation explained up to 31% of the segregation of species rich versus phylogenetically rich areas. Given these results, the increased availability of molecular data, and the known ecological effect of phylogenetically rich communities, consideration of phylogenetic diversity in conservation decision making may be feasible and informative.

Effects of genetic alterations in arbuscular mycorrhizal fungi on plant growth and on their response to a change of host

Abstract :The majority of land plants form the symbiosis with arbuscular mycorrhizal fungi (AMF). The AM symbiosis has existed for hundreds of millions of years but little or no specificity seems to have co- evolved between the partners and only about 200 morphospecies of AMF are known. The fungi supply the plants most notably with phosphate in exchange for carbohydrates. The fungi improve plant growth, protect them against pathogens and herbivores and the symbiosis plays a key role in ecosystem productivity and plant diversity. The fungi are coenocytic, grow clonally and no sexual stage in their life cycle is known. For these reasons, they are presumed ancient asexuals. Evidence suggests that AMF contain populations of genetically different nucleotypes coexisting in a common cytoplasm. Consequently, the nucleotype content of new clonal offspring could potentially be altered by segregation of nuclei at spore formation and by genetic exchange between different AMF. Given the importance of AMF, it is surprising that remarkably little is known about the genetics and genomics of the fungi.The main goal of this thesis was to investigate the combined effects of plant species differences and of genetic exchange and segregation in AMF on the symbiosis. This work showed that single spore progeny can receive a different assortment of nucleotypes compared to their parent and compared to other single spore progeny. This is the first direct evidence that segregation occurs in AMF. We then showed that both genetic exchange and segregation can lead to new progeny that differentially alter plant growth compared to their parents. We also found that genetic exchange and segregation can lead to different development of the fungus during the establishment of the symbiosis. Finally, we found that a shift of host species can differentially alter the phenotypes and genotypes of AMF progeny obtained by genetic exchange and segregation compared to their parents.Overall, this study confirms the multigenomic state of the AMF Glomus intraradices because our findings are possible only if the fungus contains genetically different nuclei. We demonstrated the importance of the processes of genetic exchange and segregation to produce, in a very short time span, new progeny with novel symbiotic effects. Moreover, our results suggest that different host species could affect the fate of different nucleotypes following genetic exchange and segregation in AMF, and can potentially contribute to the maintenance of genetic diversity within AMF individuals. This work brings new insights into understanding how plants and fungi have coevolved and how the genetic diversity in AMF can be maintained. We recommend that the intra-ir1dividual AMF diversity and these processes should be considered in future research on this symbiosis.Résumé :La majorité des plantes terrestres forment des symbioses avec les champignons endomycorhiziens arbusculaires (CEA). Cette symbiose existe depuis plusieurs centaines de millions d'années mais peu ou pas de spécificité semble avoir co-évoluée entre les partenaires et seulement 200 morpho-espèces de CEA sont connues. Le champignon fournit surtout aux plantes du phosphate en échange de carbohydrates. Le champignon augmente la croissance des plantes, les protège contre des pathogènes et herbivores et la symbiose joue un rôle clé dans la productivité des écosystèmes et de la diversité des plantes. Les CEA sont coenocytiques, se reproduisent clonalement et aucune étape sexuée n'est connue dans leur cycle de vie. Pour ces raisons, ils sont présumés comme anciens asexués. Des preuves suggèrent que les CEA ont des populations de nucleotypes différents coexistant dans un cytoplasme commun. Par conséquent, le contenu en nucleotype des nouveaux descendants clonaux pourrait être altéré par la ségrégation des noyaux lors de la fonnation des spores et par l'échange génétique entre différents CEA. Etant donné l'importance des CEA, il est surprenant que si peu soit connu sur la génétique et la génomique du champignon.Le principal but de cette thèse a été d'étudier les effets combinés de différentes espèces de plantes et des mécanismes d'échange génétique et de ségrégation chez les CEA sur la symbiose. Ce travail a montré que chaque nouvelle spore produite pouvait recevoir un assortiment différent de noyaux comparé au parent ou comparé à d'autres nouvelles spores. Ceci est la première preuve directe que la ségrégation peut se produire chez les CEA. Nous avons ensuite montré qu'à la fois l'échange génétique et la ségrégation pouvaient mener à de nouveaux descendants qui altèrent différemment la croissance des plantes, comparé à leurs parents. Nous avons également trouvé que l'échange génétique et la ségrégation pouvaient entraîner des développements différents du champignon pendant l'établissement de la symbiose. Pour finir, nous avons trouvé qu'un changement d'espèce de l'hôte pouvait altérer différemment les phénotypes et génotypes des descendants issus d'échange génétique et de ségrégation, comparé à leurs parents.Globalement, cette étude confirme l'état multigénomique du CEA Glumus intraradices car nous résultats sont possibles seulement si le champignon possède des noyaux génétiquement différents. Nous avons démontrés l'importance des mécanismes d'échange génétique et de ségrégation pour produire en très peu de temps de nouveaux descendants ayant des effets symbiotiques nouveaux. De plus, nos résultats suggèrent que différentes espèces de plantes peuvent agir sur le devenir des nucleotypes après l'échange génétique et la ségrégation chez les CEA, et pourraient contribuer à la maintenance de la diversité génétique au sein d'un même CEA. Ce travail apporte des éléments nouveaux pour comprendre comment les plantes et les champignons ont coévolué et comment la diversité génétique chez les CEA peut être maintenue. Nous recommandons de considérer la diversité génétique intra-individuelle des CEA et ces mécanismes lors de futures recherches sur cette symbiose.

