A andiroba (Carapa guianensis) é uma espécie arbórea de importância econômica na região Amazônica pelo grande interesse que vem despertando nas indústrias madeireira e cosmética. É uma planta monóica, com floração assincrônica e auto-incompatível. Ela é bastante plástica e se adapta para ocupar diferentes ambientes, sendo encontrada tanto no baixio como na terra firme. Os objetivos do presente estudo foram avaliar a estrutura genética de duas populações naturais de andiroba e quantificar a diversidade genética intrapopulacional, a autocorrelação espacial e o fluxo gênico analisando uma única população em dois ambientes distintos (terra firme e baixio) e em três classes de tamanho (plântulas, jovens e adultos). Para o estudo interpopulacional, foram avaliados 39 indivíduos adultos no município de Porto Acre e 38 em Rio Branco. Já para o intrapopulacional analisaram-se 957 indivíduos do município de Rio Branco. Foram utilizados sete locos polimórficos de microssatélites que permitiram observar 42 alelos em ambas as populações, sendo que as estimativas dos parâmetros genéticos foram muito próximas entre elas. Não foi observada endogamia e a taxa de cruzamento aparente foi alta indicando reprodução por alogamia. A maior parte da variabilidade genética (90,5%) foi encontrada dentro das populações. No entanto, a divergência genética entre as populações (9,5%) foi estatisticamente significativa e pode ser considerada intermediária. Com relação à variabilidade intrapopulacional, observou-se 85 alelos na população Rio Branco, com 67 alelos ocorrendo no ambiente de terra firme e 70 no baixio. A diversidade gênica foi semelhante nas três classes de tamanho na população total e nos dois ambientes, não tendo sido observada endogamia em nenhuma das classes de tamanho dos ambientes. Também não foi observada divergência genética entre as classes de tamanho. Já entre os indivíduos do ambiente de terra firme e os do baixio esta divergência foi baixa (1,63%), mas significativa. A taxa de cruzamento aparente foi alta tanto para os ambientes como para a população total. As analises de autocorrelação espacial dos genótipos revelaram que a população Rio Branco apresentou baixa estruturação espacial, sendo que as árvores localizadas a uma distância de até aproximadamente 370 metros tenderam a ser geneticamente similares. No ambiente de baixio encontrouse este mesmo padrão, com árvores localizadas a uma distância de até 160 metros mostrando-se mais aparentadas entre si. Quando se observou separadamente cada classe de tamanho neste ambiente, verificou-se baixa estruturação na classe dos jovens, e uma disposição quase que aleatória dos genótipos na classe dos adultos. Na terra firme não se observou estruturação espacial dos genótipos em nenhuma das classes. As analises de parentesco das plântulas indicaram que 7,3% dos parentais paternos foram encontrados no ambiente de terra firme e 9,4% no baixio. Este baixo índice encontrado mostra que é grande a quantidade de fluxo gênico vindo de fora da área amostrada. Verificou-se fluxo gênico de longo alcance dentro da população, observando-se uma distância média de até 888,8 metros entre os ambientes. Com base nos conhecimentos gerados sobre a estrutura genética, podem-se estabelecer estratégias de manejo e conservação dessas populações naturais de andiroba. / Crabwood (Carapa guianensis) is a tree of economic importance in the Amazon region, due to the great interest it has been attracting in the wood and cosmetics industries. It is a monoecious species, with asynchronic flowering and self-incompatible. This species is very plastic and adapts to occupy different habitats, and it is found in the lowland and upland habitats. The objectives of this study were to evaluate the genetic structure between two natural populations of crabwood, and to quantify the intrapopulational genetic diversity, the spatial autocorrelation and gene flow of one population, considering two habitats (upland and lowland) and three size classes (seedlings, young plants and adults). For the interpopulational study, 39 adult individuals were evaluated in the municipal district of Porto Acre and 38 in Rio Branco. For the intrapopulational studies, 957 individuals were analyzed in the municipal district of Rio Branco. Seven polymorphic microssatellite loci were used to detect 42 alleles in both populations, were the genetic parameter estimates were very similar to each other. Inbreeding was not observed and the apparent outcrossing rate was high, indicating an outcrossing breeding system for this species. Most of the genetic variability (90.5%) was found to be within populations. However, the genetic divergence between them (9.5%) was statistically significant and can be considered as intermediate. Regarding the intrapopulacional variability, 85 alleles were observed in the Rio