Our bodies contain a vast number and diversity of microbes. These microbes interact, and these interactions can define how microbes affect us. Microbial ecology and evolution, therefore, are important for both microbiology and human health. However, our understanding of microbial communities remains limited. There is a need for theory that dissects the complexity and identifies the key factors and processes affecting microbial groups. Here I develop realistic computer simulations and population models of microbial communities. My first project seeks to explain microbial communication (quorum sensing) and argues that quorum sensing is a way to infer when competing genotypes are no longer a threat. The second project proposes an evolutionary explanation for another major microbial trait: adhesion. I argue that adhesion is a weapon allowing cells to compete within microbial groups and push competitors out, particularly when growing on a host epithelium. The third project moves from microbes to the host and asks whether a host can control which microbes grow and persist inside it. I develop a model of the human gut epithelium and show that the gut architecture amplifies the ability of hosts to select helpful microbes over harmful ones using nutrient secretion. In addition to selecting particular microbial strains, a host will also benefit from stable symbiotic communities that behave in a predictable manner. But what determines whether host-associated communities are ecologically stable? My final project uses ecological network theory to show that ecological stability is likely to be a problem for gut communities that are diverse and contain species that cooperate with each other. However, I argue that the host should function as an ecosystem engineer that increases ecological stability by weakening the strong dependence of cooperating species upon one another. While host-associated communities are complex ecological systems, my thesis identifies key factors that affect their form and function.

Le suivi des populations animales et végétales nous a amené à constater une perte importante de la diversité biologique. Les objectifs de la Convention sur la diversité biologique à atteindre pour 2010 sous-tendent la poursuite détaillée de ce suivi à l’échelle mondiale (CBD 2000). Cependant, il est difficile d’avoir une perception d’ensemble de la biodiversité d’un territoire, car les écosystèmes sont des entités dynamiques et évolutives, dans l’espace et dans le temps. Le choix d’un indicateur relevant de l’ensemble des ces caractéristiques devient donc primordial, bien qu’il s’agisse d’une tâche laborieuse. Ce projet propose d’utiliser la bioacoustique comme indicateur environnemental pour faire le suivi des espèces animales en milieu tropical. Afin de faire un suivi à une échelle régionale de la biodiversité, et ce, dans l’un des biomes les plus menacés de la planète, soit celui de la Mata Atlântica brésilienne, ce projet de recherche a comme objectif général de démontrer qu’il est possible d’associer la biophonie (événements sonores), à des événements biologiques (la richesse spécifique animale) en quantifiant des événements sonores (à l’aide des chants produits par les oiseaux, les insectes chanteurs de même que par les anoures) et en tentant de les associer aux fluctuations de la biodiversité. En plus de répondre à cet objectif général, trois objectifs spécifiques ont été définis : 1) comparer la biophonie et l’anthropophonie de milieux soumis à différents niveaux d’anthropisation ou de conservation afin d’évaluer l’impact anthropique sur le milieu, 2) évaluer la variabilité spatiale de la biodiversité, de même que 3) sa variabilité temporelle. Les résultats ont démontré que la biophonie est représentative de la biodiversité d’un milieu, et ce, même dans des conditions de biodiversité maximale puisqu’il existe une très forte relation entre les deux variables. De plus, les résultats révèlent une différence significative dans le ratio anthropophonie/biophonie de milieux soumis à différents niveaux de protection du territoire. La différenciation d’indices de puissance relative (dB/kHz) nous indique également l’importance de la variabilité spatiale et temporelle de la biodiversité, et par conséquent, l’importance de faire le suivi des espèces dans divers milieux et à diverses périodes afin d’obtenir une vision adéquate de la biodiversité régionale. / Recent monitoring of plant and animal populations has led us to observe a significant loss of global biodiversity. The objectives of the Convention on Biological Diversity for 2010 are to encourage environmental monitoring worldwide (CBD 2000). However, it is difficult to have an adequate portrait of the overall biodiversity of an area, because ecosystems are dynamic and evolving in both space and time. The choice of an indicator is therefore essential. This project proposes to use bioacoustics as an environmental indicator to monitor the animal biodiversity in tropical areas, in one of the most threatened biomes on the planet, the Mata Atlantica in Brazil. Our aim is to demonstrate that it is possible to relate biophony (sound events) to biological events (punctual animal species richness), i.e. to quantify songs produced by birds, insects and anurans singers and associate them to changes in biodiversity. In addressing this overall goal, three specific objectives were put forward: 1) compare the biophony and anthropophony of different landscapes, subjected to different levels of human occupation and conservation, in order to assess the human impact on the environment, 2) assess the spatial variability of biodiversity, as well as 3) its temporal variability. Results showed that biophony is representative of the biodiversity of an area, even under conditions of maximum biodiversity such as found in Brazil because there is a very strong positive relationship between these two variables. In addition, the results show a significant difference in the ratio anthropophony/biophony in environments subject to different human impacts. Disparate indices of relative power (dB / kHz) also reveal the importance of spatial and temporal variability of biodiversity, and therefore the importance of monitoring biophony in different environments and at different times to obtain an adequate portrait of a region’s biodiversity.

