Browsing by Author "Vamosi, Steven M."
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- ItemOpen AccessBiostimulation for Enhanced Bioremediation of Crude Oil and Diesel Fuel by Marine Sediment Communities of Canada’s Subarctic: A Microcosm-Simulated Oil Spill Study(2020-01-23) Murphy, Sean Michael Colin; Hubert, Casey R. J.; Gieg, Lisa M.; Vamosi, Steven M.Increases in shipping traffic, future mining, and oil and gas developments represent significant oil spill risks in Canada’s subarctic marine environment. The impact of oil on marine ecosystems and the traditional activities of local indigenous peoples are of major concern. To understand the response of local microbial communities to oil contamination and nutrient biostimulation, microcosm-simulated oil spills contaminated with diesel fuel or crude oil and incubated at 4°C were constructed using marine sediments from Hudson Bay and the Labrador Sea. Changes in microbial community structure, diversity, and composition were monitored by DNA extraction, the amplification of 16S rRNA genes, followed by sequencing and taxonomic classifications. Additionally, hydrocarbon degradation in response to bioremediation was monitored by changes in gas compositions with GC, and through hydrocarbon extractions and GC-MS analysis. Results suggested that petroleum hydrocarbons decreased observed microbial diversity and led to dominance by Gammaproteobacteria in both sediments, where many hydrocarbonoclastic bacteria (HCB) increased heavily in abundance at both sites, including Cycloclasticus, Marinobacter, Oleispira, Paraperlucidibaca, Pseudomonas, Thalassolituus, and Zhongshania. The same OTUs were found to increase in abundance in both high and low nutrient treatments, but biostimulation was found to increase initial rates of biodegradation by accelerating the succession and dominance of these HCB. Increase in the relative abundance of Cycloclasticus was noted as signifying succession in response to hydrocarbon degradation and biostimulation. The Labrador Sea sediment community was found to be more responsive to oil spills and biostimulation mitigation strategies, which could be tied to historical exposures of the community to natural oil seepages in the region. Porticoccus and Oleispira are suggested as robust bioindicators for cold seawater environments contaminated by diesel or crude oil, respectively. A comparison of three PCR primer pairs for HCB detection found 341F/806R was the preferred choice for detecting HCB taxa and assessing environmental baselines in areas at risk of oil spills. Microbial biodiversity baselines and in situ rates of microbial degradation should be included in future environment assessments by industry. Overall, this study provided a first account of key crude oil- and diesel-degrading bacteria among marine sediments in this subarctic region.
- ItemOpen AccessChemical ecology and genetics of rough-skinned newts, Taricha granulosa(2020-05-15) Glass, Haley Cathleen; Vamosi, Steven M.; Theodor, Jessica M.; De Koning, A. P. Jason; Melin, Amanda D.Interactions between predator and prey have played a crucial role in adaptive evolutionary processes; however, phenotypic and genetic variation may also be driven by many other spatially variable biotic and abiotic factors. Rough-skinned newts, Taricha granulosa, possess a neurotoxin known as tetrodotoxin (TTX), which acts as an antipredator defense and was originally presumed to be a result of reciprocal coevolutionary interactions with resistant garter snakes across a geographic mosaic. In this thesis, I investigate several aspects of the chemical ecology and genetics of rough-skinned newts and consider how these factors play out on Vancouver Island, an interesting study region due to its isolation from mainland populations and recent non-native species introductions. By characterizing toxicity both within and among 23 populations of newts on Vancouver Island, I found significant variation in TTX and evidence for a previously unidentified hotspot, indicating selection pressures besides reciprocal coevolution may contribute to the observed patterns. Next, I present the first investigation into molecular mechanisms of tetrodotoxin expression in newts using an RNA-sequencing approach. By creating a de novo transcriptome assembly and annotation, I was able to identify novel differentially expressed genes putatively related to endogenous sources of TTX. Amphibians are also facing worldwide population declines due to factors such as negative impacts by non-native species, and Vancouver Island has experienced a recent introduction of signal crayfish and American bullfrogs. I reviewed the potential impacts of these species on rough-skinned newts and found a negative correlation between their presence and newt relative abundance, but no effect on body condition or toxicity. Using the aforementioned transcriptome assembly, I identified thousands of single nucleotide polymorphisms in 32 newts from BC and Oregon and characterized the population genetic structure at two spatial scales. Vancouver Island newts were found to belong to a cluster genetically distinct from Oregon with lower heterozygosity while displaying a lack of population structure across the island. Collectively, these results improve our understanding of the spatial variation and genetics of chemical defense in rough-skinned newts while integrating these findings with conservation implications for Vancouver Island populations.
