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Multiple surveys have taken place on Great Slave Lake with the aim of collecting data on fish populations to achieve sustainable management, however, a lack of consistency and lake coverage from these investigations’ limits data useability. Misinterpretations of data collected in early research likely contributed to the collapse of the Lake Trout, Salvelinus namaycush, stocks shortly after the commercial fishery began. The limited abundance indices available for Lake Trout, further complicated by inconsistent management areas and recording methods, prevents the incorporation of all available data into a conventional stock assessment model. Therefore, CMSY++, the most recent version of the data-limited, surplus production model, CMSY, was applied to assess the status of Great Slave Lake Trout populations. The results generated in this assessment predict that Lake Trout stocks in all current commercially fished regions are overfished, with combined Lake Trout and Lake Whitefish, Coregonus clupeaformis, quotas above estimated Lake Trout maximum sustainable yields. My findings indicate Lake Trout commercial harvest in recent years has surpassed the estimated maximum sustainable yield for the stock in some management areas. Inferences from modeling catch-time series of varied lengths suggest ~50 years of catch data should be sufficient for reference point estimation for these Lake Trout populations, as longer time series did not decrease uncertainty. The management areas with the most commercial harvest (Areas IW & IE) reveal the greatest uncertainty associated with biomass estimates, suggesting more data is required to better understand the current state of the stocks and any increases to quotas should not occur until this is done. Conclusions of my research support those suggested over 50 years ago; Lake Trout and Lake Whitefish, should be managed through separate commercial quotas to achieve sustainable management for these populations.

Beluga whales are year-round residents of the Arctic and top predators in the ecosystem. Many beluga whale populations are migratory and spend winters in polynyas and breaks in the ice to avoid entrapment. Once the ice in begins to break up and melt, beluga whale populations migrate to the same Arctic estuaries year after year. Possible uses of estuaries include feeding, aiding in skin sloughing, protection of calves from predators, and other warm water benefits. However, much is still unknown about the use of these habitats both spatially and ecologically. I investigated estuary use by Cumberland Sound beluga whales, through their distribution. Their summering area covers northern fiords of Cumberland Sound, including Clearwater Fiord where there is a large estuary. While the whales are known the frequent the fiords, the specific distribution and core areas were unknown. Using very high resolution satellite imagery, I established critical habitat within the summering region. I also provided an updated estuary abundance estimate for this small beluga whale population. Second, I explored estuary use of Hudson Bay beluga whales by investigating the primary feeding season. Migratory species often have one season where they eat the majority of their food for the year and build fat reserves, which provides energy and supports thermoregulation. This fat can be used to investigate feeding ecology of whales. Despite being the largest beluga population, fundamental ecological knowledge of Hudson Bay beluga whales, such as the primary feeding season is unknown. I used lipid content and adipocyte size throughout the blubber of Hudson Bay beluga whales to identify when they were consuming the majority of their food. I determined that there was no consistent primary feeding season, and therefore both summering and wintering areas were used for feeding. By exploring the beluga whales’ use of seasonal habitat through distribution and foraging ecology, my thesis illuminates fundame

The loss and degradation of freshwater habitats in Canada threaten the rich array of plant and animal species supported within these ecosystems, threatening the biodiversity that these ecosystems sustain. Assessing the distribution of the species in these threatened ecosystems is necessary for the effective monitoring of the well-being of their populations and the ecosystem, but it can be difficult, as some species can evade traditional survey methods due to their elusiveness, size, range, or rarity. Environmental DNA (eDNA), which describes the pool of DNA present in an environment that can be collected in and isolated from environmental samples, offers an alternative to traditional surveying that can be more sensitive and less invasive. Therefore, I developed and validated TaqMan™ MGB probe-based eDNA assays for six freshwater fishes of conservation concern in Manitoba: Bigmouth Buffalo Ictiobus cyprinellus, Chestnut Lamprey Ichthyomyzon castaneus, Golden Redhorse Moxostoma erythrurum, Hornyhead Chub Nocomis biguttatus, Northern Brook Lamprey Ichthyomyzon fossor, and Silver Lamprey Ichthyomyzon unicuspis. The designed assays were validated in situ using paired eDNA and capture-based sampling and used to map the distribution of the above species from water samples collected and filtered from 129 sites across Manitoba in 2021–2023. I detected the eDNA of four of the target species outside of their historic range: Bigmouth Buffalo in the Roseau, Morris, and Assiniboine rivers; Golden Redhorse in Hazel Creek; Hornyhead Chub in waterbodies of the Winnipeg River watershed where it has not been reported previously; and Northern Brook Lamprey in Boggy River. Apart from Northern Brook Lamprey, the eDNA of all target species was not detected in at least one site within their historic range. Further research is needed to confirm if the lack of eDNA detections of the target species within their historic range is a result of range restriction, or if a refinement of the methods

