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Le changement climatique est connu pour entraîner une redistribution spatiale des conditions climatiques et avec elle une migration des espèces vers les pôles et les sommets. De tels changements impliquent une réorganisation des communautés végétales dont la nature, l'intensité et le déterminisme sont encore peu connus. L'objectif de cette thèse est d'évaluer, à large échelle spatiale et sur de longs pas de temps, les changements de composition des communautés végétales forestières induits par le réchauffement climatique, ainsi qu'analyser les facteurs écologiques et géographiques contribuant à ces changements à l'échelle de l'espèce et des communautés. La réponse de la flore forestière vis-à-vis du réchauffement climatique a été étudiée à l'échelle du territoire français (~546000 km²) à partir de larges bases de données d'observations floristiques, de données environnementales mesurées et modélisées, et d'une approche modélisatrice basée sur le concept de niche écologique et sur le caractère bio-indicateur des espèces. Dans un premier temps, nous avons montré que le remaniement des communautés végétales a permis la compensation de 0.54°C du réchauffement climatique ayant touché les forêts de montagne entre les périodes 1965–1986 et 1987–2008 (i.e. +1.07°C) contre seulement 0.02°C pour les forêts de plaine (réchauffement = 1.11°C). Cette compensation partielle démontre l'existence d'une dette climatique de la flore induite par le réchauffement climatique. L'importance de cette dette en plaine par rapport aux montagnes provient probablement de l'effet combiné d'un déficit d'extinction et de migration des espèces en plaine conduit respectivement par une plus large tolérance thermique des plantes forestières sur cette zone et par une migration des plantes a priori (i) limitée par l'importante fragmentation des forêts de plaine et (ii) inférieure au déplacement des conditions thermiques en plaine. Les particularités écologiques et géographiques des forêts de plaine et de montagne nous ont amené à considérer deux types de menaces induites par le changement climatique : (i) l'attrition biotique en plaine, et (ii) la perte d'une biodiversité historique et spécifique en montagne (réduction de l'habitat des espèces alpines aboutissant à leur disparition) remplacée probablement par des espèces plus communes. Dans un second temps, les effets de facteurs abiotiques, biotiques et géographiques pouvant amplifier ou réduire les changements de distribution des espèces et de composition des communautés induits par le réchauffement climatique ont été caractérisés. [...] Suite et fin du résumé dans la thèse. / Climate change is known to cause a spatial redistribution of climatic conditions which is driving poleward and upward range shifts. Such shifts imply a reorganization of plant communities which is still poorly understood. Here we aimed to assess the changes in plant communities' composition induced by climate warming at a global scale and over a long time period, as well as to analyze the effects of ecological and geographical factors that contribute to these changes at the species and community levels. The response of the forest flora to the raising temperature has been studied across the French metropolitan territory (~546,000 km²) from large floristic databases, measured and modeled environmental data, and a modeling approach based on the concept of ecological niche and the bioindicator properties of plant species. First, we showed that the reshuffling of plant communities allowed to recover 0.54°C of the temperature increase between the periods 1965–1986 and 1987–2008 in highland forests (i.e. +1.07°C), while it recovered only 0.02°C in lowland forest (warming = 1.11 °C). This partial compensation demonstrates the current occurrence of a climatic debt in forest vegetation caused by climate warming. The high climatic debt observed in lowland forest compared to the highland one is likely due to extinction and migration debts caused by a wider temperature tolerance of plants in lowland communities and a plant migration capacity (i) limited by the high spatial fragmentation of the lowland forest habitat and (ii) shorter than the shift of thermal conditions in lowland areas, respectively. The ecological and geographical specificity of lowland and highland forests led us to consider two different threats induced by climate change: (i) biotic attrition in lowland areas, and (ii) loss of a specific and an historic biodiversity in highland forest (mountaintop extinction of alpine species due the surface decrease of their potential habitat) likely replaced by more common species assemblage (increase of generalist plants). Second, the effects of abiotic, biotic and geographical factors which can amplify or reduce the magnitude of both the species range shifts and the reshuffling of plant communities induced by global warming were characterized. Last and final summary in the thesis.

