As abundâncias e identidades das espécies de qualquer comunidade biológica mudam tanto ao longo do espaço quanto do tempo. Não obstante, aspectos espaciais da biodiversidade têm sido muito mais explorados do que os temporais. Um dos motivos pelos quais padrões temporais têm recebido menos atenção é a escassez de estudos de longo prazo, especialmente na região neotropical, uma das mais biodiversas e ameaçadas do planeta. Estudar a dinâmica de populações e comunidades ao longo do tempo pode revelar processos ecológicos fundamentais, bem como descrever como pressões naturais e humanas afetam a biodiversidade. Entender a dinâmica das populações e comunidades envolve entender as histórias de vida dos organismos, como eles interagem com o ambiente, o papel de interações entre espécies, o papel de processos demográficos estocásticos, dentre outros fatores. Nesta tese investigamos a dinâmica temporal de populações e comunidades de borboletas e aves, e ao longo dos capítulos avaliamos o papel de diferentes processos na regulação dessas dinâmicas. No Capítulo 1 investigamos se um comportamento sazonal observado em borboletas Ithomiini (Nymphalidae, Danainae), supostamente adaptativo à seca - os \"bolsões de Ithomiini\"- seria uma simples resposta reativa à falta de chuvas ou se mecanismos endógenos (\"relógios biológicos\") estariam envolvidos. No Capítulo 2 realizamos um estudo de dinâmica populacional comparada de borboletas miméticas da tribo Ithomiini. Algumas evidências têm sugerido que além de convergir na morfologia, espécies co-miméticas tenderiam a convergir também no comportamento, no uso de microhabitats e possivelmente em suas dinâmicas populacionais. Testamos as hipóteses de que 1) pares de espécies co-miméticas (i.e., com a morfologia convergente) ou 2) pares de espécies mais próximas filogeneticamente teriam suas dinâmicas populacionais mais correlacionadas do que pares de espécies agrupados ao acaso. No Capítulo 3 descrevemos como a composição de espécies de assembleias de aves e borboletas de nove localidades tropicais e subtropicais na América do Sul e do Norte variou ao longo do tempo (anos a décadas), e se diferenças demográficas entre espécies (nicho) seriam importantes para explicar os padrões observados. No Capítulo 1 encontramos evidências de que a agregações seriam um comportamento endógeno sincronizado com o fotoperíodo, com plasticidade limitada para lidar com as alterações no regime de chuvas previstas para a região e para o continente. No Capítulo 2 encontramos que as dinâmicas populacionais de pares de espécies de Ithomiini de um mesmo anel mimético ou mais próximas filogeneticamente não tenderam a ser mais correlacionadas do que pares reunidos ao acaso, e que as espécies, anéis miméticos e subtribos estudadas tiveram suas dinâmicas temporais mais correlacionados do que seria esperado por acaso. Estes resultados e os do Capítulo 1 sugerem que na dinâmica desse sistema as pressões seletivas exercidas por fatores ambientais seriam mais importantes do que interações entre espécies. No Capítulo 3 mostramos que a composição de espécies de assembleias de aves na Amazônia, Cerrado, Mata Atlântica e Flórida se alterou ao longo dos anos, mesmo em assembleias de áreas bem preservadas. Sobreposta a essa rotatividade (turnover) interanual também encontramos rotatividade sazonal, previsível, na composição de espécies de assembleias de aves da Amazônia e da Mata Atlântica e na assembleia de borboletas Ithomiini. Padrões de rotatividade sazonal na composição de espécies podem ser mais comuns em comunidades neotropicais do que se imagina. As estratégias temporais dos organismos neotropicais, as quais parecem ser a base dos padrões sazonais observados nas comunidades, podem ser largamente determinadas por ritmos (\"relógios\") endógenos. Estudos sobre a regulação dos ritmos e estratégias temporais dos organismos, e dos efeitos das mudanças climáticas e do uso do solo sobre eles, são essenciais. Um importante passo nesse sentido é a disseminação de estudos de longo-prazo de populações e comunidades, contínuos, sistemáticos e com resolução para detectar padrões sazonais. Além disso, a interação das perspectivas, bases teóricas e abordagens da biologia molecular, fisiologia, cronobiologia e ecologia pode avançar nosso entendimento sobre os processos que moldam a dinâmica da biodiversidade e sobre as consequências das perturbações humanas sobre os ecossistemas / The species abundances and identities of any biological community change both over space and time. Nevertheless, Spatial biodiversity dimensions have been much more exploited than temporal ones. One of the reasons for which temporal patterns have received less attention is a scarcity of long-term studies, especially in the