Department of Biology (Fredericton)

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Local and landscape effects of industrial forestry on the reproductive activity of forest songbirds in northwestern New Brunswick, Canada
Local and landscape effects of industrial forestry on the reproductive activity of forest songbirds in northwestern New Brunswick, Canada
by John Steven Gunn, In the northern hardwood forest of New Brunswick, industrial forest management affects within-stand vegetation and the landscape structure of the forest mosaic. Understanding the effects of industrial forestry on songbird populations requires the investigation of songbird reproductive success, in addition to abundance, on a landscape scale (i.e., in a mosaic of forest stands). I present a method to efficiently assess the reproductive success of multiple songbird species across a large area (e.g., > 300 ha). The method uses systematic playbacks of a recording of black-capped chickadee (Poecile atricapilla) mobbing calls to attract species to an observer. Once birds are attracted to the observer, reproduction-related activities can be recorded to infer successful pairing, hatching, or fledging. Trends in reproductive activity of two focal species obtained using this method were similar to their actual reproductive success as measured using intensive nest monitoring in the same locations. I studied the mobbing response of forest birds at different times of the year and in the presence or absence of potential avian predators. Mean duration of mobbing time was significantly longer when confronted with potential predators, but mobbing intensity was not significantly different. Mobbing group size and overall intensity were greatest early in the breeding season before the initiation of egg laying. I concluded that the variability in avian anti-predator mobbing is based on the proximate (individual safety) and ultimate (safety of offspring) risks of participation. I explored the relationship between reproductive activity and songbird abundance using Spearman correlation coefficients. Reproductive activity and songbird abundance were not significantly correlated in 56% of the comparisons (9 of 16). The lack of a consistent relationship emphasizes the importance of studying fitness parameters in addition to abundance or density. I then used canonical correspondence analysis to assess the relationship between forest management and reproductive activity of eight species of forest birds (Vireonidae, Paridae, and Parulidae) in three study grids of varying silvicultural intensity. I predicted landscape effects would become significant as silvicultural intensity increased. Reproductive activity, local vegetation, and landscape structure data were collected on one 6 x 8 systematic grid and two 8 x 8 systematic grids with stations spaced 250 m apart. Basal area of American beech (Fagus grandifolia) and sugar maple (Acer saccharum) within 100 m of the sample locations were the most significant variables associated with reproductive activity on two of the three study grids (most and least intensively managed). In the third study grid (moderately managed), the amount of tolerant hardwood forest within 1 km of the sampling locations was most significant. The relatively minor effect of landscape structure probably reflects the high proportion of suitable habitat remaining in the study area. Landscape effects on songbird populations may become more important if the proportion of suitable habitat declines.
Mercury in fish and invertebrates in the Saint John River estuary
Mercury in fish and invertebrates in the Saint John River estuary
by Bethany Reinhart, Methylmercury (MeHg) is a common toxin that affects freshwater fish and fish consumers in North America, but its accumulation has not been well studied in estuarine systems. Therefore, the spatial trends of MeHg in biota from fresh to marine waters are poorly understood. This study investigated patterns of MeHg along a salinity gradient ranging from freshwater to brackish water within the Saint John River estuary, New Brunswick, Canada. The objective was to identify how MeHg concentrations in organisms relate to this salinity gradient and other biological or environmental variables. Samples collected in 2015 and 2016 included fourspine stickleback (Apeltes quadracus), Gammarus amphipods, freshwater snails, chironomids, sediments, and water. With increasing salinity, MeHg increased in chironomids but showed no strong correlations for other samples. This research showed that salinity was not strongly associated with MeHg in abiotic and biotic compartments of this estuary and that the risk of MeHg toxicity cannot be identified based on habitat salinity. However, this work is important for building future studies predicting MeHg in estuarine food webs.
