Reynoutria spp. rank among highly invasive taxa in the Czech Republic. Therefore, a considerable effort is focused on its eradication. This is usually done by application of non- selective herbicide based on glyphosate. However, only little is known about the spontaneous recovery of the native vegetation after the eradication, as well as whether the restoration can be facilitated by additional management. In my master thesis I (i) describe the process of restoration after Reynoutria spp. eradication, (ii) evaluate the influence of factors which could potentially inhibit the succession (such as glyphosate, allelopathy, changes in soil conditions due to Reynoutria spp. invasion), and (iii) evaluate the influence of native-species seed addition on establishment of target plant communities. The process of vegetation recovery was followed on 17 sites in a forest and in ruderal forest-free area from 2007 to 2010. Over the three years of the study, the sites in the forest- free area were covered by diverse vegetation, secondary succession on sites in a forest progressed more slowly. Any soil changes were detected. The process of succession was limited probably because a dead biomass was left on the sites after the eradication. The seed addition was also not crucial for the restoration of plant communitites.

Despite its long tradition in our country, livestock grazing almost disappeared from Czech landscape. This form of land use has winded down in the middle of 20th century, when compulsory co-operative farming was introduced. Decrease of pasturage is especially visible on fragmented areas of steep slopes and in dry places. These areas are often highly valuable and protected for its nature richness. When a grazing management is introduced, its effects on plant species communities are not clear. Also the exact mechanisms of vegetation changes caused by grazing are often unknown. In 2005, administration of PLA Český kras reinstated grazing management as a mean of preservation of dry grassland ecosystems. As part of this project I studied, how generative regeneration contributes to vegetation changes. The aim of the present study is to ascertain: a) how is seedling recruitment and survival affected by grazing, b) what are limitations of generative reproduction, and c) what is the contribution of soil seed bank to vegetation changes. In 2005, monitoring of seedling recruitment and survival had started, repetitive sowing experiment was performed and species composition of persistent seed bank was analyzed. Grazing had a positive effect on seedling - both numbers of seedling and their species composition....

Le genre Cyrtorchis, groupait 18 espèces d’orchidées angraecoïdes endémiques d'Afrique tropicale, était connu pour ses grandes fleurs blanches, odorantes à long éperon bien adaptées pour des études sur la biologie de la reproduction. Il était également connu pour ses problèmes de délimitation taxonomique qui peuvent s’avérer préjudiciables pour la conservation des espèces.La présente thèse de doctorat ambitionne de résoudre les problèmes de délimitation au sein du genre au niveau inter et intraspécifique en utilisant une approche de taxonomie intégrative et de documenter sa biologie de la reproduction.Une inspection visuelle de 1752 spécimens, les analyses morphométriques et phylogénétiques ont été utilisées pour clarifier la taxonomie au sein du genre. L’inspection visuelle a permis de délimiter 27 morphogroupes à priori, desquels un échantillonnage de 171 spécimens représentant 20 morphogroupes a été utilisé pour les analyses morphométriques. Pour les reconstructions phylogénétiques, 69 spécimens représentant 21 des 27 morphogroupes ont été séquencés à partir de six marqueurs moléculaires. La caractérisation des patrons de floraison et l’observation et des pollinisateurs ont été réalisées au Cameroun grâce à un suivi phénologique en ombrière sur trois ans de 494 spécimens vivants représentant 15 taxons, et un suivi de la pollinisation naturelle in situ de deux de ces taxons. L’évaluation des facteurs affectant la production des fruits et des graines viables a été réalisée chez deux espèces du genre à travers 448 tests de pollinisation manuelle pour lesquels l’effet du système de pollinisation et de la limitation des ressources ont été examinés.Les approches morphologiques permettent de distinguer deux groupes correspondant aux deux sections préalablement identifiées pour le genre Cyrtorchis. Les analyses moléculaires quant à elles ne soutiennent que la monophylie d’une des deux sections, Cyrtorchis sect. Cyrtorchis. Huit taxons morphologiquement définis dans le genre incluant trois nouvelles espèces sont également bien supportés par les analyses morphométriques et phylogénétiques. Le point d’insertion des stipites au tier supérieur du viscidium semble être l’un des principaux caractères reproducteurs