As espécies do gênero Leishmania parasitam mamíferos do Novo e Velho Mundo e possuem ciclos de vida com alternância entre vertebrados e invertebrados. A maioria das espécies se desenvolve em artrópodes hematófagos, que podem pertencer a diversas ordens e famílias. A Leishmaniose visceral é uma importante zoonose e possui canídeos silvestres e domésticos como importantes reservatórios conhecidos na diversidade genética de Leishmania infantum chagasi no Brasil ainda não é conhecida. Leishmaniose é uma doença severa com ampla distribuição geográfica com uma incidência de dois milhões de casos por ano e 350 milhões de pessoas em áreas de risco de infecção. O objetivo deste projeto foi avaliar a variação intraespecífica e biogeografia de isolados brasileiros de Leishmania infatum chagasi baseados em genes nucleares e mitocondriais. Os marcadores SSUrDNA, gGAPDH, Citocromo b, Hsp 70, Quitinase e ITS1rDNA foram amplificados, sequenciados e comparados filogeneticamente pelos métodos de parcimônia e bayesiana através de análises concatenadas. As sequencias obtidas apresentaram variabilidade entre 0 e 1% e a topologia gerada não evidenciou diferenças intraespecíficas entre os isolados brasileiros de Leishmania infantum chagasi e consequentemente padrões biogeográficos. Apesar dos resultados obtidos não refletirem a variabilidade esperada, as diversas sequencias obtidas darão subsídios para a determinação e padronização de novos testes diagnósticos da Leishmaniose visceral canina. / The Leishmania species parasite mammals in the New World and have life cycles with alternating between vertebrates and invertebrates. Most species develops in blood-sucking arthropods, which may belong to different orders and families. Visceral leishmaniasis is an important zoonosis and has wild and domestic canids as important known reservoirs and genetic diversity of Leishmania infantum chagasi in Brazil is not yet known. Leishmaniasis is a severe disease with wide geographical distribution with an incidence of two million cases per year and 350 million people at risk in endemic areas. The aim of this study was to evaluate the intraspecific variation and biogeography based on nuclear and mitochondrial genes. The SSUrDNA markers, gGAPDH, cytochrome b, hsp 70, chitinase and ITS1rDNA were amplified, sequenced and compared phylogenetically by maximum parsimony and Bayesian methods in concatenated analysis. The variability of sequences was 0 to 1%, and the topology generated showed no intraspecific differences between Brazilian strains of Leishmania infantum chagasi and consequently biogeographic patterns. Although the results do not reflect the expected variability, the various sequences obtained will provide subsidies for the establishment and standardization of new diagnostic tests of canine visceral leishmaniasis.

Entender os processos responsáveis pela origem e manutenção da diversidade de espécies nas comunidades representa uma questão central em ecologia. Dos inúmeros processos aventados para explicar a diversidade de organismos, podemos destacar o filtro ambiental e a limitação de similaridade. O filtro ambiental atua restringindo a variação e a distribuição dos organismos em determinado ambiente, enquanto que a limitação de similaridade atua pressionando a diferenciação das características dos organismos, uma vez que a coexistência entre os indivíduos depende da divergência na utilização dos recursos. A abordagem funcional tem sido utilizada para testar os processos responsáveis pela coexistência de espécies e consiste na comparação da similaridade funcional entre as espécies de uma comunidade através da quantificação dos seus atributos. A combinação de diferentes atributos em um organismo define a sua estratégia ecológica e, consequentemente, a sua distribuição nos habitats. As florestas de restingas são ambientes propícios para testar as hipóteses de coexistência das espécies nas comunidades, por apresentarem gradientes ambientes bem marcados e que definem a disponibilidade de recursos. Nesse sentido, este trabalho teve como objetivo avaliar: i) o efeito da condição edáfica (seco e alagado) sobre os atributos funcionais e as estratégias ecológicas de espécies arbóreas de restinga alta e; ii) o efeito que os atributos funcionais e as estratégias ecológicas têm sobre a preferência de habitat pelas plantas. Realizamos este trabalho em uma área de restinga alta na Ilha do Cardoso (SP) que compreende dois tipos de solo: seco e alagado. Coletamos cinco atributos funcionais (área foliar, área foliar específica, espessura foliar, conteúdo de matéria seca foliar e densidade da madeira) de 44 espécies arbóreas. Selecionamos 30 indivíduos de cada espécie sendo 15 em cada tipo de solo. Utilizamos seleção de modelos para as análises estatísticas, sendo usados modelos lineares mistos e modelos lineares simples para avaliar o efeito do