Metabolomic analysis of derivatives of the pathways catalyzed by indolepyruvate decarboxylase and an uncharacterized aldo-keto reductase in a soil and enteric bacterium
Metabolomic analysis of derivatives of the pathways catalyzed by indolepyruvate decarboxylase and an uncharacterized aldo-keto reductase in a soil and enteric bacterium
by Danielle Harris, Enterobacter cloacae UW5 is a common enteric commensal and soil bacterium whose plant growth-promoting capabilities have been attributed to production of the signaling molecule indoleacetic acid (IAA). Mutants with deletions in the ipdC gene encoding indolepyruvate decarboxylase, a key enzyme in the IAA biosynthetic pathway no longer promote plant growth. However, indolepyruvate decarboxylases are promiscuous, and therefore the indolepyruvate pathway may produce other plant bioactive signaling molecules in addition to IAA. Moreover, ipdC is upregulated in the presence of both tryptophan (a pathway precursor) and phenylalanine (not known to be metabolized by the indolepyruvate pathway in E. cloacae). One of the aims of this study was to identify the indolepyruvate pathway-dependent metabolites produced by E. cloacae cultured in tryptophan and phenylalanine media. Expression of ipdC and an adjacent gene (akr) predicted to encode an aldo-keto reductase (AKR) are regulated by the transcription factor TyrR. Because the genes are co-regulated, I hypothesized that the pathways catalyzed by the two enzymes may be connected. Therefore, a second aim of this study was to identify metabolites in the AKR pathway, in particular those shared with the indolepyruvate pathway. Using an untargeted metabolomics approach, and ipdC and akr mutants, indolepyruvate decarboxylase-dependent changes to the metabolic profile were measured and putatively linked to tryptophan, phenylalanine, glucosinolate, sphingolipid, and linoleic acid metabolism. Additionally, 137 putative metabolites in the AKR pathway were uncovered, and pyruvate metabolism was discovered to be a potential link between the two enzymatic pathways. Many indolepyruvate-dependent changes to E. cloacae metabolism identified in this study could serve as signaling molecules or their precursors, thus shedding light on the ecological role of the indolepyruvate pathway as a potential mediator of bacteria-host or bacteria-bacteria interactions beyond its known role in IAA biosynthesis.
Molecular characterization of dieldrin in the zebrafish hypothalamus
Molecular characterization of dieldrin in the zebrafish hypothalamus
by Andrew M. Cowie, Dieldrin is a legacy pesticide that has multiple modes of action (MOA) that include being an estrogen receptor agonist, GABA receptor antagonist, and a chemical that disrupts mitochondrial function. There is also evidence that dieldrin exposure is significantly associated with an increased risk for neurodegeneration in humans. The objective of this thesis was to clarify the effects of dieldrin in the hypothalamus, the major neuroendocrine region of the brain, in the zebrafish (Danio rerio). Zebrafish were fed pellets containing 0.03, 0.15, or 1.8 μg/g dieldrin for 21 day sand a global gene expression analysis was performed to characterize cellular processes and pathways affected by dieldrin. Signaling pathways associated with T-cell receptors and several interleukin receptors were significantly down regulated in both the 0.15 and 1.8 μg/g treatment groups. Moreover, transcripts related to mitochondrial function were significantly down-regulated in the hypothalamus following dieldrin treatments. The dysregulation of immune related transcripts raises the possibility that altered immune system function may be a mechanism underlying dieldrin induced neurotoxicity and neurodegeneration.
Mortality and development of wild Atlantic salmon (Salmo salar) embryos associated with environmental conditions over winter in the Miramichi River basin
Mortality and development of wild Atlantic salmon (Salmo salar) embryos associated with environmental conditions over winter in the Miramichi River basin
by Jacqueline Michelle Lavery, Dynamic winter conditions in northern streams present considerable challenges for incubating wild Atlantic salmon (Salmo salar) embryos. How these winter conditions affect embryo mortality and development in nature is poorly understood. The goals of the present study were to 1) identify abiotic variables associated with the mortality of wild salmon embryos and 2) assess the accuracy and precision of embryonic developmental prediction methods currently used for conservation and basic research purposes. Over two study years (2013-2014 and 2014-2015), embryos were reared in artificial redds in five active spawning reaches in the Miramichi River basin and mortality was quantified at two sampling events (late March, pre-freshet and late May, post-freshet). Through partial least squares regression analyses, 37.6% of the total variation in embryo mortality was explained by abiotic predictor variables from five continuous measurements of incubation conditions in each reach (water temperature, water level, dissolved oxygen, ice conditions, and substrate characteristics). Each of the five groups of predictor variables contributed uniformly to the explained variation, which suggests that mortality is influenced by multiple interacting abiotic conditions, rather than a single variable. Developmental states based on external morphology were assigned to live embryos and alevins at various points through the incubation periods. Corresponding temperature records were used to calculate predicted developmental progression using three temperature-based relative age methods (cumulative degree-days, effective degree-days, and tau somites). Embryonic development was not observed to match any of the prediction methods. However, a linear model fitting effective degree-days to assigned developmental state was suggested as a first step to improve predictions. Population-specific adjustments to parameters within the effective degree-day or tau somite methods and the inclusion of other abiotic variables are recommended. Results from the present study support a multi-faceted ecological perspective of embryonic mortality and development in nature and may provide a baseline from which to measure the impacts of further environmental change., M.Sc. University of New Brunswick, Department of Biology, 2017.
