Department of Biology (Fredericton)
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Effects of sediment and water column acidification on growth, survival, and burrowing behaviour of invertebrates
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by Melanie Bishop, In coastal regions, sediment-dwelling animals are exposed to a high degree of variability in ocean and sediment pH which is expected to increase in the future due to anthropogenic effects. The present study examined the impacts of a 6-week exposure to reduced-pH (acidified) water on length, weight, and mortality of 2 species of molluscs and 1 species of crustaceans that inhabit mudflats: juvenile soft-shell clams (Mya arenaria), adult mud snails (Tritia obsoleta), and adult mud shrimp (Corophium volutator), and subsequently investigated the interactive effects of this exposure and sediment acidification on burrowing behaviour of these species. The predator-prey relationship between mud snails and mud shrimp was also examined by investigating the effects of water column acidification on mud shrimp mortality in the presence of mud snails. Acidified water increased mortality of mud shrimp held alone but not of those in the presence of mud snails, decreased shell length of mud snails, and had no significant effect on soft-shell clams. Sediment acidification reduced mud shrimp burrowing, and prior exposure to acidified water reduced mud snail burrowing, but neither affected soft-shell clam burrowing. These results suggest taxonomic variation in species response to ocean and sediment acidification with respect to growth, mortality, and burrowing behaviour.
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Elucidating spatiotemporal infection biology of Loma morhua (Microsporidia) in Atlantic cod (Gadus morhua) through integration of parasitological and molecular quantitative diagnostic approaches relevant for aquaculture disease mitigation
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by Aaron Paul Frenette, Assessment of Atlantic cod (Gadus morhua) as an alternative aquaculture species was driven by socio-economic consequences following the collapse of the wild fishery. Cod aquaculture failed in North America due in part to emergence of a known, but poorly characterized, microsporidian pathogen. Microsporidia are fungal parasites with almost ubiquitous distribution among wild fishes, but typically inconsequential infections. However, finfish aquaculture supports epizootics due to high host density, abiotic stressors, and high biotic potential of these parasites. Consequences of Loma morgue infections in cultured Atlantic cod are undefined. Therefore in this thesis, reliable and integrative methods for L. morhua detection, identification, and quantification have been developed to support empirical assessment of strategies to mitigate its effects during aquaculture. Spatiotemporal investigations documented the spleen as the most reliable host organ for parasite detection and quantification throughout infections. A hatchery epizootic revealed variable spleen infection among 50 Atlantic cod families. Fish growth was inversely correlated with infection intensity, and 14% fillet loss occurred in those individuals most susceptible to L. morhua infections. Whereas specific genetic markers remain elusive, broomstick selection is supported as a mechanism to help limit disease during culture. The effect of parasitism on growth was also documented experimentally with parasitized fish showing 19.3% fillet loss compared with uninfected controls. An integrative approach for parasite detection incorporated parasitological methods and a quantitative PCR (qPCR) assay developed according to Minimal Information for Quantitative Experiments guidelines. This integrative approach revealed intraperitoneal spore injection as an efficient model that both mimics epizootic infection dynamics and infects 100% of fish. Occult subclinical infections detected in 31.8% of fish promote qPCR as the new gold standard for L. morhua detection. This qPCR assay and integrative approach improves diagnostic and analytical sensitivity in detecting microsporidian infections, supports empirical assessment of preventative and therapeutic treatment of infections, and promotes studies to identify genetic markers for selection of broodstock that resist microsporidian disease. In summary, this work provides a foundation for investigation of host-parasite interactions and basic microsporidian biology that supports the development of rational mitigation strategies for this and other pathogens as aquaculture diversifies to include alternative finfish species.
