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1
Ninni, Paola. "La fonction des caroténoïdes chez les hirondelles de cheminée (Hirundo rustica)." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2003. http://tel.archives-ouvertes.fr/tel-00003369.
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La fonction des caroténoïdes chez les hirondelles de cheminée (Hirundo rustica) Un signal, pour pouvoir évoluer et se répandre doit être honnête car son coût empêche l'apparition de tricheurs. Dans cette thèse, je m'intéresse aux signaux caroténoïde-dépendants qui influencent la valeur reproductive des hirondelles de cheminée. Les caroténoïdes sont des molécules colorées que les animaux doivent nécessairement ingérer avec la nourriture. Outre la reproduction, ils conditionnent de nombreuses activités physiologiques liées à la défense immunitaire et à la neutralisation des radicaux libres. Seuls les individus de meilleure qualité sont susceptibles d'accéder à une quantité suffisante de caroténoïdes pour l'investir dans des signaux sexuels, tout en conservant un bon état de santé. J'ai considéré tout d'abord la disponibilité des caroténoïdes dans la nourriture des hirondelles, pour vérifier s'il existe une variabilité dans la capacité des individus à obtenir ces pigments. Mon étude suggère que si les hirondelles ont accès aux caroténoïdes, certains individus ne se procurent ces pigment que de façon limité. Puis j'e me suis intéressée à deux activités qui semblent être particulièrement sensibles à la présence des caroténoïdes. La date d'arrivée au site de reproduction chez les hirondelles influence la valeur reproductive tout en étant assujettie au stress oxydatif dû aux radicaux libres. La concentration et la variation de caroténoïdes dans le sang des males semblent déterminer la variabilité observée dans la date d'arrivée. Les individus de moins bonne qualité ne peuvent pas avancer leur arrivée, à cause de besoins plus importants en caroténoïdes. Dans un troisième temps j'ai analysé la quantité et la variation des caroténoïdes dans le sang des femelles pendant la reproduction, considérant que les caroténoïdes représentent une ressource, importante pour le développement de l'embryon et le poussin à l'éclosion, mais aussi particulièrement nécessaire à la femelle pour conserver un bon état de santé pendant la reproduction. On observe une diminution de la concentration en caroténoïdes dans le sang pendant la production des œufs et une différence entre les sexes lors de la saison de reproduction qui témoignent d'une utilisation importante de ces pigments par les femelles. Je me suis intéressée enfin a l'éventuel dimorphisme sexuel dans la couleur des plumes rouges de la gorge, partiellement déterminée par les caroténoïdes. Les males développent une couleur plus intense que les femelles et investissent davantage en proportion de plumes pigmentées. Les males qui développent une couleur plus intense obtiennent d'ailleurs un bénéfice en terme de possibilité de trouver un partenaire pour se reproduire. En conclusion, je rapporte plusieurs résultats empiriques qui, dans leur ensemble, suggèrent un rôle des caroténoïdes dans l'évolution des signaux honnêtes.
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Fernández, Guerra Antonio. "Ecology and evolution of microbial nitrifiers / Ecología y evolución de los microorganismos nitrificantes." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/108001.
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Ammonia oxidation, the first and the rate-limiting step in nitrification, is one of the cornerstones of the cycle. Members from the bacterial and archaeal domains are key players in ammonia oxidation in many different environ- ments. Usually these organisms are found coexisting but the most recent studies suggests that archaeal ammonia oxidizers show an incredible ability to adapt and oxidize ammonia under different environmental conditions and have displaced their bacterial counterparts in terms of importance in the global biogeochemical cycle, providing an avalanche of AOA molecular data (16S rDNA and amoA gene sequences) from very diverse environments worldwide. As far as we don’t have enough genomic data to perform an holistic approach using population genomics and reverse ecology to unveil the ecological and evolutionary mechanisms driving the adaptation; we focused our experiments on the amoA gene sequence. Because ammonia monooxygenase is supposed to be the key enzyme in the ammonia oxidation, we applied a combination of community ecology and molecular evolution methods to understand the mechanisms of the diversification patterns observed in the amoA gene. Another unsolved question in the archaeal ammonia oxidation is the unusual biochemistry found in the genome sequences from cultured archaeal ammonia oxidizers. In archaea, all the elements of the bacterial ammonia oxidizing pathway are missing but the genes coding for the presumptive AMO. To unveil missing pathways in this process, we have developed a powerful approach based on graphical models to capture all the functional associations present in metagenomes based in their ecological co-ocurrence.
The results of the analyses revealed for the first time a global picture of the phylogenetic community structure of ammonia- oxidizing assemblages. Our study unveiled larger phylogenetic richness in AOA with more dissimilar communities and clear monophyletic groups for the different habitats. The rates of diversification in AOA were higher than in AOB and the archaeal diversification dynamics showed an unusual feature, with an initial diversification process followed by a long period of stasis and a final burst of diversification. The variations observed between AOB and AOA in terms of community structure, phylogenetic diversity, diversification patterns, and habitat dispersion were unexpected just a very few years ago, and the community phylogenetics approach has nicely captured these differences.
Understand the diversification processes observed in AOA and their successful performance under a myriad of different environmental conditions such as low pH, different ammonia concentrations, high hydrostatic pressures, high light exposure, low oxygen availability among others, needs however of a deeper insight adding the evolutionary processes. Individual changes at the level of nucleotides were translated to the global diversification patterns of archaeal ammonia oxidizers. Thus, this resulted in a step further from the results obtained after applying community phylogenetics methods providing precise evolutionary information behind the phylogenetic patterns observed within an ecological context. We will gain the full picture once the results can be integrated in a comparative genomics framework.
After applying methods of reverse engineering of regulatory the associations between the known and the unknown fraction were reconstructed offering a pioneering fresh view for microbial ecology. One especially relevant result obtained from this approach on AOA was the reconstruction of the association network of the different AMO subunits to the other proteins previously reported in the marine AOA Nitrosopumilus. The information recovered from metagenomics combined with available genomes fuels hypothesis for the particular and yet unknown biochemistry of ammonia oxidation in Archaea.La oxidación del amonio es una de las piezas clave del ciclo del Nitrógeno. Tanto las bacterias como las arqueas oxidadoras del amonio se pueden encontrar coexistiendo a lo largo de diferentes ambientes. Pero cuando la primera arquea oxidadora del amonio fue aislada, se puso en relevancia la importancia de estas en comparación con las bacterias en los ciclos biogeoquímicos globales. Desde entonces hemos sido inundados por una avalancha de secuencias génicas de estas arqueas, mostrando una gran capacidad de diversificación y adaptación a ambientes diferentes. Al no disponer de suficientes datos para realizar una aproximación holistica utilizando genómica de poblaciones y de ecología inversa para poder discernir los mecanismos ecológicos y evolutivos relacionados con la adaptación; nos hemos centrado en estudiar la secuencia del amoA. La amonio monooxigenasa es la enzima responsable de la oxidación del amonio, para su estudio hemos aplicado una combinación de técnicas de ecología de comunidades y de evolución molecular con el objetivo de entender los mecanismos de los patrones de diversificación observados. Por otra banda, otro de los misterios asociados a la oxidación del amonio por parte de las arqueas, es su inusual bioquímica para realizar la oxidación del amonio. En arqueas faltan todos los elementos necesarios para llevar a cabo la oxidación del amonio a excepción del AMO. Para poder aportar algo de luz a este misterio hemos desarrollado un potente método basado en modelos gráficos para capturar todas las asociaciones funcionales presentes en los metagenomas basado en sus co-ocurrencias ecológicas.
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Caraballo, López Tatiana. "The ecology of colonial phytoplankton = Ecología del fitoplancton colonial." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/129683.
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Phytoplankton embraces a large diversity of life forms, from pioneer oxygenic photosynthetic cyanobacteria to a broad spectrum of phylogenetically distant eukaryotic organisms. In many of the evolutionary branches, colonial organisms have appeared. The evolutionary reasons for the transition to larger sizes are not yet fully understood, but multicellularity is thought to be one of its consequences. Phytoplankton ecological success or failure, under certain conditions is the result of a balance between gains and losses. Unicellular and colonial organisms have to adapt their respective functional traits related to photosynthesis, resource acquisition, and predation, to changes in the environment. The advantages of a certain life-form (unicellular or colonial), could, hence, rely in the relevance of gain processes (light, nutrient related traits), or of losses as main drivers of phytoplankton evolution.
Despite coloniality could suppose an opportunity in finding new paths to succeed, previous knowledge pointed to larger phytoplankton cells as worse competitors for nutrients than smaller cells and hence, as the size of the colonies may start to become a constraint for nutrient uptake and utilization. However, other issues changing with size can become advantageous for colonial phytoplankton. For example, large flagellate colonies can move and hence cover a greater space of resources likely to be exploited than small unicellulars, and also can have a larger storage capacity. Large cells (and colonies in particular) can take more advantage of the production of external enzymes since colonial forms, specially mucilaginous ones, could maintain exoenzymes close to the cells in this external matrix. In summary, any strategy by which there is not a proportional increase in the need for nutrients as body size enlarges can be regarded as a competitive advantage for colonial organisms. Besides, a possible advantage for large unicellulars and colonies could be related to the top-down control of the systems by grazers, as smaller unicellulars are subject of grazing by both, small and large filter feeders, whereas large colonies can override the edible size spectrum of some. Also the aggregation of cells to form large colonies harder to gulp or filter by zooplankton is considered a relative widespread defense strategy. The ubiquitousness of colonial forms of phytoplankton and its endurance until today is the basis for believing that there has been a significant selection for it in the ancient unicellular world. Yet it is difficult to guess what the main drivers for coloniality have been,
Can we find out the selective forces favoring multicellular colonial forms in phytoplankton?
Understanding the ecological advantage that colonial forms could hold in phytoplankton was the main objective of this thesis.Los orígenes de los organismos que componen la comunidad fitoplanctónica se remontan a distintos eventos endosimbióticos; por ello, una de las principales características del fitoplancton es una enorme diversidad que atañe tanto en sus atributos morfológicos y fisiológicos como en sus formas de vida. A pesar de que la multicelularidad en algunas especies de fitoplancton podría suponer una estrategia para asegurar la conservación de la línea germinal, o para generar un medio interno estable que proteja a las células que forman la colonia del cambiante ambiente que la rodea, actualmente se desconoce el motivo que pudo haber favorecido la transición desde la unicelularidad a la colonialidad. Sin embargo, la existencia de organismos coloniales evolutivamente más avanzados en los que se observa una diferenciación celular y división de tareas, podrían empezar a definir una estrategia de vida compleja y jerarquizada más allá de la simple agregación celular. La gran variedad de formas, tamaños y configuraciones presentadas por las células y colonias, es una muestra de que no hay una estructura óptima, sino un gran abanico de posibilidades exitosas para afrontar los obstáculos a los que estos organismos se enfrentan durante su ciclo de vida. Por otro lado, el paso de una forma de vida unicelular a una colonial en los organismos fitoplanctónicos, implica un número de condicionantes ecológicos que determinan cuándo y cómo las formas coloniales pueden ser más viables. En cualquier caso, el hecho de que las formas unicelulares y coloniales sean ubicuas en el fitoplancton y hayan perdurado durante millones de años, nos da a entender que deben existir ciertas ventajas ecológicas conferidas por la colonialidad. Este trabajo se centra en investigar en qué modo los organismos coloniales han llegado a compensado las desventajas derivadas de la agregación para haberse convertido en una alternativa evolutivamente exitosa a la unicelularidad.
