Phase II

Exploring a genetic approach to estimating the size of marine fisheries

Seed fund project details

About the research project

The Atlantic halibut fishery brought $90-million worth of export sales into Atlantic Canada last year. Managing a commercial fishery of this value is crucial, and doing it sustainably starts with understanding the population dynamics of the stock — a term in ecology that refers to changes to a population over time.

“We want to know whether populations are changing, if they’re declining or increasing,” says Daniel Ruzzante, a biologist at Dalhousie University.

Ruzzante is currently collaborating with Fisheries and Oceans Canada (DFO) to develop and validate a promising new alternative for estimating how many fish make up the halibut population on the Scotian Shelf, the target of the fishery off the coast of Nova Scotia. Their partnership, which will explore the application of the close-kin mark-recapture method (CKMR) for estimating population abundance, grew from an Ocean Frontier Institute Seed Fund.

“Estimating population abundance in the sea has traditionally been very challenging,” explains Ruzzante. “It can be very difficult to obtain reliable estimates of abundance in the sea because all available methods, many of which rely on measures related to catch per unit effort (CPUE), are potentially subject to various sources of unknown bias.”

A well-established technique to estimate abundance in ecology is known as the mark-recapture technique. This is how it works: a number of fish are caught, tagged or marked in a recognizable way, then released again. During a second fishing expedition, after the marked fish have had the chance to mix within their population again, more fish are caught and some of them will be marked fish from the first trip. Then a simple calculation using the numbers gathered will produce an estimate of abundance. But this approach isn’t easily applicable, or in many cases even feasible, in the marine environment or with commercially exploited and widely abundant marine fish. This leaves experts like Ruzzante looking for a more efficient and precise way to estimate abundance.

That’s where close-kin mark-recapture comes in. In this approach, genetic information from the tissue of living or dead fish bypasses the need for recapturing the same individual. One of its selling points is that genetic markers examined in the DNA extracted from tissue samples can be used to uncover patterns of parent-offspring pairs and other close relatives, the number of which, in turn, can be used to estimate population abundance in a mark-recapture framework. The statistical modelling of those patterns leads to precise estimates and fewer logistical expenses than traditional methods.

The approach was first proposed in 2001 by Hans Skaug, a professor of statistics at the University of Bergen, but the genetic tools available back then weren’t advanced enough to put the method into practice.

As technology progressed in recent years, however, a handful of researchers began testing CKMR for use in ecological research. Chief among them was a group of researchers led by Mark Bravington of the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Tasmania. His team used CKMR to study the population abundance of southern bluefin tuna, white sharks, and an assortment of other species of management and conservation concern.

“The paper that really enthused me about CKMR was the Bravington study in Nature Communications,” says Ruzzante. “It’s the kind of work that makes me tick.”

Ruzzante knew that CKMR held promise and set out to test and validate it in one of his own studies using four years of genetic data collected from brook trout, which was published in 2019. So, he also knew that such a new method came with a whole new set of intricacies. If it was really going to compete with the standard methods used in resource management and conservation today, Atlantic Canadian scientists needed to be well-versed on the topic.

Ruzzante teamed up with Joanna Mills Flemming, a statistics professor at Dalhousie, and applied for help from the OFI Seed Fund to organize a workshop on CKMR. It would train 15 highly qualified personnel (HQP) representing key fields in academia, government, and industry: statistics, bioinformatics, molecular genetics, fisheries science, and population biology.

And who better to lead the training than those who’ve pioneered the CKMR method: Skaug, Bravington, and two NOAA scientists named Eric Anderson and Robin Waples. Ruzzante invited them to Halifax, N.S. for a week-long workshop in July 2019.

“The Seed Fund gave all of us this birds-eye view introduction to CKMR,” says Ruzzante. “We needed to understand the challenges of this method and all of the things that need to be taken into consideration to develop an interdisciplinary project like this.”

Shortly afterward, Ruzzante’s partnership with the DFO began.

“CKMR is a complementary method to mark-recapture and it has the potential to provide a proper abundance estimate,” says Ruzzante. “And it’s not just abundance. This can help estimate age-specific mortality rates, and other parameters needed to understand the population dynamics of the species of interest.”