An investigation was initiated in southern British Columbia during 1984 to determine the degree of similarity between populations of coho salmon, in terms of their demographic traits and exploitation patterns. Fourteen stocks of wild or hatchery origin were subject to coded-wire tagging in nine different streams located within a 150 km region of southeast Vancouver Island during 1985,1986, and 1987. Escapement enumeration and tag recovery were conducted during the 1985-1988 period in all streams by means of counting fences and stream surveys. A new mark-recapture model was formulated specifically for estimating escapement levels in natural streams where only a partial enumeration of spawners is possible. Estimates of the number of tags recovered in various sport and commercial fisheries were generated primarily on the basis of catch and sampling records extracted from the Mark-Recovery Program database, located at the Pacific Biological Station of the Canadian Department of Fisheries and Oceans. Estimates of sampling rates in the Strait of Georgia sport fishery were determined from simulation studies based on catch and sampling statistics associated with the Georgia Strait Creel Survey and Head Recovery programs. Populations were contrasted in terms of their juvenile migration patterns, smolt-to-adult survival, catch distributions, straying rates, escapement patterns, run composition, adult sizes, and exploitation rates. Considerable variation in smolt size and juvenile migration time was detected among populations each year. The most pronounced difference was the consistently shorter migration period of smolts released from public hatcheries. Estimates of ocean survival was highly variable across years and streams, and even among stocks within the same stream. No particular stock or stock type had consistently higher survival, but hatchery fish from the Big Qualicum River exhibited consistently lower survival. Considerable variation was observed in the duration and timing of various runs within the study area. On average, the contribution of strays to each spawning population was relatively small (< 2%), but strays could account for as much as 50% of the escapement to a given stream. Average exploitation rates were in the neighborhood of 80% each year, but were as high as 96% for some stocks. Substantial differences in exploitation rate were detected between stocks from the same stream, and between stocks from adjacent streams, but exploitation rates were not consistently higher or lower for any particular stock or stock type. The influence of specific factors upon straying rates, survival rates and exploitation patterns was estimated by means of log-linear models. Stock contributions to various fisheries appeared to be related to the release location, and two stock assemblages were identified within the study area based on the level of similarity among stocks in fishery contribution. Attempts to quantify the level of co-variation among stocks in survival and exploitation rates were hampered by the lack of sufficiently long time series of data, but preliminary results gave no indication of a high level of similarity among stocks or stock types. Still, it was possible to identify stocks which could be used as indicators of the general status of all stocks in the study area in terms of escapement trends, smolt-to-adult survival and exploitation rates. Based on the level of similarity observed, indicator stocks are considered to be useful stock-assessment tools, and can provide useful information for management purposes. / Science, Faculty of / Zoology, Department of / Graduate

Visual estimation techniques were used to quantify habitat characteristics, habitat type (pool, riffle) use and longitudinal distribution of steelhead (Oncorhynchus mykiss), cutthroat trout (0. clarki), and coho salmon (0. kisutch) in spring, summer and fall in 8.8 km of Cummins Creek, a basin in the central coast of Oregon. Fish were distributed significantly different than habitat type availability in most samples. Pool habitats contained a disproportionate percent of the salmonid assemblage and 1+ fish in each sample, and the percentage of fish in pools increased as flow decreased. In spring, coho salmon fry were concentrated in side channels and valley floor tributary habitats. Large woody debris formed 57- 68% of pool habitats and was significantly correlated with pool volume, maximum pool depth, slow surface velocity in pools, and pieces of small woody debris. Longitudinal distribution of the salmonid assemblage did not differ from habitat distribution seasonally or between years, even though certain species differed Coho salmon and cutthroat trout were distributed in proportion to longitudinal habitat availability only when fish abundance was relatively high and streamflow was low. In most samples, both 0+ and 1+ steelhead were distributed in proportion to longitudinal habitat availability. Differences in coho salmon abundance between years appeared to influence longitudinal distribution of each species and age class. Certain reaches had consistent numbers of fish between years while the number of fish in other reaches varied widely. In most samples, reaches with highest abundance for steelhead were in the lower basin, cutthroat trout in the upper basin and coho salmon between the two other species. Timing of reduction in number of fish varied among species. Fifty-five percent of 0+ steelhead and 73% of 1+ steelhead lost between August 1988 and April 1989 were lost between August and October during low flow conditions. However, only 18% of the losses, for 0+ coho salmon, occurred between August and October with the remaining losses occurring after October. This study illustrates that habitat availability is not a good index of fish distribution when fish abundance is low, and it highlights the importance of habitat in the lower portions of basins when fish abundance is high. It also demonstrates that the basin wide distribution of salmonids varies among species, age classes, seasons, and years and suggests that our understanding of salmonid distribution and abundance could be greatly enhanced by adopting a basin-wide, community, and seasonal perspective. In addition, the methods used in this study offer one way to assess the seasonal distribution and abundance of salmonids in a relatively quick, inexpensive, and non-destructive manner. / Graduation date: 1994

