Scientists have identified the source of a glut of pink salmon that showed up in streams across Lower Cook Inlet this year. Suspicions that some pinks came from hatcheries proved out, but they weren’t all local stocks. In some streams, up to 70 percent were born in Prince William Sound hatcheries.

The commercial pink salmon harvest in Lower Cook Inlet wasn’t record-breaking this year, especially as compared to previous big pink years — commercial fishermen harvested about 6.4 million pinks in 2015 and about 2.1 million in 2013, according to Alaska Department of Fish and Game data — but residents saw a large number of pink salmon making their way up into streams around Kachemak Bay where they hadn’t been seen before. That sparked a question of whether more pinks from Cook Inlet Aquaculture Association’s pink salmon operations at Tutka Bay Lagoon Hatchery and Port Graham Bay were leading to salmon straying.

Fish and Game biologists have been sampling otoliths, or fish ear bones, from salmon running into various streams around Homer for the last four years. The 2017 data, released Dec. 1, showed that fish from the hatcheries strayed, but typically not far, according to a memo from area management biologist Glenn Hollowell and research biologist Ted Otis. Although the Tutka Bay Hatchery is in Kachemak Bay, except for creeks nearby, most hatchery salmon came from elsewhere.

“Similar to the previous three years, pink salmon from Tutka and Port Graham Bay hatcheries were found to have spawned in 11 of the 16 Lower Cook Inlet streams surveyed,” the memo states. “Port Graham Hatchery marks were found in samples at low levels (1%) in three streams. Tutka Bay Lagoon Hatchery marks were found in 10 of the 16 streams at widely varying proportions (15–87%) with highest proportions generally found closes to release sites.”

Otolith samples showed Tutka Bay hatchery fish at 33.9 percent in Tutka Head End Creek, 87.4 percent in Tutka Lagoon Creek, and 12.5 percent in Little Tutka Bay or Lou’s Creek. Elsewhere percentages were 4.2 percent (Sadie Cove) or less. For commercial harvest, purse seining had the highest amount of Tutka Bay hatchery pinks, 26.7 percent, while set gillnets were 15.6 percent. Most seine fisherman fish in the Tutka Bay Special Harvest Area, so it’s no surprise to see large numbers of hatchery pinks there.

Prince William Sound hatchery-marked fish, though, were present in every stream sampled. In Fritz Creek, 69.8 percent of the 96 fish sampled were from Prince William Sound hatcheries. In Beluga Slough, 56.3 percent of the 288 fish sampled were from Prince William Sound, according to data attached to the memo. Unmarked otoliths dominated in some creeks, such as Humpy Creek, where 98.4 percent were unmarked.

Hatcheries mark salmon by thermal means, where the water temperature holding fry gets raised and lowered to create a pattern in salmon otoliths something like a Morse code. In a phone interview with the Homer News on Monday, Dec. 11, Hollowell pointed out that while Tutka Bay and Prince William Sound hatcheries thermally mark otoliths, the Kitoi Bay Hatchery on Afognak Island run by the Kodiak Regional Aquaculture Association does not thermally mark salmon. That means some otolith samples that show up as unmarked could come from Kitoi Bay.

“What I would like to know is what is the percentage of wild and what is the percentage of Kitoi Bay,” Hollowell said. “Those might be 100 percent Kitoi or 100 percent wild. There’s no way for us to know that.”

Hollowell said he was surprised at how little Tutka Bay hatchery pinks strayed. Humpy Creek had no Tutka pinks and only 1.6 percent Prince William Sound pinks. He said he was scratching his head figuring out why the Tutka pinks didn’t stray.

“Whatever they’re doing, they’re doing it right,” he said of the Cook Inlet Aquaculture Association that manages the Tutka Bay hatchery. “That’s what I’ve told the CIAA board. They need to figure it out and teach Prince William Sound.”

Hollowell said he thinks the warm winters of 2015 and 2016 still might have had something to do with the glut people saw in lower Cook Inlet.

