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 highly endemic native fish fauna has experienced dramatic reductions in abundance and range because of anthropogenic activity. In addition to a highly altered flow, temperature, and physical habitat template, many non-native fish species have established populations throughout the basin. The San Rafael River, a tributary of the Green River in southeastern Utah, is home to populations of flannelmouth sucker (Catostomus latipinnis), bluehead sucker (C. discobolus), and roundtail chub (Gila robusta), and has experienced degradations representative of many rivers throughout the Colorado River Basin. Using the San Rafael River as a template, I examined (1) the effect of the non-native fishes on the food web structure of a Colorado River tributary and (2) whether any changes to the food web structure by non-native fishes impact fitness-related vital rates of native fishes in the river. Stable isotope analysis revealed that the non-native fishes present novel predator archetypes to the “three species,” but size-at-age and body condition analyses did not reveal any reduction in fitness between native fishes captured in the presence of the non-native fishes. Additionally, I used site-specific biotic and abiotic measurements to develop a model predicting “three species” relative abundance. Non-native fish abundance and spatially auto-correlated measures of physical habitat were found to be particularly important predictors of “three species” relative abundance. The model was used in combination with a longitudinal habitat survey to predict the current continuous distribution along the length of the lower San Rafael River, as well as to simulate population-level effects of relevant restoration actions. The eradication of non-native fishes resulted in significant population increases for each of the ‘three species,’ and physical habitat restoration resulted in significant population increases when executed in certain reaches, but significant population reductions if executed in other reaches. These results suggest that the restoration of physical habitat without addressing populations of non-native fishes will likely result in a limited response by the “three species,” and that the choice of restoration location is critical to its success.

Aquatic food webs are comprised of complex spatial and temporal interactions within and among trophic levels. Human manipulations, such as construction of reservoirs, enhance uncertainties in our understanding of aquatic food web structure. Reservoirs are novel ecosystems which contain a unique composition of species. Species introductions into reservoirs may disrupt interactions within an already complex and poorly understood food web. In Scofield Reservoir in central Utah, a rapidly expanding population of Utah chub poses a detrimental threat to the blue-ribbon trout fishery. The Utah Division of Wildlife Resources has recently stocked cutthroat trout and tiger trout (a brown trout x brook trout hybrid) to potentially reduce Utah chub numbers as well as to enhance the sport fishery. I used standard fisheries techniques to describe food web interactions and to assess the potential for these piscivorous trout to control the expanding Utah chub population, as well as to determine sport fish performance and quantify diet overlap amongst top predators. Using bioenergetics modeling, I estimated very high rates of Utah chub consumption by cutthroat trout and tiger trout. These two species collectively display control of Utah chub, as the chub population is no longer exponentially increasing. Cutthroat trout and tiger trout are likely not food limited and convincingly exhibit high performance, as abundance of Utah chub is still extremely high. Both diet and stable isotope analysis showed significant overlap between these top piscivores in the reservoir, but also substantial overlap between cutthroat trout and rainbow trout with respect to Utah chub. Analysis of rainbow trout suggested this species is performing poorly; rainbow trout had extremely low catch rates and never switched to a piscivorous diet at larger sizes. Utah chub and rainbow trout had similar diet compositions, and thus rainbow trout may be competing (poorly) for food and space resources. This study contributes to our understanding of interspecific interactions among these unique assemblages of top predators in this artificial system. This research also provides knowledge to fisheries managers tasked with providing optimal sport fisheries in these artificial and dynamic systems, as well as expanding on our extremely limited knowledge of tiger trout ecology.

The bioaccumulation of organic contaminants in aquatic ecosystems has been a key focus in environmental toxicology over the last decades. Bioaccumulation is a key concept in ecological risk assessments since it controls the internal dose of potential environmental contaminants. Information on the bioaccumulation of contaminants is used by regulatory authorities in the development of water quality standards, categorizing substances that are potential hazards and quantifying the risk of chemicals to human health. A basis for identifying priority chemicals has been the use of the octanol-water partition coefficient (KOW) as a criterion to estimate bioaccumulation potential. However, recognizing that the bioaccumulation process is not controlled by the hydrophobicity of a chemical alone, this thesis proposes a set of tools, incorporating chemical properties, environmental characteristics and physiological properties of organisms, to study the bioaccumulation of contaminants in aquatic ecosystems.  In striving to achieve this objective, a tool based on an equilibrium lipid partitioning approach was used in Paper I to evaluate monitoring data for bioaccumulation of organic contaminants. In Papers II and III, mechanistic based modelling tools were developed to describe bioaccumulation of hydrophobic compounds in aquatic food webs. In Paper IV, the bioaccumulation of organic compounds in aquatic food chains was studied using stable isotopes of nitrogen. The mechanistic fate and food web models developed in this thesis provide regulators and chemical manufacturers with a means of communicating scientific information to the general public and readily applicable mechanistic fate and food web models that are easily modified for evaluative assessments purposes.

