Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two nonendemic outgroups, we report a revised phylogeny of this species flock and analyse evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armour and reduction in appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate-level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca-binding muscle-related proteins, possibly indicating adaptation to Ca-deficient low mineralization Baikal waters.

Ecological processes have the potential to influence evolution through their effects on selection. This thesis explores the effects of two ecological factors - competition and ecological opportunity. Intraspecific (within-species) competition is often expected to drive adaptation and diversification by increasing selection for the use of novel resources, thereby alleviating the detrimental effects of competition. However, this is not always the expected outcome; theory suggests that intraspecific competition can also drive convergent evolution. On the other hand, interspecific (between-species) competition is usually expected to impede adaptation and diversification because competitor species occupy potential available niches, preventing the focal species from diversifying to do so. In this thesis, I review previous experimental studies exploring the effects of competition on adaptive diversification, and then directly test these effects using experimental evolution of the bacterium Pseudomonas fluorescens. I confirm that intraspecific competition drives adaptive diversification, while the effects of interspecific competition are varied. Strong interspecific competition impedes adaptation and diversification, while the presence of weak, non-diversifying interspecific competitors drives diversification through increased resource competition. The presence of ecological opportunity is essential for adaptation and diversification, and so variation in attributes of those opportunities is expected to have important effects on the dynamics of adaptive evolution. In another evolution experiment with P. fluorescens, I tested the effects of variation in ecological opportunity on adaptive evolution and found that the type and arrangement of ecological opportunities drives adaptation but, in this system, not diversification. I also show that ecological opportunity drives differences in the degree of parallel evolution at the phenotypic and genotypic level. Finally, I explore some unexpected genetic changes identified in one of these evolved populations - two synonymous mutations that conferred fitness benefits, and show that the observed fitness improvements are the result of increased gene expression. I have shown that ecological processes can play an important role in shaping the evolutionary trajectories taken by populations. Understanding the interactions between ecological and evolutionary processes is vital for our understanding of evolutionary dynamics as a whole, and the studies laid out in this thesis represent valuable contributions to this field of study.

Ecological processes have the potential to influence evolution through their effects on selection. This thesis explores the effects of two ecological factors - competition and ecological opportunity. Intraspecific (within-species) competition is often expected to drive adaptation and diversification by increasing selection for the use of novel resources, thereby alleviating the detrimental effects of competition. However, this is not always the expected outcome; theory suggests that intraspecific competition can also drive convergent evolution. On the other hand, interspecific (between-species) competition is usually expected to impede adaptation and diversification because competitor species occupy potential available niches, preventing the focal species from diversifying to do so. In this thesis, I review previous experimental studies exploring the effects of competition on adaptive diversification, and then directly test these effects using experimental evolution of the bacterium Pseudomonas fluorescens. I confirm that intraspecific competition drives adaptive diversification, while the effects of interspecific competition are varied. Strong interspecific competition impedes adaptation and diversification, while the presence of weak, non-diversifying interspecific competitors drives diversification through increased resource competition. The presence of ecological opportunity is essential for adaptation and diversification, and so variation in attributes of those opportunities is expected to have important effects on the dynamics of adaptive evolution. In another evolution experiment with P. fluorescens, I tested the effects of variation in ecological opportunity on adaptive evolution and found that the type and arrangement of ecological opportunities drives adaptation but, in this system, not diversification. I also show that ecological opportunity drives differences in the degree of parallel evolution at the phenotypic and genotypic level. Finally, I explore some unexpected genetic changes identified in one of these evolved populations - two synonymous mutations that conferred fitness benefits, and show that the observed fitness improvements are the result of increased gene expression. I have shown that ecological processes can play an important role in shaping the evolutionary trajectories taken by populations. Understanding the interactions between ecological and evolutionary processes is vital for our understanding of evolutionary dynamics as a whole, and the studies laid out in this thesis represent valuable contributions to this field of study.

No description available.

