Talking fish genomics in Gloucester

After an hour-long community talk on how genomics can support sustainable fisheries for the future in City Hall’s Kyrouz Auditorium on Wednesday, March 22, Gloucester Marine Genomics Institute fisheries research scientist Tim O’Donnell, left, stands with one of GMGI’s founders, professor Marc Vidal, who moderated the live, in-person talk before 100 people as part of the Gloucester 400+ celebration.

Gloucester Marine Genomics Institute’s 10th anniversary just happens to coincide with 400th anniversary of the nation’s oldest and one of its most storied working seaports at a time when the fishing industry has been snagged by state and federal regulations meant to keep the local fishery sustainable.

A community talk as part of the Gloucester 400+ celebration with 100 people in Kyrouz Auditorium in City Hall on Wednesday showed how the use of advanced molecular techniques at GMGI can be used to support sustainable fisheries into the future.

A team at GMGI has figured out how to identify Atlantic cod which spawn in winter versus those that spawn in the spring. Its staff have used environmental DNA techniques to survey the types of fish found in the Annisquam River, among other things.

GMGI fisheries research scientist Tim O’Donnell talked about how his team’s research may help keep fisheries sustainable so future generations “can also have the privilege of having access to the bounty of the ocean.”

When it comes to fisheries science and management, O’Donnell said, various entities collect data on their local fisheries through classic surveys or by analyzing fish biology. But certain species or areas in the ocean can be hard to study and that can create gaps in the data.

O’Donnell said his team’s research focuses not just mining the data gap but also finding the gaps using the study of DNA.

“Where are these areas where we can contribute with what we bring to the table to maybe bridge that data gap,” he said.

GMGI is using cutting-edge science to fill in the data gaps when it comes to assessing fish stocks, data that can be used to help inform federal and state regulators when it comes to when to open or close a fishery or even tell what kind of fish might be living in a certain area at a certain period of time.

One research focus is on population genetics which looks at changes in a species genome over time and geographic area to help understand a fish stock’s structure.

GMGI is also using environmental DNA techniques to assess fish from the DNA they leave behind in a sample of water. It is also looking to develop innovative tools using genomics and molecular techniques to assess fishery stocks.

Assessing Atlantic cod is quite complicated, O’Donnell said, with five different stocks in New England waters. The most complex area is in the western Gulf of Maine off Gloucester where there are two different populations — spring and winter spawners.

O’Donnell said his team worked with the Massachusetts Division of Marine Fisheries to collect 200 Atlantic cod in known spawning conditions so they knew if they were winter or spring spawners.

Then, they sequenced the cods’ genome, and found about 3 million different sites along the genome where there was some overlap. But they did not see much differentiation. When they drilled down, they found that if they just looked at 25 spots along the genome, they could tell the difference with about 90% accuracy.

Now, with a small piece of fin clipped from a cod, they can tell whether it’s a spring spawner or a winter spawner, which can help stock assessment biologists do their work.

Locally, GMGI conducted a year-long environmental DNA study looking at the fish population of the Annisquam River, where data on the population was lacking.

“We found 65 different fish species, everything ranging from the kind of the bottom of the fish food chain … all the way up to top predators and endangered species like sturgeon,” O’Donnell said.

The issue with eDNA sampling, however is fish DNA can be transported by currents. Other factors also have to be considered.

One of their sample sites was at the Mile Marker One restaurant at the Cape Ann’s Marina Resort off Essex Avenue, O’Donnell said, “and I can tell you we got a lot of tuna right at the Mile Marker. Do I think tuna is swimming around the Annisquam? No. But are they prepping a lot of tuna dishes as the Mile Marker? Yes they are.”

You can find the community talk on 1623 Studios’ Youtube channel at{em}.

Ethan Forman may be contacted at 978-675-2714,or at

Ethan Forman may be contacted at 978-675-2714,or at

Trending Video

Recommended for you