soutenant la monophylie du genre alors que d’autres traits (tels que la structure du viscidium, la forme des stipites et des lobes latéraux du rostelle) se révèlent être d’importants critères permettant d’inférer des relations phylogénétiques au sein du genre. Au final, cette analyse met en évidence 27 taxons au sein du genre(incluant six nouveaux taxons à décrire), dont 12 taxons, confirmé par les approches morphométriques et/ou phylogénétiques. La phénologie de la floraison des espèces en ombrière montre un pic de floraisons à la grande saison de pluie (entre août et octobre). Un décalage de la floraison est observé chez certains taxons distribués en sympatrie et un asynchronisme de la floraison entre population de la même espèce. La pollinisation naturelle est un évènement rare et difficile à observer chez les deux espèces étudiées (C. letouzeyi et C. okuensis). En effet, le taux de pollinisation/fructification est globalement faible (39 % de fleurs avec les pollinies emportées et 16 % de fruits produits chez C. okuensis ;31-15 % de fleurs avec les pollinies emportées et 7-4 % de fruits produits chez C. letouzeyi), et ce, à cause du nombre réduit des visites des pollinisateurs. Par ailleurs, les pollinisateurs des deux espèces ont été identifiés et la pollinisation par les sphinx est confirmée dans le genre. Les tests de pollinisation manuelles ont révélé que la pollinisation croisée semble être le système de pollinisation le plus efficace pour la production de fruits et de graines viables. Cependant, davantage d’espèces devront être testées pour confirmer ce patron. Les approches multidisciplinaires développées dans ce travail sont des bases solides pour la définition et la mise en œuvre de stratégies efficaces de conservation pour les espèces d’orchidées menacées. Afin de produire une révision taxonomique complète du genre, une phylogénie complète incluant les cinq taxons restants et ceux encore non résolus est nécessaire. Les nouveaux taxons identifiés devraient être décrits et les statuts de conservation évalués pour l’ensemble des espèces reconnues dans le genre. / The genus Cyrtorchis, grouped of 18 angraecoid orchids species endemic to tropical Africa, and was known for its large, white, fragrant flowers with a long spur well suited for studies on reproductive biology. It was also known for its taxonomic delimitation problems, which can be detrimental to the conservation of the species.This PhD thesis aims to address the delimitation problems within the genus at the inter- and intraspecific level using an integrative taxonomic approach and to investigate its reproductive biology.Visual inspection of 1752 specimens, morphometric and phylogenetic analyses was used to clarify the taxonomy within the genus. Visual inspection delineated 27 a priori morphogroups, from which a sample of 171 specimens representing 20 morphogroups was used for morphometric analyses. For phylogenetic reconstructions, 69 specimens representing 21 of the 27 morphogroups were sequenced with six molecular markers. The characterization of flowering patterns and the observation of pollinators were carried out respectively through a three-year shadehouse phenological survey of 494 living specimens representing 15 taxa and a survey of the natural in situ pollination of two taxa in Cameroon. The assessment of factors affecting fruit and viable seed production was carried out in two species of the genus through 448 hand pollination tests for which the effect of pollination system and resource limitation were examined.Morphological approaches allow to distinguish two groups corresponding to the two sections previously identified for the genus Cyrtorchis. Molecular analyses support only the monophyly of on of the sections, Cyrtorchis sect. Cyrtorchis. Eight morphologically defined taxa including three new species are also well supported by morphometric and phylogenetic analyses. The insertion point of the stipites at the rear third of the length of the viscidium appears to be one of the main reproductive characters supporting the monophyly of the genus while other traits (such as the viscidium structure, the shape of the stipites and the lateral lobes of the rostellum) are found to be important criteria for inferring phylogenetic relationships within the genus. Finally this analysis highlights 27 taxa within the genus (including six new taxa to be described), of which 12 taxa, confirmed by morphometric and/or phylogenetic approaches. Flowering of most species at the shadehouse is peaking during the main rainy season (between August and October). However, some sympatric species present non-overlapping flowering periods and an asynchronism of flowering between populations of the same species. Natural pollination is a rare event and difficult to observe in the two studied species. Indeed, the overall pollination/fruiting rate