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Snake Fall Run Second Highest Since Dams Built--Or is It? by Bill Rudolph NW Fishletter, November 11, 2011

Nearly 25,000 hatchery and wild fall chinook have been counted crossing Lower Granite Dam, making it only the second time the run has passed 20,000 fish since the dams were completed in the early 1970s, according to information on the University of Washington's DART website.

But biologists haven't yet estimated how many of the Snake fall chinook are truly wild. To do this, they must first conduct some complicated counting exercises, sorting hatchery fish with many different types of marks, and estimating how many left the river as subyearlings or yearlings.

In addition, they must now also deal with a new factor that has made the run reconstruction effort even more hazardous, and has led to some confusion and differences between what the fish counters see and what the biologists have estimated for returns at Lower Granite Dam.

A case in point -- the total fall chinook run estimated by the reconstructors came out 10,000 fish higher that what dam counters tallied in 2009.

The good ocean conditions in recent years have led to much larger numbers of fall jacks showing up than earlier in the decade. Even some jills have appeared--small females returning after their first year at sea. And these young fish are so big that many of them are being counted at dams as adult fish, said WDFW biologist Debbie Milks, who works out of the agency's Dayton, Wash., office.

Milks said fish counters figure any fall chinook less than 56 cm. long is a jack. Lately, many jacks of 70 cm. or longer have shown up; but dam counters stay with the old yardstick.

Counters at Lower Granite tallied more than 41,000 fall chinook jacks in 2009, about four times higher than the average count through the earlier 2000s. Last year, nearly 13,000 were counted. This year, the count is nearly 20,000.

Milks said the group responsible for determining the wild numbers is working on a new methodology that will probably readjust fish return numbers back to 2003.

"There are probably more wild fish than we had previously estimated in some of those years," she said, though she was quick to point out that 2010's nearly 10,000-fish wild return is still their best guess and reflects their new way of thinking.

In fact, Milks said she wouldn't be surprised if it turns out the fish should soon be delisted. The interim recovery goal of 2,500 wild fall chinook may have actually been met for the past eight or nine years. In the meantime, she will be working to sort out the age-at-return issues, which are complicated by a large number of subyearling fall chinook, mostly from the Clearwater Hatchery, that hang out in reservoirs or the Columbia estuary over the winter before they go to sea.

Glen Mendel, another WDFW biologist working with Snake fall chinook for many years, said the run reconstruction effort has been further hampered by the number of fish they must deal with, compared to previous years. The fall chinook that end up in the adult trap at Lower Granite are mixed in with thousands of returning steelhead and make random sampling efforts more difficult.

Mendel also said the large number of returning jacks has complicated hatchery operations. He said the Lyons Ferry Hatchery was worried it might not meet broodstock needs for a time this year. It has led hatchery operators to wonder if hatchery operations have something to do with the large numbers of smaller fish that are returning these days. Mendel said a recent study by researchers at Oregon State University found that the standard hatchery protocol of using random broodstock may ultimately be breeding smaller fish in future generations.

"We're now at full production," said Mendel, which means four million or five million smolts are released from various facilities on the lower Snake every year. In the 1990s, when returns were low, hatcheries only produced around 350,000 smolts a year.

Still, nobody is sure how much hatchery fish have bumped wild production by spawning in the wild. There is some evidence that wild fish are now showing some hatchery influence in their genetic structure.

But NMFS isn't ready to delist them anytime soon.

In August, when the agency released its latest status review of ESA-listed runs, it noted that very little diversity was left in the "threatened" Snake River fall chinook ESU.

By 2008, abundance levels of wild falls had more than doubled from 1999 levels, to about 4,000 fish (Last year, about 10,000 wild falls came back). However, NMFS is concerned that about 75 percent of the spawners in the Snake are hatchery fish.

The 2005 assessment found the fall chinook likely to become endangered, but the latest review was more upbeat. NMFS still considers the fall chinook ESU at "moderate risk," and it's still not considered viable, even though Idaho Department of Fish and Game's estimate of returns has been over the 2,500-fish interim recovery goal in six of the past 11 years.

USFWS researcher Billy Connor told NW Fishletter last year that the available habitat for wild spawners could well be filled. He said if the number of wild numbers started going down again, that could signal that spawning habitat had been fully tapped. After all, NMFS scientists had previously estimated that the lower Snake could only provide enough room for several thousand spawners.

Mendel said it looks like there will be fewer wild fish back this year than 2010, but spawning activity is peaking right now, and it will be some time before redd counts are in.