To help struggling salmon populations, the state of Washington is legally required to replace hundreds of culverts that divert streams under roadways. The state transportation department is replacing old, rusting metal pipes with broad, concrete promenades that provide more gradual gradients and gentler flows for salmon swimming upstream to access more spawning grounds. The of the effort will last 17 years and cost $3.8 billion.

But how successful are these projects at boosting fish traffic? A team from the 91探花 and the National Oceanic and Atmospheric Administration performed genetic sleuthing during two culvert replacements in 2021-22 near the city of Bellingham. Post-intervention monitoring shows that upgrading one culvert 鈥� which went under Interstate-5 鈥� had a big impact, and the other culvert may not have been as much of a barrier. Construction did not disrupt fish populations at either site.

The will appear in a forthcoming issue of Environmental Applications.

鈥淭his was an amazing study to work on, both in terms of the science and the broader implications. We demonstrated that we can measure the impact of management interventions using only DNA recovered from the water,鈥� said lead author , who began the project as a 91探花postdoctoral researcher in marine and environmental affairs and is now chief scientist at the UW-based .

For the study, the researchers didn鈥檛 catch or count a single fish. Instead, from March 2021 to December 2022 鈥� before, during and after the project 鈥� they collected water samples each month at locations just upstream and downstream of the culvert. Back in the lab, they sequenced the fragments of floating DNA to identify the type and amount of DNA of salmonid species present.

The study used a new type of monitoring known as 鈥渆nvironmental DNA,鈥� or eDNA. Fragments of DNA floating in the environment on scales, scat, fur or other material can help researchers detect which species are nearby, rather than relying on visual counts, cameras or traps.

A fish鈥檚 DNA stays in the water for a day or two. The researchers aimed to use the culvert project as a model for the use of eDNA in environmental impact reporting, more generally.

The study focused on along Padden Creek, a roughly 3-mile creek flowing from Padden Lake to Bellingham Bay. One culvert replacement was a major upgrade under I-5. DNA results show improvement for the four species of interest: cutthroat trout, coho salmon, rainbow trout and sockeye salmon. The other project, a smaller culvert replacement under state Route 11, or Old Fairhaven Parkway, had less impact: Trout and salmon DNA were present at similar levels before and after construction, meaning the older culvert may have been passable to fish.

鈥淚t is clear that not all things that are marked as a blockage to salmon are, in fact, blockages to salmon,鈥� Allan said. 鈥淚n the future, DNA sampling upstream of culverts might be something to add to the prioritization process.鈥�

The results could help support across the West Coast and in Alaska.

鈥淓nvironmental DNA offers a pretty different way of seeing the world,鈥� said co-lead author , a 91探花associate professor of marine and environmental affairs. 鈥淲e can see thousands of species in a liter of water, in a way that no other sampling method can. And what makes eDNA really attractive is it鈥檚 easily repeatable and scalable.鈥�

Researchers collected water samples using a high-tech backpack donated by Smith-Root, a company based in Vancouver, Washington. They sequenced about 52 million fragments of DNA in total, about half of which were for the four salmonid species of interest.

Researchers also surveyed five other creeks as controls. In the future, the authors say, engineers or surveyors could collect water samples for environmental monitoring more easily than surveying and identifying fish, making it simpler to combine with other measurements.

鈥淚f you had to go out there with another method and find and count fish, it would take all day,鈥� Kelly said. 鈥淪o eDNA offers a real savings in terms of in terms of time and effort in the field.鈥�

Other co-authors are postdoctoral researcher , master鈥檚 student and research scientist , all in the 91探花School of Marine and Environmental Affairs; and and at NOAA. The research was funded by Oceankind, a grantmaking organization based in California, and by the Washington State Department of Transportation.

For more information, contact Allan at eallan@uw.edu or Kelly at rpkelly@uw.edu.

Animals that live in groups tend to be more protected from predators. That idea might be common sense, but it鈥檚 difficult to test for some species, especially for wild populations of fish that live in the ocean.

A new 91探花 study that leverages historical data has found unique support for the 鈥渟afety in numbers鈥� hypothesis by showing that Pacific salmon in larger groups have lower risk of being eaten by predators. But for some salmon species, schooling comes at the cost of competition for food, and those fish may trade safety for a meal. The was published June 29 in the journal Science Advances.

鈥淲ith salmon, most people think of them spawning in freshwater streams, but there鈥檚 also this huge amount of time they spend in the ocean feeding and growing,鈥� said lead author , a doctoral student in the UW鈥檚 interdisciplinary Quantitative Ecology and Resource Management Program and the School of Aquatic and Fishery Sciences. 鈥淥ne of the reasons why this study is so unique is that we essentially can鈥檛 observe these fish at all in their natural ocean environment, and yet we鈥檙e able to pull out these really strong results on how grouping affects predation risk and foraging success for individual fish using this incredibly valuable dataset.鈥�

The researchers looked at four species of Pacific salmon 鈥� sockeye, chum, coho and pink 鈥� drawing on an international fisheries dataset collected for these species from 1956 to 1991. While their individual life histories vary by species, all salmon are born in freshwater streams, then migrate to the ocean to feed and grow before returning to their home streams to lay eggs, spawn and die, continuing the lifecycle for the next generation.