Ce mémoire visait à déterminer si la platanthère à gorge frangée (Platanthera blephariglottis var. blephariglottis), une orchidée, est une espèce indicatrice de l’intégrité écologique des tourbières ombrotrophes. Les indicateurs d’intégrité écologique sont des outils indispensables pour évaluer efficacement les composantes d’un écosystème. Les résultats indiquent que l’abondance de la platanthère est fortement liée à l’indice de qualité floristique (FQAI). Le FQAI est aussi un excellent prédicateur de la présence de l’espèce, avec un taux de succès à 87%. D’autre part, l’abondance de l’orchidée est négativement affectée par les activités anthropiques et la matrice environnante. D’un point de vue descriptif, les habitats renfermant une grande abondance d’orchidées sont caractérisés par une faible microtopographie de surface et un recouvrement important de bryophytes et d’éricacées de petite taille. Globalement, ce mémoire a montré que la platanthère renferme un potentiel pour être indicatrice de l’intégrité écologique des tourbières ombrotrophes au Québec. / The aim of this study was to evaluate whether White Fringed Orchid (Platanthera blephariglottis var. blephariglottis) can be used as an indicator of Sphagnum bog integrity. Ecological indicators of integrity are important tools as it is impossible to monitor efficiently all components of an ecosystem. Results indicate that White Fringed Orchid abundance is highly linked with floristic quality assessment index (FQAI). FQAI is also a good predictor of presence of the species, with an accuracy of 87%. On the other hand, orchid abundance is negatively affected by anthropogenic activities and the environmental matrix. Similarly, peatlands having low edge effect are characterized by higher orchid abundance than those more influenced by edges. From a descriptive perspective, high orchid abundance habitat is characterized by low surface microtopography, high bryophyte and small ericaceous covers. Globally, this study has shown that White Fringed Orchid has potential to evaluate ecological integrity in Sphagnum bogs in Québec.