is low (39% of flowers with pollinia removed and 16% of fruits produced in C. okuensis; 31-15% of flowers with pollinia removed and 7-4% of fruits produced in C. letouzeyi) because of the reduced number of pollinators visits. Additionally, both species were found to be pollinated by hawkmoths. Manual pollination tests revealed that cross-pollination appears to be the most efficient pollination system to produce fruits and viable seeds. However, more species will need to be tested to confirm this pattern.The multidisciplinary approaches developed in this work provide a solid basis to define and implement effective conservation strategies for threatened orchid species. To produce a complete taxonomic revision of the genus, a completed phylogeny including the five remaining and the yet unresolved taxa is required. The newly identified taxa should be described and the conservation status assessed for all species recognised in the genus. / Option Biologie des organismes du Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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Die vorliegende Arbeit behandelt das biologische Phänomen der Dormanz mit Hilfe mathematischer Modellierung. Dormanz beschreibt dabei einen reversiblen Zustand von Individuen, in dem die metabolische Aktivität reduziert wird und die Resistenz gegen Natureinflüsse erhöht ist. Der erste Teil der Arbeit widmet sich den ökologischen Eigenschaften. Hier wird zunächst ein Moranmodell vorgestellt, welches verschiedene Modellierungsarten von Dormanz aus der Populationsgenetik vereint und unter verschiedenen Skalierungen den schwachen seed-bank Koaleszenten und den starken seed-bank Koaleszenten als anzestralen Prozess innehat. Dadurch werden die Parameter der Koaleszenten vergleichbar. Als Anwendung betrachten wir die sogenannte species abundance distribution, welche mithilfe von Koaleszenten beschrieben werden kann. Der zweite Teil beschäftigt sich mit den Auswirkungen von Dormanz auf evolutionäre Eigenschaften und beginnt mit einer Einführung in die Theorie von adaptive dynamics. Dort werden auch verschiedene Möglichkeiten der Modellierung von Dormanz in individuenbasierten Modellen besprochen. Danach befassen wir uns mit der Erweiterung eines Modells für sympatrische Speziation um den Aspekt der Dormanz. Die canonical equation of adaptive dynamics wird - motiviert durch ein Modell mit Dormanz - für schnellere Mutationsraten aus dem sogenannten power-law Mutationsregime für einen Grenzfall hergeleitet. Die Arbeit schließt mit dem dritten Teil, in welchem ein individuenbasiertes Modell für die Entwicklung von Krebs unter dem Einfluss von Chemotherapie und unter Berücksichtigung von Dormanz vorgestellt wird. In Simulationsstudien wird untersucht, inwiefern Dormanz zu Misserfolg einer Therapie beiträgt. Ein weiteres Ziel ist die Analyse von Kombinationsbehandlung mit einem Medikament welches mit dormanten Zellen interagieren kann insbesondere unter Betrachtung verschiedener Therapieansätze zur Behandlung von dormanten Krebszellen. / The present thesis uses mathematical modelling to investigate the consequences of dormancy. Dormancy describes a reversible and protected state of reduced metabolic activity which enhances an individual's resilience to hazardous conditions. In this sense, dormancy acts as a protection mechanism against habitats with unfavourable environments. The thesis considers the impact of dormancy on ecological, evolutionary and in its broadest sense pathogenic properties of microbial populations. The first part is concerned with studying the impact of dormancy on ecology. For this, a Moran model is presented which unifies different models of dormancy from population genetics and exhibits the weak seed-bank coalescent and the strong seed-bank coalescent as the scaling limit of the ancestral process. As an application we consider the species abundance distribution which can be described using coalescent theory. In the second part we consider the influence of dormancy on evolutionary properties. The modelling framework for this is the theory of adaptive dynamics. We then show that competition-induced dormancy may favour sympatric speciation. A key aspect in the derivation of this result is the canonical equation of adaptive dynamics. We extend this equation - motivated by a model including dormancy - to power-law mutations in a limiting case. We conclude the thesis with the third part where we provide an individual-based model for the treatment of cancer with chemotherapy under consideration of dormant cancer cells. Using simulation studies, we investigate how dormancy may contribute to treatment failure. Another goal of this chapter is to analyse combination treatment with a drug which directly targets dormant cancer cells and to formulate general observations regarding various strategies to counter cancer cell dormancy.