This study relied on analyzing existing historical data in new ways. For more than four decades the UW鈥檚 Fisheries Research Institute in partnership with the International North Pacific Fisheries Commission recorded salmon catch data across the North Pacific Ocean as part of managing each species. The study鈥檚 authors analyzed catch data from 鈥� fishing gear that involves dropping a net and capturing all of the fish in a relatively small volume of water. By looking at numbers of fish caught in one of these nets, the researchers could estimate the size of the schools in which each fish had been swimming.

Additionally, the historical data included careful records of predator wounds on the salmon, plus the stomach contents for a subset of the fish caught. In this way, the researchers could estimate both predator encounters and feeding success for salmon across 45 years, spanning the entirety of the North Pacific Ocean 鈥� making this a unique and valuable data set.

鈥淚t was serendipitous that these data were available. They suggest that salmon are social during the ocean stage of their life and reveal the benefits and costs of this sociality,鈥� said senior author , an assistant professor in the 91探花School of Aquatic and Fishery Sciences. 鈥淕rouping is very common in marine fish and we think this is largely to help them evade predators, yet there鈥檚 actually not much empirical support showing this, especially from wild populations. I think this study is a piece of the foundation that many didn鈥檛 realize was missing.鈥�

By looking at the number of fish caught in purse seine nets as a proxy for group size, the researchers then estimated predator risk by considering the fraction of fish in each set that had predator wounds. Fish in larger groups were much less likely to be wounded, across species. For example, with sockeye salmon, an increase in 100 fish in a group cut predation risk in half. Also, wound data showed that fish whose bodies were larger or smaller than others in their group were more likely to be attacked by a predator. This suggests that the salmon鈥檚 safety in numbers comes from confusing their predators because visually distinct 鈥� larger or smaller 鈥� individuals were easier for predators to keep track of.

The researchers also found that for two salmon species 鈥� sockeye and chum 鈥� fish in larger groups had less food in their stomachs. These fish sometimes sacrificed a meal to remain protected in a group and avoid predators. The team didn鈥檛 notice this pattern for pink and coho salmon, however. One possible reason for this, the researchers said, is that sockeye and chum salmon spend a much longer portion of their lives in the ocean, and also tend to travel farther away from their home streams than other species. Spending more time and traveling farther out in the ocean generally means food is harder to find, leading to more competition and less food for fish in larger groups.

The authors hope this paper inspires eventual consideration of group size distributions and the benefits and costs of grouping in current fisheries management models 鈥� as well as dusting off other data sets to reveal relevant findings.

鈥淢any of these data sets came at great cost and I think there鈥檚 a lot in them still ready to be uncovered,鈥� Berdahl said. 鈥淚 would hope it also motivates people to think about the ecological implications of collective behavior 鈥� in this case, how grouping impacts the food web, both by changing the rate a species is being eaten as well as the rate at which it is consuming others.鈥�

Other co-authors are , a 91探花professor of aquatic and fishery sciences, and , previously a research scientist at the 91探花School of Aquatic and Fishery Sciences. This research was funded by the Fisheries Research Institute and the H. Mason Keeler Endowed Professorship at the UW.

For more information, contact聽Polyakov at polyakov@uw.edu, Quinn at tquinn@uw.edu and Berdahl at berdahl@uw.edu.

Seafood is the world鈥檚 most highly traded food commodity, by value, and the product is hard to track from source to market. Reports of seafood mislabeling have increased over the past decade, but few studies have considered the overall environmental effects of this deceptive practice.

A study by Arizona State University, the 91探花 and other institutions examined the impacts of seafood mislabeling on the marine environment, including population health, the effectiveness of fishery management, and marine habitats and ecosystems.

The , recently published in the Proceedings of the National Academy of Sciences, show that some 190,000 to 250,000 tons of mislabeled seafood are sold each year in the U.S., making up 3.4% to 4.3% of all the seafood consumed. Farmed Atlantic salmon, often labeled and sold as Pacific salmon or rainbow trout, is the second-most-consumed mislabeled seafood product in the U.S., just behind shrimp.

Co-author , an assistant professor in the 91探花School of Marine and Environmental Affairs, helped to design a statistical analysis to compare the product on the label with the one that was actually consumed.

鈥淚t鈥檚 important to consider mislabeled consumption, rather than mislabeling rates, when thinking about the various biological and environmental impacts of mislabeling,鈥� Jardine said.

鈥淵ou can have a species that鈥檚 mislabeled the majority of the time, but if the consumption of that species is low, then the amount of the mislabeled product consumed is also low, and it may not be as big of a management concern.

鈥淥n the other hand, you can get products with low mislabeling rates and high consumption, meaning that a lot of the mislabeled product is being consumed. We find this is the case for giant tiger prawns being sold as white leg shrimp, and for Atlantic salmon being sold as Pacific salmon.鈥�

The authors used the program that assesses about 85% of seafood consumed in the U.S. and offers consumer recommendations for more sustainable choices. The authors combined those scores with mislabeling and consumption rates to compare the population health and fishery management of the species actually consumed versus the one on the label.

Genetic techniques can tell whether a seafood product is being marketed as a similar, higher value species, a switch that can happen at many points in the supply chain.

The most widely-consumed mislabeled product is shrimp, the most popular seafood in America. Imported giant tiger prawns, that are in Seafood Watch鈥檚 鈥淎void鈥� category, can end up labeled as white leg shrimp, in the 鈥淏est鈥� category.

Salmon came in second on the amount of mislabeled seafood consumed. Farmed Atlantic salmon, in the 鈥淎void鈥� category, can end up labeled as Pacific salmon or rainbow trout, typically in the 鈥淏est鈥� or 鈥淕ood鈥� category.

