This study was conducted to evaluate the relative roles of trophic dynamics and nutrient concentrations in the development of cyanobacteria blooms. The motivation for this research was to gain insights into how food webs respond to ecosystem-scale changes, using Lake Champlain as a case study. I sought to link field-based observations with experimentally derived data on mechanisms to better understand the processes that drive cyanobacteria blooms. My research addressed three specific topics: (1) associations among phytoplankton and nutrient concentration trends over time, (2) the impacts of planktivory by invasive fish on the ambient zooplankton community, and (3) the role of herbivore zooplankton grazers in determining the composition of the phytoplankton community. I found little evidence of a strong association between nutrient concentrations and phytoplankton community composition during summer months in shallow bays of Lake Champlain prone to annual cyanobacteria blooms. Fish diet analysis indicated that invasive white perch (Morone americana) and alewife (Alosa pseudoharengus) selectively graze on large zooplankton, which has likely led to substantial declines in zooplankton biomass. I used these results to inform the design of a mesocosm study, which tested the effects of zooplankton grazing on phytoplankton and provided support for the theory that large zooplankton grazing pressure changes the size structure, abundance and composition of phytoplankton. High nutrient concentrations support increased levels of ecosystem productivity, but cascading trophic dynamics are additional forces that are likely contributing to the determination of phytoplankton community composition. Collectively, my research suggests that in shallow bays of Lake Champlain, selective grazing by invasive planktivorous fish is shifting the size structure of the zooplankton grazer community and has likely contributed to conditions that favor dominance by cyanobacteria in summer.

Stonecats (Noturus flavus, Rafinesque 1818) are designated as a Vermont state-listed endangered species because their known distribution is limited to two systems, the LaPlatte and Missisquoi rivers. The restricted distribution and lack of knowledge on abundance in either river is cause for concern in the continued survival of these populations. Based on the capture numbers and large size range of individuals, we predicted that the population in the LaPlatte River, which provides quality benthic habitat, is stable. However, the Missisquoi River population has the potential for increased intermittent mortalities from two sources, lampricide (3-trifluoromethyl-4-nitrophenol) treatment every four years and dewatering during drought conditions. In 2012, 2013, and 2014 we captured, PIT tagged (> 90 mm total length), and VIE marked all Stonecats collected using backpack electrofishing and minnow traps in the LaPlatte and Missisquoi rivers. A total of 1252 were PIT tagged in the LaPlatte River and 125 in the Missisquoi River. First we estimated survival and seniority of Stonecats in the LaPlatte River, using the Pradel model in Program Mark, and derived an average annual lambda of 0.9826. The population estimates from the LaPlatte River were modeled in a population viability analysis (PVA). Few Stonecats were captured in the Missisquoi River, so we used the PVA model to estimate the extinction rates with increased intermittent mortalities on 4-, 6-, and 8-year cycles to predict the long-term viability of the population. With an initial number of 2000 individuals, the population became extinct 100% of the time with an increase in mortality of 0.1 on a 4-year cycle. Our results indicate that the LaPlatte River population is stable, but the Missisquoi River population, in the area affected by lampricide, is not. These results are informative for developing future management scenarios, however, our approach has uncertainty that can only be addressed through obtaining more data on the Missisquoi River population.

Rivers deliver significant macronutrients and sediments to lakes that can vary substantially throughout the year. These nutrient and sediment loadings, exacerbated by winter and spring runoff, impact aquatic ecosystem productivity and drive the formation of harmful algae blooms. The source, extent and magnitude of nutrient and sediment loading can vary drastically due to extreme weather events and hydrologic processes, such as snowmelt or high flow storm events, that dominate during a particular time period, making the temporal component (i.e., time over which the loading is estimated) critical for accurate forecasts. In this work, we developed a data-driven framework that leverages the temporal variability embedded in these complex hydrologic regimes to improve loading estimates. Identifying the "correct" time scale is an important first step for providing accurate estimates of seasonal nutrient and sediment loadings. We use water quality concentration and associated 15-minute discharge data from nine watersheds in Vermont's Lake Champlain Basin to test our proposed framework. Optimal time periods were selected using a hierarchical cluster analysis that uses the slope and intercept coefficients from individual load-discharge regressions to derive improved linear models. These optimized linear models were used to improve estimates of annual and "spring" loadings for total phosphorus, dissolved phosphorus, total nitrogen, and total suspended loads for each of the nine study watersheds. The optimized annual regression model performed ~20% better on average than traditional annual regression models in terms of Nash-Sutcliffe efficiency, and resulted in ~50% higher cumulative load estimates with the largest difference occurring in the "spring". In addition, the largest nutrient and sediment loadings occurred during the "spring" unit of time and were typically more than 40% of the total annual estimated load in a given year. The framework developed here is robust and may be used to analyze other units of time associated with hydrologic regimes of interest provided adequate water quality data exist. This, in turn, may be used to create more targeted and cost-effective management strategies for improved aquatic health in rivers and lakes.