solo nos valores médios e na variação dos atributos e das estratégias ecológicas, respectivamente. Encontramos efeito do solo sobre os coeficientes de variação (CV) do conteúdo de matéria seca foliar (CMSF) e da área foliar específica (AFE), sendo maiores no solo alagado. No caso do CV da AFE, o efeito só foi significativo quando excluímos as palmeiras das análises. Não encontramos efeito do solo sobre a variação dos demais atributos funcionais, das estratégias ecológicas e tampouco do tipo de estratégia ecológica. Os resultados encontrados apontam que no ambiente alagado, a limitação de similaridade seja o processo preponderante na estruturação dessa comunidade. Tal resultado difere dos reportados por outros estudos em florestas tropicais. Não encontramos efeito dos atributos e das estratégias ecológicas sobre a preferência de habitat das espécies, com exceção do CV de CMSF e de AFE. Novamente, no caso do CV de AFE, o efeito só foi significativo quando excluímos Euterpe edulis (palmito-juçara) das análises. Este resultado reforça a importância da plasticidade fenotípica para definir a ocorrência das espécies em diferentes habitats / Understanding the processes underlying the origin and maintenance of species diversity in communities is a central goal in ecology. Among the numerous processes proposed to explain the organisms\' diversity, we can highlight environmental filter and limiting similarity. Environmental filter operates by restricting the variation and distribution of organisms in a given environment, while the process of limiting similarity acts by pressing differentiation in the organisms\' characteristics, because the coexistence of individuals depends on difference in resource utilization. The functional approach has been used to test the processes responsible for species coexistence and consists in the comparison of species functional similarities in a community through their traits. The combination of different traits in an organism defines its ecological strategy and, therefore, their distribution on habitats. Restinga forests are suitable to test species coexistence hypotheses in communities, because it presents a well marked environmental gradient, which is defined by resource availability. Thus, this study aimed to evaluate: i) the effect of soil condition (drained and flooded) on functional traits and on ecological strategies of restinga trees species and, ii) the effect of functional traits on plant´s habitat preference. We conducted this study in an area of high restinga at Cardoso Island (SP), which comprises two soil types: drained and flooded. We collected five functional traits (leaf area, specific leaf area, leaf thickness, leaf dry matter content and wood density) of 44 tree species. We selected 30 individuals of each species, 15 in each soil type. We used model selection for statistical analyses, being linear models to assess soil type effect on trait and ecological strategies variances and linear mixed models to assess ecological strategies mean values. We found soil effect on the coefficients of variation of leaf dry matter content (LDMC) and of specific leaf area (SLA), which was higher in the flooded soil. In the case of SLA coefficient of variance, the effect was only significant when we excluded the palms from analyses. We found no soil effect on the other functional traits and on ecological strategies variation, neither on ecological strategy type. As for the results, it was found that in the flooded soil, limiting similarity is the dominant process structuring this community. This result differs from those reported by other tropical forests researches. We found no effect of traits and ecological strategies on habitat species preference, with the exception of LDMC and SLA coefficients of variations. Again, for SLA coefficient of variation, the effect was only significant when we exclude Euterpe edulis (juçara palm) from analyses. This result reinforces the importance of phenotypic plasticity to define species occurrence in different habitats

Native plant materials are often seeded to restore biodiversity and ecosystem function in areas overtaken by exotic weeds. Plant materials are evaluated on intraspecific differences in productivity and expression of traits advantageous to establishment (e.g., phenology, seed mass, and growth rate); some investigations also consider population-level adaptation to exotic species. However, there is a lack of studies that broadly evaluate response to competition from exotic species at multiple scales within a species. In a greenhouse experiment, we used analysis of variance to assess the growth response of a perennial grass native to the Intermountain West, (Elymus elymoides), to competition from a common invasive species, (Bromus tectorum), at three levels of intraspecific differentiation: subspecies, lineage (wild vs. domestic