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Environmental drivers of stream ecosystem structure and function in subarctic Labrador, Canada
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by Allison Lynn Ritcey, The ecology of riverine ecosystems in the eastern Canadian subarctic remains
relatively unknown and, like their circumpolar counterparts, these systems are predicted
to be vulnerable to climate-induced ecological changes that are likely to affect species
composition, distribution, and overall ecosystem functioning. Thus, lotic systems in this
area must be evaluated in order to begin long-term monitoring of climate-driven
alterations to ecological structure and function. The aim of the present research was to
assess contemporary patterns in stream structure and function within the Torngat
Mountains National Park in subarctic Labrador and determine the environmental
(physicochemical) drivers of these ecological patterns. In particular, the study examined
the influence of environmental variables from multiple spatial scales on
macroinvertebrate assemblage structure, consumer trophic diversity and dietary overlap,
and cellulose decomposition rates. Environmental variables that were measured at the
reach scale ( a 1-km buffer around study sites), which included the relative area of
glaciers and various land cover types, produced the most variation in stream structure
and function. Glacier-fed streams had the lowest consumer richness and abundance, the
lowest trophic diversity and little dietary overlap, arid the lowest cellulose decay rates.
Cellulose decay rates were highest where consumer richness, trophic diversity and
dietary overlap were highest and where riparian input was greatest. Consumer diets
consisted primarily of allochthonous carbon (53 - 95%) and cellulose decay was likely
mediated primarily by shredder invertebrates, as microbial activity was not correlated
with decay rates. The present study provides baseline ecological data for long-term
stream ecosystem monitoring in the Park and suggests that changes in glacial extent,
source water contribution, and quantity and quality of riparian vegetation may cause the
greatest alteration in stream structure and function.
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Evolution in the North Atlantic: processes shaping spatial patterns of genetic diversity in introduced intertidal invertebrates
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by Anthony Leon Einfeldt, The movement of individuals and their genes across geographic space influences a species’ ecology and evolution, but it is often not possible to observe past or present movement directly. Molecular tools provide a means of inferring past movement and contemporary barriers to movement, because the known modes of mutation and inheritance underlying genetic variation provide clear predictions for patterns arising from movement and subdivision. In this thesis, I investigate how contemporary and historic patterns of movement shape evolutionary trajectories by investigating distributions of genetic variation in focal intertidal invertebrates of the North Atlantic. To determine how movement is affected by the interaction of currents with life-history traits, I sequenced mitochondrial and nuclear DNA of the intertidal amphipod Corophium volutator from discrete patches of mudflat habitat throughout the Northwest Atlantic. I detected patterns of genetic subdivision and gene flow concordant with hydrological patterns, demonstrating that currents shape evolution by determining dispersal pathways and cause fine-scale subdivision in marine communities. To test how C. valuator colonized the Northwest Atlantic coast, I investigated spatial genetic variation in populations from across its entire range using the same markers. I found that diversity in Northwest Atlantic populations was subsampled from more genetically diverse populations in the Northeast Atlantic, consistent with historic human-mediated introduction from the Northeast to the Northwest. To investigate how human-mediated dispersal affects species’ evolutionary trajectories, I characterized genomic variation in C. volutator and a co-occurring annelid Hediste diversicolor in populations from the Northeast and Northwest Atlantic coasts. I found extensive genetic divergence between the introduced and native ranges and genetic patterns consistent with historic admixture between populations within each range, providing evidence that human-mediated movement can create new allopatric lineages and erase ancestral genetic structure by promoting gene flow between otherwise isolated populations. Together, my results suggest that the increasing reach, magnitude, and frequency of global human movement will change the evolutionary trajectories of species associated with human vectors of transport. While contemporary connectivity will continue to be affected by regional processes (such as currents), uncurbed human activity will likely disrupt diversification arising from barriers at regional scales while promoting the formation of new lineages at a global scale.