Branco population, with 67 alleles occurring in the upland habitat and 70 in the lowland. The genetic diversity was similar in the three size classes in the total population, and in the two habitats. No inbreeding was observed in any of the size classes of either habitat. No genetic divergence was observed between size classes as well. Between individuals of the upland habitat and those of the lowland habitat, this divergence was low (1.63%), but significant. The autocorrelation spatial analysis of the genotypes showed that the Rio Branco population presented low spatial genetic structuring, with the trees located at a distance of approximately 370 meters tending to be genetically similar. In the lowland habitat the same pattern was found, with trees located at a distance of 160 meters tending to be more related between themselves. When each size class of this habitat was observed separately, a low spatial genetic structuring was found in the young classes and an almost random disposal of the genotypes was observed in the adult classes. In the upland habitat, a spatial genetic structure of the genotypes was not observed in any of the size classes. The paternity analysis of the seedlings indicated that 7.3% of the male parents were found in the upland habitat and 9.4% in the lowland. This low index shows that the amount of gene flow coming from outside the sampling area is high. Long-distance gene flow within the population studied was observed, with an average distance of 888.8 m found between habitats. Based in the acquired knowledge on the genetic structure, management and conservation strategies can be established for these natural crabwood populations.

As Unidades de Conservação (UCs) foram criadas para proteger e manter os remanescentes de ecossistemas naturais a fim de reduzir a perda da biodiversidade e garantir sua manutenção em longo prazo. Atualmente, muitas UCs se encontram na forma de pequenos fragmentos isolados e sob forte pressão antrópica, exigindo um manejo na forma de uma rede de fragmentos, visando reduzir as pressões das atividades do entorno. O presente trabalho teve como objetivo gerar subsídios para a criação de uma zona de amortecimento (ZA) comum para o Parque Estadual de Vassununga e para a Estação Ecológica de Jataí, visando reduzir as pressões antrópicas sobre as UCs e facilitar o fluxo biológico entre os fragmentos. Foi realizado o mapeamento da paisagem para identificar as principais formas de uso, as fontes de impactos ambientais e verificar o cumprimento da legislação de áreas de preservação permanente. Foram utilizadas métricas de paisagens para analisar a configuração espacial dos remanescentes de vegetação arbórea e selecionar fragmentos importantes para a facilitação do fluxo biológico. Foram utilizados modelos de previsão de riqueza e probabilidade de ocorrência de espécies-alvo de aves para selecionar áreas potencialmente importantes para a manutenção da biodiversidade. A paisagem da área de estudo apresenta menos de 30% de remanescentes de vegetação natural, distribuídos em pequenos fragmentos, imersos em uma matriz de cana-de-açúcar e eucalipto. O desrespeito à legislação e numerosas fontes de impacto ambiental contribuem para aumentar a pressão sobre os recursos naturais. O incremento da conectividade dos fragmentos, principalmente com a restauração das florestas ribeirinhas mostrou ser uma estratégia importante para restabelecer a conectividade funcional entre as UCs e entre os remanescentes da paisagem. Na região existem fragmentos com potencial para facilitar os fluxos biológicos, atuando como uma rede de fragmentos, e auxiliar na manutenção da biodiversidade. Porém, grande parte deles está localizada no interior de propriedades particulares, exigindo esforços para conscientização dos proprietários para proteção e incremento da conectividade destes fragmentos. / Natural reserves have been created to protect and maintain natural ecosystems remnants in order to reduce biodiversity loss and to ensure their maintenance in the long run. Nowadays, most of these reserves are small and isolated fragments under anthropogenic pressure. Such small remnants must be managed and protected as a fragment network to reduce the human pressure and to promote biological fluxes among fragments. This study aimed at producing information to help on the process of designing a common buffer zone for three public natural reserves: Vassununga State Park, Jataí Ecological Station and Luís Antônio Experimental Station. An up to date land cover/land use map was generated to identify the main activities and sources of anthropogenic impacts in the study area, their possible consequences to the environment, and also if and how much the environmental legislation is being followed. To select the most important natural fragments which could facilitate biological