Les activités humaines ont, depuis plus d'une centaine d'années, influencé de plus en plus fortement les cycles géochimiques contrôlant les niveaux d'acidité et de disponibilité en azote dans la nature. Les dépôts acides et azotés conduisent à une modification des conditions du milieu et notamment à des changements sensibles de la composition des communautés d'espèces végétales. L'objectif de cette thèse est de retracer l'évolution spatio-temporelle de l'acidité et de la disponibilité en azote des sols forestiers français au cours du 20ème siècle à partir du caractère bio-indicateur de la flore, à l'échelle locale ainsi globale. L'utilisation de la flore comme bio-indicateur vise à pallier l'absence de données de mesures directes des conditions édaphiques et des dépôts atmosphériques acides et azotés couvrant une large emprise spatio-temporelle. Premièrement, les variations de pH (indicateur d'acidité) et C:N (indicateur de disponibilité en azote) bio-indiquées ont été calculées à partir d'environ 100 000 relevés floristiques temporaires réalisés dans toute la France de 1910 à 2010. Elles ont été analysées par une méthode novatrice de comparaison spatio-temporelle, en différenciant les zones forestières sur substrat acide et non-acide ainsi que les forêts de conifères et de feuillus. Dans un second temps, nous avons analysé les changements des conditions édaphiques entre 1972 et 2011 à l'échelle de la forêt de Villey-Le-Sec, et ceux de la flore qu'ils induisent en lien avec d'autres évolutions environnementales, toujours à partir du caractère bio-indicateur de la flore.À l'échelle globale, nous avons observé une acidification des forêts françaises en milieu acide (-0.34 unités du pH en moyenne) et milieu non-acide (-0.19 unités du pH en moyenne), respectivement, jusqu'en 1984 et 1997. Nous avons ensuite mis en évidence, pour la première fois à notre connaissance, un arrêt dans l'acidification des sols forestiers et même une diminution de l'acidité sur substrat non-acide ainsi que un décalage temporel entre l'acidification des zones acides et non-acides. Cette évolution apparaît tout à fait cohérente avec celle connue des dépôts atmosphériques acidifiants en France depuis le début du 20ème siècle. Spatialement, nous confirmons la tendance temporelle, montrons une évolution régionalisée de l'acidification principalement sur substrat non-acide et soulignons la grande variabilité spatiale des changements de pH des sols forestiers. Concernant l'évolution de la disponibilité en azote, nous observons une diminution non attendue de celle-ci jusqu'en 1984 et 1997, respectivement, dans les forêts de conifères (+0.79 unités de C:N en moyenne) et de feuillus (+0.74 unités de C:N en moyenne). Une tendance à l'eutrophisation des sols forestiers a ensuite été observée dans les forêts de conifères et de feuillus à partir de 1997 (-0.10 et -0.16 unités de C:N en moyenne, respectivement). Cette évolution apparaît décalée par rapport à celle des dépôts azotés en France. [...] Suite et fin du résumé dans la thèse. / Human activities have, over the last century, strongly influenced the cycles controlling the levels of acidity and nitrogen availability in nature. Acidifying and eutrophying deposition lead to a change in environmental conditions and particularly to sensitive changes in plant communities' composition.The objective of this Ph.D work is to reconstruct the spatiotemporal evolution of the acidity and nitrogen availability in French forest soils over the 20th century using the bioindicator character of plants, into local and global scales. The use of plants as bioindicator seeks to mitigate the lack of direct measurements of soil conditions and atmospheric deposition, over a wide spatiotemporal extent. First, changes in bioindicated soil pH (indicator of acidity conditions) and C:N (indicator of nitrogen availability status) were computed from approximately 100 000 temporary floristic plots carried out throughout France from 1910 to 2010. They were analyzed using an innovative method of spatiotemporal comparison, where acidic and nonacidic forest areas and coniferous and broadleaved forests were differentiated. Secondly, and always from the bioindicator character of plants, changes in soil conditions between 1972 and 2011 across Villey forest as well as floristic changes they induce related with other environmental changes were analyzed.At the global level, we observed acidification in acidic forest areas (-0.34 pH units on average) and in nonacidic areas (-0.19 pH units on average), respectively, until 1984 and 1997. We demonstrated for the first time (to our knowledge) a cessation of acidification of forest soils and even a decrease in acidity in nonacidic forest areas, as wella as a time lag for acidification between acidic and nonacidic areas. This trend is consistent with the trend of acidifying deposition in France since the early 20th century. Spatially, our results confirm the temporal trends, show a regional geographic pattern of acidification (mainly observed in nonacidic areas), and highlight the high spatial variability of soil pH changes. Concerning the evolution of nitrogen availability conditions, we observed an unexpected decrease in available nitrogen until 1984 and 1997, respectively, in coniferous (+0.79 C:N units on average) and broadleaved forests (+0.74 C:N units on average). A trend to eutrophisation of forest soils was then observed in coniferous and broadleaved forests since 1997 (-0.10 and -0.16 C:N units on average, respectively). This trend is not consistent with the trend of nitrogen atmospheric deposition in France. ”Last and final summary in the thesis.”