Multiple stressor responses of stream benthos to nutrient enrichment and inorganic sedimentation
Multiple stressor responses of stream benthos to nutrient enrichment and inorganic sedimentation
by Justin W. Chase, There is a need to investigate freshwater ecosystem degradation as a function of multiple, often coinciding factors (stressors). Artificial stream systems known as mesocosms provide a useful means of disentangling the contributions of individual stressors acting in a multiple stressor environment while also investigating interactions between these factors. This thesis examines the impacts of locally relevant levels of nutrient loading and inorganic sedimentation on benthic invertebrate assemblages characteristic of northern temperate streams. Experimental manipulations were performed using a mesocosm system consisting of 96 self-contained artificial streams. Key questions addressed included: (1) what are the individual contributions of sedimentation and nutrient loading when simultaneously acting on benthic environments; and (2) do multiple-stressor impacts simply match the effect of the most deleterious stressor or are stressors worse in combination than alone? Complex multiple-stressor relationships were observed between nutrients and fine sediment, and combined effects could not be inferred from information on single-stressor effects. Several individual invertebrate taxa, such as Lepidostomatidae caddisflies, responded positively to additions of nutrients and fine sediment, although the apparent subsidy from single factors was often suppressed under multiple-stressor conditions. Sediment functioned exclusively as a habitat variable, and the effects on individual taxa were dependant on their specific habitat requirements (niches). Nutrients drove shifts in periphytic algal composition, from low-profile diatom dominated communities to stands of high-profile diatoms with an overstory of mostly filamentous green algae. Moderate nutrient enrichment was related to increased organism density, particularly among herbivores, although densities of several taxa declined with high enrichment, especially when coupled with sediment addition. This suggests that in highly enriched systems the food resource subsidy is confounded by habitat related stress, as excessive algal accumulation smothers the substrate and clogs interstitial spaces. Therefore, in highly impacted streams stressor mechanism overlap is probable, as both algal accumulation and sedimentation contribute to deterioration of benthic/hyporheic habitat. Given that these stressors strongly co-vary along agricultural land use gradients, it should be anticipated that with increased agricultural intensity the cooperative action of nutrients and sediment will amplify, leading to ecological impacts that far exceed that of either driver individually. Pollution standards and management practices should reflect this precept and the independent management of common non-point source pollutants should be phased out in favour of comprehensive, multiple-stressor strategies., (UNB accession number) Thesis 9167. (OCoLC) 862154481, Thesis (M. Sc.) University of New Brunswick, Dept. of Biology, 2013.
On the role of host-trait variation in insect diversification
On the role of host-trait variation in insect diversification
by Chandra Elaine Moffat, Ecology’s driving role in niche expansion and subsequent diversification has gained appreciation in recent years, but the specific mechanisms driving such processes remain poorly understood. For the herbivorous insects, diversification may be facilitated by their ability to radiate via host shifts (=host-associated differentiation, HAD). The Gape-and-Pinch (GAP) model (Heard 2012) hypothesizes that HAD may be facilitated by insects’ selective patterns of host use, both within and between host species, which may follow a predictable sequence during divergence. I provide the first tests of the GAP model and investigate a recent possible case of HAD. First, I test hypotheses derived from the GAP model, specifically that host trait variation plays a role in the divergence of specialist herbivorous insects. I quantify trait variation among phenotypes of Solidago altissima and S. gigantea and compare patterns of attacked versus available phenotypes. For specialists, results are generally consistent with GAP predictions: use of available host phenotypes depends on the stage of HAD, and there may be a link between traits diagnosing alternative host species and divergent selection acting on host-associated populations. Second, I ask whether the goldenrod ball-gall fly Eurosta solidaginis, which has evolved several host-associated races, has initiated HAD on S. rugosa. Mitochondrial DNA sequence data indicate that flies on S. altissima and S. rugosa are likely one oligophagous host race, but fine-scale interpretation of fly genotypes across the landscape suggest that S. rugosa-flies may be in the early stages of divergence. Finally, I ask whether a ‘key’ host trait may have driven divergence in one case of HAD and initiated another. For E. solidaginis, selective use of pubescent S. altissima may have promoted divergence from S. gigantea-flies and facilitated acceptance of S. rugosa, but detectability of the pattern varies across the landscape. Identifying such key traits could provide new insights into the mechanisms of HAD and ecological speciation. My results suggest that divergent use of plant phenotypes plays a role in insect diversification, and that early divergence may occur at local scales. More broadly, my work indicates adaptation to within-niche variation may facilitate colonization of novel niches and ultimately drive ecological speciation., Ph.D. University of New Brunswick, Department of Biology, 2017.