germplasm), and population. We used regression analysis to assess whether E. elymoides populations from highly invaded areas were less affected by B. tectorum competition. Finally, we explored the relationship between growth traits and competitive response using random forest regression. We found significant differences among E. elymoides subspecies in their response to B. tectorum competition, no difference between wild and domestic lineages, and no population-level differentiation within subspecies. Field abundance of B. tectorum had a significant positive relationship with E. elymoides biomass, but not competitive response, suggesting that E. elymoides has not adapted to the invader. Elymus elymoides plants which were less affected by competition were smaller, allocated more biomass to leaves, and had fewer fine roots, suggesting that light interception and tissue retention were prioritized by seedlings in this competitive greenhouse environment.

California's almond industry, valued at $2.3 billion per year, depends on the pollinator services of honey bees, although pollination by other insects, mainly solitary wild bees, is being investigated as an alternative because of recent declines in the number of honey bee colonies. Our objective is to model the movements of honey bees and determine the conditions under which they will forage in less favorable areas of a tree and its surroundings when other pollinators are present. We hypothesize that foraging in less favorable areas leads to increased movement between trees and increased cross pollination between varieties which is required for successful nut production. We use the Shigesada-Kawasaki-Teramoto model (1979) which describes the density of two species in a two-dimensional environment of variable favorableness with respect to intrinsic diffusions and intra- and interspecific interactions of species. The model is applied to almond pollination by honey bees and other pollinators with environmental favorableness based on the distribution of flowers in trees. Using the spectral-Galerkin method in a rectangular domain, we numerically approximated the two-dimensional nonlinear parabolic partial differential system arising in the model. When cross-diffusion or interspecific effects of other pollinators was high, honey bees foraged in less favorable areas of the tree. High cross-diffusion also resulted in increased activity in honey bees in terms of accelerations, decelerations, and changes in direction, indicating rapid redistribution of densities to an equilibrium state. Empirical analysis of the number of honey bees and other visitors in two-minute intervals to almond trees shows a negative relationship, indicating cross-diffusion effects in nature with the potential to increase movement to a different tree with a more favorable environment, potentially increasing nut production.

Listeria monocytogenes est un pathogène d'origine alimentaire à multiples facettes caractérisé par sa capacité d'adaptation dans des conditions défavorables et par sa prolifération dans une vaste gamme d'environnements, du sol aux cellules hôtes des mammifères. L'hétérogénéité génétique de L. monocytogenes se reflète dans sa structure clonale diversifiée, ce qui corrèle, dans une certaine mesure, avec des traits phénotypiques tels que la virulence ou la résistance au stress. La thèse portait sur deux phénotypes les plus éminents, la formation d'un biofilm et le potentiel de virulence, sous différents angles et à l'aide des technologies les plus récentes. Tout au long des études, des grands panels d'isolats ont été utilisés pour représenter la diversité intraspécifique. Stimulants défavorables tels que le choc froid et la privation d'éléments nutritifs induits par l'étape d'adhésion bactérienne. L'ajout de NaCl aux cultures de croissance a stimulé la production de biofilm et, de manière surprenante, il a considérablement intensifié la maturation du biofilm de cellules privées de nutriments. Un degré élevé de variation de la productivité relative du biofilm a été observé parmi les sérotypes, les génotypes, de même que les isolats selon les conditions de culture. Cependant, un certain génotype (complexe clonal 26) a révélé de manière caractéristique une production de biofilm plus élevée à froid (10°C), suggérant une association du génotype avec le phénotype du biofilm. Pan-GWAS a identifié un certain nombre de gènes parmi lesquels ceux impliqués dans des fonctions telles que la ‘transformation/compétence’, les ‘gènes liés aux phages’ et le ‘métabolisme du phosphate’ devront faire l'objet d'études plus approfondies sur leur rôle dans la formation du biofilm. L'analyse du séquençage de l'ARN a révélé une grande hétérogénéité intraspécifique dans les profils de transcriptome basal qui mettaient en évidence le rôle du réseau de régulation, y compris certains facteurs transcriptionnels