Depuis les années 1990, l'aulne glutineux, espèce clé des ripisylves, est affecté par un oomycète qui cause son dépérissement : Phytophthora alni subsp. alni (Paa). La genèse de Paa est liée à un événement d'hybridation interspécifique entre deux espèces proches, improprement nommées P. alni subsp. uniformis (Pau) et P. alni subsp. multiformis (Pam), car initialement considérées comme des variants de Paa. L'objectif de cette thèse était d'identifier les facteurs ayant pu jouer un rôle dans l'émergence de la maladie en Europe. Par une approche de génétique des populations, nous avons montré que Pau est une espèce invasive en Europe, probablement originaire d'Amérique du Nord. Après son introduction, l'hybridation de Pau avec Pam serait l'un des facteurs essentiels de l'apparition de Paa. Nos résultats confirment que Paa aurait été généré suite à des hybridations récurrentes, qui ont structuré géographiquement les populations en Europe. L'analyse de la variabilité génétique de Paa, révélée par des marqueurs microsatellites, a toutefois montré un faible polymorphisme, avec un génotype dominant largement répandu en Europe. Par ailleurs grâce à la modélisation, nos résultats ont établi que le dépérissement du houppier des aulnes est lié à la température. En particulier l'incidence de la maladie augmente lors des hivers doux, qui pourraient favoriser la survie du mycélium de Paa, celui-ci ne présentant pas de structure de survie hivernale (chlamydospores ou oospores). La température estivale joue également un rôle, plus complexe à interpréter. On constate en effet que l'incidence de la maladie diminue avec l'augmentation des températures estivales, mais ce phénomène pourrait dépendre d'autres facteurs tels que l'état physiologique des arbres ou le type de communautés microbiologiques présentes dans les sols. Inversement, le phénomène de guérison des arbres est favorisé par des températures hivernales basses et par des températures estivales élevées. L'émergence de la maladie ne peut pas être expliquée par le changement climatique. Cependant, une augmentation des températures hivernales dans le futur dans le cadre du changement climatique aggraverait très probablement l'épidémie / Since the early 1990's alder decline caused by the oomycete Phytophthora alni subsp. alni (Paa) is one of the most important threats to riparian ecosystems in Europe. The emergence of Paa is related to an interspecific hybridization event between two related species -initially considered as Paa variants- misnamed as Phytophthora alni subsp. uniformis (Pau) and Phytophthora alni subsp. multiformis (Pam). The objective of this thesis was to identify the factors that may have contributed to the emergence of the disease in Europe. Following a population genetics approach we showed that Pau is likely to be an invasive species in Europe, probably native to North America. Its introduction would have enabled hybridization with Pam and, consequently be a major cause on the emergence of Paa. Our results confirm that Paa has arisen from several hybridization events, which have geographically structured its European populations. Paa's genetic variability, revealed by microsatellite markers, showed low levels of polymorphism, with a dominant genotype scattered throughout Europe. In addition, a modelling approach revealed that alders' crown decline is linked to temperature. In particular, the disease incidence increases during mild winters which favours mycelium survival as Paa does not produce resistant spores (chlamydospores or oospores). The effect of summer temperatures is more complex to explain. Disease incidence decreases when summer temperatures are higher, but this phenomenon can also be linked to the physiological conditions of trees or changes in soil microbiological communities. Conversely, tree recovery is favoured by lower winter and higher summer temperatures. Climate change does not explain the emergence of the disease. However, increases in winter temperatures du to climate change may strengthen the epidemic

Acrocephalus warblers have gone through the adaptive radiation during last severalmillion years, which gave rise to thirty one species occupying mainly Eurasia,Africa and Australia. The majority of species are morphologically very similar,however, they differ in ecological requirements, migration strategy, and song.Interspecific hybridization seems to be quite common among Acrocephaluswarblers, not only between sister species, but also between more distantly relatedtaxa. The main goal of this study was to determine whether this hybridization leadsto gene flow between species and which factors affect the rate of interspecific geneflow. For this purpose we conducted population-genetic analysis in three Europeanspecies of the Acrocephalus warblers of the subgenus Notiocichla: reed warbler (A.scirpaceus), marsh warbler (A. palustris), and blyth's reed warbler (A. dumetorum).Our results based on the analysis of sequence data from eight nuclear loci indicate,that gene flow between the studied species occurs, but only in one direction. Thegene flow is higher between genetically more related species than betweenecologically more similar species. We also estimated that the reed warbler and themarsh warbler diverged approximately 1,1 million years ago. The blyth's warblerand ancestor of the reed and marsh warbler...

