New paths to survival for endangered winter run Chinook salmon

by Anna Sturrock and Corey Phillis

The chemical composition of adult Chinook salmon otoliths (“earstones”, left image) were used to reconstruct their movements through freshwater as juveniles. Otoliths grow in the inner ear of all bony fishes and reveal daily growth increments just like tree rings when you section them (right). The researchers used a laser coupled with a mass spectrometer to measure strontium isotope ratios across these layers in order to retrace the fishes’ migration history. Image courtesy of George Whitman/UC Davis.

Many Californians have seen headlines about endangered Sacramento River Winter Run Chinook salmon (“winter run”) on the “brink of extinction.” But not many people know exactly what winter run are, nor why they are endangered.

Like all salmon, winter run reproduce (spawn) in freshwater. Their offspring migrate to the ocean as juveniles, where they feed and mature before returning to their natal stream to renew the cycle.

However, the timings of these movements differ dramatically among salmon species and populations. Winter run exhibit a suite of behaviors so unique that they are treated as a separate “species” by the Endangered Species Act (ESA) and were the first Pacific salmon to be state and federally listed as endangered in 1989 and 1994, respectively.

To help protect this endangered fish during freshwater residence, most of the Sacramento River has been designated as “critical winter run habitat” by the ESA. While winter run juveniles have occasionally been observed in intermittent streams and tributaries to the Sacramento River, no one knew how frequently they showed up, how long they stayed, nor whether these “errant teens” survived to tell the tale.

In a new study published this week in Biological Conservation, researchers from the Metropolitan Water District of Southern California, UC Davis Center for Watershed Sciences, NOAA Fisheries, and Lawrence Livermore National Laboratory used salmon otolith (“earstone”) chemistry to reveal the migration patterns and secret hang out spots used by juvenile winter run on their way to the ocean.

The surprising finding was that, in their youth, around half the successful winter run adults had wandered beyond their natal reach of the Sacramento River to feed and grow before continuing their journey to the ocean. These alternative “non-natal” habitats included Deer, Mill, Battle Creeks, the Delta, Feather and American Rivers, most of which is not designated as critical habitat under the ESA.

Juvenile Chinook salmon hide in willow branches in the American River in the California Central Valley. The American River was found to be a favorite stop off for endangered winter run youths during their perilous journey to the ocean. Image courtesy of John Hannon/USBR

Let’s take a quick step back. What are winter run and why are they endangered?

Winter run exhibit a unique combination of behaviors that sets them apart spatially and temporally from all other types of salmon. For a start, they return to freshwater in winter – hence the name.

The last remaining population began declining dramatically in the 1970s to fewer than 200 spawners by 1991, and for the last decade the census has typically been below 3000. Before we built huge, impassable dams in their path, winter run spawned in cool, high-elevation, spring-fed tributaries above the Sacramento River, such as the McCloud and Pit rivers. Today, the remaining adults spawn in a small stretch of the upper Sacramento River immediately below Keswick Dam in early summer.

You might associate salmon with grizzly bears and icy Alaskan waterfalls, not summers in Chico. The California Central Valley contains the southernmost populations of native Chinook salmon in the world. Most life stages avoid the summer heat by moving into high elevation streams or escaping to the ocean.

Winter run eggs somehow need to survive and thrive through scorching summers, when air temperatures average around 100°F. Winter run literally put all their eggs into one basket – a small, very hot basket near Redding. One day, winter run may be reintroduced into the high-elevation streams above Shasta; but for now, their future is heavily reliant on cold water reserves in the reservoir that can be released through the summer.

But egg survival is only part of the story. If the warm water temperatures don’t poach the eggs, the tiny hatchlings (termed “fry”) face a perilous ~300 mile journey to the ocean. Their migration takes them down the Sacramento River, through the Delta, the estuary and bays, and finally past Golden Gate Bridge. Along the way they need to find food and territories, fight off competitors, and avoid the hungry jaws of predators.

Again, humans have upped the ante considerably. We have lined the rivers with “riprap” (large boulders or concrete blocks) to avoid erosion, facilitate flood control, and help with water delivery; but in doing so, have turned them into super highways of fast flowing water with few places for juvenile salmon to hide or rest. We have also introduced voracious predators like striped and largemouth bass, who love to dine on our winter run friends. But the results of our study showed that winter run juveniles are more resourceful than previously realized, and often wander out of the mainstem Sacramento River into smaller tributaries to feed and grow.

How did we discover their secret stop-offs?

We used otolith (“earstone”) chemistry to re-trace the migration patterns of hundreds of winter run and identify the rivers they had visited when they were making their treacherous journey to the ocean as juveniles. We extracted the otoliths from adult carcasses on the spawning grounds, representing the precious few that survived to adulthood. Otoliths are crystalline structures that grow like a pearl in the inner ear of the fish, depositing a new layer each day and forming growth rings just like a tree. The growth rings record the ambient water chemistry, providing a permanent record of the fish’s age and lifetime movements, rather like an airplane flight recorder.