neotropical region, one of the most biodiverse and endangered on the planet. Studying the dynamics of populations and communities over time can reveal key ecological processes as well as describe how natural and human pressures affect biodiversity. Understanding the dynamics of populations and communities involves understanding organisms life histories, how they interact with the environment, the role of interactions among species, the role of stochastic demographic processes, and other factors. In this dissertation we investigated the temporal dynamics of butterflies and birds populations and assemblages, and throughout its chapters we evaluate the role of different processes in the regulation of dynamics. In Chapter 1 we investigated whether a seasonal behavior observed in butterflies Ithomiini (Nymphalidae, Danainae), supposedly adaptive to dissecation - the \"Ithomiini pockets \" - is a simple reactive response to drought or there is internal time-keeping mechanisms involved. In Chapter 2, we performed a comparative population dynamics study of mimetic butterflies of the Ithomiini tribe. Some evidence has suggested that besides the convergence in morphology, co-mimetic species would tend to converge also in behavior, in the use of microhabitats and possibly in their population dynamics. We hypothesized that (1) pairs of co-mimetic species or (2) pairs of species more phylogenetically related would have their population dynamics more correlated than pairs of species grouped at random. In Chapter 3 we described how species composition of bird and butterfly assemblages from nine tropical and subtropical locations in South and North America varied over time (years and decades), and if demographic differences between species (niche) are needed to explain observed patterns. In Chapter 1 we found evidence that Ithomiini pockets are regulated by internal time-keeping mechanisms synchronized to photoperiod, and that mechanism has limited plasticity to cope with rainfall regime changes predicted for the study region and for the continent as a whole. In Chapter 2 we found that the population dynamics of Ithomiini species pairs more phylogenetically related or belonging to the same mimetic ring did not tend to be more correlated than pairs assembled at random, and that the species, mimetic rings and subtribes had their temporal dynamics more correlated than would be expected By chance These results and those of Chapter 1 suggest that this system dynamics is more influenced by selective pressures exerted by environmental factors than by species interactions. In Chapter 3 we show that the composition of bird assemblages in the Amazon, Cerrado, Atlantic Rainforest, and Florida has changed over the years, even in assemblies of well-preserved areas. Superimposed to this interannual turnover we also found seasonal, predictable turnover in species composition of bird assemblages of the Amazon and Atlantic Forest and in the Ithomiini butterflies assembly. Patterns of seasonal turnover in species composition may be more common in neotropical communities than is imagined. The temporal strategies of neotropical organisms, which appear to be the basis of the seasonal patterns observed in communities, can be largely determined by endogenous rhythms (\"biological clocks\"). Studies on the regulation of organisms\' temporal rhythms and strategies, and the effects of climate change and land use on them, are essential. An important step in this direction is the dissemination of continuous, systematic, population and community long-term studies, with sampling resolution to detect seasonal patterns. In addition, the interaction of perspectives, theoretical basis, and approaches of molecular biology, physiology, chronobiology, and ecology can advance our understanding of the processes that shape biodiversity dynamics and the consequences of human disturbances on ecosystems

Orientador: Marcus Aloizio Martinez de Aguiar / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-15T21:06:55Z (GMT). No. of bitstreams: 1 Andrade_ElizabethMachadoBaptestini_D.pdf: 4491574 bytes, checksum: 117d970a1c273ecd6ef9533aa742bb0f (MD5) Previous issue date: 2010 / Resumo: Nesse trabalho, estudamos doismecanismos de formação de espécies. No primeiro deles, consideramos um modelo espacial de especiação neutra totalmente probabilístico, sem barreiras geográficas ou interações ecológicas. A população evolui devido a influência de reprodução sexuada, mutações e recombinação. O modelo é baseado em acasalamento seletivo dependente de duas distâncias críticas, uma no espaço físico e outra no espaço dos genomas. Os vínculos introduzidos por essas duas distâncias permitem que a população se divida em grupos reprodutivamente isolados. Nossos