News & Stories

  • Gene Pollution Threatens Wild Salmon. A Solution: Sterile Farmed Fish

    August 27, 2018

    Oceans Deeply by Alastair Bland

    Scientists are proving the viability of a new idea to protect wild Atlantic salmon, a species that once spawned in great numbers in rivers from Portugal to the Arctic, as far west as Greenland and Canada and as far south as New York. Today, the Atlantic salmon is endangered or threatened in much of its range, with populations depleted by dams, water pollution and overfishing.

    The idea? Sterilizing their farmed relatives.

    A new study published in Royal Society Open Science found that triploid farmed salmon – that is, fish modified to contain three sets of chromosomes rather than the usual two – are essentially incapable of reproducing. Making farmed fish into triploids involves a process of pressure shocking their eggs minutes after fertilization, explained David Murray, a marine scientist at the University of East Anglia in the United Kingdom, who led the research. Experts said the approach could be used by salmon-farming companies to alleviate genetic pollution of wild populations, which happens when escaped farmed salmon breed with native Atlantic salmon and weaken their ability to survive or reproduce.

    Several decades ago, conservationists and scientists began to suspect that the rise of the salmon-farming industry had something to do with the fall of wild Atlantic salmon, especially when farmed salmon escaped from their nets into the ocean.
    In a 2000 experiment, researchers tagged both farmed and native Atlantic salmon and released them into the River Imsa in Norway. The farm-born fish were “inferior” in their new environment, according to the published results, and were less than a third as likely as the wild fish to succeed in breeding. But by competing for resources, their presence appeared to harm the productivity of the native salmon.

    “Farmed salmon have gone through several generations of selection for traits like rapid growth and resistance to certain diseases that are desirable for commercial production but not necessarily for survival in the wild,” said Ian Fleming, a professor at the Memorial University of Newfoundland in Canada, who led that study nearly 20 years ago.

    Those findings didn’t prove that escaped farmed fish would reduce the long-term success of wild salmon, but they did support the hypothesis. Much research in the years since has backed the same conclusion and shown how, over time, escaped farmed salmon that breed with wild salmon spread genes that diminish the genetic fitness of wild Atlantic salmon.

    Interbreeding isn’t the only risk that farmed salmon pose to wild populations. For instance, fish farms also can be breeding sites for sea lice parasites in both the Atlantic and Pacific oceans. But there is mounting evidence that what is called “genetic introgression” is a significant problem in the Atlantic, and it has been widely documented in rivers in Norway, home of the world’s largest remaining wild salmon runs and also a center of the salmon-farming industry.

    Sten Karlsson, a scientist with the Norwegian Institute for Nature Research (NINA), has studied how quickly wild populations are becoming adulterated by the genes of farm-born fish. In a paper published in 2016 in the ICES Journal of Marine Science, Karlsson and three coauthors reported “significant farmed genetic introgression” in 52 percent of the 147 Norwegian salmon rivers they studied. Another paper to which he contributed in 2017, published in Nature Ecology & Evolution, found that the interbreeding between farmed salmon and wild salmon had negative effects on “fitness-related traits” – most notably causing salmon to migrate from the sea into freshwater to spawn at a younger age. This means they were smaller, and because size is directly related to a salmon’s reproductive success, these genetically compromised fish would in theory face lower odds of producing offspring, according to the paper.

    In a 2017 paper in the ICES Journal of Marine Science, Torbjørn Forseth, a senior research scientist at NINA, concluded that genetic introgression from farmed to wild salmon is the largest current threat to the persistence of Atlantic salmon runs in Norway and other nations.

    Today, as salmon farming booms and wild salmon numbers wane almost everywhere, the new research suggests one of the most effective ways to prevent the interbreeding of farmed and wild salmon is the use of triploid fish in commercial production.

    “We show that female triploids are sterile and do not develop gonads,” Murray and his coauthors wrote in their study. And while males still produce sperm capable of fertilizing wild salmon eggs, the development and survival of the fertilized eggs was less than 1 percent compared with their two-chromosome counterparts. He said the Norwegian egg supplier AquaGen took an interest in the research, providing space and materials.

    The researchers also looked at the nutritional value of triploid fillets. It turned out the triploid salmon flesh contained lower fat overall – not necessarily a desirable thing in terms of marketability – but the ratio of healthy omega-3 fatty acids as a portion of total fat content was higher.

