Distributional ecology is a branch of ecology which aims to reconstruct and predict the geographic range of free-living and symbiotic organisms in terrestrial and aquatic ecosystems. More recently, distributional ecology has been used to map disease transmission risk. The implementation of distributional ecology for disease transmission has, however, been erroneous in many cases. The inaccurate representation of disease distribution is detrimental to effective control and prevention. Furthermore, ecological niche modeling experiments are generally developed and tested using data from terrestrial organisms, neglecting aquatic organisms in case studies. Both disease and aquatic systems are often data limited, and current modeling methods are often insufficient. There is, therefore, a need to develop data-driven models that perform accurately even when only limited amounts of data are available or when there is little to no knowledge of the species' natural history to be modeled. Here, I propose a data-driven ecological niche modeling method that requires presence-only data (i.e., absence, pseudoabsence, or background records are not needed for model calibration). My method is expected to reconstruct environmental conditions where data-limited aquatic organisms are more likely to be present, based on a density-based clustering algorithm as a proxy of the realized niche (i.e., abiotic, and biotic environmental conditions occupied by the organism). Supported by ecological theories and methods, my central hypothesis is that because density-based clustering machine-learning modeling prevents extrapolation and interpolation, it can robustly reconstruct the realized niche of a data-limited aquatic organism. First, I assembled a comprehensive dataset of abiotic (temperature) and biotic (phytoplankton) environmental conditions and presence reports using Vibrio cholerae, a well-understood aquatic bacterium species in coastal waters globally (Chapter 2). Second, using V. cholerae as a model system, I developed detailed parameterizations of density-based clustering models to determine the parameter values with the best capacities to reconstruct and predict the species' distribution in global seawaters (Chapter 3). Finally, I compared the performance of density-based clustering modeling against traditional, correlative machine-learning ecological niche modeling methods (Chapter 4). Density-based clustering models, when assessed based on model fit and prediction, had comparable performance to traditional 'data-hungry' machine-learning correlative methods used in modern applications of ecological niche modeling. Modeling the environmental and geographic ranges of V. cholerae, an aquatic organism of free-living and parasitic ecologies, is a novel approach itself in distributional ecology. Ecological niche modeling applications to pathogens, such as V. cholerae, provide an opportunity to further the knowledge of directly-transmitted emerging diseases for which only limited data are available. Density-based clustering ecological niche modeling is termed here as Marble, honoring a previous, experimental version of this analytical approach, and is expected to provide new opportunities to understand how an ecological niche modeling method influences estimates of the distribution of data-limited organisms of complex ecology. These are lessons applicable to novel, rare, and cryptic aquatic organisms, such as emerging diseases, endangered fishes, and elusive aquatic species. / Master of Science / Distributional ecology is a branch of ecology which aims to reconstruct and predict the geographic distribution of land and water organisms. In the case of diseases, a correct representation of their geographic distributions is key for successful management. Previous studies highlight the need to develop new models that perform accurately even when limited amounts of data are available and there is little to no knowledge of the organisms' ecology. This thesis proposes a data-driven method, originally termed Marble. Marble is expected to help reconstruct environmental conditions where data-limited aquatic organisms are more likely to be found. Supported by ecological theories and methods, my hypothesis is that because Marble prevents under- and over-fitting, this method will produce results which better fit the data. Using V. cholerae, an aquatic organism, as a model system, I compared the performance of Marble against other traditional modeling algorithms. I found that Marble, in terms of model fit, performed similarly to traditional methods used in distributional ecology. Modeling the ecology of V. cholerae is a new approach in and of itself in ecological modeling. Furthermore, modeling pathogens provides an opportunity to further the knowledge of directly transmitted diseases, and Marble is expected to provide opportunities to understand how algorithm selection can reconstruct (or not) the distribution of data-limited aquatic organisms of diverse ecologies.

I compared the performance of habitat models created from data of differing reliability. Because the reliability is dependent on the probability of detecting the species, I experimented to estimate detectability for a salamander species. Based on these estimates, I investigated the sensitivity of habitat models to varying detectability. Models were created using a database of amphibian and reptile observations at Fort A.P. Hill, Virginia, USA. Performance was compared among modeling methods, taxa, life histories, and sample sizes. Model performance was poor for all methods and species, except for the carpenter frog (Rana virgatipes). Discriminant function analysis and ecological niche factor analysis (ENFA) predicted presence better than logistic regression and Bayesian logistic regression models. Database collections of observations have limited value as input for modeling because of the lack of absence data. Without knowledge of detectability, it is unknown whether non-detection represents absence. To estimate detectability, I experimented with red-backed salamanders (Plethodon cinereus) using daytime, cover-object searches and nighttime, visual surveys. Salamanders were maintained in enclosures (n = 124) assigned to four treatments, daytime__low density, daytime__high density, nighttime__low density, and nighttime__high density. Multiple observations of each enclosure were made. Detectability was higher using daytime, cover-object searches (64%) than nighttime, visual surveys (20%). Detection was also higher in high-density (49%) versus low-density enclosures (35%). Because of variation in detectability, I tested model sensitivity to the probability of detection. A simulated distribution was created using functions relating habitat suitability to environmental variables from a landscape. Surveys were replicated by randomly selecting locations (n = 50, 100, 200, or 500) and determining whether the species was observed, based on the probability of detection (p = 40%, 60%, 80%, or 100%). Bayesian logistic regression and ENFA models were created for each sample. When detection was 80 __ 100%, Bayesian predictions were more correlated with the known suitability and identified presence more accurately than ENFA. Probability of detection was variable among sampling methods and effort. Models created from presence/absence data were sensitive to the probability of detection in the input data. This stresses the importance of quantifying detectability and using presence-only modeling methods when detectability is low. If planning for sampling as an input for suitability modeling, it is important to choose sampling methods to ensure that detection is 80% or higher. / Ph. D.