Combining probabilistic land-use change and tree population dynamics modelling to simulate responses in mountain forests

Altitudinal tree lines are mainly constrained by temperature, but can also be influenced by factors such as human activity, particularly in the European Alps, where centuries of agricultural use have affected the tree-line. Over the last decades this trend has been reversed due to changing agricultural practices and land-abandonment. We aimed to combine a statistical land-abandonment model with a forest dynamics model, to take into account the combined effects of climate and human land-use on the Alpine tree-line in Switzerland. Land-abandonment probability was expressed by a logistic regression function of degree-day sum, distance from forest edge, soil stoniness, slope, proportion of employees in the secondary and tertiary sectors, proportion of commuters and proportion of full-time farms. This was implemented in the TreeMig spatio-temporal forest model. Distance from forest edge and degree-day sum vary through feed-back from the dynamics part of TreeMig and climate change scenarios, while the other variables remain constant for each grid cell over time. The new model, TreeMig-LAb, was tested on theoretical landscapes, where the variables in the land-abandonment model were varied one by one. This confirmed the strong influence of distance from forest and slope on the abandonment probability. Degree-day sum has a more complex role, with opposite influences on land-abandonment and forest growth. TreeMig-LAb was also applied to a case study area in the Upper Engadine (Swiss Alps), along with a model where abandonment probability was a constant. Two scenarios were used: natural succession only (100% probability) and a probability of abandonment based on past transition proportions in that area (2.1% per decade). The former showed new forest growing in all but the highest-altitude locations. The latter was more realistic as to numbers of newly forested cells, but their location was random and the resulting landscape heterogeneous. Using the logistic regression model gave results consistent with observed patterns of land-abandonment: existing forests expanded and gaps closed, leading to an increasingly homogeneous landscape.

Plasma membrane cyclic nucleotide gated calcium channels control land plant thermal sensing and acquired thermotolerance.

Typically at dawn on a hot summer day, land plants need precise molecular thermometers to sense harmless increments in the ambient temperature to induce a timely heat shock response (HSR) and accumulate protective heat shock proteins in anticipation of harmful temperatures at mid-day. Here, we found that the cyclic nucleotide gated calcium channel (CNGC) CNGCb gene from Physcomitrella patens and its Arabidopsis thaliana ortholog CNGC2, encode a component of cyclic nucleotide gated Ca(2+) channels that act as the primary thermosensors of land plant cells. Disruption of CNGCb or CNGC2 produced a hyper-thermosensitive phenotype, giving rise to an HSR and acquired thermotolerance at significantly milder heat-priming treatments than in wild-type plants. In an aequorin-expressing moss, CNGCb loss-of-function caused a hyper-thermoresponsive Ca(2+) influx and altered Ca(2+) signaling. Patch clamp recordings on moss protoplasts showed the presence of three distinct thermoresponsive Ca(2+) channels in wild-type cells. Deletion of CNGCb led to a total absence of one and increased the open probability of the remaining two thermoresponsive Ca(2+) channels. Thus, CNGC2 and CNGCb are expected to form heteromeric Ca(2+) channels with other related CNGCs. These channels in the plasma membrane respond to increments in the ambient temperature by triggering an optimal HSR, leading to the onset of plant acquired thermotolerance.