New insights into Putah Creek salmon

by Malte Willmes, Anna Steel, Levi Lewis, Peter B. Moyle, and Andrew L. Rypel

It’s November 2016, and we’re out in canoes on Putah Creek as part of the annual salmon survey. Just as we navigate our watercraft through a narrow river section using push poles, thorny blackberry bushes and trees begin to close in from both sides of the channel. Finally, we reach a series of shallow riffles and spot our first salmon of the day. As we look it over, it’s easy to consider this fish, the ordeal it went through to get here, and how its journey symbolizes in some way the restoration of Putah Creek.

Putah Creek is a small stream originating on the East side of the Vaca Mountains. Flowing down-slope, water enters Lake Berryessa, a large impoundment created by Monticello dam. Below the dam, the creek flows to Putah Creek Diversion Dam, past the town of Winters, UC Davis, and dozens of farms and into the Yolo Bypass. From here it eventually flows into the San Francisco Estuary and the Pacific Ocean.

Chinook Salmon (Oncorhynchus tshawytscha) have become a welcome and familiar sight in recent years in Putah Creek. Considered a keystone species across the Pacific Northwest, Chinook Salmon hold a special place in our past and present as a cultural and food resource. This includes for indigenous peoples of California, such as the Patwin people, on whose land UC Davis is located. In California at the southern end of Chinook distribution, populations are in decline, due to combined effects of habitat degradation, water diversions, and climate change (Moyle et al. 2017). Putah Creek historically supported a population of fall-run Chinook Salmon (Yoshiyama et al. 1998). And while the creek had long been known to possess an intermittent hydrologic dynamic (Shapovalov 1940), reduced downstream flows after Monticello Dam was installed proved problematic. For example, areas of the creek dried more frequently during summer months, resulting in declines and extirpation of many anadromous and native fishes, including Chinook Salmon (Oncorhynchus tshawytscha). Their reappearance now is a direct result of ongoing restoration and water management efforts, particularly since ~2000.

Chinook Salmon are anadromous; they spawn in fresh water, migrate to the ocean to grow for 2-4 years (often 2 in CA), and return to natal rivers to spawn. They are also semelparous, which means they reproduce only once and die after spawning. Homing behavior of salmon allows for streams to develop evolutionarily-distinct populations with local adaptations, such as migration timing. The Central Valley Chinook Salmon population historically consisted of many smaller runs with local adaptations – this provided a critical buffer against California’s variable and unpredictable climate and ocean conditions, as it increased chances that some offspring would survive to return and reproduce under most environmental conditions. Yet a certain fraction of salmon, both historically and today, stray from their natal streams and disperse into new and previously disconnected habitats. In California, straying, especially of hatchery origin salmon, is sometimes viewed in a negative light. However straying reflects an important piece of salmon life-histories aimed at increasing fitness, and can create resilience for populations overall. Across the Pacific Rim, straying has allowed salmonids to adapt to changing habitat conditions, such as retreating glaciers in the past, or warming climates of the future.

Back to our canoe, we pass the shallow riffles, and follow the stream around a bend, where it widens and forms a series of deep pools. Carefully observing the bottom, Emily Jacinto spots a salmon carcass, and using a hook, deftly lofts it onboard the canoe. The salmon is already somewhat decayed, starting the release of valuable ocean nutrients into the creek, its smell placing a pungent twist on the peaceful and beautiful scenery (Fig. 1). We collect a few more carcasses, some in deep pools, others on the sides of the channel, and finally push the canoes onshore to process samples. Since 2016 UC Davis has been conducting annual carcass surveys in collaboration with the Solano County Water Agency, carefully tracking and counting the returning adults and collecting valuable information from the salmon carcasses.

Fig. 1. Chinook Salmon carcass survey on Putah Creek. Photo taken by Ken Davis.