En Afrique de l'Ouest, le moustique An. gambiae s.s vecteur majeur du paludisme est subdivisé en deux formes moléculaires, M et S, génétiquement et écologiquement différenciées. La forme moléculaire M se développe préférentiellement dans des collections d'eau pérennes en zone aride, généralement d'origine anthropique, permettant sa présence tout au long de l'année alors que la forme S se reproduit principalement dans des gîtes temporaires de savane humide dépendant des précipitations et disparaît en saison sèche. Cette subdivision génère des profils de dynamique de transmission palustre différents en fonction des zones où ces formes sont implantées. Dans ce contexte, cette thèse a pour objectif l'étude des facteurs écologiques de différenciation entre M et S, en se focalisant notamment sur leur écologie larvaire, afin de mieux appréhender leur distribution actuelle et future. L'étude de la distribution des populations naturelles de ces vecteurs dans une zone d'endémie palustre au Burkina Faso a permis de mettre en évidence que les niches écologiques de ces deux formes sont en étroite corrélation avec la temporalité des milieux aquatiques et la complexité des écosystèmes qu'ils hébergent. La forme M apparaît clairement liée aux habitats permanents anthropiques et à la structure des communautés qu'ils soutiennent alors que la forme S ainsi que l'espèce jumelle An. arabiensis sont associées aux habitats simples et temporaires, majoritairement retrouvés en zone rurale de savane.Cette distribution des deux formes le long d'un gradient d'hydropériode est en accord avec les interactions dominantes et les adaptations qu'elles induisent afin de pouvoir exploiter ces milieux. La forme S, associée aux milieux temporaires, s'est révélée plus compétitive que la forme M en diminuant son temps de développement larvaire en présence de compétiteurs (forme M). L'étude de la pression de sélection due à la prédation, interaction dominante dans les milieux permanents, démontre que la forme M est moins susceptible que la forme S. L'analyse du comportement larvaire a permis de mettre en évidence des différences entre ces deux formes, notamment l'existence d'un comportement plus plastique chez la forme M qui réduit son activité en présence d'un prédateur. Ce mécanisme est une des adaptations qui a favorisé le succès d'An.gambiae dans les milieux permanents.Notre approche, basée sur l'écologie larvaire des formes M et S d'An. gambiae nous a permis de mieux comprendre les processus par lesquels ces vecteurs ont évolué et se sont adaptés à différents contextes écologiques. Ces adaptations reflètent la spécialisation de ces deux formes dans leur milieu respectif et permettent en partie d'expliquer la ségrégation écologique observée sur le terrain. L'amélioration de nos connaissance sur la bio-écologie de ces vecteurs est primordiale afin d'en apprécier le potentiel évolutif dans le contexte actuel des changements globaux. / In West Africa, the main Malaria vector, the mosquito Anopheles gambiae is actually subdivided into two molecular forms named M and S, which can be genetically and environmentally differentiated. The M form preferentially breeds in permanent freshwater collections mainly resulting from human activity and is reproductively active all year round, whereas the S form thrives in temporary breeding sites and is present during the rainy season only. This subdivision generates different dynamics of Malaria transmission in areas where these forms are found. In this context, this thesis aims to study the ecological factors of differentiation between M and S, focusing on their larval ecology to better understand their current and future distribution.The study of the distribution of natural populations of these vectors in an endemic area in Burkina Faso has provided evidence that the ecological niches of these forms are closely correlated with the degree of temporality and the community complexity of aquatic ecosystems. The M form is clearly linked to permanent anthropogenic habitats and the structures they support, while the S form and its sibling species An. arabiensis are associated with simple and temporary habitats, mostly found in rural savannas.The distribution of the two forms along a hydroperiod gradient is consistent with the dominant interactions and adaptations they induce in order to be able to exploit their environments. In relation to temporary habitat, the S form was more competitive than the M form by reducing its larval development time in the presence of competitor (M form). The study of selection pressure due to predation, dominant interaction in permanent habitat, shows that the M forms suffer lesser predation rate than the S form. Analysis of larval behavior highlighted differences between these two forms, such as the existence of a more plastic behavior in the form M, which reduced its rate of activity in predator presence. This mechanism is one of the adaptations that have facilitated the success of An. gambiae in permanent aquatic habitats.Our approach, based on the larval ecology of M and S forms of An. gambiae has enabled us to better understand the processes by which these vectors have evolved and adapted to different ecological contexts. These adaptations reflect the specialization of these two forms in their respective habitats and can partially explain the ecological segregation observed in the field. Improving our knowledge on bio-ecology of these vectors is essential to appreciate their evolutionary potential in the current context of global change.

