Honours Theses

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Is the diel cycle of metabolic rate in mummichog (Fundulus heteroclitus) affected by near infrared lighting used for daytime and nighttime video recordings of behaviour?
(University of New Brunswick, 2023-04) Trembley, Annie Matilda; Speers-Roesch, Ben
Spontaneous activity, which is the routine volitional movements of an animal, is a fundamental behavioural trait that commonly shows a strong diel cycle in animals. Mummichog (Fundulus heteroclitus) are an important estuarine fish, with a historically documented diurnal diel cycle (i.e., being more active during the daylight hours). Recent laboratory studies, however, have reported that mummichog have a free-running (i.e., similarly active regardless of time of day) or nocturnal diel cycle of activity (i.e., more active at nighttime). In the laboratory, activity is often recorded using near-infrared (NIR) lights to illuminate the fish so that a NIR sensitive camera can visualize and record activity across the normal light-dark periods of the 24-hour day. A proxy for activity, when we cannot measure it directly, is whole-animal metabolic rate (MO2) because movement is correlated with oxygen consumption rate. Since NIR light is close to the visible light spectrum, and certain fish show some sensitivity to NIR, its use could explain the uncertainty about the diel cycle of activity in mummichogs. To determine if NIR lighting can influence diel cycles of activity, I measured MO2 of mummichogs over four-day (Experiment 1) or six-day (Experiment 2) periods with alternating on-off regimes of NIR lighting: NIR off-on (two days each) for Experiment 1, or NIR off-on-off (two days each) or the reverse (on-off-on) for Experiment 2. NIR lights did not influence the diel cycle of MO2, which strongly suggests that mummichog do indeed have a nocturnal, but relatively free-running, diel cycle of activity. NIR illumination is a suitable method to visualize mummichog during light-dark diel cycles.
Providing Endophytic Fungi with Taxonomic Classifications Using DNA Taxonomy and DNA Barcoding
(University of New Brunswick, 2023-04) Oh, Hannah; Gray, Christopher
Accurate taxonomic classifications are essential when conducting research about an organism. Over the years, the discovery of DNA sequence-based classification techniques (DNA barcoding and DNA taxonymy) have revolutionized this process. The Natural Products Research group (NPRG) has a library of fungi that is used to isolate bioactive molecules. In order for the NPRG to communicate the results of their studies, it is critical that the fungal isolates are provided with accurate taxonomic classifications. Therefore, this study provided fungal isolates from the NPRG’s fungal collection with taxonomic classifications by using DNA barcoding in conjunction with DNA taxonomy. In doing so, 300 of the NPRG’s fungal isolates were grouped into 158 taxonomic families.
An Assessment of Inner Bay of Fundy Atlantic Salmon (Salmo salar) Spawning Success in Fundy National Park
(University of New Brunswick, 2023-04) Nason, Jack S. J.; Samways, Kurt M.; Pavey, Scott A.
Atlantic salmon (Salmo salar) have declined precipitously throughout most of their North American range. As a result, many strategies have been implemented to try and restore Atlantic salmon (Salmo salar). One such restoration strategy, implemented by the Fundy Salmon Recovery project, involves the collection of endangered inner Bay of Fundy salmon smolts from their natal rivers to be reared at the world’s first marine conservation farm to maturity. This strategy includes both an open net ocean pen and freshwater hatchery components. Upon maturity, these salmon are returned to their natal rivers as adults. This release may be done by hand, by carrying the sexually mature salmon to the water or by carefully lowering them into pools using a helicopter, so they can naturally spawn. In my study, I aim to determine whether these differences in rearing and release strategies led to significant changes in offspring production in the adults of two Fundy National Park rivers. Single nucleotide polymorphisms (SNPs) at 185 loci were used to match parents with the next year’s offspring using Colony, a parentage analysis software. Using a fixed effects linear model, I found that there was no significant effect on offspring production caused by release strategy in both rivers. On the Point Wolfe River, rearing strategy was found to have a significant effect on offspring production – with marine-reared adults out-performing freshwater reared adults. This suggests that the marine-rearing strategy, implemented by the Fundy Salmon Recovery project can outperform, in some cases the more traditional freshwater rearing strategy in terms of releasing high-fitness adult Atlantic salmon.