Neophobia and exploratory behaviour are two processes applied in great measure in birds' reactions towards novel stimuli. The specific demonstration of these two processes may differ between different species of birds as well as within them. We compared neophobia and exploratory behaviour in two species of tits (Paridae). Adult Great tits (Parus major) and Blue tits (Cyanistes caeruleus) did not differ neither in exploring novel environment and novel object nor in neophobia towards novel object near food. We have found great differences between juveniles of these two species. Juvenile Blue tits were more neophobic towards both novel objects. Age, sex and personality affected some differences within tested species. We tested whether there exist any differences in reactions towards novel food between and within species. We used red painted mealworm (larvae of Tenebrio molitor), house cricket (Acheta domestica) and aposematic bug (Pyrrhocoris apterus) as novel food. Adult wild-caught tits with plentiful experience with various feeds did not differ in reaction towards these types of novel food. In contrast hand-reared juvenile tits differed quite a lot. Juvenile Blue tits were more neophobic than juvenile Great tits towards all three types of novel food. We found dieraty conservatism, phenomenon...

Humans affect ecosystems by changing species compositions, landscape and climate. This thesis aims to increase our understanding of anthropogenic effects on mesopredator abundance due to changes in apex predator status, landscape and climate. I show that in Eurasia the abundance of a mesopredator, the red fox (Vulpes vulpes), is limited top-down by the Eurasian lynx (Lynx lynx) and bottom-up by winter severity. However, where lynx has been eradicated, fox abundance is instead related to bottom-factors such as cropland (paper I, II). Fox abundance was highest when croplands constituted 25% of the landscape (paper II). I also project red fox abundance in Sweden over the past 200 years and in future scenarios in relation to lynx density, land use and climate change. The projected fox abundance was highest in 1920, when lynx was eradicated and the proportion of cropland was 22%. In 2010, when lynx had recolonised, the projected fox abundance was lower than in 1920, but higher than in 1830. Future scenarios indicated that lynx abundance must increase in respond to climate change to keep fox at the same density as today. The results suggest a mesopredator release when lynx was eradicated, boosted by land use and climate change, and that changes in bottom-up factors can modify the relative strength of top-down factors (paper IV). From 1846-1922, lynx, wolverine (Gulo gulo) and grey wolf (Canis lupus) declined in Scandinavia due to persecution; however I show that the change in wolverine abundance was positively related to the changes in lynx and wolf abundance. This indicates that wolverine is subsidized by carrions from lynx and wolf kills rather than limited top-down by them (paper III). This thesis illustrates how mesopredator abundance is determined by a combination of top-down and bottom-up processes, and how anthropogenic impacts not only can change the structures of predator guilds, but also may modify top-down processes through changes in bottom-up factors. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 3: Submitted. Paper 4: Manuscript.</p><p> </p>

Lucie Čadková: Lingvistické schopnosti nonhumánních živočichů 1 ABSTRACT The 20th century has witnessed significant advance in our knowledge of animal communication. Thanks to modern technology, ethologists have made great strides in decoding natural communication systems of non-human animals, while psychologist's attempts to teach a member of another species analogues of human language have met with first success. The unexpected findings called into question the unique status of human language capacities and gave rise to pressure to redefine human language in order to defend human uniqueness. One of the most influential definitions by which the communication systems of non-human animals are guaranteed a priori exclusion from the notion of language was developed by Charles F. Hockett in the 1950s and 1960s. Since then, his design-feature approach has been used, despite a series of paradigm changes in linguistics and key discoveries in cognitive ethology, in support of the claim that humans are the only living creatures endowed with language. The prevailing uncritical acceptance and usage of his theory in the field of animal communication was the impulse to write this thesis. The dissertation aims to shed light on the historical development of the question of animal linguistic abilities and presents the...