Neste trabalho realizou-se o estudo de distribuição, riqueza e conservação do gênero Davilla Vand. (Dilleniaceae) no Neotrópico. Para tal utilizou-se a modelagem de distribuição de espécies com o algoritmo Maxent. Este produz distribuição das espécies no espaço geográfico a partir de dados ambiental e de ocorrência. Foram estudadas as espécies de acordo com o bioma de ocorrência: Mata Atlântica; Cerrado; e Amazônia. Este grupo está representado no Neotrópico por 25 espécies. Para o Cerrado incluiu-se além das espécies do gênero Davilla as demais espécies da família Dilleniaceae. Os resultados indicaram que no Cerrado o grupo está representado por nove espécies de Davilla, além de Curatella americana L. e três espécies de Doliocarpus Rol., destas cinco são endêmicas (Doliocarpus elegans Eichler e 4 Davilla spp.). Para a Mata Atlântica ocorrem 12 espécies de Davilla, oito delas são endêmicas, incluindo uma espécie ameaçada de extinção. Para a Floresta Amazônica são conhecidas nove espécies, cinco delas endêmicas. Duas outras espécies são Neotropicais, portanto, compartilhadas por todos os biomas citados anteriormente. As demais espécies são de ocorrência em pelo menos dois biomas. Para estes três biomas produziu-se a distribuição e a riqueza de espécies visando comparar os resultados com as unidades de conservação, objetivando discutir questões relativas à conservação deste grupo. Os parâmetros conservacionistas como espécies raras, zonas de endemismo, zonas de alta riqueza, áreas de preservação ambiental, foram confrontados objetivando indicar áreas prioritárias para a conservação do grupo e da biodiversidade. Os resultados indicaram existir três centros de diversidade para este grupo. O principal deles está localizado na Mata Atlântica, principalmente nas florestas litorâneas do estado da Bahia. Outro centro de diversidade localiza-se na região central do Cerrado, especialmente nos estados de Goiás e Bahia. A outra área de diversidade localiza-se próximo à foz do Rio Amazonas e ao longo de seu curso. Devido ao hábito predominante das espécies serem lianas, estas são importantes componentes das florestas, das quais usamos este referencial para discutir questões relativas à conservação destes habitats, de suas espécies e da biodiversidade. As informações completas estão apresentadas nos capítulos de acordo com os respectivos biomas abordados. / In this study was realized to study the distribution, richness and conservation of the Davilla Vand. (Dilleniaceae) in the neotropics. For this purpose was used to distribution model of species with Maxent algorithm. This produces species distribution in geographic in space based on environmental and occurrence data. Species in accordance with biome of occurrence were studied: Atlantic Forest; Cerrado; and the Amazon. This group is represented by 25 species in the neotropics. For the Cerrado was included in addition to the Davilla species all species of Dilleniaceae family. The results indicated that in the Cerrado this group is represented by nine species of Davilla, and Curatella americana L. and three species of Doliocarpus Rol., to these five are endemic (Doliocarpus elegans Eichler and 4 Davilla spp.). For Atlantic Forest occur 12 Davilla species, eight of which are endemic, including an endangered species. For the Amazon are known nine species, five of these endemic. Two other neotropical species are therefore shared by all biomes mentioned above. The other species are occurring in at least two biomes. For these three biomes produced the distribution and species richness in order to compare the results with the protected areas, aiming to discuss issues relating to the conservation of this group. Conservationists parameters as rare species, areas of endemism, areas of high species richness, conservation areas, were confronted aiming indicate priority areas for conservation of biodiversity and too this group. The results indicated three centers of diversity for this group. The main one is located in the Atlantic Forest in coastal forests of Bahia. Another center of diversity is located in central region of Cerrado, especially in the states of Goias and Bahia. The other area of diversity is located near the mouth of the Amazon River and along its course. Due to the prevailing habit of the species are lianas, these are important components of forests, of which we use this framework to discuss issues relating to the conservation of these habitats, their species and biodiversity. Full details are presented in chapters according to their biomes addressed.

O piquiazeiro (Caryocar villosum (Aubl.) Pers.) é uma arbórea presente no bioma Amazônico, sendo seus principais usos os alimentícios e madeireiros. O piquiazeiro encontra-se incipientemente domesticado, e a seleção e manejo feitos por populações tradicionais pode estar promovendo a continuidade desse processo, que se iniciou na Amazônia por volta do final do Pleistoceno e inicio do Holoceno, e hoje está sendo retomado por populações tradicionais que fazem cultivos em seus quintais, entre elas o piquiazeiro. Apesar de seu uso por populações tradicionais e do potencial comercial, a diversidade e distribuição do piquiazeiro ainda foram pouco estudadas. Os objetivos desse estudo foram analisar a diversidade genética e a estrutura genética de piquiazeiros em duas situações. A primeira foi examinando o processo de domesticação do C. villosum por populações tradicionais na Floresta Nacional (FLONA) do Tapajós e a segunda foi comparando a população da FLONA do Tapajós, no Pará, com outra localizada na Reserva Extrativista (RESEX) Rio Ouro Preto, em Rondônia. Na FLONA foram genotipados, com o uso de sete marcadores microssátelites, 67 indivíduos da mata e 26 cultivados nos quintais. Maior riqueza alélica, número de alelos, número de alelos efetivos, alelos privados e heterozigosidade observada foram encontrados na mata, assim como estruturação genética espacial nos indivíduos de quintal, o que indica a domesticação da espécie, apesar da baixa estruturação genética encontrada entre os grupos mata/quintal nos métodos aplicados. Na segunda parte foram genotipados 130 piquiazeiros, sendo 92 do Pará, os mesmos utilizados no estudo da domesticação, somados a 38 de Rondônia. O Pará apresentou valores superiores para número médio de alelos/loco, número efetivo de alelos, número de alelos privados, riqueza alélica e heterozigosidade esperada, indicando um