More generally, the study shows that false labeling tends to substitute a less sustainable product. Substituted seafood was 28% more likely to be imported from other countries, which often have weaker environmental laws than the ones covering the domestic seafood listed on the label.

鈥淚n the United States, we鈥檙e actually very good at managing our fisheries,鈥� said lead author , an assistant professor at Arizona State University鈥檚 School of Sustainability. 鈥淲e assess the stock so we know what鈥檚 out there. We set a catch limit. We have strong monitoring and enforcement capabilities to support fishers adhering to the limit. But many countries we import from do not have the same management capacity.鈥�

In 86% of cases, substitutes for wild-caught species came from fisheries that performed worse in terms of population impacts 鈥� species abundance, fishing mortality, and bycatch and discards 鈥� than the species on the label. Mislabeling also tended to disguise bad management practices: 78% of the substituted seafood had lower fishery management effectiveness than the product listed on the label.

鈥淭he expected species is often really well managed,鈥� Kroetz said.

Public attention has tended to focus on frequently mislabeled species even if Americans consume less of those products.

鈥淭here鈥檚 been a lot of media attention given to the mislabeling rates of a particular species, such as halibut and snapper,鈥� Jardine said. 鈥淏ut a big-picture analysis shows that we should also focus on other species if we are concerned about the environmental impacts.鈥�

The effects of seafood mislabeling are not just environmental, the authors write, but also economic and social, affecting seafood consumers and the sustainable fishing industry.

鈥淚f the seafood sustainability movement was better integrated with seafood mislabeling testing, rate estimation and regulatory tracing programs, we could provide the consumer with better information regarding the biological, social and economic implications of the products that they consume,鈥� Jardine said.

The study was funded by the Paul M. Angell Family Foundation and Resources for the Future. The work was also supported by the National Socio-Environmental Synthesis Center in Annapolis, Maryland, with funding from the National Science Foundation.

Other co-authors are Patrick Lee, Katrina Chicojay Moore and Andrew Steinkruger at the Washington, D.C.-based nonprofit Resources for the Future; C. Josh Donlan and Gloria Luque at the Williamsburg, Virginia-based nonprofit Advanced Conservation Strategies; Jessica Gephart at American University; and Cassandra Cole at Harvard University.

For more information, contact Jardine at jardine@uw.edu or Kroetz at kailin.kroetz@asu.edu.

Adapted from an ASU . See also a from Advanced Conservation Strategies.

An ample buffet of freshwater food, brought on by climate change, is altering the life history of one of the world’s most important salmon species.

Sockeye salmon in Alaska’s Bristol Bay region are skipping an entire year in freshwater because climate change has produced more favorable conditions in lakes and streams, which allow the young fish to grow and put on weight much faster. Previously, these fish would spend up to two years in their birth lakes before heading to the ocean, where they feed and reach maturity two to three years later. Now they are more likely to head out to sea after only one year.

These were published May 27 in Nature Ecology & Evolution by 91探花 researchers.

“Climate change is literally speeding up the early part of their lifecycle across the whole region,” said senior author , a 91探花professor in the School of Aquatic and Fishery Sciences. “We know climate warming is making rivers more productive for the food juvenile salmon eat, meaning their growth rate is speeding up. That puts the salmon on a growth trajectory that moves them to the ocean faster.”

But this “jumpstart” in freshwater doesn’t necessarily benefit salmon in the long run. The same fish are now spending an extra year in the ocean, taking longer to grow and mature. This extra year at sea is likely caused by climate stressors, as well as other fish: In the ocean, wild sockeye compete for food with close to 6 billion hatchery-raised salmon released each year throughout the North Pacific Ocean. That number has grown steadily since the 1970s, when only half a billion hatchery salmon were released.

“Hatchery fish have really changed the competitive environment for juvenile salmon in the ocean,” said lead author , a postdoctoral researcher at the University of Michigan who completed this work as a doctoral student at the UW. “In Bristol Bay, the habitat is totally intact and fisheries management is excellent, but these fish are living in lakes warming with climate change, then competing with other salmon for food in the ocean.”

The researchers drew on nearly 60 years of Bristol Bay sockeye data to tease out these changes over time, including information gathered by scientists and students in the UW’s . Close to half of the world’s wild sockeye is caught from this region, and more than 40 million fish usually return each year to Bristol Bay’s nine river systems to spawn.

Higher temperatures in the region have caused lakes and rivers to warm up earlier each spring, fueling the growth of tiny plankton that young sockeye eat. This extra food essentially fattens up the fish a year earlier, triggering their migration to the ocean.

This trend could negatively impact the resiliency of the Bristol Bay sockeye population, the authors said. Before, not every fish in a particular “age class” would migrate to the ocean in the same year, and any given year would see fish of different ages moving out to sea. This diversity of ages has helped the species navigate risks and survive.

But now, most sockeye are migrating at the same time, as 1-year-olds. This could devastate an entire age class if the ocean conditions happen to be poor one year. Additionally, scientists don’t know how many salmon the North Pacific can actually support.

“With climate change, is there a limit to how productive the ocean will become? We just don’t know where there’s a tipping point, especially as we fill the ocean with hatchery competitors,” Schindler said. “We need to be really cognizant about overstressing the marine resources that support wild salmon.”

Co-author on the study is , a research scientist at the 91探花School of Aquatic and Fishery Sciences.

The study was funded by the National Science Foundation and the Gordon and Betty Moore Foundation.

