The American alligator (Alligator mississippiensis) has been frequently studied in large reservoirs and coastal marshes. Large ontogenetic shifts in their diet and morphology have been linked with changes in habitat use, with adult males using deep, open water and juveniles and nesting females relying on vegetated marsh. In certain regions of the inland portion of the alligator’s range, these different aquatic habitats are represented by seasonal wetlands and riverine systems that are separated by a terrestrial matrix. Ontogenetic habitat shifts, therefore, would require overland movements between systems, which has important implications for conservation of the species. I tested several commonly used methods of surveying alligator populations to determine the most effective method of studying alligators in seasonal wetlands. I then used systematic trapping, nest surveys and radio telemetry to determine habitat use and overland movement rates by different sex and size classes. I found that seasonal wetlands provided nesting and nursery sites for these inland alligator populations, but that both juveniles undergoing an ontogenetic shift and nesting females move between the wetlands and riverine systems. Overland movements by alligators between the wetland and riverine habitats establish a level of functional connectivity between these aquatic ecosystems. I constructed a habitat suitability index of both the wetlands and the surrounding landscape to determine which patch and landscape characteristics were important to wetland use by alligators. I found that both descriptive wetland characteristics and the spatial relationships between wetlands were important predictors of alligator use. Overland movement was related to upland landuse as well as distance between aquatic habitats. Conserving a variety of wetland sizes and types within an intact upland matrix is critical to maintaining connectivity across the landscape. Furthermore, understanding how species may act as mobile links between ecosystems, particularly those with ontogenetic niche shifts, illustrates the importance of approaching conservation from a landscape perspective.

Neurological and psychiatric disorders reveal that the basal ganglia subserve diverse functional domains, including movement, reward, and cognitive disorders (e.g., Parkinson's disease, addiction, schizophrenia). Monkey anatomical studies show that the striatum, the input structure of the basal ganglia, receives projections from nearly the entire cerebral cortex with a broad topography of motor, limbic, and association zones. However, until recently, non-invasive methods have not been available to conduct the complete mapping of the cortex to the striatum in humans. The development of functional connectivity magnetic resonance imaging (fcMRI) now allows the identification of functional connections in humans. The present dissertation reports two studies that first create a complete map of corticostriatal connectivity and then more closely examine striatal connectivity with association networks underlying cognition.

Understanding dispersal and gene flow in human-modified landscapes is crucial for effective conservation. Seed dispersal governs colonization, recruitment, and distribution of plant species, whereas both pollen and seed dispersal determine gene flow among populations. This PhD thesis tests the effect of rotational shepherding on seed dispersal and gene flow in fragmented calcareous grasslands. Calcareous grasslands (Gentiano-Koelerietum pyramidatae vegetation) in Central Europe are semi-natural communities traditionally used for rotational grazing that experienced a decline of plant species during the 20th century due to abandonment of shepherding. This PhD profits from a management project started in 1989 in Bavaria, Germany to reconnect previously abandoned calcareous grasslands in three non-overlapping shepherding systems. Two vegetation surveys in 1989 and 2009 revealed colonizations in previously abandoned grasslands reconnected by shepherding. First, I propose a comprehensive approach to identify determinants of community-level patch colonization rates based on 48 habitat specialist plants by testing competing models of pre-dispersal and dispersal effects and accounting for post-dispersal effects. Mean source patch species occupancy in 1989, and structural elements in focal patches related to establishment explained community-level patch colonization rates. Secondly, by adapting the community analysis to all 31 individual species of the same community with sufficient data, I corroborate the role of shepherding to support dispersal for a range of species, even if they lack seed morphological traits related to zoochory. Thirdly, for the habitat specialist Dianthus carthusianorum, I genotyped 1,613 individuals from 64 populations at eleven microsatellites to test the effect of dispersal by sheep on spatial genetic structure at the landscape scale. Genetic distances between grazed patches of the same herding system were related to distance along herding routes, whereas ungrazed patches showed isolation by geographic distance. Lastly, within individual grassland patches, shepherding significantly decreases the degree of relatedness among neighboring individuals (kinship structure) and increases genetic diversity. My thesis contributes towards understanding the effects of zoochory on spatial dynamics in plant populations across scales.