    “What this means is that if we can manage to get triploid fish to have the same amount of fat content as the diploids, then they should have significantly higher nutritional benefits to human beings,” Murray said. Improving the production of total body fat could require selecting new genetic strains of Atlantic salmon while also optimizing feed formulas and making them more sustainable, he noted.

    Karlsson believes the salmon-farming industry should lose no time in incorporating triploid fish into their production systems in an effort to save wild salmon. He said it’s becoming increasingly clear from the mounting body of research that the salmon-farming industry could choose to make its fish almost entirely sterile.

    “I think that there is an urgent need to stop or drastically reduce escapees and genetic introgression into wild salmon populations,” Karlsson said.

    As the scientific evidence accumulates that escaped farmed salmon weaken the survival fitness of wild populations, a fresh look at fish-farming technologies will be in order, the researchers said.

    “There was a time when we were asking, first of all, ‘Do salmon really escape?’ and then, ‘Do they really enter the rivers?’ and then, ‘Do they really interbreed with wild salmon, and if so, do they leave offspring, and if so, does it really change the wild populations?’” Karlsson said. “Now, the next really big question is whether the genetic introgression actually has a direct effect on the productivity of the wild salmon populations, and all the evidence and theoretical framework is pointing that way.”

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  • West Marin creek project underway to boost coho habitat

    August 27, 2018

    Marin Independent Journal by Adrian Rodriguez

    With the help of heavy machinery, crews are removing more than 13,000 cubic yards of dumped fill and abandoned structures from a West Marin floodplain, all to restore the habitat of the endangered coho salmon.

    The $5 million project by the Salmon Protection and Watershed Network is underway along a 1-mile stretch of Lagunitas Creek. The creek runs parallel to Sir Francis Drake Boulevard from Samuel P. Taylor State Park to Olema in areas that once were Tocaloma and Jewell.

    This will allow crews to create side channels that will serve as refuge habitat for juvenile salmon and steelhead trout, which are about 1 1/4 inch long when hatched, said Todd Steiner, executive director of the Turtle Island Restoration Network, the nonprofit parent organization of SPAWN.

    “When the big storms come, they can’t sustain themselves in the high flows,” Steiner said of the juvenile fish. “Historically, the water would spill into the floodplains and the baby fish would move into the floodplains and stay there during these big storms. So this restores that habitat.”

    The two-year project is funded by a grant from the state Department of Fish and Wildlife, the Environmental Protection Agency, the California State Water Resources Control Board, as well as SPAWN member contributions and private donors. The actual construction costs about $2.3 million. The rest of the expenses went to pay for planning and development, said Preston Brown, director of conservation at SPAWN.

    Brown said that the same type of work upstream will happen next year.

    The project also involves thinning vegetation and stockpiling wood that will later be used as woody debris structures, which will be placed in the creek to increase the stream complexity. Invasive plants will be removed to make way for 9,000 native plants from SPAWN’s plant nursery that will restore the riparian corridor.

    Steiner said that they hope to recycle the excavated materials that they collect. The gravel will be re-purposed there at the creek, and other unused sediment and fill will likely be shipped to use for other types of projects, he said.

    In the summer of 2016, the National Park Service did work in the same area, removing dilapidated and abandoned structures. This project builds on a partnership with SPAWN and the Point Reyes National Seashore to restore the areas.

    “Every small step matters for a species as imperiled as coho salmon,” Cicely Muldoon, general superintendent of the National Park Service wrote in an email. “This project restores long-impaired habitat for the coho (as well as other threatened and endangered species), and feeds into efforts throughout California to save our salmon.”

    Initial studies organized by SPAWN have indicated that tens of thousands of cubic yards of fill were placed in the floodplain during the construction of the homes decades ago.

    The Lagunitas Creek segment was historically a wide valley floodplain that served as excellent habitat for coho and steelhead trout. But in the 1930s it was developed for rural residential properties.

    The fill resulted in a 50 percent reduction of floodplain habitat along the creek. Concrete retaining walls, concrete fill, patios, fences and decks built along the creek led to unnatural channels. Nonnative plants including bamboo, vinca, ivy and Himalayan blackberry cover large areas of the property, according to a state Coastal Conservancy report.

