Conservation concerns for small, relatively unproductive populations of Chinook salmon Oncorhynchus tshawytscha limit the utility of fisheries in Canada's Fraser River. To identify population‐specific migration time and to index abundance, we analyzed 4,822 fish sampled for genetic variation in 2000 and 2001 and 580 fish with coded wire tags (CWTs) caught from 1987 to 2004 in a test fishery near the river mouth. Population sizes estimated from microsatellite variation were within 3.4% of the known‐origin population composition and were unbiased in comparison with known‐origin population sizes. All but 1 of the 30 populations detected by both genetic methods and CWTs had overlapping migration times, but these times differed significantly for only 7 populations. Migration times were identified for another 23 untagged populations identified by using genetics, which resulted in the assignment of migration timing groups (peak passage) for 53 populations as spring (March–May), early summer (June), midsummer (July), late summer (August), and fall (September–October). Population abundance indices at the test fishery were significantly associated with run size at the river mouth. When populations were aggregated by geographic stock structure and migration time, the abundance indices for the test fishery explained 80% of the variation in run size. Incorporating genetic information can substantially improve the utility of test fishery data and thereby allow more‐precise management of complex population aggregates such as those in the Fraser River.

Uncertainty can be incorporated into area‐under‐the‐curve (AUC) and peak count estimates of salmon escapement by conducting replicate fish counts and developing independent escapement estimates over several years. We describe a bootstrap procedure that follows the trapezoidal AUC method and incorporates the uncertainty associated with fish counts, the shape of the spawner curve, observer efficiency, and residence time. However, the procedure does not incorporate all sources of uncertainty or address the problems posed by sparse surveys or nonzero first or last counts. For the peak count method, the procedure was modified to include the uncertainty from fish counts, observer efficiency, the expansion factor, and the timing of scheduled flights with respect to peak spawning activity. Data from spring‐run, stream‐type chinook salmon Oncorhynchus tshawytscha in the Nicola River, British Columbia, were used to demonstrate the procedures' applications. Replicate aerial spawner counts were similar and repeatable, and annual residence times were consistent over 4 years. The AUC escapement estimates were precise, reliable, and accurate when compared with independent mark–recapture escapement estimates, whereas the peak count escapement estimates were precise but less reliable and accurate. We expect that AUC escapement estimates calculated from the mean residence time of 4 years will be less biased (−8% to +5%) than peak count estimates from the mean expansion factor of 4 years (−14% to +21%). The procedures that we describe for incorporating uncertainty into AUC and peak count escapement estimation should enable fisheries biologists to more adequately assess changes in abundance and stock status.

Two distinct populations of resident killer whales (Orcinus orca) in the north‐eastern Pacific Ocean have been listed in Canada and the USA as being of conservation concern. One of the major threats recognized for these two populations is nutritional stress associated with prey abundance levels and availability. The predominance of chinook salmon (Oncorhynchus tshawytscha) in the summer diets of both killer whale populations has been shown by recent studies, and correlations between indices of chinook salmon abundance and resident killer whale (RKW) vital rates have generated hypotheses about the potential for chinook salmon abundance to limit RKW population dynamics. This study merges statistical inference derived from linkages between RKW vital rates (survival probability and fecundity rates) and chinook salmon abundance with demographic perturbation analysis and population viability analysis to address some of the pressing questions that have recently engaged the efforts of scientists and managers interested in: (1) the role of chinook salmon abundance in the population dynamics of RKW; and (2) how RKW population viability is expected to respond to changes in chinook mortality owing to harvest. Numerous interactions between the abundance of chinook salmon aggregates and RKW vital rates were found and deemed to result from predator–prey dynamics. However, the results of this present analysis also indicated that the effects of these interactions on RKW population growth and viability are relatively small and/or uncertain and in need of further research. Other factors (genetic, environmental and/or anthropogenic) could be at play limiting RKW population growth and possibly masking and confounding the detection of stronger interactions between RKW vital rates and chinook salmon abundance. Given the current state of information, it is highly uncertain whether the allocation of chinook salmon resources for RKW would be an effective management action in RKW recovery plans. © 2014 Her Majesty the Queen in Right of Canada Ecohydrology © 2014 John Wiley & Sons, Ltd.

Escapement goals for Chinook salmon, Oncorhynchus tshawytscha (Walbaum), populations tend to be highly uncertain due to variability in, and in some cases complete absence of, spawner-recruit data. A previous study of 25 populations from Oregon to Alaska demonstrated that watershed size is a good predictor of unfished equilibrium population size. Here this relationship is further developed by evaluating a series of Bayesian hierarchical models of increasing complexity. The model that performed best included a temporal random walk to account for patterns in the spawner-recruit residuals and life history-specific distributions for the productivity parameter.K E Y W O R D S : capacity, fish-habitat model, hierarchical model, life history, maximum sustainable yield, population dynamics.

Climate change and human activities are transforming river flows globally, with potentially large consequences for freshwater life. To help inform watershed and flow management, there is a need for empirical studies linking flows and fish productivity. We tested the effects of river conditions and other factors on 22 years of Chinook salmon productivity in a watershed in British Columbia, Canada. Freshwater conditions during adult salmon migration and spawning, as well as during juvenile rearing, explained a large amount of variation in productivity. August river flows while salmon fry reared had the strongest effect on productivity—our model predicted that cohorts that experience 50% below average flow in the August of rearing have 21% lower productivity. These contemporary relationships are set within long‐term changes in climate, land use, and hydrology. Over the last century, average August river discharge decreased by 26%, air temperatures warmed, and water withdrawals increased. Seventeen percent of the watershed was logged in the last 20 years. Our results suggest that, in order to remain stable, this Chinook salmon population being assessed for legal protection requires substantially higher August flow than previously recommended. Changing flow regimes—driven by watershed impacts and climate change—can threaten imperilled fish populations.