L’objectif principal de ce projet est d’évaluer le potentiel d’un système de marais filtrants combinés pour le traitement d’un lixiviat contaminé aux agents de préservations du bois - l’arséniate de cuivre chromaté (ACC) et le pentachlorophénol (PCP) - en portant une attention particulière au rôle des plantes. Pour ce faire, une expérience en pot faisant varier la concentration d’exposition de quatre espèces de macrophyte (Typha angustifolia, Phalaris arundinacea, Phragmites australis americanus et Phragmites australis australis) a été effectuée. Le suivi de quatre marais filtrants à écoulement horizontal sous-surfacique, plantés d’une des quatre espèces de macrophyte et d’un bassin planté de saules (Salix Miyabeana SX67) a également été réalisé. La résistance des plantes au milieu contaminé, la capacité de bioaccumulation des macrophytes et les efficacités de traitement des différents systèmes ont été analysés. Nos résultats montrent que la concentration d’exposition n’influence pas la capacité des plantes à croître en milieu contaminé. Par contre, il existe une relation dose-réponse entre la concentration d’exposition et la capacité de bioaccumulation des macrophytes. Les quatre marais pilotes ont tous des efficacités de traitements supérieures à 55% en 2013 et 82% en 2014 pour les contaminants à l’étude. Le bassin de saule a la capacité théorique d’évapotranspirer jusqu’à 1200 L par jour. De plus, ses efficacités de traitements sont supérieures à 59% pour tous les composés à l’étude. L’utilisation de marais filtrants pour le traitement d’un lixiviat contaminé aux agents de préservations du bois est donc une alternative intéressante aux méthodes de traitement conventionnel. / The main objective of this project is to evaluate the capacity of a combined constructed wetland system to treat a leachate polluted with two wood preservatives-chromium copper arsenate (CCA) and pentachlorophenol (PCP)- according a particular importance to the role of plants. The effect of the exposure concentration on four macrophytes species (Typha angustifolia, Phalaris arundinacea, Phragmites australis americanus and Phragmites australis australis) was evaluated using a pot experiment. Four HSSF pilot constructed wetlands, planted with one of these plants species, were monitored. The role of an HSSF constructed wetland, planted with willow (Salix Miyabeana SX67), placed at the end of the treatment chain was also assessed. The plants growth and survival and their bioaccumulation capacity were measured, and the system treatment efficiencies were monitored. There was no effect of the concentration on plants growth but the higher exposure concentration resulted in a higher bioaccumulation in the roots of the four macrophytes. All four pilots CW showed treatment efficiencies superior to 55% in 2013 and to 82% in 2014 for the pollutants tested. The willows CW have the theorical capacity to evapotranspirate up to 1200 L of water. Its treatments efficiencies were over 59% for all the pollutants tested. A combined constructed wetland system is a good alternative to conventional methods to treat a leachate polluted with wood preservatives.

Doctor of Philosophy / Department of Biology / Michael A. Herman / Determining the genetic mechanisms involved in organismal response to environmental change is essential for understanding the effects of anthropogenic disturbance. The composition of the bacterial-feeding nematode community is an excellent biological indicator of disturbance, particularly in grassland ecosystems. We have previously shown that grassland soil nematodes are responsive to perturbations in the field including the addition of nitrogen fertilizer. We are interested in how this perturbation affects the microbial community and downstream effects on the next trophic level, the bacterial-feeding nematodes. To determine the effects of disturbance on soil bacterial communities we used massively parallel sequencing and found that chronic nitrogen addition on tallgrass prairie significantly impacts overall bacterial community diversity and the abundance of specific bacterial taxa. Because native soil nematodes lack well developed genomic tools, we employed Caenorhabditis elegans as a model for native soil nematode taxa and used transcriptional profiling to identify 204 candidate genes regulated in response to altered bacterial diets isolated from grassland soils. To biologically validate our results we used mutations that inactivate 21 of the identified genes and showed that most contribute to fitness or lifespan in a given bacterial environment. Although these bacteria may not be natural C. elegans food sources, this study aimed to show how changes in food source, as can occur in environmental disturbance, has large effects on gene expression and those genes whose expression are affected, contribute to fitness. Furthermore, we identified new functions for genes of unknown function as well as previously well-characterized genes, demonstrating the utility of this approach to further describe C. elegans genome. We also investigated the function of previously well-characterized C. elegans defense pathways in our grassland soil bacterial environments and found that some are environment specific. Additionally, we found that cuticular collagen genes are important for lifespan, and appear to function downstream of known defense pathways. Overall, our results suggest that anthropogenic disturbance in grasslands alters the most basal components of the soil food web, bacteria and bacterial-feeding nematodes through the genes they possess and how they are expressed, and resultant bottom-up effects could have profound consequences on ecosystem health and function.

