Department of Biology (Fredericton)

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Remote sensing framework reveals riverscape connectivity fragmentation and fish passability in a forested landscape
Remote sensing framework reveals riverscape connectivity fragmentation and fish passability in a forested landscape
by Michael Arsenault, Fragmentation of stream networks by anthropogenic structures such as road culverts can affect the health of a catchment by negatively affecting the ecosystem's biota, their movements, abundances, and species richness. The challenge for resource managers is the prohibitive costs of locating, evaluating, and remediating problem structures at landscape-scales. There is a need for a framework to perform a desktop, landscape-scale evaluation and prioritization process using existing data that allows managers to make cost and ecologically effective decisions. I present a framework using publicly available LiDAR and orthophotography to locate and identify road crossings and evaluate fragmentation and passability for various fish species at the landscape-scale. My approach provides a valuable and cost-effective means of identifying potential stream crossing issues for multiple management objectives, e.g., fish passage, and thus the approach is an important step in the development of prioritization tools for restoration decisions by resource managers.
Restoration potential for reproduction by Striped Bass (Morone saxatilis) in the Saint John River, New Brunswick
Restoration potential for reproduction by Striped Bass (Morone saxatilis) in the Saint John River, New Brunswick
by Samuel Nelson Andrews, In 2012 the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) listed the Striped Bass (Morone saxatilis) of the Saint John River, New Brunswick, as endangered as part of the Bay of Fundy designatable unit. This listing was due to an apparent rapid collapse and subsequent absence of presumed native origin Striped Bass, juvenile recruitment, and spawning by the species following the completion of the large Mactaquac Dam in 1968. Expert reports hypothesized that alteration in the river flow and temperature regime imposed upon the Saint John River downstream from the Mactaquac Dam were responsible for the disappearance, however, no recovery efforts or exploratory studies were conducted, and the native Striped Bass population was deemed extinct. This dissertation explored the collapse of the Saint John River Striped Bass starting with a complete historic perspective of the species in the Saint John River and concluded with a possible means to recover the population that was once believed to be lost. Within the chapters of this thesis I first summarize the history of Striped Bass in the Saint John River and explore why the current understanding of the species status needs to be updated. I locate and sample juvenile Striped Bass within the Saint John River for the first time since 1979, prove their native ancestry, and monitor their year class success. Native adult Striped Bass matching juvenile ancestry are tagged and tracked to determine the timing and location of their upstream spawning migration and the migrations of non-native adult Striped Bass within the Saint John River are also explored. I summarize information on Striped Bass winter ecology in Canada, then locate and describe four key winter habitats used by Striped Bass in the Saint John River. Finally, I draw a possible connection between the regulated discharges at the Mactaquac Generating Station to the success of Striped Bass juvenile recruitment observed in the Saint John River over six consecutive years of sampling. My general conclusion is that spawning by native Striped Bass in the Saint John River downstream of the Mactaquac Dam has been severely impacted, though not eliminated, by the regulated discharges resulting for power production. These discharge regimes have resulted in infrequently successful year classes, poor recruitment and possible spawning failures; however, spawning by surviving native origin Striped Bass may be recovered through the management of spring discharges. Managing for extended periods of moderate, sustained flow of sufficient volume and duration to keep Striped Bass eggs in suspension during the incubation period may restore successful Striped Bass spawning and juvenile recruitment in the Saint John River, New Brunswick., Electronic Only.
Role of temperature-mediated embryo development in the range expansion of cunner into the Bay of Fundy
Role of temperature-mediated embryo development in the range expansion of cunner into the Bay of Fundy
by Krystal Woodard, Increasing sea-surface temperature has been shown to affect the distribution of coastal fishes. Samples obtained from a monitoring program (2009-2015) of shallow cobble-bottom sites in southwest Bay of Fundy provided the first record (2012) of juvenile cunner Tautogolabrus adspersus in the region. The cunner range extends along the North American Atlantic coast to Newfoundland, but only occasional adults were observed in the Bay of Fundy. To determine whether this recent appearance of cunner was related to increased temperature better supporting embryo development and hatch, lab experiments were conducted to complement field observations of juvenile cunner presence/absence and density. Embryos were held in the lab at constant temperatures at 1oC increments ranging from 11-15°C. Hatch was found to increase with temperature, and was markedly greater at temperatures ≥ 13°C than at lower temperatures. Relationships observed between temperature and hatch in the lab helped explain variation in density of young-of-the-year cunner among study sites and years. This study provides evidence that increasing water temperature is resulting in range expansion of a small coastal fish into the Bay of Fundy, and that this expansion is at least partly related to increased hatching success.