possível centro de origem da espécie. A estrutura genética espacial foi significativa em ambas as localidades, o que sugere correlações de parentesco entre os indivíduos, provavelmente devido ao comportamento forrageiro de seus polinizadores e dispersores. A estruturação genética entre as duas localidades foi observada em todos os métodos, sendo que a maior parte da variação (89%) ocorre dentro das populações. A diferenciação entre as populações (11%) pode ser explicada por fatores históricos e pelo elevado fluxo gênico (Nm = 2,043). Foi também feita uma modelagem de nicho ecológico para determinar a distribuição da espécie. Foi observada a predominância de ocorrência da espécie no bioma Amazônico, com maior adaptação a climas quentes, com médias superiores a 18°C em todos os meses, e úmido, apresentando de 1 a 3 meses de seca. / Piquiá (Caryocar villosum (Aubl.) Pers.) is a tree species present in the Amazon biome, used mainly for food and timber. Piquiá is incipiently domesticated, and the selection and management by traditional populations may be promoting the continuity of this process. This process began in the Amazon around the end of the Pleistocene and the beginning of the Holocene, and today is being resumed by traditional populations, which cultivate different species in their backyards, among them is the piquiá. Despite its constant use by traditional populations and commercial potential, the diversity and distribution of piquiá have been little studied. The objectives of this study were to analyze the genetic diversity and the genetic structure of piquiás in two different cases. The first was to examine the process of domestication of C. villosum by traditional populations in the Floresta Nacional (FLONA) do Tapajós. The second one was to compare the piquiás populations from the FLONA do Tapajós, in Pará, with another one located in the Reserva Extrativista (RESEX) Rio Ouro Preto, in Rondônia. Sixtyseven individuals from the forest and 26 cultivated in the backyards were genotyped, with the use of seven microsatellite markers, in FLONA. Higher allelic richness, number of alleles, number of effective alleles, private alleles and observed heterozygosity were found in the forest, as well as spatial genetic structuring in backyard individuals, which indicates the domestication of the species, despite the low genetic structure found between the forest/backyards groups in the applied methods. In the second part, 130 piquiás were genotyped, being 92 of Pará, the same ones used in the study of domestication, and 38 of Rondônia. Pará presented higher values for average number of alleles/locus, effective number of alleles, number of private alleles, allelic richness and expected heterozygosity, indicating a possible center of origin of the species. The spatial genetic structure was significant in both localities, suggesting kinship correlations among the individuals, probably due to the forage behavior of their pollinators and dispersers. Genetic structuring between the two localities was observed in all methods, with most of the variation (89%) occurring within populations, according to AMOVA. The differentiation between populations (11%) can be explained by historical factors and high gene flow (Nm = 2,043). According to the Ecological Niche Modeling, used to verify the species distribution, the piquiá occurs predominantly in the Amazonian biome, with best suitability in hot climates, with temperature averages above 18°C, and humid, presenting between 1 and 3 months of drought.

Os Flavivírus são vírus de 40 50 nm de diâmetro, com formas esféricas e RNA de fita simples, com sentido positivo e aproximadamente 11 kb de comprimento. O Vírus da Febre Amarela, protótipo do grupo, é o agente causador da Febre Amarela, uma antiga doença que causou epidemias generalizadas na África, Américas do Norte e do Sul e Europa do século XVII ao início do século XX, e depois ressurgiu nas últimas décadas na África sub- saariana e América do Sul tropical. O presente trabalho busca a reconstrução da transmissão da Febre Amarela na América do Sul, no tempo e espaço, em especial, considerando a provável influência das populações humanas, primatas não humanos e mosquitos, na evolução e distribuição das linhagens genéticas de Febre Amarela, aplicando modelos de inferência Bayesiana para análises filogenéticas e filogeográficas e testando hipóteses de distribuição geográfica com modelagem de nicho ecológico. Os dados dão poucas evidências de que as estratégias de vacinação vigentes tenham efetivamente colaborado para a diminuição da ocorrência de Febre Amarela, indicando possíveis erros na estratégia de vacinação. A partir da análise Coalescente da população viral de Febre Amarela, a população viral apresentou um decréscimo importante iniciado em meados dos anos 90. A análise filogeográfica sugere um padrão geral de transmissibilidade Source-Sink destacando a região amazônica como fonte de diversidade para as outras áreas estudadas, com uma estrutura filogeográfica secundária em ondas. Assim, as introduções do vírus em áreas fora da amazônia tem ocorrência aleatória e podem ser ligadas temporalmente e geograficamente ao norte da America do Sul. Os modelos de distribuição geográfica corroboram esse padrão e indicam uma área possível para circulação da Febre Amarela ampla, englobando diversos ecótonos. Os resultados indicam um possível efeito em longo prazo da vacinação atuando diretamente sobre a evolução e dinâmica filogenética da Febre Amarela e sugere que monitorar a evolução do vírus da Febre Amarela é uma estratégia válida para compreender sua distribuição geográfica e evidenciar mecanismos complexos de transmissão e introdução. Por sua vez, os modelos de Nicho Ecológico mostraram ser ferramentas adequadas para calcular o risco da doença em determinadas áreas, sem sua ocorrência prévia, contribuindo como um modelo preditivos para orgãos de Vigilância prepararem suas estratégias de prevenção e controle no caso de possível introdução de patógenos / The flaviviruses are viruses of 40-50 nm in diameter, with spherical shaped and single-strand RNA with positive sense and approximately 11 kb in length. The Yellow Fever virus is the prototype of the group and the causative agent of Yellow Fever, a disease which caused widespread epidemics in Africa, North America, South America and Europe of the seventeenth century to the early twentieth century. The disease