As the human population rapidly increases, the pressures on wildlife to adapt to the changing landscape and to coexist with humans is also increasing. Understanding why wildlife matter to humans is critical in helping plan and execute conservation strategies as we move into the future. This research investigates why wildlife matter to a cohort of environmental professionals including retired and practicing wildlife biologists, as well as post-secondary students studying environmental science and studies, and explores the perspectives of Indigenous peoples on why wildlife matter to them and their culture. The qualitative research data was artistically transformed into video and song to showcase the research in diverse media. Study methods include conducting interviews, completing a literature review, as well as creating audio/visual tools to display the results of the data found within the study. This unique research initiative identified several significant findings, to conclude that wildlife matter to biologists, students, and Indigenous peoples for a variety of reasons. For example, personal perspectives on how wildlife play a direct role in their life, as well as the role wildlife play as part of the world’s ecosystems in providing balance and stability to nature’s processes. Inductive coding thematic analysis identified 5 themes within the data of why wildlife matter which includes 1) Ecosystem Importance 2) Resource for Humans 3) Personal Value – Happiness and Wellbeing 4) Recreational Purposes 5) Existential Purposes – Coexistence. The findings of the research were created into a video titled “Why Do Wildlife Matter?” and song “We Decide.” The creative works were awarded the 2020 Conservation Education Award through The Wildlife Society in recognition of outstanding media and audio-visual work which effectively conveys sound conservation concepts to the public. As a songwriter, musician, and wildlife biologist, this multidisciplinary research bridges several d

Arctic primary producer phenology is undergoing shifts attributed to the increased transmission of light resulting from climate change-induced declines in sea ice thickness, age, and extent. However, the investigation of phenological events, particularly near the ocean surface, is challenging due to limited time-series observations caused by logistical constraints and accessibility issues. Data collected from a subsurface oceanographic mooring deployed in Dease Strait, Nunavut, from 2017 to 2019 were used to determine primary producer biomass using the normalized difference index (NDI) chlorophyll-a retrieval algorithm. Sentinel-1 and RADARSAT-2 synthetic aperture radar (SAR) data and related meteorological variables were used to identify snow and sea-ice melt phase timing. The results revealed a relationship between light availability and surface primary producer timing and magnitude. Specifically, an 18-day difference in the length of ice algal blooms between 2017 and 2019 was observed, with both blooms peaking near snow melt onset and exhibiting similar daily production rates. The extended duration of the 2019 ice algal bloom was due to lower air temperatures compared to 2017, and a deeper snowpack prior to snow melt. Moreover, a 6-7 day under-ice phytoplankton bloom occurred in both years, coinciding with melt pond formation. However, the 2019 under-ice bloom exhibited a lower accumulation rate, likely due to nutrient depletion beneath the ice by the prolonged ice algal bloom. Following ice break-up in 2019, a 31-day late-summer bloom occurred via sustained wind-driven mixing, highlighting the importance of ocean-atmosphere coupling in the region following ice break-up. The findings of this thesis provide a novel approach to investigating surface primary producer phenology and suggest the potential application of this technique to support future long-term monitoring.

Studies examining biological communities in relation to environmental factors over time are essential for understanding natural sources of community variation (i.e., structure and function), as well as their response to stressors. Benthic macrofauna are important biological indicators used to assess environmental quality in marine ecosystems. Placentia Bay is a large subarctic embayment on the southeast coast of Newfoundland (NL) that has been identified as an Ecologically and Biologically Significant Area (EBSA) that is exposed to anthropogenic stressors (e.g., fisheries and hazardous substances). The overarching aim of my thesis research was to assess the influence of various environmental factors on the community structure and functional traits of macrofauna in Placentia Bay using contemporary and historical biological and environmental data. Comparison of macrofauna at 8 stations sampled in 1998 and 2019–2020 (n=77) showed significant temporal changes in community structure and function, without loss of function (i.e., 36 morphological/behavioral modalities). The historical community had significantly higher densities, but lower evenness and diversity compared to contemporary years. Macrofauna were dominated by highly tolerant (82.3%) subsurface deposit feeders (62.1%) having small body sizes, whereas contemporary communities had a higher proportion of medium tolerant species/taxa (7.2 vs. 36.7%) and nearly equal proportions of subsurface and surface deposit feeders (26.7 and 29.1%) with small-medium body sizes. These changes are likely a reflection of the large reduction in the relative proportion of polychaetes (91 vs. 58%). Community patterns were related to the sedimentary habit. Sediments have become coarser with higher levels of sedimentary total organic matter in the contemporary compared to the historical years. Interestingly, while grain size has also become coarser between 2019 and 2020 communities were similar. Moreover, even though contaminants (exam

The genus Sebastes is a morphologically and ecologically diverse genus of rockfish characterized by high longevity, late-maturity and low natural mortality. On the northwest Atlantic continental shelf, the Acadian redfish (Sebastes fasciatus) is the most common rockfish species above 300 m depth. This species has been widely exploited resulting in the depletion or collapse of most of its stocks. Management of long-lived species with intricate life-history characteristics is challenging and requires highly integrated biological and oceanographic monitoring, which allow the identification of environmental drivers and demographic and behavioral trends. The present study uses high-temporal resolution imaging and environmental data, acquired with an autonomous lander deployed for 10-months at the Sambro Bank Sponge Conservation Area (Scotian Shelf) to elucidate S. fasciatus temporal dynamics and behavioral trends in response to near-bed environmental conditions. S. fasciatus, mostly displayed passive locomotion and static behaviors, in common with other shelf-dwelling Sebastes species. Structural complexity provided by sponges positively influenced S. fasciatus presence. Fish used sponges to avoid being dragged by bottom currents. Hydrodynamics appear to act as a synchronizing factor conditioning its swimming behavior. S. fasciatus total counts exhibited a seasonal shift in rhythm’s phase likely reflecting changes in lifestyle requirements. This study provides new insights on S. fasciatus dynamics and behavior. Nonintrusive monitoring approaches, such as the one used in this study, will be key to monitor this threatened species populations. Especially, since it is expected that S. fasciatus will experience distribution shifts to higher latitudes due to future climate stressors