Drosophila buzzatii é uma espécie cactófila associada a diferentes espécies de cactos e distribuída nos diferentes Domínios fitogeográficos da América do Sul. Baseado na diversidade de inversões cromossômicas e densidade populacional, o Chaco foi considerado por alguns autores como o centro de origem da espécie. Entretanto, trabalhos recentes, utilizando aloenzimas e DNA mitocondrial, apontaram para uma possível origem na Caatinga. Os objetivos deste trabalho foram delinear rotas de dispersão da espécie para explicar sua distribuição atual e possível distribuição durante o último período glacial, na América do Sul. Foram obtidas seqüências de 714 pb da COI do mtDNA de 132 indivíduos em 44 localidades, gerando 36 haplótipos. Foram calculados os índices de diversidade nucleotídica, o teste AMOVA, testes de neutralidade, a Mismatch Distribution, Baesyan Skyline Plot, NCPA e o sentido dos movimentos migratórios (Migrate N) a fim de determinar parte da história evolutiva da espécie. As diversidades nucleotídicas encontradas por Domínio foram de 0,0030 Caatinga; 0,0019 - Mata Atlântica; 0,0020 Cerrado; 0,0011 - Pampas e 0,0004 - Chaco. A AMOVA mostrou que 68,33% da variação é intra-populacional e que uma porção significativa da variação é devido a diferenças inter-regionais (ct = 0,07124 p = 0,00196). Os testes de Neutralidade (D de Tajima = -2,4150, p = 0,0317 e Fs de Fu = -28,6719, p = 0,00001), a forma em estrela da rede e haplótipos, e a Mismatch Distribution confirmam um evento de expansão populacional estimado em aproximadamente 494.257,3 anos atrás, segundo modelo de Rogers e Harpending (1992). Entretanto, a Baesyan Skiline Plot demonstrou que esse movimento de expansão parece ser mais antigo, cerca de 550.000 650.000 anos atrás. A NCPA demonstrou que há fluxo gênico restrito com isolamento por distância, confirmado pelo teste de Mantel e alguma dispersão a longa distância em alguns dos clados analisados. O resultado do programa Migrate N indicou um padrão complexo migratório entre os domínios, porém um padrão norte/sul pôde ser verificado. A estruturação genética pode ser explicada devido à grande área de distribuição da espécie, gerando isolamento por distância e pela presença de barreiras geográficas e climáticas (entre o Cerrado e a Caatinga) e no estado do Rio de Janeiro e Espírito Santo (ao longo da Mata Atlântica) onde há pouco ou nenhum indivíduo da espécie. Os eventos de expansão ocorreram no Quaternário durante o período glacial conhecido como Ilinioian e suas subdivisões. A partir dos resultados deste trabalho foi possível traçar diversas rotas de migração possíveis entre os domínios utilizados, sendo que o movimento mais antigo partiu da Caatinga o que vai contra a hipótese de que o Centro de Origem seja o Chaco. / The fruit-fly Drosophila buzzatii is a cactophilic species in association with cactus species distributed along the Phytogeographic Domains of Caatinga, Cerrado, Atlantic Forest, Pampas and Chaco. Based in the diversity of chromosomal inversion and populational density of the species, the Chaco Domain was considered the Center of Origin of the D. buzzatii. However, recent works, using allozymes and DNAmt, showed a possible origin of the D. buzzatii in the Caatinga. The objectives of this work were trace historical dispersion routes of D. buzzatii, current and ancient areas of distribution in the South America. We obtained DNA sequences in 132 samples in 44 localities with 714 bp length from the COI mtDNA gene, generating 36 haplotypes. The diversity indexes, AMOVA, neutrality tests, Mismatch Distribution, Baesyan Skyline Plot, NCPA and sense of migration movements was calculated, to describe part of the evolutionary history of the species. The nucleotide diversity was 0,0030 - Caatinga, 0,0019 - Mata Atlântica, 0,0020 - Cerrado, 0,0011 - Pampas and 0,0004 - Chaco. The AMOVA results, grouped by Domain showed that 68,33% of the variation is intra-population and a significant portion of the variation is due to inter-regional differences (ct = 0,07124 p = 0,00196). The Neutrality tests (Tajimas D = -2,4150, p = 0,0317 and Fus Fs = -28,6719, p = 0,00001), the star-shape of the haplotype network, and Mismatch Distribution showed population expansion signs, estimated in 494.257,3 ybp, according Rogers and Harpending model (1992). However, the BSP showed that the movement is ancient, estimated in 550.000 650.000 ybp. The NCPA showed restricted gene flow with isolation by distance, confirmed by the Mantel Test and some long distance dispersion. The results of the program Migrate N showed a complex pattern of migration between the domains, but a north/south pattern could be identified. The genetic structure can be explained to the widespread distribution of the species, that could generate isolation by distance and by the presence of geographic and climatic barriers (between Cerrado and Caatinga domains) and in the States of Rio de Janeiro and Espírito Santo (along the Atlantic Forest) when there is none or few individuals of the species D. buzzatii. The expansion movements occurred in the Quaternary Period during glaciations events in the Illinoian and their subdivisions, due to the decrease of the global moisture that generated favorable conditions to the expansion of the dry vegetation and associated species. Based on the results of this work it was possible to delineate many migration routes between the phytogeographic domains, and the more ancient movement started in the Caatinga and this result not support the hypothesis that Chaco was the Center of Origin from D. buzzatii.