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Sayol, Altarriba Ferran. "Causes and consequences of brain size evolution: a global analysis on birds." Doctoral thesis, Universitat Autònoma de Barcelona, 2018. http://hdl.handle.net/10803/565697.
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Per què alguns llinatges de vertebrats, incloent els humans, han evolucionat cervells grans és un dels grans trencaclosques de la biologia evolutiva. De les varies hipòtesis que s’han plantejat per intentar resoldre aquest misteri, la variació ambiental destaca com una de les principals causes de la variació en la mida relativa del cervell. Més formalment, la hipòtesis del cervell protector (CBH, de Cognitive buffer hypothesis”, en anglès) postula que els cervells relativament més grans han evolucionat per facilitar els ajustos de comportament per augmentar la supervivència en condicions canviants. Tot i que la CBH ha rebut suport empíric els darrers anys, alguns autors qüestionen la seva rellevància for explicar l’evolució del cervell argumentant que mantenir un cervell massa gran en períodes d’escassetat de recursos és massa costós, de manera que la variació ambiental hauria de limitar més que no pas afavorir l’evolució dels cervells grans. Aquesta tesi doctoral explora les causes i conseqüències de l’evolució de la mida del cervell, amb especial atenció en la CBH, validant les seves assumpcions, assajant les seves prediccions i avaluant les seves implicacions. La tesi treu profit d’una base de dades de mesures del cervell per més de 1900 espècies d’ocells en combinació amb els més recents mètodes filogenètics comparatius per tal de descobrir els orígens de la variació en la mida del cervell en la classe de vertebrats més diversa. Com a primer objectiu, aquesta tesi valida en quina mesura la mida relativa del cervell és una bona aproximació de la variació en estructures del cervell involucrades en la capacitat de construir respostes de comportament als nous reptes. El capítol 1 mostra que les àrees associatives del cervell, tradicionalment relacionades amb la intel·ligència general, són desproporcionadament més grans en espècies de cervell gran i poden predir de forma acurada la variació en el conjunt del cervell, de manera que es validi la seva utilització en anàlisis comparatives globals. Segons la CBH, les espècies que viuen en regions amb alta variabilitat ambiental haurien de ser seleccionades per cervells grans, a menys que tinguin adaptacions especialitzades per evadir les caigudes en la disponibilitat de recursos. El Capítol 2 mostra com els ocells que viuen en ambients més estacionals i impredictibles , com les regions de latituds altes, posseeixen cervells relativament més grans que els residents d’altres regions, recolzant la CBH en ocells. En el capítol 3 es mostra com els ocells que colonitzen illes oceàniques sembla que han evolucionat cervells relativament més grans que els seus parents continentals. Aquests canvis sembla que en part s’expliquen per un augment de la incertesa en la disponibilitat de recursos que caracteritza les illes, aportant una evidència addicional per la CBH. En el capítol 4 s’estudia el rol actiu del cervell en l’evolució. Tal com prediu la hipòtesi del behavioural drive (behavioural drive hypothesis en anglès), els ajustos de comportament més freqüents com a resposta als reptes ambientals hauria d’exposar els individus més sovint a nous conjunts de pressions selectives, tot afavorint la divergència evolutiva respecte els seus ancestres i finalment afavorint l’aparició de noves espècies. El capítol 4 mostra com els llinatges amb cervells relativament més grans han tingut majors taxes de diversificació taxonòmica. Aquesta troballa recolza així la idea que els animals no són agents passius de la selecció, però que poden modificar activament la seva relació amb l’ambient i influenciar el seu propi camí evolutiu. En resum, els resultats d’aquesta tesi aporten evidència empírica per la CBH, mostrant com els cervells relativament més grans funcionen, i per tant han evolucionat, per fer front als canvis ambientals, i que l’evolució de cervells grans pot a més influir en la diversificació evolutiva d’un llinatge.Why some vertebrate lineages, including humans, evolved large brains is one of the main puzzles in evolutionary biology. Of the many hypotheses that have been launched to try to resolve this puzzle, environmental variability stands out as a major cause of relative brain size variation. More formally, the cognitive buffer hypothesis (CBH) postulates that relatively large brains evolved to facilitate behavioural adjustments to enhance survival under changing conditions. The rationale of the CBH is that advanced cognition can increase fitness in varying environments by enhancing information gathering and learning, facilitating for instance shifts between different feeding sites or food types to alleviate periods of food scarcity. While the CBH has received ample empirical support in recent years, some authors have questioned its relevance to account for the evolution of enlarged brains on the grounds that maintaining the brain during periods of food scarcity may be excessively costly, so environmental variability should constrain rather than favour the evolution of large brains. The present PhD thesis explores the causes and consequences of the CBH, validating its assumptions, testing its predictions and assessing its evolutionary implications. It takes advantage of a large database on brain size comprising more than 1900 extant bird species in combination with recently developed phylogenetic comparative methods to elucidate the origins of brain size variation in the most diverse vertebrate class. As a first objective, the thesis validates the extent to which relative brain size is a good proxy of the brain structures involved in the capacity to construct behavioural responses to new challenges. Chapter 1 thus shows that the associative areas of the brain, classically related with general intelligence, are disproportionally larger in large brained species and accurately predict variation in the whole brain, therefore validating its use in broader comparative analyses. According to the CBH, species living in regions with higher environmental variation should be selected for larger brains, unless they have adaptive specialisations to avoid drops in resource availability. Chapter 2 shows that birds living in highly seasonal and unpredictable environments, like high-latitude regions, possess relatively large brains than residents from other regions, supporting the CBH in birds. Additional support for the hypothesis is found in Chapter 3, where birds colonizing oceanic islands seem to evolve relatively larger brains than their continental relatives. These changes seem to be in part caused by the increased uncertainty in resource availability that characterizes islands, which together with limited chances to disperse and a trend toward slower life-history strategies can facilitate the evolution of enlarged brains. Finally, Chapter 4 explores the active role of brain size on evolution. As predicted by the behavioral drive hypothesis, frequent behavioral changes as a response to environmental challenges should expose individuals to new sets of selective pressures, thereby favouring evolutionary divergence from the ancestors. Chapter 4 provides evidence for the behavioural drive hypothesis, showing that avian lineages with relatively large brained have experienced higher diversification rates than those with smaller brains. This finding is in line with the view that animals are not passive agents of selection, but by actively modifying its relationship with their environment also influence their own pace of evolution. Overall, the findings of the present thesis provide empirical support for the CBH, showing that a relatively large brain functions, and hence may have evolved, to cope with environmental changes, and that the evolution of enlarged brains may subsequently influence the evolutionary diversification of the lineage.
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Nichols, Phillip Brent. "Tardigrade evolution and ecology." [Tampa, Fla] : University of South Florida, 2005. http://purl.fcla.edu/usf/dc/et/SFE0001270.
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Taupenot, Antoine. "Implication de supergènes dans l'expression de traits complexes chez la fourmi socialement et morphologiquement polymorphe Myrmecina graminicola." Electronic Thesis or Diss., Sorbonne université, 2024. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2024SORUS201.pdf.
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Les supergènes, des régions génétiques où des loci coadaptés sont transmis comme une seule unité mendélienne, jouent un rôle crucial dans la mise en place des polymorphismes complexes mais démêler la complexité de leur évolution et de leur maintien reste un défi de taille. Les fourmis offrent un contexte unique pour mettre en évidence de nouveau supergènes et étudier les principes généraux régissant leur mise en place et leur évolution puisqu'elles présentent de grandes variations inter et intra-espèces dans tous les aspects de leur organisation sociale et qu'un nombre inhabituellement élevé de supergènes a déjà été mis en évidence dans différentes espèces. Notamment, dans cinq lignées différentes un supergène en lien avec l'organisation sociale des colonies, c'est-à-dire le nombre de reines accouplées par colonie, a été mis en évidence. Cependant, son origine et son maintien restent à élucider clairement et de nouveaux modèles sont nécessaires. L'espèce de fourmi Myrmecina graminicola suscite un intérêt particulier pour l'étude des supergènes chez les insectes sociaux puisqu'elle présente à la fois un polymorphisme social (présence de colonies monogynes et de colonies polygynes) et un polymorphisme alaire (présences de reines ailées et de reines aptères).Dans cette thèse, nous avons exploré la présence de supergènes chez M. graminicola, en lien notamment avec ces deux polymorphismes. Dans le premier chapitre, à l'aide de données de reséquençage, nous avons mis en évidence la présence d'un supergène lié au polymorphisme social (~10 Mb) daté de ~1 Ma en déséquilibre de liaison avec un supergène lié au polymorphisme alaire (~110 kb) apparu plus récemment (~ 0,4 Ma). Dans le deuxième chapitre, nous avons étudié les liens entre les traits d'histoire de vie des deux principaux types de colonies retrouvés dans cette espèce, à savoir les colonies monogynes avec des reines ailées et les colonies polygynes avec des reines aptères. Nous avons montré que ces deux types de colonies ne différaient pas quant au nombre d'ouvrières et de larves au moment de l'échantillonnage. Une fois élevées en laboratoire, nous avons observé que ces deux types de colonies produisaient un nombre similaire de nymphes et d'adultes mais que les colonies polygynes produisaient plus d'œufs et de nouvelles larves que les colonies monogynes. Dans le troisième chapitre, nous avons exploré la possibilité qu'il existe dans cette espèce d'autres supergènes non liés directement à la socialité ou à la présence/absence d'ailes. Nous avons identifié un troisième supergène (~7 Mb) et démontré qu'il n'était pas associé au sex ratio des colonies. Dans l'ensemble, cette thèse révèle la présence de trois supergènes chez la fourmi M. graminicola, dont un lié au polymorphisme social, un autre au polymorphisme alaire, et propose des pistes sur les mécanismes contribuant au maintien de ces polymorphismesSupergenes, genetic regions where coadapted loci are inherited as a single Mendelian unit, play a crucial role in establishing complex polymorphisms. However, unraveling the complexity of their evolution and maintenance remains a significant challenge. Ants offer a unique context to identify new supergenes and study the general principles governing their establishment and evolution due to their extensive inter- and intra-species variations in all aspects of social organization. Notably, in five different lineages, a supergene related to colony social organization, specifically the number of mated queens per colony, has been identified. However, its origin and maintenance remain to be clearly elucidated, and new models are needed. The ant species Myrmecina graminicola is of particular interest for studying supergenes in social insects as it exhibits both social polymorphism (presence of monogynous and polygynous colonies) and wing polymorphism (presence of winged and apterous queens).In this thesis, we explored the presence of supergenes in M. graminicola, particularly in relation to these two polymorphisms. In the first chapter, using resequencing data, we identified a supergene associated with social polymorphism (~10 Mb) dating back to ~1 Mya, in linkage disequilibrium with a supergene linked to wing polymorphism (~110 kb) that appeared more recently (~0.4 Mya). In the second chapter, we examined the life history traits of the two main types of colonies found in this species, namely monogynous colonies with winged queens and polygynous colonies with apterous queens. We showed that these two colony types did not differ in the number of workers and larvae at the time of sampling. When reared in the laboratory, we observed that both types of colonies produced a similar number of nymphs and adults but that polygynous colonies produced more eggs and new larvae than monogynous colonies. In the third chapter, we explored the possibility of other supergenes in this species not directly linked to sociality or wing presence/absence. I identified a third supergene (~7 Mb) and demonstrated that it was not associated with colony sex ratio. Overall, this thesis reveals the presence of three supergenes in the ant M. graminicola, one linked to social polymorphism, another to wing polymorphism, and provides insights into the mechanisms contributing to the maintenance of these polymorphisms
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Alencar, Laura Rodrigues Vieira de. "Ecomorfologia em serpentes neotropicais: um estudo de caso com a tribo Pseudoboini." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/41/41134/tde-23092010-175653/.