Shellfish aquaculture farms, due to their coastal position, face the threat of exposure to harmful algal blooms. Such blooms can release, among others, paralytic shellfish toxins (PST) produced by the dinoflagellate Alexandrium catenella and are known to cause the restriction of bivalve harvesting sites. Shellfish can accumulate PSTs in levels that are poisonous for humans, therefore making them unfit for consumption. Thus, the ability to detect PSTs before they reach the critical threshold is crucial for minimizing losses in the industry. Previous studies have demonstrated that toxic algae detection is possible with the use of an early warning system based on the valve-gaping behaviour of blue mussel Mytilus edulis. However, some studies observed the presence of toxin resistance in other species of bivalves when they are regularly exposed to PSTs. If no resistance is observed whatever the past history of the populations would be with regard to PST exposure, this species could be appropriate as a sentinel candidate. In this study, we compare the valve-gaping behaviour of two blue mussel populations with contrasting long-term histories of PSTs events (i.e., regularly vs. not previously exposed to the PSTs producer) were compared using experimental exposure of A. catenella to M. edulis. It was found that mussels from both populations exhibited similar gaping behaviour patterns when exposed to A. catenella. For both populations, the number of valve closures and closure duration tended to increase in the presence of A. catenella, which suggested an avoidance response to the toxic dinoflagellate. In conclusion, our results support the use of M. edulis without origin discrimination

In this thesis, I used underwater images to determine patterns in lateralization and group size when beluga calves and juveniles are present. Usually, lateralization is defined by either a left or right preference, but using underwater images (an untested, non-invasive approach) provided an opportunity to analyze position bias from three distinct planes, the sagittal (left or right), coronal (dorsal or ventral), and transverse (anterior or posterior). My research found that the presence of the boat may have affected lateralization as juveniles were most frequently observed on the left. This position bias was possibly due to their mothers, who may have positioned themselves between their young and the less familiar boat. Additionally, while both calves and juveniles preferred to be positioned in ventral positions near their mother, juveniles were most frequently observed at the anterior of the head region, while calves were in the posterior or tail region or infant position. This difference is likely due to juveniles having increased swimming abilities, allowing them to compromise the hydrodynamic benefits of the infant position for the anterior position, as the head or anterior is preferred for social interactions in whales. In my second chapter, I determined if mother and calf/juvenile dyads selected larger groups. My results indicated that groups that contained calves and juveniles had more adults present than groups that contained adults only. In comparison with aerial surveys, I found that group sizes in underwater images were significantly larger across all age classes. This may be an effect of methods used, as boats used to collect camera images may have moved to locations where beluga were aggregating. However, further research is needed to determine the effect of boats on juveniles’ interactions.

In this thesis, I used underwater images to determine patterns in lateralization and group size when beluga calves and juveniles are present. Usually, lateralization is defined by either a left or right preference, but using underwater images (an untested, non-invasive approach) provided an opportunity to analyze position bias from three distinct planes, the sagittal (left or right), coronal (dorsal or ventral), and transverse (anterior or posterior). My research found that the presence of the boat may have affected lateralization as juveniles were most frequently observed on the left. This position bias was possibly due to their mothers, who may have positioned themselves between their young and the less familiar boat. Additionally, while both calves and juveniles preferred to be positioned in ventral positions near their mother, juveniles were most frequently observed at the anterior of the head region, while calves were in the posterior or tail region or infant position. This difference is likely due to juveniles having increased swimming abilities, allowing them to compromise the hydrodynamic benefits of the infant position for the anterior position, as the head or anterior is preferred for social interactions in whales. In my second chapter, I determined if mother and calf/juvenile dyads selected larger groups. My results indicated that groups that contained calves and juveniles had more adults present than groups that contained adults only. In comparison with aerial surveys, I found that group sizes in underwater images were significantly larger across all age classes. This may be an effect of methods used, as boats used to collect camera images may have moved to locations where beluga were aggregating. However, further research is needed to determine the effect of boats on juveniles’ interactions.

In certain areas of the Nova Scotian shelf, Vazella pourtalesii (Hexactinelid) forms dense monospecific aggregations. Vazella creates complex 3-dimensional structures, which provide habitat to a wide range of associated species, enhancing local diversity. In 2013, the Canadian authorities established the Sambro Bank Sponge Conservation Area, banning bottom fishing activities. However, this protection zone has not yet been incorporated into a management plan requiring implementation of monitoring strategies that account for natural variability. To elucidate assemble dynamics and response to environmental variability, a NIOZ-designed lander equipped with a HD-video camera, ADCP, CT and oxygen sensors was deployed at 154m depth for 10-months. A total of 5,151 still images were obtained of which 1157 were manually analyzed with the BIIGLE 2 software, and posteriorly used to train a mask convolutional neural network. Over 30,000 organisms belonging to 8 different species were identified. An unidentified actinian and the red fish Sebastes fasciatus were the most abundant species accounting for 93% and 4% of all observed organisms, respectively. Non-metric multidimensional scaling analysis revealed that assemblage composition did not significantly differ between seasons. However, it was observed that sessile taxa abundances decreased during benthic storms that influence the near-bed hydrodynamics. These storms could last for several days causing high sediment resuspension and the dislodgment or partial burial of sponge and actinian individuals. We also observed that sponge individuals attached to small cobbles, moved across the field of view. Moving individuals intermittently appeared laying horizontally on the seafloor or standing in an upward position, within short intervals. Bottom currents may cause Vazella individuals, attached to small cobbles, to tip and rise progressively, dislodging them from their original position depending on current intensity and direction. Ou

