SPAWNING HOME: Adult sockeye return to their birthplace, Scotch Creek, to spawn before dying. Scotch Creek is located in South Central British Columbia and feeds into the Fraser River, home to one of the world's largest wild sockeye salmon runs.
Image: © Matt Casselman
More In This Article
-
Photo Album
Salmon species potentially affected by the virus
-
The Best Science Writing Online 2012
Showcasing more than fifty of the most provocative, original, and significant online essays from 2011, The Best Science Writing Online 2012 will change the way...
Read More »
Gridlocked bridges over the Fraser River are just a part of life for commuting Vancouverites. But the industrialized motif of North America's longest dam-free river belies a rare natural treasure: a sockeye salmon run with a historical average of eight million fish worth over $1 billion. Since the early 1990s the numbers of Fraser sockeye have steadily dwindled, reaching a particularly troublesome nadir in 2009 when more than 11 million sockeye were forecast to return and only 1.4 million showed up. Since the mid-1990s, something began killing large numbers of returning sockeye on the Fraser—anywhere from 40 to 95 percent of fish in some years—before they could spawn.
Now a study bolsters the hypothesis that a mysterious pathogen working in concert with other anthropogenic stressors may be the culprit.
Led by Fisheries and Oceans Canada, a team of scientists tracked returning Fraser River sockeye to see whether the genetic activity of those that successfully spawned differed from the activity of those that perished prematurely en route.
Sure enough, salmon with a certain pattern of gene expression in their gill tissue were 13.5 times more likely to die than those that didn't carry the "you've not got long to live" signature, as co-author and University of British Columbia (U.B.C.) fish physiologist Tony Farrell puts it. Most intriguingly the mortality-related genomic signature in the fish resembled that triggered by a viral infection. "This was a needle-in-haystack investigation, so we were more than pleased that we identified a signature, and then to narrow it down to what might be a viral signature was surprising," says Farrell.
Months after the study came out mid-January in Science the research continues to make waves on Canada's west coast as journalists and environmentalists speculate as to whether the genomic signature identified in the study might be evidence of an epidemic of salmon leukemia, known to have plagued salmon fish farms along British Columbia's coast.* Lead study author Kristi Miller-Saunders, a molecular geneticist at Fisheries and Oceans Canada in Nanaimo, has not been given the green light to speak freely with the press, however she did respond to questions from Scientific American via e-mail.
"One of the most important findings of this study was the fact that salmon were already compromised before entering the river" on their journey home to spawn, she wrote. The scientists are currently studying juvenile salmon to see if the genomic signature is already present before they go out to the open ocean. Miller-Saunders also reports "there is some indication that the signature may be in Chinook and coho" salmon, too.
View a slideshow of salmon species potentially affected by the virus
Unpublished studies have found the signature in other cohorts of Fraser sockeye, suggesting that the phenomenon spans different years. But the mystery virus remains unidentified. Attempts by Miller-Saunders's lab to culture the virus from affected tissue and do molecular screenings of known pathogens have come up empty. Currently she is attempting to sequence the pathogen from the tissues of affected fish.
"The possibility of a disease affecting these fish has been on the table long before this paper came out and the usual suspect has been fish farms," says John Reynolds, a salmon conservation scientist at Simon Fraser University in Burnaby, British Columbia. "My impression is that the hard evidence isn't there yet to either implicate fish farms or to let them off the hook."
Death by a thousand cuts
The study only correlates a genomic signature with mortality, rather than proving any causal relation, but it also hints at how genomic markers can inform better management of the dwindling sockeye stocks.
"The question is: Is disease getting worse by combinations with other either natural or anthropogenic stressors?" says Jim Winton, a microbiologist at the U.S. Geological Survey's (USGS) Western Fisheries Research Center in Seattle.
He runs through a laundry list of factors that could amplify virus-driven disease mortality: fisheries shifting food chains, global warming, marine pollutant–triggered toxic algae blooms, marine pollution in the form of chemical contaminants, and endocrine disruptors altering the host–pathogen balance.
In Chinook salmon in Alaska's Yukon River, for example, the prevalence and mortality from the parasite Ichthyophonus has recently risen in concert with climate change, which has increased river temperatures by an alarming 5 degrees Celsius. "At these higher temperatures, this disease goes much faster," Winton explains.
