Interbreeding between hatchery-reared and wild salmon raises concerns that hatchery fish may increase the frequency of maladapted alleles in wild populations, yet divergence between hatchery populations and their original sources remains poorly understood. We explored phenotypic divergence in reproductive traits between hatchery and source populations of pink (Oncorhynchus gorbuscha) and coho salmon (Oncorhynchus kisutch) in Southeast Alaska, hypothesizing that relaxed selection in the hatchery would result in males with smaller snouts and humps and females with larger gonadosomatic indices and smaller, less nutrient-dense eggs. Findings partly confirmed these expectations. Our hypotheses were supported in coho salmon females and odd-year pink salmon males, but results from coho salmon males opposed our hypotheses and we observed no phenotypic divergence in even-year pink salmon, possibly due to high gene flow between hatchery and wild populations. These mixed results indicate significant yet variable phenotypic differences between hatchery and wild salmon in key reproductive traits. Our study provides a rare comparison of how hatchery rearing affects reproductive traits between species with different life histories in Southeast Alaska.

While declines in size, age at maturity, and productivity in Chinook populations have been documented in several large-scale comprehensive studies, changes in growth phenology that might underlie these phenomena have examined one to two populations at a time. We measured growth in freshwater (FW) and in the 1st through 4th year in salt water (SW1–SW4) from > 17,000 scales sampled from 14 populations across Alaska, 1966–2015. We examined correlations between increments within brood years, populations, and ages at maturity and estimated population-level growth and differences in growth for fish that matured at age 5 vs. age 6. Growth generally declined with additional years at sea. SW1 growth was above average for Bering Sea populations and below average for Gulf of Alaska populations, particularly in Cook Inlet. SW2 growth was clinal, decreasing from southeast to northwest. SW3 and SW4 growth varied regionally (Cook Inlet and Prince William Sound > Bering Sea > Southeast). Fish that matured at age 5 had higher incremental growth than those that matured at age 6, and these differences increased with each increment. Populations with greater age 5 than 6 SW1 growth had greater SW2 growth, and populations with greater age 5 than 6 SW3 growth had greater SW4 growth. Within brood years, FW growth was positively correlated with SW2 growth, but high SW2 growth was negatively correlated with SW4 growth. Our results highlight the need for research on mechanisms linking Chinook salmon growth and maturation in a rapidly changing climate, with potential negative consequences for demography.

Hatcheries are vital to many salmon fisheries, with inherent risks and rewards. While hatcheries can increase the returns of adult fish, the demographic and evolutionary consequences for natural populations interacting with hatchery fish on spawning grounds remain unclear. This study examined the impacts of stray hatchery-origin pink salmon on natural population productivity and resilience. We explored temporal assortative mating dynamics using a quantitative genetic model that assumed the only difference between hatchery- and natural-origin adults was their return timing to natural spawning grounds. This model was parameterized with empirical data from an intensive multi-generational study of hatchery-wild interactions in the world's largest pink salmon fisheries enhancement program located in Prince William Sound, Alaska. Across scenarios of increasing hatchery fish presence on spawning grounds, our findings underscore a trade-off between demographic enhancement and preservation of natural population diversity. While enhancement bolstered natural population sizes towards local carrying capacities, hatchery introgression reduced variation in adult return timing by up to 20%. Results indicated that hatchery-origin alleles can rapidly assimilate into natural populations, despite the reduced fitness of hatchery fish attributable to phenotypic mismatches. These findings elucidate the potential for long-term demographic and evolutionary consequences arising from specific hatchery-wild interactions, emphasizing the need for management strategies that balance demographic enhancement with the conservation of natural diversity.