fluxes and maintain the regional biodiversity, two approaches were used: analysis of the spatial arrangement of the fragments in the landscape applying landscape metrics, and the use of models to predict bird species richness and occurrence. The studied area presently has less than 30% of remnant natural vegetation, spread as small fragments in a sugar cane and eucalyptus matrix. Environmental legislation is not being obeyed and, together with several sources of impact, produce negative pressures on the natural resources. The restoration of riparian forests would be a good strategy to reestablish the landscape functional connectivity. Fragments able to facilitate biological fluxes and to maintain biological diversity still exist in the region, but a great deal of them are located in private properties. Therefore, efforts to warn and educate the owners are needed to increase the landscape connectivity and to conserve the regional biodiversity.

Por meio do processo conhecido como bioprospecção, propõe-se a aplicação dos lucros obtidos com a comercialização de produtos, como fármacos, em ações para conservação biológica. O objetivo deste trabalho é verificar a importância deste instrumento para a conservação a partir de estudo de caso focado na experiência do Instituto Nacional de Biodiversidade (INBio), na Costa Rica. Os procedimentos metodológicos estão baseados nas estratégias de pesquisa de: a) estudo de caso; b) documental e c) pesquisa bibliográfica. O INBio, uma associação sem fins lucrativos, se empenhou na elaboração do inventário nacional da biodiversidade e firmou diversos contratos de bioprospecção, entre eles o comentado acordo com a indústria farmacêutica Merck. Alguns pontos positivos devem ser destacados a partir dessa experiência: geração de conhecimento sobre os recursos biológicos locais em função do inventário; criação de sistema de controle ao acesso e identificação dos materiais coletados; o aparato jurídico desenvolvido; aprimoramento da capacidade de negociação; disseminação de informação em publicações científicas; atividades voltadas à Educação Ambiental e apoio a pequenas e médias empresas nacionais no desenvolvimento de produtos baseados em recursos biológicos do país. Por outro lado, os dados analisados mostram que tem sido baixo o retorno financeiro do Instituto; os pagamentos não têm sido suficientes para cobrir os gastos. Esta questão está ligada ao fato de que, ainda que tenha começado o recebimento pela comercialização de alguns produtos desenvolvidos internamente, ainda não há produtos desenvolvidos resultantes de contratos com grandes companhias e, portanto, ainda não foram correspondidas as expectativas com relação ao recebimento de royalties. Há deficiência com relação ao controle administrativo dessas atividades por parte do Estado, o que reflete na falta de transparência das fontes disponíveis de informações. A análise dos recursos financeiros obtidos versus repasse de verbas para fins de conservação fica comprometida em razão de informações incompletas ou pela falta de padronização na apresentação dos dados no decorrer dos anos. O desmatamento tem apresentado queda contínua, mas não é possível relacionar este fato com os contratos de bioprospecção, devido ao sistema variado de fontes de contribuições e pagamentos por serviços destinados à conservação biológica naquele país. Ademais, os conhecimentos tradicionais das populações locais estão sendo ignoradas em todo esse processo conduzido pelo INBio. Portanto, até o momento, o que acontece na Costa Rica está mais próximo de representar uma evolução no sentido de empreender medidas em direção ao uso e conservação dos recursos biológicos, porém ainda não representa a solução ou ajuda significativa à conservação biológica naquele país. / Using the process known as bioprospecting, it is proposed the use of the profits obtained with the commercialization of products, such as pharmaceuticals, in biological conservation activities. The objective of this work is to verify the importance of this instrument for conservation, by means of a case study focused in the experience of the National Biodiversity Institute (Instituto Nacional de Biodiversidade) (INBio), in Costa Rica. The methodology is based in the strategies of researching: a) case study; b) documents and c) bibliography research. The National Biodiversity Institute (INBio), a non-profit association which has endeavored to elaborate a national biodiversity inventory and signed various bioprospecting contracts, among them the renowned agreement with Merck pharmaceutical company. Some positive points should be emphasized from this experience: generation of knowledge about local biological resources through inventory; creation of a control system for accessing and identifying the collected materials; the development of a legal