Overwinter movement of Atlantic Puffins (Fratercula arctica) breeding in the Gulf of Maine
Overwinter movement of Atlantic Puffins (Fratercula arctica) breeding in the Gulf of Maine
by Mark A. Baran, Atlantic Puffins (Fratercula arctica) are pelagic seabirds that breed on offshore islands throughout the North Atlantic. Following the breeding season, puffins spend the nonbreeding months at sea and there is a knowledge gap regarding the factors affecting populations away from the colony. I used geolocators to determine the nonbreeding locations of North American puffins breeding on three islands in the Gulf of Maine, examining differences between colonies and within the largest colony. I also examined using stable isotopes in claw tissue to determine general overwinter position. Puffins sampled in this study typically remained in the Gulf of Maine before moving south in the late winter, though some visited waters around Newfoundland during the autumn. Movement patterns were similar among birds within and between colonies. Attempts to use stable isotope analysis of claw tissue to determine overwinter location were inhibited by the similarity of routes among sampled birds., Electronic Only.
Patterns and mechanisms of post-translational regulation of MMP-2 in vivo during zebrafish development
Patterns and mechanisms of post-translational regulation of MMP-2 in vivo during zebrafish development
by Rachael A. Wyatt, In addition to cells, multicellular tissues are made up of context-specific complexes of secreted proteins that are assembled dynamically outside cells to produce the physical characteristics of the vertebrate body and organs. The resistive strength of tendons, the elasticity and impermeability of skin and the support structure of the skeleton are functional largely because of the extracellular matrix (ECM). The development and maintenance of these tissues requires careful orchestration between assembly and degradation of components. Matrix metalloproteinases (MMPs) are one of the enzyme families known to degrade ECM. Matrix metalloproteinase-2 (MMP-2), my enzyme of interest, is known to have roles in pathologies such as arthritis, where its function is protective, and cancer metastasis, where it is activated as part of the migration and invasion of metastatic cells. It is an enzyme that requires post-translational activation by proteolytic cleavage, and therefore its role cannot be fully described by either mmp2 transcript patterns or Mmp2 protein accumulation. Using a transgenic zebrafish line with the epitope-mediated MMP activation (EMMA) assay construct, for the first time we can localize activation of Mmp2 in vivo, and here I describe its presence and activation during embryonic development. Though endogenous Mmp2 is expressed ubiquitously during the development of a zebrafish embryo, I show here that it is proteolytically activated in a much smaller set of structures. It is most strongly activated in the notochord, epithelium, fin folds and neural tube. Active Mmp2 has a role during the morphogenesis of the notochord, a driving structure in vertebrate development, and in the fin folds where actinotrichia are collagen based ECM structures that form the basis for fin rays. Further, I show that the activation mechanisms of Mmp2 are tissue- and stage-dependent: mechanisms that require metalloproteases are required for the activation of Mmp2 during fin fold development, but mechanisms dependent upon serine proteases are involved in the activation of Mmp2 in the notochord during notochord elongation and straightening. This is the first description of activation patterns in vivo and offers a starting point from which to examine the requirement of metalloproteases during development and to interrogate their mechanisms of activation.