Lots to say for a dead fish

Each carcass is carefully measured, its sex determined, and tissue samples taken for future DNA studies. We also check to see if the fish has its adipose fin intact; if the fin is missing, it’s an indication the fish originated from a hatchery, as about 25% of fall-run hatchery fish are marked this way. These marked fish also have been injected with a tiny wire tag engraved with a code, known as a Coded Wire Tag. Thus, when fish without an adipose fin are encountered, the head is sent to the CDFW Coded Wire Tag Laboratory in Sacramento to extract this valuable tag with information about the fish origin and brood year. In 2016, we recovered 23 of these marked fish, with 20 originating from the Mokelumne River Hatchery, two from the Nimbus Hatchery, and one from the Feather River Hatchery. The last step of the carcass survey is the trickiest. With a few skilled cuts with a sharp knife, Emily extracts both ear stones (otoliths) from the brain cavity of the fish (Fig. 2). Compared to the large decaying carcass next to us, these structures are tiny, but hold a wealth of information.

What can we learn from otoliths?

Fig. 2. Chinook Salmon ear stone (otolith) extraction. This tiny calcium carbonate structure holds information about age, growth, & movement histories of fish. Photo taken by Eric Chapman.

Otoliths (oto=ear, lithos=a stone) are calcium carbonate structures in the inner ear of most bony fishes, and they function to detect sound, water pressure, and depth. Otoliths grow continuously throughout the life of a fish and accrete daily layers, similar to the annual rings found in trees. The sequence of these layers can be used to estimate fish age, and their width can be used to reconstruct growth rates. In addition, distinct marks are visible in the otoliths, called ‘checks’, that were produced at hatching (hatch check), at the onset of exogenous feeding (exogenous feed check), and at ocean entry (ocean entry check). Finally, as the calcium carbonate structure grows, the chemical signature of the water surrounding the fish is incorporated as well, allowing us to reconstruct fish movement among different habitats.

One particularly useful chemical tracer in the Central Valley are strontium isotopes (87Sr/86Sr). This ratio varies among watersheds depending on the age and composition of the underlying geology, and can provide a unique geographic fingerprint (Johnson et al. 2016) as well as a tracer for migration from fresh to brackish to salt water. For our Putah Creek salmon otolith samples, we used a laser-ablation system at the ICPMS Center at UC Davis to analyze strontium isotopes across the entire otolith, reconstructing fish movements among habitats from the time the fish was born (core), across its time in freshwater (natal stream) to its time in the ocean and eventual return (edge of the otolith) (Fig. 3).

What did we find?

We recently published a paper (Willmes et al. 2020) applying this tool to 104 carcasses collected from Putah Creek in 2016 (Fig. 4). We found most Chinook Salmon returning to Putah Creek were 2 (44%) to 3 years (42%) old, with only a few 4 year old (14%) and no 5 year old fish present. This shift to a younger age distribution is not uncommon in the Central Valley and it might influence the number of juveniles being produced, as younger fish are generally smaller and produce fewer offspring. But juvenile surveys in 2017 and 2018 found large numbers (~33,000) of healthy juveniles leaving the river in spring, indicating Putah Creek supported successful spawning, and has the potential to maintain a salmon population (Miner et al. 2019).

Fig. 3. Top: Cross section of a Chinook Salmon otolith showing the position of check marks produced at hatching (hatch check), those produced by the onset of exogenous feeding (exogenous feed check), and ocean entry (ocean entry check). Fish ages were estimated based on the sequence of winter (translucent) and summer bands (opaque) and are noted in the image. The dotted white line shows the laser-ablation analysis transect. Bottom: Example 87Sr/86Sr profile of a Chinook Salmon otolith. The core forms using energy from the maternal yolk-sac, and thus has chemical signatures typical for the Pacific Ocean (red). This is followed by freshwater residence time and the start of exogenous feeding (yellow). Finally, a rapid transition to the ocean can be observed before the first annular ring forms. As with the otolith, this diagram appears semi-symmetrical since the core is at the center and otoliths grew in both directions.