Management of anadromous salmon stocks is usually based on an estimate of the spawner-recruitment relationship. A wide variety of estimation approaches have been developed, from simple to complex, and some worthwhile methodologies and auxiliary data are underutilized. The types and quality of the data available determine the most appropriate assessment methodology and the reliability of the assessment results. The management strategies available and the performance of these strategies are likewise highly dependent on the available data. This review gives an overview of the range of assessment methodologies, from the ad-hoc to hierarchical Bayesian state-space approaches. It emphasizes the central role of data; data types, data deficiencies, auxiliary information such as environmental indices, habitat characteristics, and similar stocks, and the effects of the data on the quality of guidance to managers.

Hatcheries release >4.5 billion juvenile Pacific salmon (Oncorhynchusspp.) into the North Pacific Ocean annually, raising concerns about competition with wild salmon populations. We used retrospective scale analysis to investigate how the growth of chum salmon (O. keta) from western Alaska is affected by the abundance of chum salmon from Japanese hatcheries and wild pink salmon (O. gorbuscha) from the Russian Far East. Over nearly five decades, the growth of Kuskokwim River chum salmon was negatively correlated with the abundance of Japanese hatchery chum salmon after accounting for the effects of sex and spring/summer sea-surface temperature in the Bering Sea. An effect of wild eastern Kamchatka pink salmon abundance on the growth of Kuskokwim River salmon was detectable but modest compared to the intraspecific competitive effect. A decrease in Japanese hatchery chum salmon releases in 2011-2013 was not associated with increased growth of Bering Sea chum salmon. However, the abundance of wild chum salmon from the Russian Far East increased during that time, possibly obscuring reduced competition with hatchery chum salmon. Our results support previous evidence that chum salmon are affected by intraspecific competition, and to a lesser extent interspecific competition, in the North Pacific, underscoring that the effects of salmon hatchery production transcend national boundaries.

While conservation and fisheries management are often concerned with changes in population abundance and distribution, shifts in population age–size structure are commonly observed in response to human and environmental stressors. Chinook salmon (Oncorhynchus tshawytscha) have experienced widespread declines in mean age and size throughout their North American range. We investigated the consequences of declines in body size for spawner reproductive potential in terms of total egg mass per female. Our case study is the Yukon River where Chinook salmon have supported subsistence, commercial, and recreational fisheries. Using historical observations on individual body size from throughout the Yukon River and the relationship between female size and total egg mass from the Canadian portion, we estimate a decline in average female reproductive potential of 24%–35% since the 1970s. Because spawner abundances and the population sex ratio have not shown clear trends over time, our results suggest a reduced total population reproductive potential. Changes in spawner quality should be considered when developing management reference points, and conservation of population demographic structure may be necessary to sustain productive Chinook salmon systems.

Background Archival tags that measure the Earth’s magnetic field could provide a new geolocation method for demersal fishes in the North Pacific Ocean. However, the presence of local magnetic field anomalies caused by geological formations such as volcanic rock and temporal fluctuations from solar storms could complicate its use in some high-latitude areas of the North Pacific Ocean. We assessed the potential value of adding geomagnetic data to a depth-based state-space model for geolocation of demersal fishes in Glacier Bay National Park, USA, a high-latitude magnetic anomaly area. We developed a high-resolution (100 m) magnetic field map of the study area and assessed in situ tag resolution by deploying 5 geomagnetic archival tags on a stationary mooring for 8 months. We compared performance of 4 theoretical geomagnetic tag measurement resolutions (low = ± 1000 nT, medium = ± 500 nT, high = ± 300 nT, and very high = ± 150 nT), 2 map resolutions (coarse- or fine-scale), and 5 methods of geomagnetic variance specification by estimating locations of simulated random walk trajectories under the different treatment scenarios using a hidden Markov model. Results Geomagnetic data improved model performance for both fine-scale and coarse-scale magnetic maps when tag resolutions were medium to very high and geomagnetic variance specification was based on error between measured and mapped values instead of study area attributes such as slope or roughness. Overall, the best model performance was observed for the highest tag resolution, the fine-scale map, and variance based on anomaly magnitudes. However, the coarse-scale map with a constant variance of 165 nT resulted in improvements over depth alone for all tag resolutions. In situ testing of mooring data suggests that the precision of the geomagnetic archival tags was comparable to the low and medium tag measurement resolutions tested in simulations, but variation in performance was high among tags. Conclusions Our results suggest that inclusion of geomagnetic data could improve geolocation of demersal fishes in the North Pacific Ocean, but improvements to geomagnetic tags and additional information on magnetic field values measured at the seafloor compared to the sea surface are needed to ensure its utility.

