A program to prevent the extinction of Atlantic salmon in the inner Bay of Fundy has helped maintain numbers in a few rivers but after 15 years, efforts to rebuild the stock have failed and non-native genes have mixed into the population, according to a federal report.

The review by Fisheries and Oceans Canada says the near-total loss of salmon once they reach salt water continues to prevent the re-establishment of wild self-sustaining populations of inner Bay of Fundy salmon.

The cause of extremely high mortality — 99 per cent — at sea remains unknown.

It's believed just 200 adults exist in the 50 salmon rivers that flow into the inner Bay of Fundy, which includes Chignecto Bay and the Minas Basin. But it's likely there would be none at all without the inner Bay of Fundy Live Gene Bank.

"The live gene banking program is meeting its prime objective, which is maintaining the genetic diversity of the inner Bay of Fundy salmon and is also preventing the full extirpation or extinction of that population," said Kent Smedbol, manager of population ecology for DFO's science sector in the Maritimes.

How the gene bank works

DFO has been collecting juvenile fish from the wild and rearing them at two federal hatcheries; one in Mactaquac, N.B., and another in Coldbrook, N.S.

The adults are selectively mated to maintain genetic diversity and their offspring are released in their native rivers as young as possible to them help adapt and maximize natural selection.

The goal is to maintain population in three "index" rivers, the Stewiacke and Gaspereau in Nova Scotia and the Big Salmon River in New Brunswick. Ten other rivers are also involved in the program.

More than 800,000 salmon fry were released in the index rivers in 2016.

There is no recent financial data on the program, but the annual estimated cost between 2004 and 2010 was $400,000.

What was assessed

DFO's review looked at levels of inbreeding and fitness as well as examined release strategies used in the program and found few problems.

However, during the review, scientists discovered the presence of European and other non-native salmon genetic variants in the inner Bay of Fundy population between 1997 and 2012, a genetic transfer process known as introgression.

"Analyses indicate that farm salmon escapes exhibiting European ancestry have successfully reproduced in several iBoF [inner Bay of Fundy] rivers and appear to have spawned with endangered iBoF Atlantic salmon," the report says.

DFO has never licensed the use of European-strain broodstock — mature fish used for breeding — in Nova Scotia or New Brunswick fish farms.

Testing also detected the genetic presence of Saint John River salmon, which would be considered outer Bay of Fundy, in the inner Bay of Fundy population. But it did not determine whether it was from strays or escapes from large fish farms in the area.

'The science is very clear'

Geoff Giffin of the Atlantic Salmon Federation said the findings are "alarming" and wants DFO to carry out more extensive genetic testing to determine if, in fact, farmed fish are getting into the gene pool and then take steps to cull them — one of the recommendations in the review.

"Whether or not the genetics are European or local genetics, if they are escaping from farms, farmed salmon are domesticated animals and the science is very clear on the impacts of domestication on salmon. Over time their offspring become less fit, their survival goes down, they are less adapted to the local environment," he said.

Giffin is calling on DFO to compel the aquaculture industry to release genetic databases to make tracing the source of the introgression.

The executive director of the Atlantic Canada Fish Farmers Association said she had not read the report and declined specific comment. However, Susan Farquharson said the industry only uses Saint John River-strain fish and has been screening for European gene variants for 20 years.

"DFO has the regulatory authority to check for genetics in our fish any time they want through introduction and transfer regulations," she said.

DFO screening

Smedbol said the department did not wait for publication of the review to respond to what it learned.

He said it has already implemented tests and techniques in an effort to screen out non-native gene variants. He predicts current introgression can be removed from the pedigree salmon it produces for the Stewiacke and Gaspereau rivers but it may be too late for New Brunswick's Big Salmon River.

"If you have enough mixing, so to speak, of non-native information with the genetic information it becomes very difficult to pull them apart, to parse them out when you build your mating plans," he said.

The report urges DFO to freeze salmon semen, known as milt, "before additional genetic change occurs."

"Cryopreserved milt may be used later to partially restore genetic characteristics of iBoF Atlantic Salmon," the report said.

DFO has launched a number of research projects in connection with inner Bay of Fundy salmon starting with predation. It will also consider the implications of ocean warming and releasing more smolts, which are salmon ready to go to sea.