Sediment accumulated in lakes stores valuable information about past environments and paleoclimatological conditions. Cores previously obtained from Saint Albans Bay, located in the Northeast Arm of Lake Champlain, VT record the transition from the Champlain Sea to Lake Champlain. Belrose (2015) documented the presence of a peat horizon separating the sediments of the Champlain Sea from those of Lake Champlain. Initially, this layer was thought to comprise the transition from the marine environment of the Champlain Sea to a freshwater wetland. However, based on the results from this study, the transition between marine and freshwater conditions is thought to be represented by an erosional unconformity, indicative of a lowstand at the end of the Champlain Sea period. For this study, five additional cores were collected from Saint Albans Bay along a transect following the long axis of the bay moving into progressively deeper water. These cores better constrain the spatial extent, thickness and age variability of the peat layer within the bay and allow us to better understand the environmental conditions that preceded the period of peat deposition. In each of the cores there is evidence of sediment reworking in the uppermost Champlain Sea sediments, indicated by the presence of coarse-grained sediment, which is suggestive of a lowstand at the end of the Champlain Sea period before the inception of Lake Champlain. This coarse-grained layer is immediately overlain by a thick peat horizon. The widespread occurrence of the peat layer points to a large wetland that occupied the entire inner portion of Saint Albans Bay, and lake level ~ 9 m lower than at present during the Early Holocene. Based on radiocarbon dating, this paleo-wetland existed in Saint Albans Bay from ~ 9,600-8,400 yr BP. The development of this wetland complex is time transgressive, reflecting rapidly increasing lake level during the Early Holocene. This hypothesis is supported by the basal peat radiocarbon dates, as well as by the composition of plant macrofossils recovered from the peat horizons. The shift from peat deposition to fine-grained, low organic content lacustrine sedimentation is believed to have occurred at ~8.6-8.4 ka and is likely the result of continued isostatically driven lake level rise coupled with a changing climate. Although it was not its primary focus, this study also seeks to address the variations in sediment composition in the Lake Champlain sections of the cores. Evidence from the Lake Champlain record in Saint Albans Bay indicates that there were notable fluctuations in sedimentation, which were likely linked to both climatic variations and a change in the morphology of the bay. The rebound in productivity from ~8-5 ka is likely the result of warmer conditions during the Hypsithermal period. An increase in terrigenous sedimentation during this same time suggests a change in the morphology of the bay in which the Mill River delta migrated towards the inner bay. Initially, the cooler conditions of the Neoglacial are reflected in Saint Albans Bay by a decrease in organic matter content from ~5-3 ka. During the latter part of the Neoglacial (~3-1 ka), increases in organic matter content and detrital input point to enhanced productivity in response to increased precipitation and runoff from the watershed. The most recently deposited sediments in Saint Albans Bay bear out the legacy of anthropogenic nutrient enrichment of the bay in the form of increased algal productivity.

Globally, habitat fragmentation has had a major impact on the conservation and management of many species and is one of the primary causes of species extinction. Habitat fragmentation is loosely defined as a process in which a continuous habitat is reduced to smaller, disconnected patches as the result of habitat loss, restriction of migration or the construction of barriers to movement. Aquatic systems are particularly vulnerable to habitat fragmentation, and today an estimated 48% of rivers are fragmented worldwide. My dissertation evaluates how habitat fragmentation has influenced the populations of four different species of fish in the Lake Champlain basin. In chapter 1 I summarize the current state of habitat fragmentation research, I broadly describe habitat fragmentation, review how habitat fragmentation pertains to population genetics, and describe the legacy of habitat fragmentation in the Lake Champlain basin. In chapters 2, 3 and 4 I evaluate and discuss the impact of nine lake causeways on the population structure of slimy sculpin (Cottus cognatus), rainbow smelt (Osmerus mordax), and lake whitefish (Coregonus clupeaformis). The genetic effects of causeways are limited. However, causeways appear to have had a significant influence on rainbow smelt demographics, and the genetic structure observed in lake whitefish may be a product of reduced effective population size resulted from commercial harvest in the late 1800s. In chapter 5 I evaluate how the basin-wide population of tessellated darters (Etheostoma olmstedi) is naturally structured throughout Lake Champlain and three different major tributaries and evaluates the effect that different types of habitat fragmentation (dams, causeways, and natural fall lines) have on tessellated darter populations. Tessellated darters appear to be highly structured by river drainage but not by dams, causeways or fall lines. My dissertation highlights how comparative population genetic studies can be used to identify patterns of isolation within large populations. My results stress the value of reporting both the presence and absence of barrier induced population sub-structuring.