    Sixty years ago, the estimated annual Central California coho population in the Lagunitas Creek watershed was about 6,000. Now the annual population of adult coho is fewer than 400 female spawning fish, a more than 90 percent decline from historic numbers.

    Restoration of coho habitat in Lagunitas Creek is identified as a priority by the National Oceanic and Atmospheric Administration and the California Department of Fish and Wildlife.

    Additionally, the project will help reduce flooding down stream, because the stormwater will have more room to disperse and sink into the water table, Steiner said.

    Said Muldoon: “Nature is resilient, and will do most of the work over time. We’re just lending a helping hand.”

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  • Small Amounts of Water Enable Juvenile Salmon to Survive

    August 27, 2018

    Environmental Monitor by Karla Lant

    Recent research led by California Sea Grant Extension Specialist Mariska Obedzinski reveals that even small amounts of running water in coastal California streams can mean survival instead of death for juvenile coho salmon. In fact, less than a gallon per second allows the young salmon to persevere through the heat and aridity of summer by keeping pools interconnected.

    A gallon per second may sound like a lot of water, but in the context of a stream or river, it’s negligible: “It is approximately 2.5 average garden hoses (all the way on) running through the stream channel,” clarifies Dr. Obedzinski.

    The peaks and valleys of saving Russian River coho salmon

    Since 1996, when Russian River coho salmon were listed as threatened, various conservation plans for the species have been tried—mostly without much success. By the early 2000s the species was in more serious trouble, and by 2005, they were endangered. That year, scientists monitoring the population observed fewer than 10 of the fish returning to the annual spawning grounds in the Russian River.

    To rescue the species from the brink of extinction, federal, state, and local agencies collaborated on a conservation hatchery program. The aim of the program was to breed healthy fish and release them to hospitable locations to maximize their chances of survival. California Sea Grant established a monitoring program as part of the hatchery plan to track fish released from the hatchery and study which factors were hampering the recovery of the coho. They focused on four coastal watersheds: Dutch Bill, Green Valley, Mill and Grape creeks.

    “They were chosen by the Coho Water Resources Partnership, a collaborative group funded by National Fish and Wildlife Foundation to address the low-flow bottleneck for Russian River coho salmon, because they are critical for the recovery of coho salmon in the Russian River, yet are flow-impaired,” details Dr. Obedzinski.

    “The environmental data we collected included continuous streamflow and temperature, wetted volume, days of pool disconnection, and dissolved oxygen,” states Dr. Obedzinski. “For streamflow, we collected stage data using a pressure transducer and periodic discharge measurements using a USGS Price Pygmy Current meter. These two datasets were used to generate rating curves for estimates of continuous streamflow.”

    The team also collected stream temperature data by deploying a continuous temperature logger in each of the studies reaches. In the early morning hours of each survey, the researchers collected dissolved oxygen data from each pool using a handheld DO logger. They also took measurements of length, average width, and average depth to estimate pool volume for each habitat unit.

    The researchers also estimated survival, using tracking technology and models.

    “We used an individual-based mark-recapture approach using passive integrative transponder (PIT) tags (the same microchips that are used to track pets),” Dr. Obedzinski describes. “We inserted PIT tags into individual coho salmon, and then we tracked them in the stream over the summer using a portable PIT tag detection wand that we could wave through the water. For survival estimation, we used the robust design in Program MARK which allowed us to include environmental factors as covariates and test their relative influence on survival.”

    The monitoring team discovered that low streamflow during summer’s dog days is among the greatest barriers to coho recovery. Once hatchery fish are released, they, naturally, migrate to the ocean. The dried out waterways prevent their return for spawning as adults.

    “When working at such low streamflows, measuring discharge accurately was extremely challenging,” remarks Dr. Obedzinski. “Identifying whether pools were connected or not was a useful alternative metric to streamflow that turned out to be even more important for fish survival than absolute streamflow. To document the time of disconnection in a given riffle/pool complex, we found game cameras aimed at the riffle/pool complexes to be very useful.”

    Band-aid solutions and long-term change

    Because low water levels threaten the survival of the fish, relocating fish to areas with more water is one of the strategies that the experts running the hatchery employ. It’s a time- and effort-intensive process but has been essential to keeping the species out of greater danger.