<p>I examined recruitment patterns of multiple tree species in a western Amazonian floodplain forest at three ontogenetic stages: seed fall, seedling establishment, and sapling recruitment.</p><p>From analyzing a long-term seed rain dataset collected using a high-density array of seed traps, I confirmed that seed fall decreases sharply with increasing distance from fruiting trees, with disproportionately large contributions from a very small fraction of all trees. Patterns of seed fall, although idiosyncratic for individual species, tended to relate to dispersal syndrome. Intact seeds were found at significantly greater distances away from fruiting adults than ripe fruit and almost exclusively comprised the tail of the seed shadow for most species.</p><p>Saplings of all species examined recruited in areas of very low predicted seed density at significantly higher abundances than expected under a null hypothesis of "all seeds are equal". The value of a seed in terms of its potential to produce a sapling recruit - measured as sapling/seed ratio - initially increased greatly with increasing distance from reproductive conspecific adults and leveled off at farther distances, in almost all species.</p><p>A parallel experimental study employed >1000 individual seedlings of common tree species situated near and far from conspecific adults. Overall survival for all species pooled and for eight out of 11 individual species was significantly higher at sites located far from versus close to conspecific adults, with the study design controlling for seedling density at sites. Survival analysis based on multiple censuses revealed that a "distance effect" persisted and intensified over time, although the timing of onset of distance-related differential mortality differed amongst species. The role of host-specific invertebrate herbivores and microbial pathogens in causing seedling mortality near conspecific adults was confirmed by the use of mesh exclosures. </p><p>Overall, my results provide community-level support for the influence of distance-dependent processes on recruitment patterns. Seed dispersal appears critical for successful recruitment and undispersed seeds make a minimal contribution. When de-coupled from distance-dependence, effects of competition-based density-dependent processes on recruitment were weak or undetectable. I conclude that community-level tree recruitment processes and patterns in western Amazonian lowland rainforests that harbor intact floral and faunal assemblages conform closely to predictions of the Janzen-Connell hypothesis of tropical tree recruitment.</p> / Dissertation

<p>Plants respond to changes in their local environment and, at the same time, influence the environment at a global scale. The molecular and physiological mechanisms regulating this interaction are not completely understood and this limits our capacity to predict the response of vegetation to future environmental changes. This dissertation combined tools from genomics, physiology, and ecology to examine the response of plants to environmental change. Specifically, it focused on processes affecting carbon and water exchange in forest trees because (1) trees are long-lived species that might face repeated environmental challenges; (2) relatively little information exists about the genes and the molecular mechanisms regulating structural and physiological traits in adult, long-lived woody plants; and (3) forest trees exchange a significant amount of carbon and water with the atmosphere and are therefore major players in the global carbon and water cycles. </p><p>Water flux through forests depends both on environmental conditions (e.g., soil moisture) and on the hydraulic architecture of individual trees. Resistance to xylem cavitation is an important hydraulic trait that is often associated with drought tolerance but potentially at the cost of reduced carbon uptake. The second chapter of this dissertation evaluated the variation in resistance to xylem cavitation, hydraulic conductivity, wood anatomy traits, and leaf gas exchange across 14 co-occurring temperate tree species including both angiosperms and gymnosperms. The relationship between vulnerability to cavitation (ψ₅₀) and hydraulic conductivity within specific organs (i.e. stems and roots) was not significant when considering the phylogenetic association between species. However, even after phylogenetic correction, photosynthetic carbon uptake (A) was positively correlated with both stem and root ψ₅₀, and stomatal conductance (g_s) was strongly correlated with root ψ₅₀ . These results suggest that there is a trade-off between vulnerability to cavitation and water transport capacity at the whole-plant level, and that this functional relationship reflects an adaptive response to the environment. </p><p>Forests are an important component of the global carbon cycle that can be directly impacted by a rise in atmospheric CO₂ concentration.. The