Near Burlington, Vermont, the Champlain Thrust fault placed massive Cambrian dolostones over calcareous shales of Ordovician age during the Ordovician Taconic Orogeny. Although the Champlain Thrust has been studied previously throughout the Champlain Valley, the architecture and structural evolution of its fault zone have never been systematically defined. To document these fault zone characteristics, a detailed structural analysis of multiple outcrops was completed along a 51 km transect between South Hero and Ferrisburgh, Vermont. The Champlain Thrust fault zone is predominately within the footwall and preserves at least four distinct events that are heterogeneous is both style and slip direction. The oldest stage of structures—stage 1—are bedding parallel thrust faults that record a slip direction of top-to-the-W and generated localized fault propagation folds of bedding and discontinuous cleavages. This stage defines the protolith zone and has a maximum upper boundary of 205 meters below the Champlain Thrust fault surface. Stage 2 structures define the damage zone and form two sets of subsidiary faults form thrust duplexes that truncate older recumbent folds of bedding planes and early bedding-parallel thrusts. Slickenlines along stage 2 faults record a change in slip direction from top-to-the-W to top-to-the-NW. The damage zone is ~197 meters thick with its upper boundary marking the lower boundary of the fault core. The core, which is ~8 meters thick, is marked by the appearance of mylonite, phyllitic shales, fault gouge, fault breccia, and cataclastic lined faults. In addition, stage 3 sheath folds of bedding and cleavage are preserved as well as tight folds of stage 2 faults. Stage 3 faults include thrusts that record slip as top-to-the-NW and -SW and coeval normal faults that record slip as top-to-the-N and -S. The Champlain Thrust surface is the youngest event as it cuts all previous structures, and records fault reactivation with any top-to-the-W slip direction and a later top-to-the-S slip. Axes of mullions on this surface trend to the SE and do not parallel slickenlines. The Champlain Thrust fault zone evolved asymmetrically across its principal slip surface through the process of strain localization and fault reactivation. Strain localization is characterized by the changes in relative age, motion direction along faults, and style of structures preserved within the fault zone. Reactivation of the Champlain Thrust surface and the corresponding change in slip direction was due to the influence of pre-existing structures at depth. This study defines the architecture of the Champlain Thrust fault zone and documents the importance of comparing the structural architecture of the fault zone core, damage zone, and protolith to determine the comprehensive fault zone evolution.

Mass animal migrations represent large movements of biomass, energy, and nutrients with predictable patterns and important ecosystem-level consequences. Diel vertical migration (DVM) in aquatic systems, the daily movement of organisms from deeper depths during the day to shallower depths in the water column at night, is widespread in freshwater and marine systems. Recent studies, however, suggest partial migration behavior, whereby only some portion of a population migrates, is the rule rather than the exception in a range of migratory fauna, including those that undergo DVM. Hypotheses to explain why partial migrations occur complicate traditional views on DVM and challenge conventional theories. I address intraspecific variation in DVM behavior of an aquatic omnivore, Mysis diluviana, to test several long-standing assumptions about benthic-pelagic DVM in Mysis. I evaluated the extent of partial DVM and several potential drivers within a Lake Champlain Mysis population. I used traditional net-based field observations, a novel deep-water video camera system, and a laboratory experiment, to compare distributions, demographics, abundance estimates, hunger-satiation state, and feeding behavior, of migrant and non-migrant Mysis across multiple seasons, habitats, and different times of the day. Findings from my dissertation suggest Mysis partial DVM is common, and is associated with body size and demographic differences among individuals. Partial DVM behavior, however, did not correspond to strong differences in feeding preference or hunger-satiation state of individuals. My results contribute toward a more comprehensive understanding of migration theory and mysid biology, by including the often overlooked, but important, benthic habitat component of DVM studies, and fills in several ecological knowledge gaps regarding a key omnivore in many deep lake food webs across North America where Mysis serve as both predators and prey to many organisms.

