Honours Theses

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A retrospective assessment of marine ecological research using optimal α
(University of New Brunswick, 2020) Zhao, Chuhan; Houlahan, Jeff
Null hypothesis significance testing (NHST) is and has been for many decades broadly applied across disciplines, NHST’s shortcomings have been identified and discussed since its introduction. Optimal alpha is a better method for setting statistical thresholds in NHST because it minimizes the overall probability of making errors. However, we don’t know how often using optimal α would result in a different conclusion than NHST. I calculate optimal α for 433 tests from 2009-2018 published marine biology papers and compare conclusions with NHST. I find totally 24 % of conflicting results (small ES: 22 %; medium ES: 22 %; large ES: 29 %). For disagreement, optimal alpha has 97 % significant results at small ES, 54% at medium and 24% at large. Low observed p value tends to have disagreement. These results mean that failing to use optimal alpha may be inflating the probability of making wrong conclusions in marine biology.
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.
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.
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.
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.
Change in occupancy and density of nesting Atlantic puffins and razorbills on Machias Seal Island between 2011 and 2019
(University of New Brunswick, 2020) Elisseou, Meredyth; H. Major
At Machias Seal Island (MSI), populations of nesting Atlantic Puffins (Fratercula arctica) and Razorbills (Alca torda) are stable and increasing (respectively). The purpose of my study was to determine whether the increasing Razorbill population has caused a change in the spatial distribution of nesting puffins on the island. I hypothesized that the larger, more competitive Razorbills outcompete puffins for nesting space, resulting in the movement of puffins to alternative regions of the island. Using data from Alcid surveys that occurred in 2011, 2015, 2016, and 2019, I assessed occupancy and density of puffins and Razorbills in each of 1,753 surveyed quadrats. Using generalized linear models in an information theoretic approach, I found no changes in occupancy or density of either species. However, I note the short timespan (eight years) covered in my study and suggest that continued monitoring and analysis of changes in puffin and Razorbill occupancy and density.
Changes in body size of Atlantic Puffins at Machias Seal Island (MSI) from 1995-2019
(University of New Brunswick, 2020) Georgantopoulos, Joy; Major, Heather
Body size of fledging Atlantic Puffins (Fratercula arctica) at Machias Seal Island have been decreasing over the past 25 years (1995-2019) likely due to climate change. Using fledging size data archived in the Microsoft Access data base “seabird finder” I asked three questions: 1) have puffin fledgers gotten smaller in size (wing chord and mass) over the last 25 years, 2) can small fledgers continue to grow (in wing chord) after leaving the island, and 3) are adult Atlantic Puffins decreasing in size (wing chord). Using linear regressions, I found support for the hypothesis that fledgers are getting smaller with time and that small fledgers grow more after leaving the island than large fledgers. Finally, I found a marginally insignificant result suggesting that adult size is changing in response to fledging size (i.e., adults are becoming smaller with time).
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.
Comparing the effectiveness of protein coding genes to the ITS gene as DNA barcode markers for species-level identification of Penicillium and Aspergillus fungal isolates
(University of New Brunswick, 2020) Po, Hui Ting; Gray, Christopher; Johnson, John
Penicillium and Aspergillus are important genera of fungi in the order Eurotiales that are species-rich and are found living ubiquitously. The ability to identify these fungal species allows researchers to collate and access valuable information associated with these fungi. In recent years, a molecular technique known as DNA barcoding has become a common method used for fungal identification. The internal transcribed spacer (ITS) gene was described in 2012 as the universal DNA barcode marker for fungal identifications but has limited sequence variability to identify species of Penicillium and Aspergillus. Protein coding genes; benA and calmodulin may be more effective barcode markers for identifying Penicillium and Aspergillus species, respectively, due to higher interspecific variations in the gene sequences. In the present study, we compare whether it is more effective to identify Penicillium and Aspergillus fungal isolates to the species level using protein coding genes or the ITS gene as barcode markers.
Contribution of variability in embryo development rate and status at hatch to the protracted hatch period of female American lobster Homarus americanus
(University of New Brunswick, 2018) White, Lydia; Rochette, Rémy; Zou, Liwen
Female American lobsters typically hatch their embryos over protracted hatch periods of 15-32 days. To investigate the mechanisms underlying this intra-brood variation in hatch time, I reared individual embryos from June to September 2017 at a constant temperature of 9°C, took photos of them at the beginning of the study and prior to hatch, and measured their eye size as a proxy of their development status. A multiple linear regression model explained 74% of the variability in hatch day, and indicated that embryos that hatcher earlier in the summer are (i) more developed come spring (44% of explained variance), (ii) less advanced in development (28%), and (iii) develop at a faster rate (27%). This study suggests that the process of hatching is not strictly associated with a particular role of the brooding female, but rather is perhaps mostly a function of processes or attributes of individual embryos.
Cultivation of endophytic fungi inhabiting Abies balsamea using two techniques: a comparative study
(University of New Brunswick, 2018) Fitzherbert, Tyson; Gray, Christopher; Johnson, John