The rise in mortality of Pacific herring in Puget Sound tells a similar story. There, Winton's lab has identified "three candidate diseases that we believe are now much worse than they used to be…. So there are cases in wild populations where we believe changes, and many of them man-induced, are altering the impact of natural mortality from disease."
The Fraser River itself has undergone considerable warming. Seven of the past 10 summers have broken records as the warmest. River temperatures are nearly two degrees C warmer than 50 years ago, a problem for these cold-blooded fish.
In the twilight of their brief lives adult Pacific salmon migrate back to their river of birth to spawn, perpetuating a four-year life cycle that boomerangs thousands of kilometers into the ocean. "These are very old fish, imagine these are like your grandmothers and grandfathers," says Scott Hinch, a salmon ecologist at the U.B.C. who co-authored the Science paper. By the time Pacific salmon close in on their spawning grounds, they are senescent and naturally immunosuppressed. "So any small disease, parasite, illness that is naturally occurring that is there they will pick up, and then it's often a race against time."
The salmon naturally expire after the Herculean effort of swimming upstream and spawning, but too many fish perishing prematurely before they've had a chance to lay eggs and fertilize them spells trouble.
Aquatic pollution may further exacerbate things. "We believe that some of the classes of contaminants that are now in the environment, such as these endocrine disruptors coming out of sewage treatment plants, are having an impact on the immune function in fish and altering disease resistance," Winton says. Likewise, the Fraser River sockeye are met with sewage outflows from Vancouver at the river's mouth in the Strait of Georgia.
"Personally, I think changing the environmental quality in the Strait of Georgia is a major part of this explanation for the Fraser sockeye as well," says Brian Riddell, CEO of the Pacific Salmon Foundation in Vancouver.
Dead fish swimming
To further muddy the already murky waters are the "early migrating late runs". If it sounds paradoxical, that's because everything about these fish runs counter to reason. These are sockeye that historically migrated late in the spawning season but recently have begun to jump earlier by several weeks. All one really needs to know about this cohort is the term Hinch has coined for them: "dead fish swimming". That and the fact that the majority of fish sampled in Miller-Saunders's study, the ones carrying the mortality-related genetic signature, were part of these early migrating late runs.
"Generally the earlier migrating fish are the ones that are dying," Hinch says. "The grand picture is that these fish are screwed basically when they come back."
Since 1996 a larger and larger percentage of the late runs have begun to come back two to three weeks (at most, a month) early. These days, anywhere between 40 and 95 percent of the late runs are migrating earlier when river temperatures are much higher than what they would historically encounter. Research by Hinch and his colleagues found that the early migrating late-run fish differ physiologically from their normal-timed counterparts. They are more reproductively mature, stressed, and their physiology is precociously oriented toward the freshwater environment. "So not only are they forced to deal with [river] temperatures that are potentially lethal, they're also what appears to be compromised in some fashion," Hinch says.
The nearby Columbia River's sockeye, along with steelhead (also known as rainbow trout), which face temperatures 2.5 degrees warmer than the historical average, have shifted their migration times to avoid peak summer temperatures. Not so with the Fraser's early migrating late runs, which migrate right when the river is warmest. "Clearly this is not an adaptive strategy to climate change," Hinch says. "The fact that it's not getting selected against suggests that there's something annually causing this to happen and a disease makes a sense."
Even though the Columbia River's fish seem to be better at adapting their migration patterns than the fish on the Fraser, that's not to say that it's the model to follow. "The Columbia [River] is a great cautionary tale as they consider what to do about the salmon situation up there," says the director of a new PBS documentary, Salmon: Running the Gauntlet, Jim Norton. The film investigates collapsing Pacific salmon populations all down the Pacific Northwest and examines how biologists and engineers are trying to better manage the region's threatened salmon runs.
"The Columbia's message to the Fraser is: In the consideration about how to respond to changes you don't yet understand, be very clear that once you break the system, no amount of money, creativity or engineering will ever get the pieces back together again," Norton says.
Can science save the salmon?