resultados mostram que essa dinâmica gera padrões de diversidade consistentes com padrões observados na natureza, como distribuição de abundâncias do tipo log-normal, lei de potência para curvas espécie-área, taxas de especiação e extinção constantes e maior número de espécies para baixas dimensões. No segundo, nós generalizamos um modelo de especiação simpátrica baseado em competição intraespecífica, proposto por Dieckmann e Doebeli. Nesse modelo, uma população assexuada, inicialmente idêntica, evolui por seleção direcional para um fenótipo ótimo, onde a competição intraespecífica induz à seleção disruptiva. Nós mostramos que a forma das funções de competição e distribuição de recursos afetam a probabilidade de dois fenótipos coexistirem. Nós desenvolvemos um modelo analítico e simulações computacionais e comparamos os resultados de ambas abordagens / Abstract: In this work, we have studied two different mechanisms of species formation. In the first one, we considered a probabilistic spatial neutral model of speciation, without physical barriers or any kind of ecological interaction. The population evolves under the combined influences of sexual reproduction, mutation and recombination. The model is based on assortative mating and it depends on two critical distances, one in the genetic space and one in the physical space. The constraints imposed by these two distances allow the population to split in reproductively separated groups. Our results show that this kind of dynamics creates patterns of biodiversity in agreement with observed data, like lognormal distributions of species abundance, power law species-area relationships, steady speciation and extinctions rates and more species in low dimensions. In the second model, we generalized a sympatric speciation model based on intraspecific competition, proposed by Dieckmann and Doebeli. In that model, an assexual population, initially identical, evolves by directional selection to an optimal phenotype, where intraspecific competition induces disruptive selection. We show that the shape of the competition and carrying capacity kernels affects the likelihood of emergence of two coexisting phenotypes. We developed an analytical and a computational model and we compared the results of both approaches / Doutorado / Física da Matéria Condensada / Doutora em Ciências

La distribution de l'abondance des espèces en un site, et la similarité de la composition taxonomique d'un site à l'autre, sont deux mesures de la biodiversité ayant servi de longue date de base empirique aux écologues pour tenter d'établir les règles générales gouvernant l'assemblage des communautés d'organismes. Pour ce type de mesures intégratives, le séquençage haut-débit d'ADN prélevé dans l'environnement (" ADN environnemental ") représente une alternative récente et prometteuse aux observations naturalistes traditionnelles. Cette approche présente l'avantage d'être rapide et standardisée, et donne accès à un large éventail de taxons microbiens jusqu'alors indétectables. Toutefois, ces jeux de données de grande taille à la structure complexe sont difficiles à analyser, et le caractère indirect des observations complique leur interprétation. Le premier objectif de cette thèse est d'identifier les modèles statistiques permettant d'exploiter ce nouveau type de données afin de mieux comprendre l'assemblage des communautés. Le deuxième objectif est de tester les approches retenues sur des données de biodiversité du sol en forêt amazonienne, collectées en Guyane française. Deux grands types de processus sont invoqués pour expliquer l'assemblage des communautés d'organismes : les processus "neutres", indépendants de l'espèce considérée, que sont la naissance, la mort et la dispersion des organismes, et les processus liés à la niche écologique occupée par les organismes, c'est-à-dire les interactions avec l'environnement et entre organismes. Démêler l'importance relative de ces deux types de processus dans l'assemblage des communautés est une question fondamentale en écologie ayant de nombreuses implications, notamment pour l'estimation de la biodiversité et la conservation. Le premier chapitre aborde cette question à travers la comparaison d'échantillons d'ADN environnemental prélevés dans le sol de diverses parcelles forestières en Guyane française, via les outils classiques d'analyse statistique en écologie des communautés. Le deuxième chapitre se concentre sur les processus neutres d'assemblages des communautés.