third chapter of this dissertation investigated the effects of long-term exposure to elevated CO2 on the gene expression of mature, field-grown loblolly pine trees. Using cDNA microarrays, I compared the expression of 1784 pine transcripts in trees growing under ambient and those under elevated CO₂ at monthly intervals throughout a growing season. Overall, more genes were upregulated than downregulated by elevated CO₂, although the total number of genes differentially expressed varied throughout the season. The pattern of increasing number of differentially expressed genes until the peak of the growing season (July and August) followed by a decrease in that number, matched the seasonal trend of tree growth and photosynthetic response to elevated CO₂ in this species. The seasonal trend also reflected the interaction among multiple abiotic factors intrinsic to field conditions and emphasized the relevance of evaluating the role of genes in their natural environment. Genes consistently upregulated by elevated CO₂ were functionally associated with environmental sensing, cellular signaling, and carbon metabolism, in particular the degradation of carbohydrates through respiration. An increase in carbohydrates degradation is particularly relevant in the context of carbon balance of forest trees because of the potential for enhanced leaf and tree respiration leading to a reduced sink capacity for CO₂. </p><p>Loblolly pine produces several flushes of needles throughout the year each with an average lifespan of 19 months. Each year, two age classes of needles contribute to the annual carbon sequestration of the loblolly pine forest. To address the impact of leaf age on the effects of elevated CO₂ in carbon metabolism regulation, I compared the gene expression profiles from trees under ambient and elevated CO₂ conditions in two needle cohorts: one-year-old and current-year. Differential expression under elevated CO₂ was seven times more frequent in current-year than in one-year-old needles. Despite differences in magnitude, many of the patterns within specific groups of genes were similar across age classes. For instance, there was a trend for downregulation of genes involved in the light-reactions of photosynthesis and those in photorespiration in both age classes, while genes associated with dark respiration were largely upregulated by elevated CO₂ in both cases. The difference between the two cohorts was particularly evident in the group of genes related to energy production (ATP synthesis) and the group associated with carbon partitioning (sucrose and starch metabolism). Because sucrose and starch metabolism categories included many genes known to be important regulators of gene expression and plant physiological processes, this suggests that this stage of carbon metabolism might be an important control point in age-dependent foliar responses to elevated CO₂.</p><p>This dissertation examined both structural and physiological components of plant water and carbon relations (Chapter 2) across different biological scales of organization (whole-plant level in Chapter 2; gene-level response to ecosystem-level changes in Chapters 3 and 4) and reflecting adjustments at distinct temporal scales (life-span of the organism vs. evolutionary selection of traits). An integrative approach was used to advance our understanding of how plants acclimate and adapt to their environment, and to provide a mechanistic framework for predictive models of plant response to environmental change. </p> / Dissertation

<p>Since wetlands provide many important ecosystem services, there is much interest in protecting existing wetlands and restoring degraded wetlands. Yet, degraded wetlands and restoration sites are often vulnerable to plant invasions that can hinder restoration success. Invasive plants typically reduce biodiversity and alter important ecosystem functions and services. This dissertation examines the ecological impact and management of invasive plant species during wetland restoration with a focus on three important drivers of plant community change in wetland ecosystems: disturbance, plant strategies, and environmental filters.</p><p>The investigations included in this research were conducted in a tropical dry wetland (Palo Verde Marsh, Palo Verde National Park, Costa Rica) and a temperate piedmont riparian forest (Sandy Creek, Duke Forest Stream and Wetland Assessment and Management Park, Durham, North Carolina). In these experiments, the primary species of interest are <italic>Typha domingensis</italic> Pers. (cattail; Typhaceae), <italic>Ligustrum sinense</italic> Lour. (Chinese privet; Oleaceae), <italic>Arundinaria gigantea</italic> (Walter) Muhl. (giant cane; Poaceae), and <italic>Microstegium vimineum</italic> (Trin.) A. Camus (Japanese stiltgrass; Poaceae).