Os ecossistemas de ilhas, continentais ou oceânicas, são considerados os mais sensíveis à perturbação humana. A maioria das ilhas costeiras do Brasil sofreu fortes alterações na fauna e flora silvestre. A Ilha Anchieta (Ubatuba, SP) é uma Área Protegida com um longo histórico de perturbação, tendo sido amplamente desmatada no passado e sofrido a introdução de animais. Sabe-se que a fauna possui um papel chave na composição e estrutura da comunidade vegetal, favorecendo algumas espécies e prejudicando outras. Sendo assim, a perda ou alteração dos processos de interações entre animais e plantas afetam na estrutura e composição de espécies. Este estudo analisa as interações antagônicas entre planta e animais como possíveis fatores limitantes no processo de regeneração natural em três ambientes com distintos estágios sucessionais presentes na Ilha Anchieta: campo aberto (CA) e florestas ombrófilas rala (FOR) e densa (FOD). Para isso foram testados nos três ambientes os processos pós-dispersão de sementes: a predação de sementes pós-dispersas, a germinação do banco de sementes e a herbivoria. A predação de sementes apresentou forte efeito espacial (FOD>FOR>CA) e sazonal, com maiores proporções de predação de sementes no período de escassez de alimento (estação seca). Quantitativamente o banco de sementes não representa um fator limitante, porém foi composto por uma baixa diversidade de espécies lenhosas. A capacidade de germinação do banco de sementes do solo foi similar entre os ambientes florestais apresentando menor emersão de plântulas no campo aberto, provavelmente associado ao intenso escoamento superficial no local. Adicionalmente, a mortalidade de juvenis transplantados foi de 72,27%, sendo superior nas parcelas abertas aos vertebrados para todas as espécies em todos os ambientes, demonstrando um forte efeito negativo dos herbívoros vertebrados na comunidade vegetal. Sendo assim, foram detectados distintos gargalos atuando simultaneamente na regeneração natural nos três ambientes da Ilha Anchieta, sendo necessário o estabelecimento de práticas de manejo visando minimizar os efeitos abióticos no campo aberto e floresta ombrófila rala, favorecendo as interações mutualísticas e inibindo a atividade de animais antagônicos nas florestas ombrófilas rala e densa, acelerando assim o processo de regeneração natural na Ilha Anchieta. Considerar simultaneamente os obstáculos no processo de regeneração nos auxiliará a traçar práticas de restauração e recuperação de áreas degradadas mais efetivas e viáveis economicamente. / Island ecosystems, either continental or oceanic, are considered the most sensible to anthropogenic influences. Most Brazilian coastal islands have their original fauna and flora composition altered. The Anchieta Island (southeast Brazil) is a Protected Area that suffered deforestation and introduction of alien species. It is known that the fauna plays a key role in composing and structuring the vegetal community, favoring some species and harming others. Thus, the loss or change of animal-plant interactions affects the framework and composition of species. We simultaneously analyzed the antagonistic animal-plant interactions as possible limiting factors in the natural regeneration on tree successional stages of the Anchieta Island: the old fields (OF), the early secondary forest (ESF) and old growth forest (OGF). Therefore, in each habitat we are evaluating post-dispersal seed predation processes: post-dispersal seed predation, soil seed bank, and the herbivory. We found spatial (OGF>ESF>OF) and temporal effects on seed predation, with highest rates on dry season. Quantitatively, soil seed bank did not represent a limiting factor; but qualitatively, it was composed by few woody species. Our data pointed to the absence of a viable soil seed bank in the OF, probably due to an intense runoff. The forested habitats presented similar soil bank. Moreover, the total mortality of saplings was 72.27%, being higher on the unfenced treatment for all species and in all habitats, showing a very strong negative effect of vertebrate herbivores on the vegetal community. Therefore, we are detecting distinct bottlenecks acting simultaneously in the natural regeneration process in all of the successional stages of the Anchieta Island. Our results showed that management actions are required, aiming to both minimize the abiotic effects on the old fields and in the early secondary forest and to favor the mutual interactions and inhibit the activity of antagonic animals in the old growth and early secondary forests, accelerating, this way, the natural regeneration process of the Anchieta Island. Considering simultaneously the obstacles in the regeneration process will help to define restoration and recuperation procedures of degraded areas more effective and affordable.