Sagittaria as a bioindicator of stream nutrient status: effects of nitrogen and phosphorus on leaf size and shape
Sagittaria as a bioindicator of stream nutrient status: effects of nitrogen and phosphorus on leaf size and shape
by Katherine M. Standen, Eutrophication of freshwater is an increasing problem globally as human populations, animal husbandry and agriculture intensify, and is associated with many deleterious consequences, including algal blooms, invasion of opportunistic species and, ultimately, changes in ecological functioning. These issues within Lake Winnipeg, MB, Canada, have led to research to develop bioindicators of nutrients within streams in the Red River, the largest nutrient contributing river to the lake. The research presented herein examines the use of the aquatic plant Sagittaria cuneata (Sheldon) as a bioindicator of phosphorus (P) and nitrogen (N). S. cuneata is an abundant species in rivers and streams in Manitoba, and has plastic emergent-leaf morphology and easily identifiable features. Plasticity within the genus has been linked to several factors, such as P concentration and water depth; therefore, S. cuneata was proposed as a potential bioindicator. Two studies were conducted to assess the relationship of leaf morphology with N and P: a controlled experiment where nutrients were added to either sediment or water, and a field study wherein S. cuneata leaves were collected in streams with varying water and sediment chemistry. Experimental results showed that plants used sediment nutrients to increase biomass, and that leaf morphology varied more during the growing season in sediment-enriched compared to water-enriched plants, which showed little variability of leaf morphology. Field studies indicated leaf morphology was variable at all scales of replication, and many variables contributed to leaf size, including sediment and water chemistry. Together, these results indicated that leaf morphology was affected by nutrient availability, but also complex interactions among other environmental variables. Thus, S. cuneata is not currently a reliable indicator of nutrient and future studies should further pursue the variability of leaf morphology.
Salmon aquaculture-derived nutrients and metals in biota from rocky habitats in 
the Bay of Fundy
Salmon aquaculture-derived nutrients and metals in biota from rocky habitats in the Bay of Fundy
by Jonathan Fischer-Rush, Past studies have assessed the impact of metal and nutrient loading from aquaculture, but few have examined rocky bottom habitats or quantified effects at distances greater than 200 m from salmon pens. My goal was to assess metal contamination and feed reliance at two distances from salmon pens. I deployed 7 bio-collectors at 8 pairs of sites near (68-441 m) and away (260-2750 m) from salmon pen sites across three Bay Management Areas in the Bay of Fundy to assess exposure to copper, zinc and nutrients (using stable isotopes) in five benthic species: blue mussels (Mytilus edulis), vase tunicates (Ciona intestinalis), American lobster (Homarus americanus), shorthorn sculpin (Myoxocephalus scorpius) and rock gunnel (Pholis gunnellus) in 2016 and 2017. Of the combined 41 species-site pair combinations across both years compared using t-tests, 8 and 6 showed significant differences in copper and zinc, respectively, between near and away sites, but the direction of difference was inconsistent. Some species-site pair combinations showed differences in isotope values, but only sulfur isotopes suggested a small shift towards reliance on aquaculture nutrients. Using a chi-square goodness of fit test, only sulfur in 2016 and zinc in 2017 showed significant directionality in the response to being near aquaculture. Overall, my results suggest limited impacts of aquaculture in terms of metal contamination and feed use in animals in rocky bottom habitats greater than 200 m from aquaculture pens.