- ItemOpen AccessDo molecular data support a rapid radiation of the genus nicrophorus (coleoptera: silphidae)?(2007) Venables, Chandra; Sikes, Derek S.; Vamosi, Steven M.
- ItemOpen AccessDownstream consequences of poor early life conditions: effect of larval competition on the fat content and mating propensity of adult female callosbruchus maculatus (coleoptera: bruchidae)(2009) Schade, Daynika Justine; Vamosi, Steven M.
- ItemOpen AccessEcology and Genetics of Phenotypic Integration and the Role for Adaptation in Threespine Stickleback(2019-07-09) Barry, Tegan Nicole; Rogers, Sean M.; Jamniczky, Heather A.; Theodor, Jessica M.; Vamosi, Steven M.Determining the underlying causes for the links between form, function, and the environment, and how these correlations relate to adaptation to novel environments represent integral problems in evolutionary biology. While investigations have been conducted on adaptive divergence involving single, isolated traits, adaptation is multifaceted, requiring the examination of complex, multidimensional phenotypes. In this thesis, I evaluated the hypothesis that phenotypic covariation and phenotypic integration are linked to genetic covariation and facilitate adaptation to novel environments. Phenotypic variation and covariation, along with genetic differentiation between multiple wild stickleback subpopulations and laboratory reared groups were described using three dimensional geometric morphometric data from stickleback skeletal structures as well as genomic information from high density Single Nucleotide Polymorphisms (SNPs; sensu Pool-Seq). I evaluated whether divergence in putatively adaptive traits was higher than expected under expectations for neutral evolution via PST-FST comparisons of phenotypic covariation and contrasted patterns of genetic and phenotypic variation. I determined the genetic basis of phenotypic integration using a controlled common garden experiment and investigated the genetic architecture of integrated skeletal structures through Quantitative Trait Locus (QTL) analysis carried out on linkage maps that I generated from SNPs characterized by double restriction digest reduced representation sequencing (ddRAD-Seq). Finally, I evaluated whether this genetic architecture was being maintained by selection in wild populations by testing the hypothesis that molecular divergence was higher than expected at genetic regions associated with phenotypic traits. I found the amount of phenotypic variation and strength of integration varies across the stickleback skeleton as well as among marine populations and that directional selection is acting on phenotypic integration in all observed populations. I determined that phenotypic integration across the skeleton is controlled by genetic factors, though there is a strong effect of environment on trophic traits. Finally, I characterized 33 significant QTL linked to integrated skeletal traits, finding 2702 SNP outliers within the identified QTL under selection between marine and freshwater environments. Collectively, my thesis highlights integration as an essential component of adaptive divergence and as one of the potential driving forces for the rapid adaptation of populations to novel environments.
- ItemOpen AccessEcology of Adaptive Peak Shifts in Alaskan Threespine Stickleback (Gasterosteus aculeatus)(2015-12-04) Vanderzwan, Stevi Lee; Rogers, Sean M.; Vamosi, Steven M.; Jamniczky, Heather A.; Theodor, Jessica M.Divergent natural selection is a major cause of phenotypic differentiation among populations exploiting different environments, but information on the ecological factors contributing to peak shift is largely missing from natural populations. Threespine stickleback (Gasterosteus aculeatus) is an emerging vertebrate model for studying phenotype-environment associations, as ancestral marine populations have adapted independently to postglacial freshwater environments. I characterized antipredator, foraging, and body shape phenotypes of 800+ fish from 16 ecologically diverse sites on the Alaska Peninsula. Gill rakers, antipredator traits, and body shape significantly associated with lake ecology, whereas foraging traits and body shape were influenced by geography. Stickleback from lakes ecologically similar to the ancestral state were more phenotypically similar to marine-influenced populations than fish from ecologically divergent habitats (i.e., small lakes). My study elucidates mechanisms associated with adaptive evolution and is one of relatively few that links ecological features of the adaptive landscape with phenotypic evolution in multiple populations.