L'objectif de cette thèse a été de caractériser les patrons spatiaux de diversité inter- et intraspécifique au sein des réseaux dendritiques, d'expliciter les processus évolutifs et écologiques qui les sous-tendent, et d'isoler les possibles covariations spatiales et interactions existant entre ces différentes facettes de biodiversité. Pour cela, j'ai tout d'abord développé de nouvelles méthodes statistiques permettant l'analyse, par des modèles causaux, de données sous la forme de matrices de distances, afin de pouvoir analyser plusieurs facettes de biodiversité dans un unique cadre statistique au niveau alpha et bêta. J'ai par la suite étudié de manière intégrative les patrons de diversité interspécifique et intraspécifique génétique d'une part, et intraspécifique génétique et intraspécifique phénotypique d'autre part, au sein du bassin versant Garonne- Dordogne. Enfin, j'ai utilisé un modèle de dynamique éco-évolutive afin d'étudier l'impact de la structure et des gradients environnementaux caractérisant les réseaux dendritiques sur l'adaptation locale au sein de ces réseaux. / The aim of this thesis was to characterized the spatial patterns of inter- and intraspecific diversity within riverine networks, to better understand the ecological and evolutionary processes underlying them and to explore how the different facets of biodiversity interact with one another. First, I developed novel statistical approaches allowing the application of causal modeling to data in the form of pairwise matrices, thus allowing the study within integrative frameworks of several biodiversity facets at the alpha and beta levels. I then studied integratively the patterns of interspecific and intraspecific genetic diversity and of intraspecific genetic and intraspecific phenotypic diversity within the Garonne-Dordogne river basin. Finally, I used an eco-evolutionary metapopulation dynamics model to assess the impacts of the structure and environmental gradients that characterize riverine networks on local adaptation.

Os ecossistemas aquáticos são afetados por processos que ocorrem em escalas finas (locais) e amplas (regionais). Os processos locais incluem, por exemplo, filtros ambientais e interações interespecíficas, enquanto que os regionais abrangem principalmente questões relacionadas à dispersão de indivíduos. O entendimento de como esses processos atuam sobre comunidades, populações e interações em peixes de riachos é fundamental para a conservação dos ecossistemas aquáticos, pois permite predizer as consequências de alterações antrópicas e fornece subsídios para ações de manejo e políticas de conservação. Na presente tese, eu desenvolvi cinco estudos em distintas escalas espaciais. Cada um é apresentado em capítulos distintos. Nos capítulos 1 e 2, eu abordei questões relacionadas à compreensão de como alterações antrópicas feitas em distintas escalas espaciais influenciam as diversidades alfa e beta de comunidades de peixes de riachos. No capítulo 3, eu procurei entender como processos previstos na teoria de metacomunidades influenciam mudanças temporais na composição e abundâncias de espécies em comunidades locais. No capítulo 4, eu estudei como os impactos antrópicos levam a alterações no papel trófico e no intestino de populações de uma espécie generalista e persistente. Por fim, no capítulo 5, eu usei uma abordagem de aninhamento, desenvolvida inicialmente na Ecologia de Comunidades, para avaliar a ocupação de larvas de uma espécie de quironomídeo (Diptera) sobre o corpo de seu hospedeiro (uma espécie de peixe da família Loricaridae). / Aquatic ecosystems are influenced by processes that occur at fine (local) and broad (regional) scales. Local processes include, for example, environmental filters and interspecific interactions, whereas regional processes encompass mainly questions regarding individual dispersion. Knowledge on how these processes affect communities, populations and interactions in stream fish is essential for conservation of aquatic ecosystems, as it allows predicting consequences of human-alterations and provides subsidy for management actions and conservation policies. In this dissertation, I developed five studies using distinct spatial scales. I presented each one in a separate chapter. In the 1st and 2nd chapters, I addressed questions concerned with the understanding of how human alterations at different spatial scales influence alpha and beta diversity of stream fish communities. In the 3rd chapter I looked for understanding how processes predicted in metacommunity theory influence mid- to long-term changes in composition and species abundances of local communities. In the 4th chapter, I studied how anthropic impact drives modification in the trophic role and intestine of a generalist and persistent fish species. Lastly, in the 5th chapter, I employed nestedness approach previously developed for Community Ecology to evaluate occupation of chironomid species larvae (Diptera) on the body of its host (an armored catfish species of the family Loricariidae).

Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2018-04-11T11:57:10Z No. of bitstreams: 2 Dissertação - Lucas Pereira Martins - 2018.pdf: 2113878 bytes, checksum: 4c38a4d425f42506d50aa62bf6661c3f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-04-12T11:22:54Z (GMT) No. of bitstreams: 2 Dissertação - Lucas Pereira Martins - 2018.pdf: 2113878 bytes, checksum: 4c38a4d425f42506d50aa62bf6661c3f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-04-12T11:22:54Z (GMT). No. of bitstreams: 2 Dissertação - Lucas Pereira Martins - 2018.pdf: 2113878 bytes, checksum: 4c38a4d425f42506d50aa62bf6661c3f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-03-15 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Understanding how species interact with each other is essential to advance our knowledge on community ecology. However, there are still gaps regarding how interspecific interactions affect and are affected by the variation in the composition of species that constitute the ecological networks. In particular, studies of beta diversity are interesting to understand how sets of biotic filters may affect species’ geographic distribution and persistence on communities. Another interesting question is if variations in species composition may cause changes on how ecological networks are structured. In this dissertation, we propose to evaluate patterns of beta diversity and structure on insect-plant interaction networks. Specifically, in the first chapter we aimed to test if beta diversity is affected by the trophic level to which the assemblage belongs, and by the degree of specialization of species at higher trophic levels to their host species. For this, we used a tritrophic system comprising plants of the family Asteraceae, endophagous herbivores and parasitoids sampled in remnants of Brazilian Cerrado. Our main results show that total beta diversity of parasitoids (higher trophic level) was lower than those of the other trophic levels, while there was no difference between total beta diversity of plants and herbivores. Furthermore, the degree of specialization of the assemblages of herbivores and parasitoids was positively associated to the beta diversity of these groups. In the second chapter, we evaluated if species beta diversity among sites affects dissimilarity in network structure, and if this relationship changes across time. Overall, the relationship between spatial beta diversity and dissimilarity in plant-herbivore network structure was context-dependent, thus indicating that different ecological processes (i.e., niche-based and neutral) may drive the organization of antagonistic networks across time. / Compreender como as espécies interagem entre si é essencial para avançar o nosso conhecimento em ecologia de comunidades. No entanto, ainda existem lacunas no que se refere a como interações interespecíficas influenciam e são influenciadas pela variação na composição de espécies que constituem as redes ecológicas. Em particular, estudos de diversidade beta são interessantes para entender como conjuntos de filtros bióticos podem influenciar a distribuição geográfica e persistência de espécies nas comunidades. Outra questão interessante é se variações na composição de espécies podem causar mudanças no modo como redes ecológicas são estruturadas. Nesta dissertação, propomos avaliar padrões de diversidade beta e estrutura de redes de interações inseto-planta. Especificamente, no primeiro capítulo visamos testar se a diversidade beta é influenciada pelo nível trófico ao qual a assembleia pertence, e pelo grau de especialização de espécies de níveis tróficos superiores às suas espécies hospedeiras. Para isso, utilizamos um sistema tritrófico composto por plantas da família Asteraceae, herbívoros endófagos e parasitoides amostrado em remanescentes de Cerrado brasileiro. Nossos principais resultados demonstram que a diversidade beta total de parasitoides (nível trófico superior) foi menor do que a dos demais níveis tróficos, enquanto que não houve diferença entre a diversidade beta total de plantas e herbívoros. Além disso, o grau de especialização das assembleias de herbívoros e parasitoides foi positivamente relacionado à diversidade beta destes grupos. No segundo capítulo, avaliamos se a diversidade beta de espécies entre locais influencia a dissimilaridade na estrutura de redes ecológicas, e se esta relação muda através do tempo. De modo geral, a relação entre diversidade beta espacial e dissimilaridade na estrutura de redes planta-herbívoro foi contexto-dependente, indicando assim que diferentes processos ecológicos (i.e., baseados em nicho e neutros) podem determinar a organização de redes antagonistas através do tempo.