###

For more information, contact Cline at tjcline@umich.edu or 608-381-0667 and Schindler at deschind@uw.edu or 907-842-5380.

Chemical signatures imprinted on tiny stones that form inside the ears of fish show that two of Alaska’s most productive salmon populations, and the fisheries they support, depend on the entire watershed.

Sockeye and Chinook salmon born in the Nushagak River and its network of streams and lakes in southwest Alaska use the whole basin as youngsters when searching for the best places to find prey, shelter and safety from predators. From birth until the fish migrate to the ocean a year later is a critical period for young salmon to eat and grow.

By analyzing each fish’s ear stone 鈥� called an 鈥� scientists have found that different parts of the watershed are hot spots for salmon production and growth, and these favorable locations change year to year depending on how climate conditions interact with local landscape features like topography to affect the value of habitats.

The new , led by the 91探花, appears online May 23 in Science.

“We found that the areas where fish are born and grow flicker on and off each year in terms of productivity,” said lead author , a postdoctoral researcher at the 91探花School of Aquatic and Fishery Sciences. “Habitat conditions aren鈥檛 static, and optimal places shift around. If you want to stabilize fish production over the years, the only strategy is to keep all of the options on the table.”

The Nushagak River watershed is the largest river basin in the Alaska’s , which supports the biggest sockeye salmon fishery in the world and provides about 50 percent of wild sockeye globally. It is also known for its large run of Chinook salmon.

The new study coincides with renewed efforts to gain permits for the Pebble Mine, a proposed copper and gold excavation near the headwaters of the Nushagak River. The U.S. Army Corps of Engineers’ considered only two or three years of fish counts in specific locations in proximity to the proposed mine. It states that fish habitat lost to the mine could be recreated elsewhere.

But the new Science study shows that key salmon habitat shifts year to year, and how productive one area is for a short period might not represent its overall value to the fish population or larger ecosystem.

“The overall system is more than just the sum of its parts, and small pieces of habitat can be disproportionately important,” said senior author , a professor at the 91探花School of Aquatic and Fishery Sciences. “The arrows point to the need to protect or restore at the entire basin scale if we want rivers to continue to function as they should in nature.”

The research team reconstructed the likely geographic locations of nearly 1,400 adult salmon, from their birth in a Nushagak stream until they migrated to the ocean. By looking at each fish’s otolith 鈥� which accumulates layers as the animal grows 鈥� researchers could tell where the fish lived by matching the chemical signatures imprinted on each “growth ring” of the otolith with the chemical signatures of the water in which they swam.

These chemical signatures come from isotopes of the trace element strontium, found in bedrock. Strontium鈥檚 isotopic makeup varies geographically from one tributary to another, particularly in the Nushagak basin, making it easy to tell where and when a fish spent time.

“The otolith is this natural archive that basically provides a transcript of how a fish moved downstream through the river network,” Schindler said. 鈥淓ssentially, we’re sampling the entire watershed and letting the fish tell us where the habitat conditions were most productive in that year.”

The researchers noticed significant patterns when comparing where fish lived year to year. For example, in 2011 the northwest portion of the watershed in the Upper Nushagak was highly productive for Chinook, meaning more fish were born and gained body mass in that region. But by 2014 and 2015, the population had shifted eastward to utilize resources in the Mulchatna River and its tributaries 鈥� several that are downstream of the Pebble deposit.

Similar types of shifts have been documented in a number of land- and water-based animal populations, but this is the first study to show the phenomenon at a watershed-wide scale, the authors said.

“The big thing we show is these types of dynamics are critical for stabilizing biological production through time. When you have a range of habitat available, the total production from the system tends to be more stable, reliable and resilient to environmental change,” Brennan said.

The public comment period for the Pebble Mine draft environmental impact statement recently was extended to June 29 to provide more time for groups to weigh in on the 1,400-page document.

The authors of the new study said they hope it can be used to inform the scientific analysis of the proposed mine’s impact on fish.

“Results like those we’re presenting in this paper hopefully will get people to think about what they stand to lose by starting to develop and eliminate habitat in places like the Nushagak River,” Schindler said. “The Pebble Mine environmental impact statement, which is supposed to be a mature, state-of-the-science assessment of risks, really does a poor job of assessing risks of this specific project.”

Other co-authors are at the University of Utah; and , both former 91探花graduate students who are now postdoctoral researchers at the University of Michigan and Utah State University, respectively; and at the Alaska Department of Fish and Game.

The study was funded by Bristol Bay Regional Seafood Development Association, the Bristol Bay Science Research Institute and the Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative.

###

For more information, contact Brennan at聽srbrenn@uw.edu and Schindler at聽deschind@uw.edu.

The ability to smell is critical for salmon. They depend on scent to avoid predators, sniff out prey and find their way home at the end of their lives when they return to the streams where they hatched to spawn and die.

New research from the 91探花 and NOAA Fisheries’ Northwest Fisheries Science Center shows this powerful sense of smell might be in trouble as carbon emissions continue to be absorbed by our ocean.

Ocean acidification is changing the water’s chemistry and lowering its pH. Specifically, higher levels of carbon dioxide, or CO2, in the water can affect the ways in which coho salmon process and respond to smells.

“Salmon famously use their nose for so many important aspects of their life, from navigation and finding food to detecting predators and reproducing. So it was important for us to know if salmon would be impacted by future carbon dioxide conditions in the marine environment,” said lead author , a postdoctoral researcher in ‘s lab at the 91探花Department of Environmental and Occupational Health Sciences in the School of Public Health.