The large number of missing Fraser River sockeye in 2009 prompted a Canadian federal judicial inquiry into the matter, the Cohen Commission. And just to underscore how little scientists understood of the fish, the sockeye run in 2010 was a once-in-a-century bonanza, with 34 million fish flooding the river. "From a historic low to a historic high almost—that creates a lot of uncertainty for management but it also raises questions on why it's swinging so much," says U.B.C.'s Farrell. The USGS's Winton points out that the sockeye run of 2010 was an anomaly, in the face of a steady and worrisome decline in Fraser sockeye over the years.
The Cohen Commission is currently underway and study co-author Hinch was called to the stand as a witness in mid-March. "Moving forward the real issue is whatever this is, what do we do now and how do you manage in the face of it," he says.
Miller-Saunders, for her part, will go on the stand later this summer to speak about her research, which has already been referenced in the enquiry's proceedings. Up until then, it is unlikely that she will be allowed to speak freely to the media about her research. British Columbia Supreme Court Justice Bruce Cohen, the commissioner who is overseeing the investigation, is in the unenviable position of hearing everyone out and making recommendations to ensure the future sustainability of the fishery by June 2012.
"We will have a full hearing session on diseases and the impact, if any, of aquaculture. The interplay between climate change warming and pathogens, if any, will be part of that subject," says Brian Wallace, senior commission counsel.
The Canadian Department of Fisheries and Oceans also has to juggle an immense number of stakeholders and their needs when managing the Fraser sockeye: coastal fisheries with different gear types, the in-river First Nations harvest, and one of the largest recreational fisheries in Canada.
"They were hoping that our research would tell them what do you do and our research is telling them this is tough," Hinch says. "So we're probably never going to come up with the exact cause but we may be well able to piece together a series of potential causes."
--Francie Diep wrote and produced the slide show that accompanies this
story.
*Clarification (5/5/11): This sentence was modified after publication to change the tense of the verb describing when leukemia has plagued salmon fish farms along British Columbia's coast.
See what we're tweeting about
7 Comments
Add CommentWhat makes this Fraser River salmon issue rather complicated is the extremely-high salmon returns last year and again projected for this year.
Reply | Report Abuse | Link to thisReference: Another big year for sockeye expected
http://www.timescolonist.com/Another+year+sockeye+expected/4734164/story.html
It's disappointing that Scientific American has written another article which references salmon farming without doing any scientific research on the subject.
Reply | Report Abuse | Link to thisI refer specifically to the sentence which states "Months after the study came out mid-January in Science the research continues to make waves on Canada's west coast as journalists and environmentalists speculate as to whether the genomic signature identified in the study might be evidence of an epidemic of salmon leukemia, known to plague salmon fish farms along British Columbia's coast."
First, salmon leukemia is not "known to plague salmon fish farms." The last time any farms in B.C. had a problem with salmon leukemia, also known as marine anemia or plasmacytoid leukemia, was nearly 20 years ago when B.C. salmon farms farmed almost exclusively Chinook salmon. The disease is of particular concern for Chinook salmon. Since then most farms have switched to farm mostly Atlantic salmon, and all are continually improving farming practices. Since the early 1990s the disease has not been a problem for B.C. salmon farms which farm Atlantic as well as Chinook salmon.
Second, scientific research from the late 1980s suggests the disease was not new, merely newly identified. In fact, an identical disease was identified in 1974 (before there were salmon farms in B.C.) in freshwater Chinook smolts in a Washington State hatchery, suggesting it is present before saltwater entry.
Third, farms test regularly for marine anemia and have reported to the province if any cases have been found. From 2003-2009, only three cases were found.
Finally, I found it surprising that the article gives no mention to the billions of hatchery-raised fish from Alaska, many of which carry disease, which share the same North Pacific ocean feeding grounds every year with Fraser River sockeye. Competition for food and other negative interactions between B.C. and Alaskan fish must be considered in the discussion about what is happening to Fraser River sockeye.
Dear Grant, Really briefly, I would argue that the sentences that you quote of mine are indeed accurate, although I can appreciate that given the controversial nature of this topic, perhaps they can be construed as misleading.