The Effects of Starvation and Cold on Resting Metabolism of Arctic char (Salvelinus alpinus)
(University of New Brunswick, 2023-03) Christopher, Abby R.; Speers-Roesch, Ben; Gilbert, Matthew
To cope with prolonged frigid temperatures and limited resource availability over winter, Arctic char have an overwintering strategy involving reductions in activity and fasting for up to 10 months, to minimize energy expenditure. I characterized the effects of cold and starvation on Arctic char standard (resting) metabolic rate (SMR) to determine if they confer additional energy savings beyond those achieved through inactivity. Experimental fish were acclimated to 2℃ or 8℃ in combination with either feeding or starvation. Oxygen consumption and activity were measured simultaneously and oxygen consumption at zero activity (resting) was determined to examine how SMR was affected by temperature and feeding condition. Starvation resulted in a ~40% reduction in SMR at both temperatures, suggesting a similar depression of resting energy demands during food deprivation regardless of temperature. The SMR of fish at 2°C was ~39% lower than those at 8°C (Q10=2.3) in both feeding treatments, indicating typical passive slowing of SMR in the cold. The combination of cold and starvation resulted in a ~64% decrease in SMR relative to fed fish at 8°C. Thus, cold and starvation drive reductions in Arctic char resting metabolism independently, and additively, which is likely central to energy conservation over winter.
Identification of chromosomal inversions in Gadus morhua individuals using diagnostic SNPs and Sanger sequencing
(University of New Brunswick, 2022-03) Fraser, Jillian; Pavey, Scott
Atlantic cod (Gadus morhua) is an economically valuable fish native to the Atlantic Ocean, particularly off the coast of the Canadian Atlantic. Having faced major population decline historically with little relief, understanding their genetic variation may allow for better fisheries management concerning the species. Much of the genetic variation in Atlantic cod is present in chromosomal inversions, which under current methodology are expensive and difficult to identify. The objective of this study was to develop a tool to identify the inversion on linkage group 1 in Atlantic cod using diagnostic SNPs, which would make future research into the implications of these inversions between populations much more attainable. While progress has been made in understanding how this tool could be developed, no conclusive results were able to be evaluated during the period of this study.
Tales from the Scales: Investigating the impact of restoration on smolt age class distribution & growth rates in an iBoF Atlantic salmon (Salmo salar) population
(University of New Brunswick, 2022-04) Cyr, Lauren P.; Samways, Kurt M.
The inner Bay of Fundy (iBoF) Atlantic salmon are a genetically distinct population of Atlantic salmon residing within the Bay of Fundy and northern Gulf of Maine, listed as endangered under the Species at Risk Act. Located in Fundy National Park (FNP), the Upper Salmon River is listed as critical habitat for iBoF salmon and has been the site of several restoration strategies: primarily, release of salmon though traditional (juvenile) and Fundy Salmon Recovery (FSR) models (natural spawning from adult releases). This study aims to evaluate the efficacy of adult releases to maintain a wild-like population, via interpretation of archived smolt scales. Aided by a novel scale-analysis script, I evaluated scales from 1240 individuals collected between 2002-2021 to assess age distributions and annual growth rates of smolt cohorts. I observed a shift towards smolt cohorts with more 2+ and 3+ smolts and increased growth rates, following implementation of FSR release strategies. The results of this study provide insight into the impact of this restoration strategy on annual smolt cohorts, which are a key aspect of maintaining a wild population.
Quantification and identification of potential microplastics relative to the size of juvenile soft-shell clams (Mya arenaria)
(University of New Brunswick, 2022-04) Fenech, Amanda; Hunt, Heather
Microplastics (MP) are a widespread pollutant in the marine environment. These contaminants are found in benthic organisms, including the soft-shelled clam (Mya arenaria), an ecologically and economically important filter-feeding bivalve. This study aimed to quantify the relationship between the concentration of potential MP and clam size (mm and mean tissue weight). Since filtration rates are thought to affect MP ingestion in bivalves, it is hypothesized that smaller individuals will possess a higher concentration of MP per gram of soft tissue due to their greater filtration rate. I also examined whether MP type was independent of juvenile size. Juvenile and adult M. arenaria were collected from Kouchibouguac, NB and digested in KOH to extract potential MP, which was identified under a dissecting microscope. Potential MP concentration had a significant non-linear relationship to M. arenaria size, with the highest concentrations (per g of soft tissue or individual) in small juveniles. Potential MP type was independent of juvenile size. 90% of potential MPs identified in this study were fibres and their concentration shared the same non-linear relationship to size as total potential MPs. The results of this project suggest that juvenile M. arenaria may be more vulnerable to any negative effects of MP ingestion than larger individuals.
