Aging halibut while saving halibut

Traditional methods of determining the age of halibut are generally accurate. But they have a number of drawbacks—especially for the halibut.

“The biggest limitation is that traditional aging methods are lethal,” explained Claudia Berry, a graduate student at Alaska Pacific University (APU) studying the topic “Estimating age requires extracting the otoliths, or ear bones, which means the fish must be killed.”

Berry is part of an Alaska Sea Grant-supported research team, led by Nathan Wolf of APU, Josep Planas of the International Pacific Halibut Commission, and Wes Larson of NOAA, that’s pioneering a non-lethal method of determining the age of halibut and other groundfish. By tracking a process called DNA methylation, they can calculate a halibut’s age with just a clip from its fin.

“It provides a non-lethal alternative for age estimation, therefore allowing researchers to study fish populations without sacrificing individuals,” Berry explained. “In addition, using DNA methylation as an aging tool could expand opportunities to study life history traits, population dynamics, and long-term ecosystem change.”

Extracting otoliths has long been the primary method for tracking the age of many fish. The tiny ear bones accrete layers of calcium carbonate annually over the life of the fish, which makes it possible to age a fish by counting otolith rings. There are disadvantages to the method, however. In addition to having to kill the fish to retrieve the otolith, it’s a time-consuming process, and one that can require considerable expertise to undertake.

“We need highly specialized people, and it becomes increasingly difficult to read otoliths in older fish,” Berry noted. “The rings get closer and glossy. It’s hard to find the people to do it.”

The team’s method instead relies on measuring DNA methylation, a biological process to regulate gene expression that results in patterns that change predictably with age. Researchers can model these patterns to generate molecular age predictors, known as “epigenetic clocks,” that can accurately determine a fish’s chronological age. Fortuitously, the fin clips needed for DNA methylation-based aging are already being taken from halibut for other studies, meaning the fishes’ ages can easily be determined in conjunction with existing work.

Using a set of 250 samples—10 fish each from 25 age classes—the research team is distinguishing DNA methylation signals in fin clips. Then they’re creating a map of methylation patterns on the halibut genome, and using it to develop an age predictive model. The end result, Berry said, will be a cost-effective test to estimate halibut ages on a large scale, which will benefit both researchers and fisheries managers.

“Understanding a fish’s age helps researchers determine growth and maturity rates, which are critical for setting sustainable harvest regulations,” she said. “Effective age estimation supports healthy fish populations, and helps ensure long-term availability for both fisheries and consumers.”

Kyle Kolda contributed to this story.