</p><p>The expansion of <italic>Typha</italic> into wetlands historically not dominated by cattail typically occurs in response to natural and anthropogenic perturbations. Management approaches that reduce <italic>Typha</italic> dominance, increase diversity, and restore or maintain wetland ecosystem services are of interest worldwide. The objective of the first phase of the research was to investigate a unique <italic>Typha</italic> removal method that is used in one of the most dynamic and ecologically important wetlands in Central America (Palo Verde Marsh, Palo Verde National Park, Costa Rica; a Ramsar Wetland of International Importance). Palo Verde Marsh is a tropical dry wetland with distinct and extreme wet and dry seasons; it is flooded during the wet season and has no standing water for much of the dry season. Palo Verde Marsh has historically provided important habitat for very large populations of migratory birds. However, a cattail (<italic>T. domingensis</italic>) expansion in the 1980s greatly altered the plant community and reduced avian habitat. Since then, <italic>Typha</italic> has been managed using fangueo (a Spanish word, pronounced as "fahn-gay-yo" in English). During fangueo, <italic>Typha</italic> is crushed and locally removed by a tractor with metal paddle wheels. I applied a <italic>Typha</italic> removal treatment at three levels (control, fangueo, and fangueo with fencing to exclude cattle grazing) at Palo Verde Marsh. Fangueo was applied at the beginning of the dry season resulting in a large reduction in <italic>Typha</italic> dominance (decreased aboveground biomass, ramet density, ramet height), an increase in open areas with no vegetation, and a 98 and 5-fold increase in avian density and richness, respectively. Importantly, fangueo had no apparent long-term impact on any of the soil properties measured (including bulk density). Interestingly, low soil and foliar N:P values indicate that Palo Verde Marsh and other wetlands in the region may be nitrogen limited. The fangueo process is an effective method for restricting <italic>Typha</italic> expansion and increasing plant and avian diversity. I present a model that illustrates the impact of <italic>Typha</italic> management and seasonal flooding on the plant and avian community. The technique might be adopted or modified for the restoration and management of <italic>Typha</italic> and other invasive emergent plants in other wetlands.</p><p>The second objective of this research was to better quantify the impact of the distinct and extreme anaerobic/aerobic annual cycle on the plant community in Palo Verde Marsh. Since the impact of seasonal flooding on the plant community in seasonal wetlands is often most evident after disturbance, I created gaps in the wetland vegetation via the mechanical removal of emergent vegetation and then measured plant community change using surveys of the wet and dry season standing vegetation, the seed bank, and <italic>in situ</italic> seedling recruitment. As expected, seasonal flooding acted as an environmental filter and resulted in distinct dry and wet season assemblages. The dominant plant life forms present after vegetation removal differed between seasons with emergents dominating during the dry season and floating-rooted, free-floating, and submerged species more dominant during the wet season. I identified common species that are characteristic of both seasonal assemblages and used indicator species analyses to identify species that are only likely to be found during the wet season. I also characterized the seed bank at this site; like most seasonal wetlands, plant species' resilience in this wetland were dependent upon a large and diverse seed bank which allowed many species to revegetate after disturbance and the extreme wet/dry conditions which acted like environmental filters.</p><p>In addition to the experiments conducted in Palo Verde Marsh, this dissertation also presents the results from an experiment in a temperate riparian restoration site in the North Carolina Piedmont (Sandy Creek, Duke Forest Stream and Wetland Assessment and Management Park, Durham, NC). Since riparian restoration efforts in the southeastern U.S. are often hindered by invasive non-native plants, there is much interest in approaches that can be used to reduce the impact of invasive non-native plant populations at the local level (e.g., a restoration site). In addition to the impact of non-native species-specific removal efforts, there is also much interest in the identification and assessment of native competitive-dominant plant species that can be used during riparian restoration to support important ecosystem functions and reduce non-native invasibility. <italic>Ligustrum sinense</italic> (Chinese privet) is a very common invasive non-native shrub in the region. <italic>Arundinaria gigantea</italic> (giant cane) is a native bamboo species that used to be very abundant in riparian and wetland ecosystems in the region. The objectives of this phase of the research were to: (1) measure the plant community response to