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Along the West Coast this year’s salmon fishery is a disaster. Closures mandated by the Pacific Fishery Management Council and the National Marine Fisheries Service (NMFS) in an effort to curtail the take of the parasite-ravaged Klamath chinook will mean a loss of an estimated 90 percent or more of a normal season’s catch. Lengthy closures imposed from Monterey Bay to the Columbia River with openings mostly in areas where the fish aren’t, coupled with a 75 per fish week (an ordinary day’s catch) boat quota, is going to cost fishermen and their communities at least $100 million dollars in lost revenue this season.
The tragedy, of course, is that this should have been a good year for West Coast trollers with Sacramento River fall-run chinook stocks at some of their highest levels in history and abundant runs from other rivers as well owing to good ocean conditions the past few years. It should have been the season that could have helped fishermen get well financially. Instead it is turning into one that will drive some to bankruptcy and others out of the business.
It is well known that fishing did not cause the precipitous decline in Klamath stocks. A combination of factors culminating in 2002 of low and warm flows, poor water quality, and two virulent parasites led to massive fish kills that year and the subsequent loss each of the following years of young outmigrating salmon in the mainstem of the Klamath where an estimated 80 percent of the juveniles have become infected with a moratility rate approaching 100 percent.
Even though fishermen did not cause the problem, the agencies were forced to take steps to protect the remaining fish. To date, those efforts have been focused solely on fishing and not fixing problems in the river, but that’s another story.
What the Klamath problem highlights is the problem with weak stock management, i.e., curtailing fishing on abundant runs to protect the weakest stocks. No one is saying that weak stocks don’t need protection, but the measures that are taken can be draconian and there should be better ways to accurately determine where those fish of concern are in the ocean at a given time to be able to avoid them, while at the same time targeting abundant stocks.
Fifteen years ago fisherman Nat Bingham initiated the Sacramento Winter-Run Chinook Captive Broodstock program to prevent the extinction of this unique salmon run whose spawning numbers had dwindled to less than 190 fish by 1991. Part of that program involved the utilization of new DNA-based genetic stock identification which was being developed at the time by the University of California’s Bodega Marine Laboratory – one of the partners in the broodstock effort. The DNA markers for the fish – a kind of bar code – enabled managers to clearly distinguish the winter-run from spring, fall and late-fall chinook populations that were also in the Sacramento.
Bingham was fascinated with this research, seeing its management possibilities, not simply as a tool to keep from hybridizing runs in a hatchery or determining the presence of the fish on their migratory journey to the ocean. Utilizing this technology every fish in a sense was marked, not just a fraction of hatchery production. Thus, it would be possible to dispense with marking and tagging salmon, using instead their natural markers – that DNA bar code – to be able to tell where any – not just a tagged hatchery – fish was from.
Moreover, Bingham thought with technological advances it would be possible to get to that day when essentially a fisherman could wave a wand (almost like recording the price at the check-out counter when purchasing a large item at Home Depot) over a fish coming out of the water that could then transmit what run the fish was from as well as recording the location of where it was caught, not just where it is landed. This would then provide timely data on where exactly the fish of concern, as well as the abundant stocks, were to make in-season adjustments -- directing the fleet away from areas where weak stocks may be prevalent to areas where abundant stocks (e.g., Sacramento River) were predominant.
There would be no more problems associated with inaccurate recording of where fish were caught. The information would be hours or a day old, not over a year old as is the case now. And, there would be little need for imprecise stock models. Unfortunately, Bingham’s vision seemed to die with him, coupled with the departure of key researchers from the Bodega Marine Laboratory where much of the early work was begun, and strong resistance from agencies tied to the current tagging methods, unwilling to consider a change in the status quo.
Let’s look at what presently exists. And, then let’s examine some new developments that could finally bring salmon management on the West Coast into the 21st century, enabling the protection of weak stocks without bludgeoning the fleet with massive wide spread closures based on imprecise technology.