Biodiversity, the variety of life on the planet, is declining due to climate change, population and species interactions and as the result f demographic and landscape dynamics. Integrated model-based assessments play a key role in understanding and exploring these complex dynamics and have proven use in conservation planning. Model-based assessments using Species Distribution Models constitute an efficient means of translating limited point data to distribution probability maps for current and future scenarios in support of conservation decision making. The aims of this doctoral study were to investigate; (1) the use of a hybrid genetic programming to build high quality models that handle noisy real-world presence and absence data, (2) the extension of this solution to exploit the parallelism inherent to genetic programming for fast scenario based decision making tasks, and (3) a conceptual framework to share models in the hope of enabling research synthesis. Subsequent to this, the quality of the method, evaluated with the true skill statistic, was examined with two case studies. The first with a dataset obtained by defining a virtual species, and the second with data extracted from the North American Breeding Bird Survey relating to mourning dove (Zenaida macroura). In these studies, the produced models effectively predicted the species distribution up to 30% of error rate both presence and absence samples. The parallel implementation based on a twenty-node c3.xlarge Amazon EC2 StarCluster showed a linear speedup due to the multiple-deme coarse-grained design. The hybrid fuzzy genetic programming algorithm generated under certain consitions during the case studies significantly better transferable models. / Biodiversidade, a variedade de vida no planeta, está em declínio às alterações climáticas, mudanças nas interações das populações e espécies, bem como nas alterações demográficas e na dinâmica de paisagens. Avaliações integradas baseadas em modelo desempenham um papel fundamental na compreensão e na exploração destas dinâmicas complexas e tem o seu uso comprovado no planejamento de conservação da biodiversidade. Os objetivos deste estudo de doutorado foram investigar; (1) o uso de técnicas de programação genética e fuzzy para construir modelos de alta qualidade que lida com presença e ausência de dados ruidosos do mundo real, (2) a extensão desta solução para explorar o paralelismo inerente à programação genética para acelerar tomadas de decisão e (3) um framework conceitual para compartilhar modelos, na expectativa de permitir a síntese de pesquisa. Subsequentemente, a qualidade do método, avaliada com a true skill statistic, foi examinado com dois estudos de caso. O primeiro utilizou um conjunto de dados fictícios obtidos a partir da definição de uma espécie virtual, e o segundo utilizou dados de uma espécie de pomba (Zenaida macroura) obtidos do North American Breeding Bird Survey. Nestes estudos, os modelos foram capazes de predizer a distribuição das espécies maneira correta mesmo utilizando bases de dados com até 30% de erros nas amostras de presença e de ausência. A implementação paralela utilizando um cluster de vinte nós c3.xlarge Amazon EC2 StarCluster, mostrou uma aceleração linear devido ao arquitetura de múltiplos deme de granulação grossa. O algoritmo de programação genética e fuzzy gerada em determinadas condições durante os estudos de caso, foram significativamente melhores na transferência do que os algoritmos do BIOMOD.