Genetic and phenotypic variation of Atlantic salmon (Salmo salar) young-of-the-year in the Upper Salmon River, NB, Canada
(University of New Brunswick, 2022-04) Diesbourg, Emilie; Samways, Kurt; D’Aloia, Cassidy
Determining the spatial scale at which genetic structuring occurs is one of the main goals of conservation genetics because such data can help identify management units. This study assessed the hierarchical genetic structure of Atlantic salmon young-of-the-year in the Upper Salmon River, NB at a fine spatial scale (~6 km). Using seven microsatellite loci, genetic clustering analyses and FST estimates were computed to determine the strength of genetic structure within the river. Patterns of genetic structure were then tested to detect whether they aligned with previously identified morphological groupings, using the same individuals. Subtle genetic differentiation (mean pairwise FST=0.036) and a weak isolation by distance pattern was found to exist within this ~6 km stretch of river. Additionally, not all morphological groupings were genetically distinct. This study highlights the importance of considering within-river genetic structure across small spatial scales for more informed conservation design.
Assessing the number of known-age chicks required for accurate age estimation of growing Atlantic Puffin (Fratercula arctica) and Razorbill (Alca torda) chicks
(University of New Brunswick, 2022-04) Braschuk, Arika; Major, Heather
At Machias Seal Island, chick age is used to estimate hatch dates and predict fledge dates of growing seabirds. A small percentage of chicks have a known hatch date, as the number of nest checks required to capture hatch date is limited to reduce colony disturbance. The goal of this study is to find the minimum number of known-age chicks required to accurately estimate ages of unknown-age chicks in Atlantic Puffins (Fratercula arctica) and Razorbills (Alca torda). To do this, I collected measurements of known-age chicks from the time series at MSI (1995-2021), separated these data into training and test datasets, created a series of annual linear growth models, estimated the ages of known-age chicks, and calculated the accuracy of these estimates. My results suggest that a minimum of three chicks are required to estimate chick age with 85% accuracy of puffins and four chicks for 80% accuracy in Razorbills.
Assessing Predictive Ability of Species-Area Relationship Models
(University of New Brunswick, 2022-04) Yoo, Philip J.; Houlahan, Jeff
The species-area relationship (SAR) is a well-established concept but there is still limited understanding of its predictive ability. I investigated the predictive ability of four SAR models (species/area, log-species/log-area, species/log-area, and log-species/area) to new data using linear regression models. I collected 84 SAR datasets and broke them into training and test sets. For each training set I estimated the slope and intercept for each of the 4 SAR models and then used these estimates to predict species richness in each of the 84 test sets. The predictive ability of SAR models for 68 of the 84 was more accurate than the mean. Whether I was assessing the transferability of SAR models in space (i.e., a model built using data from one geographical location in order to predict onto another location) or non-spatially (i.e., model built using randomized sites to predict richness to sites nearby) the predictive ability was similar.
Impacts of a rapidly warming environment on incubation and nestling periods of Atlantic Puffins (Fratercula arctica) on Machias Seal Island
(University of New Brunswick, 2022-03) Soriano, Francis; Major, Heather
The Gulf of Maine (GOM) is warming faster than most of the world’s oceans, cold-adapted seabirds such as Atlantic Puffins (Fratercula arctica), that are nesting at the southernmost extent of their range in the GOM, are at reproductive risk. Since 1995, researchers from the Atlantic Laboratory for Avian Research (ALAR) have collected various environmental and demographic data for puffins nesting on Machias Seal Island and have observed changes in their phenology. Specifically, puffins are now hatching later than early in the time series but fledge date has not changed. Here, I investigate changes in puffin incubation and nestling periods and how these periods are reacting to changing environmental conditions in the GOM. I found that sea surface temperatures and the North Atlantic Oscillation affect incubation periods, while hatch date and precipitation affect nestling periods. This study provides a groundwork for further research into the reproductive flux that seabirds are experiencing.
In-situ validation of American lobster (Homarus americanus) embryo hatch time predictions based on presence and abundance of stage I larvae
(University of New Brunswick, 2022-04) Kubelka, Jonathan Adam; Rochette, Rémy
Hatch time in American lobster (Homarus americanus) embryos can markedly impact larval development rates, match-mismatch with prey, dispersal, and ultimately overall success. Two temperature-dependent embryonic development functions have been proposed to predict hatch in lobsters, one linear and one exponential, but their in-situ validation has been limited. This study quantified the accuracy of these functions by comparing the hatch predictions and potential drift time of 2000 embryos sampled in the southwest Bay of Fundy to the presence and abundance of stage I larvae in the water. Predictions from several models aligned well with the observed stage I presence and abundance, supporting the use of development models to predict lobster hatch. The power function models outperformed or performed as well as the linear function models in all metrics tested, suggesting that power function models may be better suited for generating hatch predictions in southwest Bay of Fundy than linear function models.
