Fisheries oceanography often aims to link large scale atmospheric and oceanic processes to variability and trends in the productivity of economically and ecologically valuable fish species. Declines in productivity of multiple species of Pacific Salmon (genus Oncorhynchus) in recent decades have spurred the search for a 'smoking gun;' an explanation that could explain trends in productivity across populations, regions and species. Despite extensive investment of research effort and funding, such an explanation remains elusive. The lack of a unifying explanation for declining productivity of Pacific Salmon may be due to the spatial and temporal complexity of their interactions with the marine environment. This complexity has historically been understudied, in part due to logistical limitations of research on Pacific Salmon at sea. This dissertation reports the results of a detailed study of how juvenile Chinook Salmon O. tshawytscha interact with marine habitats during their first summer and fall at sea. I first developed and validated a novel, hook and line-based method of sampling juvenile Chinook Salmon (microtrolling). I then reviewed and empirically compared methods (insulin like growth factor-1 concentration, RNA to DNA ratio, and scale circulus spacing) for indexing growth rate of juvenile salmon sampled in the ocean, a variable which is hypothesized to be related to subsequent survival. I integrated microtrolling with small vessel oceanography to relate distribution, diet, size and growth of juvenile Chinook Salmon to local scale variation in water column properties (stratification) and zooplankton community composition and abundance for five sites in the Southern Gulf Islands of the Salish Sea during a single summer (2015). While both stratification and zooplankton abundance and composition varied between sites, I failed to find support for the hypothesis that juvenile salmon distribution and growth was positively related to water column stratification at fine spatial scales. Juvenile Chinook Salmon were larger and faster growing where juvenile Pacific Herring Clupea pallasii were important in their diets, suggesting that Pacific Herring may play an important role in structuring the ecology of juvenile Chinook Salmon at sea. I built on 2015 results to conduct a detailed case study of juvenile Chinook Salmon ecology at two sites in the Southern Gulf Islands: Sansum Narrows and Maple Bay. Juvenile Chinook Salmon were consistently larger, more piscivorous, and faster growing at Sansum Narrows than Maple Bay across two years (2015 and 2016) despite lower zooplankton abundance at Sansum Narrows. Hydroacoustic surveys in September 2017 confirmed prior qualitative observations of elevated occurrence of forage fish schools (likely age-0 Pacific Herring) at Sansum Narrows, and a novel, mobile acoustic tag tracking survey suggested that fish tagged at Sansum Narrows may co-locate with juvenile Pacific Herring over the tidal cycle. By relating a scale circulus spacing-based growth index to reconstructed size intervals I found that juvenile Chinook Salmon at Sansum Narrows had been faster growing that those at Maple Bay before the transition to piscivory, and perhaps before migration to the ocean. These results suggest that intrinsic growth potential, or growth conditions during freshwater rearing or the transition to marine residence, interact with fine-scale structure in marine habitats to regulate growth potential of juvenile Chinook Salmon at sea. These factors also likely interact with the basin and interannual scale processes that have received extensive study as regulators of marine survival of juvenile Pacific salmon. These complex interactions should be taken into account when designing or interpreting studies to determine factors limiting productivity of Pacific Salmon populations.

Seascape Ecology provides a comprehensive look at the state-of-the-science in the application of landscape ecology to the seas and provides guidance for future research priorities. The first book devoted exclusively to this rapidly emerging and increasingly important discipline, it is comprised of contributions from researchers at the forefront of seascape ecology working around the world. It presents the principles, concepts, methodology, and techniques informing seascape ecology and reports on the latest developments in the application of the approach to marine ecology and management. A growing number of marine scientists, geographers, and marine managers are asking questions about the marine environment that are best addressed with a landscape ecology perspective. Seascape Ecology represents the first serious effort to fill the gap in the literature on the subject. Key topics and features of interest include: The origins and history of seascape ecology and various approaches to spatial patterning in the sea The links between seascape patterns and ecological processes, with special attention paid to the roles played by seagrasses and salt marshes and animal movements through seascapes Human influences on seascape ecology—includes models for assessing human-seascape interactions A special epilogue in which three eminent scientists who have been instrumental in shaping the course of landscape ecology offer their insights and perspectives Seascape Ecology is a must-read for researchers and professionals in an array of disciplines, including marine biology, environmental science, geosciences, marine and coastal management, and environmental protection. It is also an excellent supplementary text for university courses in those fields.

Atlantic Salmon is a cultural icon throughout its North Atlantic range; it is the focus of probably the World’s highest profile recreational fishery and is the basis for one of the World’s largest aquaculture industries. Despite this, many wild stocks of salmon are in decline and underpinning this is a dearth of information on the nature and extent of population structuring and adaptive population differentiation, and its implications for species conservation. This important new book will go a long way to rectify this situation by providing a thorough review of the genetics of Atlantic salmon. Sponsored by the European Union and the Atlantic Salmon Trust, this book comprises the work of an international team of scientists, carefully integrated and edited to provide a landmark book of vital interest to all those working with Atlantic salmon.