The , published Dec. 18 in the journal Global Change Biology, is the first to show that ocean acidification affects coho salmons’ sense of smell. The study also takes a more comprehensive approach than earlier work with marine fish by looking at where in the sensory-neural system the ability to smell erodes for fish, and how that loss of smell changes their behavior.

“Our studies and research from other groups have shown that exposure to pollutants can also interfere with sense of smell for salmon,” said Gallagher, senior co-author and a 91探花professor of toxicology. “Now, salmon are potentially facing a one-two punch from exposure to pollutants and the added burden of rising CO2. These have implications for the long-term survival of our salmon.”

The research team wanted to test how juvenile coho salmon that normally depend on their sense of smell to alert them to predators and other dangers display a fear response with increasing carbon dioxide. Puget Sound’s waters are expected to absorb more CO2 as atmospheric carbon dioxide increases, contributing to ocean acidification.

In the NOAA Fisheries research lab in Mukilteo, the research team set up tanks of saltwater with three different pH levels: today’s current average Puget Sound pH, the predicted average 50 years from now, and the predicted average 100 years in the future. They exposed juvenile coho salmon to these three different pH levels for two weeks.

After two weeks, the team ran a series of behavioral and neural tests to see whether the fishes’ sense of smell was affected. Fish were placed in a holding tank and exposed to the smell of salmon skin extract, which indicates a predator attack and usually prompts the fish to hide or swim away. Fish that were in water with current CO2 levels responded normally to the offending odor, but the fish from tanks with higher CO2 levels didn’t seem to mind or detect the smell.

In the behavioral tests shown in this video, juvenile salmon in two separate tanks were exposed to an odor that would normally prompt a fear response. In the first clip, fish smell the odor coming from the left side of each tank, and avoid or swim away from the smell. In the second clip, fish have been exposed to higher levels of CO2, which has impaired their sense of smell. The fish don’t react to the odor once it is introduced to both tanks, suggesting their ability to smell has been altered.

After the behavioral tests, neural activity in each fish’s nose and brain 鈥� specifically, in the olfactory bulb where information about smells is processed 鈥� was measured to see where the sense of smell was altered. Neuron signaling in the nose was normal under all CO2 conditions, meaning the fish likely could still smell the odors. But when they analyzed neuron behavior in the olfactory bulb, they saw that processing was altered 鈥� suggesting the fish couldn’t translate the smell into an appropriate behavioral response.

Finally, the researchers analyzed tissue from the noses and olfactory bulbs of fish to see if gene expression also changed. Gene expression pathways were found to be altered for fish that were exposed to higher levels of CO2, particularly in their olfactory bulbs.

“At the nose level, we think the neurons are still detecting odors, but when the signals are processed in the brain, that’s where the messages are potentially getting altered,” Williams said.

In the wild, the fish likely would become more and more indifferent to scents that signify a predator, Williams said, either by taking longer to react to the smell or by not swimming away at all. While this study looked specifically at how altered sense of smell could affect fishes’ response to danger, it’s likely that other critical behaviors that depend on smell such as navigation, reproduction and hunting for food would also take a hit if fish aren’t able to adequately process smells.

The researchers plan to look next at whether increased CO2 levels could affect other fish species in similar ways, or alter other senses in addition to smell. Given the cultural and ecological significance of salmon, the researchers hope these findings will prompt action.

“We’re hoping this will alert people to some of the potential consequences of elevated carbon emissions,” said senior co-author , a research biologist at the Northwest Fisheries Science Center. “Salmon are so iconic in this area. Ocean acidification and climate change are abstract things until you start talking about an animal that means a lot to people.”

Other co-authors are Paul McElhany, Shallin Busch and Michael Maher of the Northwest Fisheries Science Center; and Theo Bammler and James MacDonald of the 91探花Department of Environmental and Occupational Health Sciences.

This study was funded by Washington Sea Grant and the Washington Ocean Acidification Center, with additional support from the 91探花Superfund Research Program, the NOAA Ocean Acidification Program and the Northwest Fisheries Science Center.

###

For more information, contact Williams at crw22@uw.edu and Dittman at andy.dittman@noaa.gov or 206-860-3392.

The largest and oldest Chinook salmon 鈥� fish also known as “kings” and prized for their exceptional size 鈥� have mostly disappeared along the West Coast.

That’s the main finding of a new 91探花-led published Feb. 27 in the journal Fish and Fisheries. The researchers analyzed nearly 40 years of data from hatchery and wild Chinook populations from California to Alaska, looking broadly at patterns that emerged over the course of four decades and across thousands of miles of coastline. In general, Chinook salmon populations from Alaska showed the biggest reductions in age and size, with Washington salmon a close second.

“Chinook are known for being the largest Pacific salmon and they are highly valued because they are so large,” said lead author , a research scientist in the UW’s School of Aquatic and Fishery Sciences. “The largest fish are disappearing, and that affects subsistence and recreational fisheries that target these individuals.”

Chinook salmon are born in freshwater rivers and streams, then migrate to the ocean where they spend most of their lives feeding and growing to their spectacular body size. Each population’s lifestyle in the ocean varies, mainly depending on where they can find food. California Chinook salmon tend to stay in the marine waters off the coast, while Oregon and Washington fish often migrate thousands of miles northward along the west coast to the Gulf of Alaska where they feed. Western Alaska populations tend to travel to the Bering Sea.