Seasonal migrations of the American eel, Anguilla rostrata, in the Upper Salmon River, New Brunswick
Seasonal migrations of the American eel, Anguilla rostrata, in the Upper Salmon River, New Brunswick
Stable isotope analysis of American eels (Anguilla rostrata) captured in the Upper Salmon River, New Brunswick, revealed isotopic patterns suggesting that yellow-stage eels may be migrating between saline summer foraging grounds and freshwater overwintering habitat. We examined the seasonal movements of yellow eels in the Upper Salmon River using passive integrated transponder (PIT) and radio telemetry. Comparisons of isotopic signature and seasonal movements of 288 individual eels captured in fresh water in the spring of 2009 and 2010 showed that eels with enriched vs. depleted isotopic ratios of carbon (13C/12C) and nitrogen (15N/14N), were more likely to migrate to the estuary in spring following release where they remained before exhibiting the reverse migration in fall; confirming that seasonal amphidromous migrations were driving the observed isotopic variation. Summer habitat residency in the estuary was confirmed in 2009 and 2010 using a manual PIT detection survey which showed that 36% and 34%, respectively, of spring-captured yellow eels PIT tagged and released in fresh water were identified resting in dense mats of sea lettuce (Ulva intestinalis). Freshwater overwintering of amphidromous eels was confirmed via radio tracking of select eels in the winter of 2009 and 2010. An examination of the environmental correlates of amphidromous eel migrations using count regression models determined that temperature and photoperiod were positive and negative correlates, respectively, of spring downstream migration. In addition, temperature and discharge were identified as negative and positive correlates, respectively, of fall upstream migration. Fall migration was also found to correlate significantly with the lunar cycle, with two peaks in migration occurring prior to the new and full moons. Almost all migration occurred during periods of darkness, centered about 3.3 and 4.0 h post-sunset in the springs of 2009 and 2010, and 5.9 h post sunset in the fall of 2009. In all cases, migration was centered about the midpoint of the dark period. Spring eel migrations peaked 3.7 and 6.3 h following high tide in 2009 and 2010, respectively. However, fall upstream migration was randomly distributed with respect to tide. Mark and recapture models estimated that 10,220 (97.5% CI: 6139-16,540) and 3022 (97.5% CI: 2158-5073) yellow eels >20 cm in length migrated downstream in spring 2009 and 2010, respectively. Fyke nets and rotary screw traps (RST) sampled contrasting components or size classes of the migrating eel population. An RST retention test determined that eels <20.6 cm in length were likely to escape the RST holding box. In contrast, fyke nets did not appear efficient in capturing larger eels (i.e., >20 cm in length). RST modifications are warranted for future monitoring programs., Electronic Only. (UNB thesis number) Thesis 9367. (OCoLC) 961217316., by Michael Sweezey, M.Sc., University of New Brunswick, Department of Biology, 2013.
Sequencing a seabird food chain
Sequencing a seabird food chain
by Anne Kirsten Bowser, Predator-prey interactions within food chains are used to both characterize and understand ecosystems. Traditional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool with diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here, I use multi-locus (16S and COl) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. I use NGS of puffin feces and herring stomach contents to compare traditional and molecular-derived chick diet, to test the similarity between puffin adult and chick diet, and to document herring diet at a taxonomic resolution greater than previous diet-studying methods. I identified more unique prey with our 16S compared to COl barcoding markers (51 and 39 taxa) with only 12 taxa identified by both genes. I found no significant difference between the 16S-identified diets of puffin adults (n=l 7) and chicks (n=41 ). My molecular method is more taxonomically resolved and quantitatively sensitive than traditional methods. Many likely planktonic herring prey were detected in feces from puffin chicks and adults, highlighting the impact secondary consumption may have in the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to food web analysis., Electronic Only, M.Sc. University of New Brunswick, Department of Biology, 2013.
Species diversity and phylogenetic relationships within the family Rhodomelaceae (Ceramiales, Rhodophyta) in Canada
Species diversity and phylogenetic relationships within the family Rhodomelaceae (Ceramiales, Rhodophyta) in Canada
by Amanda Marie Savoie, Biodiversity of the red algae (Rhodophyta) has typically been underestimated due to a historical reliance on traditional morphological taxonomic techniques. The simple gross morphology of most red algae leads to a paucity of useful characters for species identification, and convergent evolution and phenotypic plasticity further aggravate matters. In this thesis, species diversity, biogeography and evolutionary relationships within the red algal family Rhodomelaceae in Canada were examined using a molecularassisted approach, with a focus on the tribes Polysiphonieae and Pterosiphonieae. The Rhodomelaceae is the largest family of red algae, and despite significant study over the last 200 years, species diversity and evolutionary relationships within this group are poorly understood. Multiple molecular markers were used to delimit species boundaries and establish distributions for species of Neosiphonia in the northwest Atlantic, resolving conflict in the literature on the taxonomic status of Neosiphonia harveyi. Molecular data indicated that the Asian species Neosiphonia japonica was likely introduced to the northwest Atlantic, and sequence data from the internal transcribed spacer of the ribosomal cistron (ITS) indicated introgression of nuclear DNA from N. japonica into N. harveyi, a closely related local species. Subsequently, species diversity and evolutionary relationships were assessed for the tribes Polysiphonieae and Pterosiphonieae in Canada. The genus Pterosiphonia was reduced based on molecular phylogenetic analyses to include only the South African type and two additional species, with four North Pacific and Arctic species transferred to the newly resurrected genus Polyostea, and four Pacific species transferred to Symphyocladia. Based on DNA barcode (COI-5P) survey results, as well as morphological observations, two previously overlooked species of Symphyocladia were recognized from British Columbia (S. brevicaulis and S. rosea), and a new species of Pterosiphonia from South Africa (Pt. stegengae). Multi-gene phylogenetic analyses confirmed that the taxonomically challenging genus Polysiphonia was polyphyletic, and species of Polysiphonia were transferred to seven different genera – three extant genera, one resurrected, and three newly described here (Acanthosiphonia, Eutrichosiphonia, and Kapraunia). DNA barcode surveys revealed the presence of nine putative cryptic or overlooked species of Polysiphonieae in Canada, and several species were recorded for the first time in Canadian waters including Polysiphonia morrowii.