Pacific salmon productivity is influenced by ocean conditions and interspecific interactions, yet their combined effects are poorly understood. Using data from 47 North American sockeye salmon (Oncorhynchus nerka) populations, we present evidence that the magnitude and direction of climate and competition effects vary over large spatial scales. In the south, a warm ocean and abundant salmon competitors combined to strongly reduce sockeye productivity, whereas in the north, a warm ocean substantially increased productivity and offset the negative effects of competition at sea. From 2005 to 2015, the approximately 82 million adult pink salmon (Oncorhynchus gorbuscha) produced annually from hatcheries were estimated to have reduced the productivity of southern sockeye salmon by ∼15%, on average. In contrast, for sockeye at the northwestern end of their range, the same level of hatchery production was predicted to have reduced the positive effects of a warming ocean by ∼50% (from a ∼10% to a ∼5% increase in productivity, on average). These findings reveal spatially dependent effects of climate and competition on sockeye productivity and highlight the need for international discussions about large-scale hatchery production.

The past 50 years have seen declines in size and age of adult Chinook salmon (Oncorhynchus tshawytscha) along its entire eastern Pacific range, including Alaska. Ohlberger et al. (2018) summarized five hypotheses for the observed declines, including four previously proposed hypotheses: 1) size-selective harvest; 2) influence of hatchery production; 3) competition among Pacific salmon populations in the ocean; and 4) climate/environmental variation. The authors additionally proposed a new hypothesis: 5) increased predation upon older Chinook salmon. While none of these hypotheses are mutually exclusive, Ohlberger et al. (2018) concluded that hypotheses 1–4 were insufficient to explain the range-wide declines. Here, we suggest that hypothesis 4, climate variation, plays an important role for earlier maturation of Chinook salmon, at least towards the northern part of its range. We summarize two previously published studies (Siegel et al. 2017, 2018) demonstrating that environmental forcing, as expressed by sea surface temperature (SST), is associated with earlier maturation and thus smaller adult size of Chinook salmon.

This study combines a multi-method approach to structured expert judgment with market valuation to forecast fisheries damages from introduced invasive species. The method is applied to a case study of Alaska’s first submersed aquatic invasive plant, Elodea spp., threatening Alaska’s salmon fisheries. Assuming that Elodea spp. remains unmanaged, estimated mean damages to commercial sockeye fisheries aggregated across Alaska amount to a potential $159 million annually with a 5% chance of exceeding $577 million annually ($2015 USD). The associated mean loss of natural capital amounts to $5.1 billion cumulatively over the next 100 years reaching $400 million after 10 years. Results from the expert elicitation indicate that there is a 35% chance of positive net benefits associated with the believed positive effects of Elodea spp. on sockeye salmon (Oncorhynchus nerka). Despite the potential for positive net gains, the magnitude of the most probable damage estimate may justify substantial investment in keeping productive freshwater systems free of aquatic invasive species. The damage estimate for Alaska is significantly larger than similar estimates in the Great Lakes where ecosystems are already impaired by multiple aquatic invasive species, underscoring the value of keeping functioning ecosystems with global market value productive. This study is the first to estimate ecosystem service loss associated with introduction of an aquatic invasive species to freshwater habitat that supports the world’s most valuable wild sockeye salmon fisheries. Important policy implications related to natural resource management and efficient allocation of scarce resources are discussed This research article is available in Journal of Ocean and Coastal Economics: https://cbe.miis.edu/joce/vol6/iss1/2