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As serpentes da tribo Pseudoboini apresentam grande diversidade quanto à sua ecologia, são consideradas um grupo monofilético e possuem uma filogenia conhecida. A partir disso, tornou-se possível a análise, sob um contexto evolutivo, das possíveis associações entre a morfologia e a ecologia neste grupo. Neste estudo, analisamos a dieta da tribo, bem como, testamos hipóteses de possíveis relações adaptativas entre a morfologia e a dieta e entre a morfologia e o uso do ambiente arborícola, e exploramos a evolução destes aspectos em serpentes da tribo. Nove espécies foram consideradas generalistas e 13, especialistas, sendo seis em lagartos, três em pequenos mamíferos, duas em serpentes, uma em ovos de lagarto e uma em ovos de ave. Um aumento no consumo de pequenos mamíferos, não esteve associado com um aumento da robustez e do volume da cabeça. Especializações em lagartos, pequenos mamíferos e serpentes surgiram independentemente em táxons terminais ao menos duas vezes durante a história evolutiva da tribo. A especialização em ovos de ave é uma autapomorfia de Rhachidelus brazili. A robustez decresceu no ancestral do gênero Siphlophis, e aumentou substancialmente em R. brazili. O tamanho da cabeça decresceu no ancestral do gênero Siphlophis e em Oxyrhopus petola e aumentou substancialmente em Phimophis guianensis, no ancestral de O. trigeminus e O. rhombifer e em R. brazili. Siphlophis cervinus, S. compressus, S. pulcher e D. anomalus foram consideradas espécies semi arborícolas. A reconstrução do hábito semi-arborícola indica que este surgiu independentemente pelo menos duas vezes durante a diversificação do grupo. Não foram encontrados indícios de efeito da freqüência do uso da vegetação sobre o tamanho do corpo, a robustez, o formato da cabeça e o número de vértebras por unidade corporal. Entretanto, o hábito arborícola parece ter levado a um aumento no tamanho da cauda. O tamanho corporal diminuiu substancialmente em P. guianensis e aumentou substancialmente em Clelia rustica e no ancestral de C. clelia e C. plumbea. Já o número de vértebras por unidade corporal diminuiu substancialmente em C. rustica, no ancestral de C. clelia e C. plumbea, e em Pseudoboa haasi; aumentou substancialmente no ancestral de O. trigeminus e O. rhombifer, e em O. melanogenys e P. guianensis. O tamanho da cauda diminuiu significativamente em C. rustica, Boiruna maculata e P. haasi e aumentou consideravelmente no ancestral do gênero Siphlophis, O. petola, D. anomalus, R. brazili e no ancestral do gênero Pseudoboa. A largura da cabeça diminuiu substancialmente em Pseudoboa neuwiedii e aumentou substancialmente em S. compressus, P. guianensis e em B. maculata. As ausências de relações possivelmente adaptativas podem estar ligadas a uma forte inércia filogenética e/ou ao efeito de outros agentes seletivos. Um ancestral morfologicamente adequado a uma dieta baseada em pequenos mamíferos e ao uso da vegetação também pode ter influenciado os resultados. O conhecimento do grupo externo da tribo Pseudoboini ajudaria a esclarecer ainda mais as relações entre morfologia e ecologia nestas serpentes.Snakes of the tribe Pseudoboini are ecological diversity, considered as a monophyletic group and have a known phylogeny. Thus, the analyses of possible associations between the morphology and the ecology of this group in an evolutionary framework became possible. In the present study, we analyze the diet of pseudoboine species, and we test hypotheses of possible adaptative relationships between morphology and diet, and between morphology and microhabitat use in pseudoboine snakes. We also explore how these traits evolved during the diversification of the tribe. Nine species were considered as diet generalists and 13, as diet specialists, being six lizard specialists, three small mammal specialists, two snake specialists, one a lizard egg specialist, and one a bird egg specialist. An increase in the consumption of small mammals was not associated with an increase in robustness and head volume. Lizard, small mammal and snake specializations occurred independently at least twice in terminal taxa during the diversification of the tribe. A specialization in bird eggs seems to be an autapomorphy of Rhachidelus brazili. Robustness decreased in the ancestor of Siphlophis species, and increased substantially in R. brazili. Head volume descreased in the ancestor ofSiphlophis species and in Oxyrhopus petola, and increased substantially in Phimophis guianensis, in the ancestor of O. trigeminus and O. rhombifer and in R. brazili. Siphlophis cervinus, S. compressus, S. pulcher and D. anomalus were considered as semi-arboreal. The semi-arboreal habit reconstruction indicates that this habit evolved independently at least twice during the diversification of the group. We did not find indications of the effect of vegetation use on body size, robustness, head shape and the number of ventral scales per body unit. However, vegetation use seems to have led to an increase in tail length. Body size substantially decreased in P. guianensis and substantially increased in Clelia rustica and in the ancestor of C. clelia and C. plumbea. The number of vertebrae per body unit decreased substantially in C. rustica, in the ancestor of C. clelia and C. plumbea, and in Pseudoboa haasi. It substantially increased in the ancestor of O. trigeminus and O. rhombifer, and in O. melanogenys and P. guianensis. Tail length significantly decreased in C. rustica, Boiruna maculata and P. haasi, and increased substantially in the ancestor of the genus Siphlophis, in O. petola, D. anomalu ,R. brazili and in the ancestor of Pseudoboa spp.. Head width decreased substantially in Pseudoboa neuwiedii and increased significantly in S. compressus, P. guianensis and in B.maculata. Strong influence of phylogenetic inertia and/or the effect of alternative selective agents could be related to the absences of these possible adaptative 69 relationships. An ancestor with a morphology adequate to a diet based on small mammals and to arboreality could also have influenced the results. Knowing the outgroup of the tribe Pseudoboini would help to further clarify the relationships between morphology and ecology of these snakes.
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Vargas, Ramirez Sergio. "Evolution and ecology of antarctic sponges." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-141266.
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Ishida, Yoichi. "Secret analogies mathematics, ecology, and evolution /." abstract and full text PDF (free order & download UNR users only), 2007. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1442878.
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Veen, Franciscus Johannes Frank van. "Aphid hyperparasitoids : taxonomy, ecology and evolution." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313144.
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Reece, Sarah E. "Evolution and ecology of sex allocation." Thesis, University of Edinburgh, 2003. http://hdl.handle.net/1842/12849.
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Ricono, Angela. "Ecology and Evolution of Common Milkweed." W&M ScholarWorks, 2018. https://scholarworks.wm.edu/etd/1550154023.
Full textAbstract:
All organisms must interact with and adapt to their surrounding environment. There are myriad ways in which species accomplish this; ultimately resulting in the vast diversity of life on earth today. Changes in the environment can have profound impacts on an organisms' ability to compete and utilize their surroundings. Plants are particularly impacted by local environmental differences because of the fact that they are immobile. This environmental variation exists at both large and small spatial scales. For example, on larger scales, forces such as fire and grazers can remove dominant plant competitors. on smaller scales, variation in resource availability (e.g. light, nutrients, water) may benefit more phenotypically plastic species. to better understand how changes in the environment, on both large and small spatial scales, I established a two part study using milkweed (Asclepias spp.) as a model system. in the first chapter, I ask how fire, large grazers, and nutrients have affected milkweed abundance over relatively long time and large spatial scales. Here I found that most milkweed species increase in abundance with burning alone but expressed species-specific responses to other treatment combinations. This indicates that milkweed species have likely experienced unique fluctuations in abundance as fire and large herbivores moved across the landscape. The second aspect of this research focuses in on a single year and relatively small spatial scales. Here, using common milkweed (A. syriaca), I ask how environmental variation shapes spatial structuring of phenotypes within fine-scale physical distance and how genotypes impact phenotypes. I found that environment, not genotype, had a relatively larger role on fine-scale phenotypic variation. Combined, these results have implications for understanding the role of large and small scale environmental variations in plant phenotypes and plant abundance.
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Wilson, Howard B. "Applications of dynamical systems in ecology." Thesis, University of Warwick, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387403.
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Tompkins, Daniel Michael. "Evolutionary ecology of bird-parasite associations." Thesis, University of Oxford, 1996. http://ora.ox.ac.uk/objects/uuid:a5f5ea19-b799-490b-b738-99ff52df25c1.
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This thesis investigates the ecological determinants of chewing louse (Insecta: Phthiraptera) host-specificity on four species of Malaysian swiftlets (Aves: Apodidae). Influences of host coloniality on louse ecology were also demonstrated, illustrating the dependence which these permanent ectoparasites have on their hosts. Louse collections were made to look for incidences of host-specific lice occurring on the "wrong" host ("straggling"). Straggling was observed, implying that lice disperse among host species. Thus, opportunity for louse dispersal (or lack thereof) does not govern the host-specificity of chewing lice on swiftlets. Experimental transfers of lice between hosts were conducted. Louse survival was reduced on foreign host species. This implies adaptation to specific host characters, suggesting that specialisation governs chewing louse host-specificity on swiftlets. There was no evidence for reciprocal adaptation of swiftlets to their normal louse species. Lice had no impact on the fitness of either swiftlets or the related common swift. Furthermore, neither swiftlet nor swift lice were transmitting pathogenic endoparasites. This implies that chewing lice and Malaysian swiftlets have not "coevolved". Survival of transferred lice was determined by the relatedness of donor and recipient hosts. Closer related swiftlet species are more similar in body size and feather dimensions. When the feather dimensions of the microhabitat distributions of the same louse species on different hosts were compared the results suggested that lice keep the dimensions of barb and barbule diameter, at which they occur, "constant" through microhabitat shifts. This suggests that feather dimensions are the host characters which determine the survival (and host-specificity) of chewing lice on birds. The ability of chewing lice to survive on hosts with similar feather morphology implies that "host-switching", between distantly related hosts with similar morphological characters (due to parallel or convergent host evolution), may have been an important factor in the evolution of bird-louse associations.