We took advantage of California’s diverse geology to find a tracer for their migration to the ocean. Natural differences in strontium isotopes released from weathering rocks allowed us to develop a chemical map of river strontium-87 signatures called an “isoscape.” We used laser ablation mass spectrometry to measure the abundance of strontium-87 in tiny (~2 weekly) intervals across the otolith growth rings – from its center (the fish’s birth) to when it entered the ocean (typically 5-10 months old). Changes in the otolith strontium-87 values acted like chemical signposts, allowing us to track their movements and favorite hangout spots.

What are the implications?

An interesting finding was that the “wandering” winter run tended to leave the mainstem Sacramento River as small fry, yet left freshwater at a similar size to the rest of the population. These results suggest that these alternative habitats provide important growth opportunities and/or predator refuge.

Map of the California Central Valley winter run spawning grounds and migratory corridor, from Keswick Dam on the Sacramento River to Chipps Island, where they exit the freshwater Delta. Red shaded areas identify the regions identified isotopically as potential non-natal rearing habitats. Inset barplot shows the proportion of winter run in different “rearing groups” by escapement year, and averaged across years. Image from Phillis et al. (2018)

By using multiple habitats over their lifecycle, winter run are proving to be canny strategists. If you liken each habitat to a financial stock, winter run are effectively spreading risk by investing in a more diverse portfolio. By spreading themselves across the rich tapestry of freshwater habitats, winter run are reducing competition in natal habitats while potentially finding even better spots along the way.

Not only this, but differing growth opportunities can result in increased variability in rearing duration and ocean entry timing. Upwelling and prey dynamics are notoriously variable off the Californian coast; if a cohort all enters the ocean at the same time and miss the favorable window, they can all perish. Such “match-mismatch” dynamics are thought to be the leading cause of the precipitous stock collapse that occurred in 2007. By broadening this window, winter run are adding another layer of resiliency.

In summary, juvenile winter run have shown themselves to be masterful risk spreaders, taking their future into their own fins and using rearing habitats across a far broader geographic region than previously known. The findings open up exciting restoration and conservation opportunities for aiding species recovery, and bring new hope for the future of this endangered fish.

Anna Sturrock (@otolithgirl) is an Assistant Project Scientist at the Center for Watershed Sciences using otoliths to reconstruct juvenile salmon growth and habitat use. Her broader interests lie in linking fish ecology, science communication and data visualization, and providing empirical data to support and inform resource management. Dr. Corey Phillis, lead author of the study, can also be found in the twittersphere as @hydrophillis

 Further reading

Phillis CC, Sturrock AM, Johnson RC, Weber PK. 2018. Endangered winter-run Chinook salmon rely on diverse rearing habitats in a highly altered landscape.  Biological Conservation 217: 358-362.

Moyle PB and Lusardi RA. 2017. Moving salmon over dams with two-way trap-and-haul.

California Trout and UC Davis Center for Watershed Sciences. 2017. State of the Salmonids: Fish in Hot Water

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5 Responses to New paths to survival for endangered winter run Chinook salmon

  1. Chris Enright says:

    Congratulations on this excellent and inspiring work. I suppose we thought that juveniles are going with the flow to conserve energy. Moving up tributaries against the current might be “expensive” for small fish but the payoff in rearing resources for individuals and portfolio diversity for the population is “worth it” on balance. As you imply, perhaps the tributaries deserve more attention for conservation actions. Great job!

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  3. Keith Marine says:

    I commend the authors on a very interesting approach for substantiating the extent and potential importance of non-natal rearing behavior of CV salmon, and the WRC, in particular. However, I do take issue with the authors’ characterization of the Sacramento River reach near Redding, where most WRC currently spawn, as being typically a ” … small, very hot basket …” This is a very spatio-temporally myoptic perspective and mischaracterization of the quality, productivity, and importance of this habitat area for the WRC. While I can agree that blockage from historically available habitat above Shasta Dam poses an “ecological portfolio” risk to all CV Chinook salmon runs, particularly WRC, it has not been the lack of spawning habitat that has been the primary cause in the contemporary population declines of the WRC. Water management practices to provide for M&I and AgIrr uses and flood control practices that are incompatible with salmon life cycle requirements have been the main culprits in the current status of our CV salmon populations.

    As a fishery scientist, who has worked on understanding the biology and conservation of the WRC for over 30 years, I am disappointed in the UCD CWS’s portrayal of this habitat condition for salmon in the upper mainstem Sacramento River as typical. It is not. The recent extreme and protracted (2011-2015) drought, and water operations of the combined CVP/SWP, created the “small, very hot” conditions in the upper Sacramento River WRC spawning habitat by exhausting the available coldwater pool in Shasta Lake, which, in a majority of years, provides bone-chilling water temperatures suitable for Chinook salmon spawning and rearing all summer long for more than 30 river miles downstream of Shasta Dam. I do not know Ms. Sturrock or Dr. Phillis, but I invite them onboard my boat for a tour of the upper Sacramento River WRC spawning and rearing habitat next summer and to take a swim with me to observe, in situ, baby WRC in the “small, very hot basket” to which they refer.

    Keith Marine

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