An ecological community is complex and the mechanisms behind the assembly of such a community are still poorly understood. Here, we concentrate on the question of what mechanisms affect the proportion of specialists and the proportion of generalists in a community. First, we use an individual-based model to explore the effects of the available resource spectrum on the specialist-generalist balance in well-mixed and spatially structured environments. In the well-mixed model, we uncover a new mechanism which we term `resource spectrum engineering', in which opportunistic specialists occupying small niches in a mostly generalist community can change the resource spectrum that is experienced by other species strongly disfavouring generalists and causing a community-wide shift towards specialist strategies. Extending to a spatially structured model in which the dispersal distance of species may be limited, we find that specialism is linked to intermediate dispersal lengths, whereas generalism is linked to short and long dispersal lengths. We then investigate two real microbial systems, using 16rRNS sequence data. In the first experiment, we identify functional groups of specialists and generalists by perturbing the microbial environment with variable nutrient concentrations and establishing which groups survive across different concentrations and which do not. In the second experiment we use many replicates of samples from the same source to find co-occur find that generalist species may be more likely to be dependant on the presence of each other than on specific environmental conditions.

The emergence of the eukaryotic cell was one of the key events that paved the path to the vast variety of complex life visible all around us. A pivotal event in the process of eukaryogenesis was an endosymbiosis of two prokaryotic cells which in time resulted in the mitochondria. Phagocytosis, which is the process in which  larger cells envelope and digest smaller cells is one of the feasible explanations for how one cell came to be within another. It is common in eukaryotes, however, no contemporary examples of prokaryotes practicing phagocytosis exist. But phagocytosis had to evolve at some point, so how did it happen? This thesis gives an attempt to determine what conditions facilitate the evolution of phagocytosis. In this endeavour, we constructed chemostatic models for two different population structures where secondary consumers are subject to an invasion by a mutant with predatory capabilities. The different population structures are denoted as "competition" and "cross-feeding". By using random parameter sampling we show that the predator has a higher likelihood to invade in the cross-feeding environment. We also showed using adaptive dynamics that a mutant that is able to invade and replace its predecessor favours evolving towards a higher predation strategy in the cross-feeding case whereas in competition  such behaviour is less clear and a more balanced strategy seems preferable.

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2016-07-27T21:10:07Z No. of bitstreams: 3 Tese - Diogo Borges Provete - 2016.pdf: 3048056 bytes, checksum: 5e3c0b282d1a0790baa37204e8059ed1 (MD5) Ata de defesa - Diogo Borges Provete.PDF: 971791 bytes, checksum: d78fa4a86345ee06bcf4e49553a98347 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-07-28T11:01:30Z (GMT) No. of bitstreams: 3 Tese - Diogo Borges Provete - 2016.pdf: 3048056 bytes, checksum: 5e3c0b282d1a0790baa37204e8059ed1 (MD5) Ata de defesa - Diogo Borges Provete.PDF: 971791 bytes, checksum: d78fa4a86345ee06bcf4e49553a98347 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-07-28T11:01:30Z (GMT). No. of bitstreams: 3 Tese - Diogo Borges Provete - 2016.pdf: 3048056 bytes, checksum: 5e3c0b282d1a0790baa37204e8059ed1 (MD5) Ata de defesa - Diogo Borges Provete.PDF: 971791 bytes, checksum: d78fa4a86345ee06bcf4e49553a98347 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-03-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Phylogenetic information has increasingly been included in studies of local communities and also at broad spatial scales. Despite recent criticisms in the last four years, phylogenetic relationships may still provide insights into the organization and assembly of ecological communities. The objectives of this study were 1) to review the history of the use of phylogenetic information, as well as criticisms and perspectives of its use in community ecology; 2) understand how the size and shape of phylogenetic trees and the phylogenetic structure of metacomunidaes affect the amount of variation accounted for by a eigenvector-based method used to describe the phylogenetic composition of metacomunidaes (PCPS); 3) to test the effect of diversity of evolutionary history (MNTD and MPD) and species richness as predictors of three variables of freshwater ecosystem functioning (productivity, respiration, and decomposition); and finally 4) to test how environmental gradients, especially pond canopy cover, influence the phylogenetic structure of an anuran metacommunity from southeastern Brazil. I found that the structure of metacommunities had greater impact on eigenvalues of PCPS than tree shape metrics, such as symmetry and stemminess. In addition, decomposition and respiration were best predicted by MNTD as a linear