avec des rôles clés dans la virulence tels que σB, PrfA, et CodY. La plasticité transcriptomique entre les lignées I et II ainsi que les génotypes hyper et hypovirulents ont confirmé les caractéristiques évolutives et épidémiologiques de L. monocytogenes. De plus, la voie métabolique centrale a été impliquée dans l'infection dans le système modèle de Galleria mellonella. En conclusion, la thèse a exploré la diversité intraspécifique de L. monocytogenes et a donné lieu à de nombreux résultats phénotypiques, génomiques et transcriptomiques. Grâce à l'approche intégrative des omiques en listeriologie, le présent travail contribuera à dévoiler la physiologie et la pathogenèse de la bactérie. / Conditions and proliferation in a wide range of environments from soil to mammalian host cells. The genetic heterogeneity in L. monocytogenes is reflected on its diversified clonal structure which correlates, to some extent, with phenotypic traits such as virulence or stress resistance. The thesis investigated two most prominent phenotypes, biofilm formation and virulence potential, from various perspectives using state-of-the art technologies. Throughout the studies, large panels of isolates were used to represent the intraspecific diversity. Unfavourable stimuli such as cold shock and nutrient deprivation induced bacterial adhesion step. Addition of NaCl to growth cultures stimulated biofilm production and, surprisingly, it significantly intensified biofilm maturation of nutrient-deprived cells. High degree of variation in relative biofilm productivity was observed among serotypes, genotypes, as well as isolates across culture conditions, however, certain genotype (clonal complex 26) revealed distinctively higher biofilm production under cold temperature (10°C) suggesting an association of genotype with biofilm phenotype. Pan-GWAS identified a number of genes among which those implicated in functions such as ‘transformation/competence’, ‘phage-related genes’, and ‘metabolism of phosphate’ will need further investigations for their roles in biofilm formation. RNA sequencing analysis revealed high intraspecific heterogeneity in basal transcriptome profiles that featured the role of regulatory network including certain transcriptional factors with key roles in virulence such as σB, PrfA, and CodY. The transcriptomic plasticity between lineage I and II as well as hyper- and hypovirulent genotypes supported the evolutionary and epidemiological characteristics of L. monocytogenes. Moreover, the central metabolic pathway was implicated in the infection in Galleria mellonella model system. Conclusively, the thesis explored intraspecific diversity in L. monocytogenes and resulted in ample phenotypic, genomic, and transcriptomic findings. With the integrative omics approach in listeriology, the present work will contribute to unveiling the physiology and pathogenesis of the bacterium.

Abiotic and biotic variation has been shown to be important in regulating nutrient cycling and belowground communities in natural systems. However, genetic variation in dominant plants as a driver of rates of nutrient cycling is still poorly understood and few studies have looked at genotype interactions across multiple environments. Using Populus angustifolia and a common garden approach, we hypothesized that all three factors: tree genetic variation, environmental conditions and genetic by environment (G x E) interactions would affect soil carbon (C) storage and nitrogen (N) cycling. Replicated copies of five different reciprocally planted Populus genotypes were studied in three separate 18-21 year old common gardens at different elevations (1300m, 1384m and 1587m) in northern Utah, to measure the genotype and environmental effects on pools of soil C and N as well as rates of soil net N nitrification and net mineralization. Our results indicate that genotypes influence pools of soil C, total N and C:N, but genotype did not influence net rates of nitrogen mineralization. Environmental variation significantly influenced pools of soil C, total N, soil C:N and rates of net nitrification and net N mineralization. As predicted, G x E interactions significantly influenced both pools and processes of soil C and N cycling. Overall, we found that genetic variation in plant traits (tree diameter and leaf/root chemistry) as well as soil texture across gardens were significant predictors of soil C and N pools and fluxes across seasons. These data help us understand the relative role of genotypic variation on above- and belowground interactions in different environments and the consequences of these interactions on ecosystem processes. The results from this study show that across an environmental gradient Populus angustifolia genotypes can influence nitrogen mineralization through feedbacks between environmental variation, tree phenotype and soils.