- ItemOpen AccessEffects of diquat dibromide herbicide exposure on biomarkers of stress and chemical exposure in two non-target fish species(2018-12-20) Cribb, Emily; Jackson, Leland J.; Vijayan, Mathilakath Madathil; Hontela, Alice; Smits, Judit Emmy G.; Vamosi, Steven M.Flowering rush is an invasive plant that creates dense blooms, blocking waterways and reducing available fish habitat. Diquat dibromide was applied to eradicate flowering rush in a small water body near Innisfail, Alberta. An observational study was undertaken to assess the effects of diquat on non-target fish species under field conditions. Brook stickleback and fathead minnows were collected from the exposed water body and a reference site before and after two applications of diquat. Mass, length, condition factor, and hepatosomatic index were significantly different between the two sites, but the differences were not correlated with diquat exposure. Secondary stress (HSP70, HSC70) and chemical exposure (CYP1A) biomarkers also did not change in association with diquat exposure. The cortisol response was normal following diquat exposure. No evidence was obtained to suggest that diquat was causing sub-lethal toxic effects in these fish species following use of diquat to eradicate invasive flowering rush.
- ItemOpen AccessExtinction Risk Escalates in the Tropics(Public Library of Science, 2008) Vamosi, Jana; Vamosi, Steven M.
- ItemOpen AccessImpacts of Lake Physical Characteristics and the Presence of a Non-native Species on Diet Specialization in Threespine Stickleback (Gasterosteus aculeatus)(2018-09-21) Curley, Douglas Taylor; Vamosi, Steven M.; Vamosi, Jana C.; Galpern, Paul; Wasmuth, James D.The diet and dietary morphological adaptations of populations have been shown to be influenced by both the physical characteristics of their habitat and the presence of non-native species. In this study, I assessed how diet varies within and among populations of threespine stickleback (Gasterosteus aculeatus) in lakes with varying bathymetry in southwestern British Columbia. These lakes also differed in whether they contained the invasive signal crayfish (Pacifastacus leniusculus). Diet was evaluated through gut content analysis. I also investigated how morphology differs between these populations, as morphology has been shown to be linked to diet in stickleback. Diet data did not reveal any significant differences in diet among populations. However, morphology data did reveal significant differences among lakes and between crayfish conditions. The data suggest that diets higher in benthic invertebrates are associated with lakes with more littoral area and with the presence of signal crayfish.
- ItemOpen AccessImpacts of non-native species on the morphology of threespine stickleback (Gasterosteus aculeatus)(2018-04-16) Kienzle, Hannah Marie; Vamosi, Steven M.; Jamniczky, Heather A.; Jackson, Leland J.Invasive species have demonstrated their capability to greatly modify ecosystems and communities. Introducing multiple species can potentially alter how a native population adapts relative to when species are introduced individually. I assessed whether native threespine stickleback (Gasterosteus aculeatus) exhibit distinct morphological characteristics corresponding to a varying combination of the presence of introduced smallmouth bass (Micropterus dolomieu) and signal crayfish (Pacifastacus leniusculus) on Vancouver Island. I also examined morphological changes over 18 - 43 years to determine whether contemporary characteristics become magnified in the presence of non-native species. There are clear distinctions in stickleback traits and body shape among non-native species combinations. Bass and crayfish lake stickleback are highly armoured, whereas bass-only lakes contain stickleback with reduced armour. Klein and Dougan Lake stickleback, which coexist with signal crayfish, showed significant increases in size over time. These patterns suggest that smallmouth bass and signal crayfish may have differential impacts on stickleback morphology.
- ItemOpen AccessMacroinvertebrate Communities of Temporary Prairie Pothole Wetlands(2010) Silver, Carly Ann; Vamosi, Steven M.
