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Life-cycle models combine several strengths for estimating population parameters and biological reference points of harvested species and are particularly useful for those exhibiting distinct habitat shifts and experiencing contrasting environments. Unfortunately, time series data are often limited to counts of adult abundance and harvest. By incorporating data from other populations and by dynamically linking the life-history stages, Bayesian life-cycle models can be used to estimate stage-specific productivities and capacities as well as abundance of breeders that produce maximum sustained yield (MSY). Using coho salmon (Oncorhynchus kisutch) as our case study, we show that incorporating information on marine survival variability from nearby populations can improve model estimates and affect management parameters such as escapement at MSY. We further show that the expected long-term average yield of a fishery managed for a spawner escapement target that produces MSY strongly depends on the average marine survival. Our results illustrate the usefulness of incorporating information from other sources and highlight the importance of accounting for variation in marine survival when making inferences about the management of Pacific salmon.

Knowledge about population responses to environmental variability, including extreme climatic events, is crucial for understanding their current status and likely fate under future environmental change. The frequency and intensity of extreme events is projected to increase, especially in freshwater ecosystems. Anadromous fishes depend on freshwater habitats for spawning and juvenile rearing, making them sensitive to altered hydrologic regimes. Here, we evaluate the effect of past and projected variability in river hydrology on freshwater production of naturally spawning coho salmon populations from coastal river systems in Washington, USA. Using a stage‐based life‐cycle model, we show that juvenile production during freshwater residence depends on river flow characteristics. Most importantly, juvenile production is reduced by low minimum stream flows during summer. Based on climate model projections suggesting more extreme summer droughts in the region, we then simulate changes in river flow characteristics and quantify the effects of more frequent and severe low flows during summer on juvenile production as well as the harvest that can be sustained in these populations. Our results demonstrate that changes in hydrologic regimes due to environmental change, especially extreme low flows during summer, may significantly affect juvenile production in anadromous fishes such as coho salmon and the services these populations provide to their ecosystems and humans. Understanding population responses to extreme climatic events is thus essential for improving species conservation and risk assessments.

Fishery managers often rely on forecasts of future population abundance to set allowable harvest quotas or exploitation rates. While there has been substantial research devoted to identifying environmental factors that can predict recruitment for individual populations, such correlations often degrade over time, thereby limiting their utility for management. Conversely, examining multiple populations at once to detect shared, spatially structured patterns can offer insights into their recruitment dynamics that are advantageous for forecasting. Here, we develop a population dynamics model for natural origin coho salmon (Oncorhynchus kisutch) stocks in Washington State that leverages spatial and temporal autocorrelation in marine survival to improve one-year-ahead forecasts of adult returns. Executed in a Bayesian hierarchical integrated modelling framework, our spatiotemporal approach incorporates multiple data types and shares information among stocks to estimate key biological parameters that are informative for forecasting. Retrospective evaluation of one-year-ahead forecast skill indicated that the spatiotemporal integrated population model (ST-IPM) outperformed existing forecasts of Washington State coho salmon returns by 25–38 % on average. Moreover, the ST-IPM estimates parameters that were previously non-identifiable for many stocks, and propagates uncertainty from multiple contributing data sources into model forecasts. Our results add to a growing body of work demonstrating the utility of spatiotemporal and integrated approaches for modelling population dynamics, and the framework developed here has broad applications to the assessment and management of coho salmon in Washington State and elsewhere throughout their range.

Climate-driven changes in the oceans, such as shifts in prey timing and abundance, could influence variability in population productivity of marine fishes. For example, according to the match/mismatch hypothesis, the temporal matching of the young salmon outmigration from freshwater to the ocean relative to the timing of availability of their prey could influence their marine survival. Indeed, understanding patterns and processes of marine survival is particularly pressing in many salmon and steelhead trout populations due to recent declines. To determine whether phenological mismatches between juvenile salmonids and their prey could contribute to low ocean survival, we analyzed the migration timing and ocean survival of 22,116 tagged juvenile steelhead trout Oncorhynchus mykiss over 12 years from the Wind River, Washington State, USA. We used a Bayesian multilevel modelling approach with variable selection to assess how survival was associated with body size, river exit date, the biological spring transition date (the day when northern zooplankton first appeared in the coastal region near the Columbia River estuary), and the degree of mismatch (the effect of the interaction between individual outmigration timing and biological spring transition date). The variables with the highest probability of contributing to individual survival were fish size (100%), river exit date (99%), the interaction between year and river exit date (91%), and the biological spring transition date (64%). Fish that were larger than average at outmigration had higher ocean survival, providing further evidence that freshwater growing conditions have carryover effects on marine survival. Years with greater annual phenological mismatches such as those years with late biological spring transition dates (i.e., occurring after June 1st), or warm sea surface temperatures, had sufficiently low marine survival to compromise recovery goals. Substantial intra-annual variation in outmigration timing buffered the population from inter-annual variation in optimal outmigration timing. Collectively these findings indicate that freshwater growing conditions, migration timing, and the timing of high-quality food availability in the nearshore coastal environment work in concert to influence individual survival and annual smolt-to-adult returns.