Reply | Report Abuse | Link to thisIt is certainly true that the Kristi's study has led journalists and environmentalists to speculate about whether the genomic signature might be evidence of an epidemic of salmon leukemia. I think the key word here is "speculation". In fact, any inferences from Kristi's science paper are all speculation, which I think my article, and the study authors I quote make quite clear. Her study raises many more questions than it answers. As I write in the article, the scientists have yet to identify the viral pathogen so there's no saying that it's salmon leukemia in the first place. Nor, as I write, is there any causal evidence linking the signature to mortality. It's simply correlation.
As for salmon leukemia plaguing fish farms, it is certainly true that epidemics swept through feedlots in the early 90s. And I am sure that the industry has done its best to mitigate such risks, as would be in their own best interests no doubt! In the vein of clarifying my statement that "known to plague fish farms" I suggest that we change that to "known to have plagued fish farms".
As for the final issue of the competition with Alaskan hatchery fish, none of the six renown fisheries biologists I interviewed for the piece mentioned this issue. Infection from sea lice from the fish farms is also a commonly espoused hypothesis for explaining the shrinking numbers of spawning sockeye but I didn't mention that hot-button topic because none of the experts I interviewed mentioned it as leading hypothesis, in their opinion.
Grant, I must tell you that the point of this article is not to point the finger at fish farms. In fact, it's not about farmed salmon at all. Indeed, the point of the article is that anthropogenic stressors (such as pollution and climate change) are acting in concert with a mystery pathogen to prevent the sockeye from successfully spawning, and as a result their populations may be dwindling.
If you see me gunning for your industry in this piece then you are entirely mistaken, and I am sorry that you construed the piece in such a manner.
Thank you for making the change to the past tense "plagued." And again, this disease has not been a problem in the industry since the early 1990s, and the industry has come a long way since then.
Reply | Report Abuse | Link to thisI understand that your article was not about salmon farming, and other than the paragraph I mentioned, I found it quite excellent and informative. But given that there is a large and concerted effort on the part of some activists to make the Cohen Commission all about salmon farming, I also hope you can appreciate how seriously our industry takes any speculation linking salmon farms to diseases which may or may not exist, and which may or may not be killing massive amounts of wild salmon.
Our industry has provided more than a decade's worth of data to the Cohen Commission because we have nothing to hide, and are confident that salmon farms did not cause the decline in Fraser River sockeye returns. Despite all our openness, it is disheartening that speculation runs rampant about our operations when all people need to do is ask, or come see for themselves.
Also the question of interactions between hatchery and wild fish has been hotly debated for years: http://www.stateofthesalmon.org/marinecarryingcapacity/
Also, here is a very thorough study done by Japanese scientists, who have also noticed sockeye declines in Japan since the early 1990s similar to what is happening on the Fraser River: http://www.npafc.org/new/publications/Bulletin/Bulletin%20No.%205/NPAFC_Bull_5_293-302(Kaeriyama).pdf
They state that "biological interaction between wild and hatchery populations is an important issue in the sustainable management of Pacific salmon production at the ecosystem level."
Correlation does not equal causation, but the early 1990s was the same time there was a massive increase in hatchery production of salmon in Alaska. See Figure 8 in the study, as well as the preceding table, for detailed numbers. I certainly would like to see more science done on this issue, given that many fisheries scientists believe that all Pacific salmon go to the same feeding grounds in the North Pacific. What happens there, affects them all.
I see you use the term "feedlot" to describe salmon farms. Again, I invite you and anyone else to see for yourself that this term, chosen by anti-salmon farming activists to paint a negative word picture of salmon farms being like cattle feedlots, is inaccurate. In our net pens, the fish only take up three per cent of the pen volume. The rest is water.
I'm no expert on farmed fish.. Personally I'd wild in our ocean and super Markets.. Elizabeth May.. Green Party of Sannich Gulf Isles..Seems to think farmed fish is bad . She says farmed fish on Canada's East coast.. Has ended fishing of wild salmon there.
Reply | Report Abuse | Link to thisMay Day Walk for Wild Salmon on youtube.
http://www.youtube.com/watch?v=59hqPacgFxg
We should of learned with the killer bee's. Just leave nature alone. The earth provides.
Reply | Report Abuse | Link to thisIt would be more correct to say that Steelhead and Rainbow Trout are essentially the same species, with the exception of Steelhead being an ocean run fish.
Reply | Report Abuse | Link to this