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Evolution of retroduplicated genes in drosophila
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by Ryan Stanley O’Neill, Gene duplication is a major process that generates new genes. Duplication by retrotransposition (also called retroduplication) is thought to facilitate the evolution of novel functions in the new gene copy (retrogene), because retroduplication does not copy the original (parent) gene’s regulatory elements and therefore retrogenes are initially distinct from their parents. In this thesis, I explore the evolution of retroduplicated gene pairs (retrogenes and their parents) in the Drosophila lineage. In Chapter 2, I investigate three retroduplicated gene pairs, and find that these retrogenes, compared to their parents, tend to be less evolutionarily stable in terms of expression pattern and coding sequence. In Chapter 3, I use genetic analysis in Drosophila melanogaster to characterize the parent gene Sep2 and its retrogene Sep5, which encode cytoskeletal septin proteins. Sep2 and Sep5 have a redundant function in imaginal cell proliferation. Sep2 mutants are semisterile and have abnormal egg chambers; this Sep2 mutant phenotype is not rescued by overexpressing a Sep5 transgene, showing that Sep2’s function in oogenesis is unique. In contrast, Sep5 mutants appear wild-type, suggesting Sep5 lacks a unique function. In Chapter 4, I further explore the functions of Sep2 and Sep5. Sep2 is also required for male fertility; however, overexpressing Sep5 rescues the Sep2 mutant male sterility, showing this function is not unique to Sep2. I characterize the localization of Sep2 and Sep5 proteins in oogenesis using green fluorescent protein-tagged transgenes, finding they have similar localization patterns. Mitotic clonal analysis shows that Sep2 and Sep5 have a redundant function in follicle cells and are likely required for follicle cell proliferation. Mutations in either Sep2 or Sep5 enhance the embryonic lethal phenotype of bazooka, a key component in the establishment of cell polarity, suggesting a link between cell polarity and both Sep2 and Sep5 function. Altogether, my research provides insight into the evolution of duplicated genes by adding to the collection of functional studies and complementing the many genome-wide studies on duplicated genes, and also sheds light on our understanding of septin function, especially with respect to their functional redundancy which has not been well studied in complex multicellular animals.
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Exploring species diversity within the order Halymeniales (Rhodophyta, Florideophyceae) of predominantly southeastern Australia using molecular-assisted alpha taxonomy and multi-gene phylogenetics
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by Lesleigh Gwynyth Ka`iulani Kraft, Appreciation of the diversity of biological life is fundamentally important not only to our understanding of the world around us, but imperative in management of our environments and assessing our impact upon same. Systematics and taxonomy are the disciplines dedicated to characterizing the myriad species we share our planet with. This study was undertaken to assess species diversity in an order of red algae, the Halymeniales (Florideophyceae, Rhodophyta), from predominantly Australian collections. Modern methods have vastly increased the amount of data available to assess species diversity, with molecular barcoding being the fastest and simplest tool with which to quickly sequence large volumes of collected material and sort them into genetic species groups. From over 400 individual samples, the findings from barcode data revealed that the Halymeniales has many overlooked species (approximately doubling the biodiversity). The combination of molecular barcoding and traditional morphological assessment of anatomical features (viz. ‘alpha taxonomy’) is both more powerful than traditional taxonomy and more meaningful than simply knowing how many species groups there are, especially where novel species are uncovered by the molecular barcode. This combined approach, dubbed ‘molecular-assisted alpha taxonomy, or MAAT, was employed in this study and presented in the following chapters are many detailed observations of both existing species and species previously unknown to science.
Phylogenetic analyses placed this Australian biodiversity into a global evolutionary context, with data from Australian halymeniaceous taxa added to Halymeniales data from extra-Australian locations. Phylogenetic results indicated that some reorganization at the genus-level within the order is required, which is detailed in Chapters 2-4.
Presented here is the largest and most comprehensive molecular study of the Australian Halymeniales to date, using the combined approach of Molecular-assisted alpha taxonomy and phylogenetics to more accurately conceive the biodiversity of this large and morphologically diverse order of red algae.
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Freshwater Integrated Multi-Trophic Aquaculture (FIMTA): Developing aquaponics for cold temperate salmon, Salmo salar, hatchery systems and investigating the use of IMTA kelp biochar as a plant substrate
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by Stacy Amanda Murray, Freshwater integrated multi-trophic aquaculture (FIMTA) integrates animal aquaculture with plant culture where wastes produced by fish are either converted by microbes and/or invertebrates, then consumed by plants, or directly consumed by plants. An experimental system tested 13 plant species and measured nutrient removal from sludge effluent collected from a commercial salmon hatchery using two techniques: the floating raft and the media-filled bed. Biochar, a stable form of carbon, was produced by the pyrolysis of IMTA-grown kelps and was tested as a substrate in both techniques. After rinsing, the biochar was suitable for seedling production and in the floating raft technique; however, it was unsuccessful in the media-filled beds presumably due to its high water retention. The development of FIMTA for salmon hatcheries will aid in the completion of IMTA from “egg to plate”, which can be useful for branding purposes, product diversification, wastes reduction, water reuse and improved societal acceptance. Importantly, reducing phosphorus levels in effluents can prevent eutrophication and help farmers meet water quality guidelines.