Chapter 2 Population dynamics of forage fish species are typically characterized by extreme fluctuations. Therefore, diversity in forage fish communities creates a portfolio effect, whereby the stability of marine ecosystems is increased by sustaining their role in transferring energy between lower and higher trophic levels, a key ecosystem process. The objective of this chapter was to investigate whether inter-annual trends in abundance, distribution, and biometrics (length, mass, condition) were synchronized in key forage fish species, sand lance Ammodytes spp and capelin Mallotus villosus, across the southeastern Newfoundland Shelf during the spring using a 20-year (1996-2015) bottom-trawl dataset. I also investigated whether species-specific distribution and biometrics were influenced by abundance. Sand lance length, mass and condition decreased with increasing abundance, suggesting density-dependence, but distribution did not expand with abundance. In contrast, capelin length and mass did not decrease with increasing abundance, nor did distribution. Inter-annual variation in abundance, distribution and biometrics were not synchronized in capelin and sand lance, possibly due to species occupying different regions at different life stages. Indeed, capelin were distributed farther north and more inshore than sand lance, possibly because capelin migrate inshore to spawn during the spring and sand lance are resident in the shallower waters of the Grand Banks. These findings support the collapsed state of the Newfoundland capelin population and the lack of predator release at the meso-predator trophic level after the overfishing of a top predator, Atlantic cod, Gadus morhua, in the early 1990s. Overall, this study increased the knowledge of forage fish population dynamics on the Newfoundland Shelf, specifically the understudied sand lance Ammodytes species. Chapter 3 Non-spawning fish select habitat based on many abiotic and biotic factors. Although prey and predator

Climate change is causing the poleward redistribution of species linked to abiotic factors such as temperature. The Arctic is warming three times faster than the global average and causing a rapid climate-driven recession of sea ice, which is an added stressor to Arctic species and ecosystems. As a mobile, generalist predator, ringed seals integrate resources spatially and trophically up the Arctic marine food web, which makes them a model indicator of how the Arctic marine ecosystem will respond to environmental change. Ringed seals are also vulnerable to loss of the sea-ice habitat they depend on for pupping, nursing, moulting, and prey from sea-ice derived food webs but experience a broad range of sea-ice conditions from the southern to northern edge of their range. The objectives of this thesis were to determine how the (1) density and (2) diet of ringed seals varied over the vastly different icescapes within their latitudinal range. Our results indicated latitudinal variation in ringed seal density potentially increased with availability of preferred first-year ice habitat. We also found a shift in ringed seals diets from primarily phytoplanktonic carbon in the low Arctic to a high proportion of ice-algal carbon in the high Arctic. The observed change in the base of food webs contributing to ringed seal diets may also have implications for trophic dynamics in these food webs. Overall, we show the potential of ringed seal density and diet to indicate large scale changes to the Arctic environment and Arctic food webs. We also provide insight into the potential responses to continued sea-ice recession of a key species for Arctic ecosystems and communities, important information for cooperative management of Arctic resources.

Climate change is warming the ocean and impacting lower trophic level (LTL) organisms. Marine ecosystem models can provide estimates of how these changes will propagate to larger animals and impact societal services such as fisheries, but at present these estimates vary widely. A better understanding of what drives this inter-model variation will improve our ability to project fisheries and other ecosystem services into the future, while also helping to identify uncertainties in process understanding. Here, we explore the mechanisms that underlie the diversity of responses to changes in temperature and LTLs in eight global marine ecosystem models from the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP). Temperature and LTL impacts on total consumer biomass and ecosystem structure (defined as the relative change of small and large organism biomass) were isolated using a comparative experimental protocol. Total model biomass varied between −35% to +3% in response to warming, and -17% to +15% in response to LTL changes. There was little consensus about the spatial redistribution of biomass or changes in the balance between small and large organisms (ecosystem structure) in response to warming, an LTL impacts on total consumer biomass varied depending on the choice of LTL forcing terms. Overall, climate change impacts on consumer biomass and ecosystem structure are well approximated by the sum of temperature and LTL impacts, indicating an absence of nonlinear interaction between the models’ drivers. Our results highlight a lack of theoretical clarity about how to represent fundamental ecological mechanisms, most importantly how temperature impacts scale from individual to ecosystem level, and the need to better understand the two-way coupling between LTL organisms and consumers. We finish by identifying future research needs to strengthen global marine ecosystem modelling and improve projections of climate change impacts

Acoustic monitoring is an effective means by which to study cetaceans, such as beluga whales (Delphinapterus leucas), and can be useful in determining habitat preference and geographic variation among populations. Acoustic monitoring data were analyzed using a combination of automated detection and manual analysis to determine habitat preference of Cumberland Sound beluga in their summering range. Belugas were primarily detected in the northernmost site in Clearwater Fiord, with diel variation in call patterns at two separate sites in different years. No correlation was evident between tidal cycles and beluga detections. A second study examined geographic variation in simple contact calls (SCC’s) among four Canadian beluga populations. Results indicate variation in the measured parameters (duration, peak frequency and pulse repetition rate) among four populations and align with genetic variation previously described in the literature. These findings provide important information necessary for the conservation and management of beluga populations in Canada.