Spring migration of scoter and loon species in the Bay of Fundy: quantifying environmental influences, estimating afternoon migration, and analyzing trends between 2000 and 2017
Spring migration of scoter and loon species in the Bay of Fundy: quantifying environmental influences, estimating afternoon migration, and analyzing trends between 2000 and 2017
by James Kelley, Waterfowl migration has been monitored at the Point Lepreau Bird Observatory in the Bay of Fundy every spring since 1996. Derived scoter and loon population estimates from previous studies have suggested declines but there is uncertainty in the estimates due to unequal sampling during mornings and afternoons. This study examines: 1) if afternoon migration rates can be accurately modelled using morning rates and environmental conditions; 2) scoter and loon migration rates through the Bay of Fundy; 3) changes in migration rates between 2000 – 2017. I found: 1) morning migration and environmental data were insufficient to accurately model afternoon migration; 2) greater numbers of Black and Surf Scoter migrate through the Bay of Fundy; 3) migration rates of scoter species have declined, and loons increased between 2000 and 2017. Afternoon migration monitoring is important in maintaining effectiveness of this and similar migration monitoring projects to evaluate changes in populations over time.
Temporal dynamics of functional trait overlap in an old-field plant community
Temporal dynamics of functional trait overlap in an old-field plant community
by Hannah Ada Brazeau, Studies of trait-based plant community dynamics typically rely on null model analyses of functional trait and plot-level composition data from a single growing season. The inclusion of community-level temporal dynamics, however, is vital in investigations of community dynamics as the type and strength of biotic and abiotic filters shaping the structure of plant communities may change through time. Oscillations between filter types may help explain the conflicting findings of previous single-year studies and provide a more accurate picture of how plant communities form and persist. Here, we use multivariate and univariate approaches to determine functional overlap in a long-term herbivore exclusion experiment in Ontario, Canada. We found that functional overlap changed across time without direction, differed between individual traits, was sensitive to herbivory, and differed between pollination systems. Our findings highlight the importance of using long-term data in trait-based community dynamics studies.
Testing diagnostic bioindicators in prairie streams: are biological traits and delta 15N of aquatic insects able to detect agricultural impacts?
Testing diagnostic bioindicators in prairie streams: are biological traits and delta 15N of aquatic insects able to detect agricultural impacts?
by Sophie Nicole Cormier, Agricultural activities in the Red River watershed of Manitoba, Canada, can be significant sources of excess nutrients, sediments and pesticides leading to ecological effects in streams and downstream Lake Winnipeg. In such multiple stressor environments, it is difficult to identify, separate and diagnose the cause of environmental impacts from different agricultural activities using traditional methods (e.g., taxa assemblage). However, ecological function indicators (e.g., functional feeding groups) have potential as diagnostic indicators because they lead to the identification of ecological change pathways. This study evaluated the efficacy of two indicators of ecological function: biological traits and nitrogen isotopic signatures (δ15[15 superscript]N) of benthic macroinvertebrate. Indicator sensitivity was evaluated by their association with human activity gradients that define the type and intensity of human activities (i.e., livestock, wastewater lagoon discharge, crop production). Results indicated that biological traits and δ15[15 superscript]N of BMI were effective diagnostic bioindicators for small scale impacts (e.g., riparian condition) and point sources of stressors (e.g., wastewater discharge). However, catchment scale agricultural activities were not associated with the bioindicators likely because of hydrological factors affecting the timing of stressor transportation in these prairie catchments. This study also demonstrated the importance of testing pathways of human impacts based on conceptual models including the type and magnitude of exposure to human activities and natural gradients.

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