Currently, the Pacific Council and NMFS base season limits on predicted escapement levels, i.e., the number of fish expected to return upstream to spawn and maintain the run. In the case of the Klamath, NMFS scientists have determined that this number must be at least 35,000 natural spawning fall-chinook. Fishery managers fear that Klamath fish will be disproportionately hooked as they mingle in the open ocean with fish from larger runs, like the Sacramento, thereby pushing the number of returning fish below the 35,000 fish “floor.” Anybody who attended the contentious and often emotional spring 2006 meetings of the PFMC knows this much.
What is not well-known is that the science on which these regulatory actions are based is anything but exact. Much of what we know about how salmon live in the open ocean is based on coded-wire tags (CWT), a technology that was developed over thirty years ago for evaluating hatchery performance. Tiny strands of stainless steel 1-2 millimeters in length and factory-etched with a series of numbers are implanted into the snout of a hatchery-raised fish.
These tags are later recovered when the fish is caught by commercial or sport fishermen. Fishermen or processors turn the heads of salmon with clipped adipose fins over to state fishery agencies to be magnetically read for CWTs. Come December in California, for example, the Department of Fish & Game (CDFG) opens their large freezer of frozen salmon heads to catalog the CWT information. Based on the percentages of recovered fish from different regions, DFG will project escapement levels for rivers like the Klamath.
Klamath River stocks are based on the number of CWTs obtained from the two Klamath River Hatcheries, Iron Gate Dam Hatchery at Iron Gate Dam and the Trinity River Fish Hatchery at Lewiston Dam. However, stock numbers for hatchery fish are not always consistent with the numbers of natural spawners. Some years natural spawner numbers might be high while returning hatchery fish numbers might be low and vice versa. In addition, most Klamath chinook have a 3-4 year life cycle, so estimating population size based on last’s years’ catch of hatchery fish is not a true projection of what the next year’s stock numbers might be, which means that escapement estimates are essentially predictions based on year-old data. In some ways, this method is akin to betting on the stock market, using predictive models based on past performance to gauge future returns – not the best method for managing natural resources.
“Right now too much of fisheries management is guesswork, and when agencies guess wrong it’s always fishermen who suffer,” says Glen Spain of the Pacific Coast Federation of Fishermen’s Associations’ Northwest Regional Office.
But according to a group of researchers at Oregon State University, there is a better way.
Working hand-in-hand with commercial fishermen, scientists at OSU’s Coastal Oregon Marine Experiment Station (COMES) have come up with a uniquely collaborative process to determine from which river a harvested fish originated and the distribution patterns of these various stocks. By enlisting fishermen to collect data and tissue samples at the time a fish is caught, scientists are able to determine the fish’s origin and characteristics within weeks or even days. In this way, fish can be identified on a ‘real-time’ basis – a critical advantage over coded wire tags. Project leaders and participants hope that one day this information will enable regulatory agencies to employ the kind of in-season management practices that could avoid the sweeping closures of late that are pushing the industry to the edge of bankruptcy.
Spain notes, “The better the data on where fish are, and where they aren’t, the better fisheries management will be.”
Through funding from the Oregon Watershed Enhancement Board, the Cooperative Research for Oregon's Ocean Salmon (CROOS) project was born. The project encompasses an expansive search for technical solutions to the Klamath salmon crisis using genetic information to identify and manage ocean salmon fisheries on a real-time basis. The proposal includes additional goals, such as improved resource marketing, as well as assistance to the industry as it plays a greater role in science and management. For the full project description see: http://marineresearch.oregonstate.edu/CROOS%20blurb.doc.
With financial support from the Chinook Technical Committee, (NOAA) scientists from 10 West Coast labs (including the Hatfield Marine Science Center, home to COMES) used 13 different microsatellite markers (i.e. genetic variations), to identify 110 fish populations from Alaska to California. Fortuitously, Klamath salmon are among the most genetically distinct runs on the West Coast, making them relatively easy to identify through rapid DNA testing methods.
Now that this genetic population baseline has been established, the project is enlisting the help of Oregon salmon fishermen to collect data on captured fish through the use of an on-board sampling kit, GPS unit and data logging machine. Location, date and time of capture along with depth, temperature, salinity, and other ocean conditions are recorded. A unique barcode is assigned to the data set, which will later be uploaded to an on-line database. One copy of the barcode is attached to the fish’s operculum via a small, metal tag. A fin clip destined for laboratory DNA testing is placed into an envelope with a corresponding barcode. The fishermen then deposit the marked envelopes into a drop box on shore where it is collected by a CROOS worker, such as CIMRS Dr. Director Michael Banks.