Nas últimas décadas, em decorrência da globalização e do comércio internacional, o deslocamento de espécies para longe de suas regiões de origem tem crescido em frequência e extensão, aumentando o risco de invasões biológicas, que podem impactar significativamente a economia, o funcionamento dos ecossistemas e causar perdas de biodiversidade. A erradicação de espécies invasoras tem poucas chances de sucesso, de modo que prevenir a invasão constitui a melhor alternativa de manejo. Técnicas de modelagem preditiva de distribuição têm sido globalmente aplicadas para prever a distribuição potencial de espécies invasoras. No Brasil, são poucos e recentes os estudos sobre invasões biológicas. Visando ampliar o conhecimento sobre plantas consideradas invasoras e sua distribuição no estado de São Paulo, neste estudo aplicamos técnicas de modelagem preditiva a 10 espécies. Para cada uma delas buscamos caracterizar o padrão de invasão e identificar os fatores ambientais atuantes que limitam ou potencializam sua distribuição, por meio de modelos multi-hierárquicos de nicho ecológico. Para tanto, coletamos informações de ocorrência dessas espécies em todo o mundo e registramos coordenadas geográficas, características das populações e dos ambientes invadidos por essas espécies em todos os tipos de vegetação e em todas as regiões do estado de São Paulo. Com base nesses dados, caracterizamos o padrão de invasão de cada espécie e a invasibilidade de cada tipo vegetacional estudado. Aplicamos a metodologia de modelagem multi-hierárquica de nicho ecológico por meio do algoritmo MaxEnt em macro escala para todo o globo e em meso escala para o estado de São Paulo. Apesar das peculiaridades das espécies e dos tipos de vegetação, nossos resultados evidenciam a influência do estado de conservação do ecossistema e da posição na paisagem sobre a severidade da invasão e, também, sobre a invasibilidade dos tipos de vegetação em escala local. Mesmo os tipos de vegetação mais resistentes, como a restinga e a floresta ombrófila densa, podem se tornar suscetíveis à invasão em função de distúrbios e da pressão de propágulos. Em fragmentos conservados, porém, são raras as espécies exóticas capazes de se estabelecer e se tornar uma ameaça real à conservação. As fitofisionomias mais abertas do Cerrado mostraram-se como os tipos de vegetação suscetíveis à invasão pelo maior número de espécies, entre as estudadas. Em macro escala, os modelos de nicho ecológico identificaram as áreas potenciais de invasão e revelaram os limites fisiológicos de temperatura e precipitação para cada espécie, enquanto em meso escala, os modelos de nicho refinaram estas previsões e revelaram novos padrões associados com a distribuição das espécies na escala do estado de São Paulo. Este estudo gera contribuições importantes em termos de informação sobre as características e áreas potenciais de invasão para gestores e tomadores de decisão no processo de prevenção e controle de invasões, bem como identifica limites e fatores ambientais que contribuem para a melhor compreensão de invasões biológicas no Brasil. De forma geral, a abordagem multi-hierárquica se mostrou uma ferramenta poderosa para explorar padrões de distribuição em escalas apropriadas com os objetivos de conservação, prevenção e controle de espécies exóticas. / In recent decades, as a result of globalization and international trade, the movement of species away from their native regions has grown in frequency and extent, increasing the risk of biological invasions, which can significantly impact the economy, the functioning of ecosystems and cause biodiversity loss. The eradication of invasive species it is not an easy task, usually with little chance of success, so that prevent the invasion is still the best management alternative. Predictive species distribution modeling techniques have generally been applied to predict the potential distribution of invasive species. In Brazil, studies on biological invasions are recent and insufficient to understand the current invasive status. To enhance understanding about invasive plants and its distribution in the state of São Paulo, in this study we apply predictive modeling techniques to 10 species considered invasive. For each of the selected species we seek to characterize the invasion pattern and identify the active environmental factors that limit or leverage its distribution through multihierarchical ecological niche models. For this purpose, we collect information for these species occurring worldwide and recorded geographical coordinates characteristics of populations and environments invaded by these species in all vegetation types and in all regions of the state of São Paulo. Based on these data, we characterize the invasion pattern of each species and the invasiveness of each vegetation type studied. We applied the multihierarchical ecological niche modeling methodology through MaxEnt algorithm in macro scale for the entire globe and meso scale for the state of São Paulo. Despite the peculiarities of species and vegetation types, our results highlight the influence of ecosystem conservation status and position in the landscape on the severity of the invasion and on the invasiveness of vegetation types on a local scale. Even the most resistant types of vegetation, such as the restinga and the tropical rain forest, can become susceptible to invasion because of disturbances and seedlings pressure. In conserved fragments, however, exotic species were rarely able to settle down and become a real threat to conservation. The more open forms of the Cerrado vegetation types appeared as the most susceptible to invasion by most of the studied species. In macro scale, the ecological niche models identified the potential areas of invasion and revealed the physiological limits of temperature and precipitation for each species, while in meso scale, niche models refined these projections and revealed new patterns associated with the distribution of species on the scale of São Paulo. This study provides important contributions in terms of information about the characteristics and potential areas of invasion for managers and decision makers in prevention and control of invasions and identifies limitations and environmental factors that contribute to a better understanding of biological invasions in Brazil. In general, the multihierarchical approach proved to be a powerful tool to explore patterns of distribution at scales compatible with conservation objectives, prevention and control of alien species.