Bull Trout (Salvelinus confluentus) occur in many major watersheds in northwestern North America and are identified as “Threatened” or a “Species of Special Concern” in both Canada and the United States. Non-native fishes, including Brook Trout (Salvelinus fontinalis), are one assumed major contributor to declines of Bull Trout populations. Further understanding of how introduced species are affecting Bull Trout populations may help with their recovery. Metabolic rate is an estimate of the amount of energy being used by an organism, and one of the common ways of estimating metabolic rate in fish is through respirometry. In the following research chapters, I conducted intermittent-flow respirometry experiments both in a laboratory setting and a field setting to compare physiological performance via standard metabolic rate (SMR), maximum metabolic rate (MMR) and aerobic scope (AS) of Bull Trout and Brook Trout across a range of ecologically relevant temperatures. The temperatures tested are found in the habitat both species currently occupy, as well as temperatures that may be seen in future climate scenarios. Brook Trout tested in Chapter 2 maintained a relatively stable AS across the range of temperatures tested (5, 10, 15, 20, 23°C) and appear to be thermal generalists, well adapted to live in various thermal environments. Brook Trout showed a peak in AS at 15°C, increasing SMR with temperature, and a peak in MMR estimates between 15 and 20°C. Results from Chapter 3 revealed that wild juvenile Bull Trout and Brook Trout have comparable SMR, MMR, and AS when living in sympatry in the natural environment, at least at the temperatures tested (~3°C and ~10°C). Brook Trout have historically been seen as a major threat to Bull Trout populations based on prior studies that have looked at interactions between the species and generally found an advantage for Brook Trout over Bull Trout. However, the results from this study showed similar metabolic rates in both species livi

Individual variation in nursing duration and resource use can have cumulative effects on population growth and species resilience in response to resource changes. There have been climate-induced shifts in prey resources in the Arctic since the 1980s; however, knowledge regarding narwhal nursing and dietary variation at the individual level remain understudied. Stable isotope analysis (SIA) of sequential dentine samples can provide a longitudinal record of isotopic (13C and 15N) values that help infer age at which nursing completes, and assess diet. This study used SIA of dentine from narwhal embedded teeth to investigate individual nursing duration and dietary variation within a population over two time periods (pre- and post- 1982/1983). Embedded teeth were collected near Pond Inlet, Nunavut, from both sexes in 1982/1983 (n = 13) and 2015/2017 (n = 14). Ontogenetic 13C and 15N profiles were constructed for individual narwhals. Nursing duration was inferred based on postnatal 15N decline over age 1–10, and I found nursing in narwhals lasted for two to six years but most individuals started feeding primarily on solid food after 12 months. Nursing duration did not differ between sexes nor between the two time periods. To analyze variation in narwhal diet after nursing being completed, I evaluated 13C and 15N values and isotopic niche breadth for individuals within each period and at the population level between the two time periods. Narwhals varied significantly in their isotope values and isotopic niche, suggesting individuals may differ in resource use (prey size, proportion, and feeding locations), as well as the range and consistency of resource use over one’s lifetime. Across time periods, narwhals showed a slight niche expansion, likely reflecting a dietary shift to incorporate alternative subarctic prey that have increased in availability in the Arctic over the past 30 years. This study provides new information on narwhal life history, highlighting the v

Animal signals convey information intra- and interspecifically, but their adaptive importance is often unknown. The humpback whale (Megaptera novaeangliae) is a widespread, highly vocal cetacean known to produce both songs and non-song calls, the latter of which has been less-studied. While associations between non-song calls and behaviour have been examined throughout their range, additional investigations into their temporal patterns in understudied regions may further provide information as to their behavioural context. Using continuous 24-h passive acoustic monitoring and aural/visual surveys of recordings, I investigated the temporal patterns in non-song call activity within three broad classes (low frequency, high frequency and pulsed) on a diel and daily scale across three summers (July-August, 2015-2017) at a foraging site on the northeast coast of Newfoundland, Canada. Low frequency calls were the dominant call class (43-75%) across all time scales relative to high frequency (9-17%) and pulsed calls (8-40%), suggesting low frequency calls are vital for communication among humpback whales on the foraging grounds, as observed throughout their range. Non-song call activity in all call classes was higher during light relative to dark or twilight periods, suggesting individuals are inactive, not engaged in behaviours requiring acoustic communication, and/or remain silent to minimize predator detection. Call activity peaked when humpback whales arrived into the study area and subsequently decreased, suggesting calls are more important in mediating social interactions during movement into the area, but less-so as whales disperse to forage throughout the area. Lastly, call activity varied among years with 2016 having double the call activity of the other years, which was also associated with the highest estimated humpback whale abundance but lowest prey (capelin, Mallotus villosus) biomass, suggesting call activity may indicate humpback whale abundance. Overall, te

Marine ecosystems are influenced by multiple stressors in both linear and non-linear ways. Using generalized additive models (GAMs) fitted to outputs from a multi-ecosystem, multi-model simulation experiment, we investigated 14 major ecological indicators across ten marine ecosystems about their responses to fishing pressure under: (i) three different fishing strategies (focusing on low-, high-, or all-trophic-level taxa); and (ii) four different scenarios of directional or random primary productivity change, a proxy for environmental change. From this work, we draw four major conclusions: (i) responses of indicators to fishing mortality in shapes, directions, and thresholds depend on the fishing strategies considered; (ii) most of the indicators demonstrate decreasing trends with increasing fishing mortality, with a few exceptions depending on the type of fishing strategy; (iii) most of the indicators respond to fishing mortality in a linear way, particularly for community and biomass-based indicators; and (iv) occurrence of threshold for non-linear-mixed type (i.e. non-linear with inflection points) is not prevalent within the fishing mortality rates explored. The conclusions drawn from the present study provide a knowledge base in indicators’ dynamics under different fishing and primary productivity levels, thereby facilitating the application of ecosystem-based fisheries management worldwide