Abiotic and biotic variation has been shown to be important in regulating nutrient cycling and belowground communities in natural systems. However, genetic variation in dominant plants as a driver of rates of nutrient cycling is still poorly understood and few studies have looked at genotype interactions across multiple environments. Using Populus angustifolia and a common garden approach, we hypothesized that all three factors: tree genetic variation, environmental conditions and genetic by environment (G x E) interactions would affect soil carbon (C) storage and nitrogen (N) cycling. Replicated copies of five different reciprocally planted Populus genotypes were studied in three separate 18-21 year old common gardens at different elevations (1300m, 1384m and 1587m) in northern Utah, to measure the genotype and environmental effects on pools of soil C and N as well as rates of soil net N nitrification and net mineralization. Our results indicate that genotypes influence pools of soil C, total N and C:N, but genotype did not influence net rates of nitrogen mineralization. Environmental variation significantly influenced pools of soil C, total N, soil C:N and rates of net nitrification and net N mineralization. As predicted, G x E interactions significantly influenced both pools and processes of soil C and N cycling. Overall, we found that genetic variation in plant traits (tree diameter and leaf/root chemistry) as well as soil texture across gardens were significant predictors of soil C and N pools and fluxes across seasons. These data help us understand the relative role of genotypic variation on above- and belowground interactions in different environments and the consequences of these interactions on ecosystem processes. The results from this study show that across an environmental gradient Populus angustifolia genotypes can influence nitrogen mineralization through feedbacks between environmental variation, tree phenotype and soils.

The encroachment of woody species into grassland and savanna ecosystems has been well document since the early 1800s. Within the parkland ecoregion of western Canada, trembling aspen (Populus tremuloides Michx.) has been one of the key tree species increasing in dominance. Aspen encroachment is best explained not by single mechanism, but rather by a number of interacting ecological factors. In this study I examined the ecological consequences of the clonal biology in aspen as a means to explain persistence and observed tree-grass ratios within grassland savannas of western Canada. Results suggest that aspen stands cycle between a “stable” phase characterized by a dense mature canopy, and an “unstable” phase characterized by canopy breakup and increased regeneration from root suckers. It is during this unstable phase that clonal encroachment is likely to occur. Within these mature stands, different-aged ramets promote persistence by maximizing developmental variation. Such a mechanism overcomes the functional phenotypic uniformity of ramets within a single age-structured stand. Results from my study indicate that physiological integration is beneficial to the growth and survivorship of regenerating and encroaching aspen ramets. My results also suggest that the benefits of physiological integration are greatest in more stressful environments, and in recently established post-fire ramets. Finally, the consequences of variation in adaptive ecological relevant traits among individuals was examined by determining differences in vigor among aspen clones in relation to the production of secondary compounds (phenolic glycosides). My results demonstrate a high degree of variation in leaf phenolic glycosides production among clones. A significant amount of this variation was accounted for by differences in clone vigor (within population: individual susceptibility hypothesis), with a smaller amount related to environmental differences (among populations). In all instances, vigorous clones were significantly higher in levels of phenolic glycosides compared with dieback clones, suggesting that some individuals may be predisposed to undergo density-independent mortality. This has important ecological implications, because it implies that one of the key mechanisms regulating population dynamics, community interactions and biodiversity may be related to intrinsic adaptive differences in susceptibility among individuals.