Debris flows, common disturbances in many mountainous areas, initially scour or bury stream habitats; however, debris flows deliver vast amounts of wood, boulders, and gravel that may ultimately form complex stream habitat to potentially support a diverse salmonid assemblage. The materials deposited by debris flows would otherwise be inaccessible to streams, and thus deposits may play an important role in creating and maintaining complex salmonid habitat over time. Despite the potential of deposits for increasing habitat complexity, most fish studies have focused on the destructive effects of debris flows and short-term recovery and re-colonization in scour zones. Debris-flows that occurred during the record-setting winter storms of 1996 in western Oregon, USA, provide an opportunity to study intermediate-term effects of debris-flow deposits on abundances and habitat for juvenile salmonids. In this setting, I surveyed salmonid abundance and habitat in three Oregon Coast Range streams that contained several debris-flow deposits from the 1996 storms. I explained fish abundance using hierarchical models, accounting for heterogeneous detection probabilities with repeated counts from multiple-pass snorkeling. The "best" hierarchical model of detection probability and abundance was selected (QAIC) from pool and snorkel-pass characteristics separately for juvenile coho salmon (Oncorhynchus kisutch), age 0+ trout, and age 1+ trout (Oncorhynchus spp.) in each stream. Adding distance to the nearest 1996 debris-flow deposit (DDF) produced a significant drop-in-deviance for four of nine "best" models, including at least one in each stream and for each species/age-class. In these four models, salmonid abundance decreased with increasing distance from deposit. As a potential explanation, several pool habitat characteristics were correlated (Spearman's rank) with DDF. Results varied across streams, but generally, percent of substrate as bedrock was lower and boulder density and percent substrate as gravel were higher closer to deposits. Although repeat counts are increasingly used in hierarchical modeling of heterogeneous detection probabilities and abundance for other wildlife species, studies of fish often rely on uncalibrated, single-pass snorkel counts. When exploring the value of repeat counts, I found that juvenile salmonid abundance decreased with increasing distance from debris-flow deposits in more multiple-pass hierarchical models that accounted for heterogeneous detection probabilities than for single-pass models that did not. Thus, modeling heterogeneous detection probabilities with repeated snorkel counts may be beneficial in other situations, addressing limitations of uncalibrated indices without relying on methods such as electrofishing, which may be difficult or impossible for remote study areas, longer surveys, or sensitive species. My findings suggest that debris-flow deposits may influence salmonid abundances after 15 years, and support management of debris flow-prone hillslopes and low-order channels to deliver elements of stream habitat complexity. / Graduation date: 2013

The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. Accordingly, breeding sites should exhibit predictable habitat features linked to these components. In this study, I evaluated the relative influences of habitat features linked to fitness components on selection of breeding sites by coho salmon (Oncorhynchus kisutch). I also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. I used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. The relative likelihood of each of these models was then evaluated based on how coho salmon were observed to select breeding sites. Specific variables examined within these models included depth at the redd, width to depth ratio, stream network location, proximity to other redds, maximum depth, proximity to a pool tail, and the count of naturally occurring and artificially placed large wood. Results of this work suggest that female coho salmon most likely select breeding sites based on habitat features linked to all four hypothesized fitness components. Linkages between large wood and breeding site selection were less clear, likely due to mismatches between the scale at which availability was quantified relative to the geomorphic influences of wood, insufficient time for wood to have geomorphic influences on habitat, or the directionality in which geomorphic effects are currently manifested (i.e., upstream, downstream, or bi-directional influences). Future work focused on geomorphic processes in this system could reveal stronger linkages between instream wood and the habitat features that coho salmon select for breeding. / Graduation date: 2013

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