Recent reductions in the run sizes o f Chinook Salmon Oncorhynchus tshawytscha in Southeast Alaska have resulted in social and economic hardships within the region. Pacific salmon yearclass strength may be determined by size-selective processes during the early marine phase of their life cycle; however, the relative importance of growth during freshwater and marine residence in determining recruitment success is unknown. A scale-based retrospective analysis was conducted to examine the effects of freshwater and annual marine growth and early marine conditions on survival to reproductive maturity for female Chinook Salmon by brood year (BY) in the Taku (BYs 1979 1985, 1990 1999, 2002 2004) and Unuk (BYs 1981 1983, 1986 1988, 1994 2003, 2005 2006) rivers. First-year marine growth was positively related to survival and total return for Chinook Salmon stocks from both systems. Growth during freshwater residence (i.e., size-at-ocean entry) was not related to survival or total return o f either stock. In addition, there was a positive relationship between marine survival of Unuk River Chinook Salmon and sea-surface temperatures in Upper Chatham Strait, Icy Strait, and Auke Bay M onitor (P = 0.04) during early marine residence. The results o f my research highlight the importance of growth and marine conditions during the first year at sea in determining the survival o f Chinook Salmon in Southeast Alaska and suggest that current declines in run sizes and survival of stocks within this region may be the attributed to poor growth conditions or growth during early marine residence.

We applied an empirical model to predict hatching and emergence timing for 25 western Alaska sockeye salmon (Oncorhynchus nerka) populations in four lake-nursery systems to explore current patterns and potential responses of early life history phenology to warming water temperatures. Given the temperature regimes sockeye salmon experienced during development, we predicted hatching to occur in as few as 58 days to as many as 260 days depending on spawning timing and temperature. For a focal lake spawning population, our climate–lake temperature model predicted a water temperature increase of 0.7 to 1.4 °C from 2015 to 2099 during the incubation period, which translated to a hatching timing that was 16 to 30 days earlier. The most extreme warming scenarios shifted development to approximately 1 week earlier than historical minima and thus climatic warming may lead to only modest shifts in phenology during the early life history stage of this population. The marked variation in the predicted timing of hatching and emergence among populations in close proximity on the landscape may serve to buffer this metapopulation from climate change.

State-space geolocation models can provide valuable information on the large-scale movements of many fish species. The sensitivity of such complex models to model assumptions and fixed parameters is rarely assessed quantitatively, yet is important for interpretation of results and adaptation for new species and different geographic regions. We hypothesized that parameterization and performance of a discrete Hidden Markov Model (HMM) with a Gaussian depth-based data likelihood for demersal fishes first implemented in the flat terrain of the North Sea would be affected by the more heterogeneous depths found in the North Pacific Ocean. We ran the HMM on depth data from simulated random walk movement trajectories in flat, sloping, and heterogeneous study areas in the North Pacific Ocean where known depth distributions in each model grid cell were provided by high-resolution (5 m) multibeam bathymetry data. Performance was compared among different data likelihood specifications and grid sizes in each area. We found that model performance decreased when grid cell depth distributions departed from normal distributions. Performance decreased with increasing grid size in the heterogeneous and sloping study areas but not the flat study area. A new method for specifying grid cell depth variance based on study area slope performed better than the standard method of obtaining variance from adjacent grid cell values for larger grid sizes in heterogeneous and sloping areas. Overall model performance was highest in the heterogeneous and sloping areas at small grid sizes and in the flat area at large grid sizes. The estimated value of diffusion was also sensitive to bathymetric heterogeneity and variance-specification method. These results suggest that the degree of study area heterogeneity should be considered when choosing fixed parameters such as likelihood and grid size, and when interpreting the model results. In addition, this approach demonstrates the need for sensitivity analyses when using the model on a new species and in a new study area.