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Wanke, Stefan. "Evolution of the genus Aristolochia - Systematics, Molecular Evolution and Ecology." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1169634459488-35651.
Full textAbstract:
Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.
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Wanke, Stefan. "Evolution of the genus Aristolochia - Systematics, Molecular Evolution and Ecology." Doctoral thesis, Technische Universität Dresden, 2006. https://tud.qucosa.de/id/qucosa%3A23929.
Full textAbstract:
Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.
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Inglis, Robert Fredrik. "The evolutionary ecology of spiteful bacteriocin production." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:524eaef3-0336-4127-9cd1-60d84a00f2e3.
Full textAbstract:
Understanding the conditions that favour the evolution and maintenance of spiteful bacteriocin production combines two important questions from the fields of social evolution and microbiology. Spiteful behaviours, though, initially thought to be rare represent an important class of interactions between bacteria through the production of bacteriocins. Bacteriocins can be considered spiteful as they are costly to produce (in many cases requiring lysis) and are costly to sensitive bacteria (i.e. they are lethal). However, much about the ecology of spiteful behaviours and bacteriocin production remains unclear. Mathematical models have given us important insights into some conditions that should favour bacteriocin production, but few empirical studies exist supporting these results. In this thesis I use the bacterium Pseudomonas aeruginosa (a prolific producer of bacteriocins), to examine conditions that favour bacteriocin production. I also investigate more specific elements about this system and toxin production in general. I find that bacteriocin production in P. aeruginosa closely follows predictions made from mathematical models under a range of different conditions (e.g. frequency, scale of competition, multiple social traits). I also find that resistance can evolve to bacteriocins and biological mechanisms such as the neutralisation of one’s own toxin can have important consequences. Finally, I consider bacteriocin as a policing trait testing predictions about the role that linkage plays in policing. This work represents a comprehensive study into the importance of bacteriocin production in bacteria.
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Goddard, Matthew. "The ecology and evolution of selfish genes." Thesis, Imperial College London, 2000. http://hdl.handle.net/10044/1/11419.
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Ramon, Marina L. "Molecular ecology and evolution of intertidal sculpins /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2007. http://uclibs.org/PID/11984.
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Lee, Patricia Lee-Ming. "Ecology and evolution of swift-ectoparasite interactions." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363756.
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Clegg, Robert James. "Modelling the ecology and evolution of microorganisms." Thesis, University of Birmingham, 2015. http://etheses.bham.ac.uk//id/eprint/5608/.
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Theoretical models in microbiology have a relative short but successful history. Research presented in this thesis explores the evolutionary origin of aging and the methods used to quantify syntrophic cooperation between microbial species that are distantly related. The mathematical and computational tools used in doing so are developed and discussed in detail. Microorganisms were long thought to be capable of immortality until recent evidence demonstrated otherwise. Theoretical models suggest that aging strategies sacrificing repair for segregation of damage have highest evolutionary fitness, but this is not reflected in nature. The model developed here corrects this view of aging through more realistic assumptions regarding repair. Many estimates of the rate of interspecies metabolite transfer are based on spatial point pattern statistics and assumptions regarding cell surface concentrations. These are shown to be very inaccurate, but proposed alternatives required greater parameterisation. The system is sensitive to difficulties in determining consumption affinity constants, an issue also raised by previous authors.
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Longdon, Ben John. "Evolution and ecology of Drosophila sigma viruses." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5768.
Full textAbstract:
Insects are host to a diverse range of vertically transmitted micro-organisms, but while their bacterial symbionts are well-studied, little is known about their vertically transmitted viruses. The sigma virus (DMelSV) is currently the only natural hostspecific pathogen to be described in Drosophila melanogaster. In this thesis I have examined; the diversity and evolution of sigma viruses in Drosophila, their transmission and population dynamics, and their ability to host shift. I have described six new rhabdoviruses in five Drosophila species — D. affinis, D. obscura, D. tristis, D. immigrans and D. ananassae — and one in a member of the Muscidae, Muscina stabulans (Chapters two and four). These viruses have been tentatively named as DAffSV, DObsSV, DTriSV, DImmSV, DAnaSV and MStaSV respectively. I sequenced the complete genomes of DObsSV and DMelSV, the L gene from DAffSV and partial L gene sequences from the other viruses. Using this new sequence data I created a phylogeny of the rhabdoviruses (Chapter two). The sigma viruses form a distinct clade which is closely related to the Dimarhabdovirus supergroup, and the high levels of divergence between these viruses suggest that they may deserve to be recognised as a new genus. Furthermore, this analysis produced the most robustly supported phylogeny of the Rhabdoviridae to date, allowing me to reconstruct the major transitions that have occurred during the evolution of the family. This data suggests that the bias towards research into plants and vertebrates means that much of the diversity of rhabdoviruses has been missed, and rhabdoviruses may be common pathogens of insects. In Chapter three I examined whether the new sigma viruses in Drosophila affinis and Drosophila obscura are both vertically transmitted. As is the case for DMelSV, both males and females can transmit these viruses to their offspring. Males transmit lower viral titres through sperm than females transmit through eggs, and a lower proportion of their offspring become infected. I then examined natural populations of D. obscura in the UK; 39% of flies were infected and the viral population shows clear evidence of a recent expansion, with extremely low genetic diversity and a large excess of rare polymorphisms. Using sequence data I estimate that the virus has swept across the UK within the last ~11 years, during which time the viral population size doubled approximately every 9 months. Using simulations based on lab estimates of transmission rates, I show that the biparental mode of transmission allows the virus to invade and rapidly spread through populations, at rates consistent with those measured in the field. Therefore, as predicted by the simulations, the virus has undergone an extremely rapid and recent increase in population size. In Chapter four I investigated for the first time whether vertically transmitted viruses undergo host shifts or cospeciate with their hosts. Using a phylogenetic approach I show that sigma viruses have switched between hosts during their evolutionary history. These results suggest that sigma virus infections may be short-lived in a given host lineage, so that their long-term persistence relies on rare horizontal transmission events between hosts. In Chapter five I examined the ability of three Drosophila sigma viruses to persist and replicate in 51 hosts sampled across the Drosophilidae phylogeny. I used a phylogenetic mixed model to account for the non-independence of host taxa due to common ancestry, which additionally allows integration over the uncertainty in the host phylogeny. In two out of the three viruses there was a negative correlation between viral titre and genetic distance from the natural host. Additionally the host phylogeny explains an extremely high proportion of the variation (after considering genetic distance from the natural host) in the ability of these viruses to replicate in novel hosts (>0.8 for all viruses). There were strong phylogenetic correlations between all the viruses (>0.65 for all pairs), suggesting a given species’ level of resistance to one virus is strongly correlated with its resistance to other viruses. This suggests the host phylogeny, and genetic distance from the natural host, may be important in determining viruses ability to host switch. This work has aimed to address fundamental questions relating to host-parasite coevolution and pathogen emergence. The data presented suggests that sigma viruses are likely to be widespread vertically transmitted insect viruses, which have dynamic interactions with their hosts. These viruses appear to have switched between hosts during their evolutionary history and it is likely the host phylogeny is a determinant of such host shifts.
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Havran, J. Christopher. "Ecology and Evolution of the Hawaiian Violets." Ohio University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1210337818.
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Hackmann, Timothy Spain James Nobles. "Studies of ruminant digestion, ecology, and evolution." Diss., Columbia, Mo. : University of Missouri--Columbia, 2008. http://hdl.handle.net/10355/5688.
Full textAbstract:
The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on September 24, 2009). Thesis advisor: Dr. James Spain. Vita. Includes bibliographical references.
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Wahlberg, Niklas. "The ecology and evolution of melitaeine butterflies." Helsinki : University of Helsinki, 2000. http://ethesis.helsinki.fi/julkaisut/mat/ekolo/vk/wahlberg/.
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James, Adèle. "Ecology, evolution and virulence of environmental vibrios." Electronic Thesis or Diss., Sorbonne université, 2018. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2018SORUS477.pdf.
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Les changements globaux provoquent une augmentation des infections associées aux Vibrio. Les vibrioses affectent les humains, mais aussi des animaux marins. Un problème majeur est le manque de connaissances sur les vibrios présents dans l’environnement. Pour mieux comprendre et gérer ces maladies, nous nous sommes intéressés à l’écologie, l’évolution et la virulence de ces agents infectieux. Tout d’abord, nous avons montré que dans la nature, certains génotypes de Vibrio sont virulents pour les huîtres et que leurs mécanismes de virulence sont impliqués dans la différentiation écologique de ces souches. En France, les parcs ostréicoles font face à des évènements de mortalités massives associés à la présence d’un virus et de bactéries du genre Vibrio. Nous avons montré que le virus n’est ni essentiel, ni suffisant pour induire de fortes mortalités, contrairement aux vibrios qui jouent un rôle majeur. Les huîtres juvéniles malades sont toujours infectées par plusieurs populations, mais une seule, Vibrio crassostreae, est détectée en abondance. La virulence de cette population dépend d’un système de sécrétion de type IV codé par un plasmide conjugatif. Nos résultats suggèrent que V. crassostreae était un colonisateur peu virulent et que l’invasion du plasmide l’a rendu hautement pathogène. La distribution restreinte du plasmide de virulence suggère qu’il a été sélectionné par les hautes densités d’élevages. Enfin, nous avons montré que le transfert ou la sélection du plasmide était favorisé dans l’huître, suggérant que l’huître représente une niche propice aux transfert latéraux de gènes. Ce travail pourra permettre le développement d’outils de diagnostic et le suivi épidémiologique des vibrios pathogènesGlobal change, including anthropogenic activities, have resulted in an increase in the incidence of Vibrio-associated illnesses. These diseases not only affect humans but also marine animals. Despite strong ecological and economic consequences, little is known about population structure and virulence mechanisms of vibrios in the environment. To better understand and manage those diseases, we explored the ecology, the evolution and the virulence of these infectious agents. First, we found that some environmental strains were virulent towards oyster and we identified original virulence mechanisms related to their ecology and evolution. In France, oyster-farms are facing massive mortality events associated with the presence of a virus and bacteria of the genus Vibrio. We showed that the virus appears neither essential nor sufficient to cause high mortality rates contrary to the vibrios that play a major role. Juvenile diseased oysters were always co-infected by several populations, but only one, Vibrio crassostreae, was detected systematically and in abundance. Its virulence is dependent on a type VI secretion system that is carried by a conjugative plasmid. Our results suggest that V. crassostreae first differentiated into a low-virulent oyster colonizer and turned into a pathogen after acquisition of the virulence plasmid. The narrow distribution of the plasmid suggests that it has been selected by high density farming areas. Finally, we showed that the plasmid transfer or selection was enhanced in oysters, which suggests that oysters represent a niche for horizontal gene transfer. Overall, this work can lead to the development of diagnostic tools and epidemiological monitoring of pathogenic vibrios
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François, Sarah. "Diversité et écologie des virus associés aux arthropodes : des communautés aux génomes." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT106/document.
