TU scientists help confirm that a critical population of wild spring-run Chinook salmon still return to California’s Lower Yuba River
By Dr. Natalie Stauffer-Olsen, California staff scientist
In 2017, when I was fresh out of my PhD program at UC Berkeley and a new employee with Trout Unlimited in California, one of the first groups I engaged with was the Yuba River Management Team (RMT).
Previously, TU had been involved in litigation concerning flows released to the lower Yuba River from upstream dams. As a result of this litigation, the RMT was formed to help adaptively manage water and monitor salmon populations in the lower river.
Above: Lower Yuba River.
Adaptive stewardship of the lower Yuba River is especially important since it is understood to be one of the few remaining tributaries in the Sacramento River watershed where federally listed (threatened) Central Valley spring-run Chinook salmon still return to spawn.
However, until our recent research was published, the specifics related to this understanding were not shared by all parties working in the Yuba River. If there were indeed pure listed species remaining in the system, there might be additional management implications, which could impact water operations.
The Yuba River
The Yuba River’s North, Middle and South Forks begin high in California’s Sierra Nevada Mountains and merge to form the lower Yuba River, a key tributary of the Feather River. The Feather, in turn, eventually joins the massive Sacramento River. The watershed is a TU Priority Water.
Today dams block all but 24 miles of the lower Yuba to migratory fish, but the river remains home to critical populations of Chinook salmon, steelhead and resident rainbow trout, and other native species.
Daguerre Point Dam was built in 1910 within the lower Yuba River. Due to a pair of poorly functioning fish ladders on either side of the dam, it provides some fish passage for salmon and steelhead but completely blocks other species like sturgeon.
Like many rivers in California’s Central Valley, the Yuba watershed delivers large quantities of water to agriculture during the summer irrigation season. The Feather River is home to a hatchery that has raised and released steelhead trout and spring- and fall-run Chinook for decades. Both the Yuba and Feather Rivers are popular among California trout and steelhead anglers.
Small numbers of wild fish still return to the Yuba each year. Although Chinook populations are far below historical levels, the fish are important within the larger San Francisco Bay Delta system. Chinook returns have been so low lately that California commercial salmon fisheries completely closed during the last two years; a devastating blow to the commercial salmon fishing community and yet another wake-up call to the importance of salmon restoration and conservation work.
Image: Dan Cox, USFWS
Data gathering and monitoring
Every year, the RMT monitored the numbers of returning fish, counted redds and collected fin clips for potential future DNA analyses. Sometimes otoliths, the inner ear of fish, were also collected from salmon carcasses. Much like the rings of a tree, each year otoliths grow in a uniform layered manner and can be analyzed to identify where fish reared as juveniles (i.e. their natal stream, or further down into the SF Bay Delta) and the approximate timing of their outmigration.
Information gathered by this monitoring was useful in many regards, however, its analyses did not answer any questions specifically related to the genetics of these fish (i.e. whether they were genetically spring-run or fall-run Chinook) or their life histories as juveniles, such as when they left their natal Yuba River.
With TU’s long involvement in the RMT and the Yuba Fisheries Agreement, Rene Henery, our California Science Director, and I knew this information would be incredibly valuable for the management of the Yuba River. So, we proposed a study to better understand the genetics and life histories of Chinook Salmon in the Yuba River and how flow management could support diversity and recovery of these struggling populations.
TU Led Groundbreaking Science
In 2018, with funding provided by the Central Valley Project Improvement Act (CVPIA), I pulled together a stellar team of scientists working on Chinook salmon in the San Francisco Bay Delta. The University of Michigan’s Meek Lab focused on the genetic aspects of this work and UC Davis’s Watershed Science Center, led by Dr. Anna Sturrock, did the otolith analyses.
Image: Haley Ohms/TU
Together, our team used genetics and otoliths, a cutting-edge combination of approaches, to understand the deep, evolutionary heritage of Yuba-origin fish as well as how those genetics related to life history diversity, such as the timing of smolt (or fry) outmigration. We were interested in the occurrence and patterns of the “early-running” (i.e. spring-run) Greb-1L gene, which had been found to have only evolved once and thus is a significant aspect of Chinook diversity that must be a high priority to protect (Ford et al. 2020).