apparatus; the improvement of negotiation skills; the dissemination of information through scientific publications, activities oriented to Environmental Education and supporting national small and medium firms in the development of products based on the country\'s biological resources. On the other hand, the data analyzed show low financial return, in spite of the fact that the income for the commercialization of some internally-developed products has begun. Payments have not been enough to cover the Institute\'s expenditures and there are still no developed products resulting from contracts with big companies and, therefore, the expectations relative to the receiving of royalties were still not fulfilled. There is a deficiency relative to the administrative control of these activities by the State, which reflects the lack of transparency of the available sources of information. The analysis of the obtained resources versus the transfer of funds for conservation is jeopardized due to incomplete information or lack of standardization in the presentation of data through the years. Deforestation has declined continuously, but it is impossible to relate this fact to the bioprospecting contracts, due to the diverse system of contribution and payment sources for services destined to the conservation of that country\'s natural resources. Besides, the traditional knowledge of the local population has been ignored in the entire process conducted by INBio. Therefore, for the moment, what happens in Costa Rica is closer to represent an evolution in the sense of taking steps in the direction of using and conserving biological resources, but it still does not represent the solution or significant aid to the biological conservation in Costa Rica.

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

It has been more than two centuries since the latitudinal pattern of increase in taxonomic richness from poles to equator was first documented. After two centuries of research, and with more than two dozen hypotheses proposed, an understanding of the mechanisms underlying this pattern and their relative importance remains incomplete. Factors such as evolutionary history, area and latitude associated variables such as temperature, solar energy, climatic stability and seasonality are known to influence species richness by affecting geographic range size and location over ecological and evolutionary time. Understanding the forces that affect geographic range size is, therefore, integral to our understanding of latitudinal patterns in species richness. Using woody plants as a study system, my dissertation deciphers the latitudinal pattern, if any, in species richness within the evergreen forests of the Western Ghats. These wet evergreen forests form an evolutionarily distinct biogeographic zone, which has remained isolated from its counterparts. This has resulted in a high percentage of endemism among the evergreen woody plants and, therefore, the global geographic ranges of most of these plants are restricted within the boundaries of the Western Ghats. The first main objective of this dissertation is to understand the determinants of geographic range size in the evergreen woody plants of the Western Ghats. Further, the Western Ghats are characterized by a sharp climatic gradient in temperature and rainfall seasonality that is not correlated with mean annual temperature or annual rainfall. This allows a direct test of the hypotheses and predictions that are based on climatic seasonality, without the confounding effect of other climatic correlates of latitude. Therefore, the second main objective of this dissertation is to understand the mechanisms underlying latitudinal patterns in species richness of evergreen woody plants in the Western Ghats. Regional species richness is an outcome of two factors- local species richness of each location within the region and turnover in species composition among the locations, which in turn are a result of patterns in range size, range location and range overlap. To address these two objectives, I first test the effect of climatic niche of a species in determining geographic range size and then examine the effect of latitude associated climatic seasonality on range location and range overlap. Next, I link the observed pattern in range geometry to latitudinal patterns in species turnover and finally to latitudinal patterns in species richness. While the first part of my dissertation study deals with factors that generate spatial variation in species richness, the second part deals with the factors underlying spatial variation in species composition. Environmental heterogeneity and dispersal are considered the most important determinants of species turnover i.e. change in species composition. However, their relative importance in structuring in diverse plant