Understanding how species might respond to climate change involves disentangling the influence of co-occurring environmental factors on population dynamics, and is especially problematic for migratory species like Pacific salmon that move between ecosystems. To date, debate surrounding the causes of recent declines in Yukon River Chinook salmon (Oncorhynchus tshawytscha) abundance has centered on whether factors in freshwater or marine environments control variation in survival, and how these populations at the northern extremity of the species range will respond to climate change. To estimate the effect of factors in marine and freshwater environments on Chinook salmon survival, we constructed a stage-structured assessment model that incorporates the best available data, estimates incidental marine bycatch mortality in trawl fisheries, and uses Bayesian model selection methods to quantify support for alternative hypotheses. Models fitted to two index populations of Yukon River Chinook salmon indicate that processes in the nearshore and marine environments are the most important determinants of survival. Specifically, survival declines when ice leaves the Yukon River later in the spring, increases with wintertime temperature in the Bering Sea, and declines with the abundance of globally enhanced salmon species consistent with competition at sea. In addition, we found support for density-dependent survival limitations in freshwater but not marine portions of the life cycle, increasing average survival with ocean age, and age-specific selectivity of bycatch mortality in the Bering Sea. This study underscores the utility of flexible estimation models capable of fitting multiple data types and evaluating mortality from both natural and anthropogenic sources in multiple habitats. Overall, these analyses suggest that mortality at sea is the primary driver of population dynamics, yet under warming climate Chinook salmon populations at the northern extent of the species' range may be expected to fare better than southern populations, but are influenced by foreign salmon production.

Local adaptation has been demonstrated in spatially or temporally distant animal populations but seldom in proximate populations. To address the scale of local adaptation in Pacific salmon (Oncorhynchus spp.), two generations of hybrids between temporally separated spawning segments were made in a population of pink salmon (O. gorbuscha) and compared with controls to evaluate the genetic architecture underlying adult migration time and to test for declines in marine survival that resulted from outbreeding depression. Bayesian mixed-effects models revealed that adult migration times in hybrid lines were intermediate to those of controls and that additive sources of genetic variation were significant, thereby indicating that local adaptation has acted on additive genetic variation in shaping this trait. Similarly, a line cross analysis revealed that an additive model best described the genetic architecture of adult migration time. In contrast, marine survival was generally similar between control and hybrid lines, which suggested that the effect of outbreeding upon marine survival was minimal at such a fine scale of genetic divergence. The implications of these results are that (a) local adaptation can facilitate genetic divergence of life history traits between proximate subpopulations; (b) artificial relaxation of natural barriers to gene flow can cause maladaptive shifts in life history traits; and (c) wild populations may harbour fine-scale adaptive variation that supports productivity and sustainability.

We explored the nature of declines in size and age at maturity in 2 populations of Chinook salmon Oncorhynchus tshawytscha in western Alaska, USA, using multidimensional probabilistic maturation reaction norms (PMRNs) accounting for growth history. Individual growth histories informed by retrospective scale analysis were used to construct PMRNs and to describe the relative influence of different life-history periods on age at maturity. Similar results were found in both populations. Models accounting for growth history uniformly outperformed size-at-age models, suggesting the importance of growth history for the determination of maturation. The second year of marine growth was found to have a disproportionate influence on the age at maturity in both sexes. Males tended to grow more than females in length during the second year at sea, possibly as a consequence of females storing more energy in preparation for the high cost of female gonad development. Finally, we found that growth thresholds for maturation have shown a long-term decline in both sexes. This suggests that declines in the average age at maturity of western Alaskan Chinook salmon may have been caused in part by adaptation to environmental or fisheries-induced selection.