Understanding dispersal and gene flow in human-modified landscapes is crucial for effective conservation. Seed dispersal governs colonization, recruitment, and distribution of plant species, whereas both pollen and seed dispersal determine gene flow among populations. This PhD thesis tests the effect of rotational shepherding on seed dispersal and gene flow in fragmented calcareous grasslands. Calcareous grasslands (Gentiano-Koelerietum pyramidatae vegetation) in Central Europe are semi-natural communities traditionally used for rotational grazing that experienced a decline of plant species during the 20th century due to abandonment of shepherding. This PhD profits from a management project started in 1989 in Bavaria, Germany to reconnect previously abandoned calcareous grasslands in three non-overlapping shepherding systems. Two vegetation surveys in 1989 and 2009 revealed colonizations in previously abandoned grasslands reconnected by shepherding. First, I propose a comprehensive approach to identify determinants of community-level patch colonization rates based on 48 habitat specialist plants by testing competing models of pre-dispersal and dispersal effects and accounting for post-dispersal effects. Mean source patch species occupancy in 1989, and structural elements in focal patches related to establishment explained community-level patch colonization rates. Secondly, by adapting the community analysis to all 31 individual species of the same community with sufficient data, I corroborate the role of shepherding to support dispersal for a range of species, even if they lack seed morphological traits related to zoochory. Thirdly, for the habitat specialist Dianthus carthusianorum, I genotyped 1,613 individuals from 64 populations at eleven microsatellites to test the effect of dispersal by sheep on spatial genetic structure at the landscape scale. Genetic distances between grazed patches of the same herding system were related to distance along herding routes, whereas ungrazed patches showed isolation by geographic distance. Lastly, within individual grassland patches, shepherding significantly decreases the degree of relatedness among neighboring individuals (kinship structure) and increases genetic diversity. My thesis contributes towards understanding the effects of zoochory on spatial dynamics in plant populations across scales.

During normal development, face processing involves a gradual shift from a featurally oriented style to a mature configural style by adolescence. This shift may coincide with increased right hemispheric dominance for faces supporting configural processing. Previous studies suggest that individuals diagnosed with ASD continue to process faces using individual parts and features into adulthood. This continued bias may be due to deficits in configural processing abilities. The current study investigated measures of functional connectivity during featural and configural processing of faces in broad autism phenotype sibling (ASD-sibs) children compared to age, sex, and handedness matched normal developing (ND) controls and in children diagnosed with an Autism Spectrum Disorder compared to ASD-matched ND controls. Results indicate that children with ASD and ASD-sibs were capable of performing configural processing tasks at similar performance levels to those of ND children. Additionally, patterns of functional network connectivity for configural processing in ASD-sibs were similar to those observed in ND controls. Few network-wide hemispheric differences emerged between groups. While behavioral performance and overall network-wide patterns of connectivity suggest a face processing network that is capable of supporting configural processing in ASD and ASD-sibs, abnormalities were observed in specific regions. The amygdala and fusiform face area showed fewer interactions with the rest of the face processing network in ASD children compared to ND during configural, but not featural processing. Additionally, hemispheric comparisons show greater differences between ASD and ND controls in the right fusiform face area. The ability of these regions to communicate with other regions in the face network could be important for social motivation and attention during configural processing. Interestingly, network connectivity in ASD children during passive viewing of faces, objects, and textures without featural or configural manipulations showed a more functionally integrated, and less segregated network with a lower “wiring cost” during non-face conditions compared to ND children. ASD-sibs may demonstrate a similar milder pattern.