Orientador: Ingrid Koch / Resumo: Aspidosperma pyrifolium Mart. & Zucc. é uma espécie com distribuição ampla e disjunta, variação morfológica e taxonomia complexa. Neste estudo é tratada como um complexo de espécies, e utilizada como modelo para delimitação de espécies através de múltiplos critérios operacionais (genéticos, morfológicos e ecológicos). Consideramos que espécies são segmentos de linhagens de uma metapopulação evoluindo separadamente, pois este é um conceito universal que diminuiu as visões conflitantes do que é considerado espécie. Realizamos análises filogenéticas com dados concatenados (ITS e rpl32-trnL) e de coalescência para testar o monofiletismo do complexo e seus grupos. Desenvolvemos marcadores microssatélites polimórficos para A. pyrifolium usados na avaliação da diversidade genética e estruturação de cinco populações naturais. Analisamos a morfologia através de morfometria, incluindo características quantitativas, tanto vegetativas quanto reprodutivas. As análises ecológicas, incluíram modelagem e testes de similaridade de nicho ecológico. Nossos resultados recuperaram o complexo A. pyrifolium como monofilético, com 3 subclados relacionados a regiões geográficas e vegetações específicas, resultados também corroborados na árvore de espécies. O clado 1 ocorre na Caatinga no Nordeste do Brasil, o clado 2 nas manchas de Floresta Estacional na região Centro-Oeste no Brasil e clado 3 na vegetação chaqueana no Mato grosso do Sul, Paraguai e Bolívia. Todas as análises de estrutura populaciona... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Aspidosperma pyrifolium Mart. & Zucc. is a species with wide distribution and disjunct, morphological variation and complex taxonomy. In this study, we treated it as a species complex, and used as a model for species delimitation using multiple operational criteria (genetic, morphological and ecological). We consider species as segments of separately evolving metapopulation lineages, since this is a universal concept that diminished the conflicting visions of what is considered species. For this, we performed phylogenetic with concatenated data (ITS and rpl32-trnL) and coalescence analyzes to test the monophyly of the complex and its groups. We developed polymorphic microsatellites for complex A. pyrifolium for evaluated the genetic diversity and structure of five natural population. We analyzed morphology through morphometry, including quantitative characteristics, both vegetative and reproductive. The ecological analyzes included modeling and testing of ecological niche similarity. Our results recovered Aspidosperma pyrifolium complex as monophyletic, with 3 subclades related to geographic regions and specific vegetation, results also corroborated in the species tree. Clade 1 occurs in the Caatinga in Northeast Brazil, clade 2 in the Seasonal Forest patches in the Center-West region of Brazil and clade 3 in the Chaqueana vegetation in Mato Grosso do Sul, Paraguay and Bolivia. All analyzes of population structure suggested the formation of two genetic groups, one with the po... (Complete abstract click electronic access below) / Doutor

Quels sont les grands patrons de distribution des espèces et quels sont les facteurs qui les contrôlent? Ces questions sont au cœur des problématiques macroécologiques et prennent un intérêt tout particulier au regard du réchauffement climatique global actuel. L’objectif principal de ce travail de thèse était de déterminer les patrons de distribution actuels des espèces d’oursins antarctiques et subantarctiques à l’échelle de l’océan Austral et de mettre en évidence les facteurs qui contrôlent ces distributions. La modélisation des niches écologiques d’une vingtaine d’espèces d’oursins a permis de mettre en évidence deux grands patrons de distribution : (1) un premier représenté par les espèces dont la distribution n’est pas limitée au sud du Front Polaire et s’étend des côtes antarctiques aux zones subantarctiques et tempérées froides et (2) un deuxième constitué d’espèces restreintes à la zone antarctique. Au sein de ces deux patrons, cinq sous-patrons ont également pu être défini sur la base de différences de distribution latitudinale et bathymétrique entre groupes d’espèces. Cette approche biogéographique par modélisation de niche écologique a été complétée par l’analyse de similarité de l’ensemble des faunes d’oursins, de bivalves et de gastéropodes, au niveau spécifique et générique, entre biorégions de l’océan Austral. Cette analyse démontre qu’il existe chez les oursins et les bivalves des connexions fauniques entre l’Amérique du Sud et les zones subantarctiques ainsi qu’une séparation entre l’Est et l’Ouest antarctique. Au contraire, les faunes de gastéropodes subantarctiques montrent des affinités plutôt antarctiques que sud-américaines, l’Antarctique ne formant qu’une unique province pour ce clade. Ces différences entre clades sont interprétées comme étant le résultat d’histoires évolutive et biogéographique distinctes entre oursins et bivalves d’une part et gastéropodes d’autre part. L’hypothèse d’une réponse évolutive différente des clades aux changements environnementaux survenus au cours du Cénozoïque est avancée. Enfin, l’existence de connexions fauniques trans-antarctiques est mise en évidence dans l’étude des trois clades ; celles-ci sont interprétées comme le résultat de la dislocation de la calotte ouest-antarctique et l’ouverture de bras de mer trans-antarctiques au cours du Pléistocène. Parmi les paramètres environnementaux utilisés dans la modélisation des niches écologiques, les résultats montrent que trois paramètres jouent un rôle majeur dans la distribution des oursins : la profondeur, la couverture de glace et la température des eaux de surface. Toutefois, l’importance relative de ces paramètres diffère selon les espèces d’oursins étudiées. L’étude du genre Sterechinus souligne tout particulièrement ces différences. En effet, l’espèce S. neumayeri est plus sensible aux conditions environnementales qui prédominent près des côtes antarctiques (température des eaux de surface et couverture de glace), alors