Life history differences between natural and hatchery-origin winter-run Chinook present opportunities and challenges for managing the endangered species

By Emily Chen, Katherine Lumahan, Rachel Johnson, Corey Phillis, George Whitman, Anna Sturrock, Will Satterthwaite, and Stephanie Carlson

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Wild Pacific salmon and trout exhibit complex variation in completing their life cycle. Within a single population, some individuals leave their natal (birth) streams soon after they emerge from the nest to begin their seaward migrations, while others remain for several months or years before migrating downstream. During their downstream migration, areas throughout a watershed, such as tributaries, floodplains, and estuaries, can serve as habitat for juvenile salmon to rear and grow. Chinook salmon, in particular, have adaptable and variable life histories that allow them to spread out across the landscape and rear in diverse environments and at different times. This spreading of the population reduces competition in any one environment and increases population productivity and resilience to disturbance.

Salmon raised in hatcheries, on the other hand, are confined to the hatchery until their release. In our recent study¹ in the Sacramento River Basin, we evaluated the migratory patterns of hatchery Chinook salmon after their release and compared these patterns to those of Chinook salmon born in the river (i.e., “natural-origin”). We reconstructed their movement paths using otoliths, ear bones of fish that record, much like rings on a tree, the growth history of individual fish. The otolith chemical composition reflects the chemistry of the waters in which the fish was growing during that period of its life and thus provides a record of the different habitats the fish used during rearing and outmigration. Otoliths were collected from adult carcasses encountered by US Fish and Wildlife Service, California Department of Fish and Wildlife, and Pacific States Marine Fisheries Commission surveyors during spawning surveys and at Livingston Stone National Fish Hatchery by USFWS. Annual estimates of adult abundance and the biological samples collected from these programs are vital to understanding the status of salmon populations and reveals insights into their early lives, and which habitats they relied on as juveniles.

Cross section of an otolith viewed from under a microscope. It is gray and has the appearance of the cross section of a tree trunk's growth rings. — Figure 1. This study involved analyzing the otoliths (pictured here under a microscope) collected from adult carcasses. Like rings on a tree, otoliths grow incrementally (daily) and proportionally to body size. Otoliths incorporate elements from the surrounding water chemistry as they grow, making it possible to determine the habitat used by an individual during a specific period of life. Figure from Chen et al. (2025).

Using these otoliths, we reconstructed the movement and the different habitats used by fish born in the hatchery versus the river. We found that while natural-origin salmon spread out across the whole landscape, hatchery Chinook salmon spent less time exploring different off-channel habitats. Most hatchery Chinook salmon migrated through the system quickly and were found to rear only in the mainstem Sacramento River. In contrast, we found evidence of winter-run Chinook salmon born in the mainstem Sacramento River veering off and using multiple tributaries, including those in the Lassen region (e.g., possibly Battle Creek, Deer Creek, Mill Creek), Feather River, American River, and the Sacramento-San Joaquin Delta, before entering the ocean. These individuals, while migrating downstream, swam against the tributary flows entering the mainstem Sacramento River, stopping and rearing along the migration route. While 48% of returning natural-origin winter-run Chinook salmon were found to use these ‘non-natal habitats’, only 4% of returning hatchery Chinook salmon were found to have used those same habitats.

Figure from the manuscript showing Proportion on the y-axis and Escapement Year on the x-axis. — Figure 2. While natural-origin Chinook salmon were found to use a diversity of non-natal habitats (left), hatchery Chinook salmon were mostly only found to use the mainstem (right). The run (escapement) years 2008, 2009, and 2016 were excluded from the analysis of hatchery samples because of limited sample sizes in those years. Figure from Chen et al. (2025).

The study was performed on endangered winter-run Chinook salmon in the Sacramento River. Winter-run Chinook salmon are unique in their life history as they spawn in the summer, whereas most salmon spawn in the fall. Their unique life history is only possible because of the nature of the Sacramento River Basin. Cold spring-fed streams located in the mountains of the upper Sacramento Basin remain cold through the summer when most areas of the basin are too warm for Chinook salmon. These upper rivers, such as the Pit River, McCloud River, and upper Sacramento River, are now inaccessible to Chinook salmon due to Shasta and Keswick Dams. The inability for winter-run to spawn in their ancestral streams is the primary reason for their decline and high risk of extinction.

Landscape view of a rushing river. There are boulders and rocks in the river and a lush green forest along the banks. A small wooden bridge crossing the river is in the distance. — Figure 3. The Winnemem Waywaket (McCloud River) pictured here is one of the cold spring-fed rivers that are currently inaccessible to salmon due to dams downstream. With increasing drought frequencies and high summer temperatures, preserving and giving salmon access to year-round cold water will be crucial to their survival in the changing climate. There are multiple ongoing efforts to reintroduce winter-run Chinook salmon to these streams, led by the Winnemem Wintu Tribe, NOAA, CDFW, and USFWS, and many supporting agencies and institutions. Photo by Rachael Ryan.

The results of our study provide important information to managers and conservationists for winter-run Chinook salmon. Because of their accessibility, hatchery salmon are often used as surrogates for natural-origin fish in research and monitoring. Salmon from hatcheries provide a unique opportunity to study and understand the biology of salmon and some insights into the conditions salmon in the wild experience. For winter-run Chinook salmon, data collected using tagged hatchery fish provide scientists and managers with information that is applied to managing and conserving the natural-origin population. This includes informing models that affect the state and federal water projects in the Delta. However, our study demonstrates some ways that fish reared in hatcheries may not accurately reflect the biology and ecology of wild fish. Hatchery practices during the broodstock selection, fry cultivation, and release processes can alter the behavior and life history of those juveniles. Identifying and considering differences between hatchery- and natural-origin salmon is critical when applying insight from data collected from hatchery fish to minimize biases in management models.