Early life stress (ELS) affects the developing brain and impacts capacity for self-regulation and risk for psychopathology. The high spatial resolution of functional magnetic resonance imaging (fMRI) confers an advantage for studying specific neural regions posited to link ELS with subsequent functioning. The first chapter in this dissertation reviews the literature establishing the feasibility and utility of fMRI research with infants and young children. This chapter examines methodological issues and outlines the potential for this technique to make unique contributions to understanding how ELS influences brain development. The next two chapters present results from a study that employed a functional activation paradigm and resting state functional connectivity MRI (rs-fcMRI) to examine associations between a common source of ELS, non-physical interparental conflict, and neural functioning during infancy. The functional activation paradigm focused on emotional tone of voice as a stimulus relevant to interparental conflict, which is likely salient to infants. Higher levels of interparental conflict (as reported by mothers) were associated with infants (6 to 12 months of age) showing greater reactivity to very angry versus neutral tone of voice in neural regions associated with processing and regulation of stress and emotion (hypothalamus and rostral anterior cingulate cortex). The rs-fcMRI analysis examined coordinated neural functioning in the absence of stimuli, focusing on the amygdala as a key region for understanding the impact of ELS and the posterior cingulate cortex as part of a group of regions that show higher levels of activity in the absence of stimuli (the default network). The results replicate previous work characterizing the default network in infants and provide novel evidence for the functional connectivity of the amydgala and amygdala subregions during infancy. Interparental conflict was associated with variation in the connectivity of both regions. Thus levels of interparental conflict were associated with neural reactivity to a stressor-relevant stimulus and with patterns of coordinated neural functioning in the absence of such stimuli. These results provide support for the utility of using fMRI with infants to examine early emerging associations between common forms of ELS and brain functioning. This dissertation includes previously published and co-authored material. / 2016-10-17

The brain ages, and with it come alterations in its micro- and macro-structure which reflect in its morphology and functioning. Changes in the brain structure and functional coupling between regions can be assessed with neuroimaging, and, more specifically, magnetic resonance imaging (MRI). Using MRI data from two stages (Pilot and Enhanced) of the Nathan Kline Institute Rockland Sample (NKI-RS), totalling 613, free of neurodegenerative diseases, and right-handed, participants aged 18 to 85 years old, we measured gray-matter parameters such as cortical volume, cortical thickness, and cortical surface area, and also volume of subcortical structures. We also measured cortico-cortical functional connectivity, defined either as the Pearson correlation coefficient and partial correlation coefficient, bivariate instantaneous Granger causality and Granger causality, and generalized partial directed coherence (GPDC). GPDC was evaluated in five frequencies between the four pairs of regions displaying the strongest evidence for linear thinning, measured by their associated t-statistic, and its alterations alongside aging were assessed using a multivariate approach based on Dirichlet Regression. We also studied spatial associations between patterns of morphometric and connectivity alterations. We reproduced generalized age-related atrophy reported in the literature in cortical volume (90% of the studied structures), surface area (68%) and thickness (90%), and volumetric atrophy of several subocortical structures. We observe a positive association in the joint distribution of the expected cortical thickness at 18 years old and the yearly percentage reduction in cortical thickness. We showed, projecting these two quantitities into their principal axes and analyzing the spatial distribution of the scores, that the first principal component correlates with neocortical granularity while the second principal component represents cortical type admixture. On functional connectivity, we gathered evidence for overall increased Pearson correlation coefficient (6% of the connections in the Pilot NKI-RS and 2% in the Enhanced NKI-RS), with proportionally smaller number of decreases (0.1% in the Pilot NKI-RS and 0.3% in the Enhanced NKI-RS). The Pearson partial correlation coefficient between 12 out of 65 homotopic region pairs shows a pattern of decline with age, suggesting inter-hemispheric disconnection. However, predictive causality, as measured by both Granger causalities, do not share the same degree of changes observed in the correlational metrics. We observe increased GPDC from