Replicating nature 

Can DNA research help bring back Champlain salmon?

By Mike Lynch

Fish biologist Kurt Heim waded through the waist deep Saranac River current as technician Dylan Jennison’s feet splashed through the shallows along the shoreline. Each man, dressed in a tan dry suit, held the end of a net. 

“Yeah, we got a fish,” Jennison yelled.

It was early November. Trees were mostly bare, snow had started gathering in the highest peaks, and Atlantic salmon were finishing up their fall migration up Lake Champlain tributaries. 

On this day, a U.S. Fish and Wildlife Service crew was working on a new 9-year stocking study that relies on parentage-based tagging, a novel method of tracking fish by tracing their familial roots through DNA. Traditionally, the agency has marked its stocked fish by clipping a fin. The genetic tagging method is considered less invasive, labor intensive, and able to track more fish.

The study—which is being aided by the state Department of Environmental Conservation and Ausable River Association—will help the agency evaluate their stocking methods and aims to build upriver runs and natural reproduction by salmon.  

“It’s really about learning which techniques in our toolbox are working the best,” Heim said. 

The Atlantic salmon population was eliminated from the Lake Champlain watershed in the 1800s because of dams impeding spawning runs, pollution, and loss of habitat.

But there have been signs of improvement in recent years, indicated by young wild salmon spotted in the Boquet River. But only hundreds of those fish have been found and management agencies still consider stocking salmon the best way of sustaining the population in the watershed. 

Tens of thousands of 1-year smolts and fry (recently hatched fish) are stocked into Champlain tributaries on the New York side. Adult salmon are also stocked upstream in the Boquet, with the hope that the females lay eggs and produce young fish.

Assessing the fish

The crew netted five fish in about 45 minutes and began fish assessments. Reaching into a container, technician Shelby Scarfo lifted a two-pound salmon. With one hand she gripped the tail. She wrapped her other hand around the body below the pectoral fin. Turning over the fish, she called out that it was a “female” and “not a recap,” meaning it hadn’t been netted yet.

Scarfo reported that it had one sea lamprey wound. Lamprey are parasitic and attach themselves to salmon with their suction disk mouth, draining the fish of its body fluids. They have harmed salmon and lake trout populations in Lake Champlain. 

Next, Scarfo extracted part of a fin with a tool similar to a hole puncher and handed it to Heim, who stuck it to a sheet with other samples. 

The fin piece contained the DNA material that is added to the U.S. Fish and Wildlife’s database. If a fish they catch had been stocked for this particular study, they will find its parents in their database. Female salmon lay thousands of eggs, so the fish can be traced to a limited number of parents.

Scarfo, with the help of Jennison, went on to measure and weigh the fish, before putting it back into the container. After repeating these steps with the four other fish, they released them back into the river. 

This was the third river—including the Ausable and Boquet—the crew visited this day. It was also the final one for the season, finishing a process begun in late September. 

For the season, they netted 84 salmon in the Saranac, 26 in the Ausable and 60 in the Boquet employing two netting methods. One required dragging a net through the water and another required the gear to be set up overnight during weekdays.

In addition to sampling the fish in the fall, the crews do summer surveys of younger fish. In November and December, the crews check the Boquet for nests known as redds used by spawning salmon. 

Evaluating salmon genes

Heim said one of the main goals of the study is to evaluate how well salmon with different DNA are performing during the fall spawning run.

“The fish that evolved here in Lake Champlain over thousands of years were perfectly suited through local adaptation to thrive in this environment, so we’re working now to try to determine what genetic strain of fish that we can bring here that will perform well in this environment,” Heim said. “So that’s one of the hurdles—trying to replicate what nature did so well over thousands of years, to try to quickly bring a population back.”

He said there are a variety of salmon DNA under study. One is what he calls “maximum genetic diversity,” while another is known to have a high level of tolerance to low thiamine (also known as B1 vitamin) levels in their systems. 

Salmon that eat a lot of alewives, a small invasive fish, have been found to develop low thiamine levels. Studies have shown that adult salmon with this condition struggle navigating upstream rapids and cascades. If they overcome those obstacles, their eggs often fail to produce salmon or fry have lower survival rates.

On the Boquet River salmon must ascend a series of cascades in Willsboro to get to upriver spawning habitat.

Fish biologist Jonah Withers, who headed a radio telemetry study to track salmon on the Boquet last year, said data indicate that most fish don’t make it over the cascades.

His study found that only one of 30 salmon he tracked crossed the cascades and 20 of the 28 released upriver were swept downstream. Only two made it to prime spawning habitat.

“We’re not really too sure as to why,” said Withers.

He said the fish may have become disoriented after the tracking equipment was inserted in them—it required a minor surgery.  Habitat and low water levels may have played a role. 

In addition, the agency found 126 spawning beds below the cascades and only 56 above it. And many of those beds above the cascades—where a dam was removed several years ago—were likely created by hatchery salmon released upstream, he said.

Below the cascades is less than ideal spawning habitat because predator fish, such as bass, have easy access to the young fish, he said. In addition, the river bottom is sandy and not gravelly like the upstream spots, which have traditionally been more suitable for salmon and trout.

“It’s great sea lamprey habitat, but not very good juvenile salmon habitat,” Withers said.

RELATED: The Explorer’s “Rewilding Our Waters” series takes readers to the Boquet and Saranac rivers, where efforts are being made to restore salmon populations. READ MORE

At the hatchery, staff can place salmon eggs in a thiamine bath to increase their vitamin B levels and bolster survival, Heim said. 

But Heim said they developed the strain tolerant of low thiamine by skipping the bath for three consecutive years to study survival.

“There was massive mortality but certain families of fish, or fish with certain parents, tended to do really good,” Heim said. 

Those fish that survived are now the hatchery broodstock, or parents, with the low-thiamine tolerant genes. 

The scientists are trying to do what nature does over thousands of years. Their study will help them see if their experiment works.

“It’s hard to jumpstart from scratch a population that has been completely extirpated,” Heim said.