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Functionally specialized paralogues of Mmp11 and Timp4 interact during myotome boundary development in zebrafish
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by Emma Faith Matchett, Myotome boundary maturation occurs in zebrafish embryos between 24 and 48 hours post fertilization, and is fundamentally similar to the maturation of the myotendinous junction (MTJ) in tetrapods. During this process extracellular matrix is remodelled both mechanically and biochemically, changing shape and composition from being a rectangular fibronectin-dominated structure to a chevron-shaped laminin-dominated structure. Suggestively, both matrix metalloproteinase 11 alpha and beta (Mmp11α + β), as well as tissue inhibitor of matrix metalloproteinases 4 (Timp4) accumulate at the myotome boundary during this process. The MMPs are zinc-dependent proteinases responsible for much of the matrix remodelling that takes places during development, as well as during physiological and pathological processes like wound healing and tumour metastasis. MMP activity is regulated largely post-translationally, with TIMPs playing central roles both in the inhibition of MMP activity, and in coordinating the proteolytic activation of proMMPs. To understand better how MMP activity is regulated during maturation of MTJs, I have investigated if, when, where and how the various zebrafish paralogues of Mmp11 and Timp4 interact at the MTJ during this process. Proximity ligation assays demonstrate that Mmp11α and β interact with Timp4, and that Mmp11β interacts with fibronectin, but neither MMP appears to interact with laminin during the maturation of the myotome boundary. Depending on the domains interacting, the MMP-TIMP complex can either be inhibitory or modulatory. Using yeast two hybrid assays, I show that the interactions between Timp4β and both Mmp11 paralogues are likely of the modulatory type, but that Timp4α likely acts to inhibit Mmp11β. Taken together, I conclude that Mmp11 and Timp4 paralogues are important effectors of matrix remodelling at the MTJ, and that functional specialization of these paralogues has likely occurred., M.Sc. University of New Brunswick, Department of Biology, 2017.
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Genetic analysis and the evolutionary study of a pseudogene, CR14033, and the corresponding parent gene, CG9203
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by G. Elizabeth Sperry, Gene duplication can lead to new gene function. If a duplicated gene holds no benefit, it will acquire mutations leading to a non-functional copy or pseudogene. The purpose of this study was to see if a transcribed gene duplicate in Drosophila melanogaster, CR14033, considered a pseudogene, is involved in regulating its parent gene (CG9203), to determine the function of the genes of interest, and to study the origin of CR14033. The regulation likely occurs through the endogenous small interfering RNA pathway. Mutations in CR14033 and CG9203 and transgenic flies expressing sense and antisense transcripts of each gene were generated in this study to test this hypothesis. From the analysis of the CR14033 deletion and the overexpression of CR14033 and CG9203, it appears as though there is an interaction between the two. To study function, sterility was also explored in these genotypes. A female sterile mutant phenotype was generated from CG9203. Sequence analysis of twelve Drosophila species showed that CR14033 likely arose through a gene fusion event that occurred in the melanogaster subgroup ancestor.
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Impact of attack by gallmakers on their ancestral and novel plant hosts in a goldenrod-insect system
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by Zoryana Shibel, Through coevolution reduced virulence and increased tolerance may evolve. Novel plant hosts may experience greater impact from herbivores compared to ancestral hosts. I tested this using Solidago altissima and Solidago gigantea as host plants and Eurosta solidaginis and Rhopalomyia solidaginis as gallmakers. In 4 out of 8 data sets, both gallmakers significantly reduced the aboveground biomass (by about 30%) in the novel host. (Overall, 7 out of 8 data sets showed a trend in the expected direction.). Coupled with previous data sets from Heard and Kitts 2012 on Gnorimoschema gallaesolidaginis, 6 out of 10 data show significant support for this coevolutionary hypothesis (9 out of 10 in the expected direction; sign test P = 0.011). In addition to herbivory, plants may also experience abiotic stressors. By inducing water stress and clipping on S. altissima and S. gigantea I found that S. altissima experiences synergistically greater damage when two stressors are present., Degree Name mislabeled as "Masters of Biology" on the title page.