reemerged in recent decades in sub-Saharan Africa and tropical South America. This manuscript aims to reconstruct, in time and space, the transmission of yellow fever in South America, through the applying of a Bayesian inference model, considering the probable influence of human populations, nonhuman primates and mosquitoes on the evolution and distribution of Yellow Fever genetic lineages. Distributional pattern hypothesis will be tested by computational modeling of ecological niche. The data provide little evidence that current vaccination strategies have effectively contributed to reducing the occurrence of Yellow Fever, indicating possible errors in the vaccination strategy. From the analysis of the Yellow Fever population Coalescence, the viral population showed a significant decrease started in the mid-90s. The phylogeographic analysis suggests a general pattern of transmissibility \"Source-Sink\" highlighting the Amazon region as a source of diversity for the other areas studied, with a secondary phylogeographic wave like structure. Thus, the introductions of the virus into areas outside the Amazon has random occurrence and can be linked temporally and geographically to the north of South America The geographical distribution models corroborate this pattern and indicate a broad possible area for Yellow Fever circulation, encompassing many ecotones. The results indicate a possible long-term effect of vaccination acting directly on the evolution and phylogenetic dynamics of Yellow Fever and suggests that monitoring the evolution of the Yellow Fever virus is a valid strategy to understand the geographical distribution and highlight complex transmission mechanisms and spatial movements. In turn Ecological Niche models showed as an appropriate tool to calculate disease risk in certain areas without previous occurrence of the disease, working as a predictive model for Surveillance institutions prepare their strategies for prevention and control in the case of possible pathogen introduction

Submitted by William Justo Figueiro (williamjf) on 2015-08-11T21:04:47Z No. of bitstreams: 1 13e.pdf: 3156102 bytes, checksum: da00a19d9782f6ac017289a5d272ac1f (MD5) / Made available in DSpace on 2015-08-11T21:04:47Z (GMT). No. of bitstreams: 1 13e.pdf: 3156102 bytes, checksum: da00a19d9782f6ac017289a5d272ac1f (MD5) Previous issue date: 2013 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / CNPQ – Conselho Nacional de Desenvolvimento Científico e Tecnológico / INCT-APA - Instituto Nacional de Ciência e Tecnologia Antártico de Pesquisas Ambientais / PROANTAR - Programa Antártico Brasileiro / SECIRM - Secretaria Interministerial para os Recursos do Mar / MMA - Ministério do meio Ambiente / INCT-APA - Instituto Nacional de Ciência e Tecnologia Antártico de Pesquisas Ambientais / UNISINOS - Universidade do Vale do Rio dos Sinos / O nicho realizado de duas espécies precisa ser diferente, para que estas espécies possam coexistir de maneira estável. Pygoscelis papua e P. antarcticus reproduzem simpatricamente na Ilha Elefante, Antártica. Foram coletadas amostras de conteúdo estomacal e realizado biometria das duas espécies para analisar a dieta e a sobreposição de nicho. Um total de 56 amostras de P. papua e 71 amostras de P. antarcticus foram coletadas durante dois períodos de reprodução austral, 2010/11 e 2011/12, na região de Stinker Point. A proporção de itens variou entre as espécies de pinguins e entre os táxons representados. E. superba foi a presa de maior abundância comparado com outros itens alimentares, com aproximadamente 69% FO para P. papua e 98% FO para P. antarcticus. Foram encontradas nove espécies de peixe, seis espécies de crustáceos e uma espécie de cefalópode, identificados a nível específico. Existe uma diferença significativa entre os fatores, espécie de pinguim, tamanho da carapaça e sexo de krill antártico, quando comparados entre si. Além disso, a biometria indica que o comprimento do bico e peso de P. papua são maiores que em P. antarcticus, da mesma forma que o bico é mais alto e mais largo em P. antarcticus. Tais diferenças morfológicas podem explicar as diferenças no forrageio. Foi observada uma sobreposição de nicho trófico entre as espécies, pela utilização dos mesmos recursos, uma vez que estas espécies ocorrem simpatricamente na mesma região. Este estudo demonstra que a variação específica do nicho trófico ocupado pelas espécies pode ser definida pelo comportamento de forrageio e pela seleção dos recursos alimentares de cada espécie. É importante a recomendação destas espécies como indicadores de qualidade ambiental, adicionando questões como a variabilidade local, pois o nicho trófico pode alterar ao longo do tempo. / The two species realized niche needs to be different, since these species can coexist stably. Pygoscelis papua and P. antarcticus breed simpatricaly on Elephant Island, Antarctica. Stomach content samples were collected and biometrics of both species was measured in order to analyze the diet and the niche overlap. A total of 56 P. papua samples and 71 P. antarcticuss samples were collected, during the two austral breeding seasons, 2010/11 and 2011/12, on the Stinker Point region. The proportion of items ranged from the penguin species and among the taxa represented. E. superba was the most abundant prey compared with other food items, with approximately 69% FO for P. papua, and 98% FO for P. antarcticus. We found nine species of fish, six species of crustaceans and one species of cephalopod, identified by the specific level. There is a significant difference between the factors, species of penguin, carapace length and sex of antarctic krill, when compared with each other. In addition, the biometrics indicates that length of P. papua’s beak and weight are larger than P. antarcticus, but P. antarcticus has the highest and widest beak measures. Such morphological differences may explain differences in foraging. We observed a niche overlap of species, by the use of the same food resources, once these species occurs simpatricaly in the same region. This study also demonstrated that the specific variation of trophic niches occupied by the species may be defined by the foraging behavior and by the selection of the food resources. It is important the recommendation of these species as indicators of environmental quality, adding issues such as local variability since the trophic niche may change over the time.