“Maybe the hatchery fish were following the few wild fish that made it into the streams and survived,” he said. “If that doggone Kitoi fish ahd been marked, we might know.”

At a Regional Planning Team meeting held at Cook Inlet Aquaculture Association’s headquarters on Dec. 7, the otolith sampling study came up as a topic of concern for the public. The Regional Planning Team, a stakeholder group coordinated by the state to advise on hatchery permit issues, includes fishermen, hatchery representatives and regional Fish and Game officials. Nancy Hillstrand, a Sadie Cove resident, said at the meeting that she was very concerned about the straying issue. She asked that Fish and Game regulators prioritize wild fish health over hatchery production.

“We have portfolio stocks that are being invaded and desecrated down in Lower Cook Inlet by Prince William Sound fish,” she said. “This needs to be fixed and stopped. It means we’re raising too many fish.”

Otis, who attended the meeting, said Fish and Game researchers were concerned too and were gathering data to determine a future course of action. This winter, the researchers plan to work with Fish and Game’s genetics department on the problem, he said.

“Nobody’s got their heads in the sand — everybody is trying to look into this,” he said.

Sam Rabung, the section chief in Fish and Game’s Aquaculture Section and a member of the Regional Planning Team, said at the meeting the presence of Prince William Sound hatchery fish in the Homer streams is likely not new. Salmon naturally stray from their home streams as a survival tactic, so it’s likely that straying has been going on from the Prince William Sound hatcheries since their inception in the 1970s, he said.

“Presumably these Prince William Sound pinks that we’re finding in Lower Cook Inlet didn’t just start now,” he said.

Fish and Game is currently in the sixth year of a long-range study on the impacts of hatchery salmon straying, focusing largely on Prince William Sound and Southeast Alaska. The study is expected to continue through 2023, though Rabung said the researchers might like to extend it further to capture another salmon life cycle in their data.

“The main driver is we understand that salmon stray, but we don’t know what that means in terms of fitness, and that’s why we’re following the generations,” he said.

CIAA has recently reopened operations at the two Lower Cook Inlet hatcheries for pink salmon. In building up brood stock at both facilities, the operations have sparked controversy in Homer, particularly the Tutka Bay Lagoon Hatchery. Tutka Bay is within the borders of Kachemak Bay State Park. At a hearing in May regarding a permit for CIAA to move its net pens into Tutka Bay, dozens of locals turned out to protest the operations, saying they were concerned about the introduction of millions of hatchery pink salmon damaging the marine ecology of the bay.

Ultimately, CIAA received its permit, but plans to scale back the number of fry released from the net pens in the open bay versus in the lagoon. At the planning team meeting, CIAA Board of Directors President Brent Johnson said they scaled back the number of fry as a calculated risk because they’ve never had the net pens out in the open bay before. They also plan to put a different otolith mark on the fish released from the bay to help determine their survival rate, he said.

Tutka Bay Hatchery ran into a number of snags this year; early in the year, the fry line between the hatchery and the net pens, where the salmon are imprinted, was frozen and the staff had to thaw it out before the salmon could be transferred. In the middle of the egg-take season, a fire consumed one of the sheds on site, and in September, a flood in Tutka Creek made collecting salmon difficult, though the weir the staff use wasn’t lost, said CIAA Executive Director Gary Fandrei.

On top of that, egg survival has been “disappointing,” he said — between 50 and 60 percent survive, in part due to high sediment levels in the water available at the hatchery. The organization is looking into ways to solve the siltation problem, has installed new fire equipment after the shed burned down and is working with the Alaska Department of Environmental Conservation on methods to sell the fish carcasses from egg-takes to processors rather than disposing them in Tutka Bay.

Reach Elizabeth Earl at elizabeth.earl@peninsulaclarion.com. Michael Armstrong from the Homer News contributed to this article. Reach him at michael.armstrong@homernews.com