several regions to themselves in many frequencies (25% out of a total of 40 self-connections), indicating a degree of disconnection to the other regions. Given seed regions, we uncovered spatially distributed significant patterns of association between the standardized effect of age on the connectivity to its targets and on their targets thicknesses. Regions with smaller evidence for age-related thinning, such as several occipital areas, tend to have fewer alterations in functional connectivity than regions with greater evidence for age-related thinning, like many frontal regions. We hypothesize that regions showing a negative association (5% of the seed regions) are part of compensatory systems, being increasingly correlated with regions displaying most atrophy. Regions showing a positive association (5%) do not have compensatory mechanisms available, and therefore are losing connectivity to atrophyc regions. Overall, we found evidence for brainwide alterations in connectivity and cortical and subcortical morphometry throughout the human adult lifespan. We also found a specifc pattern of associations between the atrophic trends and age-related alterations in connectivity in the brain / O cérebro envelhece, e com isso vêm à tona alterações em sua micro e macroestrutura que se refletem em sua morfologia e funcionamento. Mudanças na estrutura cerebral e acoplamento funcional entre suas regiões podem ser averiguadas através da neuroimagem, e, mais especificamente, imagem por ressonância magnética (IRM). Usando dados de IRM das duas etapas (Pilot and Enhanced) do Nathan Kline Institute Rockland Sample (NKI-RS), totalizando 613 participantes destros, livres de doenças neurodegenerativas, com idade entre 18 e 85 anos, medimos parâmetros de substância cinzenta como volume, espessura, e área de superfície corticais, e também volume de estruturas subcorticais. Também medimos conectividade funcional cortico-cortical, definida como o coeficiente de correlação de Pearson, coeficiente de correlação parcial de Pearson, causalidade instântanea de Granger e causalidade de Granger bivariadas, e coerência parcial direcionada generalizada (GPDC). A GPDC foi medida em cinco frequências entre quatro pares de regiões que demonstraram a mais forte evidência para diminuição da espessura cortical linearmente, medido pela estatística-t associada, e suas alterações ao longo do envelhecimento foram estudadas usando uma abordagem multivariada baseada na Regressão de Dirichlet. Também estudamos associações espaciais entre padrões de alterações morfométricas e na conectividade. Reproduzimos a atrofia generalizada devido à idade reportada na literatura no volume cortical (90% das estruturas estudadas), área de superfície (68%) e espessura (90%), e atrofia volumétrica de várias estruturas subcorticais. Observamos uma associação positiva na distribuição conjunta do valor esperado da espessura cortical aos 18 anos de idade e a redução percentual anual na espessura cortical. Mostramos, ao projetar ambos em seus eixos principais e analizar a distribuição espacial desses índices, que a primeira componente principal correlaciona-se com a granularidade neocortical enquanto que a segunda componente principal representa o tipo cortical. Sobre a conectividade funcional, colhemos evidências para um aumento geral no coeficiente de correlação de Pearson (6% das conexões no Pilot NKI-RS e 2% no Enhanced NKI-RS), com menor proporção de decréscimos (0.1% no Pilot NKI-RS e 0.3% no Enhanced NKI-RS). O coeficiente de correlação parcial de Pearson entre 12 de 65 pares de regiões homotópicas demonstra um padrão de declínio com a idade, sugerindo desconexão inter-hemisférica. No entanto, a causalidade preditiva, como medida através de ambas as métricas de causalidade de Granger, não aparenta o mesmo grau de mudanças observado nas medidas correlacionais. Observamos aumentos na GPDC de várias regiões para si próprias em muitas frequências (25% de um total de 40 auto-conexões), que indica um grau de disconexão às outras regiões. Dadas regiões semente, revelamos padrões significativos espacialmente distribuídos de associação entre efeitos padronizados da idade na conectividade para seus alvos e das espessuras dos alvos. Regiões com menor evidência para o desbastamento relacionado com a idade, como várias áreas occipitais, tendem a ter menos alterações em sua conectividade funcional que regiões com maior evidência suportando o desbastamento cortical relacionado à idade, como diversas regiões frontais. Hipotetizamos que regiões cuja associação é negativa (5% das regiões semente) são parte de sistemas compensatórios, estando correlacionadas com regiões que demonstram os maiores graus de atrofia de modo crescente. Regiões cuja associação é positiva (5%) não teriam mecanismos compensatórios à disposição, e portanto perdem conectividade para regiões atróficas. No geral, encontramos evidências para alterações na conectividade e na morfometria cortical e subcortical no cérebro todo ao longo da extensão da vida adulta humana. Também achamos um padrão específico de associações entre tendências atróficas e alterações na conectividade cerebral devido à idade