Distintos padrões de composição de espécies de plantas podem ser observados ao longo de metacomunidades, pois espécies variam de acordo com os diferentes tipos de ambiente e também com a distância geográfica, dado o processo de dispersão. Ainda, estes mecanismos podem causar variação temporal na composição ou abundância de espécies em um sítio devido a alterações que estes mecanismos podem sofrer. Compreender como as mudanças na composição de espécies no espaço, definida como beta diversidade, ou no tempo estão relacionadas ao clima passado, atual ou futuro podem ajudar no planejamento de conservação de uma região. Assim, esta tese esta dividida em quatro capítulos e aborda questões relacionadas com mudanças espaçotemporais na composição de espécies sob uma perspectiva de planejamento de conservação e mudanças climáticas na Mata Atlântica. O primeiro capítulo apresenta um banco de dados com a informação de ocorrência de 1917 espécies de plantas arbóreas distribuídas em 206 comunidades na Mata Atlântica, em diferentes formações florestais (Floresta Atlântica stricto sensu (s.s.), Floresta com Araucária e Floresta Estacional). O segundo capítulo relacionou padrões de beta diversidade com a efetividade da rede de áreas protegidas nas formações florestais do sul da Mata Atlântica (Floresta Atlântica, Floresta com Araucária e Floresta Estacional). Encontramos altos valores de turnover e baixo aninhamento para todas as formações florestais, por isso recomendamos que esforços adicionais precisam almejar o aumento no número de áreas protegidas, especialmente para a Floresta com Araucária e a Floresta Estacional. A maioria das áreas protegidas no sul da Mata Atlântica estão concentradas na região leste, priorizando a Floresta Atlântica s.s. O terceiro capítulo trouxe novas perspectivas sobre a dinâmica da Floresta com Araucária no tempo através da modelagem de nicho ecológica. Durante as flutuações climáticas do Quaternário, estudos palinológicos indicavam uma expansão da Floresta com Araucária, porém nossos resultados demonstraram uma retração da área de cobertura desta floresta, principalmente nas zonas de contato com outras formações florestais. Também observamos que futuramente, se a temperatura continuar aumentando como previsto, a Floresta com Araucária sofrerá uma drástica redução na sua distribuição. Por fim, o capítulo quatro investigou como as espécies de árvores estão respondendo aos efeitos de mudanças climáticas em parcelas permanentes localizadas em ecótonos de florestas Atlânticas. Os resultados mostram que espécies tropicais estão migrando em direção a áreas de maior altitude, ou seja mais frias. Espécies tropicais que já ocorrem em áreas vi de Floresta com Araucária estão apresentando maiores taxas de recrutamento e crescimento, e menor mortalidade do que espécies temperadas, características da Floresta com Araucária. / Distinct patterns of plant species composition can be observed along metacommunities, as species vary in relation to different types of environment and also to the geographic distance, given the dispersal process. These mechanisms may yet lead temporal variation in species composition or abundance in a given place due to fluctuations on these mechanisms. Understanding how changes in species composition across the space, defined as beta diversity, or in time are related with past, current and future climate changes can help conservation planning in a given region. Thus, this thesis is divided into four chapters and discusses shifts in species composition across space and time under the perspective of conservation planning and climate changes in the Atlantic Forest. The first chapter shows a database with 1917 tree species occurrence distributed in 206 sites across distinct forest formations in the Atlantic Forest biome (Atlantic Rainforest, Araucaria Forest and Seasonal Forest). The second chapter related beta diversity patterns with the effectiveness of the current network of protected areas in southern Brazilian Atlantic forests (Atlantic Rainforest, Araucaria Forest and Seasonal Forest). We found high values of turnover and low nestedness for all forest formations, thus additional conservation efforts must target an increase in the number of protected areas, especially for the Araucaria Forest and the Seasonal Forest. Most protected areas are currently limited to the eastern region and prioritize the Atlantic Rainforest. The third chapter brought new insights about the Araucaria Forest dynamics in time through ecological niche models. During the climatic fluctuations of the Quaternary, palynological studies indicated an expansion of the Araucaria Forest, however our results demonstrated an overall retraction of the cover area, mainly in boundary zones with other forest formations. Yet, we showed that in the future, if the temperature continues to increase as expected, the Araucaria Forest would suffer a drastic reduction in its distribution. Finally, the fourth chapter investigated how tree species are responding to climatic changes in permanent plots located in Atlantic forests ecotones. Our results showed that tropical species are migrating towards to colder areas in higher altitudes. Tropical species that already occur in Araucaria Forest areas are even presenting higher rates of recruitment and growth, and lower mortality than temperate species characteristics from the Araucaria Forest.