Two cultivation techniques: leaf segment cultivation and dilution-series cultivation, were compared for recovery of endophytes from needles of Abies balsamea collected in Saint John, New Brunswick, Canada. Endophytes were cultured on 2% malt extract agar and morphology of the endophytic growth was used to aid identification of distinct isolates. Endophytes were isolated from A. balsamea needles using the leaf segment cultivation method at a frequency of 13%, all replicates of two distinct isolates. Endophytes were isolated form eight of 25 prepared isolation plates for the dilution-series method. All endophytic growth from the dilution-series method was single-celled yeast species, while the endophytic growth from the leaf segment method was exclusively filamentous fungal species; thus, dichotomy was seen between the two methods of isolation.
Determination of a link between the taxonomic relationship of Canadian medicinal plants and the exhibited antibiotic activity of their crude extracts
(University of New Brunswick, 2019) Therrien, Julie K.; Gray, Christopher
Chemotaxonomy is effective in determining the expected chemical compounds found in extracts from different organisms. However, this is time-consuming and costly, as it is based on purified fractions of a chemical extract. Utilizing biological activity data of extracts and relating it to the taxonomic relationship of plants may be a more effective approach. The aim of this study was to determine if a link exists between the taxonomic relationship of plants and the exhibited antibiotic activity of their extracts. The antibiotic activity of methanolic extracts of 90 plants were evaluated against eight microorganisms. Bioactivity profiles were created and analyzed, using two separate methods. It was found that the lowest taxonomic level that correlated with the bioactivity profiles of the extracts was family.
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.
Does land-use affect bird abundance?
(University of New Brunswick, 2019) Prosser, Jacob; Houlahan, Jeff
Over the last 50 years many species have seen negative population trends and scientists have identified habitat loss, change, and fragmentation as possible causes. I investigated the ability of random forest and boosted trees models to predict bird abundances based on land-use throughout the United States. Bird abundance data was acquired from the North American Breed Bird Survey (BBS) and land-use data was gathered by the Multi-Resolution Land Characteristics (MRLC) consortium. The models had a mixed transferability between the training and test data with 14 of 21 models better fit the training data. The models were mixed in their ability to accurately predict abundances based on land-use compared to the mean; 14 of 21 models more accuracy predict abundance compared to the mean suggesting an effect of land-use on abundance. Six models were classified as “good,” 11 as “cautious,” and 4 as “poor.”
Effects of environmental conditions on egg-laying dates in Atlantic puffin Fratercula arctica
(University of New Brunswick, 2019) Fana, Natalia; Major, H.L.; Whidden, S.E.
Climate change trends may have an impact on the timing of seasonal activities, and in particular the phenology of Atlantic Puffins. The purpose of this study was to investigate if changes in environmental conditions, such as Sea Surface Temperature (SST), are responsible for the observed delay in egg laying at Machias Seal Island (MSI), New Brunswick. I used monthly means for SST and egg laying dates over a period of 24 years (1995-2018) from MSI. I used general linear models in an AICc framework and found a positive relationship between egg laying dates and SST over time. I suggest continued long-term monitoring to assess future changes and the puffin’s ability to continue to adapt to those changes.
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.
Human behavioural ecology in the middle palaeolithic : a comparative study based on how we quantify the use of raw material
(University of New Brunswick, 2020) Mears, Peter; Wilson, Lucy; Browne, Constance
Resource Selection Function (RSF) analyses can be used to understand what variables influenced hominin choices for selection of lithic raw materials. Previous work examined stone tool assemblages from the Bau de l’Aubesier (Vaucluse, France), quantifying raw material use by the number of lithics from a particular source area. My study compares this to quantifying use by the weight of those pieces, using Generalized Linear Models that describe the sources of raw material used in each archaeological layer. Independent variables describe raw material characteristics or the surrounding terrain. In the older layers of the site, terrain variables contribute more towards source area use. In the younger layers, raw material characteristics drive source use, but less so in models that quantify lithics by their weight. k-fold cross-validation analyses suggest the best method of quantifying lithic artefacts for use in RSFs may vary depending on the hominin behaviour that led to the assemblage.
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.
Identification and DNA taxonomic analysis of a library of endophytic fungi
(University of New Brunswick, 2019) Stack, Ryleigh A.; Gray, Christopher; Johnson, John
Endophytes represent a largely untapped source of natural products. Despite a growing body of research, data and knowledge relating to endophyte biology and chemistry, one of the difficulties in endophyte research remains the accurate identification of endophytes. The advancements and development of molecular methods have provided researchers with tools that allow them to obtain an identification based on the endophyte’s DNA sequence, rather than its morphological and/or phenotypic characteristics. In the present study, the DNA extracted from 155 endophytes was analyzed following a DNA taxonomy methodology and compiled to give phylogenetic trees to obtain identifications based on the molecular properties of the endophytes, rather than their morphology. Of the 155 endophytes; 57 were identified to the species level, 65 to genus, 5 to class, 2 to subdivision, 10 to order, 15 to family, and 1 to subclass.
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.

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Browsing Honours Theses by Subject "Biology"

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