- ItemOpen AccessPhylogeography and local adaptation in prickly sculpin, Cottus asper(2013-12-23) Dennenmoser, Stefan; Vamosi, Steven M.; Rogers, Sean M.This thesis examined historical and contemporary effects on genetic population structuring of prickly sculpin (Cottus asper) in British Columbia, Canada. A phylogeographic study was conducted, which disproved the traditional view that prickly sculpin survived the Last Glacial Maximum in only southern coastal and inland refugia, favoring allopatric divergence and giving rise to coastal and inland “prickling” phenotypes, which vary in the degree to which spine-like scales cover the body of the fish. Instead, analyses of mitochondrial DNA and microsatellite markers suggest parallel evolution of highly prickled inland populations, which presumably have evolved independently across three glacial lineages, originating from highly differentiated ancestral coastal populations. Postglacial colonization from coastal towards inland regions and associated founder effects resulted in decreased genetic diversities, which was also evident in a subsequent study on conservation genetics of a recently discovered peripheral population in the Peace River in Alberta. While no divergent “conservation designation unit” was detected in the Peace River, a for freshswater sculpins unusual high genetic connectivity over large geographic scales was found, which could reflect high dispersal capacities of an extended, planktonic larval stage that might have been at least partially retained from an amphidromous life cycle of the putative ancestral coastal populations. While such assumptions on life history characteristics of inland populations remain speculative, the divergence between coastal, amphidromous and inland, purely freshwater life cycles is young (< 14,000 years), and may be in an early, incomplete stage of a life history transition. To better understand life history transitions from amphidromous to freshwater life cycles in C. asper, a population genetics study was conducted in the Lower Fraser River system, which identified sympatric life history ecotypes represented by amphidromous sculpins in the river main channel, and genetically differentiated freshwater sculpins in the river tributaries. These results indicate that that isolation-by-environment to discrete freshwater habitats could play a role for the early stage of amphidromy-freshwater transitions, which may be further favored by the presence of large tributary streams and lakes allowing for large effective population sizes.
- ItemOpen AccessSeafloor Sediment Bacterial Community Profiling for Baselines and Environmental Effects Monitoring at a Deep-Sea Oil Production Site Offshore Nova Scotia, Canada(2019-02-22) Stacey, Deidra Kathryn; Hubert, Casey R. J.; Dunfield, Peter F.; Vamosi, Steven M.; Else, Brent G. T.Monitoring effects of environmental pollution is a critical aspect to preserving ecosystem health, but is challenging if baseline conditions are never established. Microorganisms are the first responders in a marine pollution event, hence oil-degrading bacteria can be used to monitor dispersion and biodegradation of oil spills. Deep-water subsurface oil reservoirs are predicted to exist along the Scotian Slope offshore Nova Scotia. Seafloor sediment from 19 Scotian Slope stations spanning a ~70,000 km2 area were used to generate 51 bacterial 16S rRNA gene amplicon libraries (V3-V4 region) to form a DNA baseline. A 300-day-long mock oil spill experiment using Scotian Slope sediment identified potential bacterial bioindicators of pristine and contaminated conditions, relative to baseline, underpinning an environmental monitoring approach that is proposed. This study shows that bacterial rRNA gene amplicon sequencing offers a novel parameter for baselines and environmentally responsible development of offshore deep-water oil drilling in Canada and beyond.
- ItemOpen AccessThe effects of predaceous dragonfly larvae (odonata, anisoptera) on community composition in dytiscid diving beetles (coleoptera, dytiscidae)(2010) Wohlfahrt, Bianca; Vamosi, Steven M.
- ItemOpen AccessThe Landscape Genetic Patterns of Culaea inconstans(2013-05-01) Kremer, Cory S.; Rogers, Sean M.; Vamosi, Steven M.Landscape genetics is a new field that investigates the consequences of landscape features on population genetic patterns. The small lakes of Alberta, and the brook stickleback (Culaea inconstans) that inhabit them, provide a unique system where populations are highly fragmented and isolated from one another. These lakes are prone to winterkills hypothesized to precipitate frequent bottleneck events in brook stickleback populations. As predicted, brook stickleback populations exhibited a high degree of population structure, and were hierarchically structured by small scale watersheds. AIC analyses of the role of spatial features found support for basin characteristics in driving patterns of genetic diversity, which was also consistent with the detection of recent bottlenecks in at least five of the sampled lakes. These results suggest that brook stickleback population genetic patterns are primarily controlled by processes that accelerate genetic drift, reinforcing the importance of connectivity in the maintenance of genetic diversity in fragmented landscapes.