Le premier objectif de ce travail de thèse était de déterminer quel est le degré de ségrégation écologique entre cinq espèces sympatriques de cétacés odontocètes (i.e. le dauphin commun Delphinus delphis, le marsouin commun Phocoena phocoena, le grand dauphin tursiops truncatus, le dauphin bleu et blanc Stenella coeruleoalba et le globicéphale noir Globicephala melas) fréquentant l’aire marine restreinte et très productive du Nord-Ouest de la Péninsule Ibérique (NOPI). Pour cela, des paramètres chimiques ont été analysés dans les tissus biologiques, en tant que “ méthode alternative ” pouvant refléter de façon précise le régime alimentaire et l’habitat de ces animaux à différents échelles de temps d’intégration, et ainsi compléter les informations apportées par des méthodes plus traditionnelles tels que l’analyse des contenus stomacaux ou des fèces, ou encore les données d’observations en mer. Le second objectif de ce travail était d’évaluer l’état de contamination de ces espèces, pour acquérir une base de données de référence complète les concernant et estimer le risque toxicologique auquel elles peuvent faire face. Dans ce contexte, les éléments traces, les isotopes stables du carbone et de l’azote, et les polluants organiques persistants (POPs) sont les paramètres chimiques qui ont été sélectionnés pour répondre aux objectifs fixés.Dans un premier temps, les paramètres chimiques ont été utilisés comme traceurs écologiques des populations (ou de segments de population), procurant une image du régime alimentaire et de l’habitat des espèces à différentes échelles de temps. Nous avons calculé que le réseau trophique du NOPI avait cinq niveaux trophiques, au sein duquel les espèces étudiées occupaient les plus hautes positions, comprises entre 4,3 à 5,3, et sans qu’il y ait de différence significative de position trophiques entre les espèces. Alors que l’analyse d’un seul paramètre chimique ne permettait pas ségréger les cinq espèces, les informations apportées par l’analyse de plusieurs traceurs de long terme (i.e. rapport des isotopes stables du carbone et de l’azote dans les dents et concentrations de cadmium dans les reins) ont révélé une ségrégation de leur niche écologique dans deux des dimensions possibles (les dimensions trophique et spatiale). Cependant, les variations pouvant survenir d’une année sur l’autre ou saisonnières n’ont pas pu être étudiées, excepté pour le dauphin commun, et un chevauchement temporaire des niches ne peut donc pas être totalement exclu. De plus, nous avons montré que les profils de polychlorobiphényles (PCBs) pouvaient être un traceur pertinent de l’écologie trophique d’espèces taxinomiquement proches, en permettant une séparation fine des espèces telles que le marsouin commun et le dauphin bleu et blanc, d’après les différents profiles d’accumulation de ces deux espèces.Dans un second temps, l’état de contamination des espèces dans la zone d’étude a été évalué. Les concentrations ont été interprétées à la lumière des facteurs biologiques et écologiques pouvant influencer ces concentrations, et la bioaccumulation des éléments traces s’est révélée moins prévisible que celle des POPs. Le grand dauphin et le marsouin commun présentaient les concentrations de PCBs les plus élevées par rapport aux autres cétacés odontocètes du NOPI et par rapport à d’autres individus des eaux adjacentes de l’Atlantique Nord-Est.Les résultats principaux de ce travail de thèse ont mis en évidence la pertinence d’utiliser ces paramètres chimiques comme traceurs écologiques, et leur utilité dans la compréhension de la structure et le fonctionnement des écosystèmes à travers le rôle des prédateurs supérieurs. En combinant ces résultats à des informations concernant les activités anthropiques, ce travail peut contribuer au développement et à l’implémentation de mesures de gestion pour ces cinq espèces de cétacés odontocètes du NOPI. / The first objective of this PhD was to determine the degree of ecological segregation between five sympatric species of toothed whales (i.e. common dolphin Delphinus delphis, harbour porpoise Phocoena phocoena, bottlenose dolphin Tursiops truncatus, striped dolphin Stenella coeruleoalba and long finned pilot whale Globicephala melas) inhabiting a restricted and highly productive area, the North West Iberian Peninsula (NWIP). To this end, chemical parameters analyses were used as an “alternative method” of assessing diet and habitat of these animals over different periods of integration, complementing the information given by traditional methods of investigation such as stomach contents, faeces analyses and field observations. The second objective was to evaluate the contamination status of these species in order to estimate the toxicological risk these populations face and to complete the existing database. In this context, trace elements, carbon and nitrogen stable isotopes, as well as persistent organic pollutants (POPs) were selected as chemical parameters for our investigations.Firstly, the chemical parameters were used as ecological tracers of populations (or parts of populations) by drawing an image of the diet and habitat of the species at different time scales. We estimated that the food web has five trophic levels, with toothed whales occupying the top positions, with no significant