Banks, who began his career at the Bodega Marine Laboratory and worked with Bingham in the winter-run program, foresees potential management applications of the CROOS project. “We’re excited about using real-time data to predict the distribution and behavior of fish,” says Banks. “This could allow us to target stocks of choice and avoid stocks of concern, like those of the Klamath.”
The CROOS project also has potential marketing applications to help fishermen achieve greater profit margins on their catch. Banks cites the recent focus on Alaskan Copper River salmon, which is touted as being of particularly high quality.
“It’s a value-added concept,” says Banks. “Consumers like to know where their fish came from. It’s likely that some river systems are better than others.” If consumers come to identify runs for their particular characteristics, Banks notes that certain salmon could fetch several extra dollars per pound.
Another leader on the project, COMES Superintendent Gil Sylvia, notes that the bar code system – in which the source information of fish is publicly available on the Internet – could help avoid the kind of fraud that has seen salmon purveyors passing off farm-raised as wild.
Sylvia sees the integrative nature of the research as a one of the great CROOS successes and a key to its future. “Not only are we testing to get scientific information on distribution, location and timing of runs, we’re working from the basins to the upper management to keep boats on the water.”
Indeed, seemingly everybody is in on the act. Local salmon processors and buyers who purchase bar code-tagged fish are returning some the fish heads and stomachs to the OSU Hatfild Marine Science Center. The heads are valuable for their otoliths, the inner ear structures that record the age and chemical environment of the fish. Examining stomach contents indicate the salmon’s diet and what portion of its diet is made up of baitfish, which varies by location and season.
In other words, when you’ve got fishermen, university and government scientists, and managers working side-by-side, everybody wins. And thanks to digital information sharing made possible by the Internet, from the catch to the marketplace to the dinner plate, everybody knows the origin of their food.
To be truly effective, notes Sylvia, the project must be expanded to include the entire coastline, from California to Washington and possibly Canada, as well. “We need to share more information and protocol,” he says. “To do the science right we need to develop a coordinated approach. The nature of salmon is that they move around a lot.”
The challenge CROOS now faces is convincing the Congressional delegation to commit the money to extend the project for another 3-4 years, which could require an addition $10 million. If the project is shown to be successful in its first year, however, it is hoped that the Klamath crisis will focus attention on better management practices, pushing the issue forward and spurring swifter adoption of the new concepts and technologies. The resulting long-term solutions could come at a small marginal cost, and may well prove to be a more cost-effective scheme than the current strategy of closures and prohibitive take limits.
Along the California coast, a scientist and statistician have also been working hard to develop another form of Genetic Stock Identification (GSI) that would further expand upon existing GSI technology, which can only give information on stock estimates and cannot give fish age or brood year. Carlos Garza and Eric Anderson of the National Marine Fisheries Service’s Southwest Fisheries Science Center have been developing Full Parental Genotyping (FPG) for salmon. As part of an expert panel with the Salmon Council, which was chaired by David Hankin, Chair of the Fisheries Biology department at HSU, Carlos Garza and his mathematician colleague wrote a report evaluating the technologies that might be able to supplement CWTs. Out of that report came the development of FPG. For more information see: Genetic Stock Identification and Full Parental Genotyping for Management of California’s Chinook Salmon Fisheries, by Carlos Garza and Eric Anderson, Supplemental Informational Report to the Pacific Council: www.pcouncil.org/bb/2006/0406/info_rpt8.pdf.
FPG or Parentage-Based Tagging would be able to give fishery managers cohort of origin (or age of fish) as well as stock of origin, which is important for the management of fish like chinook who may return to spawn in their 3rd, 4th or 5th year, which can dramatically alter escapement estimates. Current GSI and CWT methods are not able to return cohort of origin information.
“We needed to find a way to overcome not being able to have the age of the fish that were caught for managerial purposes. FPG is in every way comparable to the information that CWT gives you,” says Carlos Garza, Research Geneticist and Molecular Ecology Team Leader for the National Marine Fisheries Service.