One surprise finding from our otolith study was the diversity of origins of Putah Creek salmon. In 2016, fish came from at least seven different natal sources, overwhelmingly from hatcheries. Fall-run Chinook Salmon in the Central Valley are largely supported by hatcheries, which has increased straying rates and in turn created genetic and life-history homogenization. In addition, a high priority in hatchery operations is to increase fish survival to the ocean. This resulted in the trucking of juvenile salmon to downstream or estuary release sites during drought years with otherwise expected high migration mortality (Sturrock et al. 2019). However, this practice also increases straying rates (presumably because of a lack of natal stream imprinting), and appeared to be an important driver of fish straying into Putah Creek. While in many circumstances, high rates of straying can cause harm to salmon populations by reducing local adaptation, for Putah Creek the stray rates have been beneficial, as they bring added numbers and genetic diversity to the stream. Into the future, however, continued high stray rates may reduce the extent of new local adaptations to develop within this emerging run.

To date, we do not have enough information to determine whether Putah Creek Chinook Salmon represent the beginning of a newly established and self-sustaining run. In 2016, we found only one fish that originated in Putah Creek, and unfortunately our strontium isotope tracer was not able to distinguish it from wild Feather River origin fish. The fish returning in 2016 would represent juveniles migrating out in 2013 and 2014, before large numbers of Chinook returned to Putah Creek so finding a Putah Creek origin fish in 2016 was unlikely. Over time we expect to gather more evidence about reestablishment of the Putah Creek run.

Fig. 4. Natal origins of 104 Chinook Salmon analyzed from Putah Creek in 2016.

What does this mean for Putah Creek and Chinook Salmon in the Central Valley?

Rehabilitating a degraded and deeply incised stream ecosystem is a difficult proposition and a long process. Transitioning from small and shrinking salmon population to a robust and resilient one may take even longer. But by leveraging and restoring many small, spatially distinct systems, like Putah Creek, and restoring the core ecological processes that generate biological complexity, we may be able to achieve this goal over time. Locally-adapted salmon runs differ in susceptibility to natural and anthropogenic risks (Beechie et al. 2010). Furthermore, this work reveals an upside to straying salmon that is rarely discussed, but that upside is only realized if salmon have a good place to go. Reconnecting migratory pathways and restoring other degraded small streams like Putah Creek thus provides an opportunity to increase salmon life-history diversity and help strengthen and recover Chinook Salmon populations.

Putah Creek is a special place in many ways. It has a long history of habitat degradation, and the road to restoration has been a long and difficult one. Ongoing persistence of Chinook Salmon adds to this success story, and continued salmon returns may spark changes to the ecosystem overall. Because salmon die after spawning, carcasses nurish freshwater ecosystems with a supply of marine nutrients, connecting this small stream in our backyard to the expansive Pacific Ocean. As numbers increase, marine-derived nutrients will enrich vegetation, and enhance the productivity of all animals that feed on it. We are only at the beginning of our scientific program on Putah Creek and continued monitoring and the application of a vast toolset of scientific methods will be required to see if and how salmon establish a new population here.


We would like to thank the Solano County Water Agency (Roland Sanford and Rich Marovich) for funding and support of the study (Contract #03-00206VR). In addition, we thank the members of the Biotelemetry lab at UC Davis for assisting with carcass surveys in 2016: Tommy Agosta, Colby Hause, Christopher Bolte, Patrick Doughty, and Alexandra McInturf. Additional thanks to Kyle Brandt for his help during carcass surveys and rotary screw trapping and to Rick Fowler and Rick Poor for assistance with the preparation and deployment of the screw trap. Special thanks to John and Erin Hasbrook for graciously allowing us access to their property to deploy and tend the rotary screw trap.

Malte Willmes is a Postdoc at University of California Santa Cruz in the Institute of Marine Sciences and NOAA Fisheries Collaborative Program.

Anna Steel is a Postdoc in the Department of Wildlife, Fish & Conservation Biology at the University of California, Davis, and works within the Ecophysiology Laboratory of Nann Fangue.

Levi Lewis is a Research Scientist in the Department of Wildlife, Fish & Conservation Biology at the University of California, Davis and leads the Otolith Geochemistry & Fish Ecology Laboratory.