The advent of steam contributed heavily to the economic transformation of early America, facilitating trade through the transportation of goods along the country’s lakes, rivers, and canals. Serious experimentation with steam navigation began in the last quarter of the 18th century. By the turn of the 19th century, fledgling US steamboat companies vied for control of navigation rights in the country’s northern waterways. The second steamboat to be launched on Lake Champlain, Phoenix, operated as a passenger steamer between 1815 and 1819, when she caught fire and sank in the lake. The intention of this study is to advance our knowledge of early steamboat design and use in the United States through the archaeological investigation of the country’s earliest-known steamboat wreck. As little is known about the development of these early steam vessels, the study of Phoenix offers a unique opportunity to gain new information related to steamboat design in the early 19th century as well as a glimpse into life on the lakes and rivers of North America during this era. The dissertation presents detailed information on Phoenix’s construction, operation, and sinking based on historical and archaeological analysis and interpretation. In combination with the available archival record and analytical comparisons with steamboats of similar size and age, a more comprehensive understanding of the developmental phases of steam travel and its impact on early America can be gained.

En 2004, un projet de caractérisation des dépôts meubles (cartographie, sédimentologie et lithostratigraphie) a été amorcé dans la région de Mont-Laurier. L'objectif principal de cette étude réalisée dans le cadre d'une maîtrise visait à définir l'histoire glaciaire et post-glaciaire de cette région. L'orientation des marques d'érosion glaciaire durant la dernière glaciation démontre un écoulement principalement vers le SSE. Cette phase d'écoulement a été confirmée par les formes fuselées et par la thématique de dispersion glaciaire réalisée à partir des affleurements de marbre localisés à l'est de la ville de Mont-Laurier. Les dépôts quaternaires de la région de Mont-Laurier-Grand-Remous reposent en discordance angulaire sur le socle du Bouclier canadien. Le till sableux typique des Laurentides est surmonté, en plusieurs endroits, de sables et graviers fluvioglaciaires. L'une des problématiques principales de ce projet de recherche consistait à analyser les vestiges possiblement associés à l'invasion de la Mer de Champlain ou à la présence de lacs proglaciaires dans les vallées de la rivière Gatineau et du Lièvre. La photo-interprétation du territoire, les levés des coupes, les analyses sédimentologiques et l'inventaire des indicateurs biologiques effectué par Dadswell (1974) indiquent que la vallée de la rivière Gatineau et la vallée de la rivière du Lièvre ont été occupées par deux plans d'eau différents. Dans la vallée de la rivière du Lièvre, on a observé des séquences de rythmites qui présentent des caractéristiques sédimentologiques de varves; elles témoignent de la présence d'un paléolac. En tenant compte de l'hypothèse où chacun des couplets de rythmites représente une année de sédimentation, on estime que cet environnement glaciolacustre a pu exister durant environ 350 ans. Ces varves ont une épaisseur moyenne de 1,5 cm. La diminution de l'épaisseur des varves vers le haut des séquences est interprétée comme un indice du recul de la marge glaciaire. Ces varves sont constituées d'une importante quantité d'argile (35%) et ce principalement dans les lits d'hiver. Elles s'apparentent ainsi à certaines varves des lacs Barlow et Ojibway, décrites par Veillette (1996), dans la région de l' Abitibi-Témiscamingue. Les littoraux associés à ce plan d'eau indiquent que l'altitude maximale atteinte a été d'environ 255 m. La vallée de la rivière Gatineau présente un modèle géomorphologique et sédimentologique différent. Les levés de coupes stratigraphiques n'ont pas permis d'identifier des séquences de varves. L'altitude maximale des dépôts littoraux est également inférieure à celle observée dans la vallée de la rivière du Lièvre, soit 235 m. Dans le cadre de la reconstitution de l'étendue des mers et des lacs post-glaciaires, Dadswell (1974) a utilisé la répartition spatiale de bioindicateurs afin de caractériser ces paléenvironnements. Le Mysis Relicta représente le bioindicateur le plus répandu et le plus fréquemment utilisé. Ses résultats démontrent la présence du Mysis Relicta dans la majorité des lacs du secteur de la rivière Gatineau; ce qui semble indiquer que ce bassin était relié avec celui de la Mer de Champlain. À l'opposé, dans la vallée de la rivière du Lièvre, aucun lac échantillonné ne contenait ce crustacé. Compte tenu des nombreux autres indices tel que l'altitude plus élevé de ce plan d'eau, la présence de sédiments rythmés qui s'apparentent à des varves et d'un mécanisme de retenu des eaux (seuil topographique) situé à l'aval glaciaire, il semble probable qu'un lac proglaciaire ait inondé la vallée de la rivière du Lièvre alors que les eaux marines envahissaient celle de la rivière Gatineau. Il serait donc question de deux bassins indépendants: l'un paramarin à l'ouest et glaciolacustre à l'est. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Cartographie, Paléogéographie, Stratigraphie quaternaire, Sédimentologie, Mer de Champlain, Lac proglaciaire.

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