que S. antarcticus semble être beaucoup moins contraint par ces mêmes paramètres. La distribution potentielle de S. antarcticus est d’ailleurs beaucoup plus étendue en latitude. Cependant, S. antarcticus n’est pas présent sur l’ensemble de son aire de distribution potentielle, ceci pouvant être expliqué alternativement par le résultat (1) de facteurs océanographiques (rôle de barrière biogéographique joué par le Front Polaire), (2) d’interactions biotiques (phénomènes de compétition inter-spécifique) et (3) du contexte temporel (colonisation toujours en cours). / What are the forcing factors and main patterns of species distribution? This question is the core of macroecological issues and is of particular interest in the present context of global warming. The main objectives of this thesis were to determine the current distribution patterns of Antarctic and sub-Antarctic echinoid species at the scale of the whole Southern Ocean and to highlight the forcing factors that control them. The ecological niche modelling of 19 echinoid species showed that distribution is mainly structured in two patterns: (1) a first one represented by species that are not limited to the south of the Polar Front and distributed from the Antarctic coasts to the sub-Antarctic and cold temperate areas, and (2) a second one with species restricted to the Antarctic area. Within these two main patterns, five sub-patterns were also identified that depend on differences in the latitudinal and depth range of species groupings. In addition to this approach of biogeography by ecological niche modelling, a similarity analysis of echinoid, bivalve and gastropod fauna between bioregions of the Southern Ocean was performed at species and genus levels. This analysis reveals faunal connections between southern South America and sub-Antarctic areas in echinoids and bivalves, along with a partition between the East and West Antarctic. On the contrary, sub-Antarctic gastropod fauna show Antarctic rather than South American affinities and the Antarctic form a sole and unique province in this clade. These differences between clades are interpreted as the result of distinct biogeographic and evolutionary histories between echinoids and bivalves on the one hand, and gastropods on the other hand. The proposed hypothesis is that clades developped different evolutionary responses to the environmental changes that occurred during the Cenozoic. Finally, in the three clades, trans-Antarctic faunal connections are shown and interpreted as a result of West Antarctic Ice Sheet collapses and the setting up of trans-Antarctic sea-ways during the Pleistocene. Among the environmental parameters used for the ecological niche modelling, results show that the three following parameters play the main part in echinoid distribution: depth, sea-ice cover and sea surface temperature. However, the relative importance of these parameters depends on the species under studies. These differences are particularly emphasized in the case study of the genus Sterechinus. The species S. neumayeri is indeed the most dependent on environmental conditions that prevail along the Antarctic coasts (sea surface temperature and sea-ice cover), while S. antarcticus doesn’t seem to be so much under the control of these parameters. Accordingly, the potential distribution of S. antarcticus in latitude is the most extended. However, S. antarcticus is not present over the whole area of its potential distribution, what can be explained as the result of either (1) oceanographic factors (role of the Polar Front as a biogeographical barrier), (2) biotic interactions (inter-specific competition) or (3) the temporal context (still ongoing colonization).

Para se compreender o papel ecológico dos cetáceos são necessários maiores conhecimentos sobre suas ocorrências e distribuições. A distribuição potencial das espécies pode ser determinada a partir das áreas geográficas de ocorrência dos seus nichos. Estes podem ser definidos com o uso de variáveis ambientais, o que se demonstra uma vantagem por serem estáticas e não serem dinamicamente afetadas pelas atividades biológicas. O presente estudo tem como objetivo determinar a ocorrência e distribuição dos cetáceos ao largo da costa sudeste do Brasil com base em dados de avistagens, bem como delimitar os nichos fundamentais e a sobreposição das áreas de distribuição potencial das espécies avaliadas. Os dados de avistagem foram obtidos por meio de cruzeiros oceanográficos realizados entre 2012 e 2015. Os modelos ecológicos de nicho foram elaborados com o uso das variáveis ambientais disponibilizadas pelo MARSPEC e com o uso do software NicheA. Foram avistadas doze espécies com a realização dos cruzeiros, sendo as seis mais frequentes utilizadas para a determinação das áreas de distribuição potencial. Apesar de apresentarem diferenças quanto às preferências ambientais, a maioria das espécies de cetáceos amostrada apresentou sobreposição parcial de nicho e da área de distribuição potencial. / It is deemed important to understand cetacean occurrence and distribution to comprehend their ecological roles. The geographical occurrence of species\' niche can be used to evaluate their potential distribution. The niche can be defined using environmental variables. Those variables are considered static and are not affected by biological activities. The present study goal is to access the occurrence and distribution of cetaceans along the southeastern Brazilian coast, as well as to define the fundamental niche of the species and the overlap between their potential distribution areas. Sighting data were obtained through oceanographic surveys conducted between 2012 and 2015. The environmental variables available on MARSPEC and the software NicheA were used for the ecological niche modeling. A total of twelve cetacean species were identified during the cruises. The potential distribution areas of the six commonest species were defined. Even though the species presented different environmental preferences, most of them had partial overlap between niches and potential distribution areas.