Loss of biodiversity is one of the most severe threats to the ecosystems of the world. The major causes behind the high population and species extinction rates are anthropogenic activities such as overharvesting of natural populations, pollution, climate change and destruction and fragmentation of natural habitats. There is an urgent need of understanding how these species losses affect the ecological structure and functioning of our ecosystems. Ecological communities exist in a landscape but the spatial aspects of community dynamics have until recently to large extent been ignored. However, the community’s response to species losses is likely to depend on both the structure of the local community as well as its interactions with surrounding communities. Also the characteristics of the species going extinct do affect how the community can cope with species loss. The overall goal of the present work has been to investigate how both local and regional processes affect ecosystem stability, in the context of preserved biodiversity and maintained ecosystem functioning. The focus is particularly on how these processes effects ecosystem’s response to species loss. To accomplish this goal I have formulated and analyzed mathematical models of ecological communities. We start by analyzing the local processes (Paper I and II) and continue by adding the regional processes (Paper III, IV and V). In Paper I we analyze dynamical models of ecological communities of different complexity (connectance) to investigate how the structure of the communities affects their resistance to species loss. We also investigate how the resistance is affected by the characteristics, like trophic level and connectivity, of the initially lost species. We find that complex communities are more resistant to species loss than simple communities. The loss of species at low trophic levels and/or with high connectivity (many links to other species) triggers, on average, the highest number of secondary extinctions. We also investigate the structure of the post-extinction community. Moreover, we compare our dynamical analysis with results from topological analysis to evaluate the importance of incorporating dynamics when assessing the risk and extent of cascading extinctions. The characteristics of a species, like its trophic position and connectivity (number of ingoing and outgoing trophic links) will affect the consequences of its loss as well as its own vulnerability to secondary extinction. In Paper II we characterize the species according to their trophic/ecological uniqueness, a new measure of species characteristic we develop in this paper. A species that has no prey or predators in common with any other species in the community will have a high tropic uniqueness. Here we examine the effect of secondary extinctions on an ecological community’s trophic diversity, the range of different trophic roles played by the species in a community. We find that secondary extinctions cause loss of trophic diversity greater than expected from chance. This occurs because more tropically unique species are more vulnerable to secondary extinctions. In Paper III, IV and V we expand the analysis to also include the spatial dimension. Paper III is a book chapter discussing spatial aspects of food webs. In Paper IV we analyze how metacommunities (a set of local communities in the landscape connected by species dispersal) respond to species loss and how this response is affected by the structure of the local communities and the number of patches in the metacommunity. We find that the inclusion of space reduces the risk of global and local extinctions and that lowly connected communities are more sensitive to species loss. In Paper V we investigate how the trophic structure of the local communities, the spatial structure of the landscape and the dispersal patterns of species affect the risk of local extinctions in the metacommunity. We find that the pattern of dispersal can have large effects on local diversity. Dispersal rate as well as dispersal distance are important: low dispersal rates and localized dispersal decrease the risk of local and global extinctions while high dispersal rates and global dispersal increase the risk. We also show that the structure of the local communities plays a significant role for the effects of dispersal on the dynamics of the metacommunity. The species that are most affected by the introduction of the spatial dimension are the top predators.

Coral reefs, seagrass beds and mangroves constitute a complex mosaic of habitats referred to as the tropical seascape. Great gaps exist in the knowledge of how these systems are interconnected. This thesis sets out to examine ecological connectivity, i.e. the connectedness of ecological processes across multiple scales, in Zanzibar and Mafia Island, Tanzania. Paper I examined the current knowledge of interlinkages and their effect on seascape functioning, revealing that there are surprisingly few studies on the influences of cross-habitat interactions and food-web ecology. Furthermore, 50% of all fish species use more than one habitat and 18% of all coral reef fish species use mangrove or seagrass beds as juvenile habitat in Zanzibar. Paper II examined the seascape of Menai Bay, Zanzibar using a landscape ecology approach and studied the relationship between fish and landscape variables. The amount of seagrass within 750m of a coral reef site was correlated with increased invertebrate feeder/piscivore fish abundance, especially Lethrinidae and Lutjanidae, which are known to perform ontogenetic and feeding migrations. Within patch seagrass cover was correlated with nursery species abundance. Paper III focused on a seagrass-dominated seascape in Chwaka Bay, Zanzibar and showed that small-scale habitat complexity (shoot height and density) as well as large-scale variables such as distance to coral reefs affected abundance and distribution of a common seagrass parrotfish Leptoscarus vaigiensis. Paper IV studied the connectivity and functional role of two snappers (Lutjanus fulviflamma and L. ehrenbergii) using stable isotopes (δ15N and δ13C) and found that connectivity between habitats was maintained by ontogenetic and foraging migrations by these species. The thesis concludes that ecological connectivity and multi-habitat usage by fish is a general and important characteristic in the Western Indian Ocean and should be considered in management planning. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 4: Submitted.</p>