After one to five years in the ocean, the fish return to their home streams, where they spawn and then die.

Despite these differences in life history, most populations analyzed saw a clear reduction in the average size of the returning fish over the last four decades 鈥� up to 10 percent shorter in length, in the most extreme cases.

These broad similarities point to a cause that transcends regional fishing practices, ecosystems, or animal behaviors, the authors said.

“This suggests that there is something about the larger ocean environment that is driving these patterns,” Ohlberger said. “I think fishing is part of the story, but it’s definitely not sufficient to explain all of the patterns we see. Many populations are exploited at lower rates than they were 20 to 30 years ago.”

It used to be common to find Chinook salmon 40 inches or more in length, particularly in the Columbia River or Alaska’s Kenai Peninsula and Copper River regions. The reductions in size could have a long-term impact on the abundance of Chinook salmon, because smaller females carry fewer eggs, so over time the number of fish that hatch and survive to adulthood may decrease.

There are likely many reasons for the changes in size and age, and the researchers say there is no “smoking gun.” Their analysis, however, points to fishing pressure and marine mammal predation as two of the bigger drivers.

Commercial and sport fishing have for years targeted larger Chinook. But fishing pressure has relaxed in the last 30 years due to regulations to promote sustainable fishing rates, while the reductions in Chinook size have been most rapid over the past 15 years. Resident killer whales, which are known Chinook salmon specialists, as well as other marine mammals that feed on salmon are probably contributing to the overall changes, the researchers found.

“We know that resident killer whales have a very strong preference for eating the largest fish, and this selectivity is far greater than fisheries ever were,” said senior author , a 91探花professor of aquatic and fishery sciences.

While southern resident killer whales that inhabit Puget Sound are in apparent decline, populations of northern resident killer whales, and those that reside in the Gulf of Alaska and along the Aleutian Islands, appear to be growing at extremely fast rates. The paper’s authors propose that these burgeoning northern populations are possibly a critical, but poorly understood, cause of the observed declines in Chinook salmon sizes.

Scientists are still trying to understand the impacts of orcas and other marine mammals on Chinook salmon, and the ways in which their relationships may have ebbed and flowed in the past. It may not be possible, for example, for marine mammals and Chinook salmon populations to be robust at the same time, given their predator-prey relationship.

“When you have predators and prey interacting in a real ecosystem, everything can’t flourish all the time,” Schindler said. “These observations challenge our thinking about what we expect the structure and composition of our ecosystems to be.”

Co-authors are Eric Ward of NOAA’s Northwest Fisheries Science Center and Bert Lewis of the Alaska Department of Fish and Game.

This study was funded by the Pacific States Marine Fisheries Commission.

###

For more information, contact Ohlberger at janohl@uw.edu聽and Schindler at deschind@uw.edu.

A multi-year survey of the nutritional, physiological and reproductive health of endangered southern resident killer whales suggests that up to two-thirds of pregnancies failed in this population from 2007 to 2014. The study links this orca population’s low reproductive success to stress brought on by low or variable abundance of their most nutrient-rich prey, Chinook salmon.

The , published June 29 in the journal , was conducted by researchers from the at the 91探花, along with partners at the National Oceanic and Atmospheric Administration’s and the . The team’s findings help resolve debate about which environmental stressors 鈥� food supply, pollutants or boat traffic 鈥� are most responsible for this struggling population’s ongoing decline.

“Based on our analysis of whale health and pregnancy over this seven-year period, we believe that a low abundance of salmon is the primary factor for low reproductive success among southern resident killer whales,” said lead author , a 91探花professor of biology and director of the Center for Conservation Biology. “During years of low salmon abundance, we see hormonal signs that nutritional stress is setting in and more pregnancies fail, and this trend has become increasingly common in recent years.”

Southern resident killer whales typically feed from May to October in the Salish Sea, and spend winters in the open Pacific Ocean along the West Coast. Unlike transient orca populations that feed on marine mammals, more than 95 percent of the diet of southern resident orcas consists of salmon, with Chinook salmon alone making up about three-quarters of their total diet.

Scientists already knew that the southern residents, just 78 individuals in Dec. 2016, had a lower fecundity rate compared with orcas in northern British Columbia and southern Alaska. But the data gathered by Wasser’s team indicate that dwindling and variable salmon runs do more direct damage to the reproductive success of the southern resident population than increasing boat traffic in the Salish Sea. Impacts of nutritional stress on pregnancy failure are further compounded by the release of toxins, which accumulate in their fatty tissues.

To gather data about orca health and reproduction, Wasser and his team measured the breakdown products of key physiological and sex hormones in orca fecal samples, or scat. They also used orca DNA extracted from the scat to determine sex, family pod and identity of the individual responsible for the leavings.

Obtaining fresh orca scat is no ordinary task. Through the Center’s program, the team trained dogs to sniff out floating orca scat from the bow of research boats that trailed southern resident pods. The dogs could detect scat up to one nautical mile away. Using this approach, they collected 348 scat samples from 79 orcas between 2007 and 2014. On these fecal searches, the researchers also gathered extensive data on boat traffic in the area, which increased significantly during the study period.

The hormone levels they calculated from scat include progesterone, testosterone, glucocorticoid and thyroid hormone. Glucocorticoid and thyroid hormones play key roles in physiological stress responses 鈥� and determining levels of both hormones allowed researchers to differentiate between stress due to poor nutrition and stress due to external responses, such as boat traffic.