    “In early June, a team of biologists from California Sea Grant, the California Department of Fish, and the Army Corps of Engineers relocated about 1,200 stranded juvenile salmon, greatly improving their fate by moving them to a location in the watershed that is known to remain wet all summer,” explains Dr. Obedzinski. “However, relocating fish is just a band-aid solution to a problem that needs a long-term solution. While it improves the chances that the rescued fish will survive, there are countless others that are stranded each year because no one is there to observe the pools drying and there are not enough resources to move all of the fish that are found stranded.”

    In the meantime, the experts are faced with even tougher questions, including how much additional water the salmon need, and where that water might come from.

    “The long-term solution is to work at a watershed-scale to reduce and better coordinate our water use to replenish the water table and keep streams flowing during the summer season,” comments Dr. Obedzinski. “The Coho Water Resources Partnership is working to find alternative ways for landowners to acquire the water they need while increasing the amount that flows through the streams. Examples of projects include rainwater catchment systems, water storage tanks and ponds, efficient irrigation systems, coordinated water withdrawals, and frost protection fans.”

    California is no stranger to drought, and given the state’s booming economy and population growth, water is an even more limited resource. However, the actual amounts of water that can save this species are relatively modest. Whether that will be the case for other species remains to be seen.

    “We have observed other aquatic species in drying pools as well: steelhead, Chinook, sculpin, roach, tadpoles, newt larva, and aquatic invertebrates,” remarks Dr. Obedzinski. “We expect the problem to increase with climate change and an increasing human demand for water during the dry season.”

    For now, this research is allowing managers to make smarter decisions about water and wildlife.

    “This work underscores the importance of considering the size, character and geomorphic context of watershed when considering different flow management actions,” comments Dr. Obedzinski. “Existing flow models that predict fish habitat are based on larger stream systems and don’t hold true in the small intermittent streams typical of coastal California. More studies like these that link flow-related variables to direct biological responses are needed to inform managers, especially in the face of increasing drought due to climate change and an increasing demand for water with population growth.”

    “Repurposing even a little bit of water back into the streams can improve the fate of aquatic species, and simple actions on all of our parts, like converting to a drip irrigation system, storing water in tanks or putting in drought-tolerant plants can make a big difference,” adds Dr. Obedzinski.

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  • Eel River salmon spawners may face tough run this fall, local officials say

    August 16, 2018

    Eureka Times Standard By Will Houston

    Critical pools on the lower Eel River where migrating salmon swim toward their upriver spawning grounds are once again saturated with sediment, according to local researchers and river surveyors.

    Eel River Recovery Project board member and salmon surveyor Eric Stockwell said the shallow pools and channels make it more likely fish will contract disease or become stranded as had occurred in previous years.

    “I feel like they’re the worst they’ve ever been,” Stockwell said about the pools.

    Heavy winter rains in 2016-2017 are believed to have flushed out sediment-filled spawning territory in the upper reaches of the river, according to Stockwell, but that sediment is believed to have been carried downriver and filled in the holding pools.

    National Oceanic and Atmospheric Administration fisheries biologist Matt Goldsworthy of Arcata said no one has a definite answer as to why the pools are filling. He hoped rains in the 2017-18 winter would flush out this fill-in, but that didn’t come to pass.

    “It was perfect for fish migration and everything, but the problem this winter was actually a lack of sustained flows so the bed load didn’t really move much this winter,” he said. “My guess would be that it wasn’t a bunch of bedload and sediment coming from upstream; it was more that this winter didn’t really mobilize much so the channel didn’t really change much and there wasn’t much velocity to scour anything out.”

    Goldsworthy said this same scenario played out in other local rivers.

    Another concern raised by Goldsworthy and Stockwell is an island in the river north of Fortuna which used to flow to the right of the island where there were holding pools but is now flowing left, where there are none.

    “So there is no holding water for about 3 miles between Fernbridge and Fortuna where fish can get to [the 12th Street] pool, which is 14 feet deep and a large area, lots of volume. Deeper holes have a little cold water, they can get stratified down on the bottom and the fish want that because around the low 70s it’s lethal to these salmonids, so they’re not going to cruise too early.”

    Goldsworthy said that the river used to flow on the left side of the island a few decades back, and that the river does change naturally.

    However, it still has Stockwell worried because he believes more fish will be sitting in the much shallower Warswick pool downriver. Three years earlier during the drought, Stockwell observed blinded, lethargic fish sitting in the algae-laden pool with many fish having been infected by a parasitic fluke and a virus.