Dans un contexte de destruction des zones humides à l’échelle mondiale, conséquence des activités d’origine anthropique, la restauration écologique de ces milieux et de leurs fonctions est devenue un enjeu écologique et sociétal. L’objectif de ce projet est de recréer des prairies humides à vocation agricole aux caractéristiques pédologiques et floristiques aussi proches que possible de celles des prairies totalement détruites par l’exploitation de matériaux alluvionnaires. L’étude présentée ici se focalise sur l’incidence des matériaux pédologiques utilisés pour la recréation de quatre sols sur les fonctions du sol et les cortèges floristiques associés. L’hypothèse principale est que la recréation d’un sol morphologiquement proche de celui détruit devrait permettre d’orienter la restauration écologique.L’hypothèse sous-jacente est qu’en utilisant différents matériaux pédologiques locaux, on hérite de leurs caractéristiques physico-chimiques et biologiques ce qui permettait de conserver les fonctions pédologiques qui leur sont associées et favorisait le retour d’un cortège floristique compatible avec un usage agricole. La première partie est consacrée à l’étude de deux fonctions remplies par les sols de zones humides à savoir le stockage du carbone organique et la dénitrification. Deux années et demi après la fin des travaux de comblement de ballastières, ces deux fonctions sont conservées au sein des quatre types de sols recréés. Les principaux résultats montrent un niveau d’efficience des matériaux pédologiques testés, fonction de leur sol origine et de leurs caractéristiques physico-chimiques. La deuxième partie est consacrée à l’étude des mécanismes de structuration des communautés végétales. Le suivi de la colonisation spontanée de la végétation a permis d’appréhender la forte contribution de la banque de graines issue des matériaux pédologiques locaux. Malgré la mise en évidence d’un début de trajectoires dynamiques au sein des quatre sols recréés, la similarité entre les communautés obtenues et les communautés cibles des prairies de référence n’excède pas 50 %. Les productions de biomasses aériennes associées à ces communautés sont comparables en quantité à celles des prairies de référence mais pas en qualité. La mise en place d’une gestion par semis associée à une fauche montre dès la première année une production de biomasses de qualité se rapprochant de celles des prairies locales.La dernière partie de ce manuscrit est consacrée à l’effet de trois niveaux d’engorgement des sols sur le processus de dénitrification et sur les traits de réponse d’une espèce prairiale, Holcus lanatus. Placer les quatre matériaux pédologiques dans des conditions identiques d’engorgement permet de souligner l’importance de l’héritage des communautés bactériennes dénitrifiantes sur le processus de dénitrification. Parallèlement, ces conditions expérimentales permettent de mettre en évidence les traits de réponses morphologiques et fonctionnels de l’espèce considérée. À l’issue de ces suivis, le meilleur compromis de restauration alliant sol, végétation et coûts économiques doit prendre en considération l’origine et l’histoire (i.e. gestion) des matériaux utilisés lors de la recréation écologique. / In a worldwide context of wetland destruction, a consequence of anthropic activities, ecological restoration of such habitats and their functions has become a societal and ecological issue. The objective of this project is to recreate agriculture-oriented wet grasslands with pedological and floristical properties as similar as possible to typical grasslands destroyed by alluvial materials extraction. The study presented here focuses on the impact of pedological materials, used in the re-creation of four soils, on soil functions and associated floristic processions. The main hypothesis is that re-creation of a soil morphologically similar to the previously destroyed one should drive ecological restoration. The underlying hypothesis is that different local pedological materials inherit their previous physicochemical and biological properties. This should conserve associated pedological functions and favor the return of a floristic procession compatible with agricultural exploitation. The first part is dedicated to the study of carbon storage and denitrification, two wetlands soils functions. These two functions are retained within the four re-created soils two and a half year after gravel-pit filling. Main results highlight functional efficiency levels of tested pedological material inherited from their respective initial topsoil physico-chemical properties. The second part is devoted to the study of mechanisms structuring plant communities. The