Abstract The negative impact of invasive plant species on biodiversity and ecosystem functions, such as productivity and nutrient cycling has been deemed a global epidemic. To address this worldwide concern, information is needed on how the invasion process happens and how to control an existing invasion. The main aim of the research presented in this thesis was to develop a better understanding of the interacting role different mechanisms play in facilitating invasion and then link this understanding to the design of more effective control strategies. This aim is significant because traditional weed control strategies are not working. The estimated cost of controlling weeds in Australia is $1.4 billion per year in agricultural landscapes. Despite this substantial investment, invasive weed species are estimated to continue to cost the agricultural industry $2.2 billion per year in loss of yield. Current control strategies tend to focus on killing or removing an invasive plant species directly with the application of herbicides and/or mechanical removal. These strategies have proven ineffectual because the plant communities that assemble after management often remain dominated by the same invader or another. In this thesis, I use a combination of empirical and modelling techniques to investigate how disturbance regimes and competitive interactions between invasive plants and native plants can be manipulated to improve the efficacy of restoration efforts. To do this, I use the model scenario of the invasion of Eragrostis curvula (African lovegrass), an invasive grass species introduced into Australia in the early 1900s from South Africa. This species has now spread into every Australian state and territory (chapter 2). I specifically focus on two mechanisms: (1) disturbance, i.e. cattle grazing, and (2) competitive interactions. In chapter 3, I examine connections between dominance and competitive differences among African lovegrass and several functionally similar native grass species in a pasture community. To test the displacement hypothesis, I used a glasshouse competition trial to investigate interactions between African lovegrass and two non-persisting native grass species (Themeda australis and Bothriochloa decipiens) with manipulations of resources, neighbour density, and establishment order. To test the partitioning hypothesis, I compared in situ water use patterns among African lovegrass and two coexisting native grass species (Aristida calycina and Aristida personata) based on the assumption that water is the most limiting resource in this system. The key finding of this chapter is that competition can have important, but contingent, impacts on dominance. Competitive differences appear to partially contribute to abundance patterns after establishment, but may be relatively unimportant during the establishment phase where disturbance appears more critical. In chapter 4, I provide evidence that the identification of mechanisms that led to an invasion, while crucial for the development of effective preventative measures and understanding the invasion process, may not be necessary for the design of more effective control strategies. To examine the effects of different control strategies on African lovegrass and the resultant community, I established a large factorial field-trial with a split-plot design. I manipulated grazing, soil nutrient levels and the presence of the invader. The most common control strategy (removing the causal disturbance and killing the invasive grass), based implicitly on traditional equilibrium models, was not an effective option for restoring a desirable native community. Instead, this strategy led to the dominance of a secondary invader. The most effective control strategy was based on alternative stable states models and involved maintaining grazing, and increasing the palatability of the invader with fertilizers. The key finding of this chapter is that novel approaches for control, which consider the dynamics of the invader-dominated system, are needed. In chapter 5, I investigate the benefits of explicitly incorporating actions that manipulate disturbance (natural or imposed) into control efforts. To do this, I first developed a process model that described the dynamics of an invader whose establishment is preferentially favoured by disturbance. I then couched this model in a decision theory framework, a stochastic dynamic program, and applied a case-study of another invasive plant species, Mimosa pigra (a perennial legume shrub and pan-tropical weed). The key finding of this chapter is that strategies should not only focus on existing invader-dominated sites, but should also protect sites occupied by native species from disturbances that facilitate invasion. The research discussed in this thesis makes three key contributions to a better understanding of the invasion process and the design of more effective control strategies: 1) the search for one key mechanism is not sufficient because multiple mechanisms can interact or shift in importance to facilitate different stages of invasion, 2) a novel approach is needed to restore a more desirable native community because the dynamics of the invader-dominated system can differ from the historical native community, and 3) control efforts should be broadened in focus to include protection of the integrity of native communities from disturbances that facilitate invasion.

