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NOAA Fisheries scientists work to bring back a historic salmon run in Southern California

a Tag being inserted in the body cavity of a hatchery fall-run Chinook salmona (11) Tag being inserted in the body cavity of a hatchery fall-run Chinook salmon

September 14, 2011

Scientists from the NOAA Fisheries Service’s Southwest Region have years of experience working to prevent the extinction of endangered and threatened species.  Now they are teaming up with the U.S. Fish and Wildlife Service, the California Department of Fish and Game, and other organizations to do something they’ve never done before: bring back a salmon run that has been gone for more than 60 years.

The spring run of Chinook salmon on the San Joaquin River once numbered over 300,000 fish. But after the construction of the Friant Dam in the 1940s, that number dropped to zero.  The San Joaquin went dry in several locations and the salmon run was wiped out.

“While scientists have been able to restore populations of some animals threatened with extinction, this is the first time we’ve attempted to bring back an entire salmon run that hasn’t existed for such a long period of time,” said fishery biologist Elif Fehm-Sullivan of the Southwest Region’s Sacramento office.  “This restoration goes above and beyond previous conservation efforts.  We are restoring more than 150 miles of river.”

Elif implanting tagElif implanting tag

The reintroduction stems from a lawsuit against the Bureau of Reclamation by the Natural Resources Defense Council and other groups over the negative impact of the Friant Dam on the San Joaquin watershed.  After 18 years of litigation, a settlement reached in 2006 requires the flow of the river to be restored and salmon to be reintroduced by the end of 2012.

In accordance with the settlement, USFWS was tasked with submitting an Enhancement of Species Permit to NOAA Fisheries Service.  In this permit USFWS proposes to establish a population of 500 breeding adult spring-run Chinook salmon. With the assistance of NOAA Fisheries Service and other agencies, USFWS eventually wants to restore the population to 30,000. While the main focus is on reintroducing the spring run, USFWS also hopes to eventually restore a fall run of Chinook salmon to a population of 10,000.

The first step, said Fehm-Sullivan, was restoring flow to the river – which was not as simple as just allowing more water to be released from the dam.

“Some sections of the original riverbed have limited to no capacity for water,” she said.  “It has been several decades since the river was allowed to flow, and the river has been physically altered at various locations as a result of water operations, encroachments by agriculture, and other structures. Much
of that land was reclaimed and developed for other uses.”

Implanting Coded Wire TagsImplanting Coded Wire Tags

The river is now flowing to the ocean through the use of existing flood control structures, Fehm-Sullivan said, so it’s now time to move on to step two:  reintroducing the salmon.  NOAA Fisheries Service is working with USFWS and the California Department of Fish and Game to determine the best approach.

First, because the San Joaquin spring-run Chinook salmon were wiped out, donor fish need to be brought in.  “They will come from both wild and hatchery populations in Northern California,” Fehm-Sullivan said.  “Additionally, we want to make sure that removing fish won’t have a negative impact on those spring-run populations.” 

Strict criteria are used for the selection of donor stock:   the population of the run must exceed 2,500 fish, it must not have experienced a catastrophic event (such as a wildfire) within the past 10 years, and the population must not be in decline.

Scientists are currently discussing the best life phase at which the salmon should be taken from the donor stream/hatchery and  reintroduced to the San Joaquin River.  One possibility is to transplant eggs between rivers.  However, Fehm-Sullivan said this process could involve suctioning eggs out of redds
(i.e., nests where salmon lay their eggs and cover them with gravel.)  Disturbing
a redd can harm the eggs remaining inside, and taking eggs from only one or
two redds won’t work. 

San Joaquin River before and afterSan Joaquin River before and after

“In order to maintain genetic diversity, we would have to take eggs from many redds, and disturbing too many redds would likely have a significant negative impact on the population,” she said.

Another possibility would be to use adult salmon, but according to Fehm-Sullivan, “Adults often experience too much stress during transportation and die.  It could be that transporting juveniles is best.  Also, we may try to capture and transport adults from other streams that, due to low water levels or blockages, are trapped below their spawning grounds and would otherwise die.”

Fehm-Sullivan added that, while scientists are hoping to use wild fish, they may need to use fish from the Feather River hatchery.  In addition, a temporary conservation facility is being proposed at the Friant Dam to help increase San Joaquin salmon numbers.

Restoring salmon to the San Joaquin is a complicated process that must be adaptively managed.  “We have to remain flexible,” Fehm-Sullivan said.  “We’re thinking of all scenarios that could possibly work.”

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