- ItemOpen AccessThe molecular systematics of the Agabinae Thomson, 1867 (Coleoptera, Dytiscidae)(2016) Venables, Chandra; Vamosi, Steven M.; Theodor, Jessica M.; Rogers, SeanEarly 19th century classifications of the predaceous diving beetle subfamily Agabinae have been continuously reworked by subsequent systematists, but remain in flux at all taxonomic levels. Morphological characters have not produced sufficient evidence for a robust phylogeny, as there are few informative characters on which to base the taxonomy below the level of subfamily. It has been 12 years since the only comprehensive analysis of the molecular systematics and biogeography of the subfamily was published by Ribera et al. (2004). In the current project I update the molecular systematics of the Agabinae, addressing problems of biogeography, diversification rate, and taxonomy, at the subfamily, genus, and species levels. I apply dense taxon sampling, including data from the previously underrepresented Neotropical, Northern Nearctic, Eastern Palearctic, and Afrotropical regions, to a dataset of 10 gene sequences; (five mitochondrial, five nuclear). Using Bayesian and likelihood approaches, as well as fossil data, I infer time-calibrated phylogenies for the subfamily and for the genus Agabus. My results indicate the Agabinae originated during the early Paleogene in the Northern Hemisphere, with expansions to Australasia and South America likely via long distance dispersal. The tribes Agabini and Platynectini were consistently recovered as monophyletic, as was Hydrotrupini; however, results suggest that Hydrotrupes should be elevated to subfamily Hydrotrupinae. Relationships within and between genera were consistently recovered with strong Bayesian support with the exceptions of the relationship between Platambus and Agabus, species groups of Ilybius and Agabus, and for the subgenera of Agabus. In addition to polyphyletic Platambus occurring in Agabus, 44% of the current Agabus species groups (not monotypic) were not recovered as monophyletic. Collections in Northern Canada and Alaska yielded new locality data for 9 species, and identified possible refugial populations of Agabus arcticus (Paykull, 1798) in the Peel watershed (Yukon Territory). Further study of A. arcticus in the Nearctic will likely support the recognition of unique Nearctic subspecies. Molecular phylogenetic results provide new insights into Agabinae systematics, and also find support for many taxonomic hypotheses developed by the pre-cladistic workers in the group, underscoring the importance of integrative taxonomy combining molecular (this project) and morphological data (past workers).
- ItemOpen AccessToxic cyanobacteria in relation to sulfate, molybdenum, nitrogen and phosphorus in Alberta's shallow prairie lakes(2018-10-19) Anderson, Susan Marie; Jackson, Leland J.; Kinniburgh, David W.; Vamosi, Steven M.; Vamosi, Jana C.Cyanobacteria are characteristic of poor global water quality. They create a public health concern and threaten biodiversity, particularly when they produce toxins such as microcystins. It is poorly understood why cyanobacteria produce microcystins, or how cyanobacteria in shallow prairie lakes will respond to increased salinity under changing climate. To study the effects of variable sulfate concentrations on cyanobacteria and to elucidate environmental patterns of microcystin production, I sampled 25 shallow lakes over four months for total nitrogen (TN), dissolved inorganic nitrogen (DIN), total phosphorus (TP), soluble reactive phosphorus (SRP), sulfate, molybdenum, microcystins, and the cyanobacteria-specific pigments canthaxanthin, myxoxanthophyll and echinenone. There was a negative relationship between cyanobacteria pigment and sulfate, and a positive relationship between cyanobacteria pigment and molybdenum and total nitrogen. Microcystins positively correlated with cyanobacteria pigment and turbidity. When microcystin samples above 10 µg·L-1 were removed, microcystins correlated with TN:TP in June and July. My results suggest that increasing sulfate leads to less cyanobacteria pigment. With the prairies expected to get hotter and dryer in the future, shallow prairie lakes are likely to see less cyanobacteria as they increase in salinity. My results also indicate that higher cyanobacteria pigments correlate with higher microcystins. Although low TN:TP can lead to high microcystins, low TN:TP is not enough to differentiate between high and low microcystins. No thresholds were found in either analysis, meaning there was no evidence for a tipping point where sulfate limits cyanobacteria nor the existence of environmental triggers associated with microcystin production over the season.