1. Theory and previous studies have shown that commercial fishers with a diversified catch across multiple species may experience benefits such as increased revenue and reduced variability in revenue. However, fishers can only increase the species diversity of their catch if they own fishing permits that allow multiple species to be targeted, or if they own multiple single-species permits. Individuals holding a single permit can only increase catch diversity within the confines of their permit (e.g. by fishing longer or over a broader spatial area). 2. Using a large dataset of individual salmon fishers in Alaska, we build a Bayesian variance function regression model to understand how diversification impacts revenue and revenue variability, and how these effects have evolved since the 1970s. 3. Applying these models to six salmon fisheries that encompass a broad geographic range and a variety of harvesting methods and species, we find that the majority of these fisheries have experienced reduced catch diversity through time and increasing benefits of specialization on mean individual revenues. 4. One factor that has been hypothesized to reduce catch diversity in salmon fisheries is large-scale hatchery production. While our results suggest negative correlations between hatchery returns and catch diversity for some fisheries, we find little evidence for a change in variability of annual catches associated with increased hatchery production. 5. Synthesis and applications. Despite general trends towards more specialization among commercial fishers in Alaska, and more fishers exclusively targeting salmon, we find that catching fewer species can have positive effects on revenue. With increasing specialization, it is important to understand how individuals buffer against risk, as well as any barriers that prevent diversification. In addition to being affected by environmental variability, fishers are also affected by economic factors including demand and prices offered by processors. Life-history variation in the species targeted may also play a role. Individuals participating in Alaskan fisheries with high contributions of pink salmon - which have the shortest life cycles of all Pacific salmon - also have the highest variability in year-to-year revenue.

In salmon populations, local adaptation to seasonally varying incubation temperature is characterized by temperature-adjusted development times [measured in degree days – accumulated temperature units (ATUs)] that differ between control and F1 hybrid crosses that were made between temporally separated population segments, a contrast not expected in a panmictic population. We examined adaptation of embryo development time to seasonally cooling temperature in a population of pink salmon by estimating genetic components of variation in control and hybrid F1 crosses made between members of early- and late-spawning subpopulations, and replicated our observations in independent odd- and even-year brood lines. In each brood line, both sire and dam components of variation of development time were significant and accounted for a substantially larger portion of variation than their interactions, which suggested that natural selection has acted primarily on additive genetic variation. The implications of these results are that (1) spatially or temporally proximate salmon populations may be structured by distinct adaptations; (2) artificial relaxation of local geneflow barriers may lead to depression of fitness; and (3) populations of salmon genetically structured by local adaptation may carry variation that enhances their persistence during rapid climate change.

The Exxon Valdez oil spill occurred in March 1989 in Prince William Sound, Alaska, and was one of the worst environmental disasters on record in the United States. Despite long-term data collection over the nearly three decades since the spill, tremendous uncertainty remains as to how significantly the spill affected fishery resources. Pacific herring (Clupea pallasii) and some wild Pacific salmon populations (Oncorhynchus spp.) in Prince William Sound declined in the early 1990s, and have not returned to the population sizes observed in the 1980s. Discerning if, or how much of, this decline resulted from the oil spill has been difficult because a number of other physical and ecological drivers are confounded temporally with the spill; some of these drivers include environmental variability or changing climate regimes, increased production of hatchery salmon in the region, and increases in populations of potential predators. Using data pre- and post-spill, we applied time-series methods to evaluate support for whether and how herring and salmon productivity has been affected by each of five drivers: (1) density dependence, (2) the EVOS event, (3) changing environmental conditions, (4) interspecific competition on juvenile fish, and (5) predation and competition from adult fish or, in the case of herring, humpback whales. Our results showed support for intraspecific density-dependent effects in herring, sockeye, and Chinook salmon, with little overall support for an oil spill effect. Of the salmon species, the largest driver was the negative impact of adult pink salmon returns on sockeye salmon productivity. Herring productivity was most strongly affected by changing environmental conditions; specifically, freshwater discharge into the Gulf of Alaska was linked to a series of recruitment failures—before, during, and after EVOS. These results highlight the need to better understand long terms impacts of pink salmon on food webs, as well as the interactions between nearshore species and freshwater inputs, particularly as they relate to climate change and increasing water temperatures.