Patterns of natal recruitment in the Atlantic puffin (Fratercula arctica)
Patterns of natal recruitment in the Atlantic puffin (Fratercula arctica)
by S. Erin Whidden, Seabirds exhibit considerable variation in demographic parameters within a typical K-selected framework. Identification of the most sensitive of these parameters for population change is crucial for successful management and conservation. When adult survival is high and stable in seabird populations, bottom-up forces prevail and reproductive success and subsequent recruitment of juveniles will govern population dynamics. Recruitment is difficult to study, requiring large samples from throughout a metapopulation. The Atlantic puffin (Fratercula arctica) colony on Machias Seal Island is the largest in the Gulf of Maine population, and is ideally suited to explore recruitment in this species since the entire metapopulation is monitored. I first assessed trends in hatch-year parameters since the 1980s and studied whether hatch year conditions for Atlantic puffins affected the probability of natal recruitment. Despite significant declines in hatch-year parameters (wing growth, fledging body condition, quality food delivered to chicks, fledge date), none had a statistically significant effect on the probability of natal recruitment. The number of islands visited between fledging and recruiting was the only parameter with a statistically significant effect on natal recruitment. Puffins are less likely to recruit to their natal island the more islands they visit between fledging and recruitment age. I conclude that conditions experienced between fledge and recruitment may be more important in the process of natal recruitment than conditions experienced by chicks on their natal colony. These findings highlight the importance of multi-year, multi-site metapopulation-level studies when tracking changes in seabird dynamics.
Population dynamics of the ribbed mussel (Geukensia demissa) near its northern range limit, Maritime Canada
Population dynamics of the ribbed mussel (Geukensia demissa) near its northern range limit, Maritime Canada
by Spencer Donald Stuart Virgin, Ribbed mussels (Geukensia demissa) are important ecosystem engineers in salt marshes along the east coast of North America, but their populations are not well studied at their northern range limit, Maritime Canada. To learn more about ribbed mussel populations in Maritime Canada, I monitored their population dynamics over 2 years at several salt marshes in 2 microhabitats (the exposed seaward marsh edge and the edge of marsh creeks). I also reared larval ribbed mussels in the laboratory to monitor their survival, growth, and settlement at a range of temperatures (15–28°C). I then used survival, growth, and age data from my research and the scientific literature to parameterize a matrix model for ribbed mussel populations in two regions: Maritime Canada and southern New England/New York. Density of individuals, population size structure and demographic variables of ribbed mussels in Maritime Canada were variable within and among sites, but were not consistently affected by different microhabitats. Larval ribbed mussels had high mortality at low temperatures and grew significantly faster and settled earlier at higher temperatures. Elasticity analyses of my matrix model indicated that ribbed mussel populations, independent of the region examined, were more sensitive to fluctuations in adult survival than recruitment. However, ribbed mussel populations in Maritime Canada were more sensitive to fluctuations in adult survival than those in southern New England and New York; ribbed mussels in Maritime Canada are more affected by winter disturbance (ice scour and storms), but nevertheless appear to have a longer life span potentially because of low predation pressure and absent intraspecific competition. Overall, this thesis provides the first integrated assessment of ribbed mussel population dynamics at their northern range limit, Maritime Canada.
Quantitative modelling of existing and future fish habitat in the Saint John River, NB, Canada
Quantitative modelling of existing and future fish habitat in the Saint John River, NB, Canada
by Bernhard Wegscheider, The aging Mactaquac Hydroelectricity Generating Station (MGS) on the Wolastoq | Saint John River (SJR) is one of Canada's largest dams and it is reaching the end of its service life. My research focused on quantifying existing and future fish habitat downstream of the MGS, considering current management options to renew the infrastructure in the short-term with a longer-term solution of rebuilding or removing. In detail, my project applied a hydraulic-habitat model to assess habitat change and predicted effects on fish communities for future regulated and climate-induced flow regimes. Fish communities were surveyed and related to habitat characteristics both up- and downstream of the facility, and habitat requirements were defined for three distinct fish assemblages based on meso-scale habitat use and expert opinion. Modelling predictions suggest that dam operation and flow regulation resulted in a general decrease in habitat availability for each fish assemblage when being compared to the historic flow regime prior to the construction of the MGS. Furthermore, under the current dam operation scheme, rheophilic species were predicted to be limited in habitat conditions during the critical summer low flow period, with habitat availability averaging below 20% and never exceeding 30% of the wetted channel area at any day in the time record (1968 to 2015). The implementation of environmental flows ranging around the proposed Q50 flow rate was predicted to minimize the duration of stress events and increase the availability of suitable habitats on a community scale. Similarly, a future climate induced flow regime under a dam removal scenario was predicted to result in improved conditions for fish species. Recommendations informed by this thesis aim to improve habitat conditions for multiple species and are given to hydropower and fisheries managers. Proposed strategies include: i) implementing environmental flows ranging around a Q50 flow rate for the SJR, and ii) continuing fish community monitoring in the SJR and extending surveys to seasons other than the summer period to gain better insights into flow-ecology relationships of imperiled species.

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