Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. / Graduate / 2019-04-19

This dissertation describes a proposed methodology for Cumulative Effects Assessment (CEA) with the purpose of improving the process by making it both more substantive and quantitative. The general principles of the approach include the following: use of effect-based analyses where selected Valued Component (VC) sensitivities are identified first and then effect pathways are determined building bottom-up linkages from VC sensitivities to potential stressors or combinations of stressors to effect drivers and forces behind the drivers. Models were developed based on statistical or historic trend analysis or literature review that predicted the responses of the VCs to changes in effect drivers. Further, scenarios of divergent futures were created that involved different developments of each effect driver or force, and finally the models were applied to each scenario to project the state of the studied VCs. A practical implementation was conducted to demonstrate the use of the proposed methods on future population trends of two anadromous salmon species from the Cowichan River, British Columbia, Chinook and Coho. The assessment was conducted for both early freshwater and marine phases of their life. For the freshwater phase, the assessment focused on two main factors affecting salmon survival, streamflow and stream temperature and established two main drivers affecting these stressors, land use and climate change, and two main forces behind these drivers, Local and Global human development driven change, respectively. Effects of stream temperature and streamflow on salmon freshwater survival were simulated using two models; one was based on Chinook freshwater survival correlations with stream temperature and was developed only for Chinook, and the other was based on literature-derived temperature and streamflow thresholds and was developed for both species. Connections between the stressors (stream temperature and streamflow) and drivers (land use and climate change) were established through a hydrologic model and stream temperature regression model. For the marine environment, models were created using Pearson correlation and stepwise regression analysis examining links between survival of Cowichan River Chinook and Strait of Georgia hatchery-raised and wild Coho and various environmental variables of the nearshore zone of Strait of Georgia and Juan de Fuca Strait. The models were applied to project future salmon survival under four future scenarios for 2050 that were created by combining two opposite scenarios of land use in the watershed, forest conservation and development, and two climate change scenarios, extreme and moderate. Scenario projections showed a decrease in overall (combined early freshwater marine) survival by 2050 for all three studied salmon populations. None of them are likely to survive in scenarios with extreme climate change, while scenarios with moderate climate change showed positive survival rates although lower than present-day baseline levels. Analysis also showed that land use management within the Cowichan River watershed can also affect freshwater survival of both Chinook and Coho and marine survival of Chinook through influence of river discharge on nearshore processes. However, our land-use management scenarios have considerably weaker effect than climate change on salmon survival. Therefore, we conclude that land use management alone is not sufficient to offset effects of climate change on salmon survival. / Graduate

Aquatic ecosystems continue to be increasingly affected by climate warming. For salmonids in the Pacific Northwest of North America, increasing temperatures pose tighter thermal constraints on their habitat use as well as aspects of their individual performance, such as disease resistance. This thesis examines the effect of temperature on the phenology of the Ceratomyxa shasta life cycle, the effect of thermal refugia on disease risk in juvenile salmonids in the Klamath River, CA, and the spatial and temporal distribution of C. shasta in the Willamette River, OR. We developed a biological model that predicts an acceleration of the C. shasta life cycle development due to climate shifts in the Klamath River, resulting in more generations per year and earlier seasonal parasite occurrence. We showed that in early summer the Beaver Creek-Klamath River confluence provides juvenile Chinook and coho salmon an area of lower parasite doses and cooler temperatures than the main stem, thus lessening disease risk. By accelerating the development of C. shasta in its hosts, increasing temperatures will result in earlier parasite transmission to juvenile salmonids and a longer season of infectivity. These fish may find disease refuge at cold tributary inflows to the main stem of the Klamath River in early summer, further adding to the benefit of these important thermal habitats. To determine if similar disease patterns occur in other rivers with the parasite, we described spatial and temporal occurrence of C. shasta in the Willamette River. By collecting weekly water sampling at four sites over 28 months we characterize seasonal and annual differences of parasite abundance, which varies with weekly temperature. We also collected samples along the length of the main stem and its tributaries and identified spatial differences in C. shasta spore densities. Identification of spatial and temporal variation of C. shasta in the Willamette River provides a foundation for understanding future patterns of disease occurrence in this river where conservation of anadromous fisheries is also of concern. This thesis identifies likely responses of C. shasta to climate warming in the Klamath River, with useful application to other rivers in the Pacific Northwest. / Graduation date: 2013