With declining wild fisheries and increasing seafood demand from a growing population, attention has turned to aquaculture in general, and shellfish aquaculture in particular, to meet this demand. Aquaculture has grown dramatically in the last twenty years through intensification of operations and the expansion of the industry into new areas. This growth has been associated with environmental degradation and social conflict leading some to question its sustainability. However, those studying the problem point to significant opportunities for sustainable forms of aquaculture by focusing on the cultivation of species such as shellfish and the adoption of ecosystem-based management (EBM). Shellfish aquaculture has a long history in British Columbia (B.C.), Canada with an abundance of coastline and suitable water conditions. There is significant development potential for shellfish aquaculture in B.C., which creates an opportunity to ensure this development occurs in an ecologically sound way through the use of governance approaches like ecosystem-based management. Transitioning from conventional approaches to resource management to an ecosystem-based approach presents several challenges particularly for the management of one sector. This study highlights how an understanding of the industry and the existing governance context can inform the implementation of EBM. The specific research objectives include: (1) to understand the governance system for shellfish aquaculture in B.C.; (2) to understand the shellfish aquaculture industry within the context of EBM; and (3) to explore EBM as an approach to governance in the shellfish aquaculture industry in B.C. The main method of inquiry is a questionnaire survey (October 2006 to February 2008) of the shellfish aquaculture industry. Supporting methods include an analysis of industry data, an in-depth analysis of government documents, policies and regulations, and targeted interviews with federal and provincial government regulators. The empirical knowledge gained through the main research instrument was combined with the contextual knowledge gained through the supporting methods to achieve a more holistic understanding of the case study. The results show that the governance setting for the shellfish aquaculture industry is multi-lateral and the lack of comprehensive and targeted legal instruments, and the ill-use of marine spatial planning and conflicts with other coastal users have together contributed to an inefficient and costly site application process. EBM has the potential to address some of these challenges with the current governance process by making some decisions on an ecosystem-scale as opposed to an application-by-application basis, such as assessing the presence of fish habitat and consulting with stakeholders. The results of the survey of the shellfish aquaculture industry show that the industry is geographically diverse, and understands and values the connection between their business and the large ecosystem. This suggests that the industry may be supportive of EBM. However, the industry faces many economic challenges that may influence their capacity to participate, as such regulators should look towards the use of economic incentives to achieve policy objectives. Although this research provided several recommendations for management and the industry in moving forward with this new approach to governance, three fundamental elements are needed: • marine spatial planning that is integrated within the governance framework; • the integration science and management through adaptive management including an ongoing monitoring framework that informs governance strategies; and, • engaging the industry as active partners in this governance approach through co-management. This research makes significant contribution to understanding the shellfish aquaculture industry in B.C. Prior to this study there was little information available characterizing the structure and socio-economic make-up of the industry. The results of the survey and the in-depth analysis of the governance context for the shellfish aquaculture industry provide a previously unavailable base of information from which to build future studies. In addition this research contributes to the growing body of literature on EBM assessing the potential challenges and opportunities for moving the theoretical concept into practice. / Graduate

In the northeast Pacific, salmon are an integral part of ecology, economics and culture. Nearshore areas, where juvenile salmon reside upon leaving their natal streams, are important habitat during a critical time where growth can determine overall survivorship. With the rise in human development in coastal areas, these valuable habitats are becoming increasingly modified, however, the ecological ramifications are not fully understood. This study focuses on two types of anthropogenic influence including shellfish aquaculture, which modifies intertidal areas by adding structures such as intertidal fencing and anti-predator nets, and plastic marine pollution in the form of microplastics. We beach seined at sites within an area extensively modified for shellfish aquaculture (Baynes Sound) to examine juvenile salmon abundance, condition, feeding intensity and prey at aquaculture and non-aquaculture areas. In addition, we also beach seined, and along the east coast of Vancouver Island to determine the incidence of microplastics in juvenile Chinook salmon and their nearshore environments. No significant differences were found between areas in the abundance, diets, condition or feeding intensity of juvenile Coho and Chinook. Chum had different prey and a higher condition and feeding intensity at aquaculture sites, suggesting that species such as Chum feeding on more benthic prey items have a higher probability of being impacted by shellfish aquaculture modifications and in