Because spring-run Chinook salmon in the Central Valley are a listed species, this information would further shine a light on the importance of the Yuba River for conserving remaining spring-run Chinook in California and the importance of restoring flows and habitat to allow both spring-run and fall-run salmon to thrive in the system.
The third aspect of our research focused on how stream flows in the Yuba River were related to juvenile outmigration patterns. This outmigration information and how life history strategies related to fish survival indicate which outmigration strategies are safest and most effective for juvenile fish, and thus, informs how flows can support the protection and recovery of anadromous fish populations.
In 2024, our team published two new papers about this work.
“Remnant salmon life history diversity rediscovered in a highly compressed habitat”
This paper explores adult return migration timing data and the gene that codes for early/spring-running life histories. This work reached the exciting conclusion that ESA-listed wild spring-run Chinook salmon are indeed spawning in the Yuba River, despite the highly compressed habitat created by impassable dams and the impacts of the Feather River fish hatchery.
Image: NOAA
We also found that the timing of Chinook salmon crossing Daguerre Point Dam, located within the lower Yuba River, was tightly correlated with their genotype. Pure spring-run Chinook salmon, and even fish that were only half genetically early-running, entered the system earlier. Fish documented as genetically pure for late migration (i.e. fall-run Chinook salmon) entered the system later. This indicates that the genotypes and phenotypes (i.e. expression) are correlated. So, in this system, timing of returning fish can reliably indicate the presence of the spring-running allele (gene), which helps inform management actions.
“Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population”
Another paper we published looked at genetics and otoliths to describe the genetic makeup and phenotypes (physical attributes) of Chinook salmon in the Yuba River to help understand the life history diversity within these populations and whether there was still a gene pool unique to the Yuba River. We also compared different groups of juvenile salmon that experienced a wide range of hydroclimatic conditions (such as wet, normal and dry years) and when they left the Yuba during their outmigration.
We learned that many spawners (42 percent over 6 years) were Yuba-origin (naturally spawned) fish, and among those, 30 percent were spring-run Chinook. This is important because before this research, we were uncertain what impact the nearby hatchery (on the Feather River) was having on Yuba fish genetics. It was very exciting to discover that even with all the environmental degradation, loss of habitat, unnatural flow regimes and hatchery impacts from straying, there was still a unique Yuba River genetic imprint – with traits specifically adapted to the Yuba River from countless generations of adult salmon returning to their natal habitat to spawn – on many of the fish spawning in the Lower Yuba River.
We also found that returns of adult Chinook were dominated by fish who had left the Yuba early as small fry. The contribution rates of these early migrating juvenile salmon were especially pronounced during drier years, suggesting disproportionately low survival of larger, later migrating parr, smolts and yearlings along the migratory corridor when flows were lower. This highlights the importance of salmon life history diversity in terms of outmigration timing so that different strategies (i.e. leaving earlier or later) can buffer the population in different years, which inevitably will vary through a range of water conditions.
In addition, otolith data we analyzed indicated generally faster growth in non-natal habitats (i.e. in areas other than the Yuba River), which means that fish who decided to stay in their natal Yuba River did not grow as fast as fish who left earlier. This indicates that the Yuba River doesn’t currently provide the best habitat or growth potential for Chinook, suggesting that habitat restoration and flow management to improve in-river growing conditions for young fish should be a high priority for those looking to support and restore Chinook salmon in the Yuba River and the San Francisco Bay Delta.
Implications for the Yuba River’s Chinook
In the massive Sacramento River watershed, populations of spring-run Chinook only remain in a few tributaries. This new research confirms that the Lower Yuba is one of those important places.
Our hope is that the new information we gathered will highlight the necessity of a healthy Yuba River that supports the diversity of native salmonids in the system. With flows that support diverse life history strategies and more restored habitat, we can focus on conservation and recovery of federally listed spring-run Chinook salmon and commercially important fall-run Chinook salmon as well.
Of course, TU and our allies will continue to do this type of work, share information we gather, and collaborate on ways to make the river systems we love healthier and more productive for salmon and trout.