Sabe-se que diversas regiões do cérebro humano trabalham em sincronia, mesmo anatomicamente separadas, sugerindo conexões funcionais e estruturais. Dessa forma, nosso cérebro pode ser considerado uma rede que pode ser estudada para diferenças entre indivíduos e entre tarefas, em que os nodos podem ser diferentes regiões e as arestas podem ser medidas de conectividade funcional entre séries temporais de um sinal de ressonância magnética de cada região. Neste estudo, propomos analisar como conectividade funcional e parâmetros de rede cerebral se relacionam com desempenho intelectual e um estado de atenção sustentada. Foram adquiridas imagens de ressonância magnética de 30 indivíduos saudáveis jovens em estado de repouso e de atenção sustentada, a partir delas foram calculadas as conexões funcionais entre 90 regiões cerebrais usando o coeficiente de correlação entre pares de series temporais. Destes sujeitos foram estimados sete índices de inteligência a partir da aplicação do teste WAIS-III. As matrizes de conectividade evidenciariam um comportamento de rede complexa de mundo pequeno para limiares entre 0,2 e 0,5. Não foram encontradas associações entre parâmetros globais das redes ponderadas em estado de repouso e os índices de inteligência. Conectividade funcional e alguns parâmetros de rede locais evidenciaram correlações com pontuações de inteligência, principalmente nas regiões frontal, pré-central, parietal e occipital, giro fusiforme e supramarginal e caudado. Embora o p-valor não-corrigido seja bem pequeno e/ou haja simetria entre hemisférios em alguns resultados, ao ser considerado o efeito de múltiplas comparações para análise inteira não foram encontradas associações estatisticamente significativas, por isso as análises foram corrigidas para cada região (p-valor corrigido pelo FDR<0,05). Ainda assim, possivelmente um aumento do número de sujeitos levaria a resultados mais conclusivos. Não foram encontrados resultados que confirmassem a hipótese de que, para indivíduos normais, haveria uma maior anti-correlação de redes extrínsecas e intrínsecas como um todo para o estado de atenção focada em relação ao estado de repouso. Entretanto, durante o estado de atenção sustentada, foram encontradas algumas diferenças estatisticamente significantes nas conexões locais dentro das redes positivas e negativas à tarefa, evidenciadas por um aumento na magnitude das correlações positivas ou negativas durante a atenção sustentada, além de uma tendência de anti-correlação em conexões entre regiões positivas e negativas à tarefa. / It\'s known that some regions of the human brain work synchronously, even if they are anatomically separated, suggesting functional and structural connections. In this way, our brain can be considered a network that can be studied for individual or task differences and in which nodes can be the different regions and edges can be the measurements of functional connectivity between blood oxygen level-dependent signal time series from each region. In this study, we aim to analyze how functional connectivity and brain network parameters relate to intellectual performance and to sustained attention state. Resonance Magnetic images were acquired in 30 healthy young volunteers in resting and attentional state. The functional connections between 90 brain regions were computed from them using correlation coefficient between pairs of temporal series. Seven intelligence indices were estimated from these subjects through WAIS-III test application and associations between functional connectivity values or brain network parameters were sought. Connectivity matrices evidenced a small-world complex network behavior for thresholds between 0.2 and 0.5. No associations between global parameters using weighted networks were found. Functional connectivity and network parameters have evidenced some correlations with intelligence scores, mainly in frontal, pre-central, parietal, occipital regions, fusiform and supramarginal gyrus and caudate nucleus. Even that the uncorrected p-value was small and/or there was symmetry between hemispheres in several results, statistical significant associations were not found considering multiple comparisons correction for the entire analysis, therefore the analysis were corrected for each region (FDR corrected p-value <0.05). Even, increasing the number of subjects possibly would get more conclusive results. Results corroborant to the initial hypothesis of greater anti-correlation between default mode network and task-positive regions were not found for the sustained attention state. However, during sustained attention state, some statistically significant differences in local connections within task-positive and negative regions were found, evidenced by the increase of the strength of positive and negative correlations, besides of a trend of anti-correlation in connections between task-positive and negative regions.