Deep-sea environmental datasets are ever-increasing in size and diversity, as technological advances lead monitoring studies towards long-term, high-frequency data acquisition protocols. This study presents examples of pre-analysis data treatment steps applied to the environmental time series collected by the Internet Operated Deep-sea Crawler “Wally” during a 7-year deployment (2009–2016) in the Barkley Canyon methane hydrates site, off Vancouver Island (BC, Canada). Pressure, temperature, electrical conductivity, flow, turbidity, and chlorophyll data were subjected to different standardizing, normalizing, and de-trending methods on a case-by-case basis, depending on the nature of the treated variable and the range and scale of the values provided by each of the different sensors. The final pressure, temperature, and electrical conductivity (transformed to practical salinity) datasets are ready for use. On the other hand, in the cases of flow, turbidity, and chlorophyll, further in-depth processing, in tandem with data describing the movement and position of the crawler, will be needed in order to filter out all possible effects of the latter. Our work evidences challenges and solutions in multiparametric data acquisition and quality control and ensures that a big step is taken so that the available environmental data meet high quality standards and facilitate the production of reliable scientific results

Conservation physiology is a field of study that focuses on physiological changes in response to human activity and environmental change, including elevations in stress hormones, changes in metabolism, and declines in reproductive hormones, body condition and immune function. Physiological changes such as these can indicate environmental pressures and be used to monitor the health of wildlife populations. In this study, I analyzed endocrine data of two Arctic cetaceans, the Western Hudson Bay beluga population and the Eastern Canada-West Greenland bowhead whale population to better understand how they may respond to climate change. In Chapter 2, I demonstrated, for the first time, that it was possible to collect blow samples from free-swimming beluga whales and that cortisol and urea concentrations could be reliably measured in beluga blow samples. Urea was found to be an unsuitable dilution marker to normalize blow samples. Absolute cortisol concentrations were influenced by sample device, quantity rating, and age class, while urea concentrations were only influenced by sample device. In Chapter 3, I determined baseline triiodothyronine (T3) and corticosterone concentrations measured from baleen plates collected from bowhead whales and conservatively concluded that bowhead whales foraged year-round, based on a lack of observed seasonal variation in T3 and a lack of correlation between T3 and stable isotope values. Interestingly, we found a strong positive correlation between T3 and corticosterone in each whale, which requires further investigation. This research provides important baseline information about Arctic marine mammal endocrinology and establishes key recommendations for carrying out physiological studies.

Understanding the vocal repertoire of a species can help researchers understand many aspects of its ecology. As acoustic communication is often the most effective form of communication in aquatic environments, many marine mammals rely on vocalizations for various aspects of their lives. Therefore, acoustic studies have become a crucial tool to answer many ecological questions about marine mammals and to inform conservation and management, particularly as marine mammals spend much of their lives underwater, making them difficult to study visually. Humpback whales (Megaptera novaeangliae) are a highly vocal species for which passive acoustics have been used to extensively study their song, and, to a lesser extent, their calls. Calls have been studied on a small number of foraging grounds and migration routes, but many regions are understudied, for example, northeast Newfoundland. Therefore, the goals of this thesis were to characterize the call repertoire of northeast Newfoundland humpback whales during July-August over two years (2015, 2016), and to identify whether five call types that have been previously described (i.e., swops, droplets, teepees, growls, whups) were present on both the Newfoundland foraging ground in 2015 and on a Hawaiian breeding ground from 1981-82. Twenty-two potential call types in four broad classes were qualitatively identified in the Newfoundland repertoire over the two years, with 12 of the call types qualitatively determined to be present in both years. The five previously described call types appear to be present in both Newfoundland years as well as in the Hawaiian recordings, though some differences in characteristics were present. These findings suggest that the Newfoundland humpback whales have an extensive and possibly stable repertoire as found in other regions. They also suggest that some of the humpback repertoire could be both fixed and innate, which gives clues as to the function of some of the calls and points towards potenti

Inconnu (Stenodus leucichthys) in Great Slave Lake (GSL), NT have been over-fished resulting in declines in some stocks. By characterizing the population genetics of fish in this area, management can better understand how over-exploitation and other factors affect stocks and use this knowledge to inform their monitoring strategies. Nearly 1000 tissue samples were collected throughout their geographic range in NT from 1988-2017. Population genetic analyses with 17 microsatellite markers were performed to determine the influence of geography, post-glacial colonization, and philopatry on the genetic diversity and structure of Inconnu in NT. Geographic distance significantly affected the genetic differentiation of Inconnu. Significantly lower genetic diversity was observed in GSL populations compared to fish from the upper/lower Mackenzie River region due to post-glacial colonization. Genetic structuring was detected among Inconnu stocks associated with particular river systems suggesting philopatric behaviour. River sampling is critical to understanding the genetic dynamics of Inconnu in GSL.