Rodents often colonise agricultural lands and become pests that cause economic loss and crop damage. Eradicating or regulating pest numbers has economic and environmental costs and has always been of great interest to farmers and nature conservationists. To reduce rodent numbers poison baits are used more often than biological control. However, poisoning has adverse environmental impacts and ignores the underlying biological factors that influence pest abundance. This study examined the interactions of the common rat species of oil palm plantations, namely Rattus rattus diardii, R. argentiventer and R. tiomanicus, with their food resource, habitat structure and introduced predators in an attempt to provide a better understanding and approach for their control. To investigate the interrelationships among rodents, owls and oil palms, rodent trapping was conducted simultaneously with pellet collection and assessment of the breeding of owls over six study plots and seven trapping intervals in one oil palm plantation. Trapping records suggested that relative abundances of rodent species differed in plots with palms of differing ages. There were more R. r. diardii as a proportion of the total captures in older palms (seven years old) while R. argentiventer was the most common rat captured in younger palms (three years old). The abundance of R. tiomanicus remained low throughout trapping sessions for palms of all ages. A numerical response of rats to fruit availability in older palms was demonstrated by a positive and significant correlation between the numbers of fruit bunches present and the total number of rats captured. This relationship was observed in both older and younger palms only for R. argentiventer but not R. r. diardii or R. tiomanicus in either age of palms. This suggests that the competitiveness of R. argentiventer may be higher than that of the other two species providing that there were no factors other than food availability that limit the numbers of other two species. However, the levels of damage to palm fruit were significantly correlated with the relative abundance of R. argentiventer only in younger palms, not in older ones where R. r. diardii were more abundant. The more terrestrial nature of R. argentiventer may have restricted their acquisition of food when the palms became taller. In addition to differences in feeding niche, habitat heterogeneity may also be important in determining the rat species compositions at different ages of palms. Vegetation cover may act as a refuge for rats; the overall occurrence of rats, and especially R. argentiventer, was positively correlated with vegetation cover and height, and even certain vegetation associations. This study supported the continued use of the barn owl Tyto alba javanica for biological control of rodent pests in the palm oil plantations. The numbers of different rat species consumed by owls, as measured by pellet numbers, were proportional to prey captures with R. r. diardii dominating the prey items. Weights and sexes of rats, based upon sizes of bones recovered from owl pellets, indicated that the birds did not preferentially prey on any size or sex classes of rats. Although there was no differential predation by the owls, a functional, and possibly a numerical, response of the birds to changes in rat numbers was demonstrated. A functional response of barn owls to prey abundance was evidenced by a significant positive relationship between the relative abundance of rats captured and numbers of pellets collected. Some form of numerical response of barn owls was suggested by higher breeding records when rat abundances were significantly higher. Since both functional and numerical responses are important determinants of whether predators are likely to be able to regulate prey numbers, the role of barn owls as a practical biological control agent in oil palm plantations was supported. This study suggested that the regulation of rodent pests in oil palm plantations should not be limited to chemical measures but can be complemented by other biological factors including interspecific interactions, manipulation of the availability and density of food and habitat structure, in addition to predation by barn owls. The findings suggested that an integrated approach to rodent control, considering all biological factors that influence rat numbers, should be properly applied if an environmentally friendly and possibly cost effective approach is to be applied for the palm oil industry.