function, while productivity was affected by the quadratic term of MNTD. Finally, pond canopy cover and floating vegetation strongly affected the phylogenetic structure of the anruan metacommunity, influencing lineage sorting. These findings 1) can help users interpret the results of PCPS; 2) provide better understand of the effect of species loss in multitrophic, freshwater ecosystems; and 3) improve our knowledge about the effect of canopy cover on the lineage composition in anuran metacomunities. / Informações filogenéticas tem sido cada vez mais incluídas em estudos de comunidades locais e em larga escala espacial. Apesar das críticas dos últimos quatro anos, relações de parentesco ainda podem fornecer idéias sobre a organização e montagem de comunidades ecológicas. Os objetivos deste estudo foram 1) revisar o histórico do uso de informações filogenéticas, bem como críticas e perspectivas quanto ao seu uso em ecologia de comunidades; 2) entender como o formato e tamanho de árvores filogenéticas e a estrutura filogenética da metacomunidade afetam a quantidade de variação capturada por um método baseado em autovetores usado para descrever a composição filogenética de metacomunidaes (PCPS); 3) testar o efeito da diversidade de história evolutiva (MNTD e MPD) e da riqueza de espécies como preditores de três métricas de funcionamento de ecossistemas aquáticos (produtividade, respiração, e decomposição); e por fim 4) testar como gradientes ambientais, especialmente cobertura de dossel, influenciam a estrutura filogenética de uma metacomunidade de anuros no sudeste do Brasil. Encontrei que a estrutura da metacomunidade teve maior impacto nos autovalores do PCPS do que métricas de formato de árvore, tais como simetria e enraizamento (stemminess). Além disso a decomposição e respiração foram melhor preditas por MNTD, enquanto produtividade foi melhor predita pelo termo quadrático desta medida. Por fim, a cobertura de dossel e vegetação flutuantes afetaram fortemente a estrutura filogenética da metacomunidade de anuros, influenciando a distribuição de linhagens. Estes resultados 1) podem auxiliar na interpretação dos resultados do PCPS por usuários; 2) permitem compreender melhor o efeito da perda de espécies em ecossistemas aquáticos multitróficos; e 3) ampliam o conhecimento sobre o efeito da cobertura de dossel sobre a composição de linhagens em metacomunidades de anuros.

Microbes form complex communities on Earth. They are crucial for global nutrient recycling in soil and oceans. Inside our body, our intestinal microbiome contributes to our metabolism and protects us against diseases. The dynamics of these microbial communities and their response to environmental changes depend on intra- and inter-species interactions. Computational models are useful to simulate the behavior of such systems and to predict their response to prebiotics or to antibiotics for example. However, due to the multiple, nutrient-dependent interactions, modeling the behavior of such communities remains a real challenge. Mathematical modeling allows for an understanding of the general principles underlying the nonlinear dynamics of microbial communities. Population-based models are based on the abundances of each species but typically do not incorporate the interaction mechanism. Interactions can be mediated by the metabolism of microbes. Therefore, explicit modeling of nutrients is required for a mechanistic understanding of the dynamical behavior of interacting communities. In this thesis we developed and analyzed models accounting for the nutrient-mediated microbial interactions, focusing on competition and mutualistic cross-feeding. In the first part of the thesis, we constructed a nutrient-explicit model that reproduced experimental time series of a small synthetic microbial community, consisting of three species that interact via cross-feeding and competition. The comparison of mono-culture and co-culture dynamics reveals emergent behaviors in co-cultures and highlights the influence of key factors on the population dynamics. In the second part of the thesis, we showed how nutrient-explicit models for mutualistic cross-feeding are related to population-based models, such as the Lotka-Volterra equations. This allows to predict the occurrence of bistability and the presence of a survival threshold. Finally, we extended these results by considering the spatial dimension, and studied how diffusion and advection influence the survival of the community. Our results demonstrate that nutrient-explicit models are able to reproduce experimental time series of microbial communities and to predict the factors determining survival or extinction. By providing a mechanistic understanding of the nonlinear behavior related to microbial interactions, we take a step forward towards the development of predictive models of microbial communities. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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<img src="http://vg00.met.vgwort.de/na/806c85cec18906a64e06" width="1" height="1" alt=""> Subject of this work is the possibility to synchronize nonlinear systems via correlated noise and automatic control. The thesis is divided into two parts.