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Les nouvelles technologies de séquençage des génomes ont permis de révéler l’extraordinaire diversité des séquences virales dans des groupes d’hôtes jusque-là largement inexplorés. Ainsi, notre connaissance des virus d’arthropodes, infectant les animaux les plus diversifiés et abondants sur Terre, était jusque-là essentiellement réduite à des espèces d’intérêt économique et médical. Les nouvelles données de diversité virale chez les arthropodes illustrent le besoin d’étendre l’inventaire viral à l’échelle de l’écosystème et d’inclure les virus comme une composante essentielle de leur fonctionnement et de leur évolution.Dans ces travaux de thèse, j’ai développé et appliqué deux approches d’étude de la diversité virale chez des arthropodes, ainsi que de la circulation des virus dans des écosystèmes, en me focalisant sur des espèces d’intérêt agronomique : i) une approche virus-centrée par fouille de bases de données nucléotidiques, en recherchant la présence d’un groupe de petits virus à ADN inféodés aux arthropodes, les densovirus ii) une approche arthropode-centrée, utilisant une méthode séquençage haut débit de génomes viraux (métagénomique virale) pour analyser des communautés virales associées à des arthropodes de différents niveaux trophiques échantillonnés dans des agroécosystèmes.Mes résultats ont permis de :(i) Mettre en évidence que les densovirus sont largement présents dans l’ensemble du règne animal - notamment chez une grande diversité d’arthropodes - et qu’ils sont très diversifiés génétiquement, ce qui a permis de mieux appréhender histoire évolutive de ce groupe de virus ;(ii) Découvrir de nouveaux virus chez certains ravageurs de cultures : le tétranyque tisserand (Tetranychus urticae, Acarien) provenant de populations de laboratoires, ainsi que le puceron vert du pois (Acyrthosiphon pisum, Hémiptère), le phytonome de la luzerne (Hypera postica, Coléoptère) et l’armigère de la tomate (Helicoverpa armigera, Lépidoptère) provenant de populations naturelles échantillonnées dans des cultures de luzerne et des prairies. Ces études ont permis de mettre en évidence la présence de viromes spécifiques de chaque espèce d’arthropode et de caractériser la distribution de certains virus dans des communautés d’arthropodes d’un même écosystème. Plus de 60 nouvelles espèces de virus d’arthropodes et de plantes ont été découvertes. Leurs liens évolutifs avec des espèces de virus connues ont été caractérisés par des analyses phylogénétiques.(iii) Enfin, les travaux menés en (ii) ont également permis d’optimiser la méthodologie permettant d’obtenir et d’analyser des viromes obtenus à partir d’échantillons multiplexés, optimisant notamment l’étape d’attribution taxonomique des séquences obtenues par séquençage à haut débit, réduisant ainsi leur proportion en « matière noire » inhérente aux analyses des viromesHigh throughput sequencing technologies have revealed the extraordinary diversity of viral sequences in hitherto largely unexplored host groups. Thus, our knowledge about arthropod viruses, infecting the most diverse and abundant animals on Earth, was hitherto essentially reduced to species of economical and medical interest. New data on viral diversity in arthropods illustrate the need to expand viral inventory at the scale of the ecosystem and to include viruses as an essential component of their functioning and their evolution.In my thesis, I developed and applied two approaches to study the diversity of viruses in arthropods and how virus circulate in ecosystems, focusing on species of agronomic interest: (i) a virus-centered approach by exploring nucleotidic sequence databases, searching for the presence of a group of small DNA viruses infecting arthropods, the densoviruses (ii) an arthropod-centered approach at the scale of the ecosystem, using a viral metagenomic method to analyze viral communities associated with arthropods from different trophic levels from the same agroecosystems.My results showed that:(i) Densoviruses are spread throughout the animal kingdom - particularly in a wide diversity of arthropods - and are highly diverse genetically, which led to a better understanding of the evolutionary history of this group of viruses;(ii) A number of new viruses can be described in pests: the spider mite (Tetranychus urticae, Acari) from laboratory populations, as well as the green pea aphid (Acyrthosiphon pisum, Hemiptera), the alfalfa weevil (Hypera postica, Coleoptera) and the cotton bollworm (Helicoverpa armigera, Lepidoptera) from natural populations sampled from alfalfa crops and grasslands. These studies also highlighted that specific viromes are associated with each pest species, and I characterized the distribution of some of these viruses in arthropod communities. In total, more than 60 new species of arthropod and plant viruses were discovered. Their evolutionary links with known virus species was characterized by phylogenetic analyzes.(iii) The work realized in (ii) also contributed to optimize a methodology to prepare and analyze viromes from multiplexed samples, that is particularly suitable to optimize the taxonomic allocation of sequences and thus reduce the "dark matter" that is inherent to viral metagenomics analyses
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Cornejo, Castillo Francisco Miquel. "Diversity, ecology and evolution of marine diazotrophic microorganisms." Doctoral thesis, Universitat Politècnica de Catalunya, 2017. http://hdl.handle.net/10803/461801.
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Biological N2 fixation, the reduction of dinitrogen (N2) gas to biologically available nitrogen, is a fundamental process since it represents a source of new nitrogen for marine life in areas where this important element can be limiting, supporting primary productivity and thus biological carbon export to the deep ocean. This process is performed by the nitrogen-fixing prokaryotic microorganisms (the so-called diazotrophs). However, very little is still known about the identity and ecology of diazotrophs, which largely limits our capacity to understand the global significance of this process, and to predict potential variations in nitrogen fixation upon changes in environmental conditions. In this thesis, we aimed at improving the knowledge on the diversity, ecology and evolution of the marine nitrogen-fixing microorganisms in the open ocean.
Most current knowledge on diazotrophic diversity has been obtained using the nifH marker gene, which encodes for a structural protein of the enzymatic complex that performs the N2 fixation reaction. Thus, in Chapter 1 we first conducted a global exploration of the nifH gene extracted from metagenomic data derived from 68 globally distributed stations collected during the Tara Oceans expedition. This approach differs from previous studies in that it does not rely on primers to detect the nifH genes, and thus allows a more quantitative estimation of the contribution of these microorganisms and a more realistic view of their diversity. This study provides a first `primer-free¿ global map of the distribution of open ocean diazotrophic communities across ocean basins and throughout the water column, showing that diazotrophs often occurred at very low abundances, and that in general they were significantly more abundant in the mesopelagic than in photic waters. Likewise, we uncovered novel diversity that had remained unnoticed in all previous primer-based studies, since we demonstrate that more than half of the detected nifH variants cannot be captured by the primers used. This suggests that most diazotroph diversity studies may be disregarding an important fraction of the nitrogen-fixing community members.
Among the diazotrophs detected in Chapter 1, the most abundant was the unicellular cyanobacterium C. Atelocyanobacterium thalassa (UCYN-A), which lives in symbiosis with a prymnesiophyte alga and has been shown to be a relevant player in nitrogen fixation. Thus, in Chapter 2 and Chapter 3, we explored aspects related to the ecology, diversity and evolution of this remarkable microorganism. We detected UCYN-A in the South Atlantic Ocean using not only metagenomic approaches but also microscopic visualization techniques (CARD-FISH). This allowed us to unveil that different UCYN-A lineages, UCYN-A1 and UCYN-A2, live in symbiosis with two distinct prymnesiophyte partners of different sizes. Both UCYN-A lineages showed a streamlined genome expression towards nitrogen fixation. We estimated that these two lineages diverged almost 100 Mya under a strong purifying selection process. Finally, in Chapter 3 we focused on the study of UCYN-A3, another lineage of which very little was known, to gain insight into its ecology. Using an array of methods (PCR, qPCR, CARD-FISH and metagenomes) we could visualize and identify for the first time UCYN-A3 and its association with an alga of different size, which suggests that different UCYN-A lineages occupy different planktonic compartments that are not always considered when nitrogen fixation of nifH diversity are studied. Finally, we manage to reconstruct a significant fraction of its genome, establishing that this lineage constitutes a new UCYN-A genomic species.