[...] / Integrative patterns of biodiversity, such as the distribution of taxa abundances and the spatial turnover of taxonomic composition, have been under scrutiny from ecologists for a long time, as they offer insight into the general rules governing the assembly of organisms into ecological communities. Thank to recent progress in high-throughput DNA sequencing, these patterns can now be measured in a fast and standardized fashion through the sequencing of DNA sampled from the environment (e.g. soil or water), instead of relying on tedious fieldwork and rare naturalist expertise. They can also be measured for the whole tree of life, including the vast and previously unexplored diversity of microorganisms. Taking full advantage of this new type of data is challenging however: DNA-based surveys are indirect, and suffer as such from many potential biases; they also produce large and complex datasets compared to classical censuses. The first goal of this thesis is to investigate how statistical tools and models classically used in ecology or coming from other fields can be adapted to DNA-based data so as to better understand the assembly of ecological communities. The second goal is to apply these approaches to soil DNA data from the Amazonian forest, the Earth's most diverse land ecosystem. Two broad types of mechanisms are classically invoked to explain the assembly of ecological communities: 'neutral' processes, i.e. the random birth, death and dispersal of organisms, and 'niche' processes, i.e. the interaction of the organisms with their environment and with each other according to their phenotype. Disentangling the relative importance of these two types of mechanisms in shaping taxonomic composition is a key ecological question, with many implications from estimating global diversity to conservation issues. In the first chapter, this question is addressed across the tree of life by applying the classical analytic tools of community ecology to soil DNA samples collected from various forest plots in French Guiana. The second chapter focuses on the neutral aspect of community assembly.[...]

This thesis investigates the molecular evolutionary and macroevolutionary consequences of flight loss in insects. Chapter 2 tests the hypothesis that flightless groups have smaller effective population sizes than related flighted groups, expected to result in a consistent pattern of increased non-synonymous to synonymous ratios in flightless lineages due to the greater effect of genetic drift in smaller populations. Chapter 3 tests the hypothesis that reduced dispersal and species-level traits such as range size associated with flightlessness increase extinction rates, which over the long term will counteract increased speciation rates in flightless lineages, leading to lower net diversification. The wide-spread loss of flight in insects has led to increased molecular evolutionary rates and is associated with decreased long-term net diversification. I demonstrate that the fundamental trait of dispersal ability has shaped two forms of diversity—molecular and species—in the largest group of animals, and that microevolutionary and macroevolutionary patterns do not necessarily mirror each other. / Generously funded by NSERC with a Canada Graduate Scholarship and the Government of Ontario with an Ontario Graduate Scholarship to T. Fatima Mitterboeck; NSERC with a Discovery Grant to Dr. Sarah J. Adamowicz

Les modèles d'occupation de niche au sein des communautés locales, la variabilité spatiale de la biodiversité le long des gradients environnementaux du stress et des perturbations, et les processus de succession végétale sont plusieurs sujets fondamentaux en écologie. Récemment, l'approche basée sur les traits est apparue comme un moyen prometteur de comprendre les processus structurant les communautés végétales et cette approche a même été proposée comme méthode pour reconstruire l'écologie communautaire en fonction des traits fonctionnels. Par conséquent, lier ces thèmes fondamentaux en utilisant une lentille fonctionnelle devrait nous donner un aperçu de certaines questions fondamentales en écologie et sera l'objectif principal de ma thèse. En général, mon projet de doctorat vise à étudier les structures de l'occupation de l'espace fonctionnel dans les gradients spatio-temporels. Plus précisément, l'objectif du chapitre 2 est (i) d'étudier les modèles d'occupation de la niche fonctionnelle en calculant trois métriques clés de niche (le volume total de niche fonctionnelle , le chevauchement des niches fonctionnelles et le volume de niche fonctionnel moyen) des communautés pauvres en espèces aux communautés riches en espèces et (ii) de déterminer le principal facteur de la structure observée de l'occupation de la niche fonctionnelle dans les communautés végétales du monde entier. Dans le chapitre 3, je vise à prédire et à expliquer la variation de la richesse en espèces selon les gradients de stress et de perturbation, en reliant le modèle d'équilibre