Because natural-origin fish use the watershed more extensively and for longer durations, they have greater habitat needs than what would be suggested from data collected on hatchery fish alone. Endangered species, including winter-run Chinook salmon, and their habitats are protected under the Endangered Species Act. Currently, the critical habitat for winter-run Chinook salmon designated by the Endangered Species Act includes only the mainstem migratory corridor – but does not include the tributaries and most of the Delta, where they rear and grow before entering the ocean. While most of the habitats used by the hatchery population are protected (i.e., the mainstem migratory corridor) under the Endangered Species Act, the habitats used by nearly half of natural winter-run Chinook salmon are not, limiting the ability of the Endangered Species Act to apply to its intended extent. A growing body of work^1,2,3 provides evidence on the importance of non-natal habitats in tributaries and the Delta to winter-run Chinook salmon, and suggests a need to update the critical habitat designation under the Endangered Species Act and explicitly consider winter-run Chinook salmon in these non-natal habitats during habitat restoration and environmental flow management to better support the productivity and resilience of winter-run Chinook salmon.

Chinook salmon historically flourished in the Sacramento-San Joaquin River Basin, despite the Basin being located at the very southern end of the species’ range. Despite extensive habitat loss and degradation, the Sacramento-San Joaquin River Basin continues to provide a mosaic of rich habitats that are capable of producing very large and numerous runs of Chinook salmon. Although hatchery programs can produce large numbers of juvenile salmon, they do not compare to the volume of salmon that would be produced in intact and functioning rivers. Furthermore, altered and homogenous behaviors and life histories among hatchery individuals will more frequently result in volatile and inconsistent returns of hatchery populations.⁴ The ability of Chinook salmon to express diverse life histories and distribute across suitable habitats is an evolved trait of the species that contributes to their productivity and resilience to disturbance, including more frequent droughts caused by climate change. Providing this mosaic of habitats is the best strategy for rebuilding this and other Chinook populations in California. By restoring and maintaining habitat diversity and river connection through environmental flow management, watersheds can provide habitats that produce abundant, stable, and resilient salmon runs.

Acknowledgements

This study was possible because of existing U.S. Fish and Wildlife Service and California Department of Fish and Wildlife monitoring programs, and the numerous individuals involved in collecting and managing biological samples across many years. We thank the U.S. Fish and Wildlife Service, California Department of Fish and Wildlife, and Pacific States Marine Fisheries Commission staff for raising the fish, surveying escapement, and collecting otoliths. Assistance with otolith preparation and isotope analysis was provided by Pedro Morais. We thank Elise Allen and Audrey Kuptz for their contribution to collecting the otolith increment data.

About the Authors

Emily Chen completed a PhD in Environmental Science, Policy, and Management at UC Berkeley in 2024 with a dissertation focused on the life history and population dynamics of Chinook salmon in the Central Valley. She is currently a research scientist at California Trout focused on the population ecology of salmonids in California and using quantitative tools to inform conservation and management.

Katherine Lumahan was an otolith research assistant who majored in Molecular Environmental Biology and graduated from UC Berkeley in 2023. She is currently a medical student at Drexel University College of Medicine.

Rachel Johnson is a Program Lead with NOAA Fisheries, Fisheries Ecology Division, and Center for Watershed Sciences at UC Davis with a research lab group focused on endangered and commercial species, specialized in developing isotope tools to understand their migration, habitat use, contaminant exposure, and connectivity.

Corey Phillis is a Senior Resource Specialist at the Metropolitan Water District of Southern California with expertise in salmon evolutionary ecology and salmon migration, particularly in the context of water project management decisions.

George Whitman is a Staff Researcher at the Center for Watershed Science, UC Davis that specializes in understanding the life history of fishes from their otoliths and other structures.

Anna Sturrock is an Associate Professor at the University of Essex in the UK and Center for Watershed Sciences affiliate. Her research interests center on using fish tissues to reconstruct their migration patterns, phenology, and trophic ecology of vulnerable and commercial species.

Will Satterthwaite is a Research Ecologist in the Fisheries Ecology Division at NOAA Fisheries with an expertise in salmon population dynamics and management in California.

Stephanie Carlson is a Professor in Environmental Science, Policy, and Management at UC Berkeley with a research lab group focused on freshwater ecology, salmon life history, and human impacts on fish ecology and evolution.

Further Reading

¹Chen E. K., Lumahan, K., Johnson, R. C., Phillis, C. C., Whitman, G. E., Sturrock, A. M., Satterthwaite, W. H., and S. M. Carlson. 2025. Juvenile life history, migration, and habitat use of natural- versus hatchery-origin Chinook salmon. Transactions of the American Fisheries Society 154:440-455. https://doi.org/10.1093/tafafs/vnaf021

²Maslin, P. E., McKinney, W. R., and T. L. Moore. 1996. Intermittent streams as rearing habitat for Sacramento River Chinook Salmon. Anadromous Fish Restoration Program, United States Fish and Wildlife Service:1–29. Available at: https://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/california_waterfix/exhibits/docs/CSPA%20et%20al/part2/aqua_279.pdf

³Phillis, C. C., Sturrock, A. M., Johnson, R. C., and P. K. Weber. 2018. Endangered winter-run Chinook Salmon rely on diverse rearing habitats in a highly altered landscape. Biological Conservation 217:358–362. https://doi.org/10.1016/j.biocon.2017.10.023⁴Satterthwaite, W. H., and S. M. Carlson. 2015. Weakening portfolio effect strength in a hatchery-supplemented Chinook salmon population complex. Canadian Journal of Fisheries and Aquatic Sciences 72:1860–1875. http://dx.doi.org/10.1139/cjfas-2015-0169