high contribution of local pedological materials seed bank during the colonization process and its impact on aforementioned mechanisms was highlighted from our monitoring. Despite demonstration of the start of a dynamic trajectory in the four created soils similarity between obtained and target communities never exceeds 50%. Aerial biomass production associated to these communities is comparable to the production in reference wet grasslands in terms of quantity, but not quality. Implementation of management (sowing and mowing) shows biomass production of comparable quality to reference grassland from the first year onwards. The last part focuses on the effect of three soil waterlogging levels on the denitrification process and the response traits of Holcus lanatus, a meadow species. Pedological materials placement in identical waterlogging conditions highlights the importance of denitrifying bacteria communities inheritance on the denitrification process. These experimental conditions also enabled us to highlight the considered species morphological and functional response traits. To conclude and following our monitoring the best compromise for concurrent restoration of soil and vegetation while considering cost-effectiveness needs to account for topsoils origin and history (i.e. management).

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Global environmental changes, especially land-use changes, have profound effects on both ecosystem functioning and biodiversity, having already altered many ecosystem services. These losses emphasize the need to preserve what remains; however when conservation programs are not sufficient, restoring areas that have been destroyed or disturbed can improve conservation efforts and mitigate damages. This work focuses on campos rupestres, Neotropical grasslands found at altitudes, which are part of the Cerrado (Brazilian savannas). They host a great biodiversity with a high level of endemism and, like other mountain ecosystems, provide valuable ecosystem services, such as water purification and recreational services. They have been and still are being impacted by human activities, such as civil engineering construction, quarrying or mining. The first objective of this thesis was to describe the reference ecosystem in order to aim for a clear restoration target and to monitor progress and success. We show that campos rupestres are composed of at least two distinct plant communities (i.e. sandy and stony grasslands), each having a specific composition and structure, hosting a great biodiversity. Several phenological patterns occur among the herbaceous communities: the majority of species flowers and fruits appear during the rainy season but other patterns can be observed. During our 2-year survey, some dominant species belonging to Poaceae, among others, were not observed reproducing, which implies limited chances to disperse on degraded areas. Campo rupestre vegetation is not resilient following a strong disturbance: several years after the disturbance, almost no native species are encountered on the degraded areas, soils are completely altered and seed bank recomposes only with non-target ruderal species. According to the filter model, a local community is a subset of the regional species pool determined by a set of dispersal, abiotic and biotic filters. Acting on the different filters to influence the plant community was the core of our restoration interventions. We then applied three in-situ restoration protocols (hay transfer, species translocation and turf translocation) to restore both kinds of grassland. Hay transfer does not allow the restoration of campo rupestre vegetation because of soil alteration and mainly because of poor seed quality. Indeed, germination studies show that, while some Xyridaceae and Velloziaceae have a high germinability, some dominant Poaceae, Cyperaceae or Asteraceae species have embryoless, unviable or dormant seeds, which makes seeding less efficient. There is no evidence that fire-related cues enhance germination in campos rupestres. Species translocation is successful for only one species, Paspalum erianthum; for the others, root damages probably impede survival. Finally, turf translocation is the most successful method, since numerous species are re-introduced on degraded areas. However due to the low resilience of pristine campos rupestres where turfs are taken from, turf translocation can only be considered in the case of habitat rescue, in circumstances when complete habitat destruction is otherwise unavoidable. Face to the difficulty to restore these peculiar grasslands, the protection and the conservation of campos rupestres must be made a high priority