Estuaries provide juvenile salmonids with highly productive feeding grounds, refugia from tidal fluctuations and predators, and acclimation areas for smoltification. However, these dynamic, fluctuating salinity environments may also be physiologically stressful to growing juvenile fish. In order to evaluate the costs and benefits of estuarine marshes to juvenile Chinook salmon, I observed habitat use, diet, and growth of fish in the Nehalem Estuary on the Oregon coast. I also examined physiological costs associated with salmon living in fluctuating salinities and growth rates in laboratory experiments. I collected growth, diet and osmoregulation information from juvenile Chinook salmon in three tidal marsh sites in the Nehalem Bay and from juveniles in the Nehalem River. Stomach contents indicated that a high proportion of the diet is derived from terrestrial prey. These allochthonous prey resources likely become available during the flood stages of tidal cycles when drift, emergent and terrestrial insects would become available from the grasses surrounding the water. This field study confirmed that juvenile Chinook salmon utilized fluctuating salinity habitats to feed on a wide range of items including terrestrial-derived resources. Although field studies indicate that fish in estuarine habitats grow well and have access to quality prey resources, experimental manipulations of salinities were used to quantify the physiological costs of residing in the freshwater-saltwater transitional zone. In the laboratory, I designed an experiment to investigate the physiological responses to fluctuating salinities. Experimental treatments consisted of freshwater (FW), saltwater (SW) (22-25%o); and a fluctuating salinity (SW/FW) (2 - 25%o). These treatments were based on typical salinity fluctuations found in estuarine habitats. I measured length, weight, plasma electrolytes and cortisol concentrations for indications of growth and osmoregulatory function. The fluctuating salinity treatment had a negative effect on growth rate and initial osmoregulatory ability when compared with constant freshwater and saltwater treatments. The results indicated that fluctuating salinities had a small but marginally significant reduction in growth rate, possibly due to the additional energetic requirements of switching between hyper- and hypo-osmoregulation. However, 24-hour saltwater challenge results indicated that all fish were capable of osmoregulating in full-strength seawater. In a second experiment, I manipulated feed consumption rates of juvenile spring Chinook salmon to investigate the effects of variable growth rates on osmoregulatory ability and to test the validity of RNA:DNA ratios as indication of recent growth. The treatments consisted of three different feeding rates: three tanks of fish fed 0.7 5% (LOW) body weight; three tanks fed 3% (HIGH) body weight; and three tanks were fasted (NONE) during the experiment. These laboratory results showed a significant difference in the osmoregulatory ability of the NONE treatment compared to the LOW and HIGH treatments which indicates that a reduction in caloric intake significantly effected osmoregulatory capabilities during a 24 hour saltwater challenge. Furthermore, this suggests that there is a minimum energetic requirement in order to maintain proper ion- and osmoregulation in marine conditions. Estuarine marshes have the potential to provide productive feeding grounds with sufficient prey input from terrestrial systems. However, utilization of these marshes in sub-optimal conditions could alter behavior or impair physiological condition of juvenile Chinook salmon prior to their seaward migration by providing insufficient prey resources in a potentially stressful, fluctuating environment. Therefore, the physiological costs associated with estuarine habitat use should be well understood in order to aid future restoration planning.

The early marine phase following freshwater emigration has been identified as a critical period in salmonid (Oncorhynchus spp.) life history, characterized by high but variable mortality. Consistent with the “growth-mortality” and “bigger-is-better” hypotheses, at least some of the mortality during the critical period appears to be size-dependent – with smaller or slower growing individuals less likely to survive than larger, faster growing conspecifics. Size and growth are flexible morphological traits that vary with prey availability, yet there is incomplete information on the temporal and spatial match/mismatch between juvenile salmonids and their marine prey in the Northern California Current Ecosystem. This work addressed a gap in the understanding of seasonal variability in prey community composition, abundance, and quality during early marine residence. Three studies were conducted using a population of subyearling (age-0) Chinook salmon (O. tshawytscha) from the upper Columbia River in order to evaluate the effects of prey on salmon growth, biochemistry, and performance. The first was a laboratory study that tested for growth rate and swimming speed differences in salmon reared on three treatment diets followed by three fasting treatments to assess the effects of variability in summer diet quality and winter diet quantity. Significant differences in growth were detected among fasting treatments but not diet treatments. Also, larger salmon with more storage lipids swam faster than smaller leaner fish following fasting, indirectly supporting the notion that growth during the critical period provides a carryover benefit important for overwinter survival. Salmon fatty acids and bulk stable isotopes of carbon and nitrogen were measured throughout the experiment to provide estimates of turnover and incorporation rates. The next study was a longitudinal field study that measured variation in salmon size and prey field community throughout the early ocean period (May – September) over two years of high marine survival (2011 and 2012) to better understand the relationship between prey community composition and salmon growth. Maximum growth rates were associated with high biomass of northern anchovy (Engraulis mordax) which peaked in abundance at different times in each year. The final bioenergetics modeling study combined data from the laboratory and field studies to evaluate the relative importance of prey availability, prey energy density, and temperature on salmon growth. Variation in feeding rate was related most with growth rate variability and least with prey energy density. Throughout their range, subyearlings can grow at high rates in the ocean (>2% body weight per day) by consuming both invertebrate and marine fish prey. However, when marine fish prey are highly abundant they likely provide an energetic advantage over invertebrate prey by reducing overall foraging costs. Quantifying the abundance, size, diet, and distribution of juvenile salmonids relative to their prey field throughout early ocean residence will contribute to a better understanding of seasonal differences in trophic interactions that are associated with differences in annual growth and survival rates. Moreover, an integrated approach that combines sampling of prey with measurements of predator growth, diet, fatty acids, and stable isotopes provides a useful framework for assessing trophic dynamics and evaluating the effects of climate variability and change on predator and prey communities.