communities within tropical regions across different scales is poorly understood. Hence, the third objective of this dissertation is to understand the processes that influence change in species composition of woody plants within the Western Ghats. Geographic range size and population size are important attributes of species rarity, which are directly linked to their extinction risk. Hence, data on distribution and population status of species can help us focus our efforts on those species that require conservation attention. This is achieved through carrying out species threat assessments based on attributes such as range and population size and then assigning then to a threat category. A majority of species endemic to the Western Ghats have not yet been assessed, largely due to lack of data on their population and distribution status. Therefore, the fourth and the final part of my dissertation explores the application of information on species range size and abundance in prioritizing species for conservation. To address these objectives, I sampled the wet evergreen forests of the Western Ghats along a series of locations distributed across its entire latitudinal gradient. Based on 156 plots, covering a latitudinal gradient of more than 1200 km and comprising of more than 20,000 occurrence locations belonging to more than 450 species of woody plants, I derived quantitative estimates of latitudinal gradients in range size, local and regional richness as well as species turnover. I used a combination of statistical and simulation approaches to discern the mechanisms underlying large-scale pattern in species ranges, richness and turnover. My dissertation is structured as follows.

Ce travail de thèse s'insère dans une démarche globale d'acquisition des connaissances sur la tortue verte (Chelonia mydas) dans l'océan Indien occidental et ce afin de disposer d'éléments scientifiques essentiels à la mise en place d'une gestion cohérente et efficace de cette espèce menacée. Dans un premier temps, appliquant différentes modèles statistiques, ce travail a visé à établir des données de référence sur l'abondance des tortues vertes femelles en reproduction et les tendances sur le long terme des principales populations. Dans un second temps, il a consisté à déterminer la structure génétique et les relations qui existent entre les différentes populations de cette espèce. Enfin, la conservation des tortues marines étant étroitement liée aux pressions extérieures, ce travail a tenté dans un troisième temps de caractériser les pressions anthropiques qu'elles subissent, et notamment celles liées à la pêche. L'ensemble de ces résultats a permis de réaliser des avancées majeures dans la connaissance de la biologie et de l'écologie de la tortue verte et de disposer d'une vision régionale fiable de l'état de conservation de cette espèce dans l'océan Indien occidental. Leur compilation a ainsi permis d'identifier des zones régionales prioritaires de protection mais aussi des sites de vigilance plus spécifiques comme celui d'Europa. Enfin cette synthèse met en lumière les priorités de recherche et les approches scientifiques à favoriser à l'avenir pour améliorer les connaissances et affiner les priorités de conservation non seulement des tortues marines, mais aussi de la mégafaune marine en général. / This thesis is a comprehensive work aiming to improve scientific knowledge on the green turtle (Chelonia mydas) in order to provide key scientific evidences needed for the implementation of coherent and effective management measures to protect at the Western Indian Ocean scale this threatened species. In a first step, this work aimed to established baseline data on the abundance of green turtles nesting females and long term trends of some key nesting populations of the region by applying different modelling methods. In a second step, this work determined the regional genetic structure of this species and the relationships that exists between the different populations. Finally, the conservation of marine turtles being closely dependant to external pressures, this work tried to characterize theanthropogenic pressures they face, more specifically those related to fishing activities. All these results allowed unraveling some key gaps on the biology and ecology of the green turtle in the region and led to a global vision of the conservation status of this species in the Western Indian Ocean. The compilation of the results enabled the identification of regional priority areas for protection, but also some more specific threatened sites such as Europa. Finally, this synthesis shedslight on research priorities and scientific approaches to be promote in the future to unlock other keyscientific issues and refine conservation priorities, not only of marine turtles, but also of marine megafauna as a whole.