difference in trophic positions among them, ranging from 4.3 to 5.3. While the analysis of a single chemical parameter did not completely segregate between the five species, the information gained by combining the analyses of several long-term ecological tracers (i.e. nitrogen and carbon stable isotopes in teeth and renal cadmium concentrations) revealed ecological niche segregation in two dimensions of this niche (the trophic and the spatial dimensions). However, year-to-year or seasonal variations could not be investigated, except for in common dolphin, and thus temporary overlap cannot be excluded. Additionally, we showed that polychlorinated biphenyls (PCBs) profiles could be a relevant tracer of the foraging ecology of taxonomically close species, allowing a fine separation of the species as result of their different patterns. This was particularly clear for the harbour porpoise and striped dolphin.Secondly, the contamination status of the species in this area was evaluated, with concentrations interpreted in the light of biological and ecological factors. But the bioaccumulation of trace elements appeared to be less predictable than that of POPs. Bottlenose dolphins and harbour porpoises were found to have higher PCBs concentrations than the rest of the analysed NWIP toothed whales, as well as those of adjacent NE Atlantic waters.The main results of this PhD highlight the relevance of exploiting these chemical parameters as ecological tracers, as well as their usefulness in the comprehensive study of structure and function of ecosystems through the role of top predators. Combined with the information on anthropogenic activities, this work can also contribute to the development and implementation of management plans and mitigation measures for these five species of toothed whales in the NWIP.

Kakapo (Strigops habroptilus) are a flightless, nocturnal parrot endemic to New Zealand. Thought to be extinct within their natural range, kakapo are currently listed as nationally critical. The current population of 86 individuals is managed by the Department of Conservation’s National Kakapo Team on two offshore islands in southern New Zealand, with all females of breeding age on Codfish Island (Whenua Hou). Kakapo only breed once every two to five years, coinciding with the mast fruiting of specific plant species. On Codfish Island, the proportion of adult female kakapo that breed in rimu (Dacrydium cupressinum) fruiting years is dependent on the quantity of fruit produced, with fewer females attempting to breed during low mast years. The purpose of this research is to investigate why only some adult female kakapo breed in low rimu fruiting years on Codfish Island, specifically assessing if foraging home range size and/or habitat selection influence breeding. A total of 506 location points were collected at night for 18 adult female kakapo between March and May 2006. These were used to estimate foraging home ranges and to assess if kakapo select for particular types of vegetation. Ecological Niche Factor Analysis was used to determine the relative importance of habitat variables in the distribution of female kakapo and to predict areas of suitable breeding habitat when rimu fruit is limited. The breeding success of individuals in 2005, a low rimu mast year, was used to identify if differences in home ranges or habitat selection occurred between breeding and non-breeding females. The large variation in foraging home range sizes recorded in this research was consistent with previous studies. Foraging home range sizes were on average twice the size for breeders than for non-breeders, suggesting that adult female kakapo may be limited in their ability to breed by the size of the area they occupy. Adult female kakapo did not randomly use vegetation on Codfish Island as some vegetation types were not used, while others were common inside foraging home ranges. Adult female kakapo utilise a broad niche and are capable of surviving in a wide range of habitats. However, breeding females were more specialised in their niche requirements than non-breeders, with breeders utilising areas with higher abundances of mature rimu trees. Females occurred in high elevation, flat areas of the island but this may have been because this is where appropriate vegetation types occurred. During low rimu mast years, breeding adult females were predicted to occupy habitat in high elevation, plateau areas with a high abundance of rimu. Areas identified as sub-optimal habitat for breeding included the coastal areas, the lower elevation area of the main valley and some ridgelines. The home ranges of all 10 breeding females contained some optimal habitat, while females who did not breed were more likely to be located in sub-optimal habitat. Although there were significant areas of optimal breeding habitat not occupied by adult female kakapo, other kakapo may have been present in these areas. To increase the proportion of females that breed in low rimu mast years, it may be necessary to remove sub-adult females or surplus adult males living in optimal breeding habitat from the island. Alternatively, females in sub-optimal breeding habitat could be fed supplementary foods or transferred to other islands where there is unoccupied suitable breeding habitat available.