The perirhinal cortex (PRC) is a medial temporal lobe (MTL) structure known to be involved in assessing whether an object is familiar (i.e., meaningful) or novel. Recent evidence shows that the PRC is sensitive to the familiarity of both whole object configurations and their parts, and suggests the PRC may modulate part familiarity responses in V2. Here, using functional magnetic resonance imaging (fMRI), we investigated age-related decline in the PRC's sensitivity to part/configuration familiarity and assessed its functional connectivity to visual cortex in young and older adults. Participants categorized peripherally presented silhouettes as familiar ("real-world") or novel. Part/configuration familiarity was manipulated via three silhouette configurations: Familiar (parts/configurations familiar), Control Novel (parts/configurations novel), and Part-Rearranged Novel (parts familiar, configurations novel). "Real-world" judgments were less accurate than "novel" judgments, although accuracy did not differ between age groups. The fMRI data revealed differential neural activity, however: In young adults, a linear pattern of activation was observed in left hemisphere (LH) PRC, with Familiar > Control Novel > Part-Rearranged Novel. Older adults did not show this pattern, indicating age-related decline in the PRC's sensitivity to part/configuration familiarity. A functional connectivity analysis revealed a significant coupling between the PRC and V2 in the LH in young adults only. Older adults showed a linear pattern of activation in the temporopolar cortex (TPC), but no evidence of TPC-V2 connectivity. This is the first study to demonstrate age-related decline in the PRC's representations of part/configuration familiarity and its covariance with visual cortex.

Les troubles du spectre autistique (TSA) sont des troubles neurodéveloppementaux fortement héritables. En parallèle, la théorie de l'hypoconnectivité fronto – postérieure semble être au coeur de la physiopathologie des TSA. Afin de comprendre la contribution des facteurs de risque familiaux de ce trouble, nous avons conduit conjointement une étude de connectivité anatomique et fonctionnelle chez des parents non atteints de sujets atteints de TSA. Nous avons réalisé une étude de tractographie en cerveau entier afin de comparer les valeurs de l'anisotropie fractionnelle généralisée le long des principaux faisceaux de substance blanche chez 85 sujets adultes : 39 parents non atteints, 18 sujets atteints de TSA comparés à 28 sujets contrôles. Après avoir corrigé pour les tests multiples, nous avons mis en évidence une diminution significative de l'anisotropie fractionnelle généralisée le long du faisceau fronto- occipital inférieur bilatéral chez les parents non atteints, les sujets atteints de TSA en comparaison aux sujets contrôles. Afin de comprendre l'implication fonctionnelle de la dysconnectivité anatomique fronto – occipitale retrouvée en tractographie, nous avons calculé la connectivité fonctionnelle entre les régions fronto – occipitales selon les extrémités du faisceau frontal - occipital inférieur bilatéral. En comparaison à 28 sujets contrôles, nous avons ainsi observé une augmentation significative de la connectivité fonctionnelle fronto - occipitale chez 38 parents non atteints et chez 13 sujets atteints de TSA. Une étude de connectivité fonctionnelle en cerveau entier serait une perspective prometteuse quant à l'interprétation de l'augmentation de la connectivité fronto – occipitale observée. Les anomalies fronto – occipitales montrées chez les parents non atteints, les sujets atteints de TSA pourraient correspondre à la mise en évidence d'un endophénotype dans les TSA. / Autism Spectrum Disorder (ASD) are neurodevelopmental disorders highly heritable.In parallel, the underconnectivity theory of ASD assumes that fronto-posterior brain disconnectivity is at the core of its pathophysiology. Our goal was to assess long-range structural and functional connectivity in unaffected parents of subjects with ASD to better understand the contributions of familial factors to heightened risk of ASD. We performed a diffusion weighted imaging (DWI) based whole brain tractography to compare generalized fractional anisotropy (gFA) in the main deep long white matter tracts in 85 adults: 39 unaffected parents, 18 probands compared to 28 controls. After corrections for multiple comparisons, we identified a significant decrease in gFA in the bilateral inferior frontal occipital fasciculus (IFOF) in both probands with ASD and unaffected parents when compared to controls. To understand the functional implication of fronto – occipital anatomical disconnectivity, we assessed the functional connectivity between the regions linked by IFOF exhibiting significant alterations in gFA. We also showed that both probands and unaffected parents exhibited a significantly increased functional connectivity between the frontal and occipital regions linked by the IFOF. In order to better understand and extend this interesting results, to evaluate the global functional connectivity of our sample in order to be able to interpret the increase of fronto-occipital functional connectivity would be an important perspective. These findings highlight an altered fronto-occipital connectivity in subjects with ASD and unaffected parents suggesting that fronto-occipital disconnectivity may be an endophenotype of ASD.