Overall, this thesis has significantly contributed to expand the knowledge on marine diazotrophic organisms, unveiling new diversity and new planktonic compartments that could potentially lead to a better understanding of the marine nitrogen cycle.La fijación biológica de nitrógeno, es decir, la reducción del nitrógeno (N2) a amonio, es un proceso fundamental ya que representa una fuente de nitrógeno para la vida marina en áreas donde este elemento es limitante, posibilitando la producción primaria y por tanto la exportación de carbono al océano profundo. Este proceso se lleva a cabo por microorganismos procariotas, los llamados diazotrofos. Sin embargo, aún sabemos muy poco sobre la identidad y la ecología de estos microorganismos, lo que limita enormemente nuestra comprensión de la importancia global de este proceso, y nuestra capacidad de predecir cambios en la fijación de N2 ligados a cambios en el ambiente. El objetivo de esta tesis, por tanto, fue ahondar en el conocimiento de la diversidad, ecología y evolución de los microorganismos diazotrofos en el océano. La mayoría del conocimiento actual sobre la diversidad de diazotrofos se deriva del gen marcador nifH, que codifica una proteína estructural del complejo enzimático responsable de la fijación de nitrógeno. Por tanto, en el Capítulo 1 realizamos una exploración global del gen nifH usando datos metagenómicos de 68 estaciones muestreadas durante la campaña oceanográfica Tara Oceans. Nuestra aproximación se diferencia de los estudios anteriores ya que no se basa en el uso de cebadores para detectar el nifH y posibilita por tanto una cuantificación más precisa de la diversidad real. Este estudio representa el primer mapa global (no basado en cebadores) de la distribución de diazotrofos en el océano desde superficie hasta el mesopelágico. Aunque la abundancia de diazotrofos fue muy baja en general, era significativamente mayor en el océano profundo. Asimismo, descubrimos nuevos diazotrofos que habían pasado desapercibidos en los estudios basados en cebadores: más de la mitad de los diazotrofos detectados no se capturan por los cebadores para el nifH. Esto sugiere que la mayoría de estudios previos pueden haber obviado una fracción importante de las comunidades de fijadores de nitrógeno. Entre los diazotrofos detectados en el Capítulo 1, el más abundante fue la cianobacteria unicelular C. Atelocyanobacterium thalassa (UCYN-A), que vive en simbiosis con un alga primnesiofita y que juega un papel importante en la fijación de nitrógeno. En los capítulos 2 y 3 nos dedicamos a estudiar en detalle los aspectos relacionados con la ecología, diversidad y evolución de este diazotrofo. Mediante el análisis de metagenomas y de técnicas de visualización microscópicas como el CARD-FISH pudimos detectar UCYN-A en el atlántico sur, revelando que UCYN-A1 y UCYN-A2, dos linajes diferentes de UCYN-A, viven en simbiosis con dos hospedadores diferentes, dos primnesiofitas de tamaños distintos. Además, el análisis del perfil de expresión del genoma de ambos linajes mostró una dedicación optimizada a la fijación de nitrógeno. La edad de divergencia de UCYN-A se estimó en unos 100 millones de años, y presumiblemente ocurrió bajo presiones evolutivas de tipo estabilizadora. Por último, en el Capítulo 3, nos centramos en el estudio de UCYN-A3, otro linaje del que se sabe muy poco. Mediante el uso de varios métodos (PCR, qPCR, CARD-FISH y metagenomas) se logró visualizar e identificar por primera vez el linaje UCYN-A3 asociado con una alga de tamaño diferente, lo que sugiere que los distintos linajes de UCYN-A ocupan diferentes compartimentos planctónicos que no siempre se consideran en estudios de diversidad de nifH o de fijación de nitrógeno. Finalmente, pudimos reconstruir una fracción importante del genoma de UCYN-A3, estableciendo que representa una especie genómica diferente a las anteriores. En definitiva, esta tesis ha contribuido significativamente al conocimiento de los diazotrofos en el océano mediante el descubrimiento de nueva diversidad como de nuevos compartimentos del plancton donde puede darse la fijación de nitrógeno y que podrían ayudar a entender mejor el ciclo marino del nitrógeno.
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Zukewich, Joshua William Anthony. "Space matters : evolution and ecology in structured populations." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/43512.
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The inclusion of spatial structure in biological models has revealed important phenomenon not observed in “well-mixed” populations. In particular, cooperation may evolve in a network-structured population whereas it cannot in a well-mixed population. However, the success of cooperators is very sensitive to small details of the model architecture. In Chapter 1 I investigate two popular biologically-motivated models of evolution in finite populations: Death-Birth (DB) and Birth-Death (BD) processes. Under DB cooperation may be favoured, while under BD it never is. In both cases reproduction is proportional to fitness and death is random; the only difference is the order of the two events at each time step. Whether structure can promote the evolution of cooperation should not hinge on a somewhat artificial ordering of birth and death. I propose a mixed rule where in each time step DB (BD) is used with probability δ (1 − δ). I then derive the conditions for selection favouring cooperation under the mixed rule for all social dilemmas. The only qualitatively different outcome occurs when using just BD (δ = 0). This case admits a natural interpretation in terms of kin competition counterbalancing the effect of kin selection. Finally I show that, for any mixed BD-DB update and under weak selection, cooperation is never inhibited by population structure for any social dilemma.
Chapter 2 addresses the Competitive Exclusion Principle: the maximum number of species that can coexist is the number of habitat types (Hardin, 1960). This idea was borne out in island models, where each island represents a different well-mixed niche, with migration between islands. A specialist dominates each niche. However, these models assumed equal migration between each pair of islands, and their results are not robust to changing that assumption. Débarre and Lenormand (2011) numerically studied a two-niche model with local migration. At the boundary between niches, generalists may stably persist. The number of coexisting species may be much greater than the number of habitat types. Here, I derive the conditions for invasion of a generalist using an asymptotic approach. The prediction performs well (compared with numerical results) even for not asymptotically small parameter values (i.e. epsilon ≈ 1).
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Buckley, Yvonne Maria. "Ecology, evolution and manipulation of invasive plant populations." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271748.
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Segar, Simon T. "The ecology and evolution of fig wasp communities." Thesis, University of Reading, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.558774.
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I use the fig/fig wasp system to address several questions in the fields of evolutionary and community ecology. I present a general review of speciation and community ecology in insects on plants in general and in fig trees (genus Ficus) and fig wasps (Hymenoptera: Cha1cidoidea) in particular. Following on from this introduction are four experimental chapters. The first experimental chapter investigates the contrasting impact of two genera of parasitic, or non-pollinating fig wasps, on their host Ficus and its pollinating wasps. I present my findings in terms of community ecology and mutualism stability. In the second experimental chapter I describe the community of fig wasps associated with two Ficus species from the Australasian Ficus section Ma/vanthera. Using behavioural, ecological and molecular barcoding data I investigate the host Ficus specificity and trophic role of each genus of wasp. Furthermore I carry out a detailed investigation into the mode of speciation in a key kelptoparasite genus: Sycoscapter (Pteromalidae: Sycoryctinae), highlighting the role of ecological speciation in generating diversity. In the next chapter I present a global multi-gene phylogeny of the subfamily Sycoryctinae before evaluating its age, origins and mode of radiation in relation to other major components of fig wasp communities. The final experimental chapter addresses the assembly of fig wasp communities over evolutionary time. I combine phylogenetic and ecological data from three wasp communities associated with three Ficus species from different continents to investigate the roles of niche stasis and niche lability in shaping community structure. I fmd that overall, general ecological rules appear little constrained by the local pool of insect species in these complex, globally dispersed and multi-trophic communities. A general discussion is presented in the fmal chapter in which I highlight areas for future research and provide closing comments. /.
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García, Víctor Manuel Rodríguez. "Molecular ecology and evolution of Ariocarpus Scheidweiler (Cactaceae)." Thesis, University of Reading, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608363.
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Mexico is a centre of diversity for cacti. The predominantly Mexican genus Ariocarpus Scheidweiler, comprises geophytic cacti endemic to the Chihuahuan Desert. Recent authors recognise seven species in the genus, and many infraspecific taxa have been recognised by these and other authors. All the species are threatened. Proficient management of the Ariocarpu5 species genetic resource, with respect to conservation programs, requires a good understanding of the phylogenetic relationships of the genus and its evolutionary history as well as the levels of genetic diversity in-situ and ex-situ, and population genetic structure across natural populations. In this conservation paradigm, the aims of this project were focused on evolutionary and ecological questions, combining sequence data in phylogenetic analysis, and microsatellite markers in population analysis. Employing a Bayesian Concordance Analysis (BCA), seven nuclear microsatellite flanking regions (MFRs) and two chloroplast markers provide an estimation of past events in the evolution of the genus. Results are . suggestive of hybridisation early in evolution of the group. Ten microsatellite loci were amplified across 407 individuals collected from 18 populations representing all seven species of Ariocarpus. Genetic parameters and population structures were described per species. Gene flow between populations and correlation between genetic and geographic distances were calculated when all species data were combined. Results suggest vicariance events playa critical role in the speciation process. The same microsatellite loci were characterized in a putative hybrid. Bayesian cluster analysis showed ongoing natural hybridization between two sympatric species. Eleven microsatellite loci were analysed for two populations of the critically endangered A. bravoanus. Selective removal of plants from natural populations is shown to diminish genetic variability and substructure. The use of ex-situ genetic resources might be considered to improve genetic diversity whenever this material can be allocated to its natural source.
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Cubillos-Ruiz, Andrés Fernando, Jessica Weidemier Thompson, Jamie William Becker, Sallie W. Chisholm, Yanxiang Shi, der Donk Wilfred A. Van, and Audrey Olshefsky. "Ecology and evolution of lanthipeptides in marine picocyanobacteria." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/101829.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.Cataloged from PDF version of thesis. Each chapter with its own abstract. Each appendix with its own summary.
Includes bibliographical references.
Microbial secondary metabolites are among the most structurally and functionally complex molecules in nature. Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive post-translational modification. Most lanthipeptides are bactericidal but they are also known to act as signaling molecules or morphogenetic peptides, nevertheless the function of many lanthipeptides remains unknown. Prochlorosins are a diverse group of lanthipeptides produced by strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Unlike other lanthipeptide-producing bacteria, picocyanobacteria utilize an unprecedented mechanism of catalytic promiscuity for the production multiple structurally diverse lanthipeptides using a single biosynthetic enzyme. Also unprecedented is the production of lanthipeptides by single celled, planktonic gram-negative bacteria in a dilute nutrient-limited habitat, which suggests that they may have an unconventional biological function. The overarching goal of this thesis is to further our understanding of the ecology and evolution of the prochlorosins, and provide insights into their biological role in the marine environment. Here, we demonstrate that the prochlorosin genes are widespread in the ocean and that globally distributed populations of marine picocyanobacteria have the genetic potential of producing thousands of different lanthipeptide structures. The diversity of prochlorosin structures provides an interesting model to study the evolutionary forces that drive the creation of new lanthipeptide structures. We present evidence that there is a unique evolutionary interplay between the components of prochlorosin biosynthesis pathway; while the peptide substrates independently expand and diversify within the genome, the catalytically promiscuous biosynthetic enzyme evolves under a strong purifying selection that maintains its substrate tolerant state. This relationship indicates that the lanthipeptide production trait in marine picocyanobacteria might find its evolutionary advantage in the plasticity of the production of multiple cyclic peptides with diverse ring topologies. The remarkable diversity of prochlorosins poses many questions regarding their biological role in the marine environment. In laboratory experiments, we explore of some of the potential bioactivity of the prochlorosins, namely their potential as signaling molecules, antimicrobials and nutrient sources. The results from this exploration open new perspectives for the role of the lanthipeptides in the natural environment - more specifically the oligotrophic ocean.
by Andrés Fernando Cubillos-Ruiz.
Chapter 1. Chapter 2. Chapter 3. Chapter 4. Chapter 5. Appendix A. Appendix B. Introduction -- Evolutionary radiation of lanthipeptides in natural populations of marine picocyanobacteria / Andres Cubillos-Ruiz ; Jessica W. Berta-Thompson ; Jamie Becker ; Sallie W. Chisholm -- Exploring the biological role of prochlorosins / Andres Cubillos-Ruiz ; Jamie Becker ; Yanxiang Shi ; Wilfred van der Donk ; Sallie W. Chisholm -- Amino acid toxicity and tolerance in prochlorococcus / Andres Cubillos-Ruiz ; Audrey Olshefsky ; Sallie W. Chisholm -- Conclusion and future directions -- Proposed molecular mechanism for the expansion and diversification of prochlorosins - Hawaii Ocean experiment : prochlorosin amendment.
Ph. D.
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Allen, Richard Charles. "Secreted virulence factors : evolution, ecology and therapeutic manipulation." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/25789.