The researchers used progesterone and testosterone levels in scat from females to determine reproductive state. They could even determine whether a pregnant female was in the early or later stages of the 18-month gestation period for orcas. They then correlated these data and the date of collection with calf sightings to determine whether each pregnancy was successful.

In total, these hormone data detected 35 unique pregnancies among southern resident females from 2007 to 2014. In 11 cases, the individual female gave birth and was seen with a calf thereafter. But in 24 cases 鈥� 69 percent of total pregnancies 鈥� no live calf was subsequently seen, indicating that these pregnancies failed.

In most cases, the pregnancies likely ended in spontaneous abortion during the first half of gestation. But in one-third of the failed pregnancies, hormone levels indicated that the calf was lost in the latter half of pregnancy or moments after birth 鈥� stages at which the mother has already invested significant resources and is at higher risk of infection or complications when a pregnancy fails. These females also showed signs of nutritional stress, with ratios of thyroid hormone relative to glucocorticoid hormone nearly seven times lower than females who successfully gave birth.

“These findings indicate that pregnancy failure 鈥� likely brought on by poor nutrition 鈥� is the major constraining force on population growth in southern resident killer whales,” said Wasser.

The team compared their hormone data to records of Chinook salmon runs in the Columbia and Fraser rivers, the two most significant sources of Chinook in the southern residents’ natural range. They saw that large runs at those watersheds coincided with periods of lower nutritional stress in the orcas. But in years with poor runs at either site, signs of nutritional stress were higher. Boosting Columbia River and Fraser River salmon runs could help the killer whales recover, Wasser said.

“As it stands now, the orca numbers just keep declining with no signs of recovery,” said Wasser. “We’re losing a valuable resource here.”

Co-authors are , Elizabeth Seely and Rebecca Booth at UW; Deborah Giles and Kenneth Balcomb at the Center for Whale Research; and Jennifer Hempelmann and with the NOAA Northwest Fisheries Science Center. Lundin is now a postdoctoral researcher at NOAA. The research was funded by Washington SeaGrant, NOAA’s Northwest Fisheries Science Center, the Canadian Consulate General, the 91探花Center for Conservation Biology, the Northwest Science Association and the U.S. Environmental Protection Agency.

###

For more information, contact Wasser at wassers@uw.edu or 206-853-4730.

Grant numbers: NA10OAR417005, 91735201.

The fish hatch in the rivers and streams that feed into Puget Sound and almost immediately rely on eating small organisms near the shore, including in the heart of Seattle’s commerce-filled waterfront.

Though salmon share the busy Elliott Bay waters with boats and barges, scientists suspect built-up, “armored” shorelines and large piers may be the main culprits disrupting fish habitat. These artificial structures block light and confuse the fish as they make their way to the ocean.

But are concrete seawalls actually affecting what the salmon eat, and by how much? A 91探花 , with small chum salmon seeming to be most affected.

The study looked at the diets of young salmon passing through Elliott Bay. Researchers measured the types of prey in the water along armored shorelines and along restored beaches. Scientists then collected young salmon in nets 鈥� corralled by boats or divers 鈥� and flushed out their stomachs to look at what they ate recently.

The stomach contents showed that young pink and Chinook salmon that feed on organisms either floating in the water or on the water’s surface were able to eat the same amount of food, whether they were feeding near a concrete shoreline such as Seattle’s ferry terminal at Coleman Dock or along shoreline that has been restored to look like a natural beach, including along Seattle Art Museum’s Olympic Sculpture Park.

However, young chum salmon that munch on critters found mainly in bottom habitats had a noticeable change in their eating patterns depending on the type of shoreline. These small chum salmon ate more invertebrates floating in the water when swimming by armored sites, and more bottom-dwelling crustaceans 鈥� which they prefer 鈥� when feeding near beaches. Larger juvenile chum behaved more like their pink and Chinook counterparts.

“Our study shows that armoring affects what species of prey are available,” said lead author Stuart Munsch, a 91探花doctoral student in aquatic and fishery sciences. “Fish that normally eat those missing prey will feed on alternative species at armored sites, but we don’t know what the costs of that change are to the fish.”

The were published Sept. 15 in the journal .

The article details the latest in a series of recent studies along Seattle’s waterfront that is trying to better understand how fish behave in urban, industrial waterways. The shores of Elliott Bay are almost fully walled-in with concrete and , a layer of large stones designed to keep soil from eroding. The most natural shorelines are along several manmade sandy beaches, restored recently for public recreation and natural beauty.

The study confirmed that areas converted to look like beaches attract more diverse organisms, including small crustaceans known as . These weren’t seen much along armored shorelines, which instead had more barnacles 鈥� not an appetizing choice for young salmon.

“Engineered shorelines like these manmade beaches are going to have more components of a natural ecosystem than a featureless wall,” said co-author , lead investigator on the project and a 91探花research scientist with aquatic and fishery sciences. “Manmade beaches will produce more diversity and numbers of the kinds of food juvenile salmon utilize.”

The researchers found that while the types of organisms in the water did indeed change depending on shoreline, only the small chum salmon actually adjusted what they ate.

Maybe the other fish, the pink, Chinook and larger chum salmon, ate prey that wasn’t directly affected by the type of shorelines present 鈥� such as plankton, which was in the water at both locations 鈥� or were large and strong enough to swim through both areas, eating along the way, before their stomach contents were measured.