<br> The first part is motivated by field studies on feral sheep populations on two islands of the St. Kilda archipelago, which revealed strong correlations due to environmental noise. For a linear system the population correlation equals the noise correlation (Moran effect). But there exists no systematic examination of the properties of nonlinear maps under the influence of correlated noise. Therefore, in the first part of this thesis the noise-induced correlation of logistic maps is systematically examined. For small noise intensities it can be shown analytically that the correlation of quadratic maps in the fixed-point regime is always smaller than or equal to the noise correlation. In the period-2 regime a Markov model explains qualitatively the main dynamical characteristics. Furthermore, two different mechanisms are introduced which lead to a higher correlation of the systems than the environmental correlation. The new effect of "correlation resonance" is described, i. e. the correlation yields a maximum depending on the noise intensity. <br> In the second part of the thesis an automatic control method is presented which synchronizes different systems in a robust way. This method is inspired by phase-locked loops and is based on a feedback loop with a differential control scheme, which allows to change the phases of the controlled systems. The effectiveness of the approach is demonstrated for controlled phase synchronization of regular oscillators and foodweb models. / Gegenstand der Arbeit ist die Möglichkeit der Synchronisierung von nichtlinearen Systemen durch korreliertes Rauschen und automatische Kontrolle. Die Arbeit gliedert sich in zwei Teile.<br> Der erste Teil ist motiviert durch Feldstudien an wilden Schafspopulationen auf zwei Inseln des St. Kilda Archipels, die starke Korrelationen aufgrund von Umwelteinflüssen zeigen. In einem linearen System entspricht die Korrelation der beiden Populationen genau der Rauschkorrelation (Moran-Effekt). Es existiert aber noch keine systematische Untersuchung des Verhaltens nichtlinearer Abbildungen unter dem Einfluss korrelierten Rauschens. Deshalb wird im ersten Teils dieser Arbeit systematisch die rauschinduzierte Korrelation zweier logistischer Abbildungen in den verschiedenen dynamischen Bereichen untersucht. Für kleine Rauschintensitäten wird analytisch gezeigt, dass die Korrelation von quadratischen Abbildungen im Fixpunktbereich immer kleiner oder gleich der Rauschkorrelation ist. Im Periode-2 Bereich beschreibt ein Markov-Modell qualitativ die wichtigsten dynamischen Eigenschaften. Weiterhin werden zwei unterschiedliche Mechanismen vorgestellt, die dazu führen, dass die beiden ungekoppelten Systeme stärker als ihre Umwelt korreliert sein können. Dabei wird der neue Effekt der "correlation resonance" aufgezeigt, d. h. es ergibt sich eine Resonanzkurve der Korrelation in Abbhängkeit von der Rauschstärke. <br> Im zweiten Teil der Arbeit wird eine automatische Kontroll-Methode präsentiert, die es ermöglicht sehr unterschiedliche Systeme auf robuste Weise in Phase zu synchronisieren. Die Methode ist angelehnt an Phase-locked-Loops und basiert auf einer Rückkopplungsschleife durch einen speziellen Regler, der es erlaubt die Phasen der kontrollierten Systeme zu ändern. Die Effektivität dieser Methode zur Kontrolle der Phasensynchronisierung wird an regulären Oszillatoren und an Nahrungskettenmodellen demonstriert.

Ce projet explore la valeur épistémologique des collections historiques pour aborder des questions scientifiques actuelles sur les changements environnementaux dans les écosystèmes marins. Le challenge principal est de pouvoir caractériser le processus d'assimilation des connaissances dans un champ scientifique particulier, l'écologie. Les réseaux émergents de collections de données et d'objets permet l'exploration de questions sur comment le contexte historique a pu biaiser les observations qui sont utilisées maintenant pour analyser les tendances écologiques et environnementales du passé. Cette démarche devrait permettre in fine de contribuer à l'amélioration de nos connaissances sur la dynamique des réponses des systèmes écologiques. Plusieurs exemples différents sont traités en détail, couvrant le contexte historique de la recherche dans les stations marines et l'examen récursif des concepts de base en écologie tels que la dynamique des populations, la théorie de l'exclusion compétitive, et l'estimation de l'impact sur l'environnement. / This project explores the epistemic value of heritage collections for addressing modern scientific questions about environmental change in marine ecosystems. The main challenge is to investigate processes of knowledge assimilation within a specific scientific discipline, ecology. Emerging networks of data and object collections permit addressing questions about how historical context may bias observations used for analysis of ecological and environmental trends. The main goal is to synthesize historical concepts and data using meta-analysis and recursive techniques to reconstruct ecological trends. It is hoped that this will ultimately contribute to improving our understanding of the dynamics of ecological systems responses. Several different examples are treated in detail, covering the historical context of research work in marine stations as well as a critical re-examination of basic ecological concepts of population dynamics, competitive exclusion, and the estimation of environmental impact.