Moving toward ecosystem-based fisheries management (EBFM) necessitates a suite of ecological indicators that are responsive to fishing pressure, capable of tracking changes in the state of marine ecosystems, and related to management objectives. In this study, we employed the gradient forest method to assess the performance of 14 key ecological indicators in terms of specificity, sensitivity and the detection of thresholds for EBFM across ten marine ecosystems using four modelling frameworks (Ecopath with Ecosim, OSMOSE, Atlantis, and a multi-species size-spectrum model). Across seven of the ten ecosystems, high specificity to fishing pressure was found for most of the 14 indicators. The indicators biomass to fisheries catch ratio (B/C), mean lifespan and trophic level of fish community were found to have wide utility for evaluating fishing impacts. The biomass indicators, which have been identified as Essential Ocean Variables by the Global Ocean Observing System (GOOS), had lower performance for evaluating fishing impacts, yet they were most sensitive to changes in primary productivity. The indicator B/C was most sensitive to low levels of fishing pressure with a generally consistent threshold response around 0.4*F (fishing mortality rate at maximum sustainable yield) across nine of the ten ecosystems. Over 50% of the 14 indicators had threshold responses at, or below ∼0.6* F for most ecosystems, indicating that these ecosystems would have already crossed a threshold for most indicators when fished at F. This research provides useful insights on the performance of indicators, which contribute to facilitating the worldwide move toward EBFM

With climate change, temperate species are becoming increasingly able to occupy Arctic regions that were previously unsuitable. In Cumberland Sound, Nunavut, the forage fish capelin has become abundant in recent decades, as has the seasonally-migrant harp seal during the summer months. Coincident have been reported decreases to resident ringed seal numbers. While capelin foraging is well studied in other regions, it is less so in Cumberland Sound. In addition, no research has yet examined whether harp seals may act as competitors to Cumberland Sound ringed seals. The objectives of this thesis were to (1) quantify capelin diet and isotopic niche characteristics, and (2) examine ringed and harp seal diet and isotopic niches and determine the degree of overlap. Results from this thesis have provided insight into trophic interactions within the Cumberland Sound food web and provide a baseline for future studies examining the impacts of climate change in Arctic ecosystems.

Capelin (Mallotus villosus) is a small, short-lived forage fish species, which is a key prey for many top predators. Newfoundland capelin spawn during the summer, after which most are thought to die. I evaluated the reliability of a spawning zone in the otolith in female capelin by comparing direct (histological) and indirect (otolith-based) indicators of spawning. 50% of individuals with a spawn check identified in the otolith had residual oocytes. This suggests that otolith-based determination may not be a reliable method of identifying previous spawning. I also examined inter-annual variation in growth and links with environmental conditions. Age-specific annual growth was quantified using otolith-based techniques. Generalized Additive Models revealed that higher growth occurred during 2010-2012 and a Principal Components Analysis on environmental factors indicated that these years were characterized by warmer conditions, with earlier and higher magnitude spring blooms, but the abundance of capelin prey varied widely. This suggests that temperature and bloom dynamics may have a larger influence on capelin growth. We highlight the importance of understanding environmental conditions influencing population dynamics, as well as the importance of further characterizing the life history of capelin.

Knowledge of critical foraging areas in time and space, of large marine predators are important to inform management plans. An important foraging ground for humpback whales is coastal Newfoundland. The goal of this study was to investigate the foraging movements and site fidelity of humpback whales, as well as diet in relation to their primary prey, capelin, on their summer foraging grounds off the east coast of Newfoundland. I determined that humpback whale movement patterns within their Newfoundland foraging grounds were associated with the availability of capelin. At the regional scale, humpback whales were consistently abundant within bays when capelin was present. At bay scale, humpback whale presence was influenced by the timing of spawning, rather than capelin shoal characteristics, and individual humpback whales returned to a small area (10 km2) centered on a cluster of capelin deep-water spawning sites. Using stable isotope analysis, I found minimal dietary niche overlap between years (9%). These differences, were driven by inter-annual variation in prey 13C values and, thus, diet reconstruction resulted in capelin/herring comprising > 90% of humpback whale diet in both years. Together, our findings suggest that persistent capelin deep-water spawning sites may be important foraging areas for humpback whales in coastal Newfoundland.

There is an increasing need to understand ecosystem responses to multiple stressors in that such complex responses depend not only on species-level responses, but also on species interactions and ecosystem structure. In this study, we used a multi-model ecosystem simulation approach to explore the combined effects of fishing and primary productivity on different components of the food-web across a suite of ecosystems and a range of model types. Simulations were carried out under different levels of primary productivity and various fishing scenarios. In addition to exploring synergistic, additive or antagonistic combined effects of multiple stressors, we included a fourth category “dampened”, which refers to less negative or less positive impacts compared to additive ones, and in contrast to previous studies, we explicitly considered the direction (positive or negative) of the combined effects. We focused on two specific combined effects (negative synergism and positive dampened) associated with the risk of resultant lower fish biomass than expected under additive effects. Through a meta-analysis of the multi-models' simulation results, we found that (i) the risk of negative synergism was generally higher for low-trophic-level (LTL) taxa, implying that following an increase of fishing pressure on a given LTL stock, the subsequent decrease of biomass under low primary productivity would be larger than expected under additive effects and (ii) the risk of positive dampened effects was generally higher for high-trophic-level (HTL) taxa, implying that given a management measure aimed at reducing the impact of fishing on HTL stocks, the subsequent rebuilding of these stocks would be slower than expected. Our approach to categorizing and exploring cumulative effects can be applied to evaluate other community properties, and provide guidance for fisheries management