But small chum salmon are especially dependent on the tiny crustaceans more common along restored beach sites. And while none of the fish studied were starving, the fish whose diets changed may have used up considerable energy trying to keep a balanced diet.

“The [type of] copepods that chum salmon usually feed on are brightly colored and they’re found near the bottom,” Munsch said. In other words, the chum’s typical diet is easy prey. “We think that chum salmon along armored shorelines might have to spend more energy searching for prey that are harder to see, or chasing prey that are more evasive, when that energy should be allocated to growth or migration.”

This study and other recent papers by Cordell’s research team are informing Seattle’s , which is replacing the current waterfront wall with a structure that intends to be friendlier to fish while protecting city infrastructure.

The research was funded by the Seattle Department of Transportation and a National Science Foundation Graduate Research Fellowship. 聽 Jason Toft, a research scientist in 91探花fisheries, is another co-author on this paper.

###

For more information, contact Cordell at jcordell@uw.edu or 206-543-7532 and Munsch at smunsch@uw.edu.

This bone, called an , accumulates layers as a fish grows, similar to trees. These “growth rings” are produced throughout a salmon’s life. Scientists can tell where the fish lived by matching the chemical signatures of the otolith with the chemical signatures of the water in which they swim, according to a published May 15 in the online, open-access journal .

“Each fish has this little recorder, and we can reveal the whole life history of the fish from the perspective of the otolith. Each growth ring is a direct reflection of the environment the fish was swimming in at the time it was formed,” said lead author Sean Brennan, who completed the study as a doctoral student at the University of Alaska Fairbanks. He is now a postdoctoral researcher in the 91探花’s .

This chemical signature comes from isotopes of the trace element , found in bedrock. Strontium’s chemical makeup varies geographically. As rushing water weathers the rocks, the element is dissolved and released into the water. The dissolved strontium ions get picked up by fish, either through the gills or gut lining, then are deposited onto the otolith.

As strontium makes its way from rocks into the otoliths of fish swimming in the rivers, its chemical signature does not change, and so it serves as a robust tag that can tie each fish as being in a specific location in the river at a specific time.

“This particular element and its isotopes are very strongly related to geography,” said Matthew Wooller, director of the Alaska Stable Isotope Facility at University of Alaska Fairbanks and a co-author of the paper. “It is a really good marker for where animals have been and whether they move around in their environment.”

This process relies on a river system that has been mapped extensively for its strontium isotope variation. In general, watersheds that are diverse in the types and ages of rocks will also have a lot of variation in strontium isotope signatures 鈥� and thus are good candidates for using this technique, Brennan said.

“Alaska is a mosaic of geologic heterogeneity,” he added. “As long as you can look at a geologic map and see rocks that are really different, that’s a good potential area.”

The Bristol Bay region in Alaska produces some of the last remaining wild salmon runs in the world. The area is perhaps best known for its sockeye salmon commercial fishery, but Chinook salmon, particularly those in the where this study took place, supply important subsistence and sport fisheries for the region. The Nushagak Chinook salmon are also the third biggest run in Western Alaska, ranking it as one of the largest worldwide.

About 200,000 Chinook make their way each summer from the ocean to spawn in the river’s upper tributaries and streams. When their eggs hatch in the spring, young Chinook salmon spend a whole year in the river, feeding and growing before migrating to the Bering Sea and the Pacific Ocean.

Scientists need a way to determine the birth streams of adult Chinook when they are caught in coastal fisheries. Once they have that information, they can begin to understand how freshwater habitat, the movement of fish and environmental factors can affect fish survival. Alaska’s Chinook salmon populations have declined dramatically in the past decade, and scientists are still trying to determine why.

“This is science responding to a societal issue and need,” said co-author , U.S. Geological Survey ecologist and chief of water and interdisciplinary studies at the USGS Alaska Science Center in Anchorage. “Using this approach, we will be able to map salmon productivity and determine how freshwater habitats influence the ultimate number of salmon. With declines in Chinook salmon in Western Alaska, fishery and land-use managers need better information about freshwater habitats to guide conservation.”

Using data collected from adult salmon in 2011, the researchers not only determined which parts of the river produced the most fish but also found that the majority of Chinook salmon in the Nushagak watershed stayed in the same place for their entire first year before they migrated to the ocean. About 20 percent left their birthplace for short forays in the river’s lower main stem before swimming to the ocean.

Brennan now works with at the UW, where they will expand this work to include sockeye salmon in the same river. They will collect three years of Chinook data and two years of sockeye by end of the project, which will help determine whether birth and life history patterns in Alaskan rivers vary across years, or remain consistent.

The techniques used in Brennan’s study can also help scientists understand the behavior of other animal populations. Strontium also accumulates in things like bird feathers and teeth and also survives even after being fossilized. This allows researchers to study the movements of a wide range of animals including seals, whales, bison, ancient human populations and even dinosaurs.

Other co-authors are Diego Fernandez and Thure Cerling at the University of Utah, where all of the analyses for this research were conducted, and Megan McPhee at the University of Alaska Fairbanks.

This research was funded by Alaska Sea Grant and the U.S. Geological Survey National Institute of Water Resources program.

###

For more information, contact Brennan at srbrenn@uw.edu or 801-633-7906; Zimmerman at czimmerman@usgs.gov or 907-786-7071; Cerling at thure.cerling@utah.edu or 801-581-5558; and Wooller at mjwooller@alaska.edu or 907-474-6738.

Grant numbers: R/100-02 (Alaska Sea Grant); 2012AK108B (U.S. Geological Society)