Andrew Rypel is an Associate Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Co-Director of the Center for Watershed Sciences

Peter Moyle is a Distinguished Professor Emeritus in the Department of Wildlife, Fish & Conservation Biology at the University of California, Davis and Associate Director of the Center for Watershed Sciences.

Further reading

Beechie, T.J., Sear, D.A., Olden, J.D., Pess, G.R., Buffington, J.M., Moir, H., Roni, P., and Pollock, M.M. 2010. Process-based Principles for Restoring River Ecosystems. Bioscience 60(3): 209–222. doi:10.1525/bio.2010.60.3.7.

Johnson, R.C., Garza, J.C., MacFarlane, R.B., Grimes, C.B., Phillis, C.C., Koch, P.L., Weber, P.K., and Carr, M.H. 2016. Isotopes and genes reveal freshwater origins of Chinook salmon Oncorhynchus tshawytscha aggregations in California’s coastal ocean. Mar. Ecol. Prog. Ser. 548: 181–196. doi:10.3354/meps11623.

Miner, M., Moyle, P.B., Jacinto, E., Steel, A.E., Cocherell, D.E., Fangue, N.A., and Rypel, A.L. 2019. Origin and Abundance of Chinook Salmon in Putah Creek. Annual Report to Solano County Water Agency.

Moyle, P.B., Lusardi, R., Samuel, P., and Trout, C. 2017. State of the Salmonids II: Fish in Hot Water.

Shapovalov, L. 1940. Report on the possibilities of establishment and maintenance of salmon and steelhead runs in Cache and Putah Creeks. Bureau of Fish Conservation, California Division of Fish and Game. Technical Report.

Sturrock, A., Satterthwaite, W.H., Cervantes‐Yoshida, K.M., Huber, E.R., Sturrock, H.J.W., Nusslé, S., and Carlson, S.M. 2019. Eight Decades of Hatchery Salmon Releases in the California Central Valley: Factors Influencing Straying and Resilience. Fisheries 44(9): 433–444. doi:10.1002/fsh.10267.

Willmes, M., Jacinto, E.E., Lewis, L.S., Fichman, R.A., Bess, Z., Singer, G., Steel, A., Moyle, P., Rypel, A.L., Fangue, N., Glessner, J.J.G., Hobbs, J.A., and Chapman, E.D. 2020. Geochemical tools identify the origins of Chinook Salmon returning to a restored creek. Fisheries: fsh.10516. doi:10.1002/fsh.10516.

Yoshiyama, R.M., Fisher, F.W., and Moyle, P.B. 1998. Historical Abundance and Decline of Chinook Salmon in the Central Valley Region of California. North Am. J. Fish. Manag. 18(3): 487–521. doi:10.1577/1548-8675(1998)018<0487:HAADOC>2.0.CO;2.

Putah Creek Council a community of nature enthusiasts and volunteers who enhance and restore the Putah Creek Watershed.

The Putah Creek Legacy: A five-part multimedia series by The Davis Enterprise and Climate Confidential.

About Andrew Rypel

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.
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3 Responses to New insights into Putah Creek salmon

  1. Mitch Dion says:

    Love this project. Was quite interested in the author(s) thoughts on straying hatchery fish actually contributing to the resiliency of population. Makes me ponder the definition of a wild salmon. We have certainly heard that wild fish are genetically ‘superior’ and that genetic diversity is beneficial to resilience. I have heard that domestic animals, such as pigs and chickens, once they go feral, start to develop their ‘wild’ characteristics almost immediately. For pigs, growing longer hair, longer tusks and producing more testosterone and thus becoming more aggressive. Apparently, even after years of domestication, the wild ‘stealth genes’ that have been submissive for generations, immediately come back. I would love to hear any of the authors thoughts on how ‘wild’ a Putah Creek salmon run will be if, indeed there is a breeding population established.

  2. josh restad says:

    How do the fish return up the Putah during Nov/Oct when the Board dam is still present in the Yolo bypass? Are they still removing it in December or have they moved up that time frame?

    • andrewrypel says:

      Salmon can’t access Putah Creek when the boards are in place. However, boards were removed on 11/9 this year and salmon have been sighted in the creek.

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