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Bacterial infections are an increasing cause for concern as resistance spreads to the majority of our front line antibiotics. To counter antibiotic resistance, new treatment regimens and drug targets are being investigated, including directly targeting bacterial virulence (pathogen-induced harm to the host), and therapies which target resistance mechanisms. The outcome of successful treatment with these compounds is not always killing or halting growth of bacteria, therefore selection for resistance to these types of therapeutics is complex. This complexity is increased by the secretion of many virulence factors, meaning their effects are shared with neighbouring individuals. In addition virulence factors show high phenotypic plasticity due to regulation by processes like quorum sensing (QS), which further complicates treatments targeting virulence, or the regulatory processes themselves. Using the example of quorum sensing inhibitors this study shows the importance of understanding the function and ecology of targeted virulence factors, to predict the selection for resistance to anti-virulence drugs. Later chapters elaborate on this to show how quorum sensing control affects selection on secreted virulence factors. The use of anti-virulence drugs as adjuvants is discussed, with a study showing that the interaction between QS inhibition and translation inhibitors is dependent on the environment. The selection for resistance to combinations of antibiotics and adjuvants is investigated using co-amoxiclav as an example, showing that treatment with high doses of adjuvant are robust to the evolution of resistance.
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Coyte, Katharine. "The ecology and evolution of complex microbial communities." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:61ef24cb-93b5-4c5a-8a49-f2aea4eff3db.
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Microbial communities colonise virtually every habitable environment on earth. They live on us, inside us, and all around us, and are key components of the earth's ecosystem. However, due to the complexity of microbial communities we still understand relatively little about the mechanisms that drive their ecology and evolution. The aim of this thesis is to develop novel experimental and mathematical approaches, in order to investigate complex microbial communities. Specifically, this thesis is split into two parts, focussing in turn on how environmental complexity, and interspecies interactions shape microbial ecology and evolution. In the first part I have studied microbial evolution in porous environments such as one might find in soil or aquifers. Here I have combined microfluidic experiments, mechanistic models, and game theory to study how hydrodynamics mediate competition between bacterial genotypes. With these I have demonstrated how even subtle environmental complexity can fundamentally affect microbial competition, enabling slow growing genotypes to outcompete their faster counterparts. In the second part of this thesis I have investigated how interspecies interactions influence the stability and initial assembly of microbial communities. Here I have developed new tools - from theoretical ecology - in order to study the microbial communities within the mammalian gastro-intestinal tract. With these I have demonstrated how strong, cooperative interactions between species can undermine both the stability, and the assembly of communities. Moreover, I have illustrated how these tools can be applied to real microbiome data, in order to better understand these important communities. In sum, this thesis explores two key drivers of microbial ecology and evolution, and presents a new set of tools for the future investigation of complex microbial communities.
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De, Winter Gunnar. "The ecology and evolution of individual behavioural variation." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/44995/.
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Central to this thesis is the investigation of how several factors (e.g. morphology, ecology, and social conditions) co-vary with consistent individual behavioural variation. Additionally, conceptual work explores the reach of consistent inter-individual behavioural variation in several novel contexts. In doing so, the aim is to contribute novel findings to the quickly growing compendium of knowledge concerning 'animal personality' in various settings. In summary, during this PhD the following research has been performed: • Through the use of lab-reared juvenile three-spined stickleback (Gasterosteus aculeatus) whose parents came from different habitats, I investigated the relative contribution of plasticity and (epi)genetic mechanisms on three behaviours (boldness, activity, and sociality). While these behaviours did not differ between juveniles from both populations, correlations of body length with specific behaviours did. (Chapter 2) • During fieldwork on the Scottish island of North Uist, seven populations of wild three-spined stickleback were surveyed for boldness, exploratory behaviour, and activity. Furthermore, the defensive morphology of these fish was quantified following an armour-staining protocol. Bold fish were found to be less armoured, directly contradicting the phenotypic compensation hypothesis, while more active fish were more armoured, which contradicts the idea that armour is energetically costly. (Chapter 3) • Spurred on by the findings on morphology-behaviour correlations, the ecology of the studied populations was assessed with a focus on parasitism by three common macro-parasites of three-spined stickleback, predation by trout, competition with the nine-spined stickleback, and the availability of resources. I found that all these factors, to some extent, influence individual behavioural variation. Importantly, this study provides the first observational evidence that less-explored factors, such as resource availability and interspecific competition, can be highly relevant influences on individual behaviour. (Chapter 4) • Next, a study on the effect of group behavioural composition on group foraging behaviour was done. With the help of a research visit to Aarhus University, similar experiments were performed on stickleback and social spiders (Stegodyphus dumicola). Group behavioural composition had a strong effect in both study systems, but experience was a more relevant influence on group foraging behaviour in stickleback. By using two different study organisms from quite disparate animal taxa, this allows me to develop hypotheses concerning the evolutionary origin and maintenance of individual behavioural variation and its tentative link with sociality. (Chapter 5) • Lastly, the phenomenon of consistent individual variation in behaviour is explored in novel contexts through conceptual essays (Chapter 6). o Do bacteria offer a suitable system to study ‘personality’? o How can animal personality be leveraged to improve animal welfare? o Are non-antagonistic interspecific interactions an overlooked yet important factor in the study of animal personality?
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Oliver, Thomas Henry. "The ecology and evolution of ant-aphid interactions." Thesis, Imperial College London, 2008. http://hdl.handle.net/10044/1/4412.
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The evolution of species interactions is a fascinating subject, and one of vital importance if we are to understand how biological communities change over time. This thesis considers the interaction between aphids (Homoptera) and ants (Formicidae). Ants tend aphids for sugary honeydew and in return provide a variety of protective services. A literature review in Chapter 1 introduces the subject and provides background information. Chapter 2 considers ant- aphid interactions in a community setting. Specifically, I consider the fitness effects of the ant- aphid interaction on host plants. Net benefits or costs to plants depend on the densities of ants and aphids; these densities may themselves change depending on context dependent factors. Chapters 3 and 4 consider how semiochemicals can allow species to respectively maintain or avoid synchrony in space and time with mutualists or antagonists. Chapter 3 shows ladybirds avoid prey patches guarded by ants by reducing oviposition in response to ant semiochemicals. Chapter 4 shows that aphid walking dispersal can be limited by ant semiochemicals. This may be adaptive for aphids to remain in areas of enemy- free space. Alternatively, if levels of kin competition are high limited dispersal could be costly to aphids. In Chapter 5 I consider interactions between invasive and native ants. Ecological dominance in ants may be mediated by the ability to monopolise honeydew- producing resources. Chapter 6 explores ants’ decisions whether to tend or prey upon aphids. Predation of aphids depends on colony demand (e.g. through cues from the presence of larvae) as well as the quality or quantity of supply (e.g. increased predation of unproductive aphids). Finally, Chapter 7 deals with macroevolutionary patterns in the interaction between ants and aphids. Specifically, I identify ecological traits that characterise aphid- tending ants. A final discussion chapter summarises how ant-aphid interactions fit into existing mutualism theory.
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Stireman, John Oscar. "The ecology and evolution of tachinid-host associations." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/289745.
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The Tachinidae is a taxonomically and ecologically diverse clade of parasitoids for which evolutionary and ecological relationships with hosts are largely unknown. Here, I employed a multidisciplinary approach to evaluate the determinants of patterns of host use in the Tachinidae. First, I examined spatio-temporal variation in the tachinid-dominated parasitoid assemblage of one lepidopteran species Grammia geneura . The parasitoid assemblage and parasitism rates varied dramatically among and within sampling sites, seasons, and years. I show that this variability may be a function of habitat-specific parasitism and indirect interactions between this host and other Macrolepidoptera through shared tachinid parasitoids. I then experimentally examined the host selection process in the tachinid Exorista mella. Host movement was an important elicitor of attack behavior. Flies also responded to odors associated with food plants of their host. Experienced flies attacked hosts more readily than did inexperienced flies. Based on these results, I proposed a host selection scenario for this tachinid species. E. mella also teamed to associate colors with hosts and avoided deterrent models that they had experienced. However, I failed to find evidence for odor learning. Learning of host-associated cues by E. mella may allow this parasitoid to take advantage of abundant host populations and maintain host-searching efficiency in an unpredictable environment. To examine how host-associated characteristics evolved in the Tachinidae, I reconstructed the evolutionary relationships within the subfamily Exoristinae using molecular data. Phylogenetic analyses generally supported recent classifications. Analyses of host-related characters indicated that tachinids show great evolutionary lability in behavior, morphology, and host range. Finally, I sampled host species to assess the determinants of tachinid community structure and host range. Several host characteristics were found to affect tachinid species richness. These patterns may be due to the opportunistic use of abundant hosts by polyphagous tachinids, enemy-free space provided by well-defended hosts, and the process of host location. Patterns of tachinid host use varied significantly with sample size, host diet breadth, host gregariousness, plant form, and host morphology. Taken together, these studies indicate high levels of plasticity in tachinid-host associations. This may be responsible for their ecological and evolutionary success.
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Dillard, Jacqueline Rae. "ECOLOGY, MONOGAMY, AND THE EVOLUTION OF ANIMAL FAMILIES." UKnowledge, 2019. https://uknowledge.uky.edu/biology_etds/59.
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Family-living has been recognized as a necessary prerequisite for the evolution of advanced cooperative societies, yet the evolutionary and ecological processes that drive the coupling of different forms of cooperation in family-based societies are still poorly understood. In my dissertation, I investigate the correlated evolution of parental care, monogamy, and cooperative breeding in a variety of family-based taxa. I explore the mating and social behavior of family-living beetles with incipient cooperation to better understand the factors driving these social traits. Specifically, I evaluate different causes of extra-pair mating in socially monogamous beetles, the potential benefits that young adult offspring may gain from remaining in the family group, and how these behaviors correspond to different ecological niches. These studies demonstrated that many of the factors predicted to favor family-living in cooperatively breeding animals fail to explain delayed dispersal and family cohesion in this beetle group. In a phylogenetic comparative study of birds, I further evaluate how ecological selective pressures drive the correlated evolution of monogamy, biparental cooperation, and cooperative breeding. Taken together, these studies have implications for our general understanding of the evolution of cooperation, and suggest the action of previously unrecognized processes in shaping and pairing social behaviors.
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Coelho, de Souza Fernanda. "The evolution of carbon cycle in tropical forests : integrating ecology and evolution." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/20880/.