Across the Pacific Northwest, at least 17 intensively monitored watershed projects have been implemented to test the effectiveness of a broad range of stream restoration actions for increasing the freshwater production of salmon and steelhead and to better understand fish–habitat relationships. We assess the scope and status of these projects and report on challenges implementing them. We suggest that all intensively monitored watersheds should contain key elements based on sound experimental design concepts and be implemented within an adaptive management framework to maximize learning. The most significant challenges reported by groups were (1) improving coordination between funders, restoration groups, and researchers so that restoration and monitoring actions occur based on the project design and (2) maintaining consistent funding to conduct annual monitoring and evaluation of data. However, we conclude that despite these challenges, the intensively monitored watershed approach is the most reliable me...

Changes in density-independent mortality can alter the spatial extent of populations through patch extinction and colonization, and spatial contraction may alter population productivity and compensatory capacity. Here, we analyze a time series of steelhead (Oncorhynchus mykiss) abundance and examine the hypothesis that spatial contraction can decrease compensatory capacity. Over the last 20 years, steelhead in the Keogh River have declined by an order of magnitude because of a period of poor smolt-to-adult survival. Low abundance has been associated with more depressed production of out-migrating smolts than would be expected based on traditional models of compensatory dynamics. Patterns of juvenile density over time show changes in the spatial distribution of the population. We developed a spatially explicit population model to explore spatial structure and juvenile recruitment under varying marine survival. Results suggest that spatial contraction during a period of poor marine survival can strengthen density-dependent population regulation, reducing smolt production at the watershed scale. Our results highlight that spatial contraction can alter the fundamental density-dependent relationships that define population dynamics, recovery trajectories, and sustainable harvest levels of spatially structured populations.

Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine migrations and residents that complete their life cycle in fresh water. Many populations’ anadromous components are threatened or endangered, prompting interest in understanding ecological and evolutionary processes underlying anadromy and residency. In this paper, we synthesize information to better understand genetic and environmental influences on O. mykiss life histories, identify critical knowledge gaps, and suggest next steps. Anadromy and residency appear to reflect interactions among genetics, individual condition, and environmental influences. First, an increasing body of literature suggests that anadromous and resident individuals differ in the expression of genes related to growth, smoltification, and metabolism. Second, the literature supports the conditional strategy theory, where individuals adopt a life history pattern based on their conditional status relative to genetic thresholds along with ultimate effects of size and age at maturation and iteroparity. However, except for a generally positive association between residency and high lipid content plus a large attainable size in fresh water, the effects of body size and growth are inconsistent. Thus, individuals can exhibit plasticity in variable environments. Finally, patterns in anadromy and residency among and within populations suggested a wide range of possible environmental influences at different life stages, from freshwater temperature to marine survival. Although we document a number of interesting correlations, direct tests of mechanisms are scarce and little data exist on the extent of residency and anadromy. Consequently, we identified as many data gaps as conclusions, leaving ample room for future research.

In many species, males may exhibit alternative life histories to circumvent the costs of intrasexual competition and female courtship. While the evolution and underlying genetic and physiological mechanisms behind alternative reproductive tactics are well studied, there has been less consideration of the ecological factors that regulate their prevalence. Here, we examine six decades of age composition records from thirty-six populations of sockeye salmon (Oncorhynchus nerka) to quantify associations between spawning habitat characteristics and the prevalence of precocious sneakers known as 'jacks'. Jack prevalence was independent of neutral genetic structure among stream populations, but varied among habitat types and as a function of continuous geomorphic characteristics. Jacks were more common in streams relative to beaches and rivers, and their prevalence was negatively associated with stream width, depth, elevation, slope and area, but positively related to bank cover. Behavioural observations showed that jacks made greater use of banks, wood and shallows than guard males, indicating that their reproductive success depends on the availability of such refuges. Our results emphasize the role of the physical habitat in shaping reproductive tactic frequencies among populations, likely through local adaptation in response to variable fitness expectations under different geomorphic conditions.