Investigating the Use of Atlantic Silverside (Menidia menidia) as a Biomonitor for Polycyclic Aromatic Hydrocarbon (PAH) Pollution in the Saint John Harbour
(University of New Brunswick, 2022-04) MacDonald, Morgan; Crémazy, Anne
The Saint John Harbour (SJH) in Saint John, New Brunswick, is exposed to polycyclic aromatic hydrocarbons (PAHs) from several sources, and these contaminants can have significant adverse effects on wildlife. Biomonitors are species that accumulate and respond to contaminants, and can provide an indication of pollutant bioavailability to wildlife. The objective of this project was to determine whether the Atlantic silverside (Menidia menidia) is a good biomonitor for PAH pollution in the SJH. Sediment and fish were collected from four sites in the SJH, and PAH concentrations in sediment and fish tissue, fish condition indices, and hepatic ethoxyresorufin-O-deethylase (EROD) activity were measured. It was found that PAHs did not accumulate in detectable levels in fish tissue. Contrary to our predictions, we found that fish condition indices and hepatic EROD were not related to sediment PAH levels. Fish collected at Hazen Creek exhibited higher hepatic EROD activity than fish collected from the three other sites, despite Hazen Creek having the lowest sediment PAH concentrations. The high levels of EROD activity observed at this site could have been due to physiochemical factors, biological factors, or the presence of other contaminants.
Comparative Analysis of Cytokine Levels in Multiple Myeloma Patients: Implications for Natural Killer Cells and Therapeutic Monoclonal Antibodies
(University of New Brunswick, 2024-04) Lee, Sungmok; Reiman, Tony
Multiple myeloma (MM) is a lethal cancer affecting bone marrow (BM) plasma cells, with dysregulated natural killer (NK) cells and cytokine production contributing to disease progression. Monoclonal antibody therapies (mAbs) can induce NK cell responses against tumours, which can potentially be enhanced by cytokine manipulation. This study evaluates cytokine levels in MM patients’ blood compared to the blood of healthy controls (CTR) and the BM of MM patients to assess their potential as therapeutic targets. Using Bio-Plex profiling, eight cytokines (IL-2, IL-8, IL-10, IL-12, IL-15, IL-18, IFN-γ, and TGF-β1) were quantified. Significant differences in cytokine profiles were observed between MM patients and CTR, as well as between MM patients' blood and BM. These findings underscore cytokines’ potential role in MM progression, emphasizing them as potential therapeutic targets. The study lays the groundwork for future research aimed at modulating the cytokine network in MM to augment NK cell responsiveness to mAbs.
Bioautographic fractionation of antibiotic natural products from a marine-derived fungus
(University of New Brunswick, 2024-04) Newlands, Camryn R.; Gray, Chrisopher A.
The development of antibiotic resistance in recent decades is a major concern that has urged natural product researchers to investigate new biological sources of antimicrobial compounds. Fungi isolated from marine environments have proven to be a potent source of bioactive molecules. The crude extract of an unidentified seafoamderived fungus, SC1-077G, demonstrated strong inhibition of Staphylococcus aureus in an antimicrobial activity screening in 2016. The objective of this research was to isolate the compound(s) responsible for the bioactivity of the crude extract using immersion bioautography guided fractionation. Flash chromatography and high-performance liquid chromatography generated an impure sample containing two putatively new natural products, which demonstrated strong inhibition of S. aureus, that could not be further purified chromatographically. Acetylation of the impure sample facilitated the isolation of two acetylated, putatively new natural product derivatives. Immersion bioautography proved to be an efficient method for directing the fractionation of bioactive natural products.
Reproductive success of inner Bay of Fundy Atlantic salmon (Salmo salar) exposed to modified feeding regimes
(University of New Brunswick, 2024-03) Armstrong, Kristin; Samways, Kurt M.
Atlantic salmon (Salmo salar) are widely considered to be at-risk across much of their natural distribution. Reproductive success was investigated for inner Bay of Fundy (iBoF) Atlantic salmon reared from smolt to one sea winter maturity under various feeding regimes. The experiment measured fecundity, egg weight and diameter, and survival to the eyed-stage of development from 13 females and across 39 unique crosses. Fecundity and egg metrics (i.e., egg weight and diameter) did not vary significantly across feeding treatments, however egg mortality was significantly higher in the commercial-style feeding control group (SS4) than any experimental, food-limiting treatment group. Females of treatment group SS5, which experienced the second-most food limitation, produced the greatest number of eggs per centimeter fork length, as well as the lowest mortality rates. The results of this study suggest feeding limitation influences reproductive success in iBoF salmon and inform conservation strategies for the recovery of this species.
