A secret to survival for California’s most endangered salmon
Chinook need cold water in first weeks for their eggs to survive
image:
A slice of an ear bone, or otolith, from a juvenile winter-run Chinook salmon. The otolith measures about the size of the eye of a needle, with daily growth increments that resemble tree rings indicating when the fish hatched. White circles indicate where an ion microprobe measured oxygen isotopes to reconstruct temperatures the fish experienced just before emerging from their gravel nests, called redds.
view moreCredit: George Whitman/UC Davis Center for Watershed Sciences
Sacramento River winter-run Chinook salmon are California’s most endangered salmon, with a single surviving population and an average of a few thousand returning fish in recent decades. Shasta Dam blocks their original habitat in cold mountain rivers draining Mount Shasta, leaving them to spawn in the low-lying Sacramento River heated by the summer sun.
The research, published this week in Science Advances, found that cool river temperatures in the first 15 days after their eggs were fertilized was crucial for their survival. In warm years with less water, cold water barely covered this critical thermal window, sharply limiting survival in what may become an increasing reality for salmon as the climate warms.
“Salmon may spawn throughout the summer season, but our results suggest that only a small fraction of those spawning events ultimately produced the juveniles that survived,” said Kohma Arai, who authored the research as a postdoctoral scholar at UC Davis with other scientists from the university, NOAA Fisheries, UC Santa Cruz, UCLA, and the Norwegian Institute for Nature Research.
“This helps us understand the connection between what individuals experience during development and how populations respond to environmental change, which is becoming increasingly important as climate change continues to reshape aquatic ecosystems,” he said.
Water managers try to release cold water from Shasta Reservoir to cool the river enough for salmon eggs incubating in river gravel to survive, while also delivering water to farms and cities vital to California’s economy. The balance grows more difficult in low-water years. Water agencies, water users, such as irrigators, and federal and state fish agencies prioritized the new research to address science questions key to salmon survival in a changing climate. The U.S. Bureau of Reclamation and California State Water Board funded the research.
Behind the Spawning
Fisheries biologists long measured the annual success of winter-run Chinook salmon by the number of adult salmon returning upriver to spawn, presuming many were successful. However, laboratory studies suggested eggs may be sensitive to river temperatures. The new research probing that connection shows that in some years the true success of the species may be much more limited.
“We learned that even when surveys show many salmon spawning over an extended season, only those eggs that experience the right temperatures are likely to survive,” said Rachel Johnson, a research scientist at NOAA’s Southwest Fisheries Science Center and University of California Davis who helped lead the research. “In some years, that number can be shockingly small. It’s this number of successful spawners that we need to track to assess the true risk of extinction and goals towards recovery.”
This survival bottleneck can dramatically reduce population size and erode diversity that helps salmon adapt to a changing climate, she said. She cautioned against using the results to target limited cold water to the key 15-day window for only part of the spawning season, favoring a reduced number of redds, or nests.
“Selecting the winners at this life stage can have unintended consequences by narrowing the chance that salmon encounter favorable conditions at later life stages— it’s like putting all your eggs in one basket.” Instead, the findings argue for strategies such as reintroduction to historical habitat that give fish more options to survive, benefiting the environment, tribal communities, and economy in the long run.
“For endangered species, we have removed so many options, we don’t have the luxury of further selecting certain survivors,” Johnson said.
Instrument Examines Ear Bones
The team, for the first time, combined established salmon spawning surveys, river temperature models, and analysis of salmon otoliths, or ear bones, to track the factors affecting juvenile salmon developing inside their eggs. Researchers also collaborated with a UCLA laboratory that operates an ion microprobe, an advanced instrument that measures oxygen isotopes in the otoliths that indicate the temperatures the salmon were exposed to.
By combining those temperature records with salmon hatch dates estimated from otolith growth increments, river temperature models, and spawning surveys, the researchers identified the redds that likely produced the surviving salmon.
When the team compared the incubation temperatures of surviving juveniles to temperatures for spawning areas where juveniles did not survive, “the pattern was remarkably clear,” Arai said. “The juveniles that survived had experienced cooler incubation temperatures during their earliest stages of development, whereas unsuccessful locations were consistently associated with warmer temperatures over the same developmental period.
“That was one of those rare moments in research where the biological story became immediately apparent from the data,” he said.
For each 1.8°F (1°C) increase in the average river temperature during the 15-day thermal window, the probability of juveniles in a redd surviving declined about 73 percent, researchers found.
The fish that survived the narrow thermal window appeared to tolerate higher temperatures later in their development. The findings also suggest that the timing of favorable river temperatures may be as important as the temperatures themselves. Even short mismatches between salmon spawning and available cold water can substantially reduce the number of juveniles that survive.
New Framework Provides Insight
Combining the sensitivity of the ion microprobe with complementary analyses may open a new window on the early development of salmon and other species sensitive to temperatures and changing environmental conditions, the researchers said. It may someday reveal the experiences of individual animals across species and long time periods.
“I will never cease to admire the way our students and researchers see new technology and envision new ways to apply it to answer questions that may have seemed out of reach,” said Carson Jeffres, a senior researcher at UC Davis who leads a fisheries laboratory with Johnson and is a co-author of the new research. “Suddenly we have new insight into the very earliest and—now we know—key stages of salmon survival.”
The researchers praised collaboration with the U.S. Fish and Wildlife Service, which collected juvenile fish for the study; the California Department of Fish and Wildlife, which documented spawning locations in the river; NOAA Fisheries and University of California Santa Cruz, which tracked river temperatures connected to the otolith data; and the UCLA team that focused the ion microprobe on otoliths at very fine scales.
“It is incredibly gratifying to see scientific innovation, collaborative research, and strong agency-academic partnerships come together to identify critical bottlenecks limiting recovery. Those insights allow us to focus conservation actions with our partners where they can make the greatest difference for the species,” Johnson said.
FOR MORE INFORMATION
Recovery Through Reintroductions for California’s Central Valley Salmon
Tribe, State, and Federal Partners Join To Return Endangered Salmon to Historic Habitat
Journal
Science Advances
Method of Research
Observational study
Subject of Research
Animals
Article Title
Thermal bottlenecks constrain early-life survival of native fish in regulated rivers
Article Publication Date
21-Aug-2026
The chamber of an ion microprobe, an advanced instrument that occupies an entire room at UCLA. The instrument measures oxygen isotopes in salmon otoliths, or ear bones, inside the chamber to determine temperatures the fish experienced inside their eggs.
Credit
Rachel Johnson/NOAA Fisheries
Juvenile winter-run Chinook salmon circle a bucket waiting before they are marked for later release.
The Sacramento River near the main spawning area of winter-run Chinook salmon blocked by dams from their original mountain spawning habitat. The Sundial Bridge in Redding rises in the background.
Credit
Larisa Thacher/UC Davis Center for Watershed Sciences.
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