The encroachment of woody species into grassland and savanna ecosystems has been well document since the early 1800s. Within the parkland ecoregion of western Canada, trembling aspen (Populus tremuloides Michx.) has been one of the key tree species increasing in dominance. Aspen encroachment is best explained not by single mechanism, but rather by a number of interacting ecological factors. In this study I examined the ecological consequences of the clonal biology in aspen as a means to explain persistence and observed tree-grass ratios within grassland savannas of western Canada. Results suggest that aspen stands cycle between a “stable” phase characterized by a dense mature canopy, and an “unstable” phase characterized by canopy breakup and increased regeneration from root suckers. It is during this unstable phase that clonal encroachment is likely to occur. Within these mature stands, different-aged ramets promote persistence by maximizing developmental variation. Such a mechanism overcomes the functional phenotypic uniformity of ramets within a single age-structured stand. Results from my study indicate that physiological integration is beneficial to the growth and survivorship of regenerating and encroaching aspen ramets. My results also suggest that the benefits of physiological integration are greatest in more stressful environments, and in recently established post-fire ramets. Finally, the consequences of variation in adaptive ecological relevant traits among individuals was examined by determining differences in vigor among aspen clones in relation to the production of secondary compounds (phenolic glycosides). My results demonstrate a high degree of variation in leaf phenolic glycosides production among clones. A significant amount of this variation was accounted for by differences in clone vigor (within population: individual susceptibility hypothesis), with a smaller amount related to environmental differences (among populations). In all instances, vigorous clones were significantly higher in levels of phenolic glycosides compared with dieback clones, suggesting that some individuals may be predisposed to undergo density-independent mortality. This has important ecological implications, because it implies that one of the key mechanisms regulating population dynamics, community interactions and biodiversity may be related to intrinsic adaptive differences in susceptibility among individuals.

The overarching goal of my dissertation is to explore the potential and limits of a trait-based approach to plant ecology. Together, the different studies presented here address two explicit and implicit foundational assumptions underpinning the trait-based approach: (1) that the correlation patterns and biological significance of traits transfer across scales and (2) that the phenotypic complexity of plants can accurately be synthesized into a few meaningful traits to study their ecology. Moreover, the last chapter focuses on a third key assumption: (3) that traits are strong predictors of plant performance (Shipley et al. In Press). I examine these assumptions by exploring multivariate patterns of phenotypic variation and integration across different ecological scales (e.g., individuals, populations, species) while explicitly considering the phenotypic complexity of trees, both in terms of their multidimensional and integrated nature. Two themes thus permeate this body of work: scales and phenotypic complexity. Much of what we know about the relationships among key traits comes from species-scale studies. Trait variation at smaller scales are often interpreted in the context of these interspecific relationships, but it is not clear that interspecific patterns observed at global scales apply to smaller scales. Moreover, although plants are complex, integrated organisms with intricate relationships among their traits, single traits are often studied and interpreted without considering the rest of the phenotype. Yet, examining individual traits outside of their phenotypic context might provide limited insight or be misleading. To address these shortcomings, this body of work examines multidimensional patterns of trait variation and correlation across ecological scales. It uses (1) a set of six ecophysiological leaf traits from mature trees in a lowland tropical rainforest, and (2) a set of twenty leaf, root, stem, branch and whole-plant ecophysiological traits from deciduous saplings in a temperate forest. The combination of our findings point to three main conclusions: (i) local interspecific and intra-population trait integration structures differ from each other and from the global interspecific patterns reported in the literature, such that global-scale interspecific patterns cannot readily be transferred to more local scales; (ii) considering the complexity of the plant phenotype provides better insights into ecological patterns and processes than what we can learn from considering individual or a handful of traits; and (iii) traits strongly affect individual plant performance, although there is no relationship between a species' trait correlation structure and its environmental niche, which suggests that there are multiple alternative optimal phenotypes in a given environment.