Non-indigenous species can profoundly alter the ecosystems they invade and impact local economies. Growth and body condition declines of commercially fished Great Lakes lake whitefish coincide with the establishment of non-native dreissenid mussels and the cladoceran Bythotrephes longimanus. Declines in lake herring abundance—a key prey item for other commercially important species—have also been reported. Though additional stressors such as climate change may have contributed to changes in coregonid populations, they have not been thoroughly evaluated. Here, I present data that condition and contaminant declines in coregonids are associated with increasing density or warming climate, but growth declines in lake whitefish are likely due to ecosystem changes associated with dreissenids and Bythotrephes. In South Bay, Lake Huron, changes in lake whitefish diet composition and stable isotope signatures were consistent with increased reliance on nearshore resources after dreissenid establishment; lake whitefish occupied shallower habitats and experienced declines in mean diet energy densities post-dreissenid invasion. Growth of South Bay lake whitefish declined after environmental effects were statistically removed, whereas condition declines were explained best by changes in lake whitefish density. Among four lake whitefish populations, growth declined after dreissenids established, but not in uninvaded reference populations. Growth also declined among four lake whitefish populations after the establishment of Bythotrephes relative to reference populations. In contrast with growth, condition of lake whitefish did not change as a result of dreissenid or Bythotrephes invasion. Bioenergetic models revealed that activity rates increased and conversion efficiencies decreased in lake whitefish populations exposed to dreissenids, despite higher consumption rates in populations with dreissenids present. Condition declines among many lake whitefish and lake herring populations (and declines in mercury among herring populations) reflected regional differences and were not related to the presence of Bythotrephes or Mysis relicta. Declines in condition were more pronounced in northwest Ontario populations where climate has changed more dramatically than in southern Ontario. This work suggests that projected range expansions of dreissenid mussels and Bythotrephes will likely affect native fisheries, and their effect on these fisheries may be exacerbated by declining fish condition associated with climate change.

I compared changes in offshore Lake Ontario major species-group biomass, production and diets before (1987-1991) and after (2001-2005) invasion-induced ecological change. I synthesized the observations into carbon-based mass-balanced food webs linking two pathways of energy flow; the grazing chain (phytoplankton-zooplankton-fish) and the microbial loop (autotrophic bacteria-heterotrophic protozoans) and determined how the structure and function of the food web changed between time-periods. I use the food web descriptions to simulate the reestablishment of native deepwater bloater. I developed empirical models describing spatial variation in temperature and applied them to investigate predator temperature distributions, bioenergetic consequences of alewife diet and distribution shifts, and zooplankton productivity. Primary production declined as did the biomass and production of all species-groups except Chinook salmon. Total zooplankton production declined by approximately half with cyclopoid copepod production declining proportionately more. Zooplankton species richness and diversity were unaffected. Alewife adapted to low zooplankton production by consuming more Mysis, increasing their trophic level. The increased prey-size and exploitation of spatial heterogeneity in resource patches and temperature may have allowed alewife to maintain their growth efficiency. The trophic level also increased for smelt, adult sculpin, adult alewife and Chinook salmon. Phytoplankton grazing rates declined and predation pressure increased on Mysis, adult smelt and alewife, and decreased on protozoans. Resource to consumer trophic transfer efficiencies changed; increasing for protozoans, Mysis, Chinook salmon and other salmonines and decreasing for zooplankton, prey-fish and benthos. The changes suggest both bottom-up and top-down influences on food web structure. The direct trophic influences of invasive species on the offshore Lake Ontario food web were minor. Carbon flows to Mysis indicated an important, and changing ecological role for this species and we hypothesize that Mysis may have contributed to Diporeia declines. Simulations suggest that only a small reestablished bloater population, limited by Diporeia production, could be sustained.