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Impacts and monitoring of climate-driven changes to wetland hydroperiods on wood frog populations
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by Paul S. Crump, Climate change has the potential to alter the strength of species interactions, but not only do we lack sufficient information about possible species responses, we also lack the tools to monitor and document these changes over meaningful spatial scales. Due to their physiology and life history, ectotherms such as amphibians, are particularly sensitive to changes in prevailing environmental conditions. Amphibians breed in a variety of standing water body types and one of the main structuring variables is the amount of time the water body holds water, the hydroperiod. The province of New Brunswick in Canada is expected to warm by ~4.5°C and see anywhere from a 5-50% increase in precipitation over the next 100 years and, as a result, it is anticipated that pond hydroperiods could change. I conducted translocation experiments with wood frogs (Lithobates sylvaticus) to determine the effect of different hydroperiods on embryo and larval survivorship. Permanent ponds that contained overwintered green frog larvae (Lithobates clamitans) had lower embryo and larval survival than both permanent ponds without green frog larvae and ephemeral ponds. To investigate the population-level impacts I conducted simulations using a population projection model of different climate change and hydroperiod scenarios. I found that wetter conditions (i.e., longer hydroperiods) had a negative effect while drier conditions (i.e., shorter hydroperiods) had a positive effect, at least initially, on wood frog populations. In order to facilitate monitoring improvements for these and other population-level impacts, I used automated recorders and automated sound recognition models. I found that choice of variable settings had a greater impact on recognizer performance than the amount and type of training data, but increases in the number of sites used did improve performance slightly, and that by optimizing variable settings on new data it was possible to create reliably transferable models that minimized false negative (Type II) errors but not false positive (Type I) errors. I then used these bioacoustic monitoring tools to predict abundance in wood frog populations based on vocalization activity. The best model predicted egg mass abundance with an average absolute error of 16 masses and a relative error of 59%. Overall, I have provided evidence of an additional mechanism by which climate change can alter amphibian communities, as well as developed and evaluated a methodology to detect those alterations., Ph.D. University of New Brunswick, Department of Biology, 2017.
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Impacts of retrogressive thaw slump disturbances on biological structure and function in Arctic streams, Peel Plateau, NWT
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by Brianna Michele Levenstein, The northwestern Canadian Arctic has undergone a period of rapid warming which has promoted the formation of thermokarst across the region. Among the most dramatic thermokarst features are retrogressive thaw slumps - large depressions of melted permafrost that form on the landscape. Thaw slumps often flow into nearby streams, driving increases in sediments, nutrients, and major ions. The Peel Plateau, Northwest Territories has seen an increase in the size and frequency of thaw slumps associated with increases in precipitation and warmer air temperatures. Thus, it is important to evaluate the impacts of thaw slump disturbance on the structure and function of biological communities as they are strongly linked to water quality. Chin et al. (2016)1 performed an extensive survey of thaw slump impacts on benthic macroinvertebrate (BMI) communities in the Peel Plateau and found a negative relationship between thaw slump disturbance and abundance, but were lacking information on minimally-disturbed sites. The aim of the present research was to build on Chin et al. (2016) by evaluating primary production and decomposition and looking at patterns in BMI community structure and function at undisturbed and minimally-disturbed sites in the same region. Minimally-disturbed sites showed stronger nutrient effects than the highly-disturbed sites sampled in Chin et al. (2016), but sediments were still the main drivers of change in impacted streams. Total suspended solids strongly reduced primary production and BMI abundance, while decomposition was driven by nutrients, temperature and pH. Finally, BMI drift densities were lower at thaw-slump impacted sites, but the proportion of drifting BMIs increased with higher rates of settling sediments. The present study suggests that thaw slumps are non-selective and chronic stressors of stream food webs in the Peel Plateau, NWT.
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