With the development of FPG, fisheries managers would be able to identify salmonid offspring based on specific genetic information obtained from the juveniles’ individual parents. Garza said of FPG, “The great thing about it is an individual female chinook will produce 5,000 eggs, so a single female and male produced in a hatchery effectively produce 5,000 tags and you never even have to touch the juvenile fish. The novelty of our method is that it is highly efficient.”
Every fish’s DNA (their genome) is inherited from their individual parents. In hatchery populations, if a fin sample is taken and all of the individually spawned fish are genotyped, hatcheries could effectively identify specific genetic tags for all juveniles in the hatchery without having to individually plant a coded wire tag on each fish.
For example in a hatchery setting, all of the spawning adults would receive a dorsal clip, the clipped material would be sent to a lab, where each fish would be genotyped. The result would be that all juvenile offspring from the spawned stock would be identifiable using the genome information from the parents. With this information, a fish caught in the ocean could have a fin sample removed, a parentage analysis run and within days (or hours if you had an ever ready lab) the lab would be able to identify its stream of origin, as well as its age and brood year and parents.
While FPG sounds radical, FPG could use the same infrastructure that is already in place for Coded Wire Tags (CWT) and could either be used to complement or supplement the use of CWTs in existing fishery management. While FPG could most easily be used in a hatchery setting, existing weirs and traps could be used to bring FPG to manage wild stocks as well as hatchery stocks. FPG could be used with natural stocks if a “substantial fraction” of adult spawners could be sampled (before they are rotting carcasses) by taking small fin samples from adults during migration.
Using FPG would necessitate the use of weirs or trapping at fish ladders, which are already in place in some river systems. Although it is easy to perform FPG in a hatchery environment where genotyping of all spawned individuals and the maintenance of breeding records in hatcheries could effectively tag all the juveniles in a hatchery, it would take a great deal of effort to adequately sample wild stocks. Most of the infrastructure is in place, but managers would need convincing that their extra time is worth it and technical training would be required for workers to learn tissue sampling techniques.
At this point FPG is a dream, but it is a dream that will not have to wait long for its realization, and once it is fully developed, it will revolutionize current fishery management practices. In all, Genetic Stock Identification (GSI) is here to stay and ready to be widely utilized. “Genetic Stock Identification holds promise as a powerful tool for fisheries management, and one advantage of this technique over current practices is that you needn't insert a piece of metal into each fish for marking,” said Dr. Kristen Arkush, research scientist at the UC Davis Bodega Marine Laboratory. While current technology does not allow us to move away from the use of CWTs yet, CWT and GSI technology can be used conjunctively to real-time manage our fisheries in a way that really reflects what is happening in our ocean.
The technology is ready and waiting and it is just a matter of funding the programs to support the scientists. With smart scientists working hard to find solutions that could be used to supplement our ailing fishery management system, it is hoped in the future that Genetic Stock Identification, Full Parental Genotyping and programs like the Cooperative Research for Oregon's Ocean Salmon can be an integral part of the solution rather than just novel ideas.
The last component to any of these programs working as a management tool is commercial fishermen participation. When asked if fishermen would be supportive of experimental technologies in fishery management, Larry Collins, Vice President of the San Francisco Crab Boat Owner’s Association said, “Yes, yes I would. I would support anything that will keep us fishing. As commercial salmon fishermen we need to be able to concentrate on fishing those abundant Sacramento stocks and not the less abundant Klamath River fish. Anything that helps us do that is good news.”
Nat’s vision is alive after all.
Jeffrey Blumenthal and Crescent Calimpong are with the Institute for Fisheries Resources (IFR), working out of IFR’s San Francisco Office. They can be reached at the SF IFR Office at: PO Box 29196, San Francisco, CA 94129-0196, (415)561-3474, or by email to: jblumenthal@ifrfish.org. IFR is closely affiliated with the Pacific Coast Federation of Fishermen’s Associations (PCFFA) and manages PCFFA’s salmon conservation programs. IFR's web site is at: www.ifrfish.org. PCFFA’s web site is at: www.pcffa.org.
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