Capelin (Mallotus villosus (Müller, 1776)) is an important marine forage fish species that typically inhabits sub-Arctic and temperate circumpolar waters. Capelin have recently been reported in greater abundance in Arctic regions, and are considered an indicator for warming climate in the northern marine ecosystem. The goal of this thesis is to examine intrinsic factors among capelin populations, and whether niche overlap among sympatric capelin and Arctic cod (Boreogadus saida (Lepechin, 1774)) will affect the abundance and persistence of capelin in the Arctic as temperatures continue to rise. Life history comparisons of capelin from two Arctic regions (Western Beaufort Sea, Cumberland Sound) relative to a sub-Arctic population (Newfoundland) show that body size, body condition, growth rate and age-at-maturity vary among these regions. Life history characteristics that are adapted to northern environments and increasing temperatures will allow the presence and persistence of this species to increase in the Arctic. The consequence of increased abundance of capelin in the Arctic environment could be competition between capelin and Arctic cod, an Arctic species within a similar dietary niche. Stomach contents indicated that both species feed primarily on calanoid copepods and this result was corroborated with high dietary overlap in isotopic bivariate space (carbon and nitrogen stable isotopes). The occurrence of capelin is expected to increase in the Arctic with rising temperatures, thus adaptation in life history traits in capelin specific to each region may facilitate increased abundance and persistence, and possibly contribute to competitive pressure on Arctic cod. Potential competition will be particularly important in nearshore and shelf habitats where shifts in availability of intermediate trophic level taxa will influence diet and distribution of key predators such as beluga, sea birds, and anadromous fishes. As the Arctic environment changes with climate shif

Environment-phenotype interactions are significant particularly during early life history as they often dictate physiological performance, growth and ultimately ecological fitness of individuals. Temperature, dissolved oxygen and substrate are all important factors for developing metabolic phenotypes in fish. In this thesis, effects of temperature, dissolved oxygen (DO) and substrate on standard metabolic rate (SMR), forced maximum metabolic rate (FMR), metabolic scope (MS), energy density (ED), enzyme activity associated with ATP regeneration (pyruvate kinase, lactate dehydrogenase and cytochrome c oxidase), condition factor (K), hepatosomatic index (HSI) and critical thermal maxima (CTmax) of developing age-0 Lake Sturgeon, Acipenser fulvescens, including a simulated overwintering event, were examined. This research revealed that temperature, dissolved oxygen and substrate all significantly influenced development of metabolic phenotypes in Lake Sturgeon. While reduced temperature significantly increased SMR, increased temperature substantially decreased the survival rate. Lower DO (80%) did not impact FMR and MS in the short term, however, prolonged exposure to mild hypoxia, particularly during the stressful condition of overwintering, significantly reduced FMR and MS. Inclusion of substrate was found to significantly enhance K and SMR, and it was suggested that substrate be used at the early yolk-sac stage to enhance growth and survival. Further, a strong linear relationship between dry to wet mass ratio and ED was found, which can be used practically to estimate energetic status of Lake Sturgeon. This research provides information regarding environment-phenotype interaction during the first year of life in Lake Sturgeon. This information will contribute to a better understanding of critical factors influencing the successful recruitment of populations that are endangered throughout most of their natural range.

Arctic Cod, Boreogadus saida (Lepechin 1774) occur throughout the circumpolar north at all levels of the water column depending on their life history stage, the time of day, the season, and their activity. Arctic Cod are the most abundant fish species in the Canadian Beaufort Sea (CBS) ecosystem, and are an important link in the flow of energy within the food web. This study examined differences in energy acquisition and usage in Arctic Cod among three depth zones in the CBS (from 15-800m) by examining stomach contents and physiological indicators, taking into account sex, age and body size. Nonparametric comparison analyses found no differences with depth, but support for an ontogenetic shift in diet regarding prey size, a difference in energy content of an average diet between size classes 1 (30-60mm) and 2-4 (2: 60-90mm; 3: 90-120mm; 4: >120mm), and a slight positive relationship between physiological indicators and body size.

Previous understanding of the winter ice regime in Hudson Bay was limited. This investigation demonstrates the existence of a large coastal polynya in northwestern Hudson Bay. Measuring approximately 600 km long by 60 km wide, this polynya is typically opened and maintained by surface winds for periods of one to five days. Closing mechanisms result from decline in wind maintenance and apparent thermodynamic ice formation. Open water is present on the northwest coast at some size for up to 70% of the winter between ice formation and breakup. Observation of this open water during the period of the winter ice pack indicates that the ‘ice factory’, modelled previously, in northwest Hudson Bay exists. This furthers understanding of the freshwater budgets, stratification, and atmosphere-ocean interactions while presenting new questions about climate change and the future of the Hudson Bay physical system.

This study documents the introduction of the European Baltic prawn, Palaemon adspersus Rathke, 1837 to the coastal waters of northeastern North America, specifically the west coast of Newfoundland and the Magdalen Islands in the Gulf of St. Lawrence, Canada. Species identification was verified using morphological and genetic criteria. In September 2011, the first specimens of P. adspersus were collected in Gulf of St. Lawrence waters near Stephenville Crossing, Newfoundland, Canada. In 2012, additional P. adspersus specimens were collected in this area and at St. Andrew’s, located further south in western Newfoundland and in 2013 several egg-bearing females were collected further north in York Harbour. Accidental transport by ballast water of ships seems the likely vector for transport of Baltic prawn to the Gulf of St. Lawrence from Northern Europe or the Caspian Sea. It is possible that this shrimp has a wider presence in Atlantic Canadian waters but, due to its close resemblance to native shrimp species, it may have been previously misidentified, as occurred with specimens collected from the Magdalen Islands. We further expect that other species of the genus Palaemon, including P. elegans Rathke, 1837 from the Baltic Sea or northeastern United States, and P. macrodactylus Rathbun, 1902 from the northeastern United States, may invade the Gulf of St. Lawrence. We provide an illustrated key for the identification of these exotic Palaemon species and to differentiate them from native members of the subfamily Palaemoninae.