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. Read More > at California Department of Water Resources
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