dynamique et l'occupation de la niche fonctionnelle en fonction du cadre développé au chapitre 2. L'objectif du chapitre 4 est de tester expérimentalement l’application d'une méthode d'ordination CSR évaluée globalement en fonction de trois traits de feuilles (surface foliaire, teneur en matière sèche des feuilles et surface foliaire spécifique) dans les études locales. Enfin, l'objectif du chapitre 5 est de tester expérimentalement les hypothèses qui concilient les points de vue déterministes et historiquement contingents de la succession végétale, en étudiant la variation des divergences taxonomiques et fonctionnelles entre les communautés selon des gradients de stress et de perturbation. L'étude globale (chapitre 2) est basée sur une collection de 21 jeux de données, couvrant les biomes tropicaux et tempérés, et se compose de 313 communautés végétales représentant différentes formes de croissance. Les études locales (chapitre 3, 4 et 5) sont basées sur le même système expérimental constitué de 24 mésocosmes présentant différents niveaux de stress et de perturbation. L'expérience a commencé en 2009 avec le même mélange de graines de 30 espèces herbacées semées sur les 24 mésocosmes et s'est terminée en 2016. Nous avons permis la colonisation naturelle de graines de la banque commune de graines de sol et de l'environnement pendant la succession de sept ans. Dix traits ont été mesurés sur cinq individus (échantillonnés directement à partir des mésocosmes) par espèce par mésocosme en 2014 (chapitre 3 et 4). Un autre ensemble de traits (16 traits, y compris certains traits qui ne pouvaient pas être mesurés directement dans les mésocosmes), ont été mesurés au niveau de l'espèce (valeurs moyennes des traits) pour les 34 espèces les plus abondantes (certaines espèces disparues dans les mésocosmes) au cours des sept Ans, en les regroupant séparément pour une saison de croissance. Au chapitre 2, nous avons constaté que les communautés étaient plus diverses en termes fonctionnels (une augmentation du volume fonctionnel total) dans les communautés riches en espèces et que les espèces se chevauchaient davantage au sein de la communauté (augmentation du chevauchement fonctionnel), mais ne divisaient pas plus finement l'espace fonctionnel (aucune réduction du volume fonctionnel moyen). En outre, le filtrage de l'habitat est un processus répandu qui conduit à la caractérisation de l'occupation de niche fonctionnelle dans les communautés végétales. Dans le chapitre 3, nous avons trouvé un modèle similaire d'occupation de niche fonctionnelle sur un système expérimental avec une taille spatiale communautaire constante et un effort d'échantillonnage des traits, qui, avec le chapitre 2, nous a fourni une image plus complète et plus solide de l'occupation de niche fonctionnelle dans les communautés végétales. De plus, nous avons réussi à relier le modèle de l'occupation de la niche fonctionnelle et le modèle d'équilibre dynamique et avons constaté que le filtrage concurrentiel était le processus dominant qui détermine le mode d'occupation de la niche fonctionnelle et la richesse des espèces le long du stress et de la perturbation des gradients. Au chapitre 4, nous fournissons un soutien empirique à une méthode d'ordination CSR calibrée globalement en montrant une relation entre l'abondance relative d'espèces en croissance dans les mésocosmes ayant différents niveaux de fertilité du sol et mortalité indépendante de la densité et leur classification CSR. Au chapitre 5, nous avons montré que la succession d'installations au cours de sept ans dans ces mésocosmes était plus déterministe d'un point de vue fonctionnel, mais plus historiquement contingent d'un point de vue taxonomique et que l'importance relative de la contingence historique a diminué à mesure que l'environnement devenait plus stressé ou perturbé. En conclusion, les structures de l'occupation de l'espace fonctionnel dans (le volume fonctionnel total, le chevauchement fonctionnel et le volume fonctionnel moyen, les Chapitre 2 et 3) ou entre les communautés locales (dissimilarité fonctionnelle, chapitre 5) sont déterministes plutôt que neutres (ou contingence historique ). Les espèces tolératrices de stress sont plus avantagées dans les mésocosmes moins fertiles tandis que les espèces rudérales sont plus avantagées dans les mésocosmes avec plus de mortalité indépendante de la densité. / Abstract : The patterns of niche occupancy within local communities, the spatial variability of biodiversity along environmental gradients of stress and disturbance, and the processes of plant succession are several fundamental topics in ecology. Recently, the trait-based approach has emerged as a promising way to understand the processes structuring plant