Developing and testing a lab protocol to study the feeding ecology of American lobster (Homarus americanus) larvae
(University of New Brunswick, 2024-04) Power, Brooke-Lyn; Rochette, Rémy
Little is known about the natural feeding ecology of American lobster larvae. Through a lab experiment using different sizes of natural zooplankton, this study aims to develop a lab protocol to raise lobster larvae on a natural diet. Shortly after hatch, larvae were placed in individual containers and fed zooplankton collected from surface tows, with survival, inter-moult duration, and carapace length measured. This protocol showed promise, since it resulted in the complete development of some larvae, and it showed differences in survival rate and inter-moult period among larvae in the different zooplankton treatments. Development was sub-optimal when compared to a well-known lab study that raised lobster larvae from the same general region on an artificial diet, with lower survival and higher inter-moult duration for some or all stages. With improvements this protocol is expected allow raising lobster larvae on natural zooplankton to gain insight into their feeding ecology.
Ichnology of the Pennsylvanian-aged Boss Point Formation at Cape Enrage, New Brunswick: Implication for the paleoenvironmental context for the Lower Boss Point Formation in the Cumberland Subbasin of the Maritimes Basin
(University of New Brunswick, 2024) Hannberg, Alexia T.; Wilson, Lucy; Stimson, Matthew
The Langsettian aged Boss Point Formation (i.e. ~320 million years old) outcrops at Cape Enrage in southeastern New Brunswick along the shores of the Chignecto Bay, Bay of Fundy. Although traces have been noted from the type section at Joggins Nova Scotia, newly discovered invertebrate repichnia tracks at Cape Enrage represent the first ichnofossil assemblage to be systematically described from the Boss Point Formation in Atlantic Canada. The tracks described in this thesis include: Diplichnites, Diplopodichnus, Kouphichnium, Protichnites, Selenichnites and Stiaria. Given the presence of some diagnostic ichnotaxa, some of the lithofacies can be interpreted as shallow coastal and channel bar lithofacies conformable to the poorly-drained to openwater lithofacies assemblage transition described from the Joggins Formation. The implications of this ichnoassemblage, specifically the presence of horseshoe crab traces, indicate that the Boss Point Formation, at least in part, was more closely connected to open-water depositional settings than previously thought.
Investigating the Life History of Returning iBoF Atlantic Salmon (Salmo salar) using Passive Integrated Transponder (PIT) Technology
(University of New Brunswick, 2024-02) Morrissey, Alexandra M.; Samways, Kurt M.
Since the 1980s, the inner Bay of Fundy (iBoF) Atlantic salmon (Salmo salar) population has significantly declined, in which it was listed as endangered under the Species at Risk Act (SARA) in 2003. Fundy National Park (FNP) contains critical habitat for this population, including the Upper Salmon and Point Wolfe rivers, in which ongoing recovery efforts are being implemented. This study assesses current restoration strategies by evaluating the life history characteristics of successfully returning Atlantic salmon to FNP. Among the 385 salmon that returned to FNP rivers between 2016-2023, I found that fish reared in modified open net pens in the Bay of Fundy exhibited a return rate 1.59 times greater than fish reared in a traditional hatchery environment and juvenile salmon collected as wild smolt returned at a rate twofold higher than that of wild-exposed parr. It was found that maximizing wild exposure is crucial for the restoration of endangered salmon populations and should be a vital component to consider when captive-rearing fish. These findings allow users to adaptively manage and understand the different strategies currently being implemented by the Fundy Salmon Recovery program.
Seasonal and Temporal Variations in the Underwater Vocal Behaviour of Weddell Seals (Leptonychotes weddellii) Near Davis, Antarctica: Insights from Passive Acoustic Monitoring
(University of New Brunswick, 2024-04) Simmonds, Emma; Terhune, John M.; Samways, Kurt M.
Within the Antarctic environment, marine mammals rely on sound for communication. This study investigated the vocal behaviours of Weddell seals (Leptonychotes weddellii) using passive acoustic monitoring of calls recorded under landfast ice near Davis, Antarctica (68°34'S, 77°58'E), provided by the Australian Antarctic Division (AAD). Vocalizations were examined throughout austral winter and summer. I analyzed hourly data—sampled every ten days from July 24th, 2021, to December 31st, 2021—and recorded the number of calls and elements for eight minutes. Statistical analyses included generalized linear models with a negative binomial distribution. Results show increased vocalizations before dawn and after sunset until 24 hours of sunlight. Furthermore, underwater vocalizations varied across seasons, with high calling rates during winter, low calling rates during breeding season, and a sharp decline in mid-November. These findings produce insights into the vocalization trends of Weddell seals and will be utilized by AAD for environmental impact assessments.

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