removal of mature <italic>L. sinense</italic> individuals; and (2) quantify planted <italic>A. gigantea</italic> clonal expansion in the presence of other plants, particularly common non-native invasive species. Due to its potential for rapid growth and expansion, it was hypothesized that <italic>A. gigantea</italic> would be able to compete with common non-native species and reduce non-native invasibility. In a three-year split-plot experimental design, I applied a Privet-Presence treatment at two levels (Privet Present, Privet Removed) and a Cane-Planting treatment also at two levels (Cane, No Cane). The privet removal treatment resulted in 100% mortality of mature privet individuals. After privet removal, <italic>L. sinense</italic> seedlings recruited into these plots but growth has been very slow and these <italic>L. sinense</italic> individuals are not yet dominant. The privet canopy allows minimal understory plant recruitment and growth and privet removal resulted in an increase in species richness and diversity in the first year. However, in these Privet-Removed plots, a non-native invasive annual grass (<italic>Microstegium vimineum</italic>) invaded, became the most dominant species, and reduced species richness and diversity. In Privet-Removed plots, <italic>A. gigantea</italic> clonal expansion (i.e., ramet density, genet area, ramet diameter, and ramet height) was small in the first year but increased in the second and third years. Importantly, in Privet-Removed plots where <italic>A. gigantea</italic> was planted, <italic>M. vimineum</italic> cover was lower and species richness and diversity were greater; planting <italic>A. gigantea</italic> appears to have facilitated the establishment of other species and, in the process, increased diversity.</p><p>Our results emphasize several general conclusions that are applicable to other restoration efforts in other ecosystems with other plant species. First, during ecological restoration, invasive non-native plant removal alone will typically not restore native plant communities. Non-native invasive plant populations are typically very resilient to removal. Hence, long-term reductions in non-native invasibility will often require additional management efforts. For example, in the tropics my research showed the effectiveness of Fangueo for reducing <italic>Typha</italic> monocultures and increasing native plant and bird diversity. Another approach for improving ecosystems functions and reducing non-native invasibility after invasive plant removal is to carefully select and plant native species with competitive-dominant traits that will be able to compete with invading non-native species and resist invasion. Although this seemingly simple approach is often used by restoration practitioners, the results are rarely monitored and surprisingly few studies are designed to explicitly identify and investigate the performance of these important native competitive-dominant species.</p> / Dissertation

<p>Because species respond individually to climate change, understanding community assembly requires examination of multiple species from a diversity of forest niches. I present the post-glacial phylogeographic history of an understory, parasitic herb (<italic>Epifagus virginiana</italic>, beechdrop) that has an obligate and host specific relationship with a common eastern North American hardwood tree (<italic>Fagus grandifolia</italic>, American beech). The migration histories of the host and parasite are compared to elucidate potential limits on the parasite's range and to understand their responses to shared climate change. Two chloroplast DNA regions were sequenced and 9 microsatellite loci genotyped from parasite specimens collected throughout the host's range. These data were compared with available cpDNA sequences from the host (McLachlan et al. 2005) and host fossil pollen records from the last 21,000 years (Williams et al. 2004). Analyses of genetic diversity reveal high population differentiation in the parasite's southern range, a possible result of long term isolation within multiple southern glacial refuges. Estimates of migration rates and divergence times using Bayesian coalescent methods show the parasite initiating its post-glacial range expansion by migrating northward into the northeast from southern areas, then westward into the midwest, a pattern consistent with the development of high density beech forests. This result is strongly confirmed through spatial linear regression models, which show host density plays a significant role in structuring parasite populations, while the initial migration routes of the host are irrelevant to parasite colonization patterns. Host density is then used as a proxy for the parasite's habitat quality in an effort to identify the geographic locations of its migration corridors. Habitat cost models are parameterized through use of the parasite's genetic data, and landscape path analyses based on the habitat map show a major migration corridor south of the Great Lakes connecting the northeast and midwest. Host density was the major determinant controlling the parasite's range expansion, suggesting a lag time between host and parasite colonization of new territory. Parasites and other highly specialized species may generally migrate slower due to their complex landscape requirements, resulting in disassociation of forest assemblages during these times. From these results, the low migration capacities of highly specialized species may be insufficient to outrun extirpation from their current ranges.</p> / Dissertation