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Present-day patterns of species diversity and their ecological characteristics in the tropics result from more than 100 million years of evolution. The environmental conditions in which species evolved have left a fingerprint on their functional traits, so investigating this legacy may improve our understanding of current patterns of ecosystem function and potentially guide us in managing our resources more wisely as the climate changes. Amazonian forests are ideal for such a study as they play a major role in the global carbon cycle and harbour a remarkable diversity of angiosperm lineages and species with a broad range of ecologies. Here, I linked data from long-term forest inventory plots, environmental conditions, and a newly constructed phylogeny in order to investigate the legacy of evolution on modern-day patterns of ecosystem function and diversity. I show first that evolutionarily related taxa are more similar in their demography and carbon storage and processing ability (i.e. wood density, potential size, growth and mortality-rates) than expected by chance. Thus, the degree of evolutionary history shared between lineages is a good proxy for their carbon traits. Next, using the evolutionary relationships among lineages I find a legacy of evolutionary history on current patterns of whole ecosystem productivity across the Amazon, such that communities with more evolutionarily distinct lineages have greater wood productivity. Finally, I compare the role of heritability versus selection on shaping lineages preferences for certain environments (i.e. soils and climate). I show that there is a tendency for evolutionarily related taxa to have more similar environmental preferences than expected by chance, but that certain kinds of habitat specialisation have also occurred repeatedly and independently in many lineages. These findings are important for understanding the future of Amazonian forests under global change and support an evolutionary perspective as an important component of conservation strategies.
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Gonçalves-Souza, Thiago [UNESP]. "Decifrando a função de processos ecológicos e evolutivos na distribuição local e regional de artrópodes em plantas." Universidade Estadual Paulista (UNESP), 2012. http://hdl.handle.net/11449/100505.
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An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial for inferring the mechanisms governing the assembly of species. As closely related species often share similar morphological traits, both phylogeny and ecology can explain the convergence or divergence of species morphology. We evaluated the relative importance of spiders’ phylogeny and ecological niche to the variation in spider body size and shape by comparing spiders (i) between bromeliads and dicot plants and (ii) among bromeliads with distinct architectural features. We tested whether bromeliad-living spiders have similar morphological traits to spiders from surrounding dicots and whether the differences in spider body size and shape are related to bromeliad architecture or to the spiders’ phylogeny. Spiders from bromeliads were larger and flatter than spiders associated with the surrounding dicots; this pattern was explained only by the spiders’ phylogeny. However, spider flatness was related to both phylogeny and ecological niche, suggesting that both historical processes and recent adaptations drive the evolution of spider body shape. Bromeliads appear to favour larger and flatter spiders because they provide a larger resource supply and their leaves are tightly interlocked compared to surrounding dicot plants, providing shelters from predators. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape
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Gonçalves-Souza, Thiago. "Decifrando a função de processos ecológicos e evolutivos na distribuição local e regional de artrópodes em plantas /." São José do Rio Preto, 2012. http://hdl.handle.net/11449/100505.
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Orientador: Gustavo Quevedo RomeroCoorientador: Karl Cottenie
Banca: Mário Almeida-Neto
Banca: Leandro Duarte
Banca: Paulo de Marco Junior
Banca: Thomas M. Lewinsohn
Resumo: Não disponível
Abstract: An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial for inferring the mechanisms governing the assembly of species. As closely related species often share similar morphological traits, both phylogeny and ecology can explain the convergence or divergence of species morphology. We evaluated the relative importance of spiders' phylogeny and ecological niche to the variation in spider body size and shape by comparing spiders (i) between bromeliads and dicot plants and (ii) among bromeliads with distinct architectural features. We tested whether bromeliad-living spiders have similar morphological traits to spiders from surrounding dicots and whether the differences in spider body size and shape are related to bromeliad architecture or to the spiders' phylogeny. Spiders from bromeliads were larger and flatter than spiders associated with the surrounding dicots; this pattern was explained only by the spiders' phylogeny. However, spider flatness was related to both phylogeny and ecological niche, suggesting that both historical processes and recent adaptations drive the evolution of spider body shape. Bromeliads appear to favour larger and flatter spiders because they provide a larger resource supply and their leaves are tightly interlocked compared to surrounding dicot plants, providing shelters from predators. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape
Doutor
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Monks, Neale. "Ecology, stratigraphy and phylogeny of the heteromorph ammonoidea of the Albian." Thesis, Imperial College London, 1998. http://hdl.handle.net/10044/1/8952.
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Mondor, Edward Brian. "The ecology and evolution of aphid alarm signaling behaviour." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ61665.pdf.
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Dunlop, Jennifer Michelle. "The evolution of behaviour and ecology in emballonuridae (Chiroptera)." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ27289.pdf.
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Puebla, Oscar. "Molecular ecology and evolution in "Hypoplectrus" coral reef fishes." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=95551.
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The marine environment presents fewer absolute geographic barriers to gene flow than its terrestrial and freshwater counterparts. In addition, the prevalence of planktonic larval stages in marine taxa provides potential for gene flow across large geographic distances. These observations raise two fundamental questions. How do new species arise in the marine environment? Considering the potential for gene flow in marine systems, it remains unclear to what extent allopatric speciation alone can account for the high levels of diversity observed in the marine realm, whether marine speciation also operates in the presence of gene flow, and if it does under what specific mechanisms. How far do planktonic larvae travel with marine currents? The generally low levels of genetic structure among marine populations suggests extensive dispersal, yet planktonic larvae are notoriously difficult to track owing to their small size and as a consequence the spatial scale of marine dispersal is still largely eluding ecologists. Here, I consider brightly colored coral reef fishes in the genus Hypop/ectrus (Serranidae) as a model system to address these two questions. I demonstrate the potential for ecological speciation with gene flow to operate in this system through the pleiotropic effect of color pattern, which appears to be involved both in mimicry and mate choice. I show that local processes are operating at the Caribbean scale in this system, suggesting dispersal limitation. I test and confirm this hypothesis by reporting genetic isolation by distance in the barred hamlet (Hypop/ectrus puel/a) at spatial scales ranging from 175 to 3,200 km. In order to estimate mean dispersal distance, I complement genetic data with SCUBA surveys of population densities covering 94,000 m2 of reef and provide dispersal estimates ranging between 2 and 14 km for specific dispersal functions notwithstanding the three-week pelagic larval stage of H. puel/a and very low levels of genetic structure aL'environnement marin présente moins de barrières au flux génétique que ses équivalents terrestres et d'eau douce. De plus, les phases planctoniques larvaires prévalences chez les espèces marines peuvent potentiellement maintenir un flux génétique a travers de grandes distances géographiques. Ces observations soulèvent deux questions fondamentales. Comment se développent de nouvelles espèces dans le milieu marin? Considérant le flux génétique potentiellement important, il demeure incertain dans quelle mesure la spéciation allopatrique peut expliquer la grande diversité observée dans le milieu marin, si la speciation opère également en présence de "flux génétique, et si oui par quels mécanismes. Quelle distance parcourent les phases larvaires planctoniques avec les courants marins? La structure génétique généralement faible parmi les populations marines suggère une dispersion extensive, mais les larves planctoniques sont notoirement difficiles a suivre en raison de leur petite taille et par conséquent I’ échelle spatiale de la dispersion marine échappe encore largement aux écologues.lci, je considère les poissons de récifs coralliens brillamment colores du genre HypopJectrus (Serranidae) comme systeme modèle pour aborder ces deux questions. Je démontre comment la speciation écologique avec flux génétique peut opérer dans ce système par I’ effet plëiotropique du patron de coloration, qui semble être impliquée dans le mimétisme ainsi que dans le choix d'un partenaire sexuel. Je montre que des processus locaux opèrent a I’ échelle des Caraïbes dans ce systeme, ce qui suggère une dispersion limitée. Je teste et confirme cette hypothèse en reportant de I’ isolement génétique par la distance chez HypopJectrus puella des échelles spatiales allant de 175 a3,200 km. Afin d'estimer la distance de dispersion moyenne je complémente les données génétiques avec des relèves de densités de population couvrant
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Harrison, Elizabeth Freya. "Cooperative behaviour in Pseudomonas aeruginosa : ecology, evolution and pathology." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.444928.
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Keeling, Matthew James. "The ecology and evolution of spatial host-parasite systems." Thesis, University of Warwick, 1995. http://wrap.warwick.ac.uk/30/.
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All ecological and epidemiological systems are embedded in space and composed of individuals; these facts often have a profound effect on the dynamics and means many tools and definitions require reformulation. Modelling has always been about taking highly complex dynamical systems, such as the natural environment, and attempting to simplify them to a leve that can be conceptualised, in the process losing all the features that are not understood or not anticipated. The individual based spatial models which form the basis of this work start from the simple rules for individuals and build up to a complex system, allowing new, unexpected phenomenon to arise naturally. The local interactions in spatial models lead to short scale correlations and self-induced spatial heterogeneity as the small fluctuations of environmental noise are amplified into macro-scale patterns. These spatial patterns can lead to ephemeral refuges for hosts from where they can disperse stabilising the dynamics. After discussing the importance and variety of host-parasite interactions several techniques to be used in this work are developed and explained on simple examples. Chapters III and IV introduce a caricature host-pathogen model and how how this deviates from the standard mean field theory approximations. Attention is then turned to host-parasitoid systems and the spatially extended Nicholson-Bailey equations; probems with this coupled map lattice are highlighted and an alternative artificial ecology is formulated. Remaining with the Nicholson-Bailey equations these are forced to be integer based by utilising stochastic events, this greatly stabilises the dynamics hence the method was applied to the persistence of measles epidemics in small populations (=500000). Chapter VII demonstrates how the inclusion of space enhances the effects of parasitism in increasing the evolutionary advantage of sexual hosts over asexual ones. Finally general techniques are developed to implicitly model the effects of spatial correlations and stochastic individual based interactions.
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Goodwin, Nicholas B. "The evolution and ecology of parental care in fishes." Thesis, University of East Anglia, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323386.
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Hayward, Alex. "The evolution and ecology of oak gall wasp communities." Thesis, University of Edinburgh, 2005. http://hdl.handle.net/1842/14033.
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Oak cynipids initiate the growth of highly complex galls on plants in the genus Quercus and related genera in the family Fagaceae. These galls support closed communities consisting of high diversities of gall inducers, inquilines and natural enemies. Key questions regarding the evolution and ecology of these communities remain unanswered. In particular, the role that phylogeography of component species plays remains unclear. Communities associated with different gall wasps vary in composition and structure, but little is known about the processes generating such variation. This thesis addresses the question of the ‘community phylogeography’ of the oak wasp system, using tree-based Bayesian analyses of mitochondrial sequence data. Work already done on the gall wasp hosts is extended to the next trophic level through examination of the European phylogeography of several chalcid parasitoids. The resulting patterns are examined for concordance between parasitoids and the gall wasps, and hypotheses regarding ancient and more recent range expansion are evaluated. The phylogeny of the oak gall wasp attacking Torymidae one of the major families of parasidoid attach oak cynipids, is estimated and hypotheses regarding the evolution of the group are considered. In addition, the use of cytochrome oxidase barcodes as a means of data collection from oak gall wasp communities is evaluated. Current methods are time consuming, labour intensive, and often error prone and an efficient standardised data collection procedure would be beneficial to further analyses.