Orientador: Márcio Silva Araújo / Resumo: A variação individual no uso de recursos alimentares pode depender de fatores ecológicos como a competição intra e interespecífica, predação, além da diversidade e abundância de recursos. O objetivo deste trabalho foi identificar as causas da variação individual no uso de recursos alimentares em populações do peixe Characidium schubarti, conh’ecido como “charutinho” e descrito como insetívoro bentônico. O estudo foi realizado em riachos de Mata Atlântica no Parque Estadual Carlos Botelho, núcleo São Miguel Arcanjo, região sudeste do Estado de São Paulo. Os charutinhos foram coletados ao longo de transectos em 11 riachos diferentes. Foram coletadas amostras da comunidade de invertebrados bentônicos em cada riacho para a obtenção de estimativas da diversidade e abundância de recursos alimentares. Identificamos e quantificamos todas as possíveis espécies de peixes competidoras (insetívoros bentônicos). Nossos resultados sugerem significativa variação na dieta dos indivíduos de todas as populações, porém com baixo grau de especialização individual. Nós não encontramos efeito significativo da oportunidade ecológica (diversidade de recursos), produtividade secundária (biomassa de recursos) e competição (densidade de charutinhos e competidores) sobre o grau de variação na dieta nas populações estudadas. / Abstract: Individual variation in food resource use can depend on ecological factors such as intra and interspecific competition, predation, and the diversity and abundance of resources. Our main goal in this study was to identify the ecological causes of individual variation in the use of food resources in natural populations of the fish Characidium schubarti, part of a group popularly known as “South American darters”, described as benthic insectivores. The study was conducted in Atlantic Forest streams at the Carlos Botelho State Park, at São Miguel Arcanjo, in the southeast of the state of São Paulo. Specimens were collected along transects in 11 streams. We collected samples from the benthic invertebrate community in each stream to estimate the diversity and abundance of food resources. We identified and quantified all possible competing species of fishes (benthic insectivores). Our results suggest significant variation in the diet of individuals from all populations, however, with a low degree of individual specialization. We found no significant effect of ecological opportunity (resource diversity), secondary productivity (resource biomass) and competition (density of charutinhos and competitors) on the degree of dietary variation in the studied populations. / Mestre

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2018-07-12T20:09:09Z No. of bitstreams: 2 Tese - João Fabrício Mota Rodrigues - 2017.pdf: 7026938 bytes, checksum: bb5eb1fc81f363b414aa3c9e80fb3429 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-07-13T10:42:29Z (GMT) No. of bitstreams: 2 Tese - João Fabrício Mota Rodrigues - 2017.pdf: 7026938 bytes, checksum: bb5eb1fc81f363b414aa3c9e80fb3429 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-07-13T10:42:30Z (GMT). No. of bitstreams: 2 Tese - João Fabrício Mota Rodrigues - 2017.pdf: 7026938 bytes, checksum: bb5eb1fc81f363b414aa3c9e80fb3429 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-05-03 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Understanding the processes that shape the current distribution patterns of species is one of the main goals of Ecology. In this thesis, we aimed to understand which factors are related to the distribution of the turtle diversity, a group of ectothermic animals whose diversity patterns are still little known, over time and space. To that end, we used distribution data from continental chelonian species, as well as life history information (habitat type and body size), and reconstructed a phylogenetic hypothesis for the group using molecular data. Turtles had a burst of lineage diversification during the irradiation of the Emydidae family, which is probably linked to an event of ecological opportunity. In addition, aquatic animals had higher rates of diversification than terrestrial animals, which helps to explain the current greater diversity of aquatic animals. Turtle richness distribution along the continents is mainly influenced by climatic variables such as temperature and precipitation, but the time when lineages first colonized the continental regions also influences this pattern. Beta diversity among chelonian communities is mainly influenced by the geographical distance between communities, and communities from different biogeographic realms are structured by different drivers. Finally, body size diversity of turtles is also influenced by temperature, and small animals are more common in cold areas. / Compreender os processos responsáveis pelos padrões de distribuição atuais das espécies é um dos principais objetivos da Ecologia. Nesta tese, visamos entender quais fatores estão relacionados à distribuição da diversidade de quelônios, grupo de animais ectotérmicos cujos padrões de diversidade ainda são pouco conhecidos, ao longo do tempo e do espaço. Para esse fim, usamos dados de mapas de distribuição das espécies de quelônios continentais, além de informações de história de vida (tipo de hábitat e tamanho corporal), e reconstruímos uma hipótese filogenética para o grupo usando dados moleculares. O grupo dos quelônios apresentou uma explosão de diversificação durante a irradiação da família Emydidae, o que está provavelmente ligado a um evento de oportunidade ecológica. Além disso, animais aquáticos apresentaram taxas de diversificação mais elevadas que os animais terrestres, o que ajuda a explicar a maior diversidade de animais aquáticos atuais. A distribuição da riqueza de quelônios ao longo dos continentes é influenciada principalmente por variáveis climáticas tais como temperatura e precipitação, porém o intervalo de tempo desde o qual as áreas foram colonizadas também influencia nesse padrão. A diversidade beta entre as comunidades de quelônios é influenciada principalmente pela distância geográfica entre as comunidades, e comunidades de diferentes de domínios biogeográficos são estruturadas de modo diferenciado. Finalmente, a diversidade de tamanhos corporais dos quelônios também é influenciada pela temperatura, de modo que animais menores são mais comuns em áreas mais frias.