Using Genetic Identification to Find Spring-run Salmon and More

Balancing the water supply needs of millions of Californians while protecting the environment is no easy task. The Department of Water Resources is committed to using and advancing the best available science to operate the State Water Project to get water to the people who need it while protecting native fish species.

One important way DWR is doing just that is through the advanced use of genetics to identify different runs of Chinook salmon to monitor and protect the runs that are listed as threatened or endangered. Knowing which runs are present and where they are being found in the water system ultimately helps rebuild salmon populations in California. DWR has released a video showing the genetic identification process in action.

DWR leads an interagency effort, which includes California Department of Fish and Wildlife (CDFW) and U.S. Fish and Wildlife Service (USFWS), to calculate a Juvenile Production Estimate (JPE) for spring-run Chinook salmon, which estimates the size of the salmon population entering the Delta from upstream tributaries. Part of the interagency effort means other agencies send collected DNA from juvenile salmon to DWR. DWR’s genetic monitoring program then uses that collected DNA to determine run type, which is essential to producing an accurate Juvenile Production Estimate.

There are four different run types of Chinook salmon: spring-run, fall-run, late-fall run, and winter-run. Spring-run Chinook salmon are listed as “threatened” under the State and federal Endangered Species Acts. Fall-run and late-fall-run Chinook Salmon are a “Species of Concern” federally, while winter-run are listed as “endangered” under State and federal levels.

“All four run types look exactly the same,” said Melinda Baerwald, DWR environmental program manager. “Since we can’t tell them apart by looking at them, we have to use other methods to confirm run-type.”

Originally to determine the run-type, scientists would swab some mucus from the fish. Now, the preferred method is to clip a small portion of the dorsal fin of each fish, since it provides more DNA.

This type of DNA testing uses a specific technology called ‘SHERLOCK’ which stands for Specific High-sensitivity Enzymatic Reporter un-LOCKing. SHERLOCK was originally developed for viral diagnostics, much like the tests to detect COVID in people, but it has very recently been applied to conservation biology. Along with identifying spring-run Chinook, DWR has developed or is developing SHERLOCK tests for the three smelt species in the Delta: Delta smelt, Longfin smelt, Wakasagi; and three invasive species: nutria, zebra mussels, and quagga mussels. The development of the specific tests is done in collaboration with UC Davis.

SHERLOCK leverages another fun acronym ‘CRISPR,’ which stands for Clustered Regularly Interspersed Short Palindromic Repeats. Since spring-run salmon have different DNA than the other salmon runs, DWR scientists use the CRISPR enzyme to distinctly detect the DNA from spring-run, winter-run, and fall-run salmon.

“Mucus or a fin clip has some DNA in it. So, we put it in a tube, put that in another tube, let it sit, and if that specific DNA for a specific run type is detected it’ll glow. It’ll fluoresce,” said Sean Canfield, DWR senior environmental scientist.

SHERLOCK has an advantage over some previous genetic tests because it’s extremely rapid. The run type results can be ready within one or two hours. SHERLOCK is also very sensitive and only needs a tiny amount of DNA to detect a species. DWR environmental scientist Sarah Stinson explained the technology has other benefits such as being cost effective and the potential for mobility.

“You can use SHERLOCK in the field, as long as you have access to ice and a power source.” Stinson said. “Our long-term goal is to use it in the field, but our current method is to process samples in our genetics laboratory. The field crews bring us thousands of samples at a time from the field, and then we can process all the samples at once.”

Since Chinook salmon in California are found in a wide geographic distribution, DWR needs to be able to collect the samples as efficiently and effectively as possible.

“We are leveraging our partners across different State and federal agencies to make that happen, so that we can get the samples that we need to do the genetic analyses as quickly as possible,” Baerwald said.

The information gathered from the genetic tests will help managers track different salmon runs throughout the watershed. DWR works to ensure salmon that originate in the Sacramento River, stay in the Sacramento River, so they can migrate through the Delta to the Bay and the ocean before eventually returning to the Sacramento River to spawn. Since the Sacramento River ties into a number of other water sources like sloughs, channels, and rivers it is possible for salmon to veer off course. Correctly identifying runs allows DWR to make decisions on how to protect the fish that are listed as threatened or endangered, which works toward the project’s long-term goal to help all salmon populations recover.

Beyond generating a Juvenile Production Estimate, SHERLOCK has the potential to identify salmon runs near infrastructure like fish screens. However, because SHERLOCK is still being piloted, DWR partners with CDFW’s Genetics Laboratory to verify the run type using additional genetic approaches.

Additionally, DWR works with Cramer Fish Sciences Genetics Laboratory which also conducts genetic tests to determine run type. This verifies that the two genetic methods give the same results. These decisions can inform State Water Project water managers, who make operational adjustments and provide water to 27 million Californians. The State Water Project must adjust its operations if listed species are detected near the fish screens at the facilities. SHERLOCK’s speed could make it possible to quickly determine if water from the State Water Project can continue to pump and export or if pumping would need to be reduced.

Visit DWR’s Protecting California’s Salmon StoryMap to see more of the work being done to help salmon in California.