Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.

Knowledge of the migratory habits of juvenile Pacific salmon Oncorhynchus spp. is required to test the hypothesis that ocean food resources are a limiting factor in their production. Using DNA stock identification techniques, we reconstructed the regional and seasonal changes in the stock composition of juvenile sockeye salmon O. nerka (n ¼ 4,062) collected from coastal Washington to the Alaska Peninsula in coastal trawl surveys from May to February 1996-2007. Individuals were allocated to 14 regional populations. The majority were allocated to stocks from the Fraser River system (42%), while west coast Vancouver Island stocks accounted for 15% of the total catch; Nass and Skeena River sockeye salmon constituted 14% and Rivers Inlet 6% of the total. The remainder of the stocks identified individually contributed less than 5% of the sockeye salmon analyzed. These proportions generally reflected the abundance of those populations. In spring and summer, the majority of fish were caught in close proximity to their rivers of origin, lending further support to the allocations. By fall, sockeye salmon were caught as far north and west as the Alaska Peninsula, the majority being caught from central British Columbia to Southeast Alaska. Juvenile sockeye salmon generally disappeared from the coast by winter, suggesting dispersion into the Gulf of Alaska. Within each region, the proportional stock composition changed as the seasons progressed, with northward (and in some cases, rapid) migration along the coast. We also demonstrated stock-specific differences in migration patterns. For each stock identified, body size and energy density were higher at northern latitudes, suggesting that there is an environmental or food web influence on growth or that faster growing fish initiated their northward migration earlier.

Bioenergetic models frequently rely on published values or models for estimating the energy density of fish, principally because of the cost and effort of obtaining direct measurements. In this study, we developed empirical models of energy density for free‐ranging juvenile coho salmon Oncorhynchus kisutch and Chinook salmon O. tshawytscha sampled at sea from the west coast of Oregon to Kodiak Island, Alaska, and we evaluated the accuracy of published energy density models commonly used for these species. Our analyses showed that the energy density of juvenile coho and Chinook salmon was strongly correlated to percent dry weight and proximate constituents (especially lipid and, to a lesser extent, protein concentrations) but poorly correlated to body size and condition factor. Percent dry weight of whole fish was the single best predictor of energy density for both species, accounting for more than 90% of the variance in energy density. We also found that percent dry weight in the muscle tissue accounted for 65% of the variance in energy density. Changes in energy density mainly reflected changes in lipid composition. These results indicate that accurate estimates of energy density could be obtained at low effort and cost for juvenile coho and Chinook salmon simply by determining the water contents in whole‐fish or muscle samples. Published models overestimate the energy density of juvenile coho and Chinook salmon collected from the Pacific Ocean. This may result from the extrapolation of the models to different size‐classes, life stages, or habitats. More caution is needed when models are extrapolated to conditions beyond those that were used for their development.

The ocean feeding grounds of juvenile Pacific salmon Oncorhynchus spp. range over several thousand kilometers in which ocean conditions, prey quality and abundance, and predator assemblages vary greatly. Therefore, the fate of individual stocks may depend on where they migrate and how much time they spend in different regions. Juvenile (n = 6,266) and immature (n = 659) Chinook salmon Oncorhynchus tshawytscha were collected from coastal Washington to Southeast Alaska in coastal trawl surveys from February to November 1998–2008, which allowed us to reconstruct changes in stock composition for seasons and regions by means of DNA stock identification techniques. Individuals were allocated to 12 regional stocks. The genetic stock assignments were directly validated by showing that 96% of the 339 known‐origin, coded‐wire‐tagged fish were accurately allocated to their region of origin. Overall, the analyses performed in this study support the main findings of previous work based on tagging. However, given that the sample sizes for all stocks were larger and additional stocks were analyzed, we can extend those results; coastal residency of local stocks in their first year at sea with differences between smolt classes for southern stocks. Notably, yearling Chinook salmon moved quickly into waters north of the west coast of Vancouver Island, including Southeast Alaska. Furthermore, subyearling salmon were found over shallower bottom depths than yearling fish. Summer catches in all regions were dominated by Columbia River yearling fish, which suggests a rapid northward migration. In contrast, very few Columbia River subyearling fish were recovered north of Vancouver Island. Columbia River fish were a minor component of the catches in fall and winter, as fish originating from other southern stocks dominated catches off the west coast of Vancouver Island while northern British Columbia and Southeast Alaska stocks dominated northern regions during these time periods. In addition, we found no effect of hatchery origin on the distribution of fish.

Through the 137Cs mass balance method, annual consumption rates were estimated for juvenile Atlantic salmon (Salmo salar) parr and precocious males as well as for brook trout (Salvelinus fontinalis) at four sites in the Ste-Marguerite River system, Québec. With explicit age analysis, consumption rates and growth rates were derived on an individual fish and age-class basis. These represent the first consumption estimates for Atlantic salmon in the wild. Precocious males had consumption rates 1.5 times greater than nonmaturing parr, while Atlantic salmon parr consumption rates were 2.7 times greater than brook trout. There was a strong positive relationship between individual annual consumption and growth rates for Atlantic salmon and brook trout at all sites. Subsequently the concept of field maintenance ration was introduced as the intercept of consumption over growth. Maintenance rations for Atlantic salmon parr ranged from 0.010 to 0.016 g·g-1·day-1 between sites. Brook trout had maintenance rations approximately half those of Atlantic salmon at 0.0059 g·g-1·day-1. Precocious male growth efficiencies were half those of nonmaturing parr despite higher feeding and growth rates. Brook trout growth efficiencies were significantly greater than those of Atlantic salmon parr. The lower growth efficiencies observed for Atlantic salmon are likely due to increased metabolic costs associated with higher activity. On average, Atlantic salmon parr spent 2.4-fold more energy in activity than brook trout. Atlantic salmon precocious males spent 1.7 times more energy in activity than parr.