Genomics confirms fish farm escapees breeding with wild Atlantic salmon in Newfoundland

Researchers with Fisheries and Oceans Canada (DFO) have confirmed that farmed salmon are interbreeding with wild Atlantic salmon in rivers along the south coast of Newfoundland—something that may be putting the already threatened local population of wild salmon at additional risk.

Dr. Ian Bradbury, the DFO Research Scientist in St. John's who led the study, says whether salmon that escape from aquaculture operations in the region interbreed with wild salmon has always been an unanswered question. "Offspring of farmed Atlantic salmon and wild Atlantic salmon look the same—they're the same species," says Dr. Bradbury. "We had no way to tell whether escaped farm fish were even getting into the spawning grounds, let alone whether they were breeding with the wild salmon."

Enter genomics

The answer would be found at the molecular level—decades of selective breeding for characteristics such as faster growth have resulted in farmed salmon having a unique genetic fingerprint. With funding from the Government of Canada's Genomics Research and Development Initiative (GRDI), Dr. Bradbury was able to conduct a detailed analysis of the genome of both wild and farmed Atlantic salmon. This was a significant undertaking in itself—with more than three billion base pairs, the Atlantic salmon genome rivals the human genome in size and complexity.

"Comparing the two, we were able to identify a number of specific areas in each genome where their DNA varied in the same way," says Dr. Bradbury. "With these genetic markers, along with the analytical software we developed as part of the project and a next-generation genotyping platform, we had everything we needed to quickly distinguish a wild Atlantic salmon from a salmon bred for aquaculture."

Interbreeding confirmed

Dr. Bradbury's team collected DNA from thousands of salmon in 18 rivers along the south coast of the island. At the Bedford Institute of Oceanography in Dartmouth, Nova Scotia, biologist Lorraine Hamilton and her team in the Aquatic Biotechnology Laboratory examined the samples, searching for the markers identified by Dr. Bradbury.

"We identified both wild and farmed salmon, but we also found that, for a third of the fish, the DNA had some combination of the genetic markers identified for the wild and farmed salmon—a clear indication that these fish were hybrids, the result of the farmed salmon interbreeding with the wild salmon."

Salmon farm off southern Newfoundland. Fish can escape when their cages are damaged—by bad weather, or predators such as tuna and whales, for example. Fish also escape while being moved to and from their cages. (photo: DFO)

A threat to wild salmon?

While the study found widespread interbreeding—hybrid salmon were found in 17 of the 18 rivers included in the study—what's less clear is the impact it may be having on wild salmon populations.

"Wild salmon populations are adapted to life in a certain set of conditions—generation after generation, a population will follow the same ocean migration routes and return to the same river to spawn," explains Dr. Bradbury. "On the other hand, farmed salmon are adapted to life in very different conditions. They are bred to reach sexual maturity later and to grow to market size quickly—we know very little about how they or their hybrid offspring perform in the wild."

Dr. Bradbury notes that wild salmon populations are declining throughout southern Newfoundland, and rivers where wild salmon numbers were lowest had the highest rates of interbreeding—suggesting that small salmon populations may be most at risk.

The results of the research have been shared internationally, and Dr. Bradbury is now part of a study on the impacts of interbreeding on wild salmon populations with scientists in a number of other countries where fish farming is common, including the U.K., Denmark, Norway and others.

Informing aquaculture management

Geoff Perry, DFO's Director of Aquaculture Management for Newfoundland and Labrador, says the research led by Dr. Bradbury adds a whole new dimension to aquaculture management. "Before now, we had no way of knowing if interbreeding was even happening," says Mr. Perry. "Now we know it happens, and we can also see where and when it's happening—information that's critical to developing measures to mitigate the risk."

Mr. Perry notes that genomics-based identification also provides the capacity to trace an escaped salmon back to its farm of origin. "With that information, regulators will be able to take whatever corrective action is necessary to ensure the farm in question is complying with industry standards for containment."

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