Chinook salmon diversity contributes to fishery stability and trade-offs with mixed-stock harvest

Variation among populations in life history and intrinsic population characteristics (i.e., population diversity) helps maintain resilience to environmental change and dampen interannual variability in ecosystem services. As a result, ecological variation, and the processes that generate it, is considered central to strategies for managing risks to ecosystems in an increasingly variable and uncertain world. However, characterizing population diversity is difficult, particularly in large and remote regions, which often prevents its formal consideration in management advice. We combined genetic stock identification of archived scale and tissue samples with state-space run-reconstruction models to estimate migration timing and annual return abundance for eight geographically and genetically distinct Chinook salmon populations within the Canadian portion of the Yukon River. We found that among-population variation in migration timing and return abundances resulted in aggregate return migrations that were 2.1 times longer and 1.4 times more stable than if they had composed a single homogeneous population. We then fit state-space spawner-recruitment models to the annual return abundances to characterize among-population diversity in intrinsic productivity and population size and their consequences for the fisheries they support. Productivity and carrying capacity varied among populations by approximately 2.4-fold (2.9 to 6.9 recruits per spawner) and three-fold (8800 to 27,000 spawners), respectively. This diversity implies an equilibrium trade-off between harvesting of the population aggregate and the conservation of individual populations whereby the harvest rate predicted to maximize aggregate harvests comes at the cost of overfishing ~40% of the populations but with a relatively low risk of extirpating the weakest ones. Our findings illustrate how population diversity in one of the largest salmon-producing river basins in the world contributes to fishery stability and food security in a region where salmon have high cultural and subsistence value. More generally, our work demonstrates the utility of molecular analyses of archived biological material for characterizing diversity in biological systems and its benefits and consequences for trade-offs in decision-making.

Insights into Chinook salmon movement ecology in the terminal reaches of the upper Yukon River during the spawning migration

Chinook salmon (Oncorhynchus tshawytscha, Walbaum 1792) from the upper Yukon River are highly unique, with some populations migrating nearly 3,000 km to spawning habitat near the northern range limit for the species. We conducted a 4-year study to understand the behaviour of Chinook salmon in the terminal reaches of their migration by tagging salmon with acoustic and radio transmitters in Whitehorse, Yukon, ~2800 rkm from the ocean. Various migration characteristics were quantified for Chinook salmon including en route mortality, diel behaviour, migration rates, and homing patterns, and associations with salmon origin (wild vs. hatchery), sex, size, and migration timing were explored. Salmon had high survival to spawning grounds (>98%) and migrated throughout all hours of the day, with higher proportions of nighttime movements in a smaller spawning tributary than in the Yukon River mainstem. Migration rates were faster for larger salmon as well as late-arriving salmon, which was likely necessary to ensure they had sufficient time and suitable conditions on spawning grounds to reproduce. Non-direct homing movements (e.g. tributary exploration) were more common in male salmon and considerably increased migration distance through the study area. Findings from this study may help to inform the complex international and inter-nation management of these increasingly threatened Chinook salmon populations.

High egg retention in Chinook Salmon Oncorhynchus tshawytscha carcasses sampled downstream of a migratory barrier

Barriers in rivers have the potential to severely decrease functional connectivity between habitats. Failure to pass barriers and reach natal spawning habitat may compromise individual reproductive success, particularly for semelparous, philopatric species that rely on free-flowing rivers to reach natal habitat during their once-in-a-lifetime spawning migrations. To investigate the consequences of in-river barriers on fish spawning success, we quantified egg retention and spawning effort (caudal fin wear) in female Chinook Salmon Oncorhynchus tshawytscha carcasses collected downstream of the Whitehorse Hydro Plant on the upper Yukon River and at a nearby free-flowing tributary (Teslin River) from 2018 to 2020 (~2900 km migrations). Previous studies have demonstrated that a large proportion of fish attempting to reach spawning locations upstream of the hydro plant fail to pass the associated fishway. We estimated nearly all female salmon failing to pass the hydro plant attempted spawning in non-natal habitat downstream, but that these females retained ~34% of their total fecundity compared to ~6% in females from the free-flowing river. Females downstream of the hydro plant also had lower wear on their caudal fin, a characteristic that was correlated with increased egg deposition. Egg retention did not vary across years with different run sizes, and we propose that egg retention downstream of the hydro plant was not driven by density-dependent mechanisms. Findings from this work indicate that female Chinook Salmon can still deposit eggs following failed fish passage and failure to reach natal spawning sites, though egg retention rates are considerably higher and uncertainties remain about reproductive success. We encourage researchers to incorporate carcass surveys into fish passage evaluations for semelparous species to fully account for consequences of failed passage.

Can late stage marine mortality explain observed shifts in age structure of Chinook salmon?

Chinook salmon (Oncorhynchus tshawytscha) populations have experienced widespread declines in abundance and abrupt shifts toward younger and smaller adults returning to spawn in rivers. The causal agents underpinning these shifts are largely unknown. Here we investigate the potential role of late-stage marine mortality, defined as occurring after the first winter at sea, in driving this species’ changing age structure. Simulations using a stage-based life cycle model that included additional mortality during after the first winter at sea better reflected observed changes in the age structure of a well-studied and representative population of Chinook salmon from the Yukon River drainage, compared with a model estimating environmentally-driven variation in age-specific survival alone. Although the specific agents of late-stage mortality are not known, our finding is consistent with work reporting predation by salmon sharks (Lamna ditropis) and marine mammals including killer whales (Orcinus orca). Taken as a whole, this work suggests that Pacific salmon mortality after the first winter at sea is likely to be higher than previously thought and highlights the need to investigate selective sources of mortality, such as predation, as major contributors to rapidly changing age structure of spawning adult Chinook salmon.

Signals of large scale climate drivers, hatchery enhancement, and marine factors in Yukon River Chinook salmon survival revealed with a Bayesian life history model

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.