Cette thèse a pour objet la modélisation de systèmes multi-proies–prédateurs. Elle s’intéresse particulièrement à l’influence du comportement d’un prédateur sur les interactions indirectes entre ses proies, i.e. l’effet de l’ajout d’une proie sur la densité des autres. La théorie classique prédit l’occurrence d’effets indirects négatifs entre les proies, ou compétition apparente, résultant de l’interaction avec un prédateur commun ; des résultats plus récents identifient certains mécanismes à même d’atténuer ces effets négatifs. Nos travaux revisitent les hypothèses autour de ces mécanismes dans des systèmes composés de deux proies et de leur prédateur commun. Après avoir fixé le cadre écologique en rappelant les principaux types d’interactions directes et indirectes, nous introduisons les modèles proies-prédateurs classiques. Les travaux se concentrent ensuite sur une famille de modèles présentant de la densité-dépendance négative chez les prédateurs couplés à différentes modélisations du comportement des prédateurs lorsqu’ils sont confrontés à plusieurs types de proies. Nous montrons notamment que les interactions entre ces mécanismes peuvent inverser la compétition apparente et, contre intuitivement, accroître la densité des proies par l’intermédiaire d’un prédateur commun. Nos résultats trouvent pour partie application en lutte biologique, où il est courant de chercher à favoriser les auxiliaires en aménageant leur environnement (apport de nourriture alternative, refuge, ...). Ils suggèrent que de telles pratiques peuvent se révéler contre-productives, le contrôle des ravageurs pouvant être affaibli du fait d’une distraction de leurs prédateurs. / This thesis deals with multi-prey–predators modeling. It is particularly focused on the influence of the behavior of a predator on indirect interactions between its prey, i.e, the effect of the addition of a prey on the other prey. Classical theory predicts the occurrence of negative indirect effects between prey, or apparent competition, resulting from the interaction with a common predator. More recent results identify mechanisms that mitigate these negative effects. Our work revisits the assumptions about these mechanisms in systems composed of two prey and their common predator. After setting the ecological framework by recalling the main types of direct and indirect interactions, we introduce classical predator-prey models. The work then focuses on a family of models with predator negative density-dependence coupled with different models of predator behavior when faced with different types of prey. We show that the interactions between these mechanisms can reverse apparent competition and counter-intuitively, increase prey density through their common predator. Our results are relevant to biological control programs, where a common practice aims at fostering biological control agents by providing them with alternative food or shelters. Our theory suggests that such practices may be counter-productive, pest control being disrupted by a predator distraction effect.

Conservation in the EU and all over the world aims at reducing biodiversity loss which has become a great issue in the last decades. However, despite existing efforts, Earth is assumed to face a sixth mass extinction. One major challenge for conservation is to reconcile the targets with conflicting interests, e.g. for food production in intensively used agricultural landscapes. Agriculture is an example of a coupled human-environment system that is approached in this thesis with the help of mathematical models from two directions. Firstly, the ecological subsystem is considered to find processes relevant for the effect of habitat connectivity on population abundances. Modelling theory predicts that the species-specific growth parameters (intrinsic growth rate and carrying capacity) indicate whether dispersal has a positive or negative effect on the total population size at equilibrium (r-K relationship). We use laboratory experiments in combination with a system of ordinary differential equations and deliver the first empirical evidence for a negative effect of dispersal on the population size in line with this theory. The result is of particular relevance for the design of dispersal corridors or stepping stones which are meant to increase connectivity between habitats. These measures might not be effective for biological conservation. A second population model, consisting of two coupled Ricker maps with a mate-finding Allee effect, is analyzed in order to examine the effect of bistability due to the Allee effect in combination with overcompensation in a spatial system. The interplay can cause complex population dynamics including multiple coexisting attractors, long transients and sudden population collapses. Essential extinction teaches us that not only small populations are prone to extinction but chaotic dynamics can drive a population extinct in a short period of time as well. By a comprehensive model analysis, we find that dispersal can prevent essential extinction of a population. In the context of conservation that is: habitat connectivity can promote rescue effects to save a population that exhibits an Allee effect. The two findings of the first part of this thesis have contrasting implications for conservation which shows that universal recommendations regarding habitat connectivity are impossible without knowledge of the specific system. Secondly, a model for the socio-economic subsystem is presented. Agri-environment schemes (AES) are payments that compensate farmers for forgone profits on the condition that they improve the ecological state of the agricultural system. However, classical economic models that describe the cost-effectiveness of AES often do not take the social network of farmers into account. Numerical simulations of the socio-economic model presented in this thesis suggest that social norms can hinder farmers from scheme participation. Moreover, social norms lead to multistability in farmers’ land-use decision behaviour. Informational campaigns potentially decrease the threshold towards more long-term scheme participation and might be a good tool to complement compensation payments if social norms affect land-use decisions. Finally, a coupled human-environment system is analyzed. An integrated economicecological model is studied to investigate the cost-effectiveness of AES if the species of concern exhibits an Allee effect. A numerical model analysis indicates large trade-offs between agricultural production and persistence probability. Moreover, conservation success strongly depends on the initial population size, meaning that conservation is well advised to start before the species is threatened. Spatial aggregation of habitat can promote rescue effects, suggesting land-sparing solutions for conservation. In that case,agglomeration bonuses may serve to increase the effectiveness of AES. Possible causes for population declines are diverse and can be a combination of human influences, e.g. due to habitat degradation and inherent ecosystem properties. That complicates the task of conservation. The models presented in this thesis simplify complex systems in order to extract processes relevant for biological conservation. The analysis of spatial effects and dynamical model complexity, e.g. due to Allee effects or a nonlinear utility function, allows us improve the understanding of coupled human-environment systems.