this case we observed positive effects. Microplastic analysis showed juvenile Chinook salmon contained 1.15 1.41 (SD) microplastics per individual while water and sediment samples had 659.88 520.87 microplastics m-3 and 60.2 63.4 microplastics kg-1 dry weight, respectively. We found no differences in microplastic concentrations in juvenile Chinook and water samples among sites but observed significantly higher concentrations in sediment at our Deep Bay site compared to Nanaimo and Cowichan Bay. These differences may be due to site bathymetry and oceanographic differences facilitating settlement at the Deep Bay site and/or may be a result of differential plastic sources in the area including shellfish farming and a marina. Shellfish aquaculture had negligible or positive effects on juvenile salmon abundance, diet, condition and feeding intensity and Chinook microplastic concentrations were relatively low compared to literature values. Although fitness consequences and ecosystem-wide implications must be addressed in the future, it appears shellfish aquaculture and microplastics are not immediate threats to juvenile Pacific salmon along the east coast of Vancouver Island at this time. However, continued monitoring programs and larger-scale studies should be implemented as shoreline modification and plastic use continues to increase. / Graduate / 2017-08-14

Background: The blue mussel, Mytilus edulis L., is an important contributor to the shellfish sector of Scottish aquaculture, with 7,270 tonnes worth £8.8 million being produced for the year 2015. Since 2010, production values have fluctuated as a result of inconsistent spat settlement, several business closures, and heightened levels of marine toxins in some areas. On Scotland’s west coast, some farms (most notably Loch Etive) have suffered production losses from the appearance of non-marketable mussels with particularly fragile shells and poor quality meat. Recent research has demonstrated that these undesirable traits have a genetic factor, linked to the presence of a non-native but related species Mytilus trossulus (Gould, 1850) and often its hybrids with the native M. edulis. M. trossulus has been classed as a commercially damaging species under Scottish law, but there is insufficient data on hybridisation and introgression patterns in Scottish mussel populations to evaluate any possible impacts this could have on production. Existing research has focused on single locus genotyping to identify Mytilus spp. and their hybrids in Scotland. By instead utilising multilocus genotyping, introgression could be identified and a better understanding of population structure could be gained, with implications for management to maintain productivity and profitability. The aim of the research presented here was to develop and validate a suite of new species diagnostic markers for multilocus genotyping of field populations of Scottish mussels, thereby establishing a more complete picture of the taxonomic relationships between species than previous studies have permitted. Results: Analysis of SNPs identified with RADseq confirmed the presence of three genetically distinct Mytilus species in Scotland: M. edulis, M. galloprovincialis and M. trossulus. RADseq and KASP genotyping technology successfully identified and validated a suite of 12 highly robust diagnostic SNP markers for multilocus genotyping of Mytilus mussel populations. These markers permitted more comprehensive genotyping than previous studies had, allowing presumed pure species individuals to be distinguished from first generation (F1) hybrids and introgressed (FX) genotypes in reference populations, and subsequently presented the possibility of exploring introgression in a wider scale study. Multilocus genotyping of mussel populations from around Scotland revealed widespread introgression of M. edulis with both M. galloprovincialis and M. trossulus. No pure M. galloprovincialis was identified and pure M. trossulus was restricted to a single site in Loch Etive, possibly part of a relict population. F1 hybrids between M. edulis and M. trossulus were identified in Loch Etive and in Loch Fyne on the west coast. This was evidence of ongoing hybridisation and suggested an active hybrid zone existed in Scotland, something that previous single locus genotyping studies had not acknowledged. A link between shell fragility and M. trossulus introgression was recognised at a single site outside of Loch Etive, but this was not apparent anywhere else and the actual causes of shell fragility remain unevaluated. There was a clear difference between the genetics of most farmed stock and wild populations, which indicated an anthropogenic effect on introgression and subsequent species composition, and had implications for future farm site selection and broodstock sourcing. Temporal species composition in Loch Etive differed over a short time period, but high proportions of M. trossulus alleles were observable some 25 months after a major fallowing event had taken place. Pure M. trossulus was also identifiable, which was consistent with the presence of an established population of M. trossulus existing in this area. Conclusion: Multilocus genotyping has produced a more in depth picture of species diversity in Scottish mussel populations. SNP assays revealed widespread introgression between three genetically distinct species – M. edulis, M. galloprovincialis and M. trossulus – and furthermore recognised that, to date, single locus genotyping has overestimated the abundance of pure Mytilus mussels in Scottish waters. However, this hitherto unidentified genetic complexity does not appear disadvantageous to mussel production, despite the prevalence of M. trossulus introgression among farmed populations, and it is somewhat unlikely that genetics are the sole cause of undesirable shell characteristics among Mytilus spp. mussels.