communities and has even been proposed as a method to rebuild community ecology based on functional traits. Therefore, linking these fundamental themes through a functional lens should give us more insight into some basic questions in ecology and will be the main objective of my thesis. Generally, my PhD project is to investigate the structures of functional space occupancy along both spatial and temporal gradients. Specifically, the objective of Chapter 2 is to investigate the patterns of functional niche occupancy by calculating three key niche metrics (the total functional niche volume, the functional niche overlap and the average functional niche volume) from speciespoor communities to species-rich communities and to determine the main driver of the observed pattern of functional niche occupancy across plant communities worldwide. In Chapter 3, I aim to predict and explain the variation of species richness along gradients of stress and disturbance, by linking the dynamic equilibrium model and functional niche occupancy based on the framework developed in Chapter 2. The objective of Chapter 4 is to experimentally test the application of a globally calibrated CSR ordination method based on three leaf traits (leaf area, leaf dry matter content and specific leaf area) in local studies. Finally, the aim of Chapter 5 is to experimentally test the hypotheses reconciling the deterministic and historically contingent views of plant succession, by investigating the variation of taxonomic and functional dissimilarities between communities along gradients of stress and disturbance. The global study (Chapter 2) is based on a collection 21 trait datasets, spanning tropical to temperate biomes, and consisting of 313 plant communities representing different growth forms. The local studies (Chapter 3, 4 and 5) are based on the same experimental system consisting of 24 mesocosms experiencing different levels of stress and disturbance. The experiment started in 2009 with the same seed mixture of 30 herbaceous species broadcast over the 24 mesocosms and ended in 2016. We allowed natural colonization of seeds from the common soil seed bank and from the surroundings during the seven-year succession. Ten traits were measured on five individuals (sampled directly from the mesocosms) per species per mesocosms in 2014 (Chapter 3 and 4). Another set of traits (16 traits including some traits that were not able to measured directly in the mesocosms) were measured at the species level (species mean traits values) for the 34 most abundant species (some species disappeared in the mesocosms) over the seven years, by regrowing them separately for one growing season. In Chapter 2, we found communities were more functionally diverse (an increase in total functional volume) in species-rich communities, and species overlapped more within the community (an increase in functional overlap) but did not more finely divide the functional space (no decline in average functional volume). Moreover, habitat filtering is a widespread process driving the pattern of functional niche occupancy across plant communities. In Chapter 3, we found a similar pattern of functional niche occupancy on an experimental system with a constant community spatial size and trait-sampling effort, which together with Chapter 2 provided us a more comprehensive and robust picture of functional niche occupancy across plant communities. In addition, we succeeded in linking the pattern of functional niche occupancy and the dynamic equilibrium model and found that habitat filtering was the dominant process determining the pattern of functional niche occupancy and species richness along the gradients stress and disturbance. In Chapter 4, we provide empirical support for a globally calibrated CSR ordination method by showing a relationship between the relative abundance of species growing in mesocosms having different levels of soil fertility and density-independent mortality and their CSR classification. In Chapter 5, we showed that plant succession over seven years in these mesocosms was more deterministic from a functional perspective but more historically contingent from a taxonomic perspective, and that the relative importance of historical contingency decreased as the environment became more stressed or disturbed. In conclusion, the structures of functional space occupancy within (the total functional volume, the functional overlap and the average functional volume; Chapter 2 and 3) or between local communities (functional dissimilarity, Chapter 5) are deterministic rather than neutral (or historical contingency). Stress-tolerators were more favored in high stress communities, while ruderals are more favored in high disturbed mesocosms (Chapter 4).