Le suivi des populations animales et végétales nous a amené à constater une perte importante de la diversité biologique. Les objectifs de la Convention sur la diversité biologique à atteindre pour 2010 sous-tendent la poursuite détaillée de ce suivi à l’échelle mondiale (CBD 2000). Cependant, il est difficile d’avoir une perception d’ensemble de la biodiversité d’un territoire, car les écosystèmes sont des entités dynamiques et évolutives, dans l’espace et dans le temps. Le choix d’un indicateur relevant de l’ensemble des ces caractéristiques devient donc primordial, bien qu’il s’agisse d’une tâche laborieuse. Ce projet propose d’utiliser la bioacoustique comme indicateur environnemental pour faire le suivi des espèces animales en milieu tropical. Afin de faire un suivi à une échelle régionale de la biodiversité, et ce, dans l’un des biomes les plus menacés de la planète, soit celui de la Mata Atlântica brésilienne, ce projet de recherche a comme objectif général de démontrer qu’il est possible d’associer la biophonie (événements sonores), à des événements biologiques (la richesse spécifique animale) en quantifiant des événements sonores (à l’aide des chants produits par les oiseaux, les insectes chanteurs de même que par les anoures) et en tentant de les associer aux fluctuations de la biodiversité. En plus de répondre à cet objectif général, trois objectifs spécifiques ont été définis : 1) comparer la biophonie et l’anthropophonie de milieux soumis à différents niveaux d’anthropisation ou de conservation afin d’évaluer l’impact anthropique sur le milieu, 2) évaluer la variabilité spatiale de la biodiversité, de même que 3) sa variabilité temporelle. Les résultats ont démontré que la biophonie est représentative de la biodiversité d’un milieu, et ce, même dans des conditions de biodiversité maximale puisqu’il existe une très forte relation entre les deux variables. De plus, les résultats révèlent une différence significative dans le ratio anthropophonie/biophonie de milieux soumis à différents niveaux de protection du territoire. La différenciation d’indices de puissance relative (dB/kHz) nous indique également l’importance de la variabilité spatiale et temporelle de la biodiversité, et par conséquent, l’importance de faire le suivi des espèces dans divers milieux et à diverses périodes afin d’obtenir une vision adéquate de la biodiversité régionale. / Recent monitoring of plant and animal populations has led us to observe a significant loss of global biodiversity. The objectives of the Convention on Biological Diversity for 2010 are to encourage environmental monitoring worldwide (CBD 2000). However, it is difficult to have an adequate portrait of the overall biodiversity of an area, because ecosystems are dynamic and evolving in both space and time. The choice of an indicator is therefore essential. This project proposes to use bioacoustics as an environmental indicator to monitor the animal biodiversity in tropical areas, in one of the most threatened biomes on the planet, the Mata Atlantica in Brazil. Our aim is to demonstrate that it is possible to relate biophony (sound events) to biological events (punctual animal species richness), i.e. to quantify songs produced by birds, insects and anurans singers and associate them to changes in biodiversity. In addressing this overall goal, three specific objectives were put forward: 1) compare the biophony and anthropophony of different landscapes, subjected to different levels of human occupation and conservation, in order to assess the human impact on the environment, 2) assess the spatial variability of biodiversity, as well as 3) its temporal variability. Results showed that biophony is representative of the biodiversity of an area, even under conditions of maximum biodiversity such as found in Brazil because there is a very strong positive relationship between these two variables. In addition, the results show a significant difference in the ratio anthropophony/biophony in environments subject to different human impacts. Disparate indices of relative power (dB / kHz) also reveal the importance of spatial and temporal variability of biodiversity, and therefore the importance of monitoring biophony in different environments and at different times to obtain an adequate portrait of a region’s biodiversity.