Wild, downstream-migrating cutthroat trout, Oncorhynchus clarkii clarkii, smolts and adults were captured at a weir in Big Beef Creek, Hood Canal, Washington, surgically implanted with acoustic tags and tracked to identify spring and summer movements using stationary receivers in order to test the assumption that the species moves little while in marine waters. Overall, 93-96% migrated from the stream into the east side of the long narrow fjord, where they dispersed north and south along the shoreline. Most O. c. clarkii were detected nearshore within 10 km of the release site, with declining detection rates to 77 km. Over one-third (36%) crossed c. 2-4 km of deep water to the other side but only one O. c. clarkii left the Hood Canal basin. Movements and behaviour patterns did not differ between smolts and adults but cluster analysis revealed two modes of distribution, here categorized as residents and migrants. Within these categories of overall distribution, a range of finer-scale behaviour patterns was observed, including sedentary individuals, daily moving between proximate sites and more continuous long-distance travel. Diel movement patterns varied markedly among individuals but overall activity increased near dawn, peaked around mid-day and declined but continued at night. These patterns contrast with sympatric and closely related steelhead trout, Oncorhynchus mykiss, providing new insights into the diversity of salmonid behaviour.

Native Coastal Cutthroat Trout Oncorhynchus clarkii clarkii and Coastal Steelhead O. mykiss irideus hybridize naturally in watersheds of the Pacific Northwest yet maintain species integrity. Partial reproductive isolation due to differences in spawning habitat may limit hybridization between these species, but this process is poorly understood. We used a riverscape approach to determine the spatial distribution of spawning habitats used by native Coastal Cutthroat Trout and Steelhead as evidenced by the distribution of recently emerged fry. Molecular genetic markers were used to classify individuals as pure species or hybrids, and individuals were assigned to age-classes based on length. Fish and physical habitat data were collected in a spatially continuous framework to assess the relationship between habitat and watershed features and the spatial distribution of parental species and hybrids. Sampling occurred in 35 reaches from tidewaters to headwaters in a small (20 km2) coastal watershed in W...

Hidrostal pumps have been successfully employed in live fish transport, yet their effectiveness in fish passage is incompletely understood. This study investigates juvenile salmonid mortality in experimental passage trials through Hidrostal pumps at an agricultural pump facility in Washington State, USA. The effects of impeller pitch, rotational speed and fish body size on passage survival were examined. Hatchery-reared salmonids (Oncorhynchus mykiss (Walbaum) and Oncorhynchus kisutch (Walbaum)) were introduced to low- and high-pitch impeller assemblies operating at two speeds. Instantaneous mortality rates ranged from 0 to 4% for high-pitch trials and from 3 to 10% for low-pitch trials. Larger fish experienced sublethal injury at higher rates (approxi- mately 60% injured) than smaller fish (approximately 23% injured) and exhibited greater susceptibility to injury at higher pump speed. Injury between trials was compared by ranking according to severity and summed for each treatment; greater injury severity was found for the low-pitch impeller and from higher rotational speeds. Although injury and mortality rates to fish passing through Hidrostal pumps may be reduced through the use of higher-pitch impellers and lower operational speeds, the use of pump-bypass facilities may be warranted where acceptable impact thresholds are low.

The process of salmon colonization in the upper Cedar River and Rock Creek, Washington, following the installation of a fish ladder at Landsburg Diversion Dam in 2003, offered an opportunity to measure the effects of interspecific interactions on the dynamics of resident fish populations. Rapid recolonization by Coho Salmon Oncorhynchus kisutch provided a natural experiment to determine the influence of Coho Salmon densities on the growth, movement, and survival of resident Coastal Cutthroat Trout O. clarkii clarkii relative to other abiotic and biotic factors such as habitat quality, environmental conditions, and conspecific density. During 14 seasonal sampling events from 2005 to 2009, we PIT-tagged 1,851 and recaptured 394 Cutthroat Trout in Rock Creek, collected habitat data, enumerated fish populations, and monitored fish movements with PIT tag antenna arrays. Trout growth varied significantly among seasons and was greatest during spring and early summer. Mean juvenile Coho Salmon density in summer and fall increased eightfold from 0.04 to 0.32 and from 0.08 to 0.68 fish/m2, respectively, approaching levels seen in established populations, but did not explain variation in trout growth, movement, or survival. Summer growth of trout parr and fry were both negatively correlated with the density of conspecifics but were positively correlated with total salmonid density. Additionally, trout parr growth was positively correlated with stream discharge, whereas trout fry growth was negatively correlated with initial size and declined during the course of the study. However, abiotic and biotic explanatory variables accounted for little of the variation in trout growth, movement, and survival, suggesting that a great deal of individual variation exists. Overall, trout were largely unaffected by Coho Salmon colonists despite large increases in juvenile Coho Salmon density, though this may change if salmon populations continue to grow.