    As far as short-term solutions go, Stockwell said they’re just going to have to hope for heavy rains, but even that only goes so far.
    “We’ve changed the carrying capacity of the Eel River,” Stockwell said. “Rain doesn’t really fix those holes. ... Just because water comes up and it’s turbid and you can’t see through it doesn’t mean we still don’t have this horrible lack of habitat in the lower Eel River.”

    Both Stockwell and Goldsworthy agree that something needs to be done to create more holding habitat on the lower river.

    Goldsworthy said he would prefer something that mimics a natural process in which they install large pieces of wood and rock into the river, working to scour the riverbed and create pools. While he said funding is available for such a project, no one has taken the lead on it.

    “What we need to do is get organized and somebody needs to take the lead on getting a plan together and submitting applications for the permits and that requires funding and everything,” Goldsworthy said. “We’re definitely willing to help.”

    But Goldsworthy said it would be difficult to complete the work this late into the season, with fish expected to begin pushing up the river in the coming weeks and months.

    Stockwell said the river evolved with large redwood trees around it, but said large redwood pieces falling into the river are now often taken by people because of their value, thus leaving only willow and gravel bars.

    Goldsworthy said they had a sizeable salmon run on the river last year, with Stockwell stating that fishermen are reporting seeing several jack salmon — or two-year-old male salmon — in the ocean this summer.

    The question now is how this winter will turn out.

    “It’s all going to come down to how the rains happen,” Stockwell said.


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  • Three-day symposium focuses on coho salmon

    August 14, 2018

    Crescent City Triplicate by Julie Weeder

    Fisheries scientists will visit the South Fork of the Smith River next week for a symposium focusing on the endangered coho salmon.

    Held Aug. 24–26, the Salmonid Restoration Federation’s 21st-Annual Coho Confab will focus on watershed restoration, techniques and efforts to help coho salmon recover. The symposium will be held at Rock Creek Ranch and will include tours of stream and valley floor restoration efforts in the Lower Klamath tributaries as well as a tour of large woody debris projects led by Dan Burgess, of California State Parks.

    There will be an open forum discussing how monitoring coho salmon can inform restoration activities, featuring California Department of Fish and Wildlife scientist Justin Garwood; Julie Weeder, coho salmon recovery coordinator for NOAA Fisheries; Darren Mierau, North Coast director of Cal Trout, and Patty McCleary, co-director of the Smith River Alliance. Garwood oversees the coho monitoring program in the Smith River.

    The symposium will also include a community dinner on Friday and a presentation by geologist and climate scientist Mike Furniss on “Geology is Destiny, Why the Smith River is What It Is.”

    The Salmonid Restoration Federation is a statewide organization that puts on the largest salmon restoration conference in California, according to Executive Director Dana Stolzman. The organization hosts two symposiums focused on steelhead recovery issues and spring run chinook recovery issues. But coho salmon are much more endangered than steelhead or chinook, Stolzman said.

    The Coho Confab is one of the organization’s smaller symposiums, but it was created even before the fish was placed on the Endangered Species List for people to see what scientists were doing to help the species recover, according to Stolzman

    “For this particular event, (we’re) specifically hosting it in regions where there is still coho salmon refugia, which is the main reason we’ve returned to the Smith again and again,” Stolzman said Monday. “We really hope that by bringing leading scientists to the Smith and talking about different techniques that have been applied throughout and are definitely being applied more frequently in the Smith, we can help promote restoration efforts.”

    The people who will be presenting at the symposium include Michael Pollack, who promotes the use of beavers, which had been native to a lot of coastal streams in California and create deep pools, helping to rehabilitate lower parts of the Smith River, according to Stolzman.

    Another presentation by Humboldt State University graduate student Marisa Parish, who is working with the Smith River Alliance, will focus on recommended actions that could increase coho salmon populations, Stolzman said.

    Crescent City Triplicate by Julie Weeder
    Stolzman added that hosting the symposium alongside the Smith River simply gives many fisheries scientists a chance to see the wild and scenic stream.

    “We tour local projects, but we also bring scientists from other areas that can bring skills and techniques that are being applied to other regions,” she said.

    The cost to participate in the three-day symposium is $200, which includes meals and camping, according to Stolzman. For any locals who want to come for the dinner and keynote presentations on Aug. 24, the cost is $25.

    To register for the event, visit

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