For more than 100 years, conservationists have tried to restore stocks of Atlantic salmon in Maine rivers, including the Penobscot. Many river-specific threats to salmon, including pollution and barriers to passage in the form of dams, have been studied and demonized over the years.

Today, Maine’s rivers flow cleaner than they have in decades. Dams are being torn out, both on the Kennebec and Penobscot rivers. Salmon should be flocking back. Or should they?

Earlier this month, Katherine Mills, a research scientist at the University of Maine and the Gulf of Maine Research Institute, along with peers Andrew J. Pershing, Timothy F. Sheehan and David Mountain, published a paper that paints a grim picture of the challenge facing Atlantic salmon at sea.

In that paper, Mills points out that climate change and a decline in available food — the relocation or reduction of plankton and fish called capelin — have helped lead to a decline in salmon stocks that has been taking place since 1990. And the outlook for the future is not too bright.

“What we really are seeing is that changes in salmon can be most strongly linked to the loss of capelin as a prey source for them in the Labrador Sea, but can also be tightly linked to [water] temperature,” Mills said.

Salmon in North American rivers take different routes on their migration paths, but eventually end up — or aggregate — in a few key spots. One is the Labrador Sea, where they spend summers. Another is off west Greenland, where they spend winters. Eventually, usually after two winters at sea, Atlantic salmon swim back to the rivers where they were born or stocked.

But back in 1990, a pulse of cold water pushed their preferred bait fish — capelin — out of the area where salmon typically found them. The capelin ended up off Newfoundland instead. And they never really came back.

“So, it was a short-term cold event that lasted a very short period of time, about a year,” Mills said. “But it was enough to make the capelin move to warmer areas … and I guess the sense of understanding that I’ve been able to get from people up in Canada, who have worked on this, is that they think that [capelin] haven’t come back, not because of the water temperatures not being ideal, but because they’re doing just fine where they are.”

Not so, the salmon.

John Kocik, the chief of Atlantic salmon research for the National Oceanic and Atmospheric Administration in Orono, said that all North American salmon stocks have dwindled since about 1990.

“It’s not just the U.S.,” Kocik said. “Labrador and Newfoundland are having these same issues, and even Quebec. So farther north, they’ve had this same collapse. But when you go from 1 million fish to 300,000 fish [as has happened on some Canadian rivers], it doesn’t seem quite as bad as going from 6,000 fish to 1,000 fish, which is kind of what we’ve done [in Maine].

Kocik explained that salmon face a tough battle in their quest to go to sea and eventually return to spawn.

In the Penobscot River, for instance, for every 10,000 salmon smolts that were stocked during a period before 1990, which he called “the good old days,” about 80 would eventually return to the river. Nowadays, that return rate is more like 20 returnees per 10,000 smolts.

The Narraguagus River in Washington County generally has had a higher survival rate, in part, according to Kocik, because naturally reared fish, which spend the early part of their lives in the river, fare better than those raised in hatcheries. Still, in the 1990s scientists learned that only about 45 percent of smolts heading out to sea actually made it as far as the Gulf of Maine. On the nearby Dennys River, only 25 to 30 percent of smolts made it to the Bay of Fundy.

Kosik said Mills’ paper was eye-opening, and answered some questions that he and others have had for a long time. Among them: When the initial collapse of salmon stocks in Maine rivers began, why did some Canadian rivers fare better, at least for a time?

“Now [the Canadian rivers] are starting to go down a little bit, too, so I think it’s a numbers and distribution game,” Kocik said. “How many metric tons of capelin are there, and where are they?”

Kocik said the factors that Mills uncovered seem to explain a great deal about salmon — and other species.

“The short version is, with the temperature changes and all that, the types of zooplankton changed [in certain areas that salmon aggregated],” Kocik said. “That probably led to the capelin population collapse and that’s just cascaded through the ecosystem. And it’s probably hit cod as well as salmon.”

Warming ocean temperatures have decimated cod stocks and led to an explosion of lobsters, which have thrived without the presence of a key predator, attendees at a conference in Portland said last week.

Mills and her group studied ocean temperatures, both long- and short-term, and learned that in many parts of the salmon’s migration, waters were warming.

“What we focused on was that temperature in the Labrador Sea is warming much faster than other areas,” Mills said. “It’s warming from a half a degree to a degree [Celsius] a decade … this has a very strong direct correlation with Atlantic salmon, because temperature also shapes the whole lower trophic system in terms of phytoplankton productivity and zooplankton as well, and how well they can support forage fish like capelin.”

Harold “Hal” Borns is the founder of the University of Maine’s Climate Change Institute, and at age 86, is still working at the institute despite his “professor emeritus” status.

Borns admits that he knows little about the life history of salmon, but has studied data that reflects climate change over the past 10,000 years. Over the past 1,000 years, he said, the Gulf of Maine seems to be getting colder, not warmer. He wonders whether salmon would return to Maine rivers at all if not for substantial hatchery-based stocking efforts.

He said scientists he works with have studied piles of shells and bones — middens — that were left beside Maine rivers by Indians as much as 4,000 years ago. Not much evidence of salmon was found. The question that raised — were salmon even in Maine waters that long ago? — was more difficult to answer, Borns said.

“Maybe they’re there and they’re not preserved any more,” Borns said, pointing out that salmon bones are quite fragile.

Kocik and Mills both admitted that much of the salmon conservation work and study that has taken place has focused on the rivers; less has focused on ocean survival of the species. And below that, there are knowledge gaps that need to be filled, Kocik said.

“People study plankton. People study salmon and tuna. There’s not a lot of work done on these little silver fish, [capelin] that are the middle of the ecosystem, that makes everything click,” Kocik said.

Both Kocik and Mills say focusing on genetic diversity when making stocking decisions — making sure a wide variety of salmon, from different rivers, get the chance to use their particular genetic gifts while trying to make it to the ocean, survive, and return — should be a key part of conservation efforts in the future.

“I think this [study] doesn’t paint a good picture of what’s coming for salmon during their time at sea, but I do think there are things we can do to try to reduce the impact as much as possible,” Mills said.

Habitat improvement and capelin research are among the areas that can make a difference, she said.

“I think one thing we can do is protect those forage fish,” MIlls said.

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John Holyoke

John Holyoke has been enjoying himself in Maine's great outdoors since he was a kid. He spent 28 years working for the BDN, including 19 years as the paper's outdoors columnist or outdoors editor. While...