A filogeografia é o campo de estudo que pode revelar a história evolutiva das espécies, sua diversidade e a estrutura genética atual das populações. Neste estudo, foi avaliada a diversidade genética de 13 populações de Epidendrum orchidiflorum (Orchidaceae) utilizando uma abordagem filogeográfica, na tentativa de reconstruir a história evolutiva desta espécie ao longo da Chapada Diamantina e suas serras próximas, do litoral de Bahia e litoral do Rio de Janeiro.Foram usados como marcadores moleculares regiões de DNA de cloroplasto - cpDNA, as quais por serem de herança materna, natureza não recombinante e se encontrarem abundantemente nas plantas, são ideais para este tipo de estudos. Com os dados obtidos do seqüenciamento de duas regiões de cpDNA (rps16-trnK e rpl32-trnL), foram calculados os índices de diversidade para as 13 localidades amostradas, sendo que o número total de haplótipos foi 12. A diversidade haplotípica (Hd) variou de 0 para a população do Litoral da Bahia, Restinga (RE) a 0,889 para a população de Seabra (SE), próxima da Chapada Diamantina. O haplótipo mais freqüente foi o H2 apresentando-se em nove populações. A população RE só apresentou um haplótipo (H2), enquanto que a população de maior diversidade (SE) apresentou seis haplótipos. Além disso, em três populações (SE, Morro do Chapéu e Arraial do Cabo) foram encontrados haplótipos únicos. A análise de variância molecular (AMOVA) indicou que a diferenciação genética encontrada entre populações (FST = 47,5%) é elevada, mostrando que existem diferenças entre populações para esta espécie. No entanto, a proporção de variabilidade de haplótipos encontrados dentro das populações (52,5%, P<0,001) foi maior do que entre as populações.As análises geradas para diferentes agrupamentos testados nas AMOVAS e no programa Migrate-n, sugerem que o melhor modelo que explicaria a conectividade entre as populações seria o modelo de uma grande população panmítica que reúne as populações das serras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI e SE) com migração para as populações do litoral da Bahia (RE) e a população do Rio de Janeiro (AC). Estas análises são suportadas pelas análises geradas da Modelagem de Nicho Ecológico (EEM), indicando que as populações próximas a Chapada Diamantina se encontram conectadas desde a interglaciação e a última glaciação, porém a população do Rio de Janeiro foi separada durante a ultima glaciação, permanecendo isolada, divergindo ao longo do tempo devido à deriva genética e à mutação. / Phylogeography is the field of study that may reveal the evolutionary history of the species, their diversity and the current genetic structure of populations. In this study, we evaluated the genetic diversity of 13 populations of Epidendrum orchidiflorum (Orchidaceae ) using a phylogeographic approach in an attempt to reconstruct the evolutionary history of this species along the Chapada Diamantina and its nearby sierras, the Bahia coastline and the Rio de Janeiro coastline. We used as molecular markers chloroplast DNA regions - cpDNA, which are maternally inherited, non-recombinant and found abundantly in plants, and for these reasons are ideal for this type of studies. With the data obtained from the sequencing of two regions of cpDNA(rps16-trnK and rpl32-trnL), the diversity index for the 13 sampled locations were calculated, and the total number of haplotypes was 12.The haplotype diversity (Hd) ranged from 0.0 for the Coastal population of Bahia, Restinga (RE) to 0.889 for the population of Seabra (SE), near the Chapada Diamantina. The most common haplotype was the H2 found in nine populations. The RE population showed only one haplotype (H2), while the population of greater diversity (SE) showed six haplotypes. Moreover, in three populations (SE, Morro do Chapéu and Arraial do Cabo) unique haplotypes were found. The analysis of molecular variance (AMOVA) showed that the genetic difference found between populations (FST = 47.5%) is high, showing that there are differences between populations for this species. However, the proportion of haplotypes variability found within populations (52.5%, P <0.001) was higher than among populations. The analyses generated for different groups tested in AMOVAS and in the Migrate-n program suggest that the best model to explain the connectivity between populations would be the model of a large panmitic population that brings together the populations of the Sierras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI and SE) with migration towards the populations of the coast of Bahia (RE) and the population of Rio de Janeiro (AC). These analyses are supported by the analyses generated by the Ecological Niche Modeling (EEM), indicating that the populations near the Chapada Diamantina are connected since the interglacial and the last glaciation, but the population of Rio de Janeiro was separated during the last glaciation, remaining isolated and diverged over time due to genetic drift and mutations.