Uranium mining and milling operations at Key Lake, Saskatchewan, Canada, have been releasing effluent since 1983, resulting in the accumulation of selenium in surface water, sediment, and biota in downstream lakes relative to pre-development and reference lake conditions. Elevated selenium can pose a risk to fish and bird populations in aquatic ecosystems as a result of the trophic transfer of selenium from the base of the aquatic food web. This research program was designed to address specific knowledge gaps related to the bioaccumulation of selenium at the benthic-detrital link of aquatic food webs. To fulfill this objective, laboratory and in situ field experiments were conducted using the benthic invertebrate Chironomus dilutus to identify the exposure pathway(s) and selenium species associated with the bioaccumulation of selenium by benthic invertebrates downstream from the Key Lake operation. Laboratory bioaccumulation tests that exposed midge larvae to 4.3 µg/L as dissolved selenate for 10 d resulted in negligible accumulation of selenium. However, larvae rapidly accumulated selenium over 10 d of exposure to 3.8 and 1.8 µg/L selenite and seleno-DL-methionine (Se-met), respectively. Furthermore, once selenium was accumulated by the larvae from the selenite and Se-met treatments, the majority of it was retained after a 10 d depuration period in clean water. When additional midge larvae were exposed to selenium until emergence, selenium accumulated during the larval stage was passed onto the adults following metamorphosis, with only a small percentage of the selenium (< 5%) transferred to the exuvia. Selenium speciation analysis using X-ray absorption spectroscopy showed that increases in total selenium concentrations corresponded to increased fraction of organic selenides, modeled as selenomethionine, in C. dilutus larvae and adults. Results from the 2008 in situ caging study confirmed that surface water is not a significant selenium exposure pathway for benthic invertebrates at Key Lake. Chironomus dilutus larvae accumulated between 20- and 90-fold more selenium from exposure to sediment compared to exposure to surface water in the high exposure lake. In response to these findings, a second in situ experiment was conducted in 2009 to investigate the importance of dietary selenium (biofilm or detritus) vs. whole-sediment as an exposure pathway. Larvae exposed to sediment detritus (top 2 â 3 mm of sediment) from the exposure site had the highest selenium concentrations after 10 d of exposure (15.6 ± 1.9 µg/g) compared to larvae exposed to whole-sediment (12.9 ± 1.7 µg/g) or biofilm (9.9 ± 1.6 µg/g). Biofilm had lower total selenium concentrations than the detritus and whole-sediment fractions, but nearly 80% of the selenium was present as organic selenides similar to selenomethionine. Biofilms appear to be an enriched source of organic selenium and are important food items for many benthic consumers. Integrating the separate lines of evidence that were generated during laboratory and in situ bioaccumulation tests helped strengthen the understanding of selenium accumulation in the benthic-detrital food web and subsequent trophic transfer of selenium to benthic invertebrates.

Uranium mining and milling operations at Key Lake, Saskatchewan, Canada, have been releasing effluent since 1983, resulting in the accumulation of selenium in surface water, sediment, and biota in downstream lakes relative to pre-development and reference lake conditions. Elevated selenium can pose a risk to fish and bird populations in aquatic ecosystems as a result of the trophic transfer of selenium from the base of the aquatic food web. This research program was designed to address specific knowledge gaps related to the bioaccumulation of selenium at the benthic-detrital link of aquatic food webs. To fulfill this objective, laboratory and in situ field experiments were conducted using the benthic invertebrate Chironomus dilutus to identify the exposure pathway(s) and selenium species associated with the bioaccumulation of selenium by benthic invertebrates downstream from the Key Lake operation. Laboratory bioaccumulation tests that exposed midge larvae to 4.3 µg/L as dissolved selenate for 10 d resulted in negligible accumulation of selenium. However, larvae rapidly accumulated selenium over 10 d of exposure to 3.8 and 1.8 µg/L selenite and seleno-DL-methionine (Se-met), respectively. Furthermore, once selenium was accumulated by the larvae from the selenite and Se-met treatments, the majority of it was retained after a 10 d depuration period in clean water. When additional midge larvae were exposed to selenium until emergence, selenium accumulated during the larval stage was passed onto the adults following metamorphosis, with only a small percentage of the selenium (< 5%) transferred to the exuvia. Selenium speciation analysis using X-ray absorption spectroscopy showed that increases in total selenium concentrations corresponded to increased fraction of organic selenides, modeled as selenomethionine, in C. dilutus larvae and adults. Results from the 2008 in situ caging study confirmed that surface water is not a significant selenium exposure pathway for benthic invertebrates at Key Lake. Chironomus dilutus larvae accumulated between 20- and 90-fold more selenium from exposure to sediment compared to exposure to surface water in the high exposure lake. In response to these findings, a second in situ experiment was conducted in 2009 to investigate the importance of dietary selenium (biofilm or detritus) vs. whole-sediment as an exposure pathway. Larvae exposed to sediment detritus (top 2 â 3 mm of sediment) from the exposure site had the highest selenium concentrations after 10 d of exposure (15.6 ± 1.9 µg/g) compared to larvae exposed to whole-sediment (12.9 ± 1.7 µg/g) or biofilm (9.9 ± 1.6 µg/g). Biofilm had lower total selenium concentrations than the detritus and whole-sediment fractions, but nearly 80% of the selenium was present as organic selenides similar to selenomethionine. Biofilms appear to be an enriched source of organic selenium and are important food items for many benthic consumers. Integrating the separate lines of evidence that were generated during laboratory and in situ bioaccumulation tests helped strengthen the understanding of selenium accumulation in the benthic-detrital food web and subsequent trophic transfer of selenium to benthic invertebrates.