Codes in Cod Genes
With Sea Grant funding, two scientists scrutinize DNA sequences to help refine
strategies for managing Pacific cod stocks
By Colleen Craig
Are all cod in the north Pacific Ocean closely related?
At first glance, this might not seem unreasonable: in principle, the pelagic larvae of these fish could be easily dispersed throughout the north Pacific, resulting in a thoroughly mixed gene pool.
However, recent work by Washington Sea Grant-funded scientists Lorenz Hauser and Mike Canino suggests otherwise.
This could have a profound effect on management of fishing seasons and quotas for Pacific cod (Gadus macrocephalus) in the northeastern Pacific Ocean and Bering Sea. Those seasons and quotas are currently based on the idea that these fish comprise a genetically homogenous group.
The work of Hauser, an assistant professor with the University of Washington's School of Aquatic and Fishery Sciences, and Canino, a researcher at the NOAA/Alaska Fisheries Science Center, has shown that the population of Pacific cod is actually made up of several genetically distinct, overlapping subpopulations. When it's time to reproduce, the fish in each of these subpopulations tend to return to the same spawning grounds. In this way, they are more involved in replenishing that particular subpopulation than are cod from more distant locations. The process is called "self-recruitment."
Because there are no obvious physical barriers to the dispersal of larvae by ocean currents, scientists and resource managers had previously assumed that Pacific cod populations operated as "open" systems. "If this were true, fish removed from one area would be replenished with outside recruits," says Canino.
The notion of stock replenishment by outside recruits may have contributed to the collapse of Atlantic cod (Gadus morhua) stocks in the Maritime Provinces of Canada during the early 1990s. Subsequent studies funded by the Canadian government indicated that Atlantic cod populations were replenishing on more localized scales than were recognized at that time.
Scales of Space and Time
The degree of self-recruitment and the spatial scale at which this occurs in marine fishes are not entirely clear. Some scientists believe self-recruitment may be beneficial, especially for fishes such as cod, whose offspring develop in near-shore habitats. These waters are generally richer in nutrients than in openocean environments, providing a more favorable environment for larval survival. The developing larvae and juveniles may be retained in nursery areas, maturing to adulthood in the same waters where their lives began.
Another possibility is that, when it's time to spawn, adult Pacific cod exhibit some degree of natal homing. "There are two strategies here," says Canino. "In one, the member of certain fish stocks spawn where they were born. In the other, the stocks spawn where they spawned previously." Known respectively as natal philopatry and site philopatry, the two strategies are synonymous for salmon and several other fish. "It's unclear, though, if that's true with other marine fish, including Pacific cod," Canino says.
"There is undoubtedly some unknown degree of dispersal that occurs. However, if larvae and juveniles are largely retained within a given geographic area, the chances are greater that they will spawn in that area, rather than far away," he adds.
In a management context, self-recruitment may result in subpopulations that respond independently to fishing pressure. Hauser and Canino are striving to identify the degree that populations are subdivided in U.S. management areas. Their findings will help to support NOAA's mission to maintain sustainable fisheries.
"Currently there are two stocks of Pacific cod recognized for management purposes in our nation's waters," says Canino. "Nonetheless, I think we're beginning to see some evidence that population substructuring occurs within these management units."
Insights from Microsatellites
Determining the spatial extent of a subpopulation is difficult, because a "localized" scale in the marine environment may extend over many miles. Furthermore, since there are no physical barriers to formally separate them, the subpopulations are contiguous across the north Pacific. So the team relies on genetic studies to identify subpopulation structure in the cod stocks.
Those studies rely on microsatellite DNA markers — a class of non-coding "junk DNA," which consists of short, repetitive DNA sequences that arise naturally from transcription errors during cell division. "The microsatellites perform no real function," Canino explains.
"Think of them as the boxcars on a long freight train," he says. "The first car (the engine) and the last car (the caboose) are unique, non-repetitive DNA sequences, but the middle cars (the boxcars) are all the same."
Mutation rates for microsatellites are high and usually involve the addition or removal of a single boxcar, in a process known as "stepwise mutation." This creates a large amount of genetic variation in natural populations, which can be screened by technicians in a laboratory.
Since microsatellite DNA doesn't help or hinder an organism, it is unaffected by selection pressures. "Geographically isolated subpopulations will develop different microsatellite frequency distributions," Canino says. "That helps us figure out who's who."
Clues from Clipped Fins
For their Sea Grant-funded study, Hauser and Canino collected 100 Pacific cod from each of eight sampling sites in Puget Sound, the Bering Sea and across the north Pacific Ocean to coastal Korea and Japan. A small piece of fin tissue was clipped from each individual fish and the DNA was later screened for variation in 12 microsatellites.
The initial results of this work, presented in February at the 14th Western Groundfish Conference in Newport, Oregon, yielded three major findings. First, the team reported, the levels of population structure in Pacific cod are similar to those of the closely related Atlantic cod. Second, a clear distinction can be made between Asian and North American stocks of Pacific cod — a result consistent with an earlier study using less sensitive genetic markers. This division most likely reflects a legacy of stock separations during the Pleistocene ice age, (approximately 18,000 years ago), when tidewater glaciers extended from the Aleutian Islands to Puget Sound. Third, Pacific cod samples from North American waters show a clear genetic isolation-bydistance pattern, which infers that mating primarily occurs between adjacent groups. That pattern would not exist if mating occurred at random, throughout the northeastern Pacific Ocean.
While the genetic differences among North American samples are small, they are significant, especially when one considers the size of a Pacific cod population, which may include billions of individuals. The evolutionary force primarily responsible for population divergence, or "genetic drift," as it is commonly known, is inversely proportional to population size and is, thus, extremely weak in such large populations.
"If you see genetic structure over these scales with marine fish, you have to infer that migration and successful interbreeding are not rampant," says Canino. "That's because the exchange of only a small number of successful migrants per generation would completely homogenize any genetic signal."
More to Come
Hauser and Canino's investigations represent the most comprehensive preliminary studies of Pacific cod populates to date. They will provide important baseline information for future studies, from which strategies for successfully managing Pacific cod stocks can be devised.
The distinctiveness of Puget Sound's Pacific cod stocks, whose numbers have declined significantly since the late 1980s, may be resolved using such strategies — based upon inferences obtained from a meticulous examination of so-called "junk DNA."
Spring 2006
Contact David G. Gordon, Science Writer for Washington Sea Grant, for further information.