Das Schutzziel in der Ökotoxikologie ist die Population. Un­ter­suchungen zur Wirkung von subletalen Konzentrationen einer Umweltchemikalie auf Populationsebene, zum Beispiel mit künst­lichen Fließgewässersystemen (Mikrokosmen) können aussagekräftigere Beiträge zur ökotoxikologischen Bewertung einer Umweltchemikalie liefern. Außerdem können bei solchen Untersuchungen mögliche indirekte Effekte erfaßt werden. Über die Reaktion von Fließgewässer-Biozönosen gegenüber Um­welt­chemikalien ist relativ wenig bekannt. Die überwiegende Zahl der Untersuchungen zur Abschätzung des Ge­fähr­dungs­po­tentials von Umweltchemikalien wurde mit Testsystemen für Lebensgemeinschaften in stehenden Gewässern untersucht. Die Übertragbarkeit der Ergebnisse dieser Tests auf Fließgewässer-Lebensgemeinschaften ist meist nicht gegeben. Daher ist es notwendig Testsysteme zu etablieren, mit denen die Wirkung von Umweltchemikalien auf Fließgewässer-Le­bens­ge­mein­schaf­ten untersucht werden kann. In einem Gewächshaus wurden fünf Fließrinnen etabliert, mit denen die physikalisch-chemischen Bedingungen in einem Bach simuliert werden können. Im Ge­gensatz zu Untersuchungen einer komplexen Le­bens­ge­mein­schaft mit hoher Variabilität, wie sie sich beispielsweise durch das Einbringen von na­tür­lich­em Sediment aus Fließgewässern einstellt, wurde in diesen Experimenten die Wirkung von Che­mikalien auf eine einfache Lebensgemeinschaft untersucht. Die Le­bens­ge­mein­schaft in den Fließrinnen bestand deshalb aus wenigen, aus­ge­wählten Arten. Untersucht wurden die Kon­zen­tra­tionen 0,6, 6, 60 und 600 µg/l (Terbutryn) und 0,05, 0,5, 5 und 50 µg/l (Fenoxycarb). Gegenstand der vorliegenden Arbeit waren die Untersuchungen mit Gammarus fossarum. In einem akuten Toxizitätstest wurde die LC50 von Terbutryn für adulte und juvenile Gammariden ermittelt. In den Fließ­rin­nen­ex­perimenten mit Terbutryn und Fenoxycarb wurden po­pu­la­tions­relevante Pa­ra­meter der Gammaridenpopulationen untersucht. Ob und in welchem Um­fang sich Effekte, die mit den Stan­dard­tests gemessen wurden, auf bestimmte öko­toxi­ko­lo­gi­sche End­punkte der Population auswirken, kann nicht immer unmittelbar abgeleitet werden. Eine Möglichkeit wäre die aufwendige Durchführung von Po­pu­la­tionsexperimenten mit einfachen oder komplexeren Mo­dell­öko­systemen über eine lange Zeit. Eine andere Möglichkeit ist die Nutzung mathematischer Modelle zur Beschreibung der Populationsdynamik. Das begleitend zu den Untersuchungen entwickelte individuenbasierte Re­pro­duk­tions­modell GamMod bildet die Populationsdynamik einer ab­ge­schlos­senen Population von Gammarus fossarum in künstlichen Fließgewässersystemen ab. Es wird die Struktur und Dy­na­mik des realen Systems (Populationsdynamik) unter Ein­beziehung der Kenntnisse des Reproduktionszyklus modelliert. Mo­